UPN TCGA_id WGS_id chromosome_name start stop reference variant type gene_name transcript_name transcript_species transcript_source transcript_version strand transcript_status trv_type c_position amino_acid_change ucsc_cons domain all_domains deletion_substructures transcript_error tier NormalRefReads NormalVarReads NormalVAF TumorRefReads TumorVarReads TumorVAF RNARefReads RNAVarReads RNAVAF 104 TCGA-AB-2802 MT 13059 13059 C - DEL MT-ND5 ENST00000361567 human ensembl 54_36p 1 known frame_shift_del c.722 p.P242fs NULL HMMPfam_Oxidored_q1 "HMMPfam_Oxidored_q1_N,HMMPfam_Oxidored_q1,HMMPfam_NADH5_C" - no_errors tier1 NA NA NA NA NA NA NA NA NA 104 TCGA-AB-2802 MT 14767 14767 T C SNP MT-CYB ENST00000361789 human ensembl 54_36p 1 known missense c.20 p.I7T NULL superfamily_Transmembr_di-haem_cytochrome "HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome" - no_stop_codon:bad_bp_length_for_coding_region tier1 1696 44 2.53 2088 498 19.04 NA NA NA 104 TCGA-AB-2802 3 7478316 7478316 T A SNP GRM7 NM_181874.2 human genbank 54_36p 1 reviewed silent c.1422 p.P474 0.995 "HMMPfam_ANF_receptor,superfamily_SSF53822" "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_SSF53822" - no_errors tier1 672 10 1.46 155 52 24.88 NA NA NA 104 TCGA-AB-2802 18 12066175 12066175 A G SNP LOC728211 XR_015403.2 human genbank 54_36p -1 model rna NULL NULL 0.973 - - - pseudogene tier1 127 2 1.55 18 7 26.92 NA NA NA 104 TCGA-AB-2802 2 25310747 25310747 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2644 p.R882C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 152 0 42 17 28.33 NA NA NA 104 TCGA-AB-2802 20 34673853 34673853 C T SNP C20orf24 NM_199483.2 human genbank 54_36p 1 validated missense c.245 p.P82L 0.994 HMMPfam_Rab5ip HMMPfam_Rab5ip - no_errors tier1 375 3 0.79 32 17 34 NA NA NA 104 TCGA-AB-2802 10 37495588 37495588 C T SNP ANKRD30A NM_052997.2 human genbank 54_36p 1 validated missense c.1946 p.A649V 0.01 NULL "PatternScan_ASP_PROTEASE,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" - no_errors tier1 69 0 25 19 42.22 NA NA NA 104 TCGA-AB-2802 12 51250815 51250815 G A SNP KRT74 NM_175053.3 human genbank 54_36p -1 validated silent c.913 p.L305 0.958 HMMPfam_Filament "HMMPfam_Filament,PatternScan_IF" - no_errors tier1 249 4 1.58 60 23 27.71 NA NA NA 104 TCGA-AB-2802 12 111372548 111372548 G A SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.181 p.D61N 1 "HMMPfam_SH2,HMMSmart_SM00252,superfamily_SH2 domain" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 423 0 51 23 31.08 NA NA NA 104 TCGA-AB-2802 1 119270684 119270684 T A SNP TBX15 NM_152380.2 human genbank 54_36p -1 validated missense c.175 p.I59F 1 "HMMPfam_T-box,HMMSmart_TBOX,superfamily_P53_like_DNA_bnd" "HMMPfam_T-box,HMMSmart_TBOX,superfamily_P53_like_DNA_bnd,PatternScan_TBOX_2,PatternScan_TBOX_1" - no_errors tier1 468 7 1.47 120 54 30.68 NA NA NA 104 TCGA-AB-2802 12 131032838 131032838 G A SNP EP400 NM_015409.3 human genbank 54_36p 1 validated silent c.1788 p.Q596 0.985 NULL "HMMPfam_SNF2_N,HMMPfam_Helicase_C,HMMSmart_HELICc,HMMPfam_HSA,superfamily_Homeodomain_like,HMMSmart_HSA,HMMSmart_DEXDc,superfamily_SSF52540" - no_errors tier1 209 1 0.48 44 23 34.33 NA NA NA 104 TCGA-AB-2802 1 150324146 150324146 T C SNP TCHHL1 NM_001008536.1 human genbank 54_36p -1 provisional missense c.2636 p.Q879R 0.075 NULL "PatternScan_S100_CABP,HMMPfam_S_100,superfamily_SSF47473" - no_errors tier1 743 4 0.54 142 78 35.14 NA NA NA 104 TCGA-AB-2802 5 170767341 170767342 - GAGGAGG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.804_805 p.I268fs 0.998:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 104 TCGA-AB-2802 5 170767342 170767343 - T INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.805_806 p.N270fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 104 TCGA-AB-2802 2 208821357 208821357 C T SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.395 p.R132H 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 71 0 55 39 41.05 NA NA NA 110 TCGA-AB-2803 MT 7207 7207 G A SNP MT-CO1 ENST00000361624 human ensembl 54_36p 1 known nonsense c.1303 p.G435* NULL "HMMPfam_COX1,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^I-like" "HMMPfam_COX1,PatternScan_COX1_CUB,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^I-like" - no_stop_codon tier1 1385 1 0.07 3582 968 21.12 NA NA NA 110 TCGA-AB-2803 3 12855994 12855994 C A SNP RPL32 NM_000994.3 human genbank 54_36p -1 reviewed missense c.132 p.R44S 1 "HMMPfam_Ribosomal_L32e,superfamily_Ribosomal protein L32e" "HMMPfam_Ribosomal_L32e,superfamily_Ribosomal protein L32e,PatternScan_RIBOSOMAL_L32E" - no_errors tier1 84 0 64 56 46.28 1244 1394 52.68 110 TCGA-AB-2803 4 15178450 15178450 C T SNP CC2D2A NM_001080522.2 human genbank 54_36p 1 validated missense c.3341 p.T1114M 0.971 HMMSmart_C2 HMMSmart_C2 - no_errors tier1 123 0 102 68 39.53 NA 110 TCGA-AB-2803 6 31240983 31240983 G T SNP POU5F1 NM_002701.4 human genbank 54_36p -1 validated missense c.717 p.N239K 0.995 "HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like" "HMMPfam_Pou,HMMSmart_SM00352,PatternScan_POU_1,PatternScan_POU_2,HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like,superfamily_lambda repressor-like DNA-binding domains,PatternScan_HOMEOBOX_1" - no_errors tier1 191 0 136 106 43.44 1 3 75 110 TCGA-AB-2803 15 31835807 31835807 G A SNP RYR3 NM_001036.3 human genbank 54_36p 1 validated missense c.8524 p.V2842I 1 NULL "HMMPfam_RYDR_ITPR,HMMPfam_RyR,HMMPfam_MIR,superfamily_MIR domain (Pfam 02815),HMMPfam_SPRY,HMMPfam_Ion_trans,HMMPfam_RR_TM4-6,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_SM00472,HMMPfam_efhand,HMMSmart_SM00449,superfamily_EF-hand" - no_errors tier1 122 0 107 70 39.55 NA 110 TCGA-AB-2803 12 47865247 47865247 C T SNP TUBA1A NM_006009.2 human genbank 54_36p -1 reviewed missense c.1169 p.R390H 1 "superfamily_Tubulin C-terminal domain-like,HMMPfam_Tubulin_C" "HMMPfam_Tubulin,superfamily_Tubulin C-terminal domain-like,PatternScan_TUBULIN,HMMPfam_Tubulin_C,superfamily_Tubulin nucleotide-binding domain-like" - no_errors tier1 98 0 148 43 22.4 167 34 16.92 110 TCGA-AB-2803 4 54069006 54069006 C T SNP LNX1 NM_032622.1 human genbank 54_36p -1 reviewed missense c.238 p.E80K 0.988 NULL "HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ" - no_errors tier1 89 2 2.17 97 95 49.22 NA 110 TCGA-AB-2803 11 54789725 54789725 C A SNP TRIM48 NM_024114.3 human genbank 54_36p 1 validated missense c.485 p.T162N 0 NULL "HMMPfam_zf-B_box,HMMSmart_BBOX,HMMSmart_RING,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,superfamily_SSF57850" - no_errors tier1 24 0 44 26 37.14 NA 110 TCGA-AB-2803 8 56529203 56529203 A G SNP LOC100133234 XR_038021.1 human genbank 54_36p -1 model rna NULL NULL 0.803 - - - pseudogene tier1 25 0 28 12 30 NA 110 TCGA-AB-2803 2 61112441 61112441 G - DEL PEX13 NM_002618.3 human genbank 54_36p 1 reviewed frame_shift_del c.476 p.A160fs 1 HMMPfam_Peroxin-13_N "HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_Peroxin-13_N" - no_errors tier1 NA NA NA NA NA NA NA NA NA 110 TCGA-AB-2803 7 74889409 74889409 C G SNP POM121C NM_001099415.1 human genbank 54_36p -1 validated missense c.2062 p.G688R 0.135 NULL NULL - no_errors tier1 7 0 9 1 10 13 0 110 TCGA-AB-2803 15 81252794 81252794 C T SNP FSD2 NM_001007122.2 human genbank 54_36p -1 provisional missense c.403 p.G135R 0 NULL "HMMPfam_SPRY,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" - no_errors tier1 75 0 68 70 50.72 NA 110 TCGA-AB-2803 9 97095390 97095391 TG - DEL LOC643342 XR_016301.2 human genbank 54_36p 1 model rna NULL NULL 0.996:0.998 - - - pseudogene tier1 NA NA NA NA NA NA NA NA NA 110 TCGA-AB-2803 7 141319023 141319023 C G SNP TAS2R38 NM_176817.3 human genbank 54_36p -1 validated silent c.936 p.L312 0.001 "HMMPfam_TAS2R,superfamily_SSF81321" "HMMPfam_TAS2R,superfamily_SSF81321" - no_errors tier1 74 0 81 61 42.07 NA 110 TCGA-AB-2803 7 149658979 149658979 C T SNP C7orf29 NM_138434.2 human genbank 54_36p 1 validated silent c.553 p.L185 0.015 NULL NULL - no_errors tier1 23 0 44 18 29.03 1 0 110 TCGA-AB-2803 4 159974210 159974210 G A SNP FNIP2 NM_020840.1 human genbank 54_36p 1 validated missense c.635 p.C212Y 0.998 NULL NULL - no_errors tier1 186 0 145 87 36.86 2 1 33.33 110 TCGA-AB-2803 1 199321250 199321250 G A SNP CACNA1S NM_000069.2 human genbank 54_36p -1 reviewed missense c.1087 p.L363F 1 NULL "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_SSF81324" - no_errors tier1 90 0 107 61 36.09 NA 110 TCGA-AB-2803 1 200181928 200181928 G A SNP LMOD1 ENST00000367288 human ensembl 54_36p -1 known missense c.164 p.T55M 1 HMMPfam_Tropomodulin "HMMPfam_WH2,HMMPfam_Tropomodulin,superfamily_SSF52047" - no_errors tier1 94 0 99 78 43.58 NA 201 TCGA-AB-2804 X 18174676 18174676 G A SNP SCML2 NM_006089.2 human genbank 54_36p -1 validated silent c.1764 p.D588 0.001 NULL "HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_MBT,HMMSmart_SM00561,superfamily_SAM/Pointed domain,superfamily_Tudor/PWWP/MBT" - no_errors tier1 44 0 43 95 68.35 NA NA NA 201 TCGA-AB-2804 16 21649688 21649688 C T SNP OTOA NM_144672.3 human genbank 54_36p 1 provisional missense c.2237 p.T746M 0.021 NULL NULL - no_errors tier1 60 0 174 111 38.95 NA NA NA 201 TCGA-AB-2804 15 32602565 32602565 G C SNP LOC728770 XM_001718857.1 human genbank 54_36p 1 model missense c.752 p.C251S 0.002 NULL "HMMPfam_GED,HMMSmart_SM00302" - pseudogene tier1 12 1 7.69 4 3 37.5 NA NA NA 201 TCGA-AB-2804 19 40940951 40940951 C T SNP C19orf55 ENST00000396911 human ensembl 54_36p 1 known missense c.73 p.R25C 0 NULL NULL - no_errors tier1 19 0 50 19 27.54 NA NA NA 201 TCGA-AB-2804 19 59474649 59474649 C T SNP LILRB2 NM_005874.2 human genbank 54_36p -1 reviewed missense c.785 p.R262H 0 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 24 0 35 18 33.96 NA NA NA 201 TCGA-AB-2804 4 68302234 68302234 G A SNP GNRHR NM_000406.2 human genbank 54_36p -1 reviewed missense c.415 p.R139C 1 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 83 0 146 116 43.94 NA NA NA 201 TCGA-AB-2804 12 109249835 109249835 C T SNP ATP2A2 NM_170665.1 human genbank 54_36p 1 reviewed missense c.725 p.T242I 1 "HMMPfam_E1-E2_ATPase,superfamily_Calcium ATPase transmembrane domain M" "HMMPfam_Cation_ATPase_N,HMMPfam_Hydrolase,HMMPfam_Cation_ATPase_C,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_Calcium ATPase transmembrane domain M" - no_errors tier1 82 1 1.2 184 103 35.27 NA NA NA 201 TCGA-AB-2804 2 128128537 128128537 G C SNP LIMS2 NM_017980.1 human genbank 54_36p -1 provisional missense c.362 p.P121R 0.999 "HMMPfam_LIM,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,superfamily_SSF57716" "HMMPfam_LIM,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,superfamily_SSF57716" - no_errors tier1 18 0 35 24 40.68 NA NA NA 201 TCGA-AB-2804 3 128878804 128878805 - C INS ABTB1 NM_172027.2 human genbank 54_36p 1 reviewed frame_shift_ins c.747_748 p.E251fs 1.000:1.000 NULL "HMMSmart_SM00225,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,superfamily_POZ domain,HMMPfam_BTB" - no_errors tier1 NA NA NA NA NA NA NA NA NA 201 TCGA-AB-2804 X 133355645 133355645 G T SNP PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed nonsense c.415 p.E139* 1 NULL "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger" - no_errors tier1 25 0 15 74 83.15 NA NA NA 203 TCGA-AB-2805 1 1737088 1737088 T G SNP GNB1 NM_002074.2 human genbank 54_36p -1 reviewed missense c.170 p.K57T 1 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 318 0 130 134 49.81 227 192 45.71 203 TCGA-AB-2805 2 24904318 24904318 G A SNP ADCY3 NM_004036.3 human genbank 54_36p -1 reviewed missense c.2389 p.P797S 0.956 NULL "HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase,PatternScan_GUANYLATE_CYCLASE_1" - no_errors tier1 153 3 1.91 97 88 47.57 19 14 42.42 203 TCGA-AB-2805 13 28498513 28498513 G A SNP KIAA0774 NM_001033602.2 human genbank 54_36p 1 validated missense c.1708 p.V570M 0 NULL NULL - no_errors tier1 294 2 0.68 204 129 38.39 NA 203 TCGA-AB-2805 9 34496776 34496776 C T SNP DNAI1 NM_012144.2 human genbank 54_36p 1 reviewed silent c.1215 p.D405 0.604 "HMMSmart_WD40,superfamily_WD40_like" "HMMSmart_WD40,superfamily_WD40_like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 149 0 92 73 43.71 NA 203 TCGA-AB-2805 21 35153653 35153653 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed nonsense c.601 p.R201* 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 190 1 0.52 117 77 39.69 141 152 51.88 203 TCGA-AB-2805 21 35174809 35174810 - G INS RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed frame_shift_ins c.423_422 p.A142fs 0.921:1.000 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 NA NA NA NA NA NA NA NA NA 203 TCGA-AB-2805 18 42815075 42815075 C T SNP TCEB3B NM_016427.2 human genbank 54_36p -1 reviewed missense c.559 p.A187T 0 NULL "HMMSmart_TFS2N,HMMPfam_Elongin_A,HMMPfam_TFIIS" - no_errors tier1 6 0 4 8 61.54 NA 203 TCGA-AB-2805 17 53763621 53763621 C G SNP MIRN142 ENST00000384835 human ensembl 54_36p -1 known rna NULL NULL 1 - - - no_errors tier1 257 0 114 39 25.16 78 21 21.21 203 TCGA-AB-2805 18 55835205 55835205 C T SNP LOC728115 XR_038858.1 human genbank 54_36p -1 model rna NULL NULL 0.881 - - - pseudogene tier1 207 2 0.96 101 75 42.37 42 0 203 TCGA-AB-2805 19 56941085 56941085 G A SNP FPR1 NM_002029.3 human genbank 54_36p -1 validated silent c.975 p.T325 0.875 superfamily_Family A G protein-coupled receptor-like "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 573 0 275 178 39.04 44 45 50.56 203 TCGA-AB-2805 19 59738875 59738875 G A SNP KIR3DX1 ENST00000221567 human ensembl 54_36p 1 known missense c.608 p.R203H 0 "HMMSmart_SM00409,superfamily_Immunoglobulin" "HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 154 1 0.64 141 120 45.45 1 2 66.67 203 TCGA-AB-2805 2 73600435 73600435 C T SNP ALMS1 NM_015120.4 human genbank 54_36p 1 reviewed missense c.9562 p.L3188F 0 NULL NULL - no_errors tier1 137 0 108 77 40.96 10 14 58.33 203 TCGA-AB-2805 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 114 3 2.56 93 70 42.68 111 102 47.89 203 TCGA-AB-2805 7 102938684 102938684 A G SNP RELN NM_005045.3 human genbank 54_36p -1 reviewed silent c.8124 p.N2708 1 superfamily_Sialidase "HMMPfam_Reeler,HMMSmart_EGF,superfamily_Sialidase,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_SSF57196" - no_errors tier1 117 0 110 65 36.31 NA 203 TCGA-AB-2805 9 116838243 116838243 T C SNP TNC NM_002160.2 human genbank 54_36p -1 validated missense c.5611 p.K1871E 0.977 "HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" "HMMPfam_Fibrinogen_C,HMMSmart_FBG,superfamily_Fibrinogen_a/b/g_C,HMMPfam_fn3,HMMSmart_FN3,HMMPfam_EGF,HMMSmart_EGF,superfamily_FN_III-like,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2" - no_errors tier1 475 7 1.45 293 262 47.12 NA 203 TCGA-AB-2805 11 125376911 125376911 C T SNP CDON NM_016952.4 human genbank 54_36p -1 validated missense c.2071 p.V691M 0.118 NULL "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 552 6 1.07 354 217 37.8 NA 203 TCGA-AB-2805 1 167612485 167612485 G A SNP BLZF1 NM_003666.2 human genbank 54_36p 1 validated missense c.112 p.G38R 0.951 NULL HMMPfam_DASH_Hsk3 - no_errors tier1 119 0 102 118 52.21 10 12 54.55 203 TCGA-AB-2805 2 179150442 179150442 G A SNP TTN ENST00000375038 human ensembl 54_36p -1 known silent c.56809 p.L18937 0.869 "HMMSmart_SM00409,superfamily_Concanavalin A-like lectins/glucanases,superfamily_WD40 repeat-like,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_PPAK,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Protein kinase-like (PK-like),superfamily_WD40 repeat-like,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,HMMPfam_Pkinase,PatternScan_FGGY_KINASES_1,PatternScan_PEROXIDASE_1,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" - no_errors tier1 158 0 95 52 35.37 1 0 237 TCGA-AB-2806 1 17147969 17147969 G A SNP CROCC NM_014675.3 human genbank 54_36p 1 validated missense c.2797 p.E933K 0.87 NULL superfamily_Prefoldin - no_errors tier1 32 0 39 11 22 13 0 237 TCGA-AB-2806 18 19369601 19369601 C T SNP NPC1 NM_000271.3 human genbank 54_36p -1 validated missense c.3307 p.G1103S 0.899 "HMMPfam_Patched,superfamily_SSF82866" "HMMPfam_Patched,superfamily_SSF82866" - no_errors tier1 32 0 83 61 42.07 12 5 29.41 237 TCGA-AB-2806 10 24802598 24802598 G A SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated missense c.1282 p.A428T 0.889 NULL NULL - no_errors tier1 47 0 132 76 36.36 1 3 75 237 TCGA-AB-2806 19 42546341 42546341 G A SNP HKR1 NM_181786.2 human genbank 54_36p 1 provisional missense c.1804 p.A602T 0.993 superfamily_C2H2 and C2HC zinc fingers "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 14 0 63 48 42.48 17 22 55 237 TCGA-AB-2806 X 44803458 44803458 C A SNP UTX NM_021140.2 human genbank 54_36p 1 validated missense c.997 p.Q333K 1 "HMMPfam_TPR_1,HMMSmart_TPR,superfamily_SSF48452" "HMMPfam_TPR_1,HMMSmart_JmjC,HMMPfam_JmjC,HMMSmart_TPR,superfamily_SSF48452" - no_errors tier1 26 0 7 89 92.71 2 40 95.24 237 TCGA-AB-2806 5 45297941 45297941 G T SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated missense c.2512 p.R838S 1 NULL "HMMPfam_cNMP_binding,HMMSmart_cNMP,HMMPfam_Ion_trans,HMMPfam_Ion_trans_N,PatternScan_CNMP_BINDING_1,PatternScan_CNMP_BINDING_2,superfamily_cNMP_binding,superfamily_SSF81324" - no_errors tier1 9 0 27 24 47.06 NA 237 TCGA-AB-2806 2 47890258 47890259 - GA INS FBXO11 NM_025133.1 human genbank 54_36p -1 reviewed frame_shift_ins c.2179_2178 p.N726fs 1.000:1.000 "HMMSmart_PbH1,HMMSmart_CASH,superfamily_Pectin_lyas_like,superfamily_SSF81383" "HMMPfam_F-box,HMMSmart_FBOX,HMMPfam_zf-UBR,HMMSmart_PbH1,HMMSmart_CASH,superfamily_Pectin_lyas_like,superfamily_SSF81383" - no_errors tier1 NA NA NA NA NA NA NA NA NA 237 TCGA-AB-2806 11 48195044 48195044 C T SNP OR4B1 NM_001005470.1 human genbank 54_36p 1 provisional missense c.107 p.T36M 0.008 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 90 0 236 176 42.51 NA 237 TCGA-AB-2806 2 50611899 50611899 C T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed missense c.2317 p.A773T 0.977 "HMMSmart_SM00282,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2" "PatternScan_ASX_HYDROXYL,HMMSmart_SM00282,HMMSmart_SM00294,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,superfamily_EGF/Laminin" - no_errors tier1 30 0 119 88 42.31 NA 237 TCGA-AB-2806 14 91006957 91006957 G C SNP SMEK1 NM_032560.4 human genbank 54_36p -1 validated missense c.1598 p.S533W 1 superfamily_ARM-type_fold "HMMPfam_DUF625,superfamily_ARM-type_fold,superfamily_SSF50729" - no_errors tier1 42 0 139 90 39.3 80 66 44.9 237 TCGA-AB-2806 10 95781181 95781181 G T SNP PLCE1 NM_016341.3 human genbank 54_36p 1 validated missense c.388 p.A130S 0.089 NULL "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RA,HMMSmart_SM00314,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand" - no_errors tier1 56 0 143 94 39 NA 237 TCGA-AB-2806 12 120364769 120364769 T C SNP FBXL10 NM_032590.1 human genbank 54_36p -1 reviewed missense c.2858 p.E953G 1 NULL "HMMPfam_F-box,HMMSmart_SM00249,HMMPfam_zf-CXXC,HMMSmart_SM00558,HMMSmart_SM00367,superfamily_FYVE/PHD zinc finger,HMMPfam_JmjC,superfamily_Clavaminate synthase-like,superfamily_RNI-like" - no_errors tier1 15 0 30 17 35.42 29 16 35.56 237 TCGA-AB-2806 X 130506620 130506620 C T SNP OR13H1 NM_001004486.1 human genbank 54_36p 1 provisional missense c.892 p.R298W 0.967 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 52 0 25 167 84.34 2 100 237 TCGA-AB-2806 9 131630321 131630321 G C SNP C9orf78 NM_016520.2 human genbank 54_36p -1 validated missense c.810 p.N270K 0.973 NULL HMMPfam_Hep_59 - no_errors tier1 25 0 86 70 44.59 55 43 43.88 237 TCGA-AB-2806 8 144963727 144963727 G C SNP SCRIB NM_182706.3 human genbank 54_36p -1 validated silent c.1680 p.A560 0.044 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00364,superfamily_RNI-like" - no_errors tier1 21 0 22 8 26.67 25 9 26.47 237 TCGA-AB-2806 1 149527051 149527051 C T SNP ZNF687 NM_020832.1 human genbank 54_36p 1 provisional missense c.1660 p.R554C 1 superfamily_C2H2 and C2HC zinc fingers "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 27 0 42 30 41.1 22 17 43.59 237 TCGA-AB-2806 2 153985650 153985650 C T SNP LOC642635 XR_016188.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 33 1 2.94 109 107 48.64 NA 237 TCGA-AB-2806 6 154452709 154452709 G T SNP OPRM1 NM_001008505.3 human genbank 54_36p 1 validated missense c.346 p.D116Y 1 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 57 0 132 69 34.33 NA 237 TCGA-AB-2806 2 233389923 233389924 - CGGTAGGACGGGTC INS GIGYF2 NM_001103147.1 human genbank 54_36p 1 validated frame_shift_ins c.2370_2371 p.R791fs 0.997:0.997 NULL "HMMPfam_GYF,HMMSmart_GYF,superfamily_GYF" - no_errors tier1 NA NA NA NA NA NA NA NA NA 245 TCGA-AB-2807 19 1041936 1041936 C A SNP POLR2E NM_002695.3 human genbank 54_36p -1 reviewed nonsense c.400 p.E134* 1 superfamily_RNA_pol_Rpb5_N "HMMPfam_RNA_pol_Rpb5_C,PatternScan_RNA_POL_H_23KD,superfamily_RNApol_RPB5_like,HMMPfam_RNA_pol_Rpb5_N,superfamily_RNA_pol_Rpb5_N" - no_errors tier1 32 0 16 10 38.46 34 7 17.07 245 TCGA-AB-2807 17 3732306 3732306 G A SNP CAMKK1 NM_172207.2 human genbank 54_36p -1 reviewed missense c.793 p.R265C 0.001 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 293 3 1.01 74 49 39.84 4 2 33.33 245 TCGA-AB-2807 17 5005548 5005548 G A SNP USP6 NM_004505.2 human genbank 54_36p 1 validated missense c.2830 p.D944N 1 "HMMPfam_UCH,superfamily_Cysteine proteinases" "HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p,HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_Cysteine proteinases" - no_errors tier1 359 1 0.28 291 218 42.83 NA 245 TCGA-AB-2807 18 7026046 7026046 G T SNP LAMA1 NM_005559.2 human genbank 54_36p -1 validated nonsense c.1779 p.Y593* 0.99 "HMMPfam_Laminin_B,superfamily_Concanavalin A-like lectins/glucanases,HMMSmart_SM00281" "HMMPfam_Laminin_B,HMMSmart_SM00282,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMSmart_SM00181,HMMPfam_Laminin_N,HMMSmart_SM00136,superfamily_Galactose-binding domain-like,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_I,HMMPfam_Laminin_II,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMSmart_SM00281,superfamily_EGF/Laminin" - no_errors tier1 378 14 3.57 140 110 44 NA 245 TCGA-AB-2807 17 8066613 8066613 T C SNP C17orf44 ENST00000315707 human ensembl 54_36p -1 known missense c.316 p.I106V 0 NULL NULL - no_errors tier1 216 0 160 162 50.15 1 0 245 TCGA-AB-2807 20 20027446 20027446 C T SNP C20orf26 NM_015585.2 human genbank 54_36p 1 predicted nonsense c.847 p.R283* 0 NULL "superfamily_Acyl-CoA N-acyltransferases (Nat),superfamily_FAD/NAD(P)-binding domain" - no_errors tier1 914 2 0.22 255 229 47.31 NA 245 TCGA-AB-2807 6 29071725 29071725 G A SNP ZNF311 NM_001010877.2 human genbank 54_36p -1 provisional missense c.1033 p.R345C 0 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 575 3 0.52 179 183 50.55 2 4 66.67 245 TCGA-AB-2807 22 29596557 29596557 G C SNP OSBP2 NM_030758.3 human genbank 54_36p 1 reviewed missense c.995 p.R332P 1 NULL "HMMPfam_Oxysterol_BP,HMMPfam_PH,HMMSmart_SM00233,PatternScan_OSBP,superfamily_PH domain-like" - no_errors tier1 44 1 2.22 22 19 46.34 2 100 245 TCGA-AB-2807 20 30486388 30486388 G - DEL ASXL1 NM_015338.4 human genbank 54_36p 1 reviewed frame_shift_del c.2212 p.G738fs 0 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 245 TCGA-AB-2807 22 30885094 30885094 C A SNP C22orf42 NM_001010859.1 human genbank 54_36p -1 provisional missense c.109 p.A37S 0 NULL NULL - no_errors tier1 370 1 0.27 131 138 51.3 NA 245 TCGA-AB-2807 21 35174726 35174731 CTTCCA - DEL RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed in_frame_del c.506_501 p.SG167in_frame_del 1.000:1.000:1.000:1.000:1.000:0.990 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 NA NA NA NA NA NA NA NA NA 245 TCGA-AB-2807 13 35343426 35343426 C T SNP DCLK1 NM_004734.3 human genbank 54_36p -1 validated missense c.875 p.R292H 1 NULL "HMMSmart_S_TKc,HMMPfam_DCX,HMMSmart_DCX,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_SSF89837" - no_errors tier1 368 5 1.34 251 248 49.6 NA 245 TCGA-AB-2807 17 36294725 36294725 C T SNP KRT20 NM_019010.1 human genbank 54_36p -1 reviewed missense c.239 p.R80H 1 HMMPfam_Filament "HMMPfam_Filament,PatternScan_IF" - no_errors tier1 278 1 0.36 258 41 13.71 NA 245 TCGA-AB-2807 8 37816921 37816921 C T SNP GPR124 NM_032777.7 human genbank 54_36p 1 validated missense c.2615 p.P872L 0.875 NULL "HMMPfam_GPS,HMMSmart_SM00082,HMMPfam_LRR_1,HMMPfam_HRM,HMMSmart_SM00369,HMMSmart_SM00409,PatternScan_G_PROTEIN_RECEP_F2_2,superfamily_Hormone receptor domain (HRM Pfam 02793),superfamily_L domain-like" - no_errors tier1 185 0 96 35 26.72 3 1 25 245 TCGA-AB-2807 15 39642181 39642181 C T SNP TYRO3 NM_006293.2 human genbank 54_36p 1 provisional missense c.553 p.P185S 0.035 "HMMSmart_IG,HMMPfam_ig,superfamily_SSF48726" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,HMMSmart_IGc2,HMMSmart_IG,HMMPfam_fn3,HMMSmart_FN3,PatternScan_PROTEIN_KINASE_TYR,superfamily_FN_III-like,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 574 0 54 55 50.46 NA 245 TCGA-AB-2807 12 51196813 51196813 G T SNP LOC100129218 XM_001718439.1 human genbank 54_36p 1 model missense c.1642 p.G548C 1 NULL NULL - no_errors tier1 216 7 3.14 118 112 48.7 2 100 245 TCGA-AB-2807 7 53071334 53071334 G A SNP DKFZp564N2472 NM_182595.2 human genbank 54_36p 1 validated missense c.476 p.R159H 0.001 NULL NULL - no_errors tier1 12 0 16 7 30.43 NA 245 TCGA-AB-2807 17 53763624 53763624 T C SNP MIRN142 ENST00000384835 human ensembl 54_36p -1 known rna NULL NULL 1 - - - no_errors tier1 291 0 77 50 39.37 25 26 50.98 245 TCGA-AB-2807 18 59315520 59315520 G A SNP LOC728205 XR_015404.1 human genbank 54_36p 1 model rna NULL NULL 1 - - - pseudogene tier1 141 3 2.07 155 153 49.51 NA 245 TCGA-AB-2807 11 72623927 72623927 T C SNP P2RY2 NM_002564.2 human genbank 54_36p 1 reviewed missense c.1075 p.S359P 0 NULL "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 1258 48 3.67 84 86 50.59 5 0 245 TCGA-AB-2807 X 74674244 74674244 T G SNP LOC100128989 XM_001716779.1 human genbank 54_36p -1 model missense c.366 p.K122N 0.999 NULL NULL - no_start_codon tier1 424 2 0.47 293 166 36.17 NA 245 TCGA-AB-2807 15 80361550 80361550 C T SNP FAM154B NM_001008226.1 human genbank 54_36p 1 predicted missense c.289 p.L97F 0.864 NULL NULL - no_errors tier1 132 0 119 104 46.64 NA 245 TCGA-AB-2807 7 82376253 82376253 C T SNP PCLO NM_033026.2 human genbank 54_36p -1 validated missense c.13313 p.R4438H 1 NULL "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_zf-piccolo,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FYVE/PHD zinc finger" - no_errors tier1 97 2 2.02 182 122 40.13 NA 245 TCGA-AB-2807 15 83202326 83202326 C T SNP ALPK3 NM_020778.4 human genbank 54_36p 1 validated missense c.3959 p.A1320V 0 NULL "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_Alpha_kinase,HMMSmart_SM00811,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,superfamily_Immunoglobulin" - no_errors tier1 47 1 2.08 56 50 46.73 1 0 245 TCGA-AB-2807 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 153 1 0.65 97 82 45.81 160 132 45.05 245 TCGA-AB-2807 2 101010296 101010296 T G SNP TBC1D8 NM_001102426.1 human genbank 54_36p -1 validated missense c.2456 p.E819A 1 superfamily_EF-hand "HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p,HMMPfam_GRAM,HMMSmart_SM00568,superfamily_EF-hand" - no_errors tier1 205 3 1.44 103 97 48.5 13 13 50 245 TCGA-AB-2807 X 102222197 102222197 C T SNP NXF3 NM_022052.1 human genbank 54_36p -1 reviewed splice_site c.891-1 e10-1 0.376 - - - no_errors tier1 340 0 107 70 39.55 NA 245 TCGA-AB-2807 1 112798626 112798626 G A SNP CTTNBP2NL NM_018704.2 human genbank 54_36p 1 validated silent c.363 p.R121 1 HMMPfam_CortBP2 HMMPfam_CortBP2 - no_errors tier1 360 9 2.44 91 74 44.85 2 1 33.33 245 TCGA-AB-2807 12 119056525 119056525 G A SNP GCN1L1 NM_006836.1 human genbank 54_36p -1 validated missense c.7270 p.R2424W 1 "HMMPfam_HEAT,superfamily_ARM repeat" "HMMPfam_HEAT,superfamily_ARM repeat" - no_errors tier1 118 1 0.84 83 75 47.47 39 34 46.58 245 TCGA-AB-2807 7 128267950 128267950 C T SNP FLNC NM_001458.1 human genbank 54_36p 1 reviewed silent c.1662 p.Y554 0.972 "HMMSmart_SM00557,superfamily_E set domains,HMMPfam_Filamin" "HMMSmart_SM00557,PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_SM00033,superfamily_E set domains,superfamily_Calponin-homology domain CH-domain,HMMPfam_Filamin" - no_errors tier1 1521 59 3.73 97 88 47.57 NA 245 TCGA-AB-2807 6 151715435 151715435 G A SNP AKAP12 NM_005100.3 human genbank 54_36p 1 reviewed missense c.4216 p.V1406I 0 NULL "HMMPfam_WSK,HMMPfam_RII_binding_1" - no_errors tier1 223 1 0.45 233 205 46.8 NA 245 TCGA-AB-2807 6 160918157 160918157 C T SNP LPA NM_005577.2 human genbank 54_36p -1 validated splice_site c.4631+1 e28+1 1 - - - no_errors tier1 154 0 325 217 40.04 NA 245 TCGA-AB-2807 4 183901404 183901404 G A SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional missense c.3467 p.R1156H 1 superfamily_ConA_like_lec_gl "HMMPfam_NHL,HMMSmart_EGF,HMMPfam_RHS_repeat,superfamily_CarboxypepD_reg,superfamily_ConA_like_lec_gl,HMMPfam_Ten_N,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_SSF101898,superfamily_SSF57196,superfamily_SSF63829" - no_errors tier1 166 0 126 119 48.57 NA 245 TCGA-AB-2807 2 197302357 197302357 G A SNP CCDC150 NM_001080539.1 human genbank 54_36p 1 provisional splice_site c.2751+1 e23+1 0.997 - - - no_errors tier1 345 3 0.86 284 210 42.51 NA 245 TCGA-AB-2807 2 210491539 210491539 G A SNP uc002vdl.1 ENST00000272845 human ensembl 54_36p 1 known silent c.2577 p.P859 0.915 NULL NULL - no_start_codon tier1 243 0 227 237 51.08 NA 269 TCGA-AB-2808 18 19648425 19648425 T C SNP LAMA3 NM_198129.3 human genbank 54_36p 1 reviewed missense c.1849 p.Y617H 0.977 "HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,superfamily_EGF/Laminin" "HMMPfam_Laminin_B,HMMSmart_SM00282,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMSmart_SM00181,HMMPfam_Laminin_N,HMMSmart_SM00136,superfamily_Galactose-binding domain-like,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_I,HMMPfam_Laminin_II,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMSmart_SM00281,PatternScan_CHAPERONINS_CPN60,superfamily_EGF/Laminin" - no_errors tier1 53 3 5.36 101 96 48.24 NA 269 TCGA-AB-2808 1 35033304 35033304 G A SNP GJA4 NM_002060.2 human genbank 54_36p 1 reviewed silent c.903 p.A301 0.012 NULL "HMMPfam_Connexin,HMMSmart_SM00037,PatternScan_CONNEXINS_1,PatternScan_CONNEXINS_2,HMMPfam_Connexin_CCC" - no_errors tier1 43 1 2.27 37 42 53.16 NA 269 TCGA-AB-2808 1 36706021 36706021 G A SNP CSF3R NM_156039.2 human genbank 54_36p -1 reviewed missense c.1853 p.T618I 0.989 superfamily_FN_III-like "PatternScan_HEMATOPO_REC_L_F2,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_Lep_receptor_Ig" - no_errors tier1 61 0 184 39 17.33 250 95 27.54 269 TCGA-AB-2808 19 38484208 38484209 - TCA INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_ins c.953_952 p.318in_frame_insM 0.992:0.993 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 269 TCGA-AB-2808 6 76079603 76079603 G A SNP FILIP1 NM_015687.2 human genbank 54_36p -1 validated nonsense c.2665 p.R889* 0.294 NULL HMMPfam_CortBP2 - no_errors tier1 106 7 6.19 139 124 47.15 NA 269 TCGA-AB-2808 2 79938770 79938770 C T SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated missense c.422 p.A141V 0.999 "HMMPfam_Vinculin,superfamily_alpha-catenin/vinculin" "PatternScan_VINCULIN_1,HMMPfam_Vinculin,superfamily_alpha-catenin/vinculin" - no_errors tier1 41 3 6.82 44 51 53.68 NA 269 TCGA-AB-2808 8 113720223 113720223 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated missense c.3404 p.R1135H 1 "HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain" "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,PatternScan_GLYCOSYL_HYDROL_F10,superfamily_Complement control module/SCR domain" - no_errors tier1 74 4 5.13 95 51 34.23 NA 269 TCGA-AB-2808 1 115060267 115060267 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.38 p.G13D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 74 0 153 31 16.85 26 5 16.13 269 TCGA-AB-2808 1 115397524 115397524 G A SNP TSPAN2 NM_005725.3 human genbank 54_36p -1 reviewed missense c.599 p.T200M 1 HMMPfam_Tetraspannin "superfamily_Tetraspanin,HMMPfam_Tetraspannin,PatternScan_TM4_1" - no_errors tier1 63 4 5.97 215 120 35.61 21 2 8.7 269 TCGA-AB-2808 12 125915679 125915679 G A SNP LOC121296 XR_016630.1 human genbank 54_36p 1 model rna NULL NULL 1 - - - no_errors tier1 60 0 112 17 12.88 NA 269 TCGA-AB-2808 6 127838631 127838631 G T SNP C6orf174 NM_001012279.1 human genbank 54_36p -1 validated missense c.2233 p.R745S 1 NULL NULL - no_errors tier1 10 0 15 16 51.61 NA 287 TCGA-AB-2809 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 906 223 19.7 65 41 38.32 NA NA 287 TCGA-AB-2809 14 50293976 50293976 T C SNP NIN NM_020921.3 human genbank 54_36p -1 reviewed silent c.3522 p.E1174 0.902 NULL "HMMPfam_efhand,superfamily_EF-hand" - no_errors tier1 202 16 7.34 124 66 34.55 NA NA NA 287 TCGA-AB-2809 19 55554088 55554088 C T SNP NAPSA NM_004851.1 human genbank 54_36p -1 reviewed missense c.1027 p.V343I 1 "HMMPfam_Asp,superfamily_Pept_Aspartic" "HMMPfam_Asp,PatternScan_ASP_PROTEASE,superfamily_Pept_Aspartic" - no_errors tier1 2523 74 2.85 73 30 29.13 NA NA NA 287 TCGA-AB-2809 7 89694251 89694251 C T SNP STEAP2 NM_001040665.1 human genbank 54_36p 1 reviewed nonsense c.523 p.R175* 0.992 "HMMPfam_F420_oxidored,superfamily_NAD(P)-binding Rossmann-fold domains" "HMMPfam_F420_oxidored,HMMPfam_Ferric_reduct,superfamily_NAD(P)-binding Rossmann-fold domains" - no_errors tier1 135 5 3.55 126 49 27.84 NA NA NA 287 TCGA-AB-2809 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 295 TCGA-AB-2810 X 31764826 31764826 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed missense c.7130 p.P2377L 1 superfamily_Spectrin repeat "HMMPfam_ZZ,HMMSmart_SM00291,PatternScan_ZF_ZZ_1,HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain,PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_Spectrin,superfamily_Prefoldin,superfamily_t-snare proteins,HMMPfam_efhand_1,HMMPfam_efhand_2,superfamily_Calponin-homology domain CH-domain,HMMSmart_SM00150,superfamily_Spectrin repeat,superfamily_EF-hand" - no_errors tier1 112 9 7.38 209 161 42.93 NA 295 TCGA-AB-2810 19 36461818 36461818 C T SNP TSHZ3 NM_020856.2 human genbank 54_36p -1 validated missense c.721 p.D241N 1 NULL "HMMPfam_Homeobox,HMMSmart_HOX,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Homeodomain_like,HMMSmart_ZnF_C2H2,PatternScan_HOMEOBOX_1" - no_errors tier1 1001 126 11.14 164 146 46.79 NA 295 TCGA-AB-2810 21 36755479 36755479 C T SNP CLDN14 NM_012130.1 human genbank 54_36p -1 reviewed missense c.385 p.G129S 1 HMMPfam_PMP22_Claudin "HMMPfam_PMP22_Claudin,PatternScan_CLAUDIN" - no_errors tier1 148 10 6.33 53 19 26.39 NA 295 TCGA-AB-2810 19 47530112 47530112 G A SNP MEGF8 NM_001410.2 human genbank 54_36p 1 validated silent c.465 p.P155 0 HMMSmart_EGF "PatternScan_ASX_HYDROXYL,HMMPfam_CUB,HMMSmart_CUB,superfamily_CUB,HMMSmart_EGF_CA,HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,PatternScan_EGF_LAM_1,HMMPfam_PSI,HMMSmart_PSI,HMMSmart_EGF,HMMPfam_Kelch_1,superfamily_Gal_oxid_central,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_SSF57196" - no_errors tier1 72 10 12.2 48 44 47.31 4 2 33.33 295 TCGA-AB-2810 3 48674114 48674114 T C SNP CELSR3 NM_001407.2 human genbank 54_36p -1 reviewed missense c.958 p.N320D 1 NULL "PatternScan_ASX_HYDROXYL,HMMPfam_GPS,HMMSmart_SM00303,HMMPfam_7tm_2,HMMSmart_SM00282,HMMPfam_HRM,HMMSmart_SM00008,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Cadherin-like,PatternScan_G_PROTEIN_RECEP_F2_2,superfamily_EGF/Laminin" - no_errors tier1 78 6 7.14 30 34 53.12 NA 295 TCGA-AB-2810 19 53570758 53570758 C T SNP SYNGR4 NM_012451.2 human genbank 54_36p 1 reviewed silent c.408 p.F136 0.848 HMMPfam_MARVEL HMMPfam_MARVEL - no_errors tier1 591 62 9.47 49 41 45.05 1 100 295 TCGA-AB-2810 3 62493667 62493667 C T SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed missense c.2210 p.R737Q 1 NULL "HMMPfam_C2,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_DUF1041,superfamily_PH domain-like" - no_errors tier1 238 12 4.8 135 111 44.4 NA 295 TCGA-AB-2810 10 72721224 72721224 C T SNP UNC5B NM_170744.3 human genbank 54_36p 1 validated missense c.1324 p.P442S 1 NULL "HMMPfam_Death,HMMSmart_SM00005,HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_ZU5,HMMSmart_SM00218,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_DEATH domain,HMMPfam_I-set,superfamily_Immunoglobulin" - no_errors tier1 171 14 7.57 48 32 39.02 NA 295 TCGA-AB-2810 5 79063408 79063408 G A SNP CMYA5 NM_153610.3 human genbank 54_36p 1 validated missense c.3064 p.E1022K 0.262 NULL "HMMPfam_SPRY,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" - no_errors tier1 188 14 6.93 203 169 44.83 NA 295 TCGA-AB-2810 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 186 20 9.66 64 49 42.98 153 162 51.27 295 TCGA-AB-2810 1 100777515 100777515 C A SNP GPR88 NM_022049.2 human genbank 54_36p 1 validated silent c.405 p.A135 0.994 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 15 1 6.25 18 21 52.5 NA 295 TCGA-AB-2810 6 122017543 122017543 C T SNP LOC442255 XR_016618.2 human genbank 54_36p 1 model rna NULL NULL 0.047 - - - pseudogene tier1 215 23 9.62 189 157 45.24 35 0 295 TCGA-AB-2810 5 141009287 141009287 C T SNP FCHSD1 NM_033449.1 human genbank 54_36p -1 provisional silent c.234 p.R78 0.999 "HMMPfam_FCH,HMMSmart_SM00055" "HMMPfam_FCH,HMMSmart_SM00055,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_SH3_2" - no_errors tier1 195 21 9.72 51 34 39.53 0 295 TCGA-AB-2810 1 166227168 166227168 T C SNP IQWD1 NM_018442.1 human genbank 54_36p 1 validated missense c.655 p.Y219H 1 "HMMSmart_WD40,superfamily_WD40_like,HMMPfam_WD40" "HMMSmart_IQ,HMMSmart_WD40,superfamily_WD40_like,HMMPfam_WD40" - no_errors tier1 68 17 20 122 116 48.33 8 10 55.56 295 TCGA-AB-2810 6 168750815 168750815 G A SNP SMOC2 NM_022138.1 human genbank 54_36p 1 provisional missense c.911 p.R304Q 0.973 NULL "HMMPfam_Thyroglobulin_1,HMMSmart_TY,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin_1,HMMSmart_EFh,HMMPfam_Kazal_1,HMMSmart_KAZAL,PatternScan_EF_HAND_1,HMMPfam_SPARC_Ca_bdg,superfamily_SSF47473" - no_errors tier1 70 9 11.39 28 29 50.88 NA 295 TCGA-AB-2810 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 296 TCGA-AB-2811 MT 2779 2779 G A SNP ENSG00000210082 ENST00000387347 human ensembl 54_36p 1 known rna NULL NULL NULL - - - no_errors tier1 1745 83 4.52 3832 1399 26.7 NA NA NA 296 TCGA-AB-2811 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 73 6 7.5 91 84 48 23 26 53.06 296 TCGA-AB-2811 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 69 2 2.82 118 114 49.14 235 117 33.24 296 TCGA-AB-2811 12 49743968 49743968 T C SNP CSRNP2 NM_030809.1 human genbank 54_36p -1 provisional missense c.1460 p.E487G 0.75 NULL NULL - no_errors tier1 73 3 3.95 161 132 45.05 8 3 27.27 296 TCGA-AB-2811 X 53449304 53449304 C T SNP SMC1A NM_006306.2 human genbank 54_36p -1 reviewed missense c.1757 p.R586Q 1 "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" - no_errors tier1 22 1 4.35 8 97 92.38 5 12 70.59 296 TCGA-AB-2811 2 94906188 94906188 A G SNP TEKT4 NM_144705.2 human genbank 54_36p 1 provisional missense c.1255 p.M419V 1 HMMPfam_Tektin HMMPfam_Tektin - no_errors tier1 41 1 2.38 60 53 46.9 3 0 296 TCGA-AB-2811 9 97260346 97260346 C T SNP PTCH1 NM_000264.3 human genbank 54_36p -1 reviewed missense c.2938 p.G980S 1 HMMPfam_Patched "HMMPfam_Patched,superfamily_SSF82866" - no_errors tier1 172 23 11.56 132 107 44.77 1 0 296 TCGA-AB-2811 7 111168880 111168880 G T SNP DOCK4 NM_014705.3 human genbank 54_36p -1 reviewed missense c.4844 p.A1615E 0.994 NULL "HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_SH3_2" - no_errors tier1 50 1 1.96 126 111 46.84 NA 296 TCGA-AB-2811 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 296 TCGA-AB-2811 5 180099606 180099606 C T SNP OR2Y1 NM_001001657.1 human genbank 54_36p -1 provisional nonsense c.59 p.W20* 0.001 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 183 23 11.17 307 257 45.57 NA 104851 TCGA-AB-2812 13 23956867 23956867 C T SNP PARP4 NM_006437.3 human genbank 54_36p -1 reviewed missense c.1372 p.V458I 0.975 "HMMPfam_PARP,superfamily_SSF56399" "HMMPfam_BRCT,HMMSmart_BRCT,superfamily_BRCT,HMMPfam_VWA,HMMSmart_VWA,superfamily_PARP_reg,HMMSmart_VIT,HMMPfam_PARP,HMMPfam_VIT,superfamily_SSF53300,superfamily_SSF56399" - no_errors tier1 52 0 159 30 15.62 103 0 104851 TCGA-AB-2812 13 27506256 27506257 - TCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1800_1799 p.601in_frame_insSSDNEYFYVDFREYEYD 0.998:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 104851 TCGA-AB-2812 12 40799117 40799117 T C SNP GLT8D3 NM_173601.1 human genbank 54_36p -1 validated silent c.438 p.Q146 0.647 "HMMPfam_Glyco_transf_8,superfamily_Nucleotide-diphospho-sugar transferases" "HMMPfam_Glyco_transf_8,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 68 1 1.45 174 106 37.32 10 6 37.5 104851 TCGA-AB-2812 20 43886574 43886574 G T SNP TNNC2 NM_003279.2 human genbank 54_36p -1 reviewed missense c.166 p.L56M 1 "HMMSmart_SM00054,HMMPfam_efhand,superfamily_EF-hand" "HMMSmart_SM00054,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_EF-hand" - no_errors tier1 50 6 10.71 120 107 46.93 1 0 104851 TCGA-AB-2812 12 47602220 47602220 C A SNP FKBP11 NM_016594.1 human genbank 54_36p -1 validated silent c.420 p.L140 0.997 "HMMPfam_FKBP_C,superfamily_SSF54534" "HMMPfam_FKBP_C,superfamily_SSF54534" - no_errors tier1 79 1 1.23 166 140 45.45 22 10 31.25 104851 TCGA-AB-2812 16 55484452 55484452 C T SNP SLC12A3 NM_000339.2 human genbank 54_36p 1 reviewed missense c.2533 p.L845F 0.999 NULL "HMMPfam_AA_permease,HMMPfam_AA_permease_N" - no_errors tier1 30 0 112 103 47.47 NA 104851 TCGA-AB-2812 11 99717125 99717125 A C SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed missense c.3008 p.E1003A 1 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 88 5 5.38 211 151 41.14 NA 104851 TCGA-AB-2812 7 113307023 113307023 G T SNP PPP1R3A NM_002711.3 human genbank 54_36p -1 reviewed missense c.1360 p.P454T 0.001 NULL HMMPfam_CBM_21 - no_errors tier1 59 4 6.35 123 134 51.74 NA 104851 TCGA-AB-2812 10 115654646 115654646 T C SNP NHLRC2 NM_198514.2 human genbank 54_36p 1 provisional silent c.1785 p.P595 0.999 NULL "HMMPfam_NHL,superfamily_Thioredoxin-like,superfamily_NHL repeat" - no_errors tier1 53 5 8.62 136 108 43.9 15 3 16.67 104851 TCGA-AB-2812 5 170770150 170770151 - TGCA INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.861_862 p.W287fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 104851 TCGA-AB-2812 2 201703073 201703073 G A SNP CFLAR NM_003879.1 human genbank 54_36p 1 validated silent c.240 p.E80 0.938 NULL "HMMPfam_DED,HMMSmart_SM00031,superfamily_DEATH domain,HMMPfam_Peptidase_C14,HMMSmart_SM00115,superfamily_Caspase-like" - no_errors tier1 51 3 5.56 98 73 42.44 62 74 54.41 147796 TCGA-AB-2813 17 7519128 7519128 C T SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.527 p.C176Y 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 691 18 2.49 46 156 76.47 1 81 98.78 147796 TCGA-AB-2813 4 10054632 10054632 A T SNP ZNF518B NM_053042.2 human genbank 54_36p -1 validated missense c.2419 p.L807I 0.001 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 517 7 1.32 139 37 20.9 6 8 57.14 147796 TCGA-AB-2813 19 18237918 18237918 T C SNP KIAA1683 NM_025249.1 human genbank 54_36p -1 validated missense c.1432 p.K478E 0.02 NULL "HMMPfam_IQ,HMMSmart_SM00015,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 517 13 2.44 92 53 36.55 3 2 40 147796 TCGA-AB-2813 14 18447885 18447885 G A SNP OR11H12 NM_001013354.1 human genbank 54_36p 1 provisional missense c.292 p.V98I 0.016 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 154 1 0.65 64 29 30.53 NA 147796 TCGA-AB-2813 6 32656522 32656522 T G SNP HLA-DRB1 NM_002124.2 human genbank 54_36p -1 reviewed missense c.742 p.I248L 0.956 NULL "HMMPfam_MHC_II_beta,PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_MHC antigen-recognition domain,superfamily_Immunoglobulin" - no_errors tier1 245 43 14.93 149 24 13.71 717 1 0.14 147796 TCGA-AB-2813 1 37080106 37080106 G A SNP GRIK3 NM_000831.3 human genbank 54_36p -1 reviewed missense c.1348 p.R450W 1 "HMMSmart_PBPe,HMMPfam_Lig_chan-Glu_bd,superfamily_SSF53850" "HMMPfam_Lig_chan,HMMSmart_PBPe,HMMPfam_ANF_receptor,HMMPfam_Lig_chan-Glu_bd,superfamily_SSF53822,superfamily_SSF53850,superfamily_SSF55620" - no_errors tier1 470 5 1.04 109 48 30.19 NA 147796 TCGA-AB-2813 18 45772699 45772699 T C SNP MYO5B NM_001080467.1 human genbank 54_36p -1 provisional missense c.713 p.N238S 1 "HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_IQ,HMMSmart_SM00015,HMMPfam_Myosin_head,HMMSmart_SM00242,HMMPfam_DIL,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1810 20 1.09 96 168 61.99 1 0 147796 TCGA-AB-2813 14 60586994 60586994 T A SNP SLC38A6 NM_153811.1 human genbank 54_36p 1 provisional missense c.937 p.S313T 1 HMMPfam_Aa_trans HMMPfam_Aa_trans - no_errors tier1 665 15 2.19 155 86 35.39 4 8 66.67 147796 TCGA-AB-2813 11 92171938 92171938 G T SNP FAT3 NM_001008781.2 human genbank 54_36p 1 validated silent c.6111 p.T2037 0.992 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Cadherin-like" "PatternScan_ASX_HYDROXYL,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Cadherin-like,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 333 1 0.3 67 46 40 NA 147796 TCGA-AB-2813 9 94319819 94319819 C T SNP ECM2 NM_001393.2 human genbank 54_36p -1 reviewed missense c.452 p.G151E 1 "HMMPfam_VWC,HMMSmart_VWC,PatternScan_VWFC_1" "HMMPfam_VWC,HMMSmart_VWC,PatternScan_VWFC_1,HMMPfam_LRR_1,superfamily_SSF52058" - no_errors tier1 525 14 2.58 128 101 43.53 2 2 50 147796 TCGA-AB-2813 12 100704096 100704096 G A SNP GNPTAB NM_024312.3 human genbank 54_36p -1 validated silent c.396 p.H132 1 NULL "HMMPfam_Notch,HMMSmart_SM00004,superfamily_Notch domain,HMMPfam_DMAP_binding,PatternScan_EF_HAND_1" - no_errors tier1 791 9 1.12 194 130 39.88 56 38 40.43 147796 TCGA-AB-2813 7 107343262 107343262 G A SNP DLD NM_000108.3 human genbank 54_36p 1 reviewed missense c.760 p.D254N 1 "HMMPfam_Pyr_redox,HMMPfam_Pyr_redox_2,superfamily_SSF51905" "HMMPfam_Pyr_redox,HMMPfam_Pyr_redox_dim,PatternScan_PYRIDINE_REDOX_1,HMMPfam_Pyr_redox_2,superfamily_FAD/NAD-linked_reductase_dimer,superfamily_SSF51905" - no_errors tier1 220 3 1.33 118 71 37.17 48 36 42.35 147796 TCGA-AB-2813 X 118607987 118607987 G A SNP NKRF NM_017544.2 human genbank 54_36p -1 validated missense c.1429 p.R477C 1 "HMMSmart_SM00358,superfamily_dsRNA-binding domain-like" "HMMPfam_G-patch,HMMSmart_SM00443,HMMPfam_dsrm,HMMSmart_SM00358,HMMPfam_R3H,HMMSmart_SM00393,superfamily_dsRNA-binding domain-like,superfamily_R3H domain" - no_errors tier1 125 1 0.79 62 11 14.86 9 0 147796 TCGA-AB-2813 4 123884068 123884068 A G SNP BBS12 NM_152618.2 human genbank 54_36p 1 validated missense c.1571 p.Y524C 0.79 "HMMPfam_Cpn60_TCP1,superfamily_GroEL equatorial domain-like" "HMMPfam_Cpn60_TCP1,superfamily_GroEL equatorial domain-like,superfamily_GroEL apical domain-like" - no_errors tier1 237 3 1.23 152 58 27.1 2 100 147796 TCGA-AB-2813 X 130505772 130505772 T C SNP OR13H1 NM_001004486.1 human genbank 54_36p 1 provisional missense c.44 p.I15T 0.89 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 427 14 3.16 38 219 82.95 NA 147796 TCGA-AB-2813 X 130985068 130985068 G C SNP uc004ewl.1 ENST00000370887 human ensembl 54_36p 1 known missense c.82 p.G28R 0.001 NULL "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_start_codon tier1 55 1 1.79 2 18 90 1 15 93.75 147796 TCGA-AB-2813 9 140136178 140136178 G A SNP CACNA1B NM_000718.2 human genbank 54_36p 1 validated missense c.6926 p.R2309H 0.988 NULL "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels" - no_errors tier1 77 4 4.82 31 24 43.64 NA 147796 TCGA-AB-2813 1 151211012 151211012 C T SNP SPRR4 NM_173080.1 human genbank 54_36p 1 provisional missense c.22 p.R8W 0.928 HMMPfam_Cornifin HMMPfam_Cornifin - no_errors tier1 1083 29 2.59 203 137 39.83 NA 150951 TCGA-AB-2814 MT 7962 7962 T C SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known silent c.376 p.L126 NULL "HMMPfam_COX2,superfamily_Cupredoxins" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 2573 33 1.26 227 1109 82.09 NA NA NA 150951 TCGA-AB-2814 4 17774 17774 G A SNP LOC100133718 XM_001713866.1 human genbank 54_36p -1 model missense c.88 p.P30S 0 NULL NULL - no_start_codon:pseudogene:no_stop_codon tier1 377 33 8.05 1078 132 10.81 NA 150951 TCGA-AB-2814 X 9822449 9822449 C A SNP SHROOM2 NM_001649.2 human genbank 54_36p 1 reviewed silent c.501 p.R167 0.89 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_ASD2,HMMPfam_ASD1" - no_errors tier1 31 0 81 35 30.17 NA 150951 TCGA-AB-2814 21 18588511 18588511 G A SNP PRSS7 NM_002772.2 human genbank 54_36p -1 reviewed silent c.2433 p.G811 0.93 "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases" "HMMPfam_SEA,HMMSmart_SM00200,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMPfam_SRCR,HMMPfam_Trypsin,HMMSmart_SM00020,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,superfamily_Trypsin-like serine proteases,HMMSmart_SM00202,superfamily_SRCR-like,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER,superfamily_SEA domain" - no_errors tier1 21 0 45 30 40 NA 150951 TCGA-AB-2814 19 18824815 18824815 T A SNP UPF1 NM_002911.3 human genbank 54_36p 1 reviewed missense c.992 p.V331D 1 NULL "HMMPfam_ResIII,HMMPfam_UPF1_Zn_bind,superfamily_SSF52540" - no_errors tier1 40 0 51 31 37.8 55 42 43.3 150951 TCGA-AB-2814 13 27490640 27490640 A C SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2505 p.D835E 0.991 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 48 0 93 24 19.83 309 147 32.24 150951 TCGA-AB-2814 16 66136380 66136380 C T SNP FAM65A NM_024519.2 human genbank 54_36p 1 validated missense c.2890 p.R964W 0.018 NULL superfamily_ARM-type_fold - no_errors tier1 48 0 30 32 51.61 16 21 56.76 150951 TCGA-AB-2814 5 84881024 84881024 C T SNP LOC645181 XR_017382.2 human genbank 54_36p 1 model rna NULL NULL 0.618 - - - pseudogene tier1 33 1 2.86 71 47 39.5 8 0 150951 TCGA-AB-2814 7 102727130 102727130 G T SNP PMPCB NM_004279.2 human genbank 54_36p 1 reviewed missense c.245 p.G82V 1 "superfamily_Metalloenz_metal-bd,HMMPfam_Peptidase_M16" "PatternScan_INSULINASE,HMMPfam_Peptidase_M16_C,superfamily_Metalloenz_metal-bd,HMMPfam_Peptidase_M16" - no_errors tier1 94 1 1.05 130 63 32.47 57 75 56.82 150951 TCGA-AB-2814 1 119855801 119855801 G A SNP HSD3B1 NM_000862.2 human genbank 54_36p 1 validated missense c.298 p.V100I 0.976 "HMMPfam_3Beta_HSD,superfamily_NAD(P)-bd" "HMMPfam_3Beta_HSD,superfamily_NAD(P)-bd" - no_errors tier1 170 0 288 84 22.4 NA 150951 TCGA-AB-2814 X 128976217 128976218 - A INS BCORL1 NM_021946.2 human genbank 54_36p 1 validated frame_shift_ins c.1788_1789 p.T596fs 0.002:0.198 NULL "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" - no_errors tier1 NA NA NA NA NA NA NA NA NA 150951 TCGA-AB-2814 9 140063588 140063588 C T SNP CACNA1B NM_000718.2 human genbank 54_36p 1 validated missense c.3710 p.S1237L 1 "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels" - no_errors tier1 265 1 0.38 236 138 36.8 NA 150951 TCGA-AB-2814 1 174852074 174852074 G A SNP LOC730167 XM_001134386.1 human genbank 54_36p -1 model missense c.466 p.R156C 1 superfamily_(Phosphotyrosine protein) phosphatases II superfamily_(Phosphotyrosine protein) phosphatases II - no_errors tier1 154 1 0.65 212 137 39.03 1 0 150951 TCGA-AB-2814 3 184065947 184065947 G A SNP ATP11B NM_014616.1 human genbank 54_36p 1 validated missense c.1210 p.V404M 1 "HMMPfam_Hydrolase,superfamily_SSF56784" "HMMPfam_Hydrolase,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_SSF56784,superfamily_SSF81653,superfamily_SSF81660" - no_errors tier1 50 0 94 43 31.16 53 38 41.76 186481 TCGA-AB-2816 20 2332303 2332303 C T SNP TGM6 NM_198994.2 human genbank 54_36p 1 validated silent c.1170 p.F390 0.993 superfamily_Cysteine proteinases "HMMPfam_Transglut_N,HMMPfam_Transglut_core,HMMSmart_SM00460,HMMPfam_Transglut_C,superfamily_Transglutaminase two C-terminal domains,PatternScan_TRANSGLUTAMINASES,superfamily_E set domains,superfamily_Cysteine proteinases" - no_errors tier1 12 0 39 35 47.3 NA 186481 TCGA-AB-2816 2 25310747 25310747 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2644 p.R882C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 59 7 10.61 74 72 48.98 3 30 90.91 186481 TCGA-AB-2816 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 51 1 1.89 105 40 27.21 126 23 15.44 186481 TCGA-AB-2816 10 31033438 31033438 A T SNP LOC645954 XR_017086.2 human genbank 54_36p 1 model rna NULL NULL 1 - - - no_errors tier1 37 5 11.9 99 67 40.12 NA 186481 TCGA-AB-2816 12 48569229 48569229 G C SNP FAIM2 NM_012306.2 human genbank 54_36p -1 validated silent c.675 p.G225 0.973 HMMPfam_UPF0005 HMMPfam_UPF0005 - no_errors tier1 86 7 7.53 194 127 39.56 NA 186481 TCGA-AB-2816 1 115060267 115060267 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.38 p.G13D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 54 4 6.9 155 29 15.76 44 18 29.03 186481 TCGA-AB-2816 9 134437636 134437636 G A SNP C9orf171 NM_207417.1 human genbank 54_36p 1 predicted missense c.881 p.R294H 0.996 NULL NULL - no_errors tier1 26 3 10.34 40 35 45.45 NA 186481 TCGA-AB-2816 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 186481 TCGA-AB-2816 1 207851977 207851977 G A SNP CAMK1G NM_020439.2 human genbank 54_36p 1 reviewed missense c.1133 p.G378D 0.001 superfamily_Protein kinase-like (PK-like) "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 44 3 6.25 80 75 48.08 NA 195182 TCGA-AB-2817 MT 1311 1311 A G SNP ENSG00000211459 ENST00000389680 human ensembl 54_36p 1 novel rna NULL NULL NULL - - - no_errors tier1 1448 12 0.82 2481 2728 52.22 NA NA NA 195182 TCGA-AB-2817 MT 3434 3434 T C SNP MT-ND1 ENST00000361390 human ensembl 54_36p 1 known missense c.127 p.Y43H NULL HMMPfam_NADHdh "HMMPfam_NADHdh,PatternScan_COMPLEX1_ND1_1,PatternScan_COMPLEX1_ND1_2" - no_errors tier1 888 7 0.78 3097 1726 35.73 NA NA NA 195182 TCGA-AB-2817 MT 10493 10493 T C SNP MT-ND4 ENST00000361335 human ensembl 54_36p 1 known missense c.23 p.I8T NULL HMMPfam_Oxidored_q2 HMMPfam_Oxidored_q2 - no_errors tier1 1004 6 0.59 2833 2041 41.85 NA NA NA 195182 TCGA-AB-2817 MT 13116 13116 T C SNP MT-ND5 ENST00000361567 human ensembl 54_36p 1 known missense c.779 p.L260P NULL HMMPfam_Oxidored_q1 "HMMPfam_Oxidored_q1_N,HMMPfam_Oxidored_q1,HMMPfam_NADH5_C" - no_errors tier1 691 1 0.14 1999 1156 36.59 NA NA NA 195182 TCGA-AB-2817 3 3164779 3164779 A G SNP TRNT1 NM_182916.2 human genbank 54_36p 1 validated missense c.1246 p.K416E 1 superfamily_Poly A polymerase C-terminal region-like "HMMPfam_PolyA_pol,superfamily_Nucleotidyltransferase,superfamily_Poly A polymerase C-terminal region-like" - no_errors tier1 27 0 75 62 45.26 16 11 40.74 195182 TCGA-AB-2817 20 22964628 22964628 G A SNP SSTR4 NM_001052.2 human genbank 54_36p 1 validated missense c.508 p.V170M 0.99 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 28 0 16 7 30.43 NA 195182 TCGA-AB-2817 3 44738612 44738612 A T SNP ZNF502 NM_033210.1 human genbank 54_36p 1 validated missense c.1299 p.K433N 1 superfamily_SSF57667 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 153 1 0.64 63 47 42.73 NA 195182 TCGA-AB-2817 16 65673672 65673673 - A INS CBFB NM_022845.2 human genbank 54_36p 1 reviewed frame_shift_ins c.455_456 p.F153fs 1.000:1.000 HMMPfam_CBF_beta "HMMPfam_CBF_beta,superfamily_CBF_beta" - no_errors tier1 NA NA NA NA NA NA NA NA NA 195182 TCGA-AB-2817 5 79070167 79070167 C T SNP CMYA5 NM_153610.3 human genbank 54_36p 1 validated missense c.9823 p.P3275S 0.515 NULL "HMMPfam_SPRY,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" - no_errors tier1 73 0 149 129 46.4 NA 195182 TCGA-AB-2817 15 88215721 88215721 T C SNP AP3S2 NM_005829.4 human genbank 54_36p -1 validated missense c.335 p.H112R 1 "HMMPfam_Clat_adaptor_s,superfamily_SNARE-like" "HMMPfam_Clat_adaptor_s,PatternScan_CLAT_ADAPTOR_S,superfamily_SNARE-like" - no_errors tier1 57 0 24 14 36.84 18 13 41.94 195182 TCGA-AB-2817 10 94825672 94825672 G A SNP CYP26A1 NM_000783.3 human genbank 54_36p 1 reviewed missense c.964 p.V322I 0.887 "HMMPfam_p450,superfamily_Cytochrome_P450" "HMMPfam_p450,superfamily_Cytochrome_P450,PatternScan_CYTOCHROME_P450" - no_errors tier1 64 1 1.54 33 20 37.74 NA 195182 TCGA-AB-2817 6 110407561 110407561 G A SNP GPR6 NM_005284.3 human genbank 54_36p 1 validated missense c.553 p.V185M 1 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 35 0 44 43 49.43 NA 195182 TCGA-AB-2817 7 143204057 143204057 A G SNP FAM115A NM_014719.1 human genbank 54_36p -1 predicted missense c.578 p.F193S 0.934 NULL NULL - no_errors tier1 62 0 13 88 87.13 2 4 66.67 195182 TCGA-AB-2817 7 148135695 148135696 - ATGCA INS EZH2 NM_004456.3 human genbank 54_36p -1 reviewed frame_shift_ins c.2232_2231 p.E745fs 0.985:1.000 NULL "HMMSmart_SANT,HMMPfam_SET,HMMSmart_SET,superfamily_SSF82199" - no_errors tier1 NA NA NA NA NA NA NA NA NA 195182 TCGA-AB-2817 7 148135696 148135697 - ATGCA INS EZH2 NM_004456.3 human genbank 54_36p -1 reviewed frame_shift_ins c.2231_2230 p.I744fs 1.000:1.000 NULL "HMMSmart_SANT,HMMPfam_SET,HMMSmart_SET,superfamily_SSF82199" - no_errors tier1 NA NA NA NA NA NA NA NA NA 195182 TCGA-AB-2817 4 174456015 174456015 A G SNP GALNT7 NM_017423.2 human genbank 54_36p 1 reviewed silent c.1140 p.E380 1 "HMMPfam_Glycos_transf_2,superfamily_Nucleotide-diphospho-sugar transferases" "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,HMMPfam_Glycos_transf_2,superfamily_Ricin B-like lectins,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 42 0 67 60 47.24 25 18 41.86 195182 TCGA-AB-2817 1 188334484 188334484 G A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional missense c.1588 p.R530C 1 NULL "HMMPfam_MACPF,HMMSmart_SM00457" - no_errors tier1 29 0 90 62 40.79 NA 208027 TCGA-AB-2818 11 18271034 18271034 G A SNP HPS5 NM_181507.3 human genbank 54_36p -1 reviewed missense c.1850 p.T617I 1 NULL superfamily_WD40 repeat-like - no_errors tier1 30 0 81 65 44.52 11 8 42.11 208027 TCGA-AB-2818 8 18769577 18769577 C G SNP PSD3 NM_015310.3 human genbank 54_36p -1 validated silent c.1521 p.V507 0.111 NULL "HMMPfam_Sec7,HMMSmart_Sec7,superfamily_Sec7,HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729" - no_errors tier1 77 0 102 79 43.65 2 1 33.33 208027 TCGA-AB-2818 9 22738240 22738240 G A SNP LOC646609 XR_037907.1 human genbank 54_36p 1 model rna NULL NULL 0.042 - - - pseudogene tier1 31 0 77 74 48.68 NA 208027 TCGA-AB-2818 2 25313378 25313378 C G SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2409 p.R803S 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 24 1 4 24 14 36.84 16 5 23.81 208027 TCGA-AB-2818 X 26615585 26615585 G A SNP LOC646346 XR_017105.2 human genbank 54_36p 1 model rna NULL NULL 1 - - - pseudogene tier1 44 0 112 29 20.57 NA 208027 TCGA-AB-2818 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 41 0 71 57 44.53 141 104 42.45 208027 TCGA-AB-2818 16 33332554 33332554 G A SNP LOC647211 XR_017499.2 human genbank 54_36p 1 model rna NULL NULL 0.001 - - - pseudogene tier1 153 0 330 46 12.23 NA 208027 TCGA-AB-2818 6 43089041 43089041 G A SNP MEA1 NM_014623.2 human genbank 54_36p -1 validated silent c.93 p.P31 0.997 HMMPfam_MEA1 HMMPfam_MEA1 - no_errors tier1 125 0 73 55 42.64 16 6 26.09 208027 TCGA-AB-2818 10 95710248 95710248 C G SNP PIPSL ENST00000340582 human ensembl 54_36p -1 known missense c.896 p.R299T 0.156 "HMMPfam_PIP5K,HMMSmart_PIPKc,superfamily_SSF56104" "HMMSmart_VWA,HMMPfam_PIP5K,HMMPfam_UIM,HMMSmart_PIPKc,superfamily_SSF53300,superfamily_SSF56104" - no_errors tier1 31 0 59 51 45.95 34 0 208027 TCGA-AB-2818 8 117944678 117944679 - C INS RAD21 NM_006265.2 human genbank 54_36p -1 reviewed frame_shift_ins c.146_145 p.V49fs 1.000:1.000 HMMPfam_Rad21_Rec8_N "HMMPfam_Rad21_Rec8,HMMPfam_Rad21_Rec8_N" - no_errors tier1 NA NA NA NA NA NA NA NA NA 208027 TCGA-AB-2818 9 122764816 122764816 C A SNP C5 NM_001735.2 human genbank 54_36p -1 reviewed silent c.4458 p.G1486 0.995 "HMMPfam_A2M_recep,superfamily_AM_receptor_bind" "HMMPfam_ANATO,HMMSmart_ANATO,PatternScan_ANAPHYLATOXIN_1,HMMPfam_A2M,HMMPfam_A2M_N,superfamily_Terp_cyc_toroid,HMMPfam_A2M_recep,superfamily_AM_receptor_bind,HMMPfam_A2M_N_2,HMMPfam_A2M_comp,superfamily_Anaphylatoxin,HMMPfam_NTR,HMMSmart_C345C,PatternScan_ALPHA_2_MACROGLOBULIN" - no_errors tier1 54 1 1.82 82 57 41.01 4 6 60 208027 TCGA-AB-2818 6 146167649 146167649 C T SNP FBXO30 NM_032145.4 human genbank 54_36p -1 reviewed missense c.1586 p.R529K 1 NULL "HMMPfam_F-box,HMMSmart_FBOX,superfamily_Traf_like,superfamily_SSF81383" - no_errors tier1 54 1 1.79 97 80 45.2 16 6 27.27 208027 TCGA-AB-2818 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 208027 TCGA-AB-2818 5 179608667 179608667 C T SNP MAPK9 NM_002752.1 human genbank 54_36p -1 reviewed silent c.528 p.A176 0.606 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_MAPK,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" - no_errors tier1 22 0 45 49 52.13 22 26 54.17 208027 TCGA-AB-2818 1 201130363 201130363 T G SNP KLHL12 NM_021633.2 human genbank 54_36p -1 provisional missense c.1273 p.S425R 1 "HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central" "HMMSmart_BTB,HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central,superfamily_BTB/POZ_fold,HMMPfam_BACK,HMMPfam_BTB" - no_errors tier1 27 0 56 59 51.3 3 2 40 208027 TCGA-AB-2818 2 234510743 234510743 G A SNP TRPM8 NM_024080.4 human genbank 54_36p 1 validated missense c.199 p.V67M 0.006 NULL HMMPfam_Ion_trans - no_errors tier1 28 0 65 63 49.22 NA 263578 TCGA-AB-2819 MT 530 530 T C SNP ENSG00000223073 ENST00000411141 human ensembl 54_36p 1 novel rna NULL NULL NULL - - - no_errors tier1 680 5 0.73 292 2998 90.41 NA NA NA 263578 TCGA-AB-2819 MT 11810 11810 T C SNP MT-ND4 ENST00000361381 human ensembl 54_36p 1 known silent c.1050 p.T350 NULL HMMPfam_Oxidored_q1 "HMMPfam_Oxidored_q5_N,HMMPfam_Oxidored_q1" - no_stop_codon:bad_bp_length_for_coding_region tier1 1256 8 0.63 429 5303 91.53 NA NA NA 263578 TCGA-AB-2819 12 16444150 16444150 G T SNP LOC400011 XR_016968.2 human genbank 54_36p -1 model rna NULL NULL 0.986 - - - pseudogene tier1 59 0 159 96 37.5 87 0 263578 TCGA-AB-2819 13 18855134 18855134 G A SNP LOC727895 XM_001125866.2 human genbank 54_36p 1 model missense c.523 p.A175T 0.758 superfamily_Cyclin-like superfamily_Cyclin-like - no_errors tier1 16 0 79 48 36.92 4 0 263578 TCGA-AB-2819 1 22051263 22051263 C T SNP HSPG2 NM_005529.5 human genbank 54_36p -1 validated missense c.6775 p.G2259S 0.999 "HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_I-set,superfamily_Immunoglobulin" "HMMPfam_Laminin_B,HMMPfam_SEA,HMMSmart_SM00200,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMSmart_SM00281,superfamily_Immunoglobulin,superfamily_EGF/Laminin" - no_errors tier1 14 0 45 38 44.71 41 22 34.92 263578 TCGA-AB-2819 13 37054628 37054628 G A SNP POSTN NM_006475.1 human genbank 54_36p -1 validated missense c.1267 p.R423C 1 "HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain" "HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain,HMMPfam_EMI" - no_errors tier1 44 0 94 54 35.76 NA 263578 TCGA-AB-2819 21 40569957 40569957 G A SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated missense c.2293 p.L765F 1 "HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin" "HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 27 0 68 41 37.27 NA 263578 TCGA-AB-2819 2 47881044 47881044 C T SNP MSH6 NM_000179.2 human genbank 54_36p 1 reviewed silent c.2418 p.S806 0.392 "HMMPfam_MutS_III,HMMSmart_SM00533,superfamily_DNA repair protein MutS domain III" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_MutS_V,HMMSmart_SM00534,PatternScan_DNA_MISMATCH_REPAIR_2,HMMPfam_MutS_I,HMMPfam_MutS_III,HMMSmart_SM00533,superfamily_DNA repair protein MutS domain III,HMMPfam_MutS_II,HMMPfam_MutS_IV,superfamily_DNA repair protein MutS domain I,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 59 0 169 132 43.56 44 79 64.23 263578 TCGA-AB-2819 4 55284528 55284528 A C SNP KIT NM_000222.2 human genbank 54_36p 1 reviewed missense c.1253 p.Y418S 0.002 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 30 0 104 42 28 176 0 263578 TCGA-AB-2819 9 78510558 78510558 C T SNP PRUNE2 ENST00000376718 human ensembl 54_36p -1 known missense c.5375 p.R1792Q 0.001 NULL "HMMSmart_SM00516,superfamily_CRAL/TRIO domain,superfamily_Ferritin-like" - no_errors tier1 35 0 126 52 29.05 NA 263578 TCGA-AB-2819 X 99549148 99549148 G A SNP PCDH19 NM_001105243.1 human genbank 54_36p -1 validated silent c.1104 p.I368 0.92 "HMMPfam_Cadherin,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 7 0 21 6 22.22 NA 263578 TCGA-AB-2819 X 109583735 109583735 C A SNP RGAG1 NM_020769.1 human genbank 54_36p 1 provisional silent c.3234 p.G1078 0 NULL HMMPfam_Retrotrans_gag - no_errors tier1 31 0 103 75 42.13 NA 263578 TCGA-AB-2819 7 123296322 123296322 C G SNP HYAL4 NM_012269.2 human genbank 54_36p 1 reviewed missense c.759 p.N253K 0.993 "HMMPfam_Glyco_hydro_56,superfamily_Glyco_hydro_cat" "HMMPfam_Glyco_hydro_56,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Glyco_hydro_cat" - no_errors tier1 52 0 129 79 37.8 NA 263578 TCGA-AB-2819 5 140461079 140461079 C T SNP PCDHB3 NM_018937.2 human genbank 54_36p 1 reviewed missense c.662 p.P221L 0.028 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 19 0 62 30 32.26 NA 263578 TCGA-AB-2819 5 140989468 140989468 T C SNP HDAC3 NM_003883.3 human genbank 54_36p -1 reviewed missense c.443 p.N148S 1 "HMMPfam_Hist_deacetyl,superfamily_Arginase/deacetylase" "HMMPfam_Hist_deacetyl,superfamily_Arginase/deacetylase" - no_errors tier1 82 0 87 66 42.31 31 16 34.04 263578 TCGA-AB-2819 5 149484585 149484585 G A SNP PDGFRB NM_002609.3 human genbank 54_36p -1 reviewed missense c.1810 p.R604C 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 12 0 34 19 35.19 7 4 36.36 263578 TCGA-AB-2819 5 156852676 156852676 G T SNP ADAM19 NM_023038.3 human genbank 54_36p -1 reviewed missense c.1795 p.H599N 0 NULL NULL - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 38 0 178 96 34.66 3 0 263578 TCGA-AB-2819 1 182161933 182161933 C T SNP RGL1 NM_015149.3 human genbank 54_36p 1 validated missense c.2296 p.R766C 1 "HMMPfam_RA,HMMSmart_SM00314,superfamily_Ubiquitin-like" "HMMPfam_RA,HMMSmart_SM00314,HMMPfam_RasGEF_N,HMMSmart_SM00229,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,PatternScan_RASGEF,superfamily_Ubiquitin-like" - no_errors tier1 53 0 149 101 40.08 6 0 263578 TCGA-AB-2819 3 186393047 186393047 T C SNP EHHADH NM_001966.2 human genbank 54_36p -1 validated silent c.1833 p.P611 0.013 superfamily_6DGDH_C_like "HMMPfam_ECH,HMMPfam_3HCDH,HMMPfam_3HCDH_N,PatternScan_3HCDH,superfamily_6DGDH_C_like,superfamily_NAD(P)-bd,PatternScan_ENOYL_COA_HYDRATASE,superfamily_SSF52096" - no_errors tier1 67 0 161 92 35.38 13 9 40.91 263578 TCGA-AB-2819 3 187125967 187125967 G A SNP TRA2B NM_004593.2 human genbank 54_36p -1 validated silent c.312 p.R104 1 superfamily_RNA-binding domain RBD "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 43 0 116 87 42.65 214 226 51.36 269542 TCGA-AB-2820 MT 8103 8103 G A SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known missense c.517 p.D173N NULL "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 1765 24 1.34 1705 644 27.24 NA NA NA 269542 TCGA-AB-2820 4 44736 44736 G A SNP CEP170L XR_042173.2 human genbank 54_36p 1 model rna NULL NULL 0.002 - - - pseudogene tier1 313 38 10.8 577 95 14.01 7 0 269542 TCGA-AB-2820 8 3188242 3188242 A T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated missense c.3616 p.F1206I 0.98 NULL "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,superfamily_Complement control module/SCR domain" - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 110 6 5.04 94 140 57.85 NA 269542 TCGA-AB-2820 17 7518906 7518907 - GCGGCTC INS TP53 NM_000546.4 human genbank 54_36p -1 reviewed frame_shift_ins c.668_667 p.P223fs 0.987:0.989 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 NA NA NA NA NA NA NA NA NA 269542 TCGA-AB-2820 11 9411726 9411726 G A SNP IPO7 NM_006391.2 human genbank 54_36p 1 reviewed missense c.1915 p.V639I 1 superfamily_ARM-type_fold "HMMPfam_IBN_N,superfamily_ARM-type_fold" - no_errors tier1 66 2 2.94 89 186 67.39 17 45 72.58 269542 TCGA-AB-2820 19 18229587 18229587 G T SNP KIAA1683 NM_025249.1 human genbank 54_36p -1 validated silent c.2946 p.A982 0.384 "HMMSmart_SM00015,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_IQ,HMMSmart_SM00015,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 11 0 12 9 42.86 18 6 25 269542 TCGA-AB-2820 13 18649584 18649584 G A SNP TUBA3C NM_006001.1 human genbank 54_36p -1 reviewed missense c.539 p.A180V 1 "HMMPfam_Tubulin,superfamily_Tubulin nucleotide-binding domain-like" "HMMPfam_Tubulin,superfamily_Tubulin C-terminal domain-like,PatternScan_TUBULIN,HMMPfam_Tubulin_C,superfamily_Tubulin nucleotide-binding domain-like" - no_errors tier1 66 1 1.49 98 28 22.22 NA 269542 TCGA-AB-2820 4 21998925 21998925 G A SNP GPR125 NM_145290.2 human genbank 54_36p -1 validated missense c.3467 p.A1156V 0.998 NULL "HMMPfam_GPS,HMMSmart_SM00303,HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_7tm_2,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00409,superfamily_Hormone receptor domain (HRM Pfam 02793),superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 92 1 1.08 131 115 46 1 3 75 269542 TCGA-AB-2820 17 27291451 27291451 G A SNP SUZ12 NM_015355.2 human genbank 54_36p 1 reviewed missense c.308 p.R103Q 1 NULL "PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,HMMPfam_VEFS-Box" - no_errors tier1 98 0 30 36 54.55 19 11 36.67 269542 TCGA-AB-2820 5 39418786 39418787 AC - DEL DAB2 NM_001343.2 human genbank 54_36p -1 validated frame_shift_del c.1032_1031 p.G344fs 0.972:1.000 NULL "PatternScan_PFKB_KINASES_1,HMMPfam_PID,HMMSmart_SM00462,superfamily_PH domain-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 269542 TCGA-AB-2820 X 40635696 40635696 G A SNP LOC100131656 XR_037406.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 59 3 4.84 40 80 65.57 1 0 269542 TCGA-AB-2820 15 41313067 41313067 G A SNP TGM5 NM_201631.2 human genbank 54_36p -1 validated silent c.1986 p.L662 0.927 "HMMPfam_Transglut_C,superfamily_Transglutaminase two C-terminal domains" "HMMPfam_Transglut_N,HMMPfam_Transglut_core,HMMSmart_SM00460,HMMPfam_Transglut_C,superfamily_Transglutaminase two C-terminal domains,PatternScan_TRANSGLUTAMINASES,superfamily_E set domains,superfamily_Cysteine proteinases" - no_errors tier1 111 0 98 68 40.96 NA 269542 TCGA-AB-2820 2 102222123 102222123 C T SNP IL1RL2 NM_003854.2 human genbank 54_36p 1 reviewed missense c.1718 p.T573M 0 NULL "HMMPfam_TIR,HMMSmart_TIR,superfamily_TIR,HMMSmart_IG,HMMPfam_ig,superfamily_SSF48726" - no_errors tier1 126 2 1.56 98 50 33.56 NA 269542 TCGA-AB-2820 1 111294073 111294073 C G SNP C1orf103 NM_018372.1 human genbank 54_36p -1 validated missense c.1792 p.D598H 0 NULL NULL - no_errors tier1 217 1 0.46 354 175 32.77 23 13 36.11 269542 TCGA-AB-2820 12 117325666 117325666 C A SNP SUDS3 NM_022491.2 human genbank 54_36p 1 validated missense c.764 p.A255D 1 NULL HMMPfam_Sds3 - no_errors tier1 99 0 117 117 50 11 5 31.25 269542 TCGA-AB-2820 10 118993771 118993771 G A SNP SLC18A2 NM_003054.3 human genbank 54_36p 1 provisional missense c.421 p.V141I 0.971 "HMMPfam_MFS_1,superfamily_MFS general substrate transporter" "HMMPfam_MFS_1,superfamily_MFS general substrate transporter" - no_errors tier1 90 2 2.17 54 70 55.56 3 100 269542 TCGA-AB-2820 7 138503645 138503645 G T SNP TTC26 NM_024926.1 human genbank 54_36p 1 validated nonsense c.967 p.G323* 1 superfamily_SSF48452 superfamily_SSF48452 - no_errors tier1 191 5 2.54 104 104 49.76 NA 269542 TCGA-AB-2820 8 140700045 140700045 G T SNP KCNK9 NM_016601.2 human genbank 54_36p -1 reviewed silent c.763 p.R255 0.977 superfamily_SSF81324 "HMMPfam_Ion_trans_2,superfamily_SSF81324" - no_errors tier1 88 0 72 37 33.64 NA 269542 TCGA-AB-2820 4 172972307 172972307 A G SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated missense c.1 p.M1V 1 NULL "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,HMMPfam_Glycos_transf_2,superfamily_Ricin B-like lectins,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 33 0 49 44 47.31 NA 269542 TCGA-AB-2820 3 180562900 180562900 G A SNP MFN1 NM_033540.2 human genbank 54_36p 1 reviewed missense c.472 p.V158I 1 "HMMPfam_Dynamin_N,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Dynamin_N,HMMPfam_Fzo_mitofusin,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 123 2 1.6 105 74 40.66 14 15 50 274429 TCGA-AB-2821 4 13224941 13224941 T C SNP BOD1L NM_148894.2 human genbank 54_36p -1 validated missense c.1151 p.K384R 0.002 superfamily_SSF81995 "HMMPfam_AT_hook,HMMSmart_AT_hook,superfamily_SSF81995" - no_errors tier1 74 0 154 90 36.59 30 37 55.22 274429 TCGA-AB-2821 20 30486373 30486373 C T SNP ASXL1 NM_015338.4 human genbank 54_36p 1 reviewed nonsense c.2197 p.Q733* 0.002 NULL NULL - no_errors tier1 8 0 105 44 28.95 47 35 42.68 274429 TCGA-AB-2821 6 33517365 33517365 C T SNP SYNGAP1 NM_006772.2 human genbank 54_36p 1 validated silent c.2100 p.P700 0.996 "HMMSmart_SM00323,superfamily_GTPase activation domain GAP" "HMMPfam_C2,HMMSmart_SM00239,HMMSmart_SM00233,HMMPfam_RasGAP,HMMSmart_SM00323,PatternScan_RAS_GTPASE_ACTIV_1,superfamily_GTPase activation domain GAP,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_PH domain-like" - no_errors tier1 257 1 0.39 201 121 37.12 19 26 57.78 274429 TCGA-AB-2821 21 35174864 35174865 - CC INS RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed frame_shift_ins c.368_367 p.D123fs 0.999:1.000 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 NA NA NA NA NA NA NA NA NA 274429 TCGA-AB-2821 21 43387846 43387846 T G SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.470 p.Q157P 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 22 0 69 54 43.55 35 48 57.83 274429 TCGA-AB-2821 11 55629610 55629610 C T SNP OR8H2 NM_001005200.1 human genbank 54_36p 1 provisional silent c.516 p.N172 0.025 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 39 0 184 103 35.89 NA 274429 TCGA-AB-2821 15 86273475 86273475 A G SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed missense c.2084 p.I695T 1 "HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)" "HMMPfam_LRRNT,HMMSmart_SM00013,HMMSmart_SM00082,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMPfam_LRR_1,PatternScan_RECEPTOR_TYR_KIN_II,HMMSmart_SM00220,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 128 0 163 92 35.38 NA 274429 TCGA-AB-2821 15 88432842 88432842 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.515 p.R172K 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 40 0 144 18 11.11 169 21 11.05 274429 TCGA-AB-2821 8 93096001 93096001 G A SNP RUNX1T1 NM_175634.2 human genbank 54_36p -1 reviewed silent c.450 p.T150 0.845 "HMMPfam_TAFH,HMMSmart_SM00549" "HMMPfam_zf-MYND,PatternScan_ZF_MYND_1,HMMPfam_TAFH,HMMSmart_SM00549,HMMPfam_NHR2" - no_errors tier1 184 0 348 176 33.46 1 0 274429 TCGA-AB-2821 10 99958685 99958685 G A SNP C10orf28 NM_014472.4 human genbank 54_36p 1 validated missense c.824 p.G275D 0.015 NULL NULL - no_errors tier1 110 0 158 76 32.2 15 9 37.5 274429 TCGA-AB-2821 5 150909157 150909157 C T SNP FAT2 NM_001447.2 human genbank 54_36p -1 reviewed missense c.4681 p.E1561K 1 "HMMPfam_Cadherin,superfamily_Cadherin-like" "HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Cadherin-like,superfamily_EGF/Laminin" - no_errors tier1 27 0 91 73 44.51 NA 274429 TCGA-AB-2821 2 191009228 191009228 T G SNP MFSD6 NM_017694.3 human genbank 54_36p 1 validated missense c.228 p.F76L 1 "HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter" "HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter" - no_errors tier1 99 0 161 101 38.4 25 29 52.73 274429 TCGA-AB-2821 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 33 0 93 55 36.67 81 42 34.15 274429 TCGA-AB-2821 1 228481673 228481673 A C SNP GALNT2 NM_004481.3 human genbank 54_36p 1 reviewed missense c.1562 p.K521T 1 "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,superfamily_Ricin B-like lectins" "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,HMMPfam_Glycos_transf_2,superfamily_Ricin B-like lectins,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 36 2 5.26 91 61 39.87 48 35 42.17 274429 TCGA-AB-2821 2 233866685 233866685 T A SNP ATG16L1 NM_030803.3 human genbank 54_36p 1 validated missense c.1673 p.L558Q 0.994 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_ATG16,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 262 0 483 280 36.46 23 10 30.3 275382 TCGA-AB-2822 17 5964535 5964535 G A SNP WSCD1 NM_015253.1 human genbank 54_36p 1 validated missense c.1558 p.V520M 1 superfamily_SSF52540 "HMMPfam_WSC,HMMSmart_WSC,superfamily_SSF52540" - no_errors tier1 36 0 87 15 14.71 NA 275382 TCGA-AB-2822 1 7836067 7836067 G A SNP UTS2 NM_021995.3 human genbank 54_36p -1 reviewed silent c.12 p.N4 0 NULL "HMMPfam_Urotensin_II,PatternScan_UROTENSIN_II" - no_errors tier1 162 0 130 80 38.1 NA 275382 TCGA-AB-2822 19 10019021 10019021 C T SNP uc010dwx.1 ENST00000333905 human ensembl 54_36p 1 known silent c.184 p.L62 0.997 HMMPfam_A2M "HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp" - no_errors tier1 414 0 152 75 33.04 NA 275382 TCGA-AB-2822 17 10301589 10301589 G A SNP MYH4 NM_017533.2 human genbank 54_36p -1 validated silent c.1770 p.D590 1 "HMMPfam_Myosin_head,HMMSmart_MYSc,superfamily_SSF52540" "HMMSmart_IQ,HMMPfam_Myosin_head,HMMSmart_MYSc,HMMPfam_Myosin_tail_1,HMMPfam_Myosin_N,superfamily_SSF52540" - no_errors tier1 58 0 91 49 34.75 NA 275382 TCGA-AB-2822 6 10985374 10985374 G A SNP GCM2 NM_004752.3 human genbank 54_36p -1 reviewed missense c.328 p.R110W 0.85 "HMMPfam_GCM,superfamily_GCM_motif" "HMMPfam_GCM,superfamily_GCM_motif" - no_errors tier1 83 0 88 61 40.67 NA 275382 TCGA-AB-2822 4 17426051 17426051 C T SNP NCAPG NM_022346.3 human genbank 54_36p 1 validated silent c.747 p.L249 0.982 superfamily_ARM-type_fold superfamily_ARM-type_fold - no_errors tier1 66 0 93 44 31.65 2 3 60 275382 TCGA-AB-2822 16 19143586 19143586 G C SNP SYT17 NM_016524.2 human genbank 54_36p 1 validated missense c.1153 p.D385H 0.989 "HMMPfam_C2,HMMSmart_C2,superfamily_C2_CaLB" "HMMPfam_C2,HMMSmart_C2,superfamily_C2_CaLB" - no_errors tier1 363 0 291 159 35.25 NA 275382 TCGA-AB-2822 2 25320712 25320712 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed splice_site c.1668-1 e14-1 1 - - - no_errors tier1 12 0 10 17 62.96 7 14 66.67 275382 TCGA-AB-2822 8 31124475 31124475 G A SNP WRN NM_000553.4 human genbank 54_36p 1 reviewed missense c.3513 p.M1171I 0.995 "HMMPfam_HRDC,HMMSmart_SM00341" "HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_HRDC,HMMSmart_SM00341,HMMPfam_3_5_exonuc,HMMSmart_SM00474,HMMPfam_DEAD,superfamily_Ribonuclease H-like,HMMSmart_SM00487,HMMPfam_RQC,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 47 0 294 119 28.61 45 28 38.36 275382 TCGA-AB-2822 6 33765099 33765099 G A SNP ITPR3 NM_002224.2 human genbank 54_36p 1 validated silent c.6801 p.A2267 0.185 NULL "HMMPfam_RYDR_ITPR,HMMPfam_MIR,superfamily_MIR,HMMPfam_Ion_trans,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_MIR,superfamily_SSF100909" - no_errors tier1 110 0 75 42 35.9 4 3 42.86 275382 TCGA-AB-2822 5 35072874 35072874 G T SNP AGXT2 NM_031900.2 human genbank 54_36p -1 reviewed missense c.416 p.T139N 0.001 "HMMPfam_Aminotran_3,superfamily_PyrdxlP-dep_Trfase_major" "HMMPfam_Aminotran_3,PatternScan_AA_TRANSFER_CLASS_3,superfamily_PyrdxlP-dep_Trfase_major" - no_errors tier1 102 0 186 101 34.95 NA 275382 TCGA-AB-2822 15 50017675 50017675 G C SNP LEO1 NM_138792.2 human genbank 54_36p -1 provisional missense c.1971 p.I657M 1 NULL HMMPfam_Leo1 - no_errors tier1 337 2 0.59 160 105 39.62 24 20 45.45 275382 TCGA-AB-2822 X 53452803 53452803 G C SNP SMC1A NM_006306.2 human genbank 54_36p -1 reviewed missense c.1460 p.A487G 1 "HMMPfam_SMC_N,superfamily_SMC_hinge,superfamily_SSF52540" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" - no_errors tier1 61 1 1.61 22 68 75.56 4 31 88.57 275382 TCGA-AB-2822 X 70272893 70272893 G A SNP MED12 NM_005120.2 human genbank 54_36p 1 validated nonsense c.5063 p.W1688* 1 NULL HMMPfam_Med12 - no_errors tier1 295 0 40 95 69.34 2 38 95 275382 TCGA-AB-2822 X 73535890 73535891 - CTTGAAGAACTGTC INS LOC728748 XR_037583.1 human genbank 54_36p -1 model rna NULL NULL 1.000:0.993 - - - pseudogene tier1 NA NA NA NA NA NA NA NA NA 275382 TCGA-AB-2822 16 74134048 74134048 T C SNP FLJ22167 NM_001077416.1 human genbank 54_36p -1 validated missense c.704 p.Y235C 0.061 HMMPfam_NAcGluc_Transf HMMPfam_NAcGluc_Transf - no_errors tier1 127 0 51 29 35.8 2 2 50 275382 TCGA-AB-2822 5 83438262 83438262 C T SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed silent c.612 p.A204 1 "HMMPfam_F5_F8_type_C,HMMSmart_SM00231,PatternScan_FA58C_1,superfamily_Galactose-binding domain-like" "PatternScan_ASX_HYDROXYL,HMMPfam_F5_F8_type_C,HMMSmart_SM00231,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Galactose-binding domain-like,PatternScan_EGF_1,PatternScan_EGF_2,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 64 0 193 39 16.74 NA 275382 TCGA-AB-2822 10 87369739 87369739 T A SNP GRID1 NM_017551.2 human genbank 54_36p -1 reviewed missense c.2225 p.D742V 1 "HMMPfam_Lig_chan,HMMSmart_SM00079,superfamily_Periplasmic binding protein-like II" "HMMPfam_Lig_chan,HMMSmart_SM00079,HMMPfam_ANF_receptor,PatternScan_ALDEHYDE_DEHYDR_GLU,HMMPfam_Lig_chan-Glu_bd,superfamily_Periplasmic binding protein-like I,superfamily_Periplasmic binding protein-like II" - no_errors tier1 98 0 98 58 37.18 2 0 275382 TCGA-AB-2822 4 106375492 106375492 C - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.944 p.Q317fs 0.998 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 275382 TCGA-AB-2822 12 121243474 121243474 G A SNP LRRC43 NM_001098519.1 human genbank 54_36p 1 validated missense c.1319 p.R440H 0 NULL superfamily_Outer arm dynein light chain 1 - no_errors tier1 129 1 0.77 42 24 36.36 NA 275382 TCGA-AB-2822 6 130803775 130803775 C T SNP TMEM200A NM_052913.2 human genbank 54_36p 1 provisional missense c.515 p.T172M 0.961 NULL HMMPfam_DUF2371 - no_errors tier1 126 0 363 75 17.05 1 0 275382 TCGA-AB-2822 2 136125804 136125804 G A SNP R3HDM1 NM_015361.2 human genbank 54_36p 1 provisional missense c.1655 p.S552N 1 NULL "HMMPfam_R3H,HMMSmart_SM00393,superfamily_R3H domain" - no_errors tier1 147 1 0.68 145 79 34.96 15 23 60.53 275382 TCGA-AB-2822 5 140510496 140510496 T A SNP PCDHB6 NM_018939.2 human genbank 54_36p 1 reviewed missense c.474 p.D158E 0.982 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 51 0 82 64 43.54 NA 275382 TCGA-AB-2822 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 46 0 84 53 38.41 31 39 54.93 291696 TCGA-AB-2823 12 8268635 8268635 G - DEL FAM90A1 NM_018088.3 human genbank 54_36p -1 validated frame_shift_del c.61 p.Q21fs 0 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 294154 TCGA-AB-2824 2 25316790 25316790 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2207 p.R736H 1 "HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 37 4 9.52 36 36 50 6 9 60 294154 TCGA-AB-2824 X 53443351 53443351 C T SNP SMC1A NM_006306.2 human genbank 54_36p -1 reviewed missense c.2447 p.R816H 1 "HMMPfam_SMC_N,superfamily_SSF52540" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" - no_errors tier1 72 1 1.37 187 45 19.23 43 22 33.85 294154 TCGA-AB-2824 6 57166661 57166661 T C SNP RAB23 NM_016277.3 human genbank 54_36p -1 reviewed missense c.512 p.Q171R 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 83 1 1.19 194 40 17.09 5 0 294154 TCGA-AB-2824 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 294154 TCGA-AB-2824 2 207328068 207328068 G A SNP MDH1B NM_001039845.1 human genbank 54_36p -1 validated missense c.820 p.R274C 0.067 superfamily_NAD(P)-binding Rossmann-fold domains "superfamily_LDH C-terminal domain-like,superfamily_NAD(P)-binding Rossmann-fold domains" - no_errors tier1 201 29 12.61 154 127 44.41 NA 296361 TCGA-AB-2825 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 41 25 37.88 21 16 43.24 16 8 33.33 296361 TCGA-AB-2825 13 27506217 27506218 - CCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTATTCGTG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins in_frame_ins 1.000:1.000 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 296361 TCGA-AB-2825 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 311636 TCGA-AB-2826 12 25271542 25271542 T A SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.183 p.Q61H 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 61 5 7.58 80 26 24.53 12 4 25 311636 TCGA-AB-2826 4 55650951 55650951 C T SNP KDR NM_002253.2 human genbank 54_36p -1 validated missense c.3121 p.V1041M 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 137 13 8.67 118 92 43.81 NA 311636 TCGA-AB-2826 2 61301042 61301042 G A SNP USP34 NM_014709.3 human genbank 54_36p -1 validated nonsense c.7954 p.R2652* 1 NULL "HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_Cysteine proteinases" - no_errors tier1 87 4 4.4 137 51 26.84 35 7 16.28 311636 TCGA-AB-2826 5 78616032 78616032 T C SNP LOC643932 XR_017289.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 117 9 7.14 120 107 46.32 2 1 33.33 311636 TCGA-AB-2826 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 71 4 5.26 60 47 43.93 145 101 40.89 311636 TCGA-AB-2826 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 312340 TCGA-AB-2827 9 701981 701981 C G SNP KANK1 NM_015158.2 human genbank 54_36p 1 reviewed silent c.1215 p.A405 0.883 superfamily_ANK "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" - no_errors tier1 48 0 97 23 18.55 NA NA NA 312340 TCGA-AB-2827 22 28728934 28728934 G C SNP MTMR3 NM_021090.3 human genbank 54_36p 1 reviewed missense c.623 p.S208T 1 "HMMPfam_Myotub-related,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_FYVE,HMMSmart_SM00064,HMMSmart_SM00404,HMMPfam_Myotub-related,superfamily_FYVE/PHD zinc finger,PatternScan_TYR_PHOSPHATASE_1,superfamily_PH domain-like,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 41 0 113 83 41.92 NA NA NA 312340 TCGA-AB-2827 1 38000163 38000163 G A SNP EPHA10 NM_001099439.1 human genbank 54_36p -1 validated silent c.351 p.G117 0.531 "HMMPfam_Ephrin_lbd,HMMSmart_SM00615,superfamily_Galactose-binding domain-like" "HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),PatternScan_EGF_2" - no_errors tier1 187 2 1.06 52 8 13.11 NA NA NA 312340 TCGA-AB-2827 19 53299742 53299742 C G SNP PLA2G4C NM_003706.1 human genbank 54_36p -1 provisional missense c.172 p.A58P 0.98 "HMMPfam_PLA2_B,HMMSmart_PLAc,superfamily_Acyl_Trfase/lysoPlipase" "HMMPfam_PLA2_B,HMMSmart_PLAc,superfamily_Acyl_Trfase/lysoPlipase" - no_errors tier1 30 1 3.23 57 53 47.75 NA NA NA 312340 TCGA-AB-2827 16 66131490 66131490 C T SNP FAM65A NM_024519.2 human genbank 54_36p 1 validated missense c.448 p.R150W 1 NULL superfamily_ARM-type_fold - no_errors tier1 99 7 6.6 192 170 46.45 NA NA NA 312340 TCGA-AB-2827 15 67025715 67025715 G A SNP SPESP1 NM_145658.2 human genbank 54_36p 1 provisional missense c.788 p.R263Q 0.09 NULL NULL - no_errors tier1 6 0 134 34 20 NA NA NA 312340 TCGA-AB-2827 17 71669646 71669646 G A SNP RNF157 NM_052916.2 human genbank 54_36p -1 validated silent c.825 p.A275 0.627 superfamily_RING/U-box "HMMSmart_SM00184,HMMPfam_zf-C3HC4,superfamily_RING/U-box" - no_errors tier1 38 0 86 36 29.27 NA NA NA 312340 TCGA-AB-2827 17 74336626 74336626 G A SNP USP36 NM_025090.3 human genbank 54_36p -1 validated silent c.534 p.F178 0.979 "HMMPfam_UCH,superfamily_SSF54001" "HMMPfam_UCH,PatternScan_IG_MHC,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_SSF54001" - no_errors tier1 18 0 95 76 44.19 NA NA NA 312340 TCGA-AB-2827 17 77913366 77913366 C G SNP FLJ35767 NM_207459.1 human genbank 54_36p 1 predicted silent c.51 p.L17 0 NULL NULL - no_errors tier1 61 1 1.61 14 6 30 NA NA NA 312340 TCGA-AB-2827 7 105066182 105066182 C G SNP ATXN7L1 ENST00000297416 human ensembl 54_36p -1 known missense c.1065 p.E355D 1 NULL HMMPfam_SCA7 - no_start_codon tier1 21 0 99 81 44.75 NA NA NA 312340 TCGA-AB-2827 13 113241795 113241795 C T SNP TMCO3 NM_017905.4 human genbank 54_36p 1 validated silent c.1662 p.F554 0.996 HMMPfam_Na_H_Exchanger HMMPfam_Na_H_Exchanger - no_errors tier1 121 0 127 84 39.44 NA NA NA 312340 TCGA-AB-2827 5 122389416 122389416 C T SNP PPIC NM_000943.4 human genbank 54_36p -1 reviewed missense c.472 p.G158S 1 "HMMPfam_Pro_isomerase,superfamily_Cyclophilin-like" "HMMPfam_Pro_isomerase,PatternScan_CSA_PPIASE_1,superfamily_Cyclophilin-like" - no_errors tier1 58 6 9.38 91 50 35.21 NA NA NA 312340 TCGA-AB-2827 8 128819866 128819866 C T SNP MYC NM_002467.3 human genbank 54_36p 1 reviewed missense c.221 p.P74L 1 HMMPfam_Myc_N "HMMPfam_HLH,HMMSmart_SM00353,HMMPfam_Myc-LZ,superfamily_HLH helix-loop-helix DNA-binding domain,HMMPfam_Myc_N" - no_errors tier1 80 0 56 11 16.18 NA NA NA 312340 TCGA-AB-2827 1 149604327 149604327 C T SNP SELENBP1 NM_003944.2 human genbank 54_36p -1 reviewed missense c.1099 p.E367K 0.978 "HMMPfam_SBP56,superfamily_Cyt_cd1_haem_C" "HMMPfam_SBP56,superfamily_Cyt_cd1_haem_C" - no_errors tier1 16 1 5.88 113 94 44.98 NA NA NA 318433 TCGA-AB-2828 19 7009587 7009587 C T SNP LOC653657 XM_928697.3 human genbank 54_36p -1 model silent c.30 p.P10 0.004 NULL NULL - no_errors tier1 17 0 11 6 35.29 NA 318433 TCGA-AB-2828 10 13274457 13274457 G A SNP MCM10 NM_182751.3 human genbank 54_36p 1 reviewed missense c.1631 p.G544E 0.733 HMMPfam_Mcm10 "HMMPfam_zf-primase,HMMPfam_Mcm10" - no_errors tier1 64 5 7.25 82 55 39.86 12 14 51.85 318433 TCGA-AB-2828 1 16398232 16398232 C T SNP ARHGEF19 NM_153213.3 human genbank 54_36p -1 provisional missense c.2251 p.G751S 0.999 "HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain" "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like" - no_errors tier1 161 6 3.59 204 180 46.15 1 0 318433 TCGA-AB-2828 12 26957742 26957742 C A SNP C12orf11 NM_018164.2 human genbank 54_36p -1 validated nonsense c.1720 p.G574* 1 HMMPfam_DUF2151 HMMPfam_DUF2151 - no_errors tier1 128 4 3.03 132 112 45.53 23 10 30.3 318433 TCGA-AB-2828 8 27572859 27572859 G A SNP SCARA3 NM_016240.2 human genbank 54_36p 1 reviewed missense c.1253 p.S418N 0.997 NULL HMMPfam_Collagen - no_errors tier1 61 2 3.17 104 94 47.24 NA 318433 TCGA-AB-2828 19 41189298 41189298 G A SNP C19orf46 NM_001039876.1 human genbank 54_36p -1 validated missense c.734 p.T245I 0.973 NULL HMMPfam_KASH - no_errors tier1 68 3 4.23 41 24 36.92 NA 318433 TCGA-AB-2828 2 44784945 44784945 G A SNP C2orf34 NM_024766.3 human genbank 54_36p 1 validated silent c.396 p.E132 1 "HMMPfam_Methyltransf_16,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_Methyltransf_16,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" - no_errors tier1 119 9 7.03 112 89 44.06 4 1 20 318433 TCGA-AB-2828 19 45068786 45068786 G A SNP FCGBP NM_003890.2 human genbank 54_36p -1 validated missense c.11476 p.P3826S 0.554 NULL "HMMSmart_VWC,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_TIL_assoc,HMMSmart_FOLN,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 23 0 29 3 9.38 3 1 25 318433 TCGA-AB-2828 15 47088804 47088804 C T SNP SECISBP2L NM_014701.2 human genbank 54_36p -1 provisional missense c.1793 p.C598Y 1 NULL "HMMPfam_Ribosomal_L7Ae,superfamily_SSF55315" - no_errors tier1 178 8 4.3 178 164 47.95 18 19 51.35 318433 TCGA-AB-2828 12 51332071 51332071 G A SNP KRT2 NM_000423.2 human genbank 54_36p -1 reviewed silent c.123 p.S41 1 NULL "HMMPfam_Filament,PatternScan_IF" - no_errors tier1 23 1 4.17 38 29 43.28 NA 318433 TCGA-AB-2828 2 71650962 71650962 C T SNP DYSF NM_003494.1 human genbank 54_36p 1 reviewed silent c.3021 p.V1007 0.913 NULL "HMMPfam_C2,HMMSmart_SM00239,HMMSmart_SM00693,HMMSmart_SM00694,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_FerA,HMMPfam_FerB,HMMPfam_FerI" - no_errors tier1 51 0 135 31 18.56 43 9 17.31 318433 TCGA-AB-2828 3 123902717 123902717 C G SNP PARP14 NM_017554.2 human genbank 54_36p 1 validated missense c.2626 p.H876D 0.002 "HMMPfam_Macro,HMMSmart_SM00506,superfamily_Macro domain-like" "HMMPfam_Macro,HMMSmart_SM00506,HMMPfam_PARP,superfamily_Macro domain-like,superfamily_ADP-ribosylation" - no_errors tier1 58 2 3.33 82 85 50.6 22 21 48.84 318433 TCGA-AB-2828 1 246410626 246410626 C T SNP OR2M2 NM_001004688.1 human genbank 54_36p 1 provisional missense c.716 p.T239M 0.002 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 53 3 5.36 93 95 50 NA 327929 TCGA-AB-2829 3 4800546 4800546 G A SNP ITPR1 NM_001099952.1 human genbank 54_36p 1 validated missense c.6413 p.G2138D 0.977 NULL "HMMPfam_RYDR_ITPR,HMMPfam_MIR,superfamily_MIR domain (Pfam 02815),HMMPfam_Ion_trans,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_SM00472,superfamily_IP3 receptor type 1 binding core domain 2" - no_errors tier1 98 1 1.01 139 99 41.25 NA NA NA 327929 TCGA-AB-2829 17 7517825 7517825 T C SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.838 p.R280G 0.997 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 182 1 0.54 189 95 33.1 NA NA NA 327929 TCGA-AB-2829 17 7518334 7518334 C T SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed splice_site c.673-1 e6-1 0.99 - - - no_errors tier1 258 2 0.77 233 124 34.44 NA NA NA 327929 TCGA-AB-2829 21 14667840 14667840 T C SNP HSPA13 NM_006948.4 human genbank 54_36p -1 reviewed missense c.1385 p.N462S 1 NULL "HMMPfam_HSP70,PatternScan_HSP70_1,PatternScan_HSP70_2,PatternScan_HSP70_3,superfamily_Actin-like ATPase domain" - no_errors tier1 47 0 216 31 12.45 NA NA NA 327929 TCGA-AB-2829 11 57009230 57009230 T C SNP SLC43A1 NM_003627.4 human genbank 54_36p -1 provisional missense c.1595 p.Y532C 0.999 superfamily_MFS general substrate transporter superfamily_MFS general substrate transporter - no_errors tier1 33 0 30 26 46.43 NA NA NA 327929 TCGA-AB-2829 15 64581298 64581298 C T SNP RPL4 NM_000968.2 human genbank 54_36p -1 reviewed missense c.428 p.R143H 1 "HMMPfam_Ribosomal_L4,superfamily_Ribosomal protein L4" "HMMPfam_Ribosomal_L4,superfamily_Ribosomal protein L4,PatternScan_RIBOSOMAL_L1E,PatternScan_ALDEHYDE_DEHYDR_GLU" - no_errors tier1 28 0 126 60 32.09 NA NA NA 327929 TCGA-AB-2829 15 86471424 86471424 G A SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed silent c.1266 p.T422 1 NULL "HMMPfam_LRRNT,HMMSmart_SM00013,HMMSmart_SM00082,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMPfam_LRR_1,PatternScan_RECEPTOR_TYR_KIN_II,HMMSmart_SM00220,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 141 0 221 67 23.18 NA NA NA 327929 TCGA-AB-2829 11 93940384 93940384 G C SNP PIWIL4 NM_152431.2 human genbank 54_36p 1 validated missense c.52 p.A18P 0 NULL "HMMPfam_PAZ,HMMPfam_Piwi,superfamily_Ribonuclease H-like,superfamily_PAZ domain" - no_errors tier1 22 0 75 44 36.67 NA NA NA 327929 TCGA-AB-2829 5 179927586 179927586 G T SNP CNOT6 NM_015455.3 human genbank 54_36p 1 reviewed missense c.1004 p.R335L 1 "HMMPfam_Exo_endo_phos,superfamily_DNase I-like" "HMMPfam_LRR_1,HMMSmart_SM00369,HMMPfam_Exo_endo_phos,superfamily_DNase I-like,superfamily_L domain-like" - no_errors tier1 60 0 63 56 47.06 NA NA NA 327929 TCGA-AB-2829 1 226540582 226540582 T G SNP OBSCN NM_001098623.1 human genbank 54_36p 1 reviewed missense c.9185 p.V3062G 0.742 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin" "HMMPfam_IQ,HMMSmart_SM00015,HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMSmart_SM00219,HMMPfam_PH,HMMSmart_SM00233,HMMSmart_SM00220,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_TYR,PatternScan_PROTEIN_KINASE_ST,superfamily_Fibronectin type III,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,PatternScan_GLYCOSYL_HYDROL_F5,superfamily_Immunoglobulin,superfamily_PH domain-like" - no_errors tier1 8 0 21 17 44.74 NA NA NA 346190 TCGA-AB-2830 X 2803884 2803884 G A SNP GYG2 NM_003918.1 human genbank 54_36p 1 validated missense c.1165 p.V389M 0.001 NULL "HMMPfam_Glyco_transf_8,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 58 2 3.33 69 34 33.01 NA 346190 TCGA-AB-2830 10 5812591 5812591 G A SNP C10orf18 NM_017782.3 human genbank 54_36p 1 validated missense c.623 p.R208H 0.005 NULL NULL - no_errors tier1 77 0 72 21 22.58 19 18 48.65 346190 TCGA-AB-2830 X 18252971 18252971 C A SNP SCML2 NM_006089.2 human genbank 54_36p -1 validated missense c.139 p.A47S 1 "HMMSmart_SM00561,superfamily_Tudor/PWWP/MBT" "HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_MBT,HMMSmart_SM00561,superfamily_SAM/Pointed domain,superfamily_Tudor/PWWP/MBT" - no_errors tier1 33 3 8.11 51 34 40 22 0 346190 TCGA-AB-2830 3 24144126 24144126 G A SNP THRB NM_000461.4 human genbank 54_36p -1 reviewed missense c.1012 p.R338W 0.991 "HMMPfam_Hormone_recep,HMMSmart_SM00430,superfamily_Nuclear receptor ligand-binding domain" "HMMPfam_Hormone_recep,HMMSmart_SM00430,HMMPfam_zf-C4,HMMSmart_SM00399,PatternScan_NUCLEAR_REC_DBD_1,superfamily_Nuclear receptor ligand-binding domain,superfamily_Glucocorticoid receptor-like (DNA-binding domain)" - no_errors tier1 117 11 8.59 86 19 18.1 NA 346190 TCGA-AB-2830 2 25310746 25310746 C G SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882P 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 155 12 7.14 48 13 21.31 37 23 37.7 346190 TCGA-AB-2830 13 27506242 27506243 - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1814_1813 p.605in_frame_insSPRGGNEYFYVDFREYEYDLKWE 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 346190 TCGA-AB-2830 1 29415717 29415717 T C SNP MECR NM_016011.1 human genbank 54_36p -1 validated missense c.244 p.I82V 0.997 "superfamily_GroES-like,HMMPfam_ADH_N" "superfamily_GroES-like,HMMPfam_ADH_zinc_N,HMMPfam_ADH_N,superfamily_NAD(P)-binding Rossmann-fold domains" - no_errors tier1 290 4 1.36 59 18 23.38 15 13 46.43 346190 TCGA-AB-2830 15 39891521 39891521 G A SNP MAPKBP1 NM_014994.1 human genbank 54_36p 1 validated silent c.402 p.K134 0.999 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,PatternScan_PTS_HPR_SER,superfamily_WD40 repeat-like,HMMPfam_WD40" - no_errors tier1 260 11 4.06 65 33 33.67 24 32 57.14 346190 TCGA-AB-2830 16 46802498 46802498 G A SNP ABCC11 NM_032583.3 human genbank 54_36p -1 reviewed silent c.1470 p.I490 0 superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain "HMMPfam_ABC_membrane,HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 184 17 8.42 117 61 34.27 NA 346190 TCGA-AB-2830 22 49013906 49013906 A G SNP TUBGCP6 NM_020461.3 human genbank 54_36p -1 reviewed missense c.1082 p.I361T 0.999 HMMPfam_Spc97_Spc98 HMMPfam_Spc97_Spc98 - no_errors tier1 38 1 2.56 30 12 28.57 68 50 42.37 346190 TCGA-AB-2830 12 54092397 54092397 G A SNP PHC1B ENST00000326184 human ensembl 54_36p -1 known silent c.2391 p.L797 0.25 HMMPfam_zf-FCS "HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_zf-FCS,superfamily_SAM/Pointed domain" - no_errors tier1 16 1 5.88 25 11 30.56 41 0 346190 TCGA-AB-2830 X 105956093 105956093 T A SNP TBC1D8B NM_017752.2 human genbank 54_36p 1 validated missense c.1005 p.N335K 0.976 "HMMPfam_GRAM,HMMSmart_SM00568" "HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p,HMMPfam_GRAM,HMMSmart_SM00568,PatternScan_EF_HAND_1,superfamily_EF-hand" - no_errors tier1 19 0 125 31 19.87 4 0 346190 TCGA-AB-2830 4 106410312 106410313 - G INS TET2 ENST00000265149 human ensembl 54_36p 1 known frame_shift_ins c.547_548 p.A183fs 1.000:1.000 NULL NULL - no_start_codon tier1 NA NA NA NA NA NA NA NA NA 346190 TCGA-AB-2830 4 106413304 106413304 A - DEL TET2 ENST00000265149 human ensembl 54_36p 1 known frame_shift_del c.723 p.K241fs 0 NULL NULL - no_start_codon tier1 NA NA NA NA NA NA NA NA NA 346190 TCGA-AB-2830 X 129111222 129111222 G A SNP AIFM1 NM_004208.1 human genbank 54_36p -1 reviewed silent c.252 p.A84 1 NULL "HMMPfam_Pyr_redox_2,superfamily_FAD/NAD-linked reductases dimerisation (C-terminal) domain,superfamily_FAD/NAD(P)-binding domain" - no_errors tier1 141 3 2.08 53 24 31.17 33 0 346190 TCGA-AB-2830 X 138641542 138641542 G A SNP ATP11C NM_173694.1 human genbank 54_36p -1 validated silent c.3336 p.S1112 0.956 NULL "HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N" - no_errors tier1 62 0 96 15 13.51 4 0 346190 TCGA-AB-2830 6 143135644 143135644 C T SNP HIVEP2 NM_006734.3 human genbank 54_36p -1 provisional missense c.1925 p.R642Q 0.983 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 46 4 7.84 62 33 34.74 18 3 14.29 346190 TCGA-AB-2830 2 235615512 235615512 G A SNP SH3BP4 NM_014521.2 human genbank 54_36p 1 reviewed missense c.1360 p.V454M 0.948 NULL "HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_SH3_2" - no_errors tier1 22 0 50 10 16.67 NA 369065 TCGA-AB-2831 2 25316667 25316676 TCGAGGTATA - DEL DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed frame_shift_del c.2330_2321 p.E774fs 0.991:0.997:0.999:0.999:0.999:1.000:1.000:1.000:1.000:1.000 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 NA NA NA NA NA NA NA NA 369065 TCGA-AB-2831 6 74573288 74573288 G T SNP CD109 NM_133493.3 human genbank 54_36p 1 validated missense c.2961 p.W987C 1 "superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp" "HMMPfam_A2M,HMMPfam_A2M_N,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_recep,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_N_2,HMMPfam_A2M_comp,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN" - no_errors tier1 70 1 1.41 95 15 13.51 NA NA NA 369065 TCGA-AB-2831 7 77487021 77487021 C T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed silent c.3915 p.Q1305 1 NULL "HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_Guanylate_kin,HMMSmart_SM00072,PatternScan_GUANYLATE_KINASE_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 21 1 4.55 14 8 36.36 NA NA NA 369065 TCGA-AB-2831 10 99959110 99959110 G A SNP C10orf28 NM_014472.4 human genbank 54_36p 1 validated missense c.1249 p.G417R 0.028 NULL NULL - no_errors tier1 61 1 1.61 148 21 12.35 NA NA NA 380949 TCGA-AB-2832 16 14990830 14990830 T C SNP LOC728138 XM_001128282.2 human genbank 54_36p -1 model missense c.689 p.K230R 0.2 HMMPfam_DUF2152 HMMPfam_DUF2152 - no_errors tier1 26 0 42 11 20.75 34 1 2.86 380949 TCGA-AB-2832 19 20169074 20169074 A G SNP ZNF486 NM_052852.2 human genbank 54_36p 1 provisional missense c.555 p.I185M 0.281 superfamily_SSF57667 "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 57 0 68 59 46.46 NA 380949 TCGA-AB-2832 1 34999735 34999735 G A SNP GJB4 NM_153212.1 human genbank 54_36p 1 validated missense c.293 p.R98H 0.975 HMMPfam_Connexin "HMMPfam_Connexin,HMMSmart_SM00037,PatternScan_CONNEXINS_1,PatternScan_CONNEXINS_2,HMMPfam_Connexin_CCC" - no_errors tier1 49 2 3.92 69 51 42.15 NA 380949 TCGA-AB-2832 22 40603972 40603972 G A SNP SREBF2 NM_004599.2 human genbank 54_36p 1 reviewed missense c.1660 p.V554M 1 NULL "HMMPfam_HLH,HMMSmart_HLH,superfamily_HLH_basic" - no_errors tier1 91 6 6.19 79 50 38.76 59 71 54.62 380949 TCGA-AB-2832 14 67110289 67110289 C T SNP PLEKHH1 NM_020715.2 human genbank 54_36p 1 validated missense c.1858 p.P620S 1 "HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like" "HMMPfam_MyTH4,HMMSmart_SM00139,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_FERM_M,superfamily_Second domain of FERM,HMMSmart_SM00295,superfamily_PH domain-like" - no_errors tier1 100 8 7.41 114 69 37.1 NA 380949 TCGA-AB-2832 15 70832206 70832206 A G SNP ADPGK NM_031284.4 human genbank 54_36p -1 validated silent c.1020 p.S340 0.316 "HMMPfam_ADP_PFK_GK,superfamily_SSF53613" "HMMPfam_ADP_PFK_GK,superfamily_SSF53613" - no_errors tier1 64 3 4.48 83 60 41.67 114 125 52.3 380949 TCGA-AB-2832 9 71537035 71537035 G A SNP PTAR1 NM_001099666.1 human genbank 54_36p -1 validated missense c.482 p.T161I 0.715 superfamily_Prenyl_trans "HMMPfam_PPTA,superfamily_Prenyl_trans" - no_errors tier1 97 7 6.73 97 88 47.31 7 8 53.33 380949 TCGA-AB-2832 14 76314113 76314113 C T SNP VASH1 NM_014909.4 human genbank 54_36p 1 validated missense c.971 p.S324F 1 NULL NULL - no_errors tier1 38 2 5 34 38 52.05 9 11 55 380949 TCGA-AB-2832 16 79719117 79719117 C A SNP PKD1L2 ENST00000299598 human ensembl 54_36p -1 known silent c.6108 p.V2036 1 HMMPfam_PKD_channel "HMMPfam_GPS,HMMSmart_SM00303,PatternScan_CHANNEL_COLICIN,HMMPfam_PLAT,HMMSmart_SM00308,HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_Lipase/lipooxygenase domain (PLAT/LH2 domain),HMMPfam_PKD_channel,superfamily_C-type lectin-like" - no_errors tier1 226 13 5.44 169 138 44.52 NA 380949 TCGA-AB-2832 2 91440296 91440296 A G SNP LOC389000 XM_371534.1 human genbank 54_36p -1 model missense c.1130 p.L377P 1 HMMPfam_Na_H_Exchanger HMMPfam_Na_H_Exchanger - pseudogene tier1 30 1 3.23 78 18 18.75 1 0 380949 TCGA-AB-2832 7 98929185 98929185 C T SNP ZNF394 NM_032164.2 human genbank 54_36p -1 provisional missense c.1589 p.C530Y 1 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_SCAN,HMMSmart_SM00431,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 281 20 6.64 153 94 37.9 86 94 52.22 380949 TCGA-AB-2832 7 129453268 129453268 C T SNP ZC3HC1 NM_016478.3 human genbank 54_36p -1 validated missense c.742 p.A248T 1 NULL HMMPfam_zf-C3HC - no_errors tier1 62 4 6.06 47 38 43.68 13 15 53.57 399253 TCGA-AB-2833 19 10148990 10148990 T A SNP DNMT1 NM_001379.1 human genbank 54_36p -1 reviewed missense c.499 p.I167F 0.993 NULL "HMMPfam_BAH,HMMSmart_SM00439,HMMPfam_DNA_methylase,HMMPfam_zf-CXXC,HMMPfam_DMAP_binding,PatternScan_C5_MTASE_1,PatternScan_C5_MTASE_2,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" - no_errors tier1 173 25 12.56 64 68 51.52 97 54 35.76 399253 TCGA-AB-2833 1 17123487 17123487 G A SNP CROCC NM_014675.3 human genbank 54_36p 1 validated missense c.277 p.V93M 0.916 NULL superfamily_Prefoldin - no_errors tier1 33 2 5.71 72 25 25.77 2 2 50 399253 TCGA-AB-2833 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 44 16 26.23 58 61 51.26 12 25 67.57 399253 TCGA-AB-2833 20 40143967 40143967 C T SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed missense c.4298 p.R1433H 0.836 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMSmart_SM00404,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,PatternScan_TYR_PHOSPHATASE_1,superfamily_Immunoglobulin,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 116 20 14.6 67 63 48.09 NA 399253 TCGA-AB-2833 10 46388671 46388671 G A SNP SYT15 NM_031912.3 human genbank 54_36p -1 reviewed silent c.271 p.L91 0.005 NULL "HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),PatternScan_CNMP_BINDING_1" - no_errors tier1 26 2 7.14 92 25 21.37 1 0 399253 TCGA-AB-2833 11 65472142 65472142 C T SNP TSGA10IP NM_152762.2 human genbank 54_36p 1 validated silent c.1098 p.F366 0.005 NULL NULL - pseudogene tier1 143 14 8.86 107 56 34.36 NA 399253 TCGA-AB-2833 16 65628109 65628109 C T SNP CBFB NM_022845.2 human genbank 54_36p 1 reviewed nonsense c.232 p.R78* 1 "HMMPfam_CBF_beta,superfamily_CBF_beta" "HMMPfam_CBF_beta,superfamily_CBF_beta" - no_errors tier1 54 8 12.9 37 42 53.16 20 6 22.22 399253 TCGA-AB-2833 3 122580309 122580309 C T SNP STXBP5L NM_014980.2 human genbank 54_36p 1 validated missense c.2305 p.R769C 1 NULL "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_LLGL,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 105 15 12.4 48 34 41.46 NA 399253 TCGA-AB-2833 12 122863982 122863982 C T SNP DNAH10 NM_207437.3 human genbank 54_36p 1 validated missense c.2563 p.R855C 0.078 NULL HMMPfam_DHC_N1 - no_errors tier1 154 25 13.81 107 78 42.16 NA 399253 TCGA-AB-2833 3 124554003 124554003 G A SNP ADCY5 NM_183357.1 human genbank 54_36p -1 validated missense c.1250 p.A417V 0.999 NULL "HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase,HMMPfam_DUF1053,PatternScan_GUANYLATE_CYCLASE_1" - no_errors tier1 58 4 6.35 43 32 42.67 NA 407992 TCGA-AB-2834 13 27490640 27490640 A T SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2505 p.D835E 0.991 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 88 13 12.75 131 71 34.63 120 92 43.4 412761 TCGA-AB-2835 12 10432664 10432664 G A SNP KLRK1 NM_007360.2 human genbank 54_36p -1 reviewed missense c.13 p.R5C 0.003 NULL "HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_C-type lectin-like" - no_errors tier1 132 20 13.16 86 55 38.46 1 100 412761 TCGA-AB-2835 5 132459795 132459795 T A SNP HSPA4 NM_002154.3 human genbank 54_36p 1 validated nonsense c.1757 p.L586* 0.003 "HMMPfam_HSP70,superfamily_SSF100920" "HMMPfam_HSP70,PatternScan_HSP70_1,PatternScan_HSP70_2,PatternScan_HSP70_3,superfamily_SSF100920,superfamily_SSF100934,superfamily_SSF53067" - no_errors tier1 126 29 18.47 90 79 46.2 55 11 16.67 412761 TCGA-AB-2835 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 418499 TCGA-AB-2836 13 27506267 27506268 - TTCTCTGAAATCAACGTAGAAGTACTCATTATC INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1789_1788 p.596in_frame_insDNEYFYVDFRE 0.789:0.794 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 418499 TCGA-AB-2836 12 54703753 54703753 C T SNP IKZF4 NM_022465.3 human genbank 54_36p 1 validated missense c.119 p.P40L 1 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 172 0 121 20 14.08 3 1 25 418499 TCGA-AB-2836 1 114323708 114323708 C T SNP OLFML3 NM_020190.2 human genbank 54_36p 1 validated missense c.47 p.S16L 0 NULL "HMMPfam_OLF,HMMSmart_SM00284" - no_errors tier1 182 0 159 29 15.34 NA 418499 TCGA-AB-2836 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 427366 TCGA-AB-2837 1 143963627 143963627 G A SNP LOC100132495 XM_001722237.1 human genbank 54_36p 1 model missense c.380 p.R127K 0.016 NULL NULL - no_errors tier1 3 1 25 42 12 21.82 4 1 20 427366 TCGA-AB-2837 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 432398 TCGA-AB-2838 12 5542827 5542827 C A SNP ANO2 NM_020373.2 human genbank 54_36p -1 validated missense c.2899 p.G967C 0 NULL HMMPfam_DUF590 - no_errors tier1 379 0 96 57 37.01 NA 432398 TCGA-AB-2838 17 7520037 7520037 C T SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed silent c.375 p.T125 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 283 0 42 63 60 4 42 91.3 432398 TCGA-AB-2838 19 10389494 10389494 G T SNP PDE4A ENST00000380702 human ensembl 54_36p 1 known silent c.207 p.P69 0.941 NULL "HMMPfam_PDEase_I,PatternScan_PDEASE_I,HMMSmart_HDc,superfamily_SSF109604" - no_errors tier1 76 0 32 16 33.33 NA 432398 TCGA-AB-2838 12 14689506 14689506 T A SNP GUCY2C NM_004963.3 human genbank 54_36p -1 validated missense c.1721 p.N574I 1 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMPfam_Guanylate_cyc,HMMSmart_SM00044,superfamily_Adenylyl and guanylyl cyclase catalytic domain,HMMSmart_SM00219,HMMPfam_ANF_receptor,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase,PatternScan_GUANYLATE_CYCLASE_1,superfamily_Periplasmic binding protein-like I" - no_errors tier1 165 0 89 51 36.43 NA 432398 TCGA-AB-2838 1 17291560 17291560 G A SNP PADI2 NM_007365.2 human genbank 54_36p -1 reviewed silent c.585 p.P195 0.011 "HMMPfam_PAD_M,superfamily_PAD_central" "superfamily_Cupredoxin,HMMPfam_PAD,HMMPfam_PAD_N,HMMPfam_PAD_M,superfamily_PAD_central,superfamily_SSF55909" - no_errors tier1 94 1 1.03 47 28 37.33 40 10 20 432398 TCGA-AB-2838 11 18718847 18718847 T C SNP PTPN5 NM_006906.1 human genbank 54_36p -1 validated missense c.794 p.Y265C 0.865 NULL "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 139 0 87 32 26.89 NA 432398 TCGA-AB-2838 13 33307285 33307285 G A SNP RFC3 NM_002915.3 human genbank 54_36p 1 reviewed silent c.810 p.R270 0.995 "superfamily_DNA polymerase III clamp loader subunits C-terminal domain,HMMPfam_RFC-E_C" "HMMSmart_SM00382,superfamily_DNA polymerase III clamp loader subunits C-terminal domain,HMMPfam_RFC-E_C,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 35 0 33 21 38.89 14 11 44 432398 TCGA-AB-2838 3 47360205 47360205 T C SNP KLHL18 NM_025010.4 human genbank 54_36p 1 validated missense c.1495 p.S499P 1 "HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain" "HMMSmart_SM00225,HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain,superfamily_POZ domain,HMMPfam_BACK,HMMPfam_BTB" - no_errors tier1 112 0 67 49 42.24 13 14 51.85 432398 TCGA-AB-2838 3 48426931 48426931 G A SNP PLXNB1 NM_002673.1 human genbank 54_36p -1 validated silent c.5457 p.D1819 0.995 "superfamily_GTPase activation domain GAP,HMMPfam_Plexin_cytopl" "HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain,HMMPfam_PSI,PatternScan_LIPOCALIN,HMMPfam_TIG,HMMSmart_SM00429,PatternScan_IG_MHC,HMMSmart_SM00423,superfamily_GTPase activation domain GAP,HMMPfam_Plexin_cytopl,superfamily_E set domains,superfamily_Plexin repeat" - no_errors tier1 72 0 16 11 40.74 1 0 432398 TCGA-AB-2838 17 49255533 49255533 C T SNP KIF2B NM_032559.4 human genbank 54_36p 1 validated missense c.140 p.T47M 0.977 NULL "HMMPfam_Kinesin,HMMSmart_SM00129,PatternScan_KINESIN_MOTOR_DOMAIN1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 86 0 36 32 47.06 NA 432398 TCGA-AB-2838 10 50636573 50636573 G A SNP OGDHL NM_018245.1 human genbank 54_36p -1 validated silent c.72 p.V24 0.001 NULL "HMMPfam_E1_dh,HMMPfam_Transket_pyr,superfamily_SSF52518" - no_errors tier1 36 0 20 8 28.57 NA 432398 TCGA-AB-2838 3 62331988 62331988 T A SNP FEZF2 NM_018008.3 human genbank 54_36p -1 validated missense c.1064 p.H355L 1 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 98 0 52 33 38.82 NA 432398 TCGA-AB-2838 15 71964459 71964459 G C SNP TBC1D21 NM_153356.1 human genbank 54_36p 1 provisional missense c.541 p.E181Q 1 "HMMSmart_TBC,superfamily_RabGAP_TBC" "HMMSmart_TBC,superfamily_RabGAP_TBC" - no_errors tier1 164 3 1.78 75 44 36.97 NA 432398 TCGA-AB-2838 16 73002259 73002259 T C SNP CLEC18B ENST00000268492 human ensembl 54_36p -1 known missense c.17 p.D6G 0 NULL "HMMPfam_Lectin_C,superfamily_C-type lectin-like,PatternScan_C_TYPE_LECTIN_1" - no_start_codon tier1 18 2 10 2 8 80 1 100 432398 TCGA-AB-2838 X 89181766 89181766 C G SNP LOC100130134 XR_037810.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 77 0 17 57 77.03 7 0 432398 TCGA-AB-2838 1 115058051 115058051 T A SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.183 p.Q61H 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 95 1 1.03 77 29 26.85 77 39 33.62 432398 TCGA-AB-2838 8 124290957 124290957 G T SNP FAM83A NM_207006.4 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*40 NULL 0 - - - no_errors tier1 141 0 413 49 10.61 9 0 432398 TCGA-AB-2838 7 148085114 148085114 A G SNP CUL1 NM_003592.2 human genbank 54_36p 1 validated missense c.422 p.N141S 1 "HMMPfam_Cullin,superfamily_Cullin repeat" "HMMPfam_Cullin,PatternScan_CULLIN_1,HMMSmart_SM00182,superfamily_Cullin homology domain,superfamily_Cullin repeat,HMMPfam_Cullin_Nedd8,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 73 0 17 43 71.67 10 47 82.46 432398 TCGA-AB-2838 6 151817475 151817475 C T SNP C6orf211 NM_024573.1 human genbank 54_36p 1 predicted silent c.141 p.H47 1 "HMMPfam_DUF89,superfamily_DUF89" "HMMPfam_DUF89,superfamily_DUF89" - no_errors tier1 87 0 52 24 31.58 8 7 46.67 432398 TCGA-AB-2838 1 153198033 153198033 C G SNP PYGO2 NM_138300.3 human genbank 54_36p -1 validated missense c.1067 p.R356P 0.995 "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger,PatternScan_ZF_PHD_1,HMMPfam_PHD" "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger,PatternScan_ZF_PHD_1,HMMPfam_PHD" - no_errors tier1 93 0 25 31 55.36 28 24 46.15 432398 TCGA-AB-2838 1 153204838 153204838 C G SNP SHC1 NM_183001.1 human genbank 54_36p -1 validated silent c.1428 p.S476 0 superfamily_SH2 domain "HMMPfam_SH2,HMMSmart_SM00252,HMMPfam_PID,HMMSmart_SM00462,superfamily_PH domain-like,superfamily_SH2 domain" - no_errors tier1 854 52 5.65 42 34 44.74 22 27 55.1 432398 TCGA-AB-2838 1 155220785 155220785 G A SNP ARHGEF11 NM_198236.2 human genbank 54_36p -1 reviewed missense c.193 p.R65C 1 "HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ" "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMSmart_RGS,HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ,HMMSmart_PH,HMMPfam_RGS-like,superfamily_Regulat_G_prot_signal_superfam,superfamily_SSF50729" - no_errors tier1 160 0 76 31 28.97 5 4 44.44 432398 TCGA-AB-2838 1 188334865 188334865 G A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional missense c.1207 p.R403C 0.986 NULL "HMMPfam_MACPF,HMMSmart_SM00457" - no_errors tier1 77 1 1.28 14 11 42.31 NA 432398 TCGA-AB-2838 1 188517414 188517414 C T SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional missense c.326 p.R109H 1 "HMMPfam_MACPF,HMMSmart_SM00457" "HMMPfam_MACPF,HMMSmart_SM00457" - no_errors tier1 62 0 21 14 38.89 NA 433325 TCGA-AB-2839 3 1390299 1390299 C A SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed missense c.1798 p.P600T 1 "HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" "HMMSmart_IGc2,HMMSmart_IG,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,superfamily_SSF48726" - no_errors tier1 81 0 60 30 33.33 NA 433325 TCGA-AB-2839 12 1833394 1833394 C A SNP CACNA2D4 NM_172364.4 human genbank 54_36p -1 reviewed missense c.2230 p.A744S 0.824 NULL "HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Cache_1,HMMPfam_VWA_N,superfamily_vWA-like" - no_errors tier1 89 6 6.32 25 35 58.33 6 11 64.71 433325 TCGA-AB-2839 9 4566050 4566050 G A SNP SLC1A1 NM_004170.4 human genbank 54_36p 1 validated missense c.925 p.V309I 0.986 HMMPfam_SDF "HMMPfam_SDF,PatternScan_NA_DICARBOXYL_SYMP_1,PatternScan_NA_DICARBOXYL_SYMP_2" - no_errors tier1 141 8 5.37 71 75 51.37 NA 433325 TCGA-AB-2839 20 20558211 20558211 C A SNP C20orf74 NM_020343.2 human genbank 54_36p -1 validated missense c.1029 p.Q343H 0.972 NULL "HMMPfam_Rap_GAP,superfamily_Rap/Ran-GAP (Pfam 02145)" - no_errors tier1 78 5 6.02 74 56 43.08 9 14 60.87 433325 TCGA-AB-2839 2 25321637 25321637 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed nonsense c.1543 p.Q515* 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 18 0 12 15 55.56 27 16 37.21 433325 TCGA-AB-2839 11 32374484 32374485 - CCGA INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1144_1143 p.A381fs 0.833:0.771 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 433325 TCGA-AB-2839 9 33785590 33785590 C T SNP PRSS3 NM_002771.3 human genbank 54_36p 1 reviewed missense c.19 p.L7F 0.941 NULL "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,PatternScan_TRYPSIN_HIS" - no_errors tier1 105 8 7.08 48 37 43.53 NA 433325 TCGA-AB-2839 19 38484134 38484134 G - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_del c.1027 p.R343fs 1 HMMSmart_BRLZ "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 433325 TCGA-AB-2839 15 38642377 38642377 C T SNP C15orf57 NM_001080791.1 human genbank 54_36p -1 validated missense c.157 p.V53M 0.251 NULL NULL - no_errors tier1 119 3 2.46 33 27 45 26 20 43.48 433325 TCGA-AB-2839 21 40064940 40064940 G A SNP IGSF5 NM_001080444.1 human genbank 54_36p 1 provisional missense c.646 p.V216M 0.992 "HMMSmart_IG,superfamily_SSF48726" "HMMSmart_IG,HMMPfam_I-set,superfamily_SSF48726" - no_errors tier1 36 2 5.26 42 33 44 NA 433325 TCGA-AB-2839 15 43195656 43195656 C A SNP DUOXA2 NM_207581.2 human genbank 54_36p 1 validated missense c.248 p.T83N 0.999 HMMPfam_DuoxA HMMPfam_DuoxA - no_errors tier1 29 1 3.33 15 12 44.44 NA 433325 TCGA-AB-2839 3 51441853 51441853 T C SNP VPRBP ENST00000273612 human ensembl 54_36p -1 known missense c.1589 p.K530R 1 superfamily_ARM repeat "HMMSmart_SM00667,superfamily_WD40 repeat-like,HMMPfam_LisH,superfamily_ARM repeat" - no_errors tier1 67 6 8.22 55 43 43.88 16 7 30.43 433325 TCGA-AB-2839 12 54917304 54917304 G T SNP SLC39A5 NM_173596.1 human genbank 54_36p 1 validated silent c.1389 p.V463 0.997 HMMPfam_Zip HMMPfam_Zip - no_errors tier1 37 1 2.63 14 12 46.15 2 0 433325 TCGA-AB-2839 11 55554670 55554670 C A SNP OR5AS1 NM_001001921.1 human genbank 54_36p 1 provisional missense c.200 p.S67Y 0.965 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 67 7 9.46 83 56 40.29 NA 433325 TCGA-AB-2839 4 55675057 55675057 G A SNP KDR NM_002253.2 human genbank 54_36p -1 validated missense c.791 p.S264F 0.63 "HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 108 7 6.09 55 65 53.72 NA 433325 TCGA-AB-2839 15 81575626 81575626 C T SNP TM6SF1 NM_023003.1 human genbank 54_36p 1 validated silent c.222 p.S74 0.954 NULL NULL - no_errors tier1 222 11 4.72 56 37 39.78 NA 433325 TCGA-AB-2839 12 111424364 111424364 A C SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.1633 p.I545L 1 NULL "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 65 3 4.41 35 36 50.7 23 22 48.89 433325 TCGA-AB-2839 10 112352977 112352977 C T SNP SMC3 NM_005445.3 human genbank 54_36p 1 reviewed missense c.3521 p.T1174I 1 "HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain" - no_errors tier1 23 4 14.81 50 41 44.57 25 18 41.86 433325 TCGA-AB-2839 1 115060267 115060267 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.38 p.G13D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 92 2 2.13 58 35 37.63 37 13 26 433325 TCGA-AB-2839 5 135424452 135424452 C T SNP TGFBI NM_000358.2 human genbank 54_36p 1 reviewed missense c.1834 p.P612S 0.998 "HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain" "HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain,HMMPfam_EMI" - no_errors tier1 213 3 1.39 49 27 35.53 1 100 433325 TCGA-AB-2839 5 170770148 170770149 - TATG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 447649 TCGA-AB-2840 13 27506248 27506249 - ATTTGAGATCATATTCAT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1808_1807 p.603in_frame_insYEYDLK 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 537782 TCGA-AB-2841 21 10120604 10120604 G A SNP BAGE4 NM_181704.1 human genbank 54_36p -1 provisional missense c.5 p.A2V 0 HMMPfam_BAGE HMMPfam_BAGE - no_errors tier1 76 0 56 14 19.44 NA 537782 TCGA-AB-2841 10 46388671 46388671 G A SNP SYT15 NM_031912.3 human genbank 54_36p -1 reviewed silent c.271 p.L91 0.005 NULL "HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),PatternScan_CNMP_BINDING_1" - no_errors tier1 209 10 4.55 130 42 24 0 537782 TCGA-AB-2841 3 49543349 49543349 G A SNP DAG1 NM_004393.2 human genbank 54_36p 1 reviewed missense c.401 p.S134N 0.264 "HMMSmart_CADG,HMMPfam_DAG1,superfamily_Cadherin" "HMMSmart_CADG,HMMPfam_DAG1,superfamily_Cadherin,superfamily_SSF111006" - no_errors tier1 82 1 1.19 99 72 41.86 6 8 57.14 537782 TCGA-AB-2841 12 51504252 51504252 G A SNP KRT79 NM_175834.2 human genbank 54_36p -1 validated silent c.1017 p.T339 0.988 "superfamily_Prefoldin,HMMPfam_Filament" "superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF" - no_errors tier1 88 0 72 66 47.83 NA 537782 TCGA-AB-2841 9 100011143 100011143 A C SNP TBC1D2 NM_018421.3 human genbank 54_36p -1 validated missense c.1778 p.L593R 1 NULL "HMMPfam_TBC,HMMSmart_TBC,superfamily_RabGAP_TBC,HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729" - no_errors tier1 49 0 65 55 45.83 6 23 76.67 537782 TCGA-AB-2841 3 128398485 128398485 G A SNP C3orf56 ENST00000398112 human ensembl 54_36p 1 known missense c.267 p.M89I 0 NULL NULL - no_errors tier1 33 0 77 53 39.85 NA 537782 TCGA-AB-2841 2 203414070 203414072 GCT - DEL KRT8P15 XR_016994.2 human genbank 54_36p -1 model rna NULL NULL 1.000:0.999:0.999 - - - pseudogene tier1 NA NA NA NA NA NA NA NA NA 558395 TCGA-AB-2842 9 2071904 2071904 C T SNP SMARCA2 NM_003070.3 human genbank 54_36p 1 reviewed missense c.2257 p.L753F 1 "HMMPfam_SNF2_N,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_SNF2_N,HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain,HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_HSA,HMMPfam_BRK,HMMSmart_SM00592,HMMSmart_SM00573,HMMSmart_SM00487,HMMPfam_QLQ,PatternScan_BROMODOMAIN_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 207 22 9.57 63 19 23.17 119 61 33.89 558395 TCGA-AB-2842 1 23278197 23278197 A G SNP AOF2 NM_015013.2 human genbank 54_36p 1 reviewed silent c.1923 p.P641 0.359 "HMMPfam_Amino_oxidase,superfamily_FAD/NAD(P)-binding domain" "HMMPfam_Amino_oxidase,HMMPfam_SWIRM,superfamily_FAD/NAD(P)-binding domain,superfamily_FAD-linked reductases C-terminal domain" - no_errors tier1 84 8 8.7 41 38 48.1 40 29 42.03 569053 TCGA-AB-2843 1 40136201 40136201 T A SNP MYCL1 NM_001033081.1 human genbank 54_36p -1 validated silent c.525 p.V175 1 HMMPfam_Myc_N "HMMPfam_HLH,HMMSmart_SM00353,superfamily_HLH helix-loop-helix DNA-binding domain,HMMPfam_Myc_N" - no_errors tier1 195 2 1.01 57 34 37.36 2 3 60 569053 TCGA-AB-2843 22 41328936 41328936 A G SNP POLDIP3 NM_032311.3 human genbank 54_36p -1 reviewed silent c.234 p.L78 1 NULL "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 269 6 2.18 32 45 58.44 35 26 42.62 569053 TCGA-AB-2843 21 43397525 43397525 G A SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.101 p.S34F 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 69 0 12 13 52 48 61 55.96 569053 TCGA-AB-2843 4 55259459 55259459 C T SNP KIT NM_000222.2 human genbank 54_36p 1 reviewed missense c.590 p.S197L 0.086 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 44 0 32 19 37.25 15 20 57.14 569053 TCGA-AB-2843 4 55294078 55294078 A T SNP KIT NM_000222.2 human genbank 54_36p 1 reviewed missense c.2447 p.D816V 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 59 4 6.35 24 25 51.02 35 43 55.13 569053 TCGA-AB-2843 12 78135485 78135485 G A SNP SYT1 NM_005639.1 human genbank 54_36p 1 validated missense c.55 p.A19T 0.964 NULL "HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)" - no_errors tier1 71 0 54 32 37.21 NA 569053 TCGA-AB-2843 10 95921184 95921184 C A SNP PLCE1 NM_016341.3 human genbank 54_36p 1 validated missense c.1750 p.L584I 0.239 "HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF" "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RA,HMMSmart_SM00314,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand" - no_errors tier1 470 0 206 50 19.46 NA 569053 TCGA-AB-2843 2 98378805 98378805 C T SNP CNGA3 NM_001298.1 human genbank 54_36p 1 reviewed missense c.740 p.T247M 0.001 "HMMPfam_Ion_trans,superfamily_SSF81324" "HMMPfam_cNMP_binding,HMMSmart_cNMP,HMMPfam_Ion_trans,PatternScan_CNMP_BINDING_1,PatternScan_CNMP_BINDING_2,superfamily_cNMP_binding,superfamily_SSF81324" - no_errors tier1 268 2 0.74 53 42 44.21 NA 569053 TCGA-AB-2843 9 119515138 119515141 TTAA - DEL TLR4 NM_138554.3 human genbank 54_36p 1 reviewed frame_shift_del c.911_914 p.N305fs 0.040:0.049:0.060:0.352 superfamily_L domain-like "HMMPfam_TIR,HMMSmart_SM00255,superfamily_Toll/Interleukin receptor TIR domain,HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00365,superfamily_L domain-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 569053 TCGA-AB-2843 7 123386834 123386834 G A SNP SPAM1 NM_003117.3 human genbank 54_36p 1 reviewed missense c.1105 p.V369I 1 HMMPfam_Glyco_hydro_56 "HMMPfam_Glyco_hydro_56,superfamily_Glyco_hydro_cat" - no_errors tier1 228 2 0.87 67 41 37.96 NA 569053 TCGA-AB-2843 5 138237719 138237719 G C SNP LRRTM2 NM_015564.2 human genbank 54_36p -1 validated missense c.430 p.Q144E 1 "HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like" "HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like" - no_errors tier1 203 0 98 42 30 0 569053 TCGA-AB-2843 5 149772478 149772478 G A SNP CD74 NM_001025159.1 human genbank 54_36p -1 validated missense c.28 p.R10W 0.002 NULL "HMMPfam_Thyroglobulin_1,HMMSmart_SM00211,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin type-1 domain,HMMPfam_MHCassoc_trimer,superfamily_Class II MHC-associated invariant chain ectoplasmic trimerization domain,HMMPfam_MHC2-interact" - no_errors tier1 266 1 0.37 51 36 41.38 4335 3678 45.83 570755 TCGA-AB-2844 12 4891072 4891072 C T SNP KCNA1 NM_000217.2 human genbank 54_36p 1 reviewed silent c.267 p.F89 1 "HMMSmart_BTB,HMMPfam_K_tetra,superfamily_BTB/POZ_fold" "HMMSmart_BTB,HMMPfam_K_tetra,HMMPfam_Ion_trans,superfamily_BTB/POZ_fold,superfamily_SSF81324" - no_errors tier1 115 10 7.94 34 25 42.37 NA 570755 TCGA-AB-2844 19 19326222 19326222 C T SNP KIAA0892 NM_015329.3 human genbank 54_36p 1 validated missense c.1607 p.S536L 0.992 "HMMPfam_Cohesin_load,superfamily_TPR-like" "HMMPfam_Cohesin_load,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 39 0 8 4 33.33 50 46 47.92 570755 TCGA-AB-2844 15 19974541 19974541 T C SNP LOC642131 XM_001716834.1 human genbank 54_36p -1 model missense c.115 p.K39E 0.784 "HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" "HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" - no_errors tier1 37 4 9.76 9 8 47.06 2 0 570755 TCGA-AB-2844 8 20082748 20082748 C T SNP SLC18A1 NM_003053.2 human genbank 54_36p -1 validated missense c.8 p.R3Q 0.065 NULL "HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter" - no_errors tier1 111 9 7.38 33 21 38.89 NA 570755 TCGA-AB-2844 13 27506214 27506215 - TTACCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins in_frame_ins 0.779:0.796 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 570755 TCGA-AB-2844 11 32374486 32374487 - ACCGTACA INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1142_1141 p.S381fs 0.996:0.996 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 570755 TCGA-AB-2844 14 44703333 44703333 G A SNP FANCM NM_020937.2 human genbank 54_36p 1 reviewed missense c.1603 p.G535S 1 "HMMPfam_Helicase_C,HMMSmart_SM00490,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_ERCC4,superfamily_RuvA domain 2-like,superfamily_Restriction endonuclease-like,HMMPfam_DEAD,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 122 7 5.38 102 73 41.71 2 3 60 570755 TCGA-AB-2844 X 53458666 53458666 C T SNP SMC1A NM_006306.2 human genbank 54_36p -1 reviewed missense c.287 p.R96H 0.998 "HMMPfam_SMC_N,superfamily_SSF52540" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" - no_errors tier1 138 11 7.24 2 8 80 1 65 98.48 570755 TCGA-AB-2844 2 53982167 53982167 C A SNP PSME4 NM_014614.2 human genbank 54_36p -1 validated missense c.2767 p.G923C 1 superfamily_ARM repeat "HMMPfam_HEAT,superfamily_ARM repeat" - no_errors tier1 96 9 8.57 34 53 60.92 19 25 56.82 570755 TCGA-AB-2844 19 55190328 55190328 C T SNP VRK3 NM_016440.1 human genbank 54_36p -1 reviewed silent c.696 p.K232 0.991 HMMSmart_SM00220 "HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)" - no_errors tier1 305 10 3.14 36 25 40.98 30 29 49.15 570755 TCGA-AB-2844 9 72110092 72110092 A T SNP SMC5 NM_015110.3 human genbank 54_36p 1 validated missense c.1574 p.K525I 0.794 "HMMPfam_SMC_N,superfamily_SSF52540" "HMMPfam_SMC_N,superfamily_SSF52540" - no_errors tier1 108 9 7.5 63 53 45.69 18 18 50 570755 TCGA-AB-2844 X 85301946 85301946 G A SNP LOC100130211 XM_001717632.1 human genbank 54_36p -1 model missense c.1055 p.A352V 1 NULL "HMMPfam_GTP_EFTU,HMMPfam_GTP_EFTU_D3,HMMPfam_GTP_EFTU_D2,superfamily_Translation proteins,superfamily_EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain,superfamily_P-loop containing nucleoside triphosphate hydrolases" - pseudogene tier1 30 4 11.76 1 30 96.77 3 0 570755 TCGA-AB-2844 7 100478014 100478014 T C SNP MUC17 NM_001040105.1 human genbank 54_36p 1 provisional missense c.12433 p.S4145P 0 superfamily_EGF/Laminin "HMMPfam_SEA,HMMSmart_SM00200,PatternScan_EGF_1,superfamily_EGF/Laminin,superfamily_SEA domain" - no_errors tier1 184 8 4.06 11 12 52.17 NA 570755 TCGA-AB-2844 3 102619278 102619278 G A SNP SENP7 NM_020654.1 human genbank 54_36p -1 validated nonsense c.331 p.R111* 1 NULL "HMMPfam_Peptidase_C48,superfamily_Cysteine proteinases" - no_errors tier1 116 8 6.45 54 47 46.53 8 6 42.86 570755 TCGA-AB-2844 5 140595924 140595924 C A SNP PCDHB18 ENST00000274705 human ensembl 54_36p 1 known silent c.1455 p.S485 0.981 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 51 0 9 9 50 0 570755 TCGA-AB-2844 1 148577342 148577342 T C SNP PRPF3 NM_004698.2 human genbank 54_36p 1 reviewed missense c.1118 p.I373T 1 HMMPfam_PRP3 "HMMPfam_PWI,HMMSmart_SM00311,HMMPfam_PRP3,superfamily_PWI domain" - no_errors tier1 470 43 8.3 42 42 50 42 43 50.59 570755 TCGA-AB-2844 3 187126059 187126059 G C SNP TRA2B NM_004593.2 human genbank 54_36p -1 validated missense c.220 p.R74G 1 NULL "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 137 8 5.48 31 37 53.62 150 124 45.09 606061 TCGA-AB-2845 MT 1149 1149 G A SNP ENSG00000211459 ENST00000389680 human ensembl 54_36p 1 novel rna NULL NULL NULL - - - no_errors tier1 1394 73 4.97 103 135 56.49 NA NA NA 606061 TCGA-AB-2845 1 16347846 16347846 G A SNP EPHA2 NM_004431.2 human genbank 54_36p -1 reviewed missense c.437 p.A146V 1 "HMMPfam_Ephrin_lbd,HMMSmart_EPH_lbd,superfamily_Gal_bind_like" "HMMPfam_Ephrin_lbd,HMMSmart_EPH_lbd,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SAM,HMMPfam_fn3,HMMSmart_FN3,PatternScan_PROTEIN_KINASE_TYR,superfamily_FN_III-like,superfamily_Gal_bind_like,superfamily_Grow_fac_recept,superfamily_SAM_homology,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 128 6 4.48 21 22 51.16 8 9 52.94 606061 TCGA-AB-2845 12 30797894 30797894 C T SNP CAPRIN2 NM_001002259.1 human genbank 54_36p -1 validated nonsense c.71 p.W24* 0.015 NULL "HMMPfam_C1q,HMMSmart_SM00110,superfamily_TNF-like" - no_errors tier1 138 3 2.11 35 32 47.76 8 6 42.86 606061 TCGA-AB-2845 19 38484230 38484231 - CGGGTTCTGCTT INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_ins c.931_930 p.310in_frame_insKQNP 1.000:1.000 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 606061 TCGA-AB-2845 19 38485030 38485031 GC - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_del c.131_130 p.A44fs 0.988:0.957 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 606061 TCGA-AB-2845 19 38485031 38485031 C G SNP CEBPA NM_004364.3 human genbank 54_36p -1 reviewed missense c.130 p.A44P 0.957 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 0 0 0 0 0 0 116 90 43.48 606061 TCGA-AB-2845 4 106400342 106400342 G - DEL TET2 ENST00000265149 human ensembl 54_36p 1 known frame_shift_del c.327 p.K110fs 0.996 NULL NULL - no_start_codon tier1 NA NA NA NA NA NA NA NA NA 619751 TCGA-AB-2846 17 596213 596213 A T SNP GEMIN4 NM_015721.2 human genbank 54_36p -1 reviewed missense c.1820 p.L607H 0.999 NULL NULL - no_errors tier1 55 1 1.79 3 5 62.5 18 21 53.85 619751 TCGA-AB-2846 14 19285532 19285532 A G SNP OR4Q3 NM_172194.1 human genbank 54_36p 1 provisional missense c.106 p.I36V 0.004 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 464 12 2.52 61 46 42.59 NA 619751 TCGA-AB-2846 20 30211546 30211546 G A SNP TM9SF4 NM_014742.3 human genbank 54_36p 1 validated missense c.1609 p.V537I 1 HMMPfam_EMP70 HMMPfam_EMP70 - no_errors tier1 245 13 5.04 14 22 61.11 56 38 40.43 619751 TCGA-AB-2846 11 32374485 32374486 - A INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1143_1142 p.A382fs 0.771:0.996 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 619751 TCGA-AB-2846 X 34567329 34567329 C T SNP TMEM47 NM_031442.3 human genbank 54_36p -1 reviewed missense c.323 p.R108Q 1 NULL NULL - no_errors tier1 104 4 3.7 18 10 35.71 1 0 619751 TCGA-AB-2846 4 35829014 35829014 A G SNP ARAP2 NM_015230.2 human genbank 54_36p -1 reviewed missense c.2800 p.Y934H 1 "HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like" "HMMPfam_RA,HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_ArfGap,HMMSmart_SM00105,superfamily_Pyk2-associated protein beta ARF-GAP domain,HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_PH,HMMSmart_SM00233,superfamily_GTPase activation domain GAP,superfamily_SAM/Pointed domain,superfamily_PH domain-like" - no_errors tier1 132 5 3.65 14 6 30 7 8 53.33 619751 TCGA-AB-2846 19 54625658 54625658 G A SNP SLC17A7 NM_020309.3 human genbank 54_36p -1 reviewed missense c.1613 p.P538L 0.264 NULL "HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter" - no_errors tier1 18 0 7 4 36.36 NA 619751 TCGA-AB-2846 4 55284523 55284523 G - DEL KIT NM_000222.2 human genbank 54_36p 1 reviewed frame_shift_del c.1248 p.T417fs 0.99 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 619751 TCGA-AB-2846 4 55284527 55284528 - AGGTGGG INS KIT NM_000222.2 human genbank 54_36p 1 reviewed frame_shift_ins c.1252_1253 p.Y418fs 0.005:0.002 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 619751 TCGA-AB-2846 6 56509558 56509558 C T SNP DST NM_183380.1 human genbank 54_36p -1 reviewed missense c.9857 p.R3286Q 0.169 "HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_Spectrin repeat" "PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_Spectrin,HMMSmart_SM00054,HMMPfam_GAS2,HMMSmart_SM00243,superfamily_Calponin-homology domain CH-domain,HMMSmart_SM00150,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_Spectrin repeat,superfamily_EF-hand" - no_errors tier1 70 4 5.41 13 10 43.48 2 0 619751 TCGA-AB-2846 9 83737543 83737543 G A SNP uc004amh.1 ENST00000341875 human ensembl 54_36p 1 known missense c.2647 p.V883I 0 NULL NULL - no_errors tier1 82 0 21 18 46.15 NA 619751 TCGA-AB-2846 12 107124204 107124204 A G SNP WSCD2 NM_014653.2 human genbank 54_36p 1 validated missense c.391 p.I131V 1 "HMMPfam_WSC,HMMSmart_SM00321" "HMMPfam_WSC,HMMSmart_SM00321,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 176 12 6.38 34 24 41.38 NA 619751 TCGA-AB-2846 7 141413692 141413692 C T SNP MGAM ENST00000312952 human ensembl 54_36p 1 known missense c.5002 p.R1668C 0.019 HMMPfam_Glyco_hydro_31 "HMMPfam_Glyco_hydro_31,PatternScan_GLYCOSYL_HYDROL_F31_1,PatternScan_GLYCOSYL_HYDROL_F31_2,HMMPfam_Trefoil,HMMSmart_SM00018,superfamily_Trefoil,superfamily_(Trans)glycosidases,PatternScan_P_TREFOIL" - no_stop_codon tier1 77 7 8.33 18 9 33.33 NA 619751 TCGA-AB-2846 5 149304237 149304237 G A SNP PDE6A NM_000440.2 human genbank 54_36p -1 reviewed silent c.193 p.L65 0.999 superfamily_SSF55781 "HMMPfam_PDEase_I,PatternScan_PDEASE_I,HMMPfam_GAF,HMMSmart_GAF,HMMSmart_HDc,superfamily_SSF109604,superfamily_SSF55781" - no_errors tier1 204 3 1.45 38 25 39.68 NA 619751 TCGA-AB-2846 5 165388499 165388499 C A SNP LOC728843 XR_015391.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 93 2 2.08 25 16 39.02 1 0 619751 TCGA-AB-2846 3 171623663 171623663 G A SNP CLDN11 NM_005602.5 human genbank 54_36p 1 reviewed missense c.245 p.R82H 1 HMMPfam_PMP22_Claudin "HMMPfam_PMP22_Claudin,PatternScan_CLAUDIN" - no_errors tier1 106 0 15 14 48.28 NA 619751 TCGA-AB-2846 4 189161145 189161145 G A SNP ZFP42 NM_174900.3 human genbank 54_36p 1 validated missense c.190 p.G64R 0.001 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 71 1 1.39 19 13 40.62 NA 619751 TCGA-AB-2846 1 212886431 212886431 C G SNP CENPF NM_016343.3 human genbank 54_36p 1 reviewed missense c.6895 p.L2299V 0 NULL "superfamily_Prefoldin,HMMPfam_Rb-bdg_C_Cenp-F,HMMPfam_Cenp-F_N,HMMPfam_Cenp-F_leu_zip,superfamily_Spectrin repeat" - no_errors tier1 46 0 16 9 36 16 22 57.89 633734 TCGA-AB-2847 4 1378345 1378346 CA - DEL CRIPAK NM_175918.3 human genbank 54_36p 1 validated frame_shift_del c.46_47 p.T17fs 0.758:0.787 NULL HMMSmart_PostSET - no_errors tier1 NA NA NA NA NA NA NA NA NA 633734 TCGA-AB-2847 5 5292824 5292824 G A SNP ADAMTS16 NM_139056.2 human genbank 54_36p 1 reviewed missense c.2309 p.G770E 1 HMMPfam_ADAM_spacer1 "HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_Reprolysin,HMMPfam_Pep_M12B_propep,PatternScan_CARBAMOYLTRANSFERASE,HMMPfam_ADAM_spacer1,HMMPfam_PLAC,superfamily_Metalloproteases (""zincins"") catalytic domain" - no_errors tier1 152 2 1.29 221 108 32.73 NA 633734 TCGA-AB-2847 11 6763236 6763236 C A SNP OR2AG1 NM_001004489.1 human genbank 54_36p 1 provisional missense c.392 p.T131K 0.977 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 188 0 160 82 33.2 NA 633734 TCGA-AB-2847 16 20390039 20390039 G A SNP ACSM2A NM_001010845.2 human genbank 54_36p 1 validated missense c.740 p.G247D 0.999 "HMMPfam_AMP-binding,superfamily_Acetyl-CoA synthetase-like" "HMMPfam_AMP-binding,PatternScan_AMP_BINDING,superfamily_Acetyl-CoA synthetase-like" - no_errors tier1 233 1 0.42 214 130 37.36 NA 633734 TCGA-AB-2847 6 28651673 28651673 G A SNP SCAND3 NM_052923.1 human genbank 54_36p -1 provisional missense c.788 p.A263V 0.948 NULL "HMMPfam_rve,HMMPfam_SCAN,HMMSmart_SCAN,HMMPfam_hATC,superfamily_RNaseH_fold" - no_errors tier1 143 0 116 65 34.76 NA 633734 TCGA-AB-2847 3 39161570 39161570 C T SNP AXUD1 NM_033027.3 human genbank 54_36p -1 reviewed silent c.387 p.A129 0.036 NULL NULL - no_errors tier1 141 2 1.37 60 33 35.11 30 13 30.23 633734 TCGA-AB-2847 21 43397525 43397525 G A SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.101 p.S34F 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 74 2 2.6 45 17 27.42 64 84 56.76 633734 TCGA-AB-2847 16 55491009 55491009 C T SNP SLC12A3 NM_000339.2 human genbank 54_36p 1 reviewed silent c.2727 p.N909 1 NULL "HMMPfam_AA_permease,HMMPfam_AA_permease_N" - no_errors tier1 316 3 0.93 164 72 30.38 2 0 633734 TCGA-AB-2847 2 141190758 141190758 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated silent c.5856 p.L1952 1 "HMMPfam_Ldl_recept_b,HMMSmart_LY,superfamily_SSF63825" "HMMPfam_Ldl_recept_b,HMMSmart_LY,PatternScan_ASX_HYDROXYL,HMMPfam_NHL,HMMSmart_EGF_CA,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_SSF57196,superfamily_SSF63825" - no_errors tier1 219 3 1.35 300 175 36.08 NA 633734 TCGA-AB-2847 1 201406130 201406130 C T SNP MYBPH NM_004997.2 human genbank 54_36p -1 validated silent c.1005 p.S335 0.81 "HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" "HMMSmart_IGc2,HMMSmart_IG,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,superfamily_SSF48726" - no_errors tier1 168 1 0.58 78 47 37.3 NA 633734 TCGA-AB-2847 1 226351682 226351682 C T SNP ARF1 NM_001024226.1 human genbank 54_36p 1 reviewed silent c.165 p.T55 0.94 "HMMSmart_SM00175,HMMSmart_SM00178,HMMSmart_SM00177,HMMPfam_Arf,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00175,HMMSmart_SM00178,HMMSmart_SM00177,PatternScan_ARF,HMMPfam_Arf,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 38 0 57 30 33.71 208 190 47.74 670224 TCGA-AB-2848 5 170770152 170770153 - CAAG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 692900 TCGA-AB-2849 9 424936 424937 - T INS DOCK8 NM_203447.1 human genbank 54_36p 1 validated frame_shift_ins c.4836_4837 p.D1612fs 1.000:1.000 NULL HMMPfam_Ded_cyto - no_errors tier1 NA NA NA NA NA NA NA NA NA 692900 TCGA-AB-2849 6 3994338 3994338 T C SNP PRPF4B NM_003913.4 human genbank 54_36p 1 reviewed silent c.2025 p.Y675 0.991 superfamily_Protein kinase-like (PK-like) "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" - no_errors tier1 79 0 78 32 29.09 11 24 68.57 692900 TCGA-AB-2849 19 8949095 8949095 G T SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated missense c.3720 p.S1240R 0 NULL "HMMPfam_SEA,HMMSmart_SM00200,PatternScan_ATPASE_ALPHA_BETA,superfamily_SEA domain" - no_errors tier1 135 1 0.74 188 125 39.94 NA 692900 TCGA-AB-2849 1 12842584 12842584 C T SNP PRAMEF2 NM_023014.1 human genbank 54_36p 1 provisional missense c.737 p.T246M 0.009 superfamily_SSF52047 superfamily_SSF52047 - no_errors tier1 88 0 61 38 38.38 NA 692900 TCGA-AB-2849 1 13370462 13370462 C T SNP PRAMEF16 NM_001045480.1 human genbank 54_36p 1 provisional missense c.1172 p.T391M 0.012 superfamily_SSF52047 superfamily_SSF52047 - no_errors tier1 6 0 4 1 20 NA 692900 TCGA-AB-2849 5 14340024 14340024 G A SNP TRIO NM_007118.2 human genbank 54_36p 1 validated missense c.392 p.R131H 1 "HMMSmart_SM00516,superfamily_CRAL/TRIO domain" "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMSmart_SM00219,HMMSmart_SM00516,superfamily_CRAL/TRIO domain,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Spectrin,HMMSmart_SM00220,HMMSmart_SM00408,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_Pkinase,HMMSmart_SM00150,superfamily_Spectrin repeat,superfamily_Immunoglobulin,superfamily_PH domain-like" - no_errors tier1 76 1 1.3 76 36 31.58 1 0 692900 TCGA-AB-2849 1 16132825 16132825 G A SNP SPEN NM_015001.2 human genbank 54_36p 1 reviewed nonsense c.7503 p.W2501* 1 NULL "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_SPOC,superfamily_SPOC-like,superfamily_SSF54928" - no_errors tier1 46 0 34 30 46.88 33 30 47.62 692900 TCGA-AB-2849 11 20032211 20032211 C T SNP NAV2 NM_182964.1 human genbank 54_36p 1 validated silent c.4560 p.P1520 1 NULL "HMMPfam_CH,HMMSmart_SM00033,HMMSmart_SM00382,superfamily_Calponin-homology domain CH-domain,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 116 1 0.85 52 27 34.18 1 2 66.67 692900 TCGA-AB-2849 8 21949986 21949986 G A SNP NPM2 NM_182795.1 human genbank 54_36p 1 validated splice_region c.600+3 e7+3 0.958 - - - no_errors tier1 57 0 20 6 23.08 2 1 33.33 692900 TCGA-AB-2849 12 27070645 27070645 T C SNP MED21 NM_004264.3 human genbank 54_36p 1 provisional missense c.68 p.I23T 1 NULL NULL - no_errors tier1 59 0 112 53 32.12 9 8 47.06 692900 TCGA-AB-2849 2 32331149 32331149 G A SNP NLRC4 NM_021209.3 human genbank 54_36p -1 validated silent c.105 p.R35 0 "HMMPfam_CARD,superfamily_DEATH domain" "HMMPfam_CARD,HMMPfam_NACHT,superfamily_DEATH domain,superfamily_RNI-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 49 0 75 59 44.03 2 0 692900 TCGA-AB-2849 22 34664851 34664851 C T SNP RBM9 NM_001082578.2 human genbank 54_36p -1 reviewed missense c.227 p.R76Q 0.998 NULL "HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928" - no_errors tier1 79 0 86 16 15.69 3 2 40 692900 TCGA-AB-2849 1 36534823 36534823 G A SNP THRAP3 NM_005119.3 human genbank 54_36p 1 validated missense c.2168 p.R723H 1 NULL NULL - no_errors tier1 148 0 50 36 41.86 98 64 39.51 692900 TCGA-AB-2849 22 36653659 36653659 C A SNP MICALL1 NM_033386.2 human genbank 54_36p 1 validated silent c.1761 p.G587 0.758 NULL "HMMPfam_CH,HMMSmart_CH,HMMPfam_LIM,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,superfamily_Calponin-homology,superfamily_SSF57716" - no_errors tier1 33 0 13 5 27.78 13 3 18.75 692900 TCGA-AB-2849 15 43227458 43227458 T A SNP DUOX1 NM_017434.3 human genbank 54_36p 1 reviewed silent c.2613 p.I871 0.894 "HMMSmart_SM00054,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_EF-hand" "HMMPfam_An_peroxidase,HMMSmart_SM00054,superfamily_Heme-dependent peroxidases,HMMPfam_FAD_binding_8,HMMPfam_NAD_binding_6,HMMPfam_Ferric_reduct,superfamily_Riboflavin synthase domain-like,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_EF-hand,superfamily_Ferredoxin reductase-like C-terminal NADP-linked domain" - no_errors tier1 62 0 52 38 42.22 2 100 692900 TCGA-AB-2849 7 49993531 49993531 C G SNP ZPBP NM_007009.1 human genbank 54_36p -1 provisional missense c.914 p.G305A 0.99 HMMPfam_Sp38 HMMPfam_Sp38 - no_errors tier1 22 1 4.35 28 20 41.67 NA 692900 TCGA-AB-2849 14 64486883 64486883 G A SNP RAB15 NM_198686.2 human genbank 54_36p -1 validated missense c.458 p.T153M 0.997 NULL "PatternScan_SIGMA54_INTERACT_1,HMMSmart_RAB,HMMPfam_Ras,superfamily_SSF52540" - no_errors tier1 69 0 29 20 40.82 21 9 30 692900 TCGA-AB-2849 9 65375598 65375598 G A SNP LOC643827 XM_001714537.1 human genbank 54_36p 1 model missense c.1946 p.G649E 1 "superfamily_Concanavalin A-like lectins/glucanases,PatternScan_GLYCO_HORMONE_BETA_1" "HMMSmart_SM00282,superfamily_Fibrinogen C-terminal domain-like,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_GLYCO_HORMONE_BETA_1" - no_errors tier1 22 0 15 14 48.28 NA 692900 TCGA-AB-2849 10 76405901 76405901 C G SNP MYST4 NM_012330.2 human genbank 54_36p 1 validated missense c.1800 p.H600Q 1 NULL "HMMSmart_SM00249,HMMPfam_MOZ_SAS,HMMSmart_SM00526,superfamily_FYVE/PHD zinc finger,superfamily_Acyl-CoA N-acyltransferases (Nat),PatternScan_ZF_PHD_1,HMMPfam_PHD,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 46 0 58 34 36.96 12 13 52 692900 TCGA-AB-2849 12 79626771 79626771 G A SNP MYF6 NM_002469.1 human genbank 54_36p 1 provisional silent c.630 p.S210 0.004 NULL "HMMPfam_HLH,HMMSmart_SM00353,HMMPfam_Basic,HMMSmart_SM00520,superfamily_HLH helix-loop-helix DNA-binding domain" - no_errors tier1 95 0 52 41 44.09 NA 692900 TCGA-AB-2849 15 80123062 80123062 A G SNP MEX3B NM_032246.3 human genbank 54_36p -1 provisional missense c.1204 p.S402P 0.078 NULL "HMMSmart_SM00184,HMMSmart_SM00322,HMMPfam_KH_1,HMMPfam_zf-C3HC4,superfamily_Eukaryotic type KH-domain (KH-domain type I),superfamily_RING/U-box" - no_errors tier1 17 0 17 8 32 12 11 47.83 692900 TCGA-AB-2849 1 89293100 89293100 C A SNP GBP1 NM_002053.2 human genbank 54_36p -1 validated missense c.1518 p.L506F 0.478 "HMMPfam_GBP_C,superfamily_Interferon-induced guanylate-binding protein 1 (GBP1) C-terminal domain" "HMMPfam_GBP_C,HMMPfam_GBP,superfamily_Interferon-induced guanylate-binding protein 1 (GBP1) C-terminal domain,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 84 0 69 47 40.52 30 6 16.67 692900 TCGA-AB-2849 2 96332701 96332701 A G SNP SNRNP200 NM_014014.2 human genbank 54_36p -1 validated missense c.304 p.Y102H 1 NULL "HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_Sec63,HMMPfam_DEAD,HMMSmart_SM00487,HMMSmart_SM00611,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 50 0 50 30 37.5 80 63 43.75 692900 TCGA-AB-2849 X 135254814 135254814 T A SNP GPR112 NM_153834.3 human genbank 54_36p 1 validated missense c.1283 p.L428H 0.011 NULL "HMMPfam_GPS,HMMSmart_GPS,HMMPfam_7tm_2,superfamily_ConA_like_lec_gl,PatternScan_G_PROTEIN_RECEP_F2_2" - no_errors tier1 57 2 3.33 37 144 79.12 NA 692900 TCGA-AB-2849 5 137756942 137756942 G A SNP JMJD1B NM_016604.3 human genbank 54_36p 1 validated missense c.2813 p.R938H 1 NULL "HMMSmart_SM00558,HMMPfam_JmjC,superfamily_Clavaminate synthase-like" - no_errors tier1 85 0 16 30 65.22 4 63 94.03 692900 TCGA-AB-2849 4 184073702 184073702 G A SNP DCTD NM_001012732.1 human genbank 54_36p -1 reviewed missense c.47 p.S16F 0.752 NULL "HMMPfam_dCMP_cyt_deam_1,PatternScan_CYT_DCMP_DEAMINASES,superfamily_Cytidine_deaminase-like" - no_errors tier1 32 0 35 13 27.08 24 10 29.41 692900 TCGA-AB-2849 2 201768825 201768825 C A SNP CASP10 NM_032977.4 human genbank 54_36p 1 reviewed missense c.593 p.T198K 0.002 NULL "HMMPfam_DED,HMMSmart_DED,superfamily_DEATH_like,HMMPfam_Peptidase_C14,HMMSmart_CASc,PatternScan_CASPASE_HIS,PatternScan_CASPASE_CYS,superfamily_SSF52129" - no_errors tier1 103 0 109 60 35.5 35 10 22.22 692900 TCGA-AB-2849 2 238281927 238281927 C T SNP LRRFIP1 NM_004735.1 human genbank 54_36p 1 validated missense c.68 p.A23V 1 HMMPfam_DUF2051 HMMPfam_DUF2051 - no_errors tier1 25 0 18 11 37.93 4 8 66.67 724606 TCGA-AB-2850 21 35086465 35086487 CGCGGCGGCGAGCGCTCGCCGCC - DEL RUNX1 ENST00000300305 human ensembl 58_37c -1 known frame_shift_del c.1280_1258 p.G420fs 1.000:1.000:0.914:1.000:0.997:0.962:1.000:1.000:0.958:1.000:1.000:0.999:1.000:1.000:1.000:1.000:1.000:0.999:1.000:1.000:0.950:1.000:1.000 HMMPfam_RunxI "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 NA NA NA NA NA NA NA NA NA 724606 TCGA-AB-2850 17 49256322 49256322 C T SNP KIF2B ENST00000268919 human ensembl 58_37c 1 known missense c.929 p.T310M 1 "HMMPfam_Kinesin,HMMSmart_SM00129,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Kinesin,HMMSmart_SM00129,PatternScan_KINESIN_MOTOR_DOMAIN1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 57 0 0 32 29 47.54 NA NA NA 724606 TCGA-AB-2850 17 72244531 72244554 GGCGGCTGTGGTGTGAGTCCGGGG - DEL SFRS2 ENST00000358156 human ensembl 58_37c -1 known in_frame_del c.307_284 p.PPDSHHSR95in_frame_del 0.998:0.999:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999:0.217:0.326:0.310:0.137:0.989 superfamily_RNA-binding domain RBD "HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00361,superfamily_RNA-binding domain RBD" - no_errors tier1 NA NA NA NA NA NA NA NA NA 724606 TCGA-AB-2850 15 88432938 88432938 C T SNP IDH2 ENST00000330062 human ensembl 58_37c -1 known missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 107 0 0 73 45 38.14 NA NA NA 724606 TCGA-AB-2850 X 123052296 123052296 G A SNP STAG2 ENST00000218089 human ensembl 58_37c 1 known splice_site c.3467+1 e29+1 1 - - - no_errors tier1 124 2 1.59 79 72 47.37 NA NA NA 724606 TCGA-AB-2850 9 138514953 138514953 C T SNP NOTCH1 ENST00000277541 human ensembl 58_37c -1 known missense c.5806 p.A1936T 1 "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" "PatternScan_ASX_HYDROXYL,HMMPfam_Notch,HMMSmart_NL,superfamily_Notch_region,HMMSmart_EGF_CA,HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK,HMMPfam_EGF,HMMSmart_EGF,HMMPfam_NOD,HMMPfam_NODP,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_SSF57196" - no_errors tier1 282 2 0.7 133 116 46.22 NA NA NA 730817 TCGA-AB-2851 2 25320534 25320534 C - DEL DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed frame_shift_del c.1845 p.E616fs 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 NA NA NA NA NA NA NA NA NA 730817 TCGA-AB-2851 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 69 10 12.66 21 12 36.36 184 175 48.75 730817 TCGA-AB-2851 19 43730855 43730855 C T SNP RYR1 NM_000540.2 human genbank 54_36p 1 reviewed silent c.12237 p.Y4079 0.998 superfamily_EF-hand "HMMPfam_RYDR_ITPR,HMMPfam_RyR,HMMPfam_MIR,superfamily_MIR domain (Pfam 02815),HMMPfam_SPRY,HMMPfam_Ion_trans,HMMPfam_RR_TM4-6,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_SM00472,HMMSmart_SM00449,superfamily_EF-hand" - no_errors tier1 177 15 7.81 29 25 46.3 NA 730817 TCGA-AB-2851 19 60865717 60865718 - G INS U2AF2 NM_007279.1 human genbank 54_36p 1 reviewed frame_shift_ins c.524_525 p.L178fs 0.997:0.995 "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 NA NA NA NA NA NA NA NA NA 730817 TCGA-AB-2851 8 70698766 70698766 C T SNP SULF1 NM_015170.1 human genbank 54_36p 1 validated missense c.1630 p.R544C 1 superfamily_Alkaline_phosphatase_core "HMMPfam_Sulfatase,PatternScan_SULFATASE_2,PatternScan_SULFATASE_1,superfamily_Alkaline_phosphatase_core" - no_errors tier1 47 2 4.08 57 38 40 NA 730817 TCGA-AB-2851 2 111135776 111135776 G A SNP BUB1 NM_004336.3 human genbank 54_36p -1 reviewed missense c.1073 p.A358V 0 NULL "HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Mad3_BUB1_I,HMMSmart_SM00777,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 219 14 5.96 85 48 35.56 1 1 50 730817 TCGA-AB-2851 10 112332346 112332346 A T SNP SMC3 NM_005445.3 human genbank 54_36p 1 reviewed nonsense c.760 p.R254* 1 "HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain" - no_errors tier1 49 5 9.26 63 41 39.42 39 4 9.3 730817 TCGA-AB-2851 3 190521248 190521248 T C SNP TPRG1 NM_198485.3 human genbank 54_36p 1 validated missense c.773 p.I258T 1 NULL NULL - no_errors tier1 133 10 6.99 109 104 48.83 1 0 807615 TCGA-AB-2853 10 5193906 5193906 C T SNP AKR1CL1 NM_001007536.3 human genbank 54_36p -1 provisional silent c.291 p.L97 0.819 "HMMPfam_Aldo_ket_red,superfamily_Aldo/ket_red" "HMMPfam_Aldo_ket_red,superfamily_Aldo/ket_red,PatternScan_ALDOKETO_REDUCTASE_1" - no_errors tier1 105 8 7.08 113 113 49.56 0 807615 TCGA-AB-2853 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 98 7 6.67 62 44 41.12 34 39 53.42 807615 TCGA-AB-2853 13 27506268 27506269 - TCTCTGAAATCAACGTAG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1788_1787 p.596in_frame_insDYVDFR 0.794:0.991 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 807615 TCGA-AB-2853 4 38791161 38791161 G A SNP KLHL5 NM_015990.1 human genbank 54_36p 1 validated silent c.1953 p.T651 0.771 "HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain" "HMMSmart_SM00225,HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain,superfamily_POZ domain,HMMPfam_BACK,HMMPfam_BTB" - no_errors tier1 66 5 7.04 51 24 32 17 14 45.16 807615 TCGA-AB-2853 14 58364276 58364276 C T SNP LOC440181 XR_017581.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 128 15 10.49 116 94 44.55 NA 807615 TCGA-AB-2853 17 58851938 58851938 C T SNP TANC2 NM_025185.3 human genbank 54_36p 1 validated silent c.4863 p.A1621 0.891 NULL "HMMPfam_TPR_1,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,HMMSmart_SM00028,superfamily_TPR-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 219 5 2.23 76 91 53.53 6 4 40 807615 TCGA-AB-2853 14 77088240 77088240 T C SNP SPTLC2 NM_004863.2 human genbank 54_36p -1 validated missense c.1255 p.I419V 1 "HMMPfam_Aminotran_1_2,superfamily_PyrdxlP-dep_Trfase_major" "PatternScan_AA_TRANSFER_CLASS_2,HMMPfam_Aminotran_1_2,superfamily_PyrdxlP-dep_Trfase_major" - no_errors tier1 120 9 6.98 121 101 44.89 38 146 78.92 807615 TCGA-AB-2853 1 91880656 91880656 C T SNP HSP90B3P ENST00000370405 human ensembl 54_36p 1 known silent c.225 p.C75 0.671 NULL "superfamily_Ribosomal_S5_D2-typ_fold,HMMPfam_HSP90,superfamily_SSF110942" - no_errors tier1 185 7 3.65 170 118 40.83 NA 807615 TCGA-AB-2853 5 101862376 101862376 G A SNP SLCO6A1 NM_173488.3 human genbank 54_36p -1 validated silent c.72 p.A24 0 NULL "HMMPfam_OATP,HMMPfam_Kazal_2,superfamily_MFS general substrate transporter,superfamily_Kazal-type serine protease inhibitors" - no_errors tier1 62 3 4.62 42 33 42.31 NA 807615 TCGA-AB-2853 10 112346164 112346164 G C SNP SMC3 NM_005445.3 human genbank 54_36p 1 reviewed missense c.1982 p.R661P 1 "HMMPfam_SMC_N,superfamily_Smc hinge domain,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain" - no_errors tier1 56 4 6.67 38 50 56.18 78 68 46.58 807615 TCGA-AB-2853 4 114473772 114473772 C A SNP ANK2 NM_001148.1 human genbank 54_36p 1 reviewed missense c.3338 p.T1113N 0.998 NULL "HMMPfam_Death,HMMSmart_DEATH,HMMPfam_ZU5,HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK,superfamily_DEATH_like,PatternScan_ALDEHYDE_DEHYDR_GLU" - no_errors tier1 133 10 6.99 116 90 43.48 NA 807615 TCGA-AB-2853 7 122542939 122542939 C A SNP SLC13A1 NM_022444.3 human genbank 54_36p -1 validated missense c.1657 p.A553S 1 HMMPfam_Na_sulph_symp "HMMPfam_Na_sulph_symp,PatternScan_NA_SULFATE" - no_errors tier1 120 10 7.69 107 91 45.96 NA 807615 TCGA-AB-2853 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 826984 TCGA-AB-2854 1 12382883 12382883 G A SNP VPS13D NM_015378.2 human genbank 54_36p 1 reviewed missense c.11693 p.S3898N 0.996 NULL "HMMPfam_UBA,superfamily_UBA-like,HMMPfam_DUF1162,HMMSmart_SM00165" - no_errors tier1 160 2 1.22 39 11 22 13 4 23.53 826984 TCGA-AB-2854 8 26683778 26683778 G A SNP ADRA1A NM_033303.2 human genbank 54_36p -1 reviewed silent c.1206 p.S402 0.173 NULL "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 280 1 0.35 53 20 27.03 NA 826984 TCGA-AB-2854 16 32071067 32071067 G A SNP HERC2P4 NR_002827.1 human genbank 54_36p -1 provisional rna NULL NULL 0.793 - - - pseudogene tier1 181 1 0.55 24 4 14.29 0 826984 TCGA-AB-2854 11 34471642 34471642 G A SNP ELF5 NM_198381.2 human genbank 54_36p -1 reviewed silent c.345 p.G115 0.979 "HMMPfam_SAM_PNT,HMMSmart_SM00251,superfamily_SAM/Pointed domain" "HMMPfam_Ets,HMMSmart_SM00413,PatternScan_ETS_DOMAIN_2,HMMPfam_SAM_PNT,HMMSmart_SM00251,superfamily_SAM/Pointed domain,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 125 2 1.56 24 6 20 NA 826984 TCGA-AB-2854 17 40210925 40210925 C A SNP ADAM11 NM_002390.4 human genbank 54_36p 1 reviewed missense c.2150 p.T717K 0.071 NULL "HMMPfam_Reprolysin,HMMPfam_Disintegrin,HMMSmart_SM00050,superfamily_Blood coagulation inhibitor (disintegrin),HMMPfam_Pep_M12B_propep,HMMPfam_ADAM_CR,HMMSmart_SM00608,PatternScan_EGF_1,HMMPfam_EGF_2,PatternScan_DISINTEGRIN_1,superfamily_Metalloproteases (""zincins"") catalytic domain,superfamily_EGF/Laminin" - no_errors tier1 124 0 14 7 33.33 NA 826984 TCGA-AB-2854 5 41094054 41094054 G T SNP HEATR7B2 NM_173489.4 human genbank 54_36p -1 validated missense c.624 p.S208R 0.001 NULL superfamily_ARM repeat - no_errors tier1 385 4 1.02 60 18 23.08 NA 826984 TCGA-AB-2854 4 48262466 48262466 C T SNP FRYL NM_015030.1 human genbank 54_36p -1 validated splice_site c.3170-1 e26-1 1 - - - no_errors tier1 57 0 48 14 22.58 4 0 826984 TCGA-AB-2854 2 53969413 53969413 A C SNP PSME4 NM_014614.2 human genbank 54_36p -1 validated missense c.3995 p.L1332R 1 superfamily_ARM repeat "HMMPfam_HEAT,superfamily_ARM repeat" - no_errors tier1 71 0 60 25 29.41 60 15 20 826984 TCGA-AB-2854 10 59824797 59824797 G A SNP TFAM NM_003201.1 human genbank 54_36p 1 provisional missense c.698 p.R233H 0.053 superfamily_HMG-box "HMMPfam_HMG_box,HMMSmart_SM00398,superfamily_HMG-box" - no_errors tier1 93 0 28 16 36.36 26 6 18.75 826984 TCGA-AB-2854 17 72445737 72445737 C T SNP MGAT5B NM_198955.2 human genbank 54_36p 1 validated missense c.1528 p.R510W 1 NULL NULL - no_errors tier1 294 0 34 7 17.07 NA 826984 TCGA-AB-2854 10 124911770 124911770 G T SNP BUB3 NM_004725.2 human genbank 54_36p 1 reviewed missense c.605 p.R202L 1 superfamily_WD40 repeat-like "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" - no_errors tier1 102 0 39 7 15.22 103 39 27.46 826984 TCGA-AB-2854 5 140543532 140543532 C T SNP PCDHB16 NM_020957.1 human genbank 54_36p 1 reviewed missense c.1214 p.T405M 0.301 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 47 0 18 4 18.18 NA 852559 TCGA-AB-2855 1 7692 7692 G A SNP LOC727882 XR_015152.2 human genbank 54_36p 1 model rna NULL NULL 0.043 - - - pseudogene tier1 0 0 1 0 852559 TCGA-AB-2855 9 38605714 38605714 G A SNP ANKRD18A XM_001726105.1 human genbank 54_36p -1 model silent c.372 p.G124 0.95 "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" - no_errors tier1 25 2 7.41 60 53 46.9 NA 852559 TCGA-AB-2855 10 70120655 70120655 C T SNP TET1 NM_030625.2 human genbank 54_36p 1 validated missense c.5489 p.T1830I 0.944 NULL HMMPfam_zf-CXXC - no_errors tier1 79 16 16.67 87 65 42.21 6 5 45.45 852559 TCGA-AB-2855 12 111411235 111411235 C T SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.1472 p.P491L 1 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 261 34 11.49 333 341 50 13 17 56.67 852559 TCGA-AB-2855 X 133375569 133375570 - GGATA INS PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed frame_shift_ins c.636_637 p.F213fs 1.000:1.000 NULL "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger" - no_errors tier1 NA NA NA NA NA NA NA NA NA 852559 TCGA-AB-2855 X 134816810 134816810 G A SNP SAGE1 NM_018666.2 human genbank 54_36p 1 reviewed missense c.796 p.D266N 0.516 NULL NULL - no_errors tier1 105 22 17.32 7 75 90.36 0 884262 TCGA-AB-2857 16 3040422 3040422 C T SNP MMP25 NM_022468.4 human genbank 54_36p 1 reviewed missense c.535 p.H179Y 0.993 "HMMPfam_Peptidase_M10,HMMSmart_ZnMc,superfamily_SSF55486" "superfamily_Hemopexin,HMMPfam_Peptidase_M10,PatternScan_CYSTEINE_SWITCH,HMMPfam_PG_binding_1,superfamily_PGBD_like,PatternScan_ZINC_PROTEASE,HMMSmart_ZnMc,PatternScan_HEMOPEXIN,HMMPfam_Hemopexin,HMMSmart_HX,superfamily_SSF55486" - no_errors tier1 122 1 0.81 28 11 27.5 10 3 23.08 884262 TCGA-AB-2857 17 7531419 7531419 C T SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed splice_site c.1+1 e0+1 0.966 - - - no_errors tier1 57 0 17 20 54.05 0 884262 TCGA-AB-2857 11 12204389 12204389 C G SNP MICAL2 NM_014632.2 human genbank 54_36p 1 provisional missense c.1784 p.T595R 0.995 "HMMPfam_CH,HMMSmart_SM00033,superfamily_Calponin-homology domain CH-domain" "HMMPfam_CH,HMMSmart_SM00033,HMMPfam_LIM,HMMSmart_SM00132,PatternScan_LIM_DOMAIN_1,HMMPfam_FAD_binding_3,superfamily_Calponin-homology domain CH-domain,superfamily_FAD/NAD(P)-binding domain,superfamily_Glucocorticoid receptor-like (DNA-binding domain)" - no_errors tier1 215 0 72 20 21.51 28 16 36.36 884262 TCGA-AB-2857 17 14051012 14051012 C T SNP COX10 NM_001303.3 human genbank 54_36p 1 reviewed silent c.1089 p.A363 0.993 HMMPfam_UbiA "HMMPfam_UbiA,PatternScan_UBIA" - no_errors tier1 42 0 20 16 44.44 4 6 60 884262 TCGA-AB-2857 21 29636837 29636837 C A SNP BACH1 NM_001186.1 human genbank 54_36p 1 reviewed silent c.2023 p.R675 0.016 NULL "HMMSmart_SM00225,HMMSmart_SM00338,PatternScan_BZIP_BASIC,superfamily_A DNA-binding domain in eukaryotic transcription factors,superfamily_POZ domain,HMMPfam_bZIP_1,HMMPfam_BTB" - no_errors tier1 90 0 104 49 31.61 20 15 42.86 884262 TCGA-AB-2857 17 36831252 36831252 G A SNP KRT37 NM_003770.4 human genbank 54_36p -1 reviewed silent c.1134 p.A378 0.997 HMMPfam_Filament "HMMPfam_Filament,PatternScan_IF" - no_errors tier1 105 0 147 22 12.94 NA 884262 TCGA-AB-2857 12 51114119 51114119 G A SNP KRT75 NM_004693.2 human genbank 54_36p -1 reviewed silent c.237 p.S79 0.002 NULL "superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF" - no_errors tier1 111 0 63 21 25 NA 884262 TCGA-AB-2857 19 55241783 55241783 T G SNP ZNF473 NM_001006656.1 human genbank 54_36p 1 validated silent c.2271 p.P757 0.001 superfamily_C2H2 and C2HC zinc fingers "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 483 0 142 33 18.86 10 10 50 884262 TCGA-AB-2857 10 64637174 64637174 A G SNP JMJD1C NM_032776.2 human genbank 54_36p -1 validated missense c.4261 p.S1421P 1 NULL "HMMSmart_SM00558,HMMPfam_JmjC,superfamily_Clavaminate synthase-like" - no_errors tier1 164 0 76 31 28.7 40 27 40.3 884262 TCGA-AB-2857 16 65503312 65503312 C T SNP CDH16 NM_004062.2 human genbank 54_36p -1 reviewed missense c.1781 p.R594Q 0.023 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" - no_errors tier1 426 2 0.47 56 10 15.15 1 0 884262 TCGA-AB-2857 10 85984050 85984050 G A SNP LRIT1 NM_015613.2 human genbank 54_36p -1 validated silent c.654 p.G218 0.078 "HMMSmart_LRRCT,superfamily_SSF52058" "HMMSmart_LRRNT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMSmart_IGc2,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_ig,superfamily_SSF48726,superfamily_SSF52058" - no_errors tier1 21 0 44 24 34.78 NA 884262 TCGA-AB-2857 4 110039758 110039758 C T SNP COL25A1 NM_198721.2 human genbank 54_36p -1 validated splice_site c.861+1 e14+1 0.998 - - - no_errors tier1 288 1 0.35 137 56 28.72 NA 884262 TCGA-AB-2857 8 113747769 113747769 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated missense c.2729 p.G910E 1 "HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain" "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,PatternScan_GLYCOSYL_HYDROL_F10,superfamily_Complement control module/SCR domain" - no_errors tier1 181 0 98 56 36.13 NA 884262 TCGA-AB-2857 7 136499727 136499727 C T SNP LOC100128744 XM_001718911.1 human genbank 54_36p 1 model missense c.1061 p.P354L 0.999 "HMMPfam_Ribosomal_L18e,superfamily_Ribosomal proteins L15p and L18e" "HMMPfam_Ribosomal_L18e,superfamily_Ribosomal proteins L15p and L18e" - no_errors tier1 56 0 36 25 40.32 NA 884262 TCGA-AB-2857 2 166611561 166611561 T C SNP SCN1A NM_006920.4 human genbank 54_36p -1 validated missense c.1342 p.I448V 1 NULL "HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Ion_trans,HMMPfam_Na_trans_assoc,PatternScan_RIBONUCLEASE_P,superfamily_SSF81324" - no_errors tier1 231 3 1.28 85 43 33.33 NA 884262 TCGA-AB-2857 2 225426080 225426080 C T SNP DOCK10 NM_014689.2 human genbank 54_36p -1 validated missense c.1892 p.C631Y 1 NULL "HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Ded_cyto,superfamily_PH domain-like" - no_errors tier1 253 0 181 81 30.34 26 8 23.53 905179 TCGA-AB-2858 11 30895090 30895090 A T SNP DCDC5 ENST00000406071 human ensembl 54_36p -1 known missense c.685 p.W229R 1 NULL "HMMPfam_DCX,superfamily_RicinB_like,superfamily_SSF89837" - no_errors tier1 119 10 7.69 104 37 26.24 NA 905179 TCGA-AB-2858 9 34504416 34504416 T C SNP DNAI1 NM_012144.2 human genbank 54_36p 1 reviewed missense c.1594 p.F532L 1 "HMMSmart_WD40,superfamily_WD40_like,HMMPfam_WD40" "HMMSmart_WD40,superfamily_WD40_like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 65 2 2.99 84 44 34.38 NA 905179 TCGA-AB-2858 4 47361825 47361825 C T SNP CORIN NM_006587.2 human genbank 54_36p -1 reviewed missense c.1570 p.E524K 0.119 "superfamily_Frizzled cysteine-rich domain,HMMPfam_Fz,HMMSmart_SM00063" "superfamily_Frizzled cysteine-rich domain,PatternScan_SRCR_1,HMMPfam_Trypsin,HMMSmart_SM00020,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,superfamily_Trypsin-like serine proteases,HMMSmart_SM00202,superfamily_SRCR-like,PatternScan_TRYPSIN_SER,HMMPfam_Fz,HMMSmart_SM00063" - no_errors tier1 148 5 3.25 72 37 33.94 NA 905179 TCGA-AB-2858 X 53425957 53425957 T C SNP SMC1A NM_006306.2 human genbank 54_36p -1 reviewed missense c.3358 p.K1120E 1 "HMMPfam_SMC_N,superfamily_SSF52540" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" - no_errors tier1 117 4 3.31 87 42 32.56 34 62 64.58 905179 TCGA-AB-2858 15 56966894 56966894 A G SNP SLTM NM_024755.1 human genbank 54_36p -1 validated missense c.2513 p.L838P 1 NULL "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_SAP,HMMSmart_SAP,superfamily_SSF54928,superfamily_SSF68906" - no_errors tier1 250 8 3.08 234 114 32.76 125 82 39.61 905179 TCGA-AB-2858 17 62457324 62457324 C T SNP CACNG4 NM_014405.2 human genbank 54_36p 1 reviewed silent c.726 p.R242 0.999 NULL "HMMPfam_PMP22_Claudin,PatternScan_CLAUDIN" - no_errors tier1 244 7 2.76 206 88 29.93 NA 905179 TCGA-AB-2858 10 72030188 72030188 G A SNP PRF1 NM_001083116.1 human genbank 54_36p -1 reviewed silent c.477 p.A159 0.008 HMMPfam_MACPF "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_MACPF,HMMSmart_SM00457,PatternScan_MAC_PERFORIN,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)" - no_errors tier1 106 5 4.46 189 98 34.15 16 0 905179 TCGA-AB-2858 10 88267726 88267726 T G SNP WAPAL NM_015045.2 human genbank 54_36p -1 validated missense c.81 p.K27N 1 NULL "HMMPfam_WAPL,superfamily_ARM repeat" - no_errors tier1 118 4 3.23 116 64 35.56 47 32 40.51 905179 TCGA-AB-2858 1 89425289 89425289 C T SNP GBP4 NM_052941.4 human genbank 54_36p -1 validated missense c.1495 p.G499R 0.001 "HMMPfam_GBP_C,superfamily_GBP" "HMMPfam_GBP_C,HMMPfam_GBP,superfamily_GBP,superfamily_SSF52540" - no_errors tier1 194 8 3.96 161 78 32.64 19 21 52.5 905179 TCGA-AB-2858 12 95674471 95674471 G A SNP C12orf63 NM_198520.2 human genbank 54_36p 1 validated missense c.3220 p.G1074R 1 NULL NULL - no_errors tier1 227 13 5.31 181 66 26.72 NA 905179 TCGA-AB-2858 7 99492574 99492574 C T SNP ZSCAN21 NM_145914.2 human genbank 54_36p 1 validated silent c.9 p.T3 0.942 NULL "HMMPfam_SCAN,HMMSmart_SM00431,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 50 2 3.7 80 22 21.36 4 6 60 905179 TCGA-AB-2858 14 105305233 105305233 A G SNP IGHG3 ENST00000390550 human ensembl 54_36p -1 known silent c.1218 p.C406 1 NULL "PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin" - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 41 0 54 9 14.29 1 100 905179 TCGA-AB-2858 11 120338459 120338459 G A SNP GRIK4 NM_014619.2 human genbank 54_36p 1 reviewed missense c.2125 p.G709R 1 "HMMPfam_Lig_chan,HMMSmart_PBPe,superfamily_SSF53850" "HMMPfam_Lig_chan,HMMSmart_PBPe,HMMPfam_ANF_receptor,HMMPfam_Lig_chan-Glu_bd,superfamily_SSF53822,superfamily_SSF53850" - no_errors tier1 56 0 44 18 29.03 1 0 905179 TCGA-AB-2858 5 140549322 140549322 C T SNP PCDHB9 NM_019119.3 human genbank 54_36p 1 reviewed missense c.2246 p.T749I 0.141 NULL "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 79 4 4.82 74 29 28.16 NA 905179 TCGA-AB-2858 4 160463047 160463047 G T SNP RAPGEF2 NM_014247.2 human genbank 54_36p 1 validated nonsense c.469 p.E157* 1 "HMMPfam_cNMP_binding,HMMSmart_cNMP,superfamily_cNMP_binding" "HMMPfam_RA,HMMSmart_RA,HMMPfam_cNMP_binding,HMMSmart_cNMP,HMMPfam_RasGEF_N,HMMSmart_RasGEFN,HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ,HMMPfam_RasGEF,HMMSmart_RasGEF,superfamily_Ras_GEF,superfamily_cNMP_binding" - no_errors tier1 163 6 3.49 164 69 29.61 4 5 55.56 936028 TCGA-AB-2859 MT 14767 14767 T C SNP MT-CYB ENST00000361789 human ensembl 54_36p 1 known missense c.20 p.I7T NULL superfamily_Transmembr_di-haem_cytochrome "HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome" - no_stop_codon:bad_bp_length_for_coding_region tier1 2497 27 1.07 804 165 16.77 NA NA NA 936028 TCGA-AB-2859 11 4886017 4886017 T G SNP OR51A7 NM_001004749.1 human genbank 54_36p 1 provisional missense c.842 p.L281W 0.12 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 205 4 1.91 382 230 37.4 NA 936028 TCGA-AB-2859 6 7175590 7175590 C G SNP RREB1 NM_001003699.2 human genbank 54_36p 1 validated silent c.2259 p.T753 0.984 "HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 53 1 1.85 79 53 39.85 35 42 54.55 936028 TCGA-AB-2859 8 17586240 17586240 C T SNP MTUS1 NM_001001924.2 human genbank 54_36p -1 reviewed silent c.2715 p.L905 0.954 NULL NULL - no_errors tier1 214 1 0.46 603 218 26.17 2 0 936028 TCGA-AB-2859 5 23562543 23562543 G A SNP PRDM9 NM_020227.2 human genbank 54_36p 1 provisional missense c.1589 p.G530E 0.974 HMMSmart_ZnF_C2H2 "HMMSmart_SET,HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,HMMPfam_SSXRD,superfamily_SSF57667,superfamily_SSF82199" - no_errors tier1 144 0 369 191 33.87 NA 936028 TCGA-AB-2859 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 121 3 2.42 169 94 35.61 33 34 50.75 936028 TCGA-AB-2859 17 36587840 36587840 A T SNP KRTAP4-2 NM_033062.2 human genbank 54_36p -1 reviewed missense c.103 p.C35S 1 HMMPfam_Keratin_B2 HMMPfam_Keratin_B2 - no_errors tier1 72 1 1.37 213 52 19.55 NA 936028 TCGA-AB-2859 17 36912478 36912478 G A SNP KRT13 NM_153490.3 human genbank 54_36p -1 reviewed missense c.1010 p.S337F 0.999 "superfamily_Prefoldin,HMMPfam_Filament" "superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF" - no_errors tier1 151 0 188 93 32.63 NA 936028 TCGA-AB-2859 21 45665860 45665860 G A SNP C21orf123 ENST00000330082 human ensembl 54_36p -1 known silent c.256 p.L86 0.023 NULL NULL - no_errors tier1 42 0 35 16 31.37 NA 936028 TCGA-AB-2859 19 58931994 58931995 TT - DEL MIRN516B1 ENST00000385211 human ensembl 54_36p 1 known rna NULL NULL 0.000:0.000 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 936028 TCGA-AB-2859 16 83336744 83336744 C - DEL USP10 NM_005153.2 human genbank 54_36p 1 reviewed frame_shift_del c.1156 p.P386fs 1 NULL "HMMPfam_UCH,HMMPfam_PAM2,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_SSF54001" - no_errors tier1 NA NA NA NA NA NA NA NA NA 936028 TCGA-AB-2859 9 85781739 85781740 GA - DEL HNRNPK NM_002140.3 human genbank 54_36p -1 reviewed frame_shift_del c.204_203 p.L68fs 0.999:1.000 "HMMSmart_SM00322,HMMPfam_KH_1,superfamily_Eukaryotic type KH-domain (KH-domain type I)" "HMMSmart_SM00322,HMMPfam_ROKNT,HMMPfam_KH_1,superfamily_Eukaryotic type KH-domain (KH-domain type I)" - no_errors tier1 NA NA NA NA NA NA NA NA NA 936028 TCGA-AB-2859 1 112071820 112071820 C T SNP C1orf183 NM_019099.3 human genbank 54_36p -1 validated missense c.187 p.V63M 0.002 NULL NULL - no_errors tier1 248 2 0.8 539 325 37.1 1 3 75 936028 TCGA-AB-2859 X 132178772 132178772 G A SNP TFDP3 NM_016521.2 human genbank 54_36p -1 validated silent c.1002 p.N334 1 NULL "HMMPfam_E2F_TDP,HMMPfam_DP,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 71 0 98 193 65.87 NA 936028 TCGA-AB-2859 11 133600282 133600282 C G SNP VPS26B NM_052875.3 human genbank 54_36p 1 validated missense c.56 p.A19G 0.999 HMMPfam_Vps26 HMMPfam_Vps26 - no_errors tier1 249 20 7.43 97 90 48.13 41 36 46.75 936028 TCGA-AB-2859 5 170770150 170770151 - CTGC INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.861_862 p.W287fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 936028 TCGA-AB-2859 1 198449681 198449681 G A SNP FAM58B NM_001105517.1 human genbank 54_36p 1 inferred missense c.367 p.D123N 1 "HMMSmart_CYCLIN,superfamily_Cyclin_like" "HMMSmart_CYCLIN,PatternScan_CYCLINS,superfamily_Cyclin_like" - no_errors tier1 108 0 505 246 32.33 NA 938150 TCGA-AB-2860 17 7520294 7520295 - CCATCCAG INS TP53 NM_000546.4 human genbank 54_36p -1 reviewed frame_shift_ins c.118_117 p.M39fs 0.000:0.000 NULL "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 NA NA NA NA NA NA NA NA NA 938150 TCGA-AB-2860 19 8921849 8921849 G A SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated missense c.26597 p.S8866L 0 NULL "HMMPfam_SEA,HMMSmart_SM00200,PatternScan_ATPASE_ALPHA_BETA,superfamily_SEA domain" - no_errors tier1 176 3 1.64 110 37 24.83 NA 938150 TCGA-AB-2860 4 11010116 11010116 C T SNP HS3ST1 NM_005114.2 human genbank 54_36p -1 reviewed silent c.612 p.L204 0.999 "HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 23 0 31 19 38 13 8 38.1 938150 TCGA-AB-2860 1 11947397 11947397 G A SNP PLOD1 NM_000302.2 human genbank 54_36p 1 reviewed missense c.1438 p.D480N 0.997 NULL "PatternScan_LYS_HYDROXYLASE,HMMPfam_2OG-FeII_Oxy,HMMSmart_P4Hc" - no_errors tier1 26 0 8 5 38.46 40 31 43.66 938150 TCGA-AB-2860 19 23719583 23719584 CA - DEL ZNF681 NM_138286.2 human genbank 54_36p -1 validated frame_shift_del c.609_608 p.C203fs 1.000:0.998 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 938150 TCGA-AB-2860 7 27275629 27275629 C T SNP LOC392008 XR_017366.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - no_errors tier1 38 0 48 28 36.84 NA 938150 TCGA-AB-2860 19 43679015 43679015 G A SNP RYR1 NM_000540.2 human genbank 54_36p 1 reviewed missense c.6790 p.G2264S 1 HMMPfam_RYDR_ITPR "HMMPfam_RYDR_ITPR,HMMPfam_RyR,HMMPfam_MIR,superfamily_MIR domain (Pfam 02815),HMMPfam_SPRY,HMMPfam_Ion_trans,HMMPfam_RR_TM4-6,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_SM00472,HMMSmart_SM00449,superfamily_EF-hand" - no_errors tier1 18 0 10 6 37.5 NA 938150 TCGA-AB-2860 2 58541604 58541604 C T SNP LOC644456 XR_039438.1 human genbank 54_36p -1 model rna NULL NULL 0.005 - - - pseudogene tier1 75 2 2.6 162 50 23.36 18 0 938150 TCGA-AB-2860 11 65948991 65948991 A G SNP NPAS4 NM_178864.3 human genbank 54_36p 1 validated missense c.2054 p.D685G 0.874 NULL "HMMSmart_PAS,HMMPfam_PAS_3,superfamily_SSF55785" - no_errors tier1 57 2 3.39 13 9 40.91 NA 938150 TCGA-AB-2860 7 73428914 73428914 C T SNP CLIP2 NM_003388.4 human genbank 54_36p 1 reviewed silent c.2247 p.I749 0.992 NULL "HMMPfam_CAP_GLY,PatternScan_CAP_GLY_1,superfamily_Cap-Gly domain" - no_errors tier1 35 0 46 13 22.03 17 13 43.33 938150 TCGA-AB-2860 4 79407574 79407574 C T SNP FRAS1 ENST00000380674 human ensembl 54_36p 1 known silent c.945 p.C315 1 "HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1" "HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_Calx-beta,HMMSmart_SM00237,HMMSmart_SM00181,HMMSmart_SM00261,HMMSmart_SM00215,superfamily_Growth factor receptor domain" - no_errors tier1 49 1 2 141 44 23.78 NA 938150 TCGA-AB-2860 10 97597217 97597217 G A SNP ENTPD1 NM_001098175.1 human genbank 54_36p 1 validated missense c.859 p.D287N 0.005 HMMPfam_GDA1_CD39 "HMMPfam_GDA1_CD39,PatternScan_GDA1_CD39_NTPASE" - no_errors tier1 36 0 71 17 19.1 20 8 28.57 938150 TCGA-AB-2860 4 155473290 155473290 T A SNP DCHS2 NM_017639.1 human genbank 54_36p -1 validated missense c.2023 p.S675C 1 "HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" - no_errors tier1 29 0 50 35 41.18 NA 938150 TCGA-AB-2860 1 157082073 157082073 G A SNP MNDA NM_002432.1 human genbank 54_36p 1 reviewed missense c.643 p.V215M 0.003 HMMPfam_HIN "HMMPfam_PAAD_DAPIN,HMMPfam_HIN" - no_errors tier1 76 0 73 30 29.13 124 130 51.18 938150 TCGA-AB-2860 3 157237331 157237331 G A SNP CASRL1 ENST00000312652 human ensembl 54_36p 1 known missense c.1430 p.R477K 0.173 HMMPfam_7tm_3 "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_SSF53822" - no_errors tier1 27 0 77 29 27.36 NA 957664 TCGA-AB-2861 16 3234588 3234588 C T SNP MEFV NM_000243.2 human genbank 54_36p -1 reviewed missense c.1612 p.A538T 0.911 NULL "HMMPfam_zf-B_box,HMMSmart_SM00336,HMMPfam_SPRY,HMMPfam_PAAD_DAPIN,HMMSmart_SM00589,superfamily_DEATH domain,HMMSmart_SM00449,superfamily_B-box zinc-binding domain" - no_errors tier1 205 15 6.82 22 31 58.49 10 5 33.33 957664 TCGA-AB-2861 8 15525008 15525008 C T SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed missense c.187 p.R63C 1 "HMMPfam_OST3_OST6,superfamily_Thioredoxin-like" "HMMPfam_OST3_OST6,superfamily_Thioredoxin-like" - no_errors tier1 86 0 108 46 29.87 NA 957664 TCGA-AB-2861 9 16426735 16426735 C T SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated missense c.1457 p.R486H 1 "HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 648 3 0.46 127 45 26.16 NA 957664 TCGA-AB-2861 16 18439649 18439649 C T SNP NOMO2 NM_001004060.1 human genbank 54_36p -1 reviewed missense c.2212 p.V738M 0.986 NULL "HMMPfam_Cna_B,superfamily_Carboxypeptidase regulatory domain,superfamily_Starch-binding domain-like" - no_errors tier1 517 24 4.42 97 35 26.52 65 48 42.48 957664 TCGA-AB-2861 14 18546106 18546106 G A SNP LOC642458 XR_016116.2 human genbank 54_36p -1 model rna NULL NULL 0.986 - - - pseudogene tier1 156 2 1.27 162 23 12.43 1 100 957664 TCGA-AB-2861 12 25289551 25289551 C A SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.35 p.G12V 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 30 1 3.23 35 15 30 18 9 33.33 957664 TCGA-AB-2861 2 25320536 25320536 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed nonsense c.1843 p.Q615* 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 46 0 5 8 61.54 10 4 28.57 957664 TCGA-AB-2861 6 31860190 31860190 G A SNP VARS NM_006295.2 human genbank 54_36p -1 reviewed silent c.1536 p.F512 1 "HMMPfam_tRNA-synt_1,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Nucleotidylyl transferase" "PatternScan_AA_TRNA_LIGASE_I,HMMPfam_tRNA-synt_1,HMMPfam_GST_N,HMMPfam_GST_C,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases,superfamily_Glutathione S-transferase (GST) C-terminal domain,HMMPfam_Anticodon_1,superfamily_Nucleotidylyl transferase" - no_errors tier1 110 3 2.63 15 12 44.44 65 85 56.67 957664 TCGA-AB-2861 18 42879702 42879702 C A SNP KATNAL2 NM_031303.1 human genbank 54_36p 1 provisional missense c.1086 p.H362Q 0.999 "HMMPfam_AAA,superfamily_SSF52540" "HMMSmart_AAA,HMMPfam_AAA,superfamily_SSF52540" - no_errors tier1 223 2 0.89 39 34 46.58 3 0 957664 TCGA-AB-2861 19 43075963 43075963 A T SNP WDR87 ENST00000303868 human ensembl 54_36p -1 known silent c.2103 p.I701 1 NULL "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_C_TYPE_LECTIN_1,HMMPfam_WD40" - no_stop_codon tier1 535 17 3.07 75 62 45.26 NA 957664 TCGA-AB-2861 21 43397525 43397525 G T SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.101 p.S34Y 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 175 5 2.76 15 8 33.33 103 113 52.31 957664 TCGA-AB-2861 3 44649065 44649065 C T SNP ZNF197 NM_006991.1 human genbank 54_36p 1 reviewed silent c.739 p.L247 0.997 "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352)" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_SCAN,HMMSmart_SM00431,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 232 15 6.07 129 96 42.48 4 3 42.86 957664 TCGA-AB-2861 19 53646208 53646208 G A SNP GRWD1 NM_031485.2 human genbank 54_36p 1 provisional missense c.931 p.V311I 0.99 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 122 0 21 7 25 48 22 31.43 957664 TCGA-AB-2861 17 62471268 62471268 C T SNP CACNG1 NM_000727.2 human genbank 54_36p 1 reviewed silent c.30 p.R10 0.962 HMMPfam_PMP22_Claudin HMMPfam_PMP22_Claudin - no_errors tier1 118 8 6.35 8 8 50 NA 957664 TCGA-AB-2861 6 83938402 83938402 A T SNP PGM3 NM_015599.1 human genbank 54_36p -1 provisional missense c.1338 p.D446E 0.937 superfamily_Phosphoglucomutase C-terminal domain "HMMPfam_PGM_PMM_IV,HMMPfam_PGM_PMM_I,superfamily_Phosphoglucomutase first 3 domains,PatternScan_PGM_PMM,superfamily_Phosphoglucomutase C-terminal domain" - no_errors tier1 219 6 2.65 96 77 44.51 6 4 40 957664 TCGA-AB-2861 4 88986411 88986411 G A SNP MEPE NM_020203.2 human genbank 54_36p 1 validated missense c.1367 p.G456D 0 NULL HMMPfam_Osteoregulin - no_errors tier1 282 8 2.76 50 27 35.06 NA 957664 TCGA-AB-2861 6 114381250 114381250 C T SNP HDAC2 NM_001527.2 human genbank 54_36p -1 reviewed missense c.805 p.D269N 1 "HMMPfam_Hist_deacetyl,superfamily_SSF52768" "HMMPfam_Hist_deacetyl,superfamily_SSF52768" - no_errors tier1 90 0 80 42 34.15 58 40 40.82 957664 TCGA-AB-2861 10 124024603 124024603 C T SNP BTBD16 NM_144587.2 human genbank 54_36p 1 validated missense c.17 p.T6M 0 NULL "superfamily_POZ domain,HMMPfam_BTB" - no_errors tier1 353 1 0.28 102 73 41.71 NA 957664 TCGA-AB-2861 7 143693292 143693292 G A SNP ARHGEF5 NM_005435.3 human genbank 54_36p 1 reviewed missense c.2597 p.R866Q 0.023 NULL "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),PatternScan_DH_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_SH3_2,superfamily_PH domain-like" - no_errors tier1 573 0 475 65 12.04 NA 957664 TCGA-AB-2861 1 159410135 159410135 C T SNP B4GALT3 NM_003779.2 human genbank 54_36p -1 reviewed silent c.687 p.P229 0.701 "HMMPfam_Galactosyl_T_2,superfamily_Nucleotide-diphospho-sugar transferases" "HMMPfam_Galactosyl_T_2,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 611 17 2.7 109 76 40.86 35 45 55.56 957664 TCGA-AB-2861 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 957664 TCGA-AB-2861 2 175140981 175140981 G C SNP WIPF1 NM_001077269.1 human genbank 54_36p -1 reviewed missense c.1196 p.P399R 1 NULL "HMMPfam_WH2,HMMSmart_SM00246" - no_errors tier1 182 2 1.09 37 32 46.38 37 33 47.14 964886 TCGA-AB-2862 17 263938 263938 G A SNP C17orf97 NM_001013672.3 human genbank 54_36p 1 validated missense c.988 p.E330K 0 NULL NULL - no_errors tier1 32 1 3.03 19 7 26.92 6 0 964886 TCGA-AB-2862 X 13590684 13590684 A G SNP TCEANC NM_152634.2 human genbank 54_36p 1 validated missense c.226 p.T76A 1 "HMMPfam_TFIIS,superfamily_Conserved domain common to transcription factors TFIIS elongin A CRSP70" "HMMPfam_TFIIS_M,superfamily_Elongation factor TFIIS domain 2,HMMPfam_TFIIS,superfamily_Conserved domain common to transcription factors TFIIS elongin A CRSP70,HMMSmart_SM00510,superfamily_Zinc beta-ribbon" - no_errors tier1 179 0 107 57 34.13 5 0 964886 TCGA-AB-2862 10 38685318 38685318 C T SNP HSD17B7P2 NR_003086.1 human genbank 54_36p 1 provisional rna NULL NULL 0.033 - - - pseudogene tier1 775 38 4.67 95 56 36.84 1 0 964886 TCGA-AB-2862 7 43514204 43514204 G A SNP HECW1 NM_015052.3 human genbank 54_36p 1 validated missense c.3815 p.R1272Q 1 "HMMSmart_HECTc,superfamily_HECT" "HMMPfam_C2,HMMSmart_C2,HMMPfam_HECT,HMMSmart_HECTc,superfamily_HECT,HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,superfamily_C2_CaLB" - no_errors tier1 303 0 115 83 41.5 NA 964886 TCGA-AB-2862 19 44383213 44383213 G A SNP NCCRP1 NM_001001414.1 human genbank 54_36p 1 provisional missense c.805 p.V269M 1 "HMMPfam_FBA,superfamily_Gal_bind_like" "HMMPfam_FBA,superfamily_Gal_bind_like" - no_errors tier1 86 0 48 30 38.46 NA 964886 TCGA-AB-2862 20 47023105 47023105 G A SNP ARFGEF2 NM_006420.2 human genbank 54_36p 1 reviewed silent c.1542 p.V514 1 superfamily_ARM-type_fold "HMMPfam_Sec7,HMMSmart_Sec7,superfamily_Sec7,HMMPfam_DUF1981,superfamily_ARM-type_fold" - no_errors tier1 134 0 104 69 39.43 11 0 964886 TCGA-AB-2862 15 50673187 50673187 A G SNP KIAA1370 NM_019600.2 human genbank 54_36p -1 validated silent c.2688 p.I896 0.992 NULL NULL - no_errors tier1 113 0 89 43 31.62 14 10 41.67 964886 TCGA-AB-2862 17 59303780 59303780 G A SNP CSH2 NM_020991.3 human genbank 54_36p -1 reviewed silent c.345 p.P115 0.987 "HMMPfam_Hormone_1,superfamily_4-helical cytokines" "HMMPfam_Hormone_1,superfamily_4-helical cytokines,PatternScan_SOMATOTROPIN_1,PatternScan_SOMATOTROPIN_2" - no_errors tier1 99 0 50 11 18.03 NA 964886 TCGA-AB-2862 15 83919417 83919417 G A SNP AKAP13 NM_006738.4 human genbank 54_36p 1 reviewed silent c.714 p.P238 0.233 NULL "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMPfam_PH,HMMSmart_PH,superfamily_ANK,HMMPfam_C1_1,HMMSmart_C1,PatternScan_ZF_DAG_PE_1,PatternScan_EF_HAND_1,HMMPfam_RII_binding_1,superfamily_SSF50729,superfamily_SSF57889" - no_errors tier1 202 0 145 89 37.55 4 2 33.33 964886 TCGA-AB-2862 2 91237422 91237422 C T SNP DRD5P1 ENST00000328341 human ensembl 54_36p -1 known missense c.215 p.R72H 1 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,superfamily_SSF81321" - no_errors tier1 81 0 61 34 35.79 NA 964886 TCGA-AB-2862 1 93820716 93820716 G A SNP BCAR3 NM_003567.2 human genbank 54_36p -1 reviewed silent c.1416 p.G472 0.782 superfamily_Ras GEF "HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00147,superfamily_Ras GEF" - no_errors tier1 150 0 97 59 37.58 1 0 964886 TCGA-AB-2862 3 124554002 124554002 C T SNP ADCY5 NM_183357.1 human genbank 54_36p -1 validated silent c.1251 p.A417 0.445 NULL "HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase,HMMPfam_DUF1053,PatternScan_GUANYLATE_CYCLASE_1" - no_errors tier1 257 1 0.39 52 41 43.16 NA 964886 TCGA-AB-2862 10 132781477 132781477 A G SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated missense c.1699 p.F567L 1 "HMMPfam_FF,HMMSmart_FF,superfamily_FF" "HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,HMMPfam_FF,HMMSmart_FF,superfamily_FF" - no_errors tier1 255 0 132 86 39.27 NA 964886 TCGA-AB-2862 6 133831555 133831555 C A SNP EYA4 NM_004100.4 human genbank 54_36p 1 reviewed missense c.963 p.N321K 0.993 NULL HMMPfam_Hydrolase - no_errors tier1 235 0 117 102 46.15 NA 974749 TCGA-AB-2863 19 18513593 18513593 G A SNP FKBP8 NM_012181.3 human genbank 54_36p -1 reviewed missense c.188 p.A63V 0 NULL "HMMPfam_FKBP_C,HMMPfam_TPR_1,superfamily_SSF48452,superfamily_SSF54534" - no_errors tier1 96 9 8.49 37 24 39.34 43 52 54.17 974749 TCGA-AB-2863 16 19790845 19790845 G A SNP GPRC5B NM_016235.1 human genbank 54_36p -1 reviewed missense c.824 p.T275M 1 HMMPfam_7tm_3 "HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3" - no_errors tier1 220 12 5.11 92 82 46.86 NA 974749 TCGA-AB-2863 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 149 20 11.83 89 80 47.34 21 27 55.1 974749 TCGA-AB-2863 13 36344969 36344969 G A SNP SMAD9 NM_005905.1 human genbank 54_36p -1 validated missense c.496 p.H166Y 1 NULL "HMMPfam_MH2,HMMSmart_SM00524,HMMPfam_MH1,HMMSmart_SM00523,superfamily_SMAD/FHA domain,superfamily_SMAD MH1 domain" - no_errors tier1 510 0 315 54 14.56 NA 974749 TCGA-AB-2863 8 37851570 37851570 C T SNP RAB11FIP1 NM_001002814.1 human genbank 54_36p -1 validated missense c.1243 p.A415T 0.003 NULL "HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_RBD-FIP" - no_errors tier1 502 37 6.81 372 123 24.6 34 18 34.62 974749 TCGA-AB-2863 19 38484208 38484210 GTC - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_del c.953_951 p.T318in_frame_del 0.992:0.993:0.994 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 974749 TCGA-AB-2863 20 43315200 43315200 C T SNP SLPI NM_003064.2 human genbank 54_36p -1 reviewed missense c.251 p.R84K 0.002 superfamily_Elafin-like "HMMPfam_WAP,HMMSmart_SM00217,superfamily_Elafin-like,PatternScan_4_DISULFIDE_CORE" - no_errors tier1 229 22 8.76 128 112 46.67 NA 974749 TCGA-AB-2863 3 50355818 50355818 A C SNP ZMYND10 NM_015896.2 human genbank 54_36p -1 validated missense c.434 p.L145R 1 NULL "HMMPfam_zf-MYND,PatternScan_ZF_MYND_1" - no_errors tier1 123 9 6.82 68 48 40.34 2 100 974749 TCGA-AB-2863 7 55240593 55240593 C G SNP EGFR NM_005228.3 human genbank 54_36p 1 reviewed missense c.3422 p.T1141S 0.763 NULL "HMMPfam_Recep_L_domain,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,HMMPfam_Furin-like,HMMSmart_SM00261,PatternScan_PROTEIN_KINASE_TYR,superfamily_Growth factor receptor domain,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,superfamily_L domain-like" - no_errors tier1 269 27 9.06 107 64 36.99 NA 974749 TCGA-AB-2863 11 62120719 62120719 T C SNP MTA2 NM_004739.2 human genbank 54_36p -1 reviewed missense c.848 p.Y283C 1 "HMMSmart_SANT,HMMPfam_Myb_DNA-binding" "HMMPfam_GATA,HMMSmart_ZnF_GATA,PatternScan_GATA_ZN_FINGER_1,HMMPfam_ELM2,HMMSmart_SANT,HMMPfam_BAH,HMMSmart_BAH,HMMPfam_Myb_DNA-binding,superfamily_SSF57716" - no_errors tier1 812 70 7.88 136 102 42.5 77 63 45 974749 TCGA-AB-2863 2 75574230 75574230 T C SNP FAM176A NM_032181.1 human genbank 54_36p -1 validated silent c.99 p.R33 0.991 NULL NULL - no_errors tier1 122 16 11.51 141 109 42.75 NA 974749 TCGA-AB-2863 17 75935198 75935198 G A SNP RNF213 NM_020914.3 human genbank 54_36p 1 validated missense c.2687 p.R896Q 0.996 "HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00184,HMMSmart_SM00382,HMMPfam_zf-C3HC4,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_RING/U-box" - no_errors tier1 77 10 11.36 45 37 44.58 25 37 59.68 974749 TCGA-AB-2863 15 90472624 90472624 C G SNP SLCO3A1 NM_013272.1 human genbank 54_36p 1 validated missense c.1413 p.C471W 1 "HMMPfam_OATP,HMMPfam_Kazal_2,superfamily_MFS general substrate transporter,superfamily_Kazal-type serine protease inhibitors" "HMMPfam_OATP,HMMPfam_Kazal_2,superfamily_MFS general substrate transporter,superfamily_Kazal-type serine protease inhibitors" - no_errors tier1 626 69 9.87 254 218 45.51 32 29 47.54 974749 TCGA-AB-2863 11 92767395 92767395 A G SNP CCDC67 NM_181645.3 human genbank 54_36p 1 validated silent c.1164 p.T388 1 NULL NULL - no_errors tier1 121 13 9.7 91 68 42.5 NA 974749 TCGA-AB-2863 6 100497679 100497679 G A SNP MCHR2 NM_001040179.1 human genbank 54_36p -1 validated missense c.454 p.R152W 0.979 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 164 16 8.89 82 73 46.79 NA 974749 TCGA-AB-2863 3 122859868 122859868 A C SNP HCLS1 NM_005335.4 human genbank 54_36p -1 validated missense c.17 p.V6G 1 NULL "HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_HS1_rep" - no_errors tier1 376 28 6.86 181 125 40.72 54 27 33.33 974749 TCGA-AB-2863 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 67 12 15 63 57 47.11 73 80 52.29 974749 TCGA-AB-2863 2 215946317 215946317 C A SNP FN1 NM_212482.2 human genbank 54_36p -1 reviewed nonsense c.6220 p.E2074* 1 "HMMSmart_SM00060,superfamily_Fibronectin type III" "HMMPfam_fn1,HMMSmart_SM00058,PatternScan_FN1_1,HMMPfam_fn2,HMMSmart_SM00059,PatternScan_FN2_1,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,PatternScan_EGF_1,superfamily_Kringle-like,PatternScan_ALDEHYDE_DEHYDR_GLU,superfamily_Fibronectin type I module" - no_errors tier1 432 54 11.02 143 101 40.89 1 1 50 975684 TCGA-AB-2864 20 3714879 3714879 C T SNP CENPB NM_001810.5 human genbank 54_36p -1 reviewed nonsense c.252 p.W84* 1 "HMMSmart_CENPB,superfamily_Homeodomain_like,HMMPfam_CenpB-DNA-bind" "HMMPfam_DDE,HMMSmart_CENPB,HMMPfam_CENP-B_N,superfamily_Homeodomain_like,HMMPfam_Cenp-B_dimeris,HMMPfam_CenpB-DNA-bind,superfamily_SSF101160" - no_errors tier1 11 0 40 23 35.94 NA NA NA 975684 TCGA-AB-2864 12 9202328 9202328 A G SNP PZP NM_002864.2 human genbank 54_36p -1 validated silent c.3249 p.N1083 0.998 "superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp" "HMMPfam_A2M,HMMPfam_A2M_N,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_recep,superfamily_Alpha-macroglobulin receptor domain,PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N_2,HMMPfam_A2M_comp,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN" - no_errors tier1 253 8 3.03 242 39 13.83 NA NA NA 975684 TCGA-AB-2864 1 10638385 10638385 C T SNP CASZ1 NM_001079843.1 human genbank 54_36p -1 validated missense c.1573 p.G525S 1 NULL "PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 30 0 67 45 40.18 NA NA NA 975684 TCGA-AB-2864 17 20457554 20457554 C T SNP LOC401875 XR_042367.1 human genbank 54_36p 1 model rna NULL NULL 0.961 - - - pseudogene tier1 33 0 98 64 39.51 NA NA NA 975684 TCGA-AB-2864 12 25271549 25271549 G T SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.176 p.A59E 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 83 1 1.16 74 52 40.62 NA NA NA 975684 TCGA-AB-2864 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 178 5 2.72 63 64 50 NA NA NA 975684 TCGA-AB-2864 20 30486932 30486933 - ACCA INS ASXL1 NM_015338.4 human genbank 54_36p 1 reviewed frame_shift_ins c.2756_2757 p.S921fs 0.000:0.000 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 975684 TCGA-AB-2864 1 44241210 44241210 T A SNP SLC6A9 NM_201649.1 human genbank 54_36p -1 validated missense c.844 p.N282Y 0.955 HMMPfam_SNF "HMMPfam_SNF,PatternScan_NA_NEUROTRAN_SYMP_1,PatternScan_NA_NEUROTRAN_SYMP_2" - no_errors tier1 67 0 68 41 36.61 NA NA NA 975684 TCGA-AB-2864 12 50571180 50571180 C T SNP ANKRD33 NM_182608.1 human genbank 54_36p 1 validated missense c.1183 p.P395S 0.144 NULL "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" - no_errors tier1 59 1 1.64 67 63 48.46 NA NA NA 975684 TCGA-AB-2864 17 60020040 60020040 T C SNP SMURF2 NM_022739.3 human genbank 54_36p -1 validated missense c.314 p.N105S 1 "HMMSmart_C2,superfamily_C2_CaLB" "HMMPfam_C2,HMMSmart_C2,HMMPfam_HECT,HMMSmart_HECTc,superfamily_HECT,HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,superfamily_C2_CaLB" - no_errors tier1 352 13 3.55 65 47 41.96 NA NA NA 975684 TCGA-AB-2864 15 88432842 88432842 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.515 p.R172K 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 65 0 75 46 38.02 NA NA NA 975684 TCGA-AB-2864 7 94953408 94953408 T G SNP ASB4 NM_016116.1 human genbank 54_36p 1 reviewed splice_site c.187+2 e1+2 1 - - - no_errors tier1 65 0 109 71 39.23 NA NA NA 975684 TCGA-AB-2864 14 105206164 105206164 T C SNP ENSG00000211894 ENST00000390546 human ensembl 54_36p -1 known missense c.556 p.M186V 0.021 "HMMPfam_C1-set,superfamily_SSF48726" "PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_IGc1,superfamily_SSF48726" - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 34 0 43 28 38.89 NA NA NA 975684 TCGA-AB-2864 12 111330795 111330795 C T SNP RPL6 NM_000970.3 human genbank 54_36p -1 reviewed missense c.49 p.E17K 0.24 NULL "HMMPfam_Ribosomal_L6e,PatternScan_RIBOSOMAL_L6E,HMMPfam_Ribosomal_L6e_N" - no_errors tier1 74 1 1.32 35 17 32.08 NA NA NA 975684 TCGA-AB-2864 5 140244230 140244230 G A SNP PCDHA13 NM_018904.2 human genbank 54_36p 1 reviewed silent c.2193 p.A731 0.239 NULL "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 8 0 31 26 44.07 NA NA NA 975684 TCGA-AB-2864 5 145949924 145949924 G A SNP PPP2R2B NM_181676.1 human genbank 54_36p -1 reviewed missense c.1120 p.R374C 1 superfamily_WD40 repeat-like "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_PR55_1,PatternScan_PR55_2,HMMPfam_PP2A_B_N,HMMPfam_PP2A_B_subs_rcg,PatternScan_WD_REPEATS_1" - no_errors tier1 223 0 171 123 41.14 NA NA NA 975684 TCGA-AB-2864 6 165635643 165635643 C T SNP C6orf118 NM_144980.3 human genbank 54_36p -1 validated missense c.158 p.R53Q 0.017 NULL NULL - no_errors tier1 49 0 180 63 25.61 NA NA NA 975684 TCGA-AB-2864 3 194511175 194511175 G C SNP ATP13A5 NM_198505.2 human genbank 54_36p -1 provisional missense c.2471 p.A824G 1 "superfamily_SSF56784,superfamily_SSF81665" "HMMPfam_Cation_ATPase_N,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_SSF56784,superfamily_SSF81653,superfamily_SSF81660,superfamily_SSF81665" - no_errors tier1 157 1 0.62 123 102 45.13 NA NA NA 984036 TCGA-AB-2865 9 5063770 5063770 G T SNP JAK2 NM_004972.3 human genbank 54_36p 1 reviewed missense c.1849 p.V617F 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_SH2,HMMSmart_SH2,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,PatternScan_FERM_1,PatternScan_FERM_2,HMMSmart_B41,superfamily_SSF55550" - no_errors tier1 79 1 1.25 68 40 37.04 14 20 58.82 984036 TCGA-AB-2865 17 10296271 10296271 G A SNP MYH4 NM_017533.2 human genbank 54_36p -1 validated silent c.3450 p.I1150 1 HMMPfam_Myosin_tail_1 "HMMSmart_IQ,HMMPfam_Myosin_head,HMMSmart_MYSc,HMMPfam_Myosin_tail_1,HMMPfam_Myosin_N,superfamily_SSF52540" - no_errors tier1 61 4 6.15 60 30 32.61 NA 984036 TCGA-AB-2865 1 12842416 12842416 C T SNP PRAMEF2 NM_023014.1 human genbank 54_36p 1 provisional missense c.569 p.T190M 0.002 superfamily_SSF52047 superfamily_SSF52047 - no_errors tier1 53 1 1.85 67 56 45.53 NA 984036 TCGA-AB-2865 1 24256576 24256576 G A SNP MYOM3 NM_152372.3 human genbank 54_36p -1 validated silent c.4179 p.T1393 1 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,PatternScan_EF_HAND_1,superfamily_Immunoglobulin" - no_errors tier1 113 5 4.24 87 65 42.21 NA 984036 TCGA-AB-2865 12 25289551 25289551 C T SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.35 p.G12D 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 11 0 80 14 14.89 23 8 25.81 984036 TCGA-AB-2865 21 35153662 35153662 C T SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.592 p.D198N 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 98 1 1.01 61 97 60.62 359 705 66.2 984036 TCGA-AB-2865 21 35174810 35174810 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.422 p.S141L 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 34 1 2.86 62 22 25.88 712 326 31.41 984036 TCGA-AB-2865 22 35428399 35428399 C T SNP CACNG2 NM_006078.2 human genbank 54_36p -1 reviewed missense c.169 p.V57I 1 HMMPfam_PMP22_Claudin HMMPfam_PMP22_Claudin - no_errors tier1 316 4 1.25 48 36 42.86 NA 984036 TCGA-AB-2865 6 43338696 43338696 A G SNP TTBK1 NM_032538.1 human genbank 54_36p 1 validated missense c.1616 p.D539G 1 NULL "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 38 3 7.32 32 16 33.33 NA 984036 TCGA-AB-2865 19 48463864 48463864 C T SNP PSG9 NM_002784.3 human genbank 54_36p -1 validated silent c.342 p.R114 0.015 "HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_V-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 276 3 1.08 122 114 48.31 NA 984036 TCGA-AB-2865 13 72243998 72243998 C T SNP DIS3 NM_014953.1 human genbank 54_36p -1 validated missense c.1541 p.R514K 0.986 HMMPfam_RNB "HMMPfam_RNB,PatternScan_RIBONUCLEASE_II,HMMSmart_SM00670,superfamily_PIN domain-like" - no_errors tier1 40 5 11.11 94 66 40.49 19 14 41.18 984036 TCGA-AB-2865 4 106377387 106377387 C T SNP TET2 NM_017628.1 human genbank 54_36p 1 validated nonsense c.2839 p.Q947* 1 NULL NULL - no_errors tier1 89 7 7.29 70 46 38.98 22 18 45 984036 TCGA-AB-2865 4 106413250 106413251 - AT INS TET2 ENST00000265149 human ensembl 54_36p 1 known frame_shift_ins c.669_670 p.K223fs 1.000:1.000 NULL NULL - no_start_codon tier1 NA NA NA NA NA NA NA NA NA 984036 TCGA-AB-2865 4 106413251 106413252 - TA INS TET2 ENST00000265149 human ensembl 54_36p 1 known frame_shift_ins c.670_671 p.K224fs 1.000:1.000 NULL NULL - no_start_codon tier1 NA NA NA NA NA NA NA NA NA 984036 TCGA-AB-2865 7 107218912 107218912 C T SNP SLC26A3 NM_000111.2 human genbank 54_36p -1 reviewed silent c.387 p.P129 0.919 NULL "HMMPfam_STAS,superfamily_STAS,HMMPfam_Sulfate_transp,PatternScan_SLC26A" - no_errors tier1 59 4 6.35 86 65 42.21 NA 984036 TCGA-AB-2865 8 110481706 110481706 G A SNP PKHD1L1 NM_177531.4 human genbank 54_36p 1 validated missense c.1238 p.R413H 0.999 "HMMSmart_SM00710,HMMSmart_SM00758,superfamily_Anthrax protective antigen" "HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00710,superfamily_Cupredoxins,superfamily_Pectin lyase-like,HMMSmart_SM00758,superfamily_E set domains,HMMPfam_G8,superfamily_Anthrax protective antigen" - no_errors tier1 77 1 1.28 70 41 36.28 NA 984036 TCGA-AB-2865 7 131516835 131516835 C T SNP PLXNA4 NM_020911.1 human genbank 54_36p -1 validated missense c.3337 p.E1113K 0.997 "HMMPfam_TIG,HMMSmart_SM00429,superfamily_E set domains" "HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain,HMMPfam_PSI,HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00423,superfamily_GTPase activation domain GAP,HMMPfam_Plexin_cytopl,superfamily_E set domains,superfamily_Plexin repeat" - no_errors tier1 138 2 1.43 73 64 46.72 NA 984036 TCGA-AB-2865 3 139225231 139225231 G T SNP CLDN18 NM_001002026.2 human genbank 54_36p 1 validated missense c.262 p.V88F 0.995 HMMPfam_PMP22_Claudin "HMMPfam_PMP22_Claudin,PatternScan_CLAUDIN" - no_errors tier1 292 1 0.34 87 89 50 NA 984036 TCGA-AB-2865 7 148137095 148137095 C T SNP EZH2 NM_004456.3 human genbank 54_36p -1 reviewed splice_site c.2195+1 e18+1 1 - - - no_errors tier1 61 0 124 100 44.44 3 10 76.92 984036 TCGA-AB-2865 1 152018355 152018355 C T SNP SLC27A3 ENST00000368659 human ensembl 54_36p 1 known nonsense c.34 p.R12* 0 NULL superfamily_SSF56801 - no_errors tier1 149 8 5.1 82 42 33.87 3 1 25 984036 TCGA-AB-2865 X 152478458 152478458 G A SNP ATP2B3 NM_001001344.1 human genbank 54_36p 1 reviewed silent c.2703 p.T901 0.019 "HMMPfam_Cation_ATPase_C,superfamily_Calcium ATPase transmembrane domain M" "HMMPfam_Cation_ATPase_N,HMMPfam_Hydrolase,HMMPfam_Cation_ATPase_C,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_Calcium ATPase transmembrane domain M" - no_errors tier1 24 0 9 29 76.32 NA 984036 TCGA-AB-2865 1 169872108 169872108 G T SNP MYOC NM_000261.1 human genbank 54_36p -1 reviewed nonsense c.1095 p.Y365* 1 "HMMPfam_OLF,HMMSmart_SM00284" "HMMPfam_OLF,HMMSmart_SM00284" - no_errors tier1 111 2 1.77 128 95 42.41 NA 992966 TCGA-AB-2866 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 104 34 24.46 72 55 42.97 149 150 50.17 997292 TCGA-AB-2867 1 16608932 16608932 G A SNP SPATA21 NM_198546.1 human genbank 54_36p -1 provisional missense c.338 p.S113L 0.005 NULL "PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_SSF47473" - no_errors tier1 390 9 2.24 183 80 30.42 NA 997292 TCGA-AB-2867 13 18649388 18649388 G A SNP TUBA3C NM_006001.1 human genbank 54_36p -1 reviewed silent c.735 p.D245 0.999 "HMMPfam_Tubulin,superfamily_Tubulin nucleotide-binding domain-like" "HMMPfam_Tubulin,superfamily_Tubulin C-terminal domain-like,PatternScan_TUBULIN,HMMPfam_Tubulin_C,superfamily_Tubulin nucleotide-binding domain-like" - no_errors tier1 123 3 2.36 37 22 37.29 NA 997292 TCGA-AB-2867 14 22306396 22306396 T G SNP OXA1L NM_005015.3 human genbank 54_36p 1 validated missense c.343 p.F115V 0.001 NULL HMMPfam_60KD_IMP - no_errors tier1 107 2 1.83 43 19 30.65 65 37 36.27 997292 TCGA-AB-2867 2 25312191 25312191 T C SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2486 p.K829R 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 208 10 4.55 45 29 38.67 9 21 70 997292 TCGA-AB-2867 2 25322559 25322559 T C SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.1403 p.K468R 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 84 1 1.16 22 10 31.25 27 3 10 997292 TCGA-AB-2867 22 44192246 44192246 G A SNP RIBC2 NM_015653.2 human genbank 54_36p 1 validated silent c.93 p.Q31 0.149 HMMPfam_RIB43A HMMPfam_RIB43A - no_errors tier1 232 10 4.08 120 85 41.46 3 100 997292 TCGA-AB-2867 X 44807944 44807944 C T SNP UTX NM_021140.2 human genbank 54_36p 1 validated missense c.1861 p.R621C 1 NULL "HMMPfam_TPR_1,HMMSmart_JmjC,HMMPfam_JmjC,HMMSmart_TPR,superfamily_SSF48452" - no_errors tier1 116 7 5.65 73 39 34.82 26 9 25.71 997292 TCGA-AB-2867 14 51590184 51590184 G A SNP NID2 NM_007361.3 human genbank 54_36p -1 validated missense c.1292 p.S431L 0.063 NULL "HMMPfam_Ldl_recept_b,HMMSmart_SM00135,PatternScan_ASX_HYDROXYL,HMMPfam_Thyroglobulin_1,HMMSmart_SM00211,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin type-1 domain,HMMSmart_SM00179,HMMPfam_NIDO,HMMSmart_SM00539,HMMPfam_EGF,HMMSmart_SM00181,HMMPfam_G2F,HMMSmart_SM00682,superfamily_GFP-like,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin,superfamily_YWTD domain" - no_errors tier1 206 3 1.43 190 58 23.2 NA 997292 TCGA-AB-2867 16 79613724 79613724 C T SNP CENPN NM_001100625.1 human genbank 54_36p 1 validated missense c.553 p.H185Y 0.998 HMMPfam_CHL4 HMMPfam_CHL4 - no_errors tier1 160 5 3.01 74 39 34.51 0 997292 TCGA-AB-2867 13 100510315 100510315 C T SNP NALCN NM_052867.2 human genbank 54_36p -1 validated silent c.4761 p.Q1587 1 NULL "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" - no_errors tier1 220 10 4.35 99 55 35.71 NA 997292 TCGA-AB-2867 3 125706478 125706478 C T SNP KALRN ENST00000393496 human ensembl 54_36p 1 known silent c.39 p.N13 1 superfamily_SH3 "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMPfam_SH3_1,HMMSmart_SH3,superfamily_SH3,HMMPfam_PH,HMMSmart_PH,HMMPfam_SH3_2,superfamily_SSF50729" - no_errors tier1 260 7 2.61 123 58 31.69 NA 997292 TCGA-AB-2867 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 115 4 3.31 48 29 37.66 17 22 56.41 997292 TCGA-AB-2867 1 246433759 246433759 T A SNP OR2M3 NM_001004689.1 human genbank 54_36p 1 provisional nonsense c.767 p.L256* 0 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 136 3 2.13 143 70 32.86 NA 986000 TCGA-AB-2868 12 7140607 7140607 C T SNP C1RL NM_016546.1 human genbank 54_36p -1 provisional missense c.986 p.R329H 0.357 "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases" "HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,PatternScan_TRYPSIN_SER" - no_errors tier1 172 0 129 50 27.93 20 11 35.48 986000 TCGA-AB-2868 17 7519280 7519280 C T SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed splice_site c.376-1 e4-1 1 - - - no_errors tier1 281 0 97 80 45.2 5 5 50 986000 TCGA-AB-2868 11 8431029 8431029 C A SNP STK33 NM_030906.2 human genbank 54_36p -1 validated missense c.787 p.V263L 1 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 131 0 169 61 26.52 NA 986000 TCGA-AB-2868 6 13314308 13314308 T G SNP PHACTR1 NM_030948.1 human genbank 54_36p 1 validated missense c.947 p.L316R 1 NULL "HMMPfam_RPEL,HMMSmart_SM00707" - no_errors tier1 110 0 159 39 19.7 6 1 14.29 986000 TCGA-AB-2868 1 16127271 16127271 A C SNP SPEN NM_015001.2 human genbank 54_36p 1 reviewed missense c.1949 p.Y650S 1 NULL "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_SPOC,superfamily_SPOC-like,superfamily_SSF54928" - no_errors tier1 108 1 0.92 104 56 35 26 16 38.1 986000 TCGA-AB-2868 8 20155148 20155148 G C SNP LZTS1 NM_021020.2 human genbank 54_36p -1 validated missense c.574 p.Q192E 1 NULL HMMPfam_Fez1 - no_errors tier1 91 0 97 52 34.9 NA 986000 TCGA-AB-2868 1 26397073 26397073 C A SNP CATSPER4 NM_198137.1 human genbank 54_36p 1 validated missense c.596 p.P199H 0.993 "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" - no_errors tier1 202 1 0.49 106 30 22.06 NA 986000 TCGA-AB-2868 18 27593841 27593841 C T SNP MCART2 NM_001034172.2 human genbank 54_36p -1 validated missense c.782 p.R261Q 1 "superfamily_Mitochondrial carrier,HMMPfam_Mito_carr" "superfamily_Mitochondrial carrier,HMMPfam_Mito_carr" - no_errors tier1 70 0 54 31 36.47 1 0 986000 TCGA-AB-2868 19 44605603 44605603 C T SNP PLEKHG2 NM_022835.2 human genbank 54_36p 1 validated missense c.1943 p.S648F 0.098 NULL "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like" - no_errors tier1 214 0 272 66 19.53 25 3 10.71 986000 TCGA-AB-2868 16 62852158 62852158 G T SNP LOC729217 XR_015483.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 165 0 138 48 25.81 34 0 986000 TCGA-AB-2868 15 73769113 73769113 T A SNP CSPG4 NM_001897.4 human genbank 54_36p -1 reviewed missense c.1348 p.R450W 0.098 NULL "HMMSmart_SM00282,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_ATPASE_ALPHA_BETA" - no_errors tier1 20 0 12 4 25 NA 986000 TCGA-AB-2868 16 87193847 87193847 A G SNP ZC3H18 NM_144604.2 human genbank 54_36p 1 provisional missense c.1078 p.R360G 1 NULL "HMMPfam_zf-CCCH,HMMSmart_SM00356" - no_errors tier1 35 0 64 24 27.27 61 40 39.6 986000 TCGA-AB-2868 X 91818303 91818303 C T SNP LOC392501 XR_016267.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 74 1 1.3 36 33 47.83 128 0 986000 TCGA-AB-2868 12 105599943 105599943 G A SNP RFX4 NM_213594.3 human genbank 54_36p 1 reviewed missense c.358 p.G120R 1 "HMMPfam_RFX_DNA_binding,superfamily_SSF46785" "HMMPfam_RFX_DNA_binding,superfamily_SSF46785" - no_errors tier1 163 0 194 65 25.1 NA 986000 TCGA-AB-2868 8 142555396 142555396 C T SNP FLJ43860 NM_207414.2 human genbank 54_36p -1 validated silent c.1479 p.K493 0.033 NULL "HMMPfam_HEAT,superfamily_ARM repeat" - pseudogene tier1 55 0 120 30 20 NA 986000 TCGA-AB-2868 8 145012278 145012278 C G SNP EPPK1 NM_031308.1 human genbank 54_36p -1 provisional missense c.7057 p.D2353H 1 "HMMPfam_Plectin,superfamily_Plakin repeat" "HMMPfam_Plectin,HMMSmart_SM00250,superfamily_Plakin repeat" - no_stop_codon:bad_bp_length_for_coding_region tier1 11 0 33 10 23.26 19 2 9.52 986000 TCGA-AB-2868 7 148595232 148595232 G A SNP ZNF783 ENST00000378052 human ensembl 54_36p 1 known missense c.659 p.R220K 0.002 NULL "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box" - no_errors tier1 291 1 0.34 248 103 29.34 28 16 36.36 986000 TCGA-AB-2868 4 152040803 152040803 T C SNP LRBA NM_006726.2 human genbank 54_36p -1 validated missense c.1772 p.Y591C 1 superfamily_ARM repeat "HMMPfam_Beach,superfamily_BEACH domain,HMMSmart_SM00320,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_DUF1088,superfamily_WD40 repeat-like,superfamily_ARM repeat,HMMPfam_WD40,superfamily_PH domain-like" - no_errors tier1 197 2 1.01 101 37 26.81 22 15 40.54 141273 TCGA-AB-2869 1 8448659 8448659 G A SNP RERE NM_001042681.1 human genbank 54_36p -1 reviewed silent c.1116 p.S372 0.989 NULL "HMMPfam_GATA,HMMSmart_SM00401,HMMPfam_ELM2,HMMSmart_SM00717,HMMPfam_BAH,HMMSmart_SM00439,HMMPfam_Atrophin-1,superfamily_Homeodomain-like,HMMPfam_Myb_DNA-binding,superfamily_Glucocorticoid receptor-like (DNA-binding domain)" - no_errors tier1 75 7 8.54 134 96 40.68 28 30 51.72 141273 TCGA-AB-2869 2 25322414 25322414 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed nonsense c.1453 p.Q485* 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 16 1 5.88 44 46 51.11 37 15 28.85 141273 TCGA-AB-2869 13 27506253 27506254 - GATCATATTCATATTCTCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1803_1802 p.602in_frame_insQMGVSKRKFRVWRI*I*S 0.998:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 141273 TCGA-AB-2869 15 45843351 45843351 C T SNP SEMA6D NM_153618.1 human genbank 54_36p 1 reviewed missense c.760 p.R254C 1 "HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain" "HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain,HMMPfam_PSI,HMMSmart_SM00423,superfamily_Plexin repeat" - no_errors tier1 213 8 3.62 296 177 37.03 NA 141273 TCGA-AB-2869 10 73131787 73131787 G T SNP CDH23 NM_022124.4 human genbank 54_36p 1 reviewed silent c.2400 p.V800 1 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" - no_errors tier1 13 1 7.14 32 12 26.67 2 1 33.33 141273 TCGA-AB-2869 1 94263182 94263182 C T SNP ABCA4 NM_000350.2 human genbank 54_36p -1 reviewed missense c.4550 p.R1517H 0.994 NULL "HMMPfam_ABC_tran,HMMSmart_AAA,PatternScan_ABC_TRANSPORTER_1,superfamily_SSF52540" - no_errors tier1 203 9 4.23 197 122 38.12 NA 141273 TCGA-AB-2869 9 94687368 94687368 A G SNP LOC642943 XR_039168.1 human genbank 54_36p 1 model rna NULL NULL 0.127 - - - pseudogene tier1 73 4 5.13 148 78 34.06 NA 141273 TCGA-AB-2869 3 103058719 103058720 - ACTTTTAGAAAGCTTTAATAACC INS NFKBIZ NM_031419.1 human genbank 54_36p 1 reviewed splice_site_ins c.1935+2_1935+1 e10+2 0.997:0.000 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 141273 TCGA-AB-2869 4 111617157 111617157 C T SNP ENPEP NM_001977.3 human genbank 54_36p 1 validated silent c.138 p.S46 0 NULL "HMMPfam_Peptidase_M1,superfamily_Metalloproteases (""zincins"") catalytic domain,superfamily_Leukotriene A4 hydrolase N-terminal domain" - no_errors tier1 57 10 14.93 117 106 47.32 NA 141273 TCGA-AB-2869 9 122772344 122772344 T G SNP C5 NM_001735.2 human genbank 54_36p -1 reviewed missense c.4087 p.T1363P 0.204 NULL "HMMPfam_ANATO,HMMSmart_ANATO,PatternScan_ANAPHYLATOXIN_1,HMMPfam_A2M,HMMPfam_A2M_N,superfamily_Terp_cyc_toroid,HMMPfam_A2M_recep,superfamily_AM_receptor_bind,HMMPfam_A2M_N_2,HMMPfam_A2M_comp,superfamily_Anaphylatoxin,HMMPfam_NTR,HMMSmart_C345C,PatternScan_ALPHA_2_MACROGLOBULIN" - no_errors tier1 113 9 7.38 288 206 41.45 3 2 40 141273 TCGA-AB-2869 5 159958378 159958378 A G SNP ATP10B NM_025153.2 human genbank 54_36p -1 validated missense c.3541 p.Y1181H 0.993 NULL "HMMPfam_E1-E2_ATPase,HMMPfam_Hydrolase_3,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N" - no_errors tier1 57 3 5 181 119 38.89 NA 141273 TCGA-AB-2869 5 165388861 165388861 C T SNP LOC728843 XR_015391.1 human genbank 54_36p -1 model rna NULL NULL 0.997 - - - pseudogene tier1 91 8 8.08 148 126 45.32 NA 141273 TCGA-AB-2869 5 170770149 170770150 - CTGC INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.860_861 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 141273 TCGA-AB-2869 4 176810076 176810076 G A SNP GPM6A NM_005277.3 human genbank 54_36p -1 validated silent c.444 p.T148 1 HMMPfam_Myelin_PLP "HMMPfam_Myelin_PLP,HMMSmart_SM00002,PatternScan_MYELIN_PLP_1,PatternScan_MYELIN_PLP_2" - no_errors tier1 14 0 56 49 46.23 NA 141273 TCGA-AB-2869 2 222794334 222794334 C T SNP PAX3 NM_181459.4 human genbank 54_36p -1 reviewed missense c.809 p.R270H 1 "HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like,PatternScan_HOMEOBOX_1" "HMMPfam_Homeobox,HMMSmart_SM00389,HMMPfam_PAX,HMMSmart_SM00351,PatternScan_PAIRED_1,superfamily_Homeodomain-like,PatternScan_HOMEOBOX_1" - no_errors tier1 57 3 5 115 62 34.83 NA 146218 TCGA-AB-2870 16 5018917 5018917 G C SNP NAGPA NM_016256.2 human genbank 54_36p -1 reviewed silent c.885 p.L295 0.994 NULL "HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2" - no_errors tier1 59 6 9.09 75 82 51.25 21 27 56.25 146218 TCGA-AB-2870 19 9973274 9973274 C T SNP COL5A3 NM_015719.3 human genbank 54_36p -1 reviewed missense c.1036 p.G346R 0.014 NULL "HMMPfam_COLFI,HMMSmart_SM00038,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2" - no_errors tier1 117 7 5.65 205 138 40 NA 146218 TCGA-AB-2870 13 27506258 27506275 CATATTCATATTCTCTGA GGGGTGGGGGGG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1798_1781 p.595in_frame_insPPTP 1.000:1.000:1.000:0.999:0.789:0.821:0.816:0.676:0.765:0.789:0.794:0.991:0.997:0.996:0.999:1.000:1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 146218 TCGA-AB-2870 7 40084184 40084184 A - DEL CDC2L5 NM_003718.3 human genbank 54_36p 1 reviewed frame_shift_del c.2836 p.Y946fs 0.975 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 NA NA NA NA NA NA NA NA NA 146218 TCGA-AB-2870 11 57791808 57791808 G A SNP OR10W1 NM_207374.2 human genbank 54_36p -1 provisional silent c.99 p.N33 0.032 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 90 13 12.62 262 219 44.97 NA 146218 TCGA-AB-2870 1 63073082 63073082 G T SNP ATG4C NM_032852.2 human genbank 54_36p 1 reviewed missense c.1060 p.D354Y 1 HMMPfam_Peptidase_C54 HMMPfam_Peptidase_C54 - no_errors tier1 86 7 7.53 308 125 28.67 21 9 30 146218 TCGA-AB-2870 15 71411572 71411572 G A SNP HCN4 NM_005477.2 human genbank 54_36p -1 reviewed silent c.1324 p.L442 1 "HMMPfam_Ion_trans,superfamily_SSF81324" "HMMPfam_cNMP_binding,HMMSmart_cNMP,HMMPfam_Ion_trans,HMMPfam_Ion_trans_N,PatternScan_CNMP_BINDING_1,PatternScan_CNMP_BINDING_2,superfamily_cNMP_binding,superfamily_SSF81324" - no_errors tier1 28 1 3.45 77 64 45.07 NA 146218 TCGA-AB-2870 6 75958768 75958768 G A SNP COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed missense c.214 p.L72F 1 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III" "HMMPfam_VWA,HMMSmart_SM00327,HMMSmart_SM00210,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Collagen,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_vWA-like" - no_errors tier1 29 2 6.45 153 104 40 NA 146218 TCGA-AB-2870 12 105294314 105294314 C T SNP POLR3B NM_018082.4 human genbank 54_36p 1 provisional missense c.452 p.T151M 0.998 "HMMPfam_RNA_pol_Rpb2_1,superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase" "HMMPfam_RNA_pol_Rpb2_6,PatternScan_RNA_POL_BETA,HMMPfam_RNA_pol_Rpb2_7,HMMPfam_RNA_pol_Rpb2_2,HMMPfam_RNA_pol_Rpb2_1,HMMPfam_RNA_pol_Rpb2_3,HMMPfam_RNA_pol_Rpb2_4,HMMPfam_RNA_pol_Rpb2_5,superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase" - no_errors tier1 96 6 5.88 188 131 40.31 3 7 70 146218 TCGA-AB-2870 1 115058053 115058053 G T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.181 p.Q61K 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 73 3 3.95 245 55 18.21 96 16 14.29 146218 TCGA-AB-2870 1 154412904 154412904 A G SNP SEMA4A NM_022367.2 human genbank 54_36p 1 provisional missense c.1778 p.H593R 0.437 NULL "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema,HMMPfam_PSI,HMMSmart_PSI,superfamily_Plexin-like_fold" - no_errors tier1 229 31 11.92 348 314 47.08 58 43 42.16 146218 TCGA-AB-2870 2 220052132 220052132 C T SNP SPEG NM_005876.4 human genbank 54_36p 1 validated nonsense c.5050 p.R1684* 0.643 "HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_ST,superfamily_Fibronectin type III,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_Immunoglobulin" - no_errors tier1 79 11 12.22 88 66 42.31 NA 150288 TCGA-AB-2871 13 27506262 27506263 - TCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATC INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1794_1793 p.599in_frame_insMVQVTGSSDNEYFYVDFREYE 0.789:0.821 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 150288 TCGA-AB-2871 1 36539747 36539747 C T SNP THRAP3 NM_005119.3 human genbank 54_36p 1 validated nonsense c.2509 p.R837* 0.969 NULL NULL - no_errors tier1 135 0 128 26 16.46 35 3 7.89 150288 TCGA-AB-2871 21 38008662 38008662 C T SNP KCNJ6 NM_002240.2 human genbank 54_36p -1 reviewed missense c.668 p.R223Q 1 "HMMPfam_IRK,superfamily_Ig_E-set" "HMMPfam_IRK,superfamily_Ig_E-set,superfamily_SSF81324" - no_errors tier1 42 0 72 27 27 NA 150288 TCGA-AB-2871 19 41127523 41127523 C T SNP LRFN3 NM_024509.1 human genbank 54_36p 1 provisional missense c.1649 p.S550L 0.979 NULL "HMMSmart_LRRNT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMSmart_IGc2,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,superfamily_SSF48726,superfamily_SSF52058" - no_errors tier1 27 0 72 15 17.24 5 0 150288 TCGA-AB-2871 14 54922339 54922339 G A SNP KIAA0831 NM_014924.3 human genbank 54_36p -1 predicted missense c.638 p.T213M 0.819 HMMPfam_DUF2355 HMMPfam_DUF2355 - no_errors tier1 117 0 199 58 22.39 15 15 50 150288 TCGA-AB-2871 15 59969852 59969852 T C SNP VPS13C NM_020821.1 human genbank 54_36p -1 validated missense c.9145 p.I3049V 1 NULL HMMPfam_DUF1162 - no_errors tier1 114 0 121 36 22.78 58 21 26.58 150288 TCGA-AB-2871 14 73059207 73059207 C T SNP HEATR4 NM_203309.1 human genbank 54_36p -1 provisional missense c.262 p.A88T 0.001 NULL "HMMPfam_HEAT,superfamily_ARM-type_fold" - no_errors tier1 135 0 239 61 20.2 2 1 33.33 150288 TCGA-AB-2871 6 75917709 75917709 C A SNP COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed missense c.4015 p.D1339Y 1 "HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like" "HMMPfam_VWA,HMMSmart_SM00327,HMMSmart_SM00210,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Collagen,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_vWA-like" - no_errors tier1 129 1 0.77 109 23 17.29 NA 150288 TCGA-AB-2871 8 92077155 92077155 C T SNP TMEM55A NM_018710.2 human genbank 54_36p -1 validated missense c.700 p.G234R 1 HMMPfam_Tmemb_55A HMMPfam_Tmemb_55A - no_errors tier1 49 1 2 134 37 21.64 4 7 63.64 150288 TCGA-AB-2871 4 99483396 99483396 G A SNP RAP1GDS1 NM_001100426.1 human genbank 54_36p 1 validated missense c.199 p.A67T 1 superfamily_ARM repeat "HMMPfam_Arm,HMMSmart_SM00185,superfamily_ARM repeat" - no_errors tier1 83 0 134 35 20.59 33 19 36.54 150288 TCGA-AB-2871 12 111411292 111411292 A T SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.1529 p.Q510L 1 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 116 0 335 112 24.78 35 15 30 150288 TCGA-AB-2871 X 123019509 123019509 G A SNP STAG2 NM_001042749.1 human genbank 54_36p 1 validated splice_site c.1416+1 e13+1 1 - - - no_errors tier1 33 0 34 16 30.77 1 0 150288 TCGA-AB-2871 X 129032705 129032705 C T SNP ELF4 NM_001421.1 human genbank 54_36p -1 validated missense c.800 p.R267Q 1 "HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_2,superfamily_SSF46785" "HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_1,PatternScan_ETS_DOMAIN_2,superfamily_SSF46785" - no_errors tier1 43 0 113 62 35.23 28 93 76.86 150288 TCGA-AB-2871 5 140569962 140569962 C T SNP PCDHB12 NM_018932.3 human genbank 54_36p 1 reviewed silent c.1299 p.T433 0 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 30 0 60 18 22.5 NA 150288 TCGA-AB-2871 2 152127439 152127439 G T SNP NEB NM_004543.3 human genbank 54_36p -1 reviewed missense c.13720 p.Q4574K 1 HMMSmart_SM00227 "HMMPfam_Nebulin,HMMSmart_SM00227,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain" - no_errors tier1 129 0 208 73 25.52 NA 150288 TCGA-AB-2871 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 179016 TCGA-AB-2872 12 4576122 4576122 C T SNP DYRK4 NM_003845.1 human genbank 54_36p 1 provisional missense c.526 p.R176C 1 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 111 0 157 100 38.76 NA 179016 TCGA-AB-2872 19 12912080 12912081 - A INS CALR NM_004343.3 human genbank 54_36p 1 reviewed frame_shift_ins c.516_517 p.T172fs 1.000:1.000 "HMMPfam_Calreticulin,superfamily_Concanavalin A-like lectins/glucanases" "HMMPfam_Calreticulin,superfamily_Concanavalin A-like lectins/glucanases,PatternScan_CALRETICULIN_1,PatternScan_CALRETICULIN_2,PatternScan_CALRETICULIN_REPEAT" - no_errors tier1 NA NA NA NA NA NA NA NA NA 179016 TCGA-AB-2872 6 34616830 34616830 C T SNP SPDEF NM_012391.1 human genbank 54_36p -1 provisional silent c.543 p.K181 1 "HMMPfam_SAM_PNT,HMMSmart_SAM_PNT,superfamily_SAM_homology" "HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_1,PatternScan_ETS_DOMAIN_2,HMMPfam_SAM_PNT,HMMSmart_SAM_PNT,superfamily_SAM_homology,superfamily_SSF46785" - no_errors tier1 6 0 29 17 36.96 0 179016 TCGA-AB-2872 15 39269594 39269594 G A SNP EXD1 NM_152596.2 human genbank 54_36p -1 provisional nonsense c.715 p.R239* 0.496 "HMMSmart_SM00474,superfamily_Ribonuclease H-like" "HMMPfam_3_5_exonuc,HMMSmart_SM00474,superfamily_Ribonuclease H-like" - no_errors tier1 91 2 2.15 99 63 38.41 NA 179016 TCGA-AB-2872 6 43574797 43574797 G T SNP TJAP1 NM_080604.1 human genbank 54_36p 1 reviewed missense c.80 p.G27V 0.026 NULL NULL - no_errors tier1 51 0 109 65 36.93 11 14 56 179016 TCGA-AB-2872 10 67710237 67710237 A T SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated silent c.1881 p.I627 1 HMMPfam_Vinculin "HMMPfam_Vinculin,superfamily_alpha-catenin/vinculin" - no_errors tier1 102 1 0.96 114 87 43.07 NA 179016 TCGA-AB-2872 9 83893235 83893235 C T SNP LOC401533 XR_016904.2 human genbank 54_36p -1 model rna NULL NULL 0.975 - - - pseudogene tier1 74 0 18 64 76.19 3 0 179016 TCGA-AB-2872 X 91019745 91019745 C T SNP PCDH11X NM_032968.1 human genbank 54_36p 1 reviewed missense c.1850 p.T617I 1 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,HMMPfam_Protocadherin,superfamily_Cadherin-like" - no_errors tier1 15 0 9 29 74.36 NA 179016 TCGA-AB-2872 14 95250107 95250107 C T SNP TCL1A NM_001098725.1 human genbank 54_36p -1 validated missense c.50 p.R17H 0.953 "HMMPfam_TCL1_MTCP1,superfamily_TCL1_MTCP1" "HMMPfam_TCL1_MTCP1,superfamily_TCL1_MTCP1" - no_errors tier1 26 0 53 26 32.91 6 0 179016 TCGA-AB-2872 7 127456463 127456463 G A SNP LRRC4 NM_022143.4 human genbank 54_36p -1 validated silent c.1467 p.T489 1 NULL "HMMPfam_LRRNT,HMMSmart_SM00013,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 12 0 69 13 15.85 12 0 179016 TCGA-AB-2872 5 151764450 151764450 C T SNP NMUR2 NM_020167.4 human genbank 54_36p -1 reviewed missense c.418 p.V140I 0.391 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 18 1 5.26 70 65 48.15 NA 179016 TCGA-AB-2872 6 155195592 155195592 C A SNP RBM16 NM_014892.3 human genbank 54_36p 1 validated missense c.3187 p.P1063T 1 NULL "HMMPfam_RRM_1,HMMSmart_RRM,HMMSmart_RPR,HMMPfam_DUF618,superfamily_ENTH_VHS,superfamily_SSF54928" - no_errors tier1 54 2 3.51 134 131 48.88 39 14 26.42 179016 TCGA-AB-2872 4 155376048 155376048 G A SNP DCHS2 NM_017639.1 human genbank 54_36p -1 validated missense c.7841 p.P2614L 0.038 NULL "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" - no_errors tier1 117 0 103 70 40.23 NA 179016 TCGA-AB-2872 2 179314300 179314300 C T SNP TTN ENST00000286104 human ensembl 54_36p -1 known missense c.11398 p.V3800I 0.951 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set" "PatternScan_IG_MHC,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,PatternScan_FGGY_KINASES_1" - no_stop_codon tier1 102 2 1.92 143 105 42 NA 180168 TCGA-AB-2873 1 5347 5347 G A SNP LOC100134101 XR_036902.1 human genbank 54_36p -1 model rna NULL NULL 0.002 - - - pseudogene tier1 8 0 9 1 10 25 0 180168 TCGA-AB-2873 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 37 23 38.33 99 48 32.43 13 8 38.1 180168 TCGA-AB-2873 4 106157737 106157737 C - DEL TET2 NM_001127208.1 human genbank 58_37c 1 validated frame_shift_del c.2638 p.H880fs 0.856 NULL NULL - no_errors tier1 175 38 21.71 169 65 38.24 101 50 49.5 180168 TCGA-AB-2873 4 106377186 106377186 C - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.2638 p.H880fs 0.255 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 237983 TCGA-AB-2874 16 3239463 3239463 C T SNP MEFV NM_000243.2 human genbank 54_36p -1 reviewed missense c.1229 p.R410H 0.025 "HMMPfam_zf-B_box,HMMSmart_SM00336,superfamily_B-box zinc-binding domain" "HMMPfam_zf-B_box,HMMSmart_SM00336,HMMPfam_SPRY,HMMPfam_PAAD_DAPIN,HMMSmart_SM00589,superfamily_DEATH domain,HMMSmart_SM00449,superfamily_B-box zinc-binding domain" - no_errors tier1 140 2 1.4 61 75 54.74 NA 237983 TCGA-AB-2874 16 18760441 18760441 A G SNP SMG1 NM_015092.4 human genbank 54_36p -1 reviewed missense c.6643 p.F2215L 1 "HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,superfamily_Protein kinase-like (PK-like)" "HMMPfam_HEAT,HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_FATC,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_2" - no_errors tier1 469 12 2.49 168 145 45.45 51 49 49 237983 TCGA-AB-2874 10 23359678 23359678 C A SNP ARMC3 NM_173081.3 human genbank 54_36p 1 validated silent c.2193 p.T731 1 NULL "HMMPfam_Arm,HMMSmart_SM00185,superfamily_ARM repeat" - no_errors tier1 332 7 2.05 168 142 45.08 NA 237983 TCGA-AB-2874 11 32370142 32370142 G A SNP WT1 NM_024426.3 human genbank 54_36p -1 reviewed missense c.1384 p.R462W 1 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 142 1 0.69 124 46 26.9 16 7 30.43 237983 TCGA-AB-2874 19 38484263 38484263 G A SNP CEBPA NM_004364.3 human genbank 54_36p -1 reviewed missense c.898 p.R300C 1 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 0 0 0 65 47 41.96 260 212 44.82 237983 TCGA-AB-2874 19 39596586 39596586 T C SNP PDCD2L NM_032346.1 human genbank 54_36p 1 provisional missense c.791 p.I264T 1 HMMPfam_PDCD2_C HMMPfam_PDCD2_C - no_errors tier1 206 6 2.82 86 71 44.94 3 3 50 237983 TCGA-AB-2874 17 39831216 39831216 G A SNP GPATCH8 NM_001002909.1 human genbank 54_36p -1 validated missense c.3755 p.T1252I 1 NULL "HMMPfam_G-patch,HMMSmart_SM00443,PatternScan_ZINC_FINGER_C2H2_1" - no_errors tier1 394 10 2.44 157 154 49.36 33 24 41.38 237983 TCGA-AB-2874 19 45075959 45075959 C G SNP FCGBP NM_003890.2 human genbank 54_36p -1 validated missense c.9491 p.C3164S 1 "superfamily_Cysrich_TIL,HMMPfam_TIL" "HMMSmart_VWC,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_TIL_assoc,HMMSmart_FOLN,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 375 3 0.79 193 45 18.83 NA 237983 TCGA-AB-2874 19 62435849 62435849 C T SNP AURKC NM_001015878.1 human genbank 54_36p 1 reviewed missense c.424 p.R142C 0.983 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 250 1 0.4 156 27 14.67 1 0 237983 TCGA-AB-2874 13 83352095 83352095 G T SNP SLITRK1 NM_052910.1 human genbank 54_36p -1 validated missense c.1549 p.Q517K 1 superfamily_SSF52058 "HMMSmart_LRRNT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058" - no_errors tier1 161 7 4.17 70 61 46.21 NA 237983 TCGA-AB-2874 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 116 6 4.92 91 79 46.2 137 106 43.62 237983 TCGA-AB-2874 12 118453114 118453114 G A SNP CCDC60 NM_178499.3 human genbank 54_36p 1 validated missense c.1414 p.A472T 0.954 NULL NULL - no_errors tier1 161 3 1.83 123 112 46.86 NA 237983 TCGA-AB-2874 3 145057398 145057398 T - DEL LOC257039 XM_172230.1 human genbank 54_36p -1 model frame_shift_del c.542 p.E181fs 1 HMMPfam_Ribosomal_S17e HMMPfam_Ribosomal_S17e - no_errors tier1 NA NA NA NA NA NA NA NA NA 237983 TCGA-AB-2874 1 155371935 155371935 C T SNP ETV3 NM_005240.1 human genbank 54_36p -1 validated missense c.236 p.R79K 1 "HMMPfam_Ets,HMMSmart_ETS,superfamily_SSF46785" "HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_1,PatternScan_ETS_DOMAIN_2,superfamily_SSF46785" - no_errors tier1 317 14 4.23 177 128 41.16 6 6 50 237983 TCGA-AB-2874 1 238723327 238723327 G T SNP GREM2 NM_022469.3 human genbank 54_36p -1 reviewed missense c.72 p.N24K 1 NULL "HMMPfam_DAN,HMMSmart_CT" - no_errors tier1 47 1 2.08 66 40 37.38 NA 237983 TCGA-AB-2874 2 240617625 240617625 C A SNP OR6B2 NM_001005853.1 human genbank 54_36p -1 provisional missense c.895 p.D299Y 0.046 superfamily_Family A G protein-coupled receptor-like "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 78 0 81 71 45.81 NA 275786 TCGA-AB-2875 13 27506261 27506262 - TTCATATTCTCTGAAATCAACGTAGGCCAC INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1795_1794 p.598in_frame_insVAYVDFREYE 0.999:0.789 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 275786 TCGA-AB-2875 7 33911799 33911799 C A SNP BMPER NM_133468.3 human genbank 54_36p 1 validated missense c.49 p.R17S 0.866 NULL "HMMPfam_VWC,HMMSmart_VWC,PatternScan_VWFC_1,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 42 0 34 18 33.96 NA 275786 TCGA-AB-2875 19 45125275 45125275 G A SNP FCGBP NM_003890.2 human genbank 54_36p -1 validated silent c.834 p.Y278 0.223 NULL "HMMSmart_VWC,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_TIL_assoc,HMMSmart_FOLN,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 291 1 0.34 117 49 29.34 1 0 275786 TCGA-AB-2875 4 70634475 70634475 C T SNP SULT1B1 NM_014465.3 human genbank 54_36p -1 reviewed missense c.472 p.E158K 0.608 "HMMPfam_Sulfotransfer_1,superfamily_SSF52540" "HMMPfam_Sulfotransfer_1,superfamily_SSF52540" - no_errors tier1 21 0 125 63 32.98 5 0 275786 TCGA-AB-2875 12 87007016 87007016 G A SNP CEP290 NM_025114.3 human genbank 54_36p -1 reviewed missense c.3953 p.T1318I 1 NULL NULL - no_errors tier1 54 0 144 89 37.71 10 10 50 275786 TCGA-AB-2875 11 112786851 112786851 G A SNP DRD2 NM_000795.3 human genbank 54_36p -1 reviewed silent c.1140 p.G380 0.996 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 269 2 0.74 115 78 39.59 NA 275786 TCGA-AB-2875 7 113306227 113306227 T C SNP PPP1R3A NM_002711.3 human genbank 54_36p -1 reviewed missense c.2156 p.H719R 1 NULL HMMPfam_CBM_21 - no_errors tier1 25 0 193 123 38.68 NA 275786 TCGA-AB-2875 3 124910337 124910337 G T SNP MYLK NM_053025.3 human genbank 54_36p -1 reviewed missense c.2038 p.L680I 1 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin" "HMMSmart_SM00219,HMMSmart_SM00220,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_ST,superfamily_Fibronectin type III,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_Immunoglobulin" - no_errors tier1 121 0 105 57 34.76 NA 275786 TCGA-AB-2875 1 150544072 150544072 C T SNP FLG NM_002016.1 human genbank 54_36p -1 provisional missense c.9914 p.R3305H 0 HMMPfam_Filaggrin "PatternScan_S100_CABP,HMMPfam_Filaggrin,HMMPfam_S_100,PatternScan_EF_HAND_1,superfamily_SSF47473" - no_errors tier1 168 2 1.18 118 49 28.99 NA 275786 TCGA-AB-2875 1 157429939 157429939 G A SNP CADM3 NM_021189.1 human genbank 54_36p 1 validated missense c.587 p.R196Q 0.991 "HMMSmart_IG,HMMPfam_C2-set_2,superfamily_SSF48726" "HMMSmart_4.1m,HMMSmart_IGc2,HMMSmart_IG,HMMPfam_V-set,HMMPfam_ig,HMMPfam_C2-set_2,superfamily_SSF48726" - no_errors tier1 79 0 151 89 36.18 NA 275786 TCGA-AB-2875 2 210266427 210266427 G A SNP MAP2 NM_002374.1 human genbank 54_36p 1 reviewed missense c.1288 p.G430R 0.002 HMMPfam_MAP2_projctn "HMMPfam_Tubulin-binding,PatternScan_TAU_MAP,HMMPfam_MAP2_projctn,HMMPfam_RII_binding_1" - no_errors tier1 40 0 149 52 25.74 NA 319955 TCGA-AB-2876 18 2753718 2753718 T C SNP SMCHD1 NM_015295.2 human genbank 54_36p 1 validated silent c.4650 p.D1550 0.919 NULL "HMMPfam_HATPase_c,superfamily_ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase,HMMPfam_SMC_hinge,superfamily_Smc hinge domain" - no_errors tier1 49 3 5.77 57 50 46.73 47 41 46.59 319955 TCGA-AB-2876 6 13314113 13314114 - G INS PHACTR1 NM_030948.1 human genbank 54_36p 1 validated frame_shift_ins c.752_753 p.P254fs 0.638:0.521 NULL "HMMPfam_RPEL,HMMSmart_SM00707" - no_errors tier1 NA NA NA NA NA NA NA NA NA 319955 TCGA-AB-2876 10 26345791 26345791 G A SNP MYO3A NM_017433.4 human genbank 54_36p 1 reviewed missense c.545 p.R182Q 1 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Myosin_head,HMMSmart_MYSc,HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_SSF52540" - no_errors tier1 51 0 82 62 43.06 NA 319955 TCGA-AB-2876 8 27793118 27793118 C T SNP SCARA5 NM_173833.4 human genbank 54_36p -1 provisional missense c.1238 p.R413H 1 "HMMPfam_SRCR,PatternScan_SRCR_1,HMMSmart_SM00202,superfamily_SRCR-like" "HMMPfam_SRCR,PatternScan_SRCR_1,HMMPfam_Collagen,HMMSmart_SM00202,superfamily_SRCR-like" - no_errors tier1 43 1 2.27 41 53 56.38 NA 319955 TCGA-AB-2876 20 31065397 31065397 C T SNP BPIL1 NM_025227.1 human genbank 54_36p 1 reviewed silent c.429 p.H143 0 "HMMPfam_LBP_BPI_CETP,superfamily_Bactericidal permeability-increasing protein BPI" "HMMPfam_LBP_BPI_CETP_C,HMMSmart_SM00329,HMMPfam_LBP_BPI_CETP,superfamily_Bactericidal permeability-increasing protein BPI" - no_errors tier1 67 7 9.46 47 47 50 NA 319955 TCGA-AB-2876 18 46956764 46956764 T C SNP MEX3C NM_016626.3 human genbank 54_36p -1 validated silent c.1935 p.P645 1 "HMMSmart_RING,HMMPfam_zf-C3HC4,superfamily_SSF57850" "HMMSmart_RING,HMMSmart_KH,PatternScan_ZF_RING_1,HMMPfam_KH_1,HMMPfam_zf-C3HC4,superfamily_SSF54791,superfamily_SSF57850" - no_errors tier1 116 3 2.52 83 74 47.13 21 31 59.62 319955 TCGA-AB-2876 11 66006376 66006376 C T SNP DPP3 NM_005700.3 human genbank 54_36p 1 reviewed silent c.129 p.Y43 0.795 NULL HMMPfam_Peptidase_M49 - no_errors tier1 66 1 1.49 46 27 36.99 19 22 53.66 319955 TCGA-AB-2876 12 79635034 79635034 A G SNP MYF5 NM_005593.2 human genbank 54_36p 1 validated missense c.61 p.I21V 0.999 "HMMPfam_Basic,HMMSmart_BASIC" "HMMPfam_HLH,HMMSmart_HLH,HMMPfam_Basic,HMMSmart_BASIC,superfamily_HLH_basic" - no_errors tier1 33 3 8.33 44 21 32.31 NA 319955 TCGA-AB-2876 11 85639095 85639095 C A SNP EED NM_003797.2 human genbank 54_36p 1 reviewed nonsense c.224 p.S75* 1 NULL "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 82 4 4.65 102 57 35.85 10 5 33.33 319955 TCGA-AB-2876 4 106375989 106375989 C T SNP TET2 NM_017628.1 human genbank 54_36p 1 validated nonsense c.1441 p.Q481* 1 NULL NULL - no_errors tier1 77 4 4.94 109 96 46.83 40 45 52.94 319955 TCGA-AB-2876 4 106376562 106376562 A - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.2014 p.H672fs 0.114 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 319955 TCGA-AB-2876 X 135401946 135401946 C T SNP BRS3 NM_001727.1 human genbank 54_36p 1 validated missense c.946 p.R316W 1 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 104 5 4.59 52 44 45.83 NA 319955 TCGA-AB-2876 1 152783137 152783137 G A SNP TDRD10 NM_001098475.1 human genbank 54_36p 1 validated missense c.578 p.R193H 0 NULL "HMMPfam_RRM_1,HMMSmart_SM00360,HMMPfam_TUDOR,superfamily_RNA-binding domain RBD,superfamily_Tudor/PWWP/MBT" - no_errors tier1 169 4 2.31 126 87 40.65 NA 322110 TCGA-AB-2877 13 22826871 22826871 G A SNP SACS NM_014363.4 human genbank 54_36p -1 validated missense c.1439 p.T480M 1 NULL "superfamily_Chaperone J-domain,superfamily_ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase,HMMPfam_HEPN,HMMSmart_SM00748,superfamily_Nucleotidyltransferase substrate binding subunit/domain" - no_errors tier1 34 0 48 47 49.47 6 4 40 322110 TCGA-AB-2877 13 27506244 27506245 - TCCCATTTGAGATCATAT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1812_1811 p.605in_frame_insYDLKWE 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 322110 TCGA-AB-2877 17 30505827 30505827 C T SNP UNC45B NM_173167.1 human genbank 54_36p 1 validated missense c.593 p.A198V 1 "HMMSmart_SM00185,superfamily_ARM repeat" "HMMSmart_SM00185,HMMPfam_TPR_1,superfamily_ARM repeat,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 41 0 48 56 52.83 NA 322110 TCGA-AB-2877 21 43322005 43322005 G C SNP PKNOX1 NM_004571.3 human genbank 54_36p 1 validated missense c.1051 p.A351P 1 NULL "HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like" - no_errors tier1 26 0 36 39 52 36 20 35.71 322110 TCGA-AB-2877 X 46989747 46989747 T A SNP USP11 NM_004651.3 human genbank 54_36p 1 reviewed missense c.2321 p.M774K 0.993 "HMMPfam_UCH,superfamily_SSF54001" "HMMPfam_UCH,HMMSmart_DUSP,HMMPfam_DUF1055,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_SSF54001" - no_errors tier1 58 2 3.33 82 67 44.37 99 0 322110 TCGA-AB-2877 16 47137598 47137598 G A SNP N4BP1 NM_153029.3 human genbank 54_36p -1 validated missense c.2294 p.P765L 1 NULL NULL - no_errors tier1 53 0 100 45 30 25 18 41.86 322110 TCGA-AB-2877 12 48009233 48009233 G A SNP TROAP NM_005480.1 human genbank 54_36p 1 validated missense c.1043 p.R348H 0.009 NULL NULL - no_errors tier1 160 9 5.33 145 106 41.9 12 11 47.83 322110 TCGA-AB-2877 8 56598582 56598582 C A SNP XKR4 NM_052898.1 human genbank 54_36p 1 provisional missense c.1195 p.L399M 1 HMMPfam_XK-related HMMPfam_XK-related - no_errors tier1 177 2 1.1 160 139 46.03 NA 322110 TCGA-AB-2877 11 63640760 63640760 C T SNP FLRT1 NM_013280.4 human genbank 54_36p 1 reviewed missense c.445 p.R149C 0.943 "HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like" "HMMPfam_LRRNT,HMMSmart_SM00013,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMPfam_fn3,HMMSmart_SM00364,superfamily_L domain-like" - no_errors tier1 21 0 32 20 38.46 4 0 322110 TCGA-AB-2877 14 69782405 69782405 C T SNP ADAM21P NR_003951.1 human genbank 54_36p -1 validated rna NULL NULL 0.004 - - - pseudogene tier1 163 1 0.61 150 52 25.62 NA 322110 TCGA-AB-2877 7 73944898 73944898 G C SNP PMS2L5 ENST00000337023 human ensembl 54_36p 1 known missense c.65 p.W22S 0 NULL NULL - no_start_codon tier1 101 3 2.88 51 17 25 3 0 322110 TCGA-AB-2877 14 85157866 85157866 C T SNP FLRT2 NM_013231.4 human genbank 54_36p 1 reviewed silent c.255 p.H85 1 superfamily_SSF52058 "HMMPfam_LRRNT,HMMSmart_LRRNT,HMMPfam_LRRCT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,superfamily_SSF52058" - no_errors tier1 78 2 2.47 101 82 44.32 NA 322110 TCGA-AB-2877 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 56 0 61 44 41.51 143 108 43.03 322110 TCGA-AB-2877 2 89411214 89411214 C T SNP ENSG00000211619 ENST00000390264 human ensembl 54_36p -1 known missense c.95 p.S32N 0.823 "HMMSmart_IGv,HMMPfam_V-set,superfamily_SSF48726" "HMMSmart_IGv,HMMPfam_V-set,superfamily_SSF48726" - no_start_codon:no_stop_codon:bad_bp_length_for_coding_region tier1 62 1 1.59 87 30 25.42 0 322110 TCGA-AB-2877 7 89628094 89628094 G A SNP STEAP1 NM_012449.2 human genbank 54_36p 1 reviewed missense c.124 p.V42M 0.191 NULL HMMPfam_Ferric_reduct - no_errors tier1 106 1 0.92 128 71 35.15 NA 322110 TCGA-AB-2877 9 103126156 103126156 C T SNP PRG-3 NM_017753.2 human genbank 54_36p 1 reviewed missense c.974 p.T325I 1 NULL "HMMPfam_PAP2,HMMSmart_acidPPc,superfamily_AcPase_VanPerase" - no_errors tier1 175 2 1.13 142 85 37.12 NA 322110 TCGA-AB-2877 11 107006491 107006491 G A SNP ELMOD1 NM_018712.1 human genbank 54_36p 1 validated missense c.156 p.M52I 1 NULL HMMPfam_ELMO_CED12 - no_errors tier1 159 3 1.84 166 113 40.07 NA 322110 TCGA-AB-2877 3 121532775 121532775 C T SNP LRRC58 NM_001099678.1 human genbank 54_36p -1 validated missense c.1078 p.V360I 1 NULL "HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058" - no_errors tier1 89 1 1.11 92 65 41.14 12 10 45.45 322110 TCGA-AB-2877 3 123195313 123195313 C T SNP ILDR1 NM_175924.2 human genbank 54_36p -1 provisional missense c.841 p.V281M 0.057 NULL "HMMSmart_IG,HMMPfam_LSR,superfamily_SSF48726" - no_errors tier1 104 0 159 104 39.25 1 1 50 322110 TCGA-AB-2877 3 127554059 127554059 C T SNP KLF15 NM_014079.3 human genbank 54_36p -1 validated missense c.397 p.V133I 0.026 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 13 0 14 18 56.25 1 0 322110 TCGA-AB-2877 7 128878758 128878758 C T SNP FAM40B NM_020704.1 human genbank 54_36p 1 validated missense c.343 p.R115W 1 HMMPfam_N1221 HMMPfam_N1221 - no_errors tier1 124 1 0.8 81 56 40.88 1 2 66.67 322110 TCGA-AB-2877 11 133319468 133319468 C T SNP IGSF9B NM_014987.1 human genbank 54_36p -1 validated missense c.266 p.R89Q 1 "HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726" "HMMSmart_IGc2,HMMSmart_IG,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,HMMPfam_V-set,superfamily_SSF48726" - no_errors tier1 40 2 4.76 42 28 40 NA 322110 TCGA-AB-2877 X 135259212 135259212 C T SNP GPR112 NM_153834.3 human genbank 54_36p 1 validated missense c.5681 p.P1894L 0.002 NULL "HMMPfam_GPS,HMMSmart_GPS,HMMPfam_7tm_2,superfamily_ConA_like_lec_gl,PatternScan_G_PROTEIN_RECEP_F2_2" - no_errors tier1 111 1 0.88 195 115 36.98 NA 322110 TCGA-AB-2877 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 326772 TCGA-AB-2878 12 6567325 6567325 G A SNP CHD4 NM_001273.2 human genbank 54_36p -1 reviewed missense c.3517 p.R1173W 1 superfamily_P-loop containing nucleoside triphosphate hydrolases "HMMPfam_SNF2_N,HMMPfam_Chromo,HMMSmart_SM00298,PatternScan_CHROMO_1,HMMPfam_Helicase_C,HMMSmart_SM00490,HMMSmart_SM00249,PatternScan_DEAH_ATP_HELICASE,HMMPfam_DUF1086,HMMPfam_DUF1087,superfamily_FYVE/PHD zinc finger,HMMPfam_CHDCT2,HMMPfam_CHDNT,HMMSmart_SM00487,superfamily_Chromo domain-like,PatternScan_ZF_PHD_1,HMMPfam_PHD,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 91 0 186 90 32.26 77 73 48.67 326772 TCGA-AB-2878 17 7518931 7518931 T C SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.643 p.S215G 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 220 20 8.33 216 170 43.81 10 56 84.85 326772 TCGA-AB-2878 17 7519139 7519139 A - DEL TP53 NM_000546.4 human genbank 54_36p -1 reviewed frame_shift_del c.516 p.V173fs 0.952 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 NA NA NA NA NA NA NA NA NA 326772 TCGA-AB-2878 1 17147924 17147924 C T SNP CROCC NM_014675.3 human genbank 54_36p 1 validated missense c.2752 p.R918W 1 NULL superfamily_Prefoldin - no_errors tier1 30 1 3.23 83 24 22.43 10 3 23.08 326772 TCGA-AB-2878 15 18902635 18902635 G C SNP HERC2P2 ENST00000324413 human ensembl 54_36p -1 known missense c.2990 p.A997G 1 NULL HMMPfam_MIB_HERC2 - no_errors tier1 7 1 12.5 53 11 17.19 47 17 26.56 326772 TCGA-AB-2878 19 21208157 21208157 A T SNP LOC649299 XM_001719759.1 human genbank 54_36p 1 model nonsense c.181 p.K61* 1 "HMMPfam_Ribosomal_L44,superfamily_Zn-binding ribosomal proteins" "HMMPfam_Ribosomal_L44,superfamily_Zn-binding ribosomal proteins" - pseudogene tier1 36 3 7.69 44 45 50.56 0 326772 TCGA-AB-2878 2 28892400 28892400 A C SNP SPDYA NM_182756.1 human genbank 54_36p 1 validated missense c.16 p.M6L 1 NULL NULL - no_errors tier1 72 0 58 54 48.21 8 8 50 326772 TCGA-AB-2878 3 31592957 31592957 A G SNP STT3B NM_178862.1 human genbank 54_36p 1 provisional missense c.380 p.D127G 1 HMMPfam_STT3 HMMPfam_STT3 - no_errors tier1 110 5 4.35 254 151 37.28 101 78 43.58 326772 TCGA-AB-2878 15 46576758 46576758 C T SNP FBN1 NM_000138.3 human genbank 54_36p -1 reviewed missense c.2290 p.V764I 0.998 "HMMSmart_SM00179,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,superfamily_EGF/Laminin" "PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_TB,superfamily_TB module/8-cys domain,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Growth factor receptor domain,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 79 4 4.82 126 68 34.69 7 4 36.36 326772 TCGA-AB-2878 7 55206394 55206394 C T SNP EGFR NM_005228.3 human genbank 54_36p 1 reviewed missense c.1913 p.T638M 0 NULL "HMMPfam_Recep_L_domain,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,HMMPfam_Furin-like,HMMSmart_SM00261,PatternScan_PROTEIN_KINASE_TYR,superfamily_Growth factor receptor domain,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,superfamily_L domain-like" - no_errors tier1 172 3 1.71 145 108 42.69 NA 326772 TCGA-AB-2878 14 94003411 94003411 G A SNP SERPINA9 NM_175739.1 human genbank 54_36p -1 validated silent c.744 p.G248 0.333 "HMMPfam_Serpin,HMMSmart_SM00093,superfamily_Serpins" "HMMPfam_Serpin,HMMSmart_SM00093,PatternScan_SERPIN,superfamily_Serpins" - no_errors tier1 342 2 0.58 192 141 41.84 NA 326772 TCGA-AB-2878 6 108606021 108606021 G A SNP NR2E1 NM_003269.3 human genbank 54_36p 1 validated missense c.525 p.M175I 1 superfamily_Nuclear receptor ligand-binding domain "HMMPfam_Hormone_recep,HMMSmart_SM00430,HMMPfam_zf-C4,HMMSmart_SM00399,PatternScan_NUCLEAR_REC_DBD_1,superfamily_Nuclear receptor ligand-binding domain,superfamily_Glucocorticoid receptor-like (DNA-binding domain)" - no_errors tier1 121 0 56 31 35.23 NA 326772 TCGA-AB-2878 1 149424621 149424621 C G SNP VPS72 NM_005997.1 human genbank 54_36p -1 provisional missense c.370 p.D124H 1 HMMPfam_YL1 "HMMPfam_YL1,HMMPfam_YL1_C" - no_errors tier1 130 0 82 80 48.78 41 34 45.33 326772 TCGA-AB-2878 1 154140885 154140885 C T SNP RIT1 NM_006912.4 human genbank 54_36p -1 validated missense c.270 p.M90I 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 70 1 1.39 162 110 40 10 15 60 326772 TCGA-AB-2878 1 179994542 179994542 A G SNP CACNA1E NM_000721.2 human genbank 54_36p 1 reviewed missense c.4520 p.E1507G 1 superfamily_Voltage-gated potassium channels "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels" - no_errors tier1 320 19 5.59 207 145 40.96 NA 326772 TCGA-AB-2878 1 212609569 212609569 G A SNP PTPN14 NM_005401.3 human genbank 54_36p -1 reviewed missense c.3125 p.T1042M 1 "HMMPfam_Y_phosphatase,HMMSmart_PTPc,superfamily_SSF52799" "HMMPfam_Y_phosphatase,HMMSmart_PTPc,PatternScan_TYR_PHOSPHATASE_1,HMMPfam_FERM_N,PatternScan_FERM_1,PatternScan_FERM_2,HMMPfam_FERM_M,superfamily_FERM_3-hlx,HMMSmart_B41,superfamily_SSF50729,superfamily_SSF52799,superfamily_SSF54236" - no_errors tier1 135 6 4.26 208 139 40.06 NA 329614 TCGA-AB-2879 13 27506250 27506251 - TTGAGATCATATTCATATTCTCTGAAATCAACG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1806_1805 p.602in_frame_insNVDFREYEYDL 0.998:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 329614 TCGA-AB-2879 9 72408131 72408131 C T SNP TRPM3 NM_001007471.1 human genbank 54_36p -1 reviewed missense c.2707 p.E903K 1 NULL HMMPfam_Ion_trans - no_errors tier1 228 23 9.09 219 162 41.86 NA 329614 TCGA-AB-2879 4 106155921 106155921 C - DEL TET2 NM_001127208.1 human genbank 58_37c 1 validated frame_shift_del c.822 p.N275fs 0.881 NULL NULL - no_errors tier1 162 20 12.27 131 58 44.27 61 30 49.18 329614 TCGA-AB-2879 4 106375370 106375370 C - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.822 p.N275fs 0.379 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 329614 TCGA-AB-2879 4 106384227 106384227 C T SNP TET2 ENST00000265149 human ensembl 54_36p 1 known nonsense c.52 p.R18* 1 NULL NULL - no_start_codon tier1 130 19 12.58 96 86 46.74 24 24 50 329614 TCGA-AB-2879 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 332131 TCGA-AB-2880 13 27506251 27506252 - TGAGATCATATTCATATTCTC INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1805_1804 p.602in_frame_insREYEYDL 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 332131 TCGA-AB-2880 19 38484831 38484832 - C INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_ins c.330_329 p.A111fs 0.915:0.950 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 332131 TCGA-AB-2880 17 71979364 71979364 G A SNP RHBDF2 NM_024599.2 human genbank 54_36p -1 validated silent c.2517 p.F839 1 NULL HMMPfam_Rhomboid - no_errors tier1 47 3 6 40 9 18.37 46 8 14.81 345701 TCGA-AB-2881 19 3101277 3101277 C T SNP GNA15 NM_002068.2 human genbank 54_36p 1 validated missense c.479 p.A160V 0.608 "HMMPfam_G-alpha,superfamily_Transducin (alpha subunit) insertion domain,HMMSmart_SM00275,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_G-alpha,superfamily_Transducin (alpha subunit) insertion domain,HMMSmart_SM00275,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 30 0 22 13 36.11 109 143 56.08 345701 TCGA-AB-2881 18 8796946 8796946 G A SNP KIAA0802 NM_015210.3 human genbank 54_36p 1 predicted missense c.2492 p.R831H 0.05 NULL NULL - no_errors tier1 54 0 73 20 21.28 NA 345701 TCGA-AB-2881 5 54316851 54316851 C T SNP ESM1 NM_007036.1 human genbank 54_36p -1 reviewed silent c.252 p.Q84 0.995 HMMSmart_IB HMMSmart_IB - no_errors tier1 48 5 9.43 62 51 44.35 NA 345701 TCGA-AB-2881 4 55294077 55294077 G T SNP KIT NM_000222.2 human genbank 54_36p 1 reviewed missense c.2446 p.D816Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 53 2 3.64 111 40 26.32 172 71 29.22 345701 TCGA-AB-2881 8 93073230 93073230 G T SNP RUNX1T1 NM_175634.2 human genbank 54_36p -1 reviewed nonsense c.804 p.C268* 1 NULL "HMMPfam_zf-MYND,PatternScan_ZF_MYND_1,HMMPfam_TAFH,HMMSmart_SM00549,HMMPfam_NHR2" - no_errors tier1 161 10 5.78 154 102 39.38 NA 345701 TCGA-AB-2881 6 121475960 121475960 T C SNP C6orf170 NM_152730.4 human genbank 54_36p -1 validated missense c.3116 p.K1039R 1 NULL superfamily_Ypt/Rab-GAP domain of gyp1p - no_errors tier1 89 3 3.26 139 97 40.76 3 1 25 345701 TCGA-AB-2881 3 126010604 126010604 G A SNP ITGB5 NM_002213.3 human genbank 54_36p -1 provisional silent c.1218 p.S406 1 "HMMPfam_Integrin_beta,HMMSmart_INB,superfamily_SSF69179" "HMMSmart_VWA,HMMPfam_Integrin_beta,HMMSmart_INB,HMMSmart_PSI,HMMSmart_EGF,HMMPfam_Integrin_B_tail,superfamily_Integrin_bsu_tail,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,HMMPfam_Integrin_b_cyt,PatternScan_INTEGRIN_BETA,superfamily_SSF53300,superfamily_SSF57196,superfamily_SSF69179" - no_errors tier1 131 8 5.63 125 82 39.61 6 6 50 345701 TCGA-AB-2881 4 166454642 166454642 A T SNP KLHL2 NM_007246.2 human genbank 54_36p 1 provisional missense c.1483 p.N495Y 1 "HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central" "HMMSmart_BTB,HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central,superfamily_BTB/POZ_fold,HMMPfam_BACK,HMMPfam_BTB" - no_errors tier1 250 9 3.45 169 116 40 21 11 34.38 345701 TCGA-AB-2881 3 195561630 195561630 C T SNP LRRC15 NM_130830.1 human genbank 54_36p -1 validated missense c.1438 p.E480K 0.003 NULL "HMMSmart_LRRNT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058" - no_errors tier1 156 4 2.48 170 48 21.92 NA 400830 TCGA-AB-2882 19 3933568 3933568 A T SNP SNORD37 NR_002602.1 human genbank 54_36p -1 provisional rna NULL NULL 0 - - - no_errors tier1 106 8 7.02 12 9 42.86 4 3 42.86 400830 TCGA-AB-2882 7 3980582 3980582 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated missense c.1873 p.V625M 0.004 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 169 15 8.15 27 19 41.3 NA 400830 TCGA-AB-2882 20 7814398 7814398 C T SNP HAO1 NM_017545.2 human genbank 54_36p -1 reviewed silent c.927 p.K309 0.99 "HMMPfam_FMN_dh,superfamily_FMN-linked oxidoreductases" "HMMPfam_FMN_dh,PatternScan_FMN_HYDROXY_ACID_DH_1,superfamily_FMN-linked oxidoreductases" - no_errors tier1 379 20 5.01 142 78 35.45 NA 400830 TCGA-AB-2882 1 17612620 17612620 C T SNP RCC2 NM_018715.1 human genbank 54_36p -1 validated missense c.1207 p.G403S 1 superfamily_RCC1/BLIP-II "HMMPfam_RCC1,PatternScan_RCC1_1,PatternScan_RCC1_2,superfamily_RCC1/BLIP-II" - no_errors tier1 255 7 2.65 62 42 40.38 36 22 37.93 400830 TCGA-AB-2882 16 18757451 18757451 C T SNP SMG1 NM_015092.4 human genbank 54_36p -1 reviewed missense c.7007 p.R2336K 1 "HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,superfamily_Protein kinase-like (PK-like),PatternScan_PI3_4_KINASE_2" "HMMPfam_HEAT,HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_FATC,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_2" - no_errors tier1 229 10 4.18 93 47 33.57 56 43 43.43 400830 TCGA-AB-2882 22 28296426 28296426 T C SNP NIPSNAP1 NM_003634.2 human genbank 54_36p -1 reviewed missense c.194 p.K65R 1 NULL HMMPfam_NIPSNAP - no_errors tier1 764 20 2.55 100 74 42.53 19 12 38.71 400830 TCGA-AB-2882 20 30850048 30850048 C T SNP DNMT3B NM_006892.3 human genbank 54_36p 1 reviewed missense c.1612 p.R538C 1 superfamily_FYVE/PHD zinc finger "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 126 7 5.26 44 26 37.14 18 29 61.7 400830 TCGA-AB-2882 15 36030657 36030657 C T SNP TMCO5A NM_152453.2 human genbank 54_36p 1 provisional missense c.797 p.T266I 0.332 NULL NULL - no_errors tier1 214 8 3.59 77 61 44.2 NA 400830 TCGA-AB-2882 6 43092952 43092952 T C SNP KLHDC3 NM_057161.2 human genbank 54_36p 1 reviewed missense c.44 p.V15A 1 "superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2" "HMMPfam_Kelch_1,superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2" - no_errors tier1 383 23 5.39 40 24 36.92 56 40 41.67 400830 TCGA-AB-2882 21 43397525 43397525 G T SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.101 p.S34Y 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 142 1 0.7 19 16 45.71 67 66 49.62 400830 TCGA-AB-2882 6 51727649 51727649 C T SNP PKHD1 NM_138694.3 human genbank 54_36p -1 reviewed missense c.8689 p.V2897I 0.252 NULL "HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00710,superfamily_Pectin lyase-like,superfamily_E set domains,HMMPfam_G8" - no_errors tier1 314 9 2.79 126 70 35.71 NA 400830 TCGA-AB-2882 3 62459970 62459970 C G SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed silent c.2613 p.R871 0.921 HMMPfam_DUF1041 "HMMPfam_C2,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_DUF1041,superfamily_PH domain-like" - no_errors tier1 248 4 1.57 115 64 35.75 NA 400830 TCGA-AB-2882 1 63649475 63649475 G A SNP ALG6 NM_013339.3 human genbank 54_36p 1 reviewed missense c.565 p.G189R 1 HMMPfam_Alg6_Alg8 HMMPfam_Alg6_Alg8 - no_errors tier1 169 1 0.59 74 44 37.29 18 9 32.14 400830 TCGA-AB-2882 2 71763170 71763170 G A SNP DYSF NM_003494.1 human genbank 54_36p 1 reviewed missense c.6059 p.R2020H 1 NULL "HMMPfam_C2,HMMSmart_SM00239,HMMSmart_SM00693,HMMSmart_SM00694,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_FerA,HMMPfam_FerB,HMMPfam_FerI" - no_errors tier1 427 17 3.8 135 85 38.46 22 21 48.84 400830 TCGA-AB-2882 9 72408167 72408167 C T SNP TRPM3 NM_001007471.1 human genbank 54_36p -1 reviewed missense c.2671 p.V891M 1 NULL HMMPfam_Ion_trans - no_errors tier1 506 9 1.75 115 71 38.17 NA 400830 TCGA-AB-2882 11 102485613 102485613 T G SNP DYNC2H1 NM_001080463.1 human genbank 54_36p 1 provisional missense c.100 p.C34G 0 NULL "HMMSmart_SM00382,HMMPfam_Dynein_heavy,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 231 11 4.55 71 30 29.7 NA 400830 TCGA-AB-2882 6 155195736 155195736 G T SNP RBM16 NM_014892.3 human genbank 54_36p 1 validated missense c.3331 p.G1111C 0.996 NULL "HMMPfam_RRM_1,HMMSmart_RRM,HMMSmart_RPR,HMMPfam_DUF618,superfamily_ENTH_VHS,superfamily_SSF54928" - no_errors tier1 163 3 1.81 115 24 17.27 53 20 27.03 400830 TCGA-AB-2882 3 167031170 167031170 G - DEL BCHE NM_000055.2 human genbank 54_36p -1 reviewed frame_shift_del c.346 p.L116fs 0.974 "HMMPfam_COesterase,superfamily_SSF53474" "HMMPfam_COesterase,HMMPfam_AChE_tetra,PatternScan_CARBOXYLESTERASE_B_2,PatternScan_CARBOXYLESTERASE_B_1,superfamily_SSF53474" - no_errors tier1 NA NA NA NA NA NA NA NA NA 410324 TCGA-AB-2883 X 44854267 44854267 G A SNP UTX NM_021140.2 human genbank 54_36p 1 validated splice_site c.4006-1 e28-1 1 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 431799 TCGA-AB-2884 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 67 11 13.92 75 61 43.88 23 25 52.08 431799 TCGA-AB-2884 1 78897616 78897616 A T SNP IFI44 NM_006417.4 human genbank 54_36p 1 validated missense c.872 p.H291L 0 superfamily_SSF52540 superfamily_SSF52540 - no_errors tier1 106 13 10.83 85 48 35.56 8 11 57.89 431799 TCGA-AB-2884 14 89721037 89721038 - G INS KCNK13 NM_022054.2 human genbank 54_36p 1 reviewed frame_shift_ins c.1164_1165 p.V390fs 0.880:1.000 NULL "HMMPfam_Ion_trans_2,superfamily_Voltage-gated potassium channels" - no_errors tier1 NA NA NA NA NA NA NA NA NA 431799 TCGA-AB-2884 12 111372578 111372578 T C SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.211 p.F71L 1 "HMMPfam_SH2,HMMSmart_SM00252,superfamily_SH2 domain" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 98 17 14.41 60 66 51.97 18 10 35.71 431799 TCGA-AB-2884 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 431799 TCGA-AB-2884 2 208821357 208821357 C T SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.395 p.R132H 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 82 8 8.89 47 55 53.4 101 105 50.97 434640 TCGA-AB-2885 MT 8156 8156 G A SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known silent c.570 p.G190 NULL "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 2103 2 0.09 940 343 26.71 NA NA NA 434640 TCGA-AB-2885 9 3261010 3261010 C T SNP RFX3 NM_134428.2 human genbank 54_36p -1 reviewed missense c.1195 p.E399K 1 NULL "HMMPfam_RFX_DNA_binding,HMMPfam_RFX1_trans_act,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 386 0 93 68 42.24 11 7 38.89 434640 TCGA-AB-2885 17 7518997 7518997 G A SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.577 p.H193Y 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 161 0 17 68 79.07 1 149 99.33 434640 TCGA-AB-2885 18 29568298 29568298 C T SNP ASXL3 NM_030632.1 human genbank 54_36p 1 validated missense c.1003 p.R335W 1 NULL NULL - no_errors tier1 131 0 15 39 72.22 NA 434640 TCGA-AB-2885 20 40180498 40180498 C T SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed missense c.2998 p.A1000T 0.987 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMSmart_SM00404,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,PatternScan_TYR_PHOSPHATASE_1,superfamily_Immunoglobulin,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 234 0 58 39 40.21 NA 434640 TCGA-AB-2885 6 41663552 41663553 - A INS FOXP4 NM_001012426.1 human genbank 54_36p 1 reviewed frame_shift_ins c.916_917 p.H306fs 1.000:1.000 NULL "HMMPfam_Fork_head,HMMSmart_SM00339,PatternScan_ZINC_FINGER_C2H2_1,PatternScan_FORK_HEAD_2,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 434640 TCGA-AB-2885 3 49664602 49664602 C T SNP BSN NM_003458.3 human genbank 54_36p 1 validated missense c.2609 p.A870V 1 NULL "HMMPfam_zf-piccolo,superfamily_FYVE_PHD_ZnF" - no_errors tier1 65 0 1 8 88.89 NA 434640 TCGA-AB-2885 X 63491437 63491437 C T SNP MTMR8 NM_017677.2 human genbank 54_36p -1 provisional missense c.413 p.R138H 0.799 superfamily_(Phosphotyrosine protein) phosphatases II "HMMSmart_SM00404,HMMPfam_Myotub-related,PatternScan_TYR_PHOSPHATASE_1,superfamily_PH domain-like,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 199 4 1.97 14 53 77.94 3 100 434640 TCGA-AB-2885 11 93832293 93832293 G C SNP MRE11A NM_005591.3 human genbank 54_36p -1 reviewed missense c.1429 p.Q477E 1 NULL "HMMPfam_Metallophos,HMMPfam_Mre11_DNA_bind,superfamily_Metallo-dependent phosphatases" - no_errors tier1 331 1 0.3 165 76 31.4 53 35 39.77 434640 TCGA-AB-2885 12 111372546 111372546 G T SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.179 p.G60V 1 "HMMPfam_SH2,HMMSmart_SM00252,superfamily_SH2 domain" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 62 0 52 16 23.19 75 47 38.52 434640 TCGA-AB-2885 7 128881232 128881232 T C SNP FAM40B NM_020704.1 human genbank 54_36p 1 validated missense c.544 p.C182R 1 HMMPfam_N1221 HMMPfam_N1221 - no_errors tier1 215 0 10 21 67.74 NA 434640 TCGA-AB-2885 2 141243252 141243252 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated missense c.5758 p.E1920K 1 "HMMSmart_LY,superfamily_SSF63825" "HMMPfam_Ldl_recept_b,HMMSmart_LY,PatternScan_ASX_HYDROXYL,HMMPfam_NHL,HMMSmart_EGF_CA,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_SSF57196,superfamily_SSF63825" - no_errors tier1 104 0 39 28 41.79 NA 434640 TCGA-AB-2885 1 144253183 144253183 C T SNP ITGA10 NM_003637.3 human genbank 54_36p 1 reviewed missense c.3349 p.R1117W 0.811 superfamily_Integrin domains "HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_FG-GAP,HMMSmart_SM00191,HMMPfam_Integrin_alpha2,superfamily_vWA-like,superfamily_Integrin domains,superfamily_Integrin alpha N-terminal domain" - no_errors tier1 282 0 78 75 48.39 NA 434640 TCGA-AB-2885 2 167815650 167815650 G A SNP XIRP2 NM_152381.2 human genbank 54_36p 1 validated missense c.9502 p.A3168T 0.001 NULL HMMPfam_Xin - no_errors tier1 179 0 50 43 46.24 1 0 463352 TCGA-AB-2886 MT 8066 8066 G A SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known silent c.480 p.L160 NULL "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 3214 68 2.05 157 645 79.04 NA NA NA 463352 TCGA-AB-2886 17 263333 263333 G C SNP C17orf97 NM_001013672.3 human genbank 54_36p 1 validated missense c.383 p.R128P 0 NULL NULL - no_errors tier1 57 1 1.69 50 32 39.02 5 1 16.67 463352 TCGA-AB-2886 19 17810108 17810108 C T SNP JAK3 NM_000215.3 human genbank 54_36p -1 reviewed missense c.1533 p.M511I 0.993 "superfamily_Protein kinase-like (PK-like),superfamily_SH2 domain" "PatternScan_THIOL_PROTEASE_HIS,HMMSmart_SM00252,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMSmart_SM00295,superfamily_SH2 domain" - no_errors tier1 108 0 72 12 14.12 229 52 18.51 463352 TCGA-AB-2886 22 19437281 19437281 C A SNP PI4KA NM_058004.2 human genbank 54_36p -1 reviewed missense c.2723 p.R908L 1 NULL "HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_PI3Ka,HMMSmart_SM00145,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_1,PatternScan_PI3_4_KINASE_2" - no_errors tier1 58 0 70 37 33.64 72 56 43.41 463352 TCGA-AB-2886 7 21751198 21751198 G T SNP DNAH11 ENST00000328843 human ensembl 54_36p 1 known missense c.8523 p.M2841I 1 superfamily_P-loop containing nucleoside triphosphate hydrolases "PatternScan_THIOL_PROTEASE_HIS,HMMSmart_SM00382,HMMPfam_Dynein_heavy,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,PatternScan_WD_REPEATS_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 82 0 111 20 15.15 NA 463352 TCGA-AB-2886 6 33746445 33746445 G A SNP ITPR3 NM_002224.2 human genbank 54_36p 1 validated missense c.2461 p.A821T 0.921 NULL "HMMPfam_RYDR_ITPR,HMMPfam_MIR,superfamily_MIR,HMMPfam_Ion_trans,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_MIR,superfamily_SSF100909" - no_errors tier1 28 1 3.45 34 11 24.44 6 0 463352 TCGA-AB-2886 18 45623717 45623717 G A SNP MYO5B NM_001080467.1 human genbank 54_36p -1 provisional silent c.4503 p.P1501 0.634 NULL "HMMPfam_IQ,HMMSmart_SM00015,HMMPfam_Myosin_head,HMMSmart_SM00242,HMMPfam_DIL,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 59 0 67 42 38.53 NA 463352 TCGA-AB-2886 19 54935243 54935243 G A SNP TSKS NM_021733.1 human genbank 54_36p -1 reviewed missense c.1507 p.R503C 1 NULL NULL - no_errors tier1 87 0 82 10 10.75 9 1 10 463352 TCGA-AB-2886 12 67328806 67328806 G A SNP RAP1B NM_001010942.1 human genbank 54_36p 1 validated missense c.35 p.G12E 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 90 0 55 17 23.29 50 34 40.48 463352 TCGA-AB-2886 16 79748048 79748048 C T SNP PKD1L2 ENST00000299598 human ensembl 54_36p -1 known missense c.4042 p.V1348M 1 NULL "HMMPfam_GPS,HMMSmart_SM00303,PatternScan_CHANNEL_COLICIN,HMMPfam_PLAT,HMMSmart_SM00308,HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_Lipase/lipooxygenase domain (PLAT/LH2 domain),HMMPfam_PKD_channel,superfamily_C-type lectin-like" - no_errors tier1 76 1 1.27 27 18 40 NA 463352 TCGA-AB-2886 X 97531372 97531372 C T SNP LOC643563 XM_926863.1 human genbank 54_36p 1 model missense c.209 p.S70F 1 "HMMPfam_GTP_EFTU,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_GTP_EFTU,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 87 0 25 87 76.32 NA 463352 TCGA-AB-2886 9 99116998 99116998 T C SNP KIAA1529 NM_020893.1 human genbank 54_36p 1 predicted silent c.1293 p.T431 0.17 NULL NULL - no_errors tier1 40 0 37 4 9.76 7 0 463352 TCGA-AB-2886 8 117933479 117933479 C - DEL RAD21 NM_006265.2 human genbank 54_36p -1 reviewed frame_shift_del c.1359 p.E453fs 0.96 NULL "HMMPfam_Rad21_Rec8,HMMPfam_Rad21_Rec8_N" - no_errors tier1 NA NA NA NA NA NA NA NA NA 463352 TCGA-AB-2886 2 124891562 124891562 G T SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed missense c.454 p.V152F 0.957 "HMMPfam_F5_F8_type_C,HMMSmart_FA58C,superfamily_Gal_bind_like" "HMMPfam_F5_F8_type_C,HMMSmart_FA58C,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMSmart_LamG,PatternScan_FIBRIN_AG_C_DOMAIN,superfamily_Fibrinogen_a/b/g_C,HMMPfam_EGF,HMMSmart_EGF,superfamily_Gal_bind_like,superfamily_ConA_like_lec_gl,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2" - no_errors tier1 170 0 154 131 45.8 NA 463352 TCGA-AB-2886 3 130785924 130785925 - G INS PLXND1 NM_015103.2 human genbank 54_36p -1 validated frame_shift_ins c.2023_2022 p.N674fs 0.280:0.287 NULL "HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain,HMMPfam_PSI,HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00423,superfamily_GTPase activation domain GAP,HMMPfam_Plexin_cytopl,superfamily_E set domains,superfamily_Plexin repeat" - no_errors tier1 NA NA NA NA NA NA NA NA NA 463352 TCGA-AB-2886 7 142739951 142739951 G A SNP CLCN1 NM_000083.2 human genbank 54_36p 1 reviewed missense c.1264 p.E422K 1 "HMMPfam_Voltage_CLC,superfamily_Clc chloride channel" "HMMPfam_CBS,HMMPfam_Voltage_CLC,superfamily_Clc chloride channel,superfamily_CBS-domain" - no_errors tier1 220 2 0.9 107 57 34.34 NA 463352 TCGA-AB-2886 2 233389924 233389925 - GGCT INS GIGYF2 NM_001103147.1 human genbank 54_36p 1 validated frame_shift_ins c.2371_2372 p.R792fs 0.997:1.000 NULL "HMMPfam_GYF,HMMSmart_GYF,superfamily_GYF" - no_errors tier1 NA NA NA NA NA NA NA NA NA 498463 TCGA-AB-2887 2 667320 667320 G C SNP TMEM18 NM_152834.2 human genbank 54_36p -1 validated missense c.26 p.S9C 0.002 NULL NULL - no_errors tier1 44 4 8.16 23 20 46.51 12 11 47.83 498463 TCGA-AB-2887 19 15861324 15861324 C T SNP CYP4F2 NM_001082.3 human genbank 54_36p -1 reviewed missense c.827 p.R276H 0.027 "HMMPfam_p450,superfamily_Cytochrome_P450" "HMMPfam_p450,superfamily_Cytochrome_P450,PatternScan_CYTOCHROME_P450" - no_errors tier1 71 9 11.25 40 49 55.06 1 0 498463 TCGA-AB-2887 2 25317033 25317033 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2153 p.P718L 1 "HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 28 5 15.15 1 14 93.33 1 132 98.51 498463 TCGA-AB-2887 2 37333846 37333846 T C SNP PRKD3 NM_005813.3 human genbank 54_36p -1 reviewed missense c.2651 p.D884G 1 NULL "HMMSmart_SM00219,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_C1_1,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_PH domain-like,superfamily_Cysteine-rich domain" - no_errors tier1 122 10 7.46 76 78 50.65 42 45 51.72 498463 TCGA-AB-2887 17 46115973 46115973 C T SNP ABCC3 NM_003786.1 human genbank 54_36p 1 reviewed missense c.3811 p.P1271S 1 superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain "HMMPfam_ABC_membrane,HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 95 9 8.65 17 22 56.41 NA 498463 TCGA-AB-2887 16 54358799 54358799 G A SNP CES4 NR_003276.2 human genbank 54_36p 1 validated rna NULL NULL 0 - - - pseudogene tier1 98 9 8.33 76 62 44.93 NA 498463 TCGA-AB-2887 X 79875620 79875620 T C SNP BRWD3 NM_153252.3 human genbank 54_36p -1 validated missense c.1118 p.N373S 1 "HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,HMMPfam_WD40" "HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain,HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 151 15 8.98 47 37 44.05 31 96.88 498463 TCGA-AB-2887 12 94128011 94128011 C T SNP FGD6 NM_018351.3 human genbank 54_36p -1 validated missense c.1180 p.A394T 0 NULL "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_FYVE,HMMSmart_SM00064,HMMPfam_PH,HMMSmart_SM00233,superfamily_FYVE/PHD zinc finger,PatternScan_C_TYPE_LECTIN_1,superfamily_PH domain-like" - no_errors tier1 94 15 13.64 85 63 42.57 4 4 50 498463 TCGA-AB-2887 14 95776976 95776976 G A SNP BDKRB2 NM_000623.3 human genbank 54_36p 1 reviewed silent c.558 p.L186 0.046 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 21 1 4.55 14 25 62.5 NA 498463 TCGA-AB-2887 11 102544755 102544755 T C SNP DYNC2H1 NM_001080463.1 human genbank 54_36p 1 provisional silent c.4824 p.D1608 0.999 NULL "HMMSmart_SM00382,HMMPfam_Dynein_heavy,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 60 7 10.45 41 34 45.33 1 100 498463 TCGA-AB-2887 11 107514954 107514954 T G SNP ACAT1 NM_000019.3 human genbank 54_36p 1 reviewed silent c.555 p.T185 0.739 "HMMPfam_Thiolase_N,superfamily_Thiolase-like" "HMMPfam_Thiolase_N,HMMPfam_Thiolase_C,PatternScan_THIOLASE_1,PatternScan_THIOLASE_3,PatternScan_THIOLASE_2,superfamily_Thiolase-like" - no_errors tier1 98 7 6.6 53 51 49.04 62 42 40.38 498463 TCGA-AB-2887 1 115060270 115060270 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.35 p.G12D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 123 10 7.41 54 41 42.71 29 21 42 498463 TCGA-AB-2887 6 129746059 129746059 C T SNP LAMA2 NM_000426.3 human genbank 54_36p 1 reviewed missense c.5059 p.R1687W 1 "superfamily_ConA_like_lec_gl,HMMPfam_Laminin_I" "HMMPfam_Laminin_B,HMMSmart_LamG,HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,PatternScan_EGF_LAM_1,HMMPfam_Laminin_N,HMMSmart_LamNT,superfamily_Gal_bind_like,superfamily_ConA_like_lec_gl,HMMPfam_Laminin_I,HMMPfam_Laminin_II,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMSmart_LamB,superfamily_SSF56399,superfamily_SSF57196" - no_errors tier1 55 3 5.17 30 21 40.38 NA 498463 TCGA-AB-2887 3 134597446 134597446 A T SNP TMEM108 NM_023943.1 human genbank 54_36p 1 validated missense c.1654 p.T552S 1 NULL PatternScan_TONB_DEPENDENT_REC_1 - no_errors tier1 48 3 5.88 19 17 47.22 NA 498463 TCGA-AB-2887 7 148137376 148137376 C T SNP EZH2 NM_004456.3 human genbank 54_36p -1 reviewed missense c.2069 p.R690H 1 "HMMPfam_SET,HMMSmart_SET,superfamily_SSF82199" "HMMSmart_SANT,HMMPfam_SET,HMMSmart_SET,superfamily_SSF82199" - no_errors tier1 84 10 10.64 3 42 93.33 1 28 96.55 498463 TCGA-AB-2887 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 56 10 14.49 22 20 47.62 35 54 60.67 499294 TCGA-AB-2888 15 19941872 19941872 G A SNP LOC388076 XM_931016.1 human genbank 54_36p -1 model silent c.339 p.Y113 1 HMMPfam_Ribosomal_S8e HMMPfam_Ribosomal_S8e - pseudogene tier1 190 0 123 42 25.3 745 0 499294 TCGA-AB-2888 6 31432896 31432896 G C SNP HLA-B NM_005514.6 human genbank 54_36p -1 reviewed missense c.19 p.R7G 0 NULL "HMMPfam_MHC_I,PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_SM00407,HMMPfam_MHC_I_C,superfamily_MHC antigen-recognition domain,superfamily_Immunoglobulin" - no_errors tier1 60 0 48 15 23.44 1199 923 43.5 499294 TCGA-AB-2888 X 34872429 34872429 C T SNP FAM47B NM_152631.1 human genbank 54_36p 1 predicted silent c.1560 p.V520 0 NULL NULL - no_errors tier1 66 2 2.94 38 43 53.09 NA 499294 TCGA-AB-2888 12 47525672 47525672 C T SNP DDX23 NM_004818.2 human genbank 54_36p -1 reviewed missense c.161 p.R54Q 0.853 NULL "PatternScan_DEAD_ATP_HELICASE,HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_DEAD,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 74 1 1.32 39 16 29.09 52 35 40.23 499294 TCGA-AB-2888 4 55284528 55284529 - CTTCTT INS KIT NM_000222.2 human genbank 54_36p 1 reviewed in_frame_ins c.1253_1254 p.419in_frame_insFF 0.002:0.002 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 499294 TCGA-AB-2888 11 65865367 65865367 G A SNP BRMS1 NM_001024957.1 human genbank 54_36p -1 reviewed nonsense c.244 p.R82* 1 HMMPfam_Sds3 HMMPfam_Sds3 - no_errors tier1 54 0 34 10 22.73 31 6 16.22 499294 TCGA-AB-2888 8 87626150 87626150 A G SNP CPNE3 NM_003909.3 human genbank 54_36p 1 reviewed missense c.700 p.T234A 1 "HMMSmart_C2,superfamily_C2_CaLB" "HMMPfam_C2,HMMSmart_C2,HMMSmart_VWA,superfamily_C2_CaLB,HMMPfam_Copine,superfamily_SSF53300" - no_errors tier1 117 1 0.85 66 25 27.47 42 26 38.24 499294 TCGA-AB-2888 13 98745483 98745483 A G SNP GPR183 NM_004951.4 human genbank 54_36p -1 reviewed silent c.918 p.F306 0.972 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 124 1 0.79 78 33 29.73 584 532 47.63 499294 TCGA-AB-2888 7 123056342 123056342 C T SNP ASB15 NM_080928.3 human genbank 54_36p 1 validated missense c.1058 p.A353V 0.997 "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" "HMMPfam_SOCS_box,HMMSmart_SM00253,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" - no_errors tier1 111 1 0.89 79 37 31.62 NA 499294 TCGA-AB-2888 6 129992243 129992246 TCTT - DEL ARHGAP18 NM_033515.2 human genbank 54_36p -1 validated frame_shift_del c.734_731 p.K244fs 0.979:0.998:1.000:1.000 NULL "HMMPfam_RhoGAP,HMMSmart_SM00324,superfamily_GTPase activation domain GAP" - no_errors tier1 NA NA NA NA NA NA NA NA NA 507696 TCGA-AB-2889 X 3251845 3251845 A C SNP MXRA5 NM_015419.3 human genbank 54_36p -1 validated missense c.1881 p.H627Q 0.006 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin" "HMMSmart_SM00013,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 125 5 3.85 1 81 97.59 NA 507696 TCGA-AB-2889 15 27186269 27186269 C A SNP APBA2 NM_005503.1 human genbank 54_36p 1 reviewed silent c.1872 p.T624 1 "HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ" "HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ,HMMPfam_PID,HMMSmart_PTB,superfamily_SSF50729" - no_errors tier1 27 2 6.9 13 9 40.91 1 0 507696 TCGA-AB-2889 16 49731960 49731960 C T SNP SALL1 NM_002968.1 human genbank 54_36p -1 reviewed silent c.1674 p.P558 0.897 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 215 6 2.71 40 37 48.05 NA 507696 TCGA-AB-2889 9 78127861 78127861 G T SNP PCSK5 ENST00000376754 human ensembl 54_36p 1 known silent c.3285 p.S1095 0 "HMMSmart_SM00261,superfamily_Growth factor receptor domain" "HMMPfam_Peptidase_S8,PatternScan_SUBTILASE_SER,superfamily_Subtilisin-like,HMMPfam_P_proprotein,HMMSmart_SM00181,HMMSmart_SM00261,superfamily_Galactose-binding domain-like,superfamily_Growth factor receptor domain" - no_errors tier1 132 7 5.04 53 49 48.04 NA 507696 TCGA-AB-2889 4 114495214 114495214 C T SNP ANK2 NM_001148.1 human genbank 54_36p 1 reviewed silent c.5991 p.F1997 1 NULL "HMMPfam_Death,HMMSmart_DEATH,HMMPfam_ZU5,HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK,superfamily_DEATH_like,PatternScan_ALDEHYDE_DEHYDR_GLU" - no_errors tier1 214 7 3.17 65 63 49.22 NA 507696 TCGA-AB-2889 10 117476782 117476782 G A SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated missense c.3830 p.R1277H 1 NULL "HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMPfam_Lectin_C,HMMSmart_SM00034,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_PSI,HMMSmart_SM00423,HMMSmart_SM00181,HMMPfam_Kelch_1,superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_C-type lectin-like,superfamily_Plexin repeat,superfamily_EGF/Laminin" - no_errors tier1 96 5 4.95 56 35 38.04 NA 553863 TCGA-AB-2890 9 8366658 8366658 A G SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed silent c.4455 p.L1485 0.168 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,PatternScan_TYR_PHOSPHATASE_1,superfamily_Immunoglobulin,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 104 5 4.5 112 102 47.66 NA 553863 TCGA-AB-2890 19 15655469 15655469 C T SNP CYP4F12 NM_023944.2 human genbank 54_36p 1 reviewed missense c.814 p.R272W 1 "HMMPfam_p450,superfamily_Cytochrome P450" "HMMPfam_p450,superfamily_Cytochrome P450,PatternScan_CYTOCHROME_P450" - no_errors tier1 87 5 5.38 46 18 28.12 NA 553863 TCGA-AB-2890 22 29021731 29021732 - C INS TBC1D10A NM_031937.1 human genbank 54_36p -1 provisional frame_shift_ins c.519_518 p.H174fs 0.995:1.000 "HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p" "HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p" - no_errors tier1 NA NA NA NA NA NA NA NA NA 553863 TCGA-AB-2890 21 35153653 35153653 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed nonsense c.601 p.R201* 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 84 1 1.18 57 18 24 412 244 37.14 553863 TCGA-AB-2890 5 38487301 38487301 G A SNP EGFLAM NM_152403.2 human genbank 54_36p 1 validated missense c.2671 p.G891R 1 "HMMSmart_LamG,superfamily_ConA_like_lec_gl,HMMPfam_Laminin_G_2" "HMMSmart_LamG,HMMPfam_fn3,HMMSmart_FN3,HMMPfam_EGF,HMMSmart_EGF,superfamily_FN_III-like,superfamily_ConA_like_lec_gl,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2" - no_errors tier1 89 3 3.19 76 33 30.28 NA 553863 TCGA-AB-2890 20 48942512 48942512 T G SNP ADNP NM_015339.2 human genbank 54_36p -1 reviewed missense c.2146 p.K716Q 1 NULL "HMMPfam_Homeobox,HMMSmart_HOX,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Homeodomain_like,HMMSmart_ZnF_C2H2,PatternScan_HOMEOBOX_1" - no_errors tier1 45 3 6.25 71 42 37.17 47 38 44.71 553863 TCGA-AB-2890 4 78866545 78866545 C T SNP CNOT6L NM_144571.2 human genbank 54_36p -1 validated missense c.1255 p.V419I 1 "HMMPfam_Exo_endo_phos,superfamily_DNase I-like" "HMMPfam_LRR_1,HMMSmart_SM00369,HMMPfam_Exo_endo_phos,superfamily_DNase I-like,superfamily_L domain-like" - no_errors tier1 72 3 3.95 87 38 30.4 8 3 27.27 553863 TCGA-AB-2890 10 85981730 85981730 C T SNP LRIT1 NM_015613.2 human genbank 54_36p -1 validated missense c.1805 p.R602H 0.67 NULL "HMMSmart_LRRNT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMSmart_IGc2,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_ig,superfamily_SSF48726,superfamily_SSF52058" - no_errors tier1 22 0 32 11 25.58 NA 553863 TCGA-AB-2890 X 102751098 102751098 A G SNP TCEAL3 NM_001006933.1 human genbank 54_36p 1 reviewed silent c.450 p.Q150 1 HMMPfam_TFA HMMPfam_TFA - no_errors tier1 128 4 3.03 189 38 16.67 4 0 594368 TCGA-AB-2891 12 11930226 11930226 A G SNP ETV6 NM_001987.4 human genbank 54_36p 1 reviewed missense c.1252 p.R418G 1 "HMMPfam_Ets,HMMSmart_SM00413,superfamily_""Winged helix"" DNA-binding domain" "HMMPfam_Ets,HMMSmart_SM00413,PatternScan_ETS_DOMAIN_2,HMMPfam_SAM_PNT,HMMSmart_SM00251,superfamily_SAM/Pointed domain,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 255 16 5.84 55 67 54.47 2 40 95.24 594368 TCGA-AB-2891 2 25316811 25316811 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2186 p.R729Q 1 "HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 77 2 2.53 34 32 48.48 19 15 44.12 594368 TCGA-AB-2891 2 25320526 25320526 A G SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed splice_site c.1851+2 e14+2 1 - - - no_errors tier1 55 3 5.17 44 24 34.78 7 100 594368 TCGA-AB-2891 9 34700059 34700059 G A SNP CCL21 NM_002989.2 human genbank 54_36p -1 reviewed missense c.5 p.A2V 0.983 NULL "HMMPfam_IL8,HMMSmart_SM00199,superfamily_Interleukin 8-like chemokines" - no_errors tier1 293 9 2.96 231 148 38.44 NA 594368 TCGA-AB-2891 1 37959089 37959089 T C SNP EPHA10 NM_001099439.1 human genbank 54_36p -1 validated missense c.2161 p.I721V 1 "HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)" "HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),PatternScan_EGF_2" - no_errors tier1 164 3 1.79 61 43 41.35 NA 594368 TCGA-AB-2891 19 39592210 39592210 A G SNP PDCD2L NM_032346.1 human genbank 54_36p 1 provisional missense c.641 p.Y214C 0.998 HMMPfam_PDCD2_C HMMPfam_PDCD2_C - no_errors tier1 549 23 3.97 107 85 44.04 2 0 594368 TCGA-AB-2891 6 43274427 43274427 G A SNP CUL9 NM_015089.2 human genbank 54_36p 1 validated missense c.2906 p.R969H 0.201 superfamily_ARM repeat "HMMPfam_Cullin,HMMPfam_IBR,HMMSmart_SM00647,HMMPfam_APC10,superfamily_Galactose-binding domain-like,superfamily_ARM repeat,PatternScan_CULLIN_1,superfamily_Cullin homology domain,PatternScan_ZF_RING_1,PatternScan_CYTOCHROME_P450,superfamily_""Winged helix"" DNA-binding domain,superfamily_RING/U-box" - no_errors tier1 361 11 2.96 116 93 44.5 31 21 40.38 594368 TCGA-AB-2891 4 47100206 47100206 C T SNP GABRB1 NM_000812.3 human genbank 54_36p 1 reviewed missense c.659 p.S220F 1 "HMMPfam_Neur_chan_LBD,superfamily_Neur_chan_LBD" "HMMPfam_Neur_chan_memb,superfamily_Neu_channel_TM,HMMPfam_Neur_chan_LBD,superfamily_Neur_chan_LBD,PatternScan_NEUROTR_ION_CHANNEL" - no_errors tier1 447 16 3.4 146 69 31.36 1 100 594368 TCGA-AB-2891 3 49676911 49676911 A G SNP BSN NM_003458.3 human genbank 54_36p 1 validated missense c.11660 p.Q3887R 1 NULL "HMMPfam_zf-piccolo,superfamily_FYVE_PHD_ZnF" - no_errors tier1 52 2 3.7 43 19 30.16 NA 594368 TCGA-AB-2891 15 63243500 63243500 T C SNP CLPX NM_006660.3 human genbank 54_36p -1 provisional missense c.593 p.Y198C 1 superfamily_P-loop containing nucleoside triphosphate hydrolases "HMMSmart_SM00382,HMMPfam_AAA_2,HMMPfam_ClpB_D2-small,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 172 6 3.33 77 41 34.75 23 36 61.02 594368 TCGA-AB-2891 11 74994526 74994526 T A SNP MAP6 NM_033063.1 human genbank 54_36p -1 reviewed missense c.1291 p.N431Y 1 HMMPfam_STOP HMMPfam_STOP - no_errors tier1 382 13 3.27 106 70 39.77 NA 594368 TCGA-AB-2891 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 180 8 4.23 78 61 43.88 220 203 47.99 594368 TCGA-AB-2891 9 97051267 97051267 T C SNP FANCC NM_000136.2 human genbank 54_36p -1 reviewed missense c.128 p.E43G 0.998 HMMPfam_Fanconi_C HMMPfam_Fanconi_C - no_errors tier1 263 6 2.21 167 93 35.63 9 4 30.77 594368 TCGA-AB-2891 11 101459121 101459121 G A SNP C11orf70 NM_032930.1 human genbank 54_36p 1 predicted missense c.671 p.G224D 1 NULL NULL - no_errors tier1 243 6 2.39 65 41 38.68 NA 594368 TCGA-AB-2891 X 106032037 106032037 G A SNP RIPPLY1 NM_138382.1 human genbank 54_36p -1 provisional silent c.220 p.L74 0 NULL NULL - no_errors tier1 124 6 4.62 40 98 69.5 NA 594368 TCGA-AB-2891 9 134688504 134688504 C T SNP C9orf98 NM_152572.2 human genbank 54_36p -1 validated silent c.798 p.P266 0.982 superfamily_P-loop containing nucleoside triphosphate hydrolases "HMMPfam_ADK,superfamily_Microbial and mitochondrial ADK insert ""zinc finger"" domain,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 189 6 3 144 64 30.48 NA 671473 TCGA-AB-2892 18 5405927 5405928 - A INS EPB41L3 NM_012307.2 human genbank 54_36p -1 provisional frame_shift_ins c.1957_1956 p.A652fs 1.000:0.993 NULL "HMMPfam_SAB,HMMPfam_4_1_CTD,HMMPfam_FA,HMMPfam_FERM_N,HMMPfam_FERM_C,PatternScan_FERM_1,PatternScan_FERM_2,HMMPfam_FERM_M,superfamily_Second domain of FERM,HMMSmart_SM00295,superfamily_PH domain-like,superfamily_Ubiquitin-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 671473 TCGA-AB-2892 12 31134136 31134136 G A SNP DDX11 NM_152438.2 human genbank 54_36p 1 reviewed silent c.930 p.E310 0.981 "HMMSmart_SM00488,HMMPfam_DEAD_2,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00488,HMMSmart_SM00491,HMMPfam_DEAD_2,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 25 0 69 11 13.75 18 1 5.26 671473 TCGA-AB-2892 1 115058053 115058053 G T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.181 p.Q61K 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 9 3 25 188 92 32.86 30 10 25 690397 TCGA-AB-2893 14 19298190 19298190 T G SNP OR4H12P ENST00000316004 human ensembl 54_36p 1 known silent c.282 p.T94 0.004 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 281 19 6.33 155 41 20.81 NA 690397 TCGA-AB-2893 11 49822399 49822399 G A SNP LOC387770 XR_017307.2 human genbank 54_36p -1 model rna NULL NULL 0.515 - - - pseudogene tier1 220 32 12.6 52 32 38.1 NA 717456 TCGA-AB-2894 21 27136618 27136618 G A SNP ADAMTS1 NM_006988.3 human genbank 54_36p -1 reviewed missense c.988 p.R330W 0.998 "HMMPfam_Reprolysin,superfamily_SSF55486" "HMMPfam_TSP_1,HMMSmart_TSP1,superfamily_TSP1,HMMPfam_Reprolysin,HMMPfam_Pep_M12B_propep,PatternScan_ZINC_PROTEASE,HMMSmart_ACR,HMMPfam_ADAM_spacer1,PatternScan_DISINTEGRIN_1,superfamily_SSF55486" - no_errors tier1 212 9 4.07 63 32 33.68 NA 717456 TCGA-AB-2894 8 76091409 76091409 G A SNP CRISPLD1 NM_031461.4 human genbank 54_36p 1 validated missense c.782 p.R261Q 0.995 NULL "HMMSmart_SM00198,HMMPfam_LCCL,HMMSmart_SM00603,superfamily_LCCL domain,HMMPfam_SCP,superfamily_PR-1-like,PatternScan_CRISP_2" - no_errors tier1 81 6 6.9 33 12 26.09 9 4 30.77 717456 TCGA-AB-2894 5 140188859 140188859 T C SNP PCDHA6 NM_018909.2 human genbank 54_36p 1 reviewed silent c.999 p.H333 1 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 36 1 2.7 11 10 47.62 NA 717456 TCGA-AB-2894 8 145062821 145062821 G A SNP PLEC1 NM_201380.2 human genbank 54_36p -1 reviewed missense c.13567 p.R4523C 1 "HMMPfam_Plectin,HMMSmart_SM00250,superfamily_Plakin repeat" "HMMPfam_Plectin,HMMSmart_SM00250,PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_S10_plectin,superfamily_Calponin-homology domain CH-domain,HMMSmart_SM00150,superfamily_Spectrin repeat,superfamily_Plakin repeat" - no_errors tier1 9 1 10 3 5 62.5 46 37 44.58 717456 TCGA-AB-2894 2 210648701 210648701 C G SNP C2orf67 NM_152519.2 human genbank 54_36p -1 validated silent c.1575 p.L525 0.998 NULL NULL - no_errors tier1 217 8 3.56 67 34 33.66 4 11 73.33 721214 TCGA-AB-2895 1 3318383 3318383 G A SNP PRDM16 NM_022114.2 human genbank 54_36p 1 reviewed missense c.1762 p.V588M 0.001 NULL "HMMSmart_SM00317,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers,superfamily_SET domain" - no_errors tier1 84 0 19 12 37.5 20 16 44.44 721214 TCGA-AB-2895 17 7857964 7857964 C T SNP GUCY2D NM_000180.3 human genbank 54_36p 1 reviewed missense c.2305 p.P769S 1 "superfamily_Kinase_like,HMMPfam_Pkinase" "HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase,HMMPfam_ANF_receptor,superfamily_Kinase_like,HMMPfam_Pkinase,PatternScan_GUANYLATE_CYCLASE_1,superfamily_SSF53822" - no_errors tier1 75 0 33 19 36.54 1 100 721214 TCGA-AB-2895 17 9770743 9770743 G A SNP GAS7 NM_201433.1 human genbank 54_36p -1 reviewed silent c.954 p.C318 0.891 NULL "HMMPfam_FCH,HMMSmart_SM00055,HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain" - no_errors tier1 149 2 1.31 127 39 23.49 28 5 14.71 721214 TCGA-AB-2895 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 130 0 18 16 47.06 39 58 59.18 721214 TCGA-AB-2895 13 27506218 27506219 - CAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins in_frame_ins 1.000:1.000 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 721214 TCGA-AB-2895 17 35443150 35443150 G T SNP MED24 NM_014815.1 human genbank 54_36p -1 reviewed silent c.645 p.A215 0.346 NULL NULL - no_errors tier1 120 0 39 41 51.25 40 39 49.37 721214 TCGA-AB-2895 11 36207460 36207460 C T SNP LDLRAD3 NM_174902.2 human genbank 54_36p 1 provisional silent c.975 p.G325 0.06 NULL "HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich" - no_errors tier1 28 0 21 11 34.38 1 100 721214 TCGA-AB-2895 19 54657704 54657704 G A SNP ALDH16A1 NM_153329.1 human genbank 54_36p 1 validated silent c.978 p.R326 0.406 "HMMPfam_Aldedh,superfamily_ALDH-like" "HMMPfam_Aldedh,superfamily_ALDH-like" - no_errors tier1 23 0 32 8 20 17 7 29.17 721214 TCGA-AB-2895 12 65986521 65986521 T G SNP CAND1 NM_018448.3 human genbank 54_36p 1 validated missense c.2806 p.L936V 0.998 superfamily_ARM repeat "HMMPfam_HEAT,HMMPfam_TIP120,superfamily_ARM repeat" - no_errors tier1 47 1 2.04 56 74 56.92 43 42 49.41 721214 TCGA-AB-2895 11 76184545 76184545 G A SNP TSKU NM_015516.3 human genbank 54_36p 1 validated silent c.237 p.A79 0.722 superfamily_SSF52047 "HMMSmart_LRRNT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52047" - no_errors tier1 63 0 40 22 35.48 NA 721214 TCGA-AB-2895 6 85510728 85510728 G A SNP TBX18 NM_001080508.1 human genbank 54_36p -1 provisional missense c.974 p.A325V 1 "HMMPfam_T-box,HMMSmart_TBOX,superfamily_P53_like_DNA_bnd" "HMMPfam_T-box,HMMSmart_TBOX,superfamily_P53_like_DNA_bnd,PatternScan_TBOX_2,PatternScan_TBOX_1" - no_errors tier1 55 0 37 27 42.19 NA 721214 TCGA-AB-2895 10 127559142 127559142 A G SNP DHX32 NM_018180.2 human genbank 54_36p -1 reviewed missense c.242 p.V81A 0.861 superfamily_P-loop containing nucleoside triphosphate hydrolases "HMMPfam_HA2,HMMPfam_DUF1605,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 78 0 52 42 44.68 15 18 54.55 721214 TCGA-AB-2895 5 148386346 148386346 C T SNP SH3TC2 NM_024577.3 human genbank 54_36p -1 reviewed missense c.3035 p.R1012Q 0.998 superfamily_TPR-like "HMMPfam_TPR_1,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_SH3_2,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 33 0 78 17 17.89 11 2 15.38 721214 TCGA-AB-2895 1 158476620 158476620 A G SNP WDR42A NM_015726.2 human genbank 54_36p -1 reviewed missense c.214 p.S72P 1 NULL "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" - no_errors tier1 109 1 0.91 114 109 48.44 96 89 48.11 721214 TCGA-AB-2895 5 160045718 160045718 T C SNP ATP10B NM_025153.2 human genbank 54_36p -1 validated missense c.416 p.K139R 0.985 HMMPfam_E1-E2_ATPase "HMMPfam_E1-E2_ATPase,HMMPfam_Hydrolase_3,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N" - no_errors tier1 114 1 0.85 114 65 36.31 NA 721214 TCGA-AB-2895 5 169058032 169058032 G A SNP DOCK2 NM_004946.2 human genbank 54_36p 1 validated splice_site c.1055+1 e11+1 1 - - - no_errors tier1 119 0 130 95 42.22 3 1 25 721214 TCGA-AB-2895 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 737451 TCGA-AB-2896 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 53 28 34.15 29 22 43.14 43 56 56 737451 TCGA-AB-2896 12 54917282 54917283 - G INS SLC39A5 NM_173596.1 human genbank 54_36p 1 validated frame_shift_ins c.1367_1368 p.A459fs 0.797:0.707 HMMPfam_Zip HMMPfam_Zip - no_errors tier1 NA NA NA NA NA NA NA NA NA 737451 TCGA-AB-2896 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 757199 TCGA-AB-2897 MT 3919 3919 G A SNP MT-ND1 ENST00000361390 human ensembl 54_36p 1 known silent c.612 p.E204 NULL "HMMPfam_NADHdh,PatternScan_COMPLEX1_ND1_2" "HMMPfam_NADHdh,PatternScan_COMPLEX1_ND1_1,PatternScan_COMPLEX1_ND1_2" - no_errors tier1 3558 16 0.44 1035 1880 64.27 NA NA NA 757199 TCGA-AB-2897 16 1931315 1931315 T C SNP SEPX1 ENST00000399753 human ensembl 54_36p -1 known missense c.148 p.I50V 1 "HMMPfam_SelR,superfamily_Mss4_like" "HMMPfam_SelR,superfamily_Mss4_like" - no_errors tier1 48 0 24 10 29.41 52 48 48 757199 TCGA-AB-2897 19 12911446 12911447 - T INS CALR NM_004343.3 human genbank 54_36p 1 reviewed splice_site_ins c.397+1_397+1 e3+1 1.000:1.000 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 757199 TCGA-AB-2897 14 18448512 18448512 C A SNP OR11H12 NM_001013354.1 human genbank 54_36p 1 provisional missense c.919 p.L307I 0.968 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 63 0 32 23 41.82 NA 757199 TCGA-AB-2897 6 79792571 79792571 C A SNP PHIP NM_017934.5 human genbank 54_36p -1 validated missense c.630 p.W210C 1 "HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,HMMPfam_WD40" "HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain,HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,PatternScan_BROMODOMAIN_1,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 155 0 133 25 15.72 56 10 15.15 757199 TCGA-AB-2897 13 106620903 106620903 G A SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional silent c.1320 p.A440 0.272 NULL NULL - no_errors tier1 299 1 0.33 243 107 30.57 NA 757199 TCGA-AB-2897 6 109921318 109921318 G A SNP C6orf224 NM_173559.1 human genbank 54_36p -1 predicted missense c.880 p.H294Y 0.975 NULL NULL - no_errors tier1 105 1 0.93 115 76 39.58 4 2 33.33 757199 TCGA-AB-2897 6 168095154 168095154 G A SNP MLLT4 NM_001040001.1 human genbank 54_36p 1 validated missense c.4247 p.R1416H 1 NULL "HMMPfam_RA,HMMSmart_RA,HMMPfam_FHA,HMMSmart_FHA,HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ,superfamily_SMAD_FHA,HMMPfam_DIL,superfamily_SSF54236" - no_errors tier1 43 1 2.27 124 61 32.97 NA 851929 TCGA-AB-2898 4 2668082 2668082 G A SNP C4orf8 NM_003704.3 human genbank 54_36p 1 validated silent c.2598 p.T866 0.983 NULL NULL - no_errors tier1 91 0 89 68 43.31 26 11 29.73 851929 TCGA-AB-2898 20 13806170 13806170 C T SNP SEL1L2 NM_025229.1 human genbank 54_36p -1 validated missense c.1022 p.G341E 1 "HMMPfam_Sel1,HMMSmart_SEL1,superfamily_SSF81901" "HMMPfam_Sel1,HMMSmart_SEL1,superfamily_SSF81901" - no_errors tier1 143 0 81 79 49.38 NA 851929 TCGA-AB-2898 2 25313307 25313307 A C SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed splice_site c.2478+2 e20+2 0.998 - - - no_errors tier1 27 0 14 13 46.43 6 5 45.45 851929 TCGA-AB-2898 2 25315536 25315536 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2375 p.R792H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 26 0 26 19 42.22 20 46 69.7 851929 TCGA-AB-2898 2 25820737 25820738 - CT INS ASXL2 NM_018263.4 human genbank 54_36p -1 validated frame_shift_ins c.1973_1972 p.A658fs 1.000:1.000 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 851929 TCGA-AB-2898 21 36522005 36522005 C A SNP DOPEY2 NM_005128.2 human genbank 54_36p 1 validated missense c.1625 p.P542H 1 NULL HMMPfam_Dopey_N - no_errors tier1 126 0 40 28 41.18 18 15 45.45 851929 TCGA-AB-2898 2 46456394 46456394 C T SNP EPAS1 NM_001430.3 human genbank 54_36p 1 validated silent c.948 p.Y316 0.901 "HMMSmart_PAC,HMMPfam_PAS_3,superfamily_SSF55785" "HMMSmart_PAS,HMMPfam_HLH,HMMSmart_HLH,HMMSmart_PAC,superfamily_HLH_basic,HMMPfam_PAS_3,HMMPfam_HIF-1a_CTAD,superfamily_SSF55785" - no_errors tier1 126 2 1.56 64 58 47.54 8 0 851929 TCGA-AB-2898 19 47564893 47564893 C T SNP MEGF8 NM_001410.2 human genbank 54_36p 1 validated silent c.6339 p.D2113 1 NULL "PatternScan_ASX_HYDROXYL,HMMPfam_CUB,HMMSmart_CUB,superfamily_CUB,HMMSmart_EGF_CA,HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,PatternScan_EGF_LAM_1,HMMPfam_PSI,HMMSmart_PSI,HMMSmart_EGF,HMMPfam_Kelch_1,superfamily_Gal_oxid_central,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_SSF57196" - no_errors tier1 84 0 15 14 48.28 12 6 33.33 851929 TCGA-AB-2898 17 53317592 53317592 C T SNP CUEDC1 NM_017949.1 human genbank 54_36p -1 provisional silent c.333 p.P111 0.274 NULL "HMMPfam_CUE,HMMSmart_SM00546,superfamily_UBA-like" - no_errors tier1 18 0 32 17 34.69 7 3 30 851929 TCGA-AB-2898 10 55257274 55257274 C T SNP PCDH15 NM_033056.1 human genbank 54_36p -1 reviewed missense c.4252 p.A1418T 0.977 NULL "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" - no_errors tier1 62 0 22 22 50 NA 851929 TCGA-AB-2898 1 55361707 55361707 C T SNP USP24 NM_015306.1 human genbank 54_36p -1 validated splice_site c.3796+1 e33+1 1 - - - no_errors tier1 97 2 2.02 170 136 44.16 1 96 96 851929 TCGA-AB-2898 10 70075610 70075610 C T SNP TET1 NM_030625.2 human genbank 54_36p 1 validated missense c.3118 p.P1040S 0 NULL HMMPfam_zf-CXXC - no_errors tier1 152 0 78 62 43.66 3 1 25 851929 TCGA-AB-2898 15 72972172 72972174 GAG - DEL MPI NM_002435.1 human genbank 54_36p 1 reviewed in_frame_del c.463_465 p.E156in_frame_del 0.983:0.998:1.000 "HMMPfam_PMI_typeI,superfamily_RmlC-like cupins" "HMMPfam_PMI_typeI,superfamily_RmlC-like cupins,PatternScan_PMI_I_1,PatternScan_PMI_I_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 851929 TCGA-AB-2898 8 76092224 76092224 G A SNP CRISPLD1 NM_031461.4 human genbank 54_36p 1 validated missense c.1111 p.G371S 1 "HMMPfam_LCCL,HMMSmart_SM00603,superfamily_LCCL domain" "HMMSmart_SM00198,HMMPfam_LCCL,HMMSmart_SM00603,superfamily_LCCL domain,HMMPfam_SCP,superfamily_PR-1-like,PatternScan_CRISP_2" - no_errors tier1 64 0 38 63 62.38 7 9 56.25 851929 TCGA-AB-2898 15 87202088 87202088 C T SNP ACAN NM_013227.2 human genbank 54_36p 1 reviewed silent c.4926 p.S1642 0.969 NULL "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin" - no_errors tier1 36 1 2.7 29 18 38.3 NA 851929 TCGA-AB-2898 15 88432842 88432842 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.515 p.R172K 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 78 0 43 32 42.11 80 81 50.31 851929 TCGA-AB-2898 13 108177890 108177890 C T SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated silent c.399 p.A133 1 "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" "HMMPfam_IQ,HMMPfam_Myosin_head,HMMSmart_SM00242,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 284 0 84 67 43.79 NA 851929 TCGA-AB-2898 3 132197626 132197626 G A SNP ATP2C1 NM_001001486.1 human genbank 54_36p 1 reviewed missense c.2107 p.V703I 1 superfamily_Calcium ATPase transmembrane domain M "HMMPfam_Cation_ATPase_N,HMMPfam_Hydrolase,HMMPfam_Cation_ATPase_C,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_Calcium ATPase transmembrane domain M" - no_errors tier1 76 0 56 50 47.17 66 39 37.14 851929 TCGA-AB-2898 2 219875113 219875113 A C SNP PTPRN NM_002846.2 human genbank 54_36p -1 reviewed silent c.984 p.A328 0.007 NULL "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 98 0 127 90 41.1 NA 962561 TCGA-AB-2899 4 9607661 9607661 G A SNP SLC2A9 NM_020041.1 human genbank 54_36p -1 reviewed silent c.252 p.Y84 1 "HMMPfam_Sugar_tr,superfamily_MFS general substrate transporter" "HMMPfam_Sugar_tr,PatternScan_SUGAR_TRANSPORT_1,PatternScan_SUGAR_TRANSPORT_2,superfamily_MFS general substrate transporter" - no_errors tier1 121 6 4.69 55 33 37.5 7 3 30 962561 TCGA-AB-2899 14 22312678 22312678 C T SNP SLC7A7 NM_003982.1 human genbank 54_36p -1 reviewed missense c.1517 p.R506Q 0.01 NULL "PatternScan_AMINO_ACID_PERMEASE_1,HMMPfam_AA_permease" - no_errors tier1 193 3 1.52 117 99 45.83 39 37 48.68 962561 TCGA-AB-2899 21 35174748 35174748 T C SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.484 p.R162G 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 42 0 8 16 66.67 18 327 94.78 962561 TCGA-AB-2899 18 40785911 40785911 G A SNP SETBP1 NM_015559.1 human genbank 54_36p 1 validated missense c.2446 p.G816S 1 NULL "HMMPfam_AT_hook,HMMSmart_AT_hook" - no_errors tier1 81 5 5.81 60 46 43.4 15 19 55.88 962561 TCGA-AB-2899 5 41017295 41017297 GAA - DEL C7 NM_000587.2 human genbank 54_36p 1 reviewed in_frame_del c.2395_2397 p.E800in_frame_del 0.054:0.080:0.095 HMMSmart_FIMAC "HMMPfam_Sushi,HMMSmart_CCP,HMMPfam_TSP_1,HMMSmart_TSP1,superfamily_TSP1,HMMPfam_MACPF,HMMSmart_MACPF,PatternScan_MAC_PERFORIN,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,HMMSmart_FIMAC,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Complement_control_module,superfamily_SSF57196" - no_errors tier1 NA NA NA NA NA NA NA NA NA 962561 TCGA-AB-2899 6 47884004 47884004 C T SNP OPN5 NM_181744.1 human genbank 54_36p 1 reviewed silent c.912 p.I304 1 "HMMPfam_7tm_1,PatternScan_OPSIN,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,PatternScan_OPSIN,superfamily_SSF81321" - no_errors tier1 86 2 2.27 46 22 32.35 NA 962561 TCGA-AB-2899 12 54706920 54706920 C T SNP IKZF4 NM_022465.3 human genbank 54_36p 1 validated silent c.375 p.S125 0.437 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 85 2 2.3 61 27 30.68 4 0 962561 TCGA-AB-2899 17 71785833 71785833 T A SNP QRICH2 NM_032134.1 human genbank 54_36p -1 provisional missense c.4451 p.D1484V 0.303 NULL NULL - no_errors tier1 127 1 0.76 20 8 28.57 4 1 20 962561 TCGA-AB-2899 10 74343230 74343230 G A SNP OIT3 NM_152635.1 human genbank 54_36p 1 provisional missense c.949 p.D317N 0.436 "HMMPfam_Zona_pellucida,HMMSmart_SM00241" "PatternScan_ASX_HYDROXYL,HMMPfam_Zona_pellucida,HMMSmart_SM00241,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 106 3 2.75 68 66 49.25 NA 962561 TCGA-AB-2899 3 75674674 75674674 C T SNP LOC652670 XR_016285.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 62 2 3.12 27 68 71.58 0 962561 TCGA-AB-2899 X 101282827 101282827 C T SNP TCEAL6 NM_001006938.2 human genbank 54_36p -1 validated missense c.133 p.E45K 0.01 HMMPfam_TFA HMMPfam_TFA - no_errors tier1 67 0 152 113 42.64 NA 962561 TCGA-AB-2899 7 110313941 110313941 T C SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional missense c.352 p.I118V 1 "superfamily_LexA/Signal peptidase,PatternScan_SPASE_I_3" "superfamily_LexA/Signal peptidase,PatternScan_SPASE_I_3,HMMPfam_Peptidase_S24,PatternScan_ATPASE_ALPHA_BETA" - no_errors tier1 59 0 54 23 29.87 6 2 25 962561 TCGA-AB-2899 X 110889729 110889729 C T SNP ALG13 ENST00000394780 human ensembl 54_36p 1 known missense c.3260 p.P1087L 0.057 NULL "HMMPfam_OTU,HMMPfam_Glyco_tran_28_C,superfamily_SSF53756,superfamily_SSF54001,superfamily_SSF63748" - no_errors tier1 74 4 5.13 60 40 40 24 0 962561 TCGA-AB-2899 7 138619697 138619697 A G SNP UBN2 NM_173569.2 human genbank 54_36p 1 validated missense c.3257 p.N1086S 1 NULL PatternScan_TUBULIN - no_errors tier1 80 1 1.23 44 30 40.54 15 16 51.61 962561 TCGA-AB-2899 7 150274939 150274939 C T SNP KCNH2 NM_000238.2 human genbank 54_36p -1 reviewed missense c.3289 p.V1097I 0.872 NULL "HMMPfam_cNMP_binding,HMMSmart_SM00100,HMMSmart_SM00086,HMMPfam_Ion_trans,HMMPfam_PAS,superfamily_cAMP-binding domain-like,superfamily_PYP-like sensor domain (PAS domain),superfamily_Voltage-gated potassium channels" - no_errors tier1 25 0 23 15 39.47 2 100 962561 TCGA-AB-2899 5 172128423 172128423 T C SNP DUSP1 NM_004417.2 human genbank 54_36p -1 reviewed missense c.1052 p.N351S 0.996 NULL "HMMPfam_DSPc,HMMPfam_Rhodanese,HMMSmart_RHOD,superfamily_Rhodanese-like,PatternScan_TYR_PHOSPHATASE_1,HMMSmart_DSPc,superfamily_SSF52799" - no_errors tier1 45 1 2.17 46 39 45.88 434 374 46.23 962561 TCGA-AB-2899 2 220052978 220052978 G C SNP SPEG NM_005876.4 human genbank 54_36p 1 validated silent c.5214 p.R1738 0.999 "HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_ST,superfamily_Fibronectin type III,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_Immunoglobulin" - no_errors tier1 134 2 1.47 36 35 49.3 NA 982009 TCGA-AB-2900 MT 14964 14964 G A SNP MT-CYB ENST00000361789 human ensembl 54_36p 1 known missense c.217 p.V73M NULL "HMMPfam_Cytochrom_B_N,superfamily_Transmembr_di-haem_cytochrome" "HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome" - no_stop_codon:bad_bp_length_for_coding_region tier1 2685 32 1.17 3977 523 11.56 NA NA NA 982009 TCGA-AB-2900 18 9246666 9246666 A G SNP ANKRD12 NM_015208.1 human genbank 54_36p 1 validated missense c.3401 p.K1134R 0.977 superfamily_Ankyrin repeat "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" - no_errors tier1 69 3 4.11 143 131 47.64 16 10 38.46 982009 TCGA-AB-2900 2 11658497 11658497 C T SNP GREB1 NM_014668.3 human genbank 54_36p 1 reviewed silent c.2454 p.F818 1 NULL NULL - no_errors tier1 67 3 4.29 88 90 50 NA 982009 TCGA-AB-2900 1 16075676 16075676 C G SNP SPEN NM_015001.2 human genbank 54_36p 1 reviewed missense c.797 p.T266R 0.92 NULL "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_SPOC,superfamily_SPOC-like,superfamily_SSF54928" - no_errors tier1 59 1 1.67 61 50 44.25 12 23 65.71 982009 TCGA-AB-2900 22 16370917 16370917 G A SNP CECR2 ENST00000400585 human ensembl 54_36p 1 known missense c.877 p.V293I 0.987 NULL "HMMPfam_Bromodomain,HMMSmart_BROMO,superfamily_Bromodomain,PatternScan_BROMODOMAIN_1" - no_errors tier1 161 7 4.09 113 92 44.66 NA 982009 TCGA-AB-2900 1 18682068 18682068 C T SNP KLHDC7A NM_152375.2 human genbank 54_36p 1 validated missense c.2006 p.T669M 1 superfamily_Gal_oxid_central "HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central" - no_errors tier1 11 0 35 14 28 NA 982009 TCGA-AB-2900 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 87 5 5.43 94 57 37.5 300 252 45.57 982009 TCGA-AB-2900 17 38274388 38274388 G A SNP LOC90586 NR_002773.1 human genbank 54_36p 1 provisional rna NULL NULL 0.961 - - - pseudogene tier1 36 1 2.7 44 28 37.84 NA 982009 TCGA-AB-2900 19 38484304 38484305 - G INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_ins c.857_856 p.R286fs 1.000:1.000 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 982009 TCGA-AB-2900 X 53440262 53440262 C A SNP SMC1A NM_006306.2 human genbank 54_36p -1 reviewed nonsense c.2563 p.E855* 1 "HMMPfam_SMC_N,superfamily_SSF52540" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" - no_errors tier1 31 7 18.42 14 122 89.05 41 93.18 982009 TCGA-AB-2900 5 55491450 55491450 C T SNP ANKRD55 NM_024669.1 human genbank 54_36p -1 validated silent c.450 p.S150 0.807 "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" - no_errors tier1 108 8 6.9 173 131 42.95 1 0 982009 TCGA-AB-2900 14 64307466 64307466 C A SNP SPTB NM_001024858.4 human genbank 54_36p -1 validated silent c.5688 p.R1896 1 "HMMPfam_Spectrin,HMMSmart_SPEC,superfamily_Spectrin" "PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_CH,HMMPfam_PH,HMMSmart_PH,HMMPfam_Spectrin,superfamily_Calponin-homology,HMMSmart_SPEC,superfamily_Spectrin,superfamily_SSF50729" - no_errors tier1 26 0 95 54 36.24 1 100 982009 TCGA-AB-2900 11 67871993 67871993 C T SNP LRP5 NM_002335.2 human genbank 54_36p 1 validated missense c.194 p.A65V 1 "HMMSmart_SM00135,superfamily_YWTD domain" "HMMPfam_Ldl_recept_b,HMMSmart_SM00135,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMPfam_EGF,HMMSmart_SM00181,superfamily_EGF/Laminin,superfamily_YWTD domain" - no_errors tier1 62 1 1.59 46 45 48.91 2 0 982009 TCGA-AB-2900 4 75393698 75393698 C A SNP EPGN NM_001013442.1 human genbank 54_36p 1 provisional missense c.68 p.A23E 0.236 NULL "HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_SSF57196" - no_errors tier1 82 4 4.65 92 89 48.63 1 100 982009 TCGA-AB-2900 6 102176522 102176522 A G SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed missense c.121 p.I41V 1 superfamily_Periplasmic binding protein-like I "HMMPfam_Lig_chan,HMMSmart_SM00079,HMMPfam_ANF_receptor,HMMPfam_Lig_chan-Glu_bd,superfamily_Periplasmic binding protein-like I,superfamily_Periplasmic binding protein-like II" - no_errors tier1 87 2 2.22 139 99 40.91 NA 982009 TCGA-AB-2900 4 109168302 109168302 G T SNP HADH NM_005327.2 human genbank 54_36p 1 reviewed missense c.646 p.G216W 1 "HMMPfam_3HCDH,PatternScan_3HCDH,superfamily_6-phosphogluconate dehydrogenase C-terminal domain-like" "HMMPfam_3HCDH,HMMPfam_3HCDH_N,PatternScan_3HCDH,superfamily_6-phosphogluconate dehydrogenase C-terminal domain-like,superfamily_NAD(P)-binding Rossmann-fold domains" - no_errors tier1 127 11 7.86 218 210 48.5 42 42 50 982009 TCGA-AB-2900 2 119920929 119920929 C T SNP SCTR NM_002980.2 human genbank 54_36p -1 reviewed missense c.1016 p.R339H 0.995 "HMMPfam_7tm_2,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_2,HMMPfam_HRM,HMMSmart_SM00008,PatternScan_G_PROTEIN_RECEP_F2_1,PatternScan_G_PROTEIN_RECEP_F2_2,superfamily_Hormone receptor domain (HRM Pfam 02793),superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 34 2 5.41 70 64 46.72 NA 982009 TCGA-AB-2900 1 120266502 120266502 A T SNP NOTCH2 NM_024408.2 human genbank 54_36p -1 reviewed missense c.5093 p.I1698N 1 NULL "PatternScan_ASX_HYDROXYL,HMMPfam_Notch,HMMSmart_NL,superfamily_Notch_region,HMMSmart_EGF_CA,HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK,HMMPfam_EGF,HMMSmart_EGF,HMMPfam_NOD,HMMPfam_NODP,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_SSF57196" - no_errors tier1 80 1 1.2 85 106 54.36 42 39 48.15 982009 TCGA-AB-2900 9 137781841 137781841 T A SNP KCNT1 NM_020822.1 human genbank 54_36p 1 provisional missense c.331 p.S111T 1 NULL "HMMPfam_BK_channel_a,HMMPfam_Ion_trans_2,superfamily_NAD(P)-bd,superfamily_SSF81324" - no_errors tier1 49 2 3.85 49 22 30.56 NA 982009 TCGA-AB-2900 5 141224245 141224245 A G SNP PCDH1 NM_032420.3 human genbank 54_36p -1 reviewed missense c.1835 p.F612S 1 superfamily_Cadherin "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,HMMPfam_Protocadherin,superfamily_Cadherin,PatternScan_GREAB_2" - no_errors tier1 201 10 4.67 257 195 42.58 NA 982009 TCGA-AB-2900 5 161508763 161508763 G T SNP GABRG2 NM_198904.3 human genbank 54_36p 1 reviewed missense c.994 p.V332F 1 "HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore" "HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore,HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like,PatternScan_NEUROTR_ION_CHANNEL" - no_errors tier1 93 7 7 118 93 44.08 NA 982009 TCGA-AB-2900 5 170770152 170770153 - CGCG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 987523 TCGA-AB-2901 11 5835331 5835331 T C SNP OR52E8 NM_001005168.1 human genbank 54_36p -1 provisional missense c.178 p.S60G 0.746 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 166 8 4.6 121 86 41.55 NA 987523 TCGA-AB-2901 12 25248491 25248491 C T SNP LYRM5 NM_001001660.2 human genbank 54_36p 1 validated missense c.251 p.S84L 0.13 NULL HMMPfam_Complex1_LYR - no_errors tier1 255 8 3.02 179 94 34.06 22 18 45 987523 TCGA-AB-2901 15 31910538 31910538 T A SNP RYR3 NM_001036.3 human genbank 54_36p 1 validated missense c.11417 p.L3806Q 0.98 HMMPfam_RIH_assoc "HMMPfam_RYDR_ITPR,HMMPfam_RyR,HMMPfam_MIR,superfamily_MIR domain (Pfam 02815),HMMPfam_SPRY,HMMPfam_Ion_trans,HMMPfam_RR_TM4-6,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_SM00472,HMMPfam_efhand,HMMSmart_SM00449,superfamily_EF-hand" - no_errors tier1 162 19 10.38 110 107 48.64 NA 987523 TCGA-AB-2901 7 43558414 43558414 G A SNP HECW1 NM_015052.3 human genbank 54_36p 1 validated silent c.4464 p.A1488 0.315 "HMMPfam_HECT,HMMSmart_HECTc,superfamily_HECT" "HMMPfam_C2,HMMSmart_C2,HMMPfam_HECT,HMMSmart_HECTc,superfamily_HECT,HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,superfamily_C2_CaLB" - no_errors tier1 297 18 5.61 177 142 44.1 NA 987523 TCGA-AB-2901 11 47668631 47668631 C A SNP AGBL2 NM_024783.2 human genbank 54_36p -1 validated missense c.1204 p.D402Y 0.729 superfamily_Zn-dependent exopeptidases "HMMPfam_Peptidase_M14,superfamily_Zn-dependent exopeptidases" - no_errors tier1 545 18 3.18 197 165 45.08 3 0 987523 TCGA-AB-2901 16 56608774 56608774 C G SNP C16orf57 NM_024598.2 human genbank 54_36p 1 validated missense c.539 p.A180G 0.769 HMMPfam_HVSL HMMPfam_HVSL - no_errors tier1 434 18 3.9 116 90 43.69 31 24 43.64 987523 TCGA-AB-2901 2 160842078 160842078 C T SNP RBMS1 NM_016836.4 human genbank 54_36p -1 reviewed silent c.1125 p.T375 0.019 NULL "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 120 10 7.63 60 60 50 8 9 52.94 987523 TCGA-AB-2901 2 180387594 180387594 T C SNP LOC100131482 XM_001722616.1 human genbank 54_36p 1 model silent c.372 p.N124 1 "HMMPfam_DIM1,superfamily_Thioredoxin-like" "HMMPfam_DIM1,superfamily_Thioredoxin-like" - no_errors tier1 232 5 2.1 172 133 43.61 NA 987523 TCGA-AB-2901 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 114 5 4.2 63 59 48.36 81 70 46.36 989176 TCGA-AB-2903 MT 7782 7782 A G SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known missense c.196 p.T66A NULL "HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 1525 118 7.09 1244 417 24.94 NA NA NA 989176 TCGA-AB-2903 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 989176 TCGA-AB-2903 2 224348892 224348892 G A SNP AP1S3 NM_001039569.1 human genbank 54_36p -1 validated silent c.261 p.Y87 1 "HMMPfam_Clat_adaptor_s,superfamily_SNARE-like" "HMMPfam_Clat_adaptor_s,PatternScan_CLAT_ADAPTOR_S,superfamily_SNARE-like" - no_errors tier1 389 39 9.07 330 113 25.17 6 2 25 128392 TCGA-AB-2904 MT 15014 15014 A C SNP MT-CYB ENST00000361789 human ensembl 54_36p 1 known missense c.267 p.M89I NULL "HMMPfam_Cytochrom_B_N,superfamily_Transmembr_di-haem_cytochrome" "HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome" - no_stop_codon:bad_bp_length_for_coding_region tier1 4750 16 0.33 1675 2564 59.88 NA NA NA 128392 TCGA-AB-2904 17 1527142 1527142 C G SNP PRPF8 NM_006445.3 human genbank 54_36p -1 reviewed missense c.2059 p.A687P 1 HMMPfam_PROCN "HMMPfam_Mov34,HMMSmart_SM00232,HMMPfam_PRO8NT,HMMPfam_PROCN,HMMPfam_PROCT,HMMPfam_U6-snRNA_bdg,HMMPfam_U5_2-snRNA_bdg,HMMPfam_RRM_4" - no_errors tier1 117 0 30 41 56.94 17 102 85.71 128392 TCGA-AB-2904 1 6453706 6453706 C T SNP PLEKHG5 NM_198681.1 human genbank 54_36p -1 reviewed silent c.1554 p.E518 1 "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain" "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729" - no_errors tier1 15 0 11 14 56 1 3 75 128392 TCGA-AB-2904 17 7514743 7514743 G A SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.1009 p.R337C 0.465 "HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 104 0 63 116 64.8 5 120 94.49 128392 TCGA-AB-2904 6 7790455 7790455 G A SNP BMP6 NM_001718.4 human genbank 54_36p 1 reviewed missense c.748 p.V250M 1 HMMPfam_TGFb_propeptide "HMMPfam_TGFb_propeptide,HMMPfam_TGF_beta,HMMSmart_TGFB,PatternScan_TGF_BETA_1,superfamily_SSF57501" - no_errors tier1 194 0 150 98 39.2 3 0 128392 TCGA-AB-2904 19 8937508 8937508 G A SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated silent c.10938 p.S3646 0 NULL "HMMPfam_SEA,HMMSmart_SM00200,PatternScan_ATPASE_ALPHA_BETA,superfamily_SEA domain" - no_errors tier1 293 1 0.34 322 193 36.97 NA 128392 TCGA-AB-2904 9 15734617 15734617 G A SNP C9orf93 NM_173550.2 human genbank 54_36p 1 predicted missense c.2396 p.R799H 0.887 NULL NULL - no_errors tier1 163 0 158 67 29.52 15 6 28.57 128392 TCGA-AB-2904 3 19473266 19473266 A C SNP KCNH8 NM_144633.2 human genbank 54_36p 1 reviewed missense c.1828 p.K610Q 1 "HMMPfam_cNMP_binding,HMMSmart_cNMP,superfamily_cNMP_binding" "HMMPfam_cNMP_binding,HMMSmart_cNMP,HMMSmart_PAC,HMMPfam_Ion_trans,HMMPfam_PAS,PatternScan_CNMP_BINDING_1,PatternScan_CNMP_BINDING_2,superfamily_cNMP_binding,superfamily_SSF55785,superfamily_SSF81324" - no_errors tier1 115 0 125 81 39.13 NA 128392 TCGA-AB-2904 2 27319590 27319590 C T SNP CAD NM_004341.3 human genbank 54_36p 1 reviewed silent c.6501 p.L2167 1 "superfamily_Asp/Orn_carbamoyltranf,HMMPfam_OTCace" "HMMPfam_GATase,PatternScan_DIHYDROOROTASE_1,PatternScan_DIHYDROOROTASE_2,HMMPfam_CPSase_sm_chain,superfamily_CP_synthsmall,HMMPfam_CPSase_L_D2,PatternScan_CPSASE_1,PatternScan_CPSASE_2,HMMPfam_CPSase_L_D3,superfamily_CarbamoylP_synth_lsu_oligo,HMMPfam_CPSase_L_chain,PatternScan_CARBAMOYLTRANSFERASE,superfamily_Asp/Orn_carbamoyltranf,HMMPfam_OTCace,HMMPfam_OTCace_N,HMMPfam_Amidohydro_1,superfamily_Metalo_hydrolase,HMMPfam_MGS,superfamily_PreATP-grasp-like,superfamily_SSF51556,superfamily_SSF52317,superfamily_SSF52335,superfamily_SSF56059" - no_errors tier1 90 0 102 63 37.5 35 57 61.96 128392 TCGA-AB-2904 12 31137079 31137079 C T SNP DDX11 NM_152438.2 human genbank 54_36p 1 reviewed silent c.1275 p.Y425 0.997 HMMSmart_SM00488 "HMMSmart_SM00488,HMMSmart_SM00491,HMMPfam_DEAD_2,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 61 0 72 46 38.98 53 18 25.35 128392 TCGA-AB-2904 17 36934708 36934708 A G SNP KRT19 NM_002276.4 human genbank 54_36p -1 reviewed silent c.573 p.D191 0.633 "superfamily_Prefoldin,HMMPfam_Filament" "superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF" - no_errors tier1 29 0 35 17 32.08 NA 128392 TCGA-AB-2904 15 42743115 42743115 G C SNP SPG11 NM_025137.3 human genbank 54_36p -1 reviewed missense c.23 p.A8G 0.021 NULL PatternScan_GLYCOSYL_HYDROL_F1_1 - no_errors tier1 17 0 45 12 20.69 5 9 64.29 128392 TCGA-AB-2904 17 46028939 46028939 C T SNP CACNA1G NM_018896.3 human genbank 54_36p 1 validated silent c.2997 p.S999 0.579 NULL "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" - no_errors tier1 50 0 82 36 30.25 NA 128392 TCGA-AB-2904 10 53128702 53128702 G T SNP CSTF2T NM_015235.2 human genbank 54_36p -1 validated missense c.614 p.S205Y 0.993 NULL "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 101 1 0.98 137 79 36.57 17 9 34.62 128392 TCGA-AB-2904 5 64911118 64911118 T G SNP PPWD1 NM_015342.2 human genbank 54_36p 1 validated silent c.1272 p.S424 0.994 superfamily_WD40_like "HMMSmart_WD40,HMMPfam_Pro_isomerase,PatternScan_CSA_PPIASE_1,superfamily_WD40_like,superfamily_CSA_PPIase,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 116 0 112 55 32.54 55 38 40.86 128392 TCGA-AB-2904 16 74826910 74826910 C T SNP LOC441775 XR_042366.2 human genbank 54_36p -1 model rna NULL NULL 0.01 - - - pseudogene tier1 86 0 154 80 33.76 8 0 128392 TCGA-AB-2904 10 104965961 104965961 A G SNP LOC401648 XR_017482.1 human genbank 54_36p 1 model rna NULL NULL 0.999 - - - pseudogene tier1 46 8 14.81 26 37 58.73 15 0 128392 TCGA-AB-2904 4 107082990 107082990 A T SNP NPNT NM_001033047.1 human genbank 54_36p 1 validated missense c.841 p.T281S 0.984 NULL "PatternScan_ASX_HYDROXYL,HMMPfam_MAM,HMMSmart_SM00137,HMMSmart_SM00179,HMMSmart_SM00181,superfamily_Growth factor receptor domain,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 166 0 119 52 30.23 NA 128392 TCGA-AB-2904 8 110592224 110592224 G A SNP PKHD1L1 NM_177531.4 human genbank 54_36p 1 validated missense c.11438 p.R3813K 1 NULL "HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00710,superfamily_Cupredoxins,superfamily_Pectin lyase-like,HMMSmart_SM00758,superfamily_E set domains,HMMPfam_G8,superfamily_Anthrax protective antigen" - no_errors tier1 177 0 203 198 49.13 NA 128392 TCGA-AB-2904 2 133437771 133437771 C T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated missense c.571 p.A191T 1 NULL NULL - no_errors tier1 239 0 186 79 29.26 NA 128392 TCGA-AB-2904 5 140725202 140725202 G T SNP PCDHGA5 NM_018918.2 human genbank 54_36p 1 reviewed missense c.1121 p.G374V 0.001 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 80 1 1.2 31 41 56.94 NA 128392 TCGA-AB-2904 1 153011285 153011285 A T SNP KCNN3 NM_002249.4 human genbank 54_36p -1 reviewed missense c.1238 p.L413Q 1 superfamily_Voltage-gated potassium channels "HMMPfam_CaMBD,superfamily_Small-conductance potassium channel,HMMPfam_SK_channel,HMMPfam_Ion_trans_2,superfamily_Voltage-gated potassium channels" - no_errors tier1 53 0 75 41 35.34 NA 128392 TCGA-AB-2904 6 169775057 169775057 C T SNP WDR27 NM_182552.3 human genbank 54_36p -1 validated missense c.2134 p.V712M 0.002 "HMMSmart_SM00320,superfamily_WD40 repeat-like" "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" - no_errors tier1 43 0 62 40 38.83 2 2 50 128392 TCGA-AB-2904 1 205330396 205330396 C T SNP C4BPB NM_000716.3 human genbank 54_36p 1 reviewed missense c.179 p.T60I 0 "HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain" "HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain" - no_errors tier1 150 0 149 100 40 NA 128392 TCGA-AB-2904 2 241653487 241653487 T A SNP SNED1 NM_001080437.1 human genbank 54_36p 1 provisional missense c.2813 p.L938H 0.986 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III" "PatternScan_ASX_HYDROXYL,HMMPfam_Sushi,HMMSmart_SM00032,HMMSmart_SM00179,HMMPfam_NIDO,HMMSmart_SM00539,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_Complement control module/SCR domain,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 9 0 23 7 23.33 1 1 50 128392 TCGA-AB-2904 1 246164274 246164274 G T SNP OR2AJ1 ENST00000318244 human ensembl 54_36p 1 known missense c.581 p.R194L 0.002 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 208 0 221 117 34.41 NA 344551 TCGA-AB-2905 AML12 X 6328488 6328488 C T SNP ENSG00000217694 ENST00000405313 human ensembl 54_36p -1 known 5_prime_flanking_region c.-18803 NULL 0.001 - - - no_coding_region:pseudogene tier3 898 6 0.66 256 428 62.57 NA NA NA 344551 TCGA-AB-2905 AML12 Y 15988548 15988548 C T SNP ENSG00000218564 ENST00000406219 human ensembl 54_36p -1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 626 1 0.16 242 433 64.05 NA NA NA 344551 TCGA-AB-2905 AML12 X 16731330 16731330 A G SNP ENSG00000216596 ENST00000403161 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*16731330 NULL 0.998 - - - no_coding_region:pseudogene tier2 681 1 0.15 167 270 61.78 NA NA NA 344551 TCGA-AB-2905 AML12 X 33768630 33768630 C T SNP - - - - - - - - - - - - - - - tier3 355 0 0 147 302 67.26 NA NA NA 344551 TCGA-AB-2905 AML12 X 37550606 37550606 G A SNP CYBB NM_000397.3 human genbank 54_36p 1 reviewed missense c.1337 p.R446Q 1 "HMMPfam_NAD_binding_6,superfamily_Ferredoxin reductase-like C-terminal NADP-linked domain" "HMMPfam_FAD_binding_8,HMMPfam_NAD_binding_6,HMMPfam_Ferric_reduct,superfamily_Riboflavin synthase domain-like,superfamily_Ferredoxin reductase-like C-terminal NADP-linked domain" - no_errors tier1 1460 2 0.14 408 644 60.98 NA NA NA 344551 TCGA-AB-2905 AML12 X 48642171 48642171 A G SNP PQBP1 NM_001032381.1 human genbank 54_36p 1 validated intronic c.68-1240 e2-1240 0.007 - - - no_errors tier3 511 3 0.58 87 144 62.34 NA NA NA 344551 TCGA-AB-2905 AML12 X 130142987 130142987 C A SNP ENSG00000222814 ENST00000410882 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-46942 NULL 0.003 - - - no_errors tier3 670 0 0 419 783 65.09 NA NA NA 344551 TCGA-AB-2905 AML12 1 4760494 4760494 G A SNP LOC731656 XM_001716555.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-0 NULL 0.002 - - - rna_with_coding_region tier3 791 0 0 295 133 31 NA NA NA 344551 TCGA-AB-2905 AML12 1 5145797 5145797 G A SNP LOC100130833 XM_001713613.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-45229 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier2 2323 0 0 1532 720 31.94 NA NA NA 344551 TCGA-AB-2905 AML12 1 7049161 7049161 G A SNP CAMTA1 NM_015215.1 human genbank 54_36p 1 validated intronic c.235-24790 e4-24790 0.002 - - - no_errors tier3 1258 1 0.08 552 214 27.9 NA NA NA 344551 TCGA-AB-2905 AML12 1 16320088 16320088 G C SNP FAM131C NM_182623.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-47564 NULL 0.016 - - - no_errors tier3 1111 1 0.09 341 180 34.55 NA NA NA 344551 TCGA-AB-2905 AML12 1 16573768 16573768 C T SNP C1orf144 NM_015609.1 human genbank 54_36p 1 provisional intronic c.44+7378 e1+7378 0.001 - - - no_errors tier2 1416 3 0.21 507 226 30.83 NA NA NA 344551 TCGA-AB-2905 AML12 1 20699147 20699147 G A SNP MUL1 NM_024544.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*623 NULL 0.002 - - - no_errors tier3 782 0 0 349 177 33.59 NA NA NA 344551 TCGA-AB-2905 AML12 1 27235741 27235741 C T SNP FAM46B NM_052943.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23996 NULL 0.001 - - - no_errors tier3 1123 0 0 351 161 31.45 NA NA NA 344551 TCGA-AB-2905 AML12 1 30861142 30861142 C T SNP - - - - - - - - - - - - - - - tier2 987 2 0.2 500 317 38.8 NA NA NA 344551 TCGA-AB-2905 AML12 1 34956146 34956146 C T SNP GJB4 NM_153212.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-43297 NULL 0.003 - - - no_errors tier3 1856 3 0.16 909 348 27.68 NA NA NA 344551 TCGA-AB-2905 AML12 1 45239248 45239248 A G SNP UROD NM_000374.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11277 NULL 0.055 - - - no_errors tier3 1324 0 0 574 270 31.84 NA NA NA 344551 TCGA-AB-2905 AML12 1 50416021 50416021 C T SNP ELAVL4 NM_021952.1 human genbank 54_36p 1 validated intronic c.354+570 e3+570 0 - - - no_errors tier3 1950 0 0 658 251 27.61 NA NA NA 344551 TCGA-AB-2905 AML12 1 57027291 57027291 C T SNP C1orf168 NM_001004303.4 human genbank 54_36p -1 validated missense c.862 p.V288M 0.41 NULL superfamily_SH3-domain - no_errors tier1 1447 5 0.34 661 306 31.58 NA NA NA 344551 TCGA-AB-2905 AML12 1 59878937 59878937 A G SNP FGGY NM_018291.1 human genbank 54_36p 1 validated intronic c.885+2302 e8+2302 0.013 - - - no_errors tier3 757 0 0 735 273 27.08 NA NA NA 344551 TCGA-AB-2905 AML12 1 80743586 80743586 C A SNP ENSG00000218288 ENST00000405969 human ensembl 54_36p -1 known 5_prime_flanking_region c.-40560 NULL 0 - - - no_coding_region:pseudogene tier3 708 1 0.14 736 340 31.6 NA NA NA 344551 TCGA-AB-2905 AML12 1 81003422 81003422 C T SNP - - - - - - - - - - - - - - - tier3 786 2 0.25 629 290 31.52 NA NA NA 344551 TCGA-AB-2905 AML12 1 82652200 82652200 G A SNP - - - - - - - - - - - - - - - tier2 680 0 0 493 208 29.67 NA NA NA 344551 TCGA-AB-2905 AML12 1 90695428 90695428 C T SNP - - - - - - - - - - - - - - - tier3 1308 0 0 1358 527 27.91 NA NA NA 344551 TCGA-AB-2905 AML12 1 99695450 99695450 C T SNP ENSG00000217126 ENST00000402662 human ensembl 54_36p 1 known 5_prime_flanking_region c.-7072 NULL 0.002 - - - no_coding_region:pseudogene tier3 1339 1 0.07 1083 395 26.73 NA NA NA 344551 TCGA-AB-2905 AML12 1 115658174 115658174 G A SNP NGF NM_002506.2 human genbank 54_36p -1 reviewed intronic c.1-20280 e1-20280 0 - - - no_errors tier2 1396 3 0.21 785 300 27.6 NA NA NA 344551 TCGA-AB-2905 AML12 1 117144793 117144793 T C SNP ENSG00000220126 ENST00000405278 human ensembl 54_36p -1 known 5_prime_flanking_region c.-25025 NULL 0.001 - - - no_coding_region:pseudogene tier3 916 2 0.22 805 288 26.3 NA NA NA 344551 TCGA-AB-2905 AML12 1 117686200 117686200 C T SNP MAN1A2 NM_006699.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26129 NULL 0.001 - - - no_errors tier3 639 0 0 677 251 27.05 NA NA NA 344551 TCGA-AB-2905 AML12 1 117935539 117935539 G A SNP FAM46C NM_017709.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-31475 NULL 0 - - - no_errors tier3 1181 4 0.34 524 256 32.82 NA NA NA 344551 TCGA-AB-2905 AML12 1 118878713 118878713 C G SNP - - - - - - - - - - - - - - - tier3 1265 2 0.16 1195 561 31.95 NA NA NA 344551 TCGA-AB-2905 AML12 1 119667665 119667665 T C SNP HAO2 NM_001005783.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-57567 NULL 0.124 - - - no_errors tier3 506 0 0 422 64 13.17 NA NA NA 344551 TCGA-AB-2905 AML12 1 150286806 150286806 A T SNP S100A11 NM_005620.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-10791 NULL 0 - - - no_errors tier2 1062 0 0 1098 527 32.35 NA NA NA 344551 TCGA-AB-2905 AML12 1 161376117 161376117 C A SNP RGS5 NM_003617.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*7639 NULL 0 - - - no_errors tier3 669 1 0.15 514 186 26.53 NA NA NA 344551 TCGA-AB-2905 AML12 1 162913847 162913847 G A SNP PBX1 NM_002585.2 human genbank 54_36p 1 validated intronic c.266-114508 e3-114508 0 - - - no_errors tier2 963 5 0.52 486 233 32.36 NA NA NA 344551 TCGA-AB-2905 AML12 1 169082867 169082867 A G SNP - - - - - - - - - - - - - - - tier3 710 2 0.28 449 201 30.88 NA NA NA 344551 TCGA-AB-2905 AML12 1 175025647 175025647 C T SNP PAPPA2 NM_020318.2 human genbank 54_36p 1 validated missense c.4795 p.P1599S 0.691 "HMMSmart_SM00032,superfamily_Complement control module/SCR domain" "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Notch,HMMSmart_SM00004,superfamily_Notch domain,PatternScan_N6_MTASE,PatternScan_ZINC_PROTEASE,HMMSmart_SM00560,HMMPfam_Peptidase_M43,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Complement control module/SCR domain,superfamily_Metalloproteases (""zincins"") catalytic domain" - no_errors tier1 1924 1 0.05 1086 523 32.48 NA NA NA 344551 TCGA-AB-2905 AML12 1 188890882 188890882 A C SNP - - - - - - - - - - - - - - - tier3 1009 1 0.1 538 214 28.46 NA NA NA 344551 TCGA-AB-2905 AML12 1 193298334 193298334 A T SNP - - - - - - - - - - - - - - - tier3 532 1 0.19 552 212 27.75 NA NA NA 344551 TCGA-AB-2905 AML12 1 200043815 200043815 C G SNP NAV1 NM_020443.3 human genbank 54_36p 1 reviewed missense c.3751 p.P1251A 1 NULL "HMMSmart_AAA,PatternScan_PPASE,superfamily_SSF52540" - no_errors tier1 1948 0 728 339 31.71 NA NA NA 344551 TCGA-AB-2905 AML12 1 207643607 207643607 A T SNP LOC642587 NM_001104548.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25659 NULL 0 - - - no_errors tier3 2680 3 0.11 1558 724 31.71 NA NA NA 344551 TCGA-AB-2905 AML12 1 214818664 214818664 A G SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.590-10601 e4-10601 0.003 - - - no_errors tier3 636 2 0.31 513 221 30.11 NA NA NA 344551 TCGA-AB-2905 AML12 1 216678676 216678676 A G SNP TGFB2 NM_003238.1 human genbank 54_36p 1 validated intronic c.1086+1215 e6+1215 0.003 - - - no_errors tier3 846 0 0 480 213 30.74 NA NA NA 344551 TCGA-AB-2905 AML12 1 235389716 235389716 T C SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.49-110704 e2-110704 0.006 - - - no_errors tier3 1182 4 0.34 677 300 30.71 NA NA NA 344551 TCGA-AB-2905 AML12 2 4132868 4132868 G A SNP - - - - - - - - - - - - - - - tier3 2175 3 0.14 2242 1010 31.05 NA NA NA 344551 TCGA-AB-2905 AML12 2 6912490 6912490 G C SNP CMPK2 NM_207315.2 human genbank 54_36p -1 validated intronic c.993-3225 e4-3225 0.002 - - - no_errors tier2 1246 0 0 749 320 29.91 NA NA NA 344551 TCGA-AB-2905 AML12 2 7693009 7693009 C T SNP - - - - - - - - - - - - - - - tier3 1149 1 0.09 728 306 29.59 NA NA NA 344551 TCGA-AB-2905 AML12 2 11180520 11180520 C T SNP FLJ33534 XR_040331.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.112 - - - no_errors tier3 215 0 0 152 30 16.48 NA NA NA 344551 TCGA-AB-2905 AML12 2 13790728 13790728 C A SNP - - - - - - - - - - - - - - - tier3 178 0 0 158 35 18.13 NA NA NA 344551 TCGA-AB-2905 AML12 2 14501272 14501272 G A SNP - - - - - - - - - - - - - - - tier3 1560 7 0.45 1128 524 31.68 NA NA NA 344551 TCGA-AB-2905 AML12 2 14629670 14629670 T A SNP - - - - - - - - - - - - - - - tier3 1484 1 0.07 1076 495 31.45 NA NA NA 344551 TCGA-AB-2905 AML12 2 17307477 17307477 C T SNP ENSG00000214843 ENST00000399081 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21568 NULL 0 - - - no_coding_region:pseudogene tier3 1306 1 0.08 680 326 32.41 NA NA NA 344551 TCGA-AB-2905 AML12 2 28259904 28259904 G A SNP BRE NM_004899.3 human genbank 54_36p 1 validated intronic c.681-53669 e7-53669 0 - - - no_errors tier2 1854 3 0.16 1503 652 30.26 NA NA NA 344551 TCGA-AB-2905 AML12 2 29491461 29491461 C T SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.1155-31232 e5-31232 0.001 - - - no_errors tier3 879 3 0.34 555 237 29.92 NA NA NA 344551 TCGA-AB-2905 AML12 2 29765515 29765515 C T SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.952+5705 e3+5705 0.347 - - - no_errors tier3 2029 1 0.05 922 413 30.94 NA NA NA 344551 TCGA-AB-2905 AML12 2 29948038 29948038 C A SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.667+48325 e1+48325 0 - - - no_errors tier3 1868 1 0.05 1140 501 30.49 NA NA NA 344551 TCGA-AB-2905 AML12 2 41283150 41283150 C T SNP ENSG00000220937 ENST00000403195 human ensembl 54_36p 1 known 3_prime_flanking_region c.*44954 NULL 0 - - - no_coding_region:pseudogene tier3 875 0 0 667 285 29.94 NA NA NA 344551 TCGA-AB-2905 AML12 2 43933059 43933059 G A SNP ABCG8 NM_022437.2 human genbank 54_36p 1 reviewed missense c.624 p.M208I 0.069 "HMMPfam_ABC_tran,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_ABC_tran,HMMPfam_ABC2_membrane,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1027 0 620 365 37.06 NA NA NA 344551 TCGA-AB-2905 AML12 2 60344262 60344262 G T SNP - - - - - - - - - - - - - - - tier2 1741 6 0.34 1241 551 30.73 NA NA NA 344551 TCGA-AB-2905 AML12 2 65660118 65660118 G C SNP ENSG00000222130 ENST00000410198 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33780 NULL 0.002 - - - no_errors tier3 1350 0 0 697 294 29.67 NA NA NA 344551 TCGA-AB-2905 AML12 2 68852019 68852019 G T SNP ARHGAP25 NM_001007231.1 human genbank 54_36p 1 validated intronic c.62-3838 e2-3838 0.304 - - - no_errors tier3 1148 4 0.35 728 282 27.92 NA NA NA 344551 TCGA-AB-2905 AML12 2 77843623 77843623 G A SNP - - - - - - - - - - - - - - - tier3 273 0 0 307 153 33.19 NA NA NA 344551 TCGA-AB-2905 AML12 2 78797823 78797823 G T SNP - - - - - - - - - - - - - - - tier3 669 1 0.15 570 265 31.66 NA NA NA 344551 TCGA-AB-2905 AML12 2 79629765 79629765 G C SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1+35924 e0+35924 0 - - - no_errors tier3 643 0 0 584 229 28.1 NA NA NA 344551 TCGA-AB-2905 AML12 2 80778660 80778660 A G SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*50152 NULL 0.289 - - - no_errors tier3 1636 1 0.06 812 305 27.28 NA NA NA 344551 TCGA-AB-2905 AML12 2 81848686 81848686 C T SNP - - - - - - - - - - - - - - - tier3 1159 2 0.17 994 467 31.94 NA NA NA 344551 TCGA-AB-2905 AML12 2 88653062 88653062 C G SNP EIF2AK3 NM_004836.4 human genbank 54_36p -1 validated intronic c.2818-1388 e14-1388 0 - - - no_errors tier3 1088 1 0.09 570 276 32.62 NA NA NA 344551 TCGA-AB-2905 AML12 2 102159637 102159637 G A SNP IL1R1 NM_000877.2 human genbank 54_36p 1 reviewed missense c.1696 p.V566M 0 NULL "HMMPfam_TIR,HMMSmart_SM00255,superfamily_Toll/Interleukin receptor TIR domain,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 1704 1 0.06 985 478 32.67 NA NA NA 344551 TCGA-AB-2905 AML12 2 103204230 103204230 A T SNP - - - - - - - - - - - - - - - tier3 954 0 0 622 278 30.89 NA NA NA 344551 TCGA-AB-2905 AML12 2 108022327 108022327 C G SNP SLC5A7 NM_021815.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*28578 NULL 0.002 - - - no_errors tier3 2172 2 0.09 694 315 31.22 NA NA NA 344551 TCGA-AB-2905 AML12 2 115612034 115612034 T C SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.61-171251 e2-171251 0 - - - no_errors tier3 1353 0 0 692 316 31.35 NA NA NA 344551 TCGA-AB-2905 AML12 2 117310688 117310688 T C SNP - - - - - - - - - - - - - - - tier3 527 3 0.56 367 166 31.14 NA NA NA 344551 TCGA-AB-2905 AML12 2 122867435 122867435 G A SNP - - - - - - - - - - - - - - - tier3 2514 0 0 1164 482 29.27 NA NA NA 344551 TCGA-AB-2905 AML12 2 127375071 127375071 C T SNP LOC100128699 XM_001723387.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-18644 NULL 0 - - - no_errors tier3 962 0 0 395 198 33.39 NA NA NA 344551 TCGA-AB-2905 AML12 2 129765725 129765725 A G SNP LOC100131288 XM_001723662.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-9632 NULL 0 - - - no_errors tier3 961 2 0.21 437 213 32.77 NA NA NA 344551 TCGA-AB-2905 AML12 2 140799826 140799826 T C SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated silent c.12315 p.S4105 0.934 "HMMPfam_Ldl_recept_b,HMMSmart_LY,superfamily_SSF63825" "HMMPfam_Ldl_recept_b,HMMSmart_LY,PatternScan_ASX_HYDROXYL,HMMPfam_NHL,HMMSmart_EGF_CA,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_SSF57196,superfamily_SSF63825" - no_errors tier1 1711 2 0.12 1223 492 28.69 NA NA NA 344551 TCGA-AB-2905 AML12 2 142946641 142946641 C T SNP - - - - - - - - - - - - - - - tier3 1638 4 0.24 935 416 30.75 NA NA NA 344551 TCGA-AB-2905 AML12 2 158403328 158403328 C A SNP ACVR1 ENST00000263640 human ensembl 54_36p -1 known intronic c.1-20011 e1-20011 0.996 - - - no_errors tier2 1404 4 0.28 826 422 33.79 NA NA NA 344551 TCGA-AB-2905 AML12 2 162594057 162594057 T C SNP DPP4 NM_001935.3 human genbank 54_36p -1 reviewed intronic c.887+4240 e10+4240 0.961 - - - no_errors tier3 892 0 0 446 164 26.89 NA NA NA 344551 TCGA-AB-2905 AML12 2 171094485 171094485 A C SNP MYO3B NM_138995.1 human genbank 54_36p 1 provisional intronic c.3575+10189 e30+10189 0.008 - - - no_errors tier3 1148 0 0 478 252 34.47 NA NA NA 344551 TCGA-AB-2905 AML12 2 203878706 203878706 A G SNP CYP20A1 NM_177538.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*8830 NULL 0.014 - - - no_errors tier3 693 3 0.43 340 154 31.17 NA NA NA 344551 TCGA-AB-2905 AML12 2 206759047 206759048 - T INS GPR1 NM_001098199.1 human genbank 54_36p -1 validated intronic c.1-8804_8805 e1-8803 0.074:0.067 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 2 208590210 208590210 T G SNP PLEKHM3 ENST00000389247 human ensembl 54_36p -1 known intronic c.1+8148 e0+8148 0 - - - no_stop_codon tier3 2524 1 0.04 1385 626 31.13 NA NA NA 344551 TCGA-AB-2905 AML12 2 213204546 213204546 T A SNP - - - - - - - - - - - - - - - tier3 781 3 0.38 997 490 32.93 NA NA NA 344551 TCGA-AB-2905 AML12 2 214289534 214289534 T A SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1071-145920 e11-145920 0.054 - - - no_errors tier3 541 1 0.18 383 149 28.01 NA NA NA 344551 TCGA-AB-2905 AML12 2 222140254 222140254 C G SNP EPHA4 NM_004438.3 human genbank 54_36p -1 reviewed intronic c.159+1428 e2+1428 0 - - - no_errors tier3 1820 0 0 674 231 25.52 NA NA NA 344551 TCGA-AB-2905 AML12 2 234210397 234210397 C T SNP UGT1A10 NM_019075.2 human genbank 54_36p 1 reviewed missense c.490 p.P164S 0.874 "HMMPfam_UDPGT,superfamily_UDP-Glycosyltransferase/glycogen phosphorylase" "HMMPfam_UDPGT,PatternScan_UDPGT,superfamily_UDP-Glycosyltransferase/glycogen phosphorylase" - no_errors tier1 420 1 0.24 400 176 30.56 NA NA NA 344551 TCGA-AB-2905 AML12 2 237387111 237387111 G T SNP - - - - - - - - - - - - - - - tier3 492 0 0 371 152 29.06 NA NA NA 344551 TCGA-AB-2905 AML12 3 1218861 1218861 G A SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.56-18510 e2-18510 0.003 - - - no_errors tier3 828 0 0 681 281 29.18 NA NA NA 344551 TCGA-AB-2905 AML12 3 4446159 4446159 A G SNP SUMF1 NM_182760.2 human genbank 54_36p -1 validated intronic c.520-9329 e4-9329 0.952 - - - no_errors tier3 785 0 0 589 228 27.87 NA NA NA 344551 TCGA-AB-2905 AML12 3 4855413 4855413 T A SNP ITPR1 NM_001099952.1 human genbank 54_36p 1 validated intronic c.8046+1794 e56+1794 0.003 - - - no_errors tier3 1161 0 0 610 282 31.58 NA NA NA 344551 TCGA-AB-2905 AML12 3 8860327 8860327 C T SNP RAD18 NM_020165.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*37714 NULL 0 - - - no_errors tier3 1301 1 0.08 1188 491 29.24 NA NA NA 344551 TCGA-AB-2905 AML12 3 10879393 10879393 T G SNP SLC6A11 NM_014229.1 human genbank 54_36p 1 provisional intronic c.757-12253 e6-12253 0.002 - - - no_errors tier3 4107 7 0.17 2342 997 29.86 NA NA NA 344551 TCGA-AB-2905 AML12 3 21097283 21097283 G A SNP - - - - - - - - - - - - - - - tier3 479 0 0 386 183 32.16 NA NA NA 344551 TCGA-AB-2905 AML12 3 39800088 39800088 G T SNP MYRIP NM_015460.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-117224 NULL 0.013 - - - no_errors tier3 761 0 0 517 179 25.68 NA NA NA 344551 TCGA-AB-2905 AML12 3 52367898 52367898 G C SNP DNAH1 ENST00000273600 human ensembl 54_36p 1 known intronic c.4266+105 e24+105 0.001 - - - no_errors tier3 642 0 0 297 152 33.85 NA NA NA 344551 TCGA-AB-2905 AML12 3 53488649 53488649 C G SNP CACNA1D NM_000720.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-15585 NULL 0 - - - no_errors tier3 839 5 0.59 585 274 31.9 NA NA NA 344551 TCGA-AB-2905 AML12 3 68884727 68884727 C T SNP FAM19A4 NM_001005527.1 human genbank 54_36p -1 reviewed missense c.263 p.R88Q 1 NULL NULL - no_errors tier1 1486 0 911 438 32.42 NA NA NA 344551 TCGA-AB-2905 AML12 3 72705528 72705528 A G SNP ENSG00000199469 ENST00000362599 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-3004 NULL 0 - - - no_errors tier3 1064 9 0.84 545 223 29.04 NA NA NA 344551 TCGA-AB-2905 AML12 3 77939041 77939041 A T SNP ENSG00000206891 ENST00000384164 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*4541 NULL 1 - - - no_errors tier2 667 1 0.15 456 224 32.94 NA NA NA 344551 TCGA-AB-2905 AML12 3 78758673 78758673 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.3875+488 e25+488 0.004 - - - no_errors tier3 1683 1 0.06 1379 585 29.79 NA NA NA 344551 TCGA-AB-2905 AML12 3 79151890 79151890 A C SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.173-81123 e3-81123 0 - - - no_errors tier3 857 0 0 449 227 33.58 NA NA NA 344551 TCGA-AB-2905 AML12 3 82813147 82813147 G A SNP - - - - - - - - - - - - - - - tier3 625 2 0.32 454 243 34.86 NA NA NA 344551 TCGA-AB-2905 AML12 3 85466972 85466972 A G SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+375463 e1+375463 0 - - - no_errors tier2 341 0 0 248 108 30.34 NA NA NA 344551 TCGA-AB-2905 AML12 3 85905371 85905371 C T SNP CADM2 NM_153184.2 human genbank 54_36p 1 validated intronic c.68-28516 e2-28516 0.002 - - - no_errors tier3 459 0 0 303 142 31.84 NA NA NA 344551 TCGA-AB-2905 AML12 3 86596832 86596832 G A SNP - - - - - - - - - - - - - - - tier3 205 1 0.49 295 91 23.58 NA NA NA 344551 TCGA-AB-2905 AML12 3 98508751 98508751 G A SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.1606+62930 e5+62930 0.01 - - - no_errors tier3 925 1 0.11 905 395 29.61 NA NA NA 344551 TCGA-AB-2905 AML12 3 100683187 100683187 T G SNP - - - - - - - - - - - - - - - tier3 1116 2 0.18 842 383 31.24 NA NA NA 344551 TCGA-AB-2905 AML12 3 104439625 104439625 C A SNP ENSG00000198957 ENST00000362039 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2898 NULL 0.004 - - - no_coding_region:pseudogene tier3 657 0 0 616 244 28.34 NA NA NA 344551 TCGA-AB-2905 AML12 3 111881739 111881739 T A SNP ENSG00000201426 ENST00000364556 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46819 NULL 0.002 - - - no_errors tier3 367 0 0 426 185 30.28 NA NA NA 344551 TCGA-AB-2905 AML12 3 112975060 112975060 C T SNP PLCXD2 NM_153268.1 human genbank 54_36p 1 validated intronic c.866+59395 e3+59395 0 - - - no_errors tier3 762 2 0.26 514 232 31.1 NA NA NA 344551 TCGA-AB-2905 AML12 3 121401930 121401930 C T SNP GPR156 NM_153002.1 human genbank 54_36p -1 provisional intronic c.234-6969 e3-6969 0.027 - - - no_errors tier3 600 0 0 769 357 31.65 NA NA NA 344551 TCGA-AB-2905 AML12 3 128896697 128896697 C T SNP MGLL NM_007283.1 human genbank 54_36p -1 validated silent c.627 p.L209 0.991 "HMMPfam_Abhydrolase_1,superfamily_SSF53474" "HMMPfam_Abhydrolase_1,PatternScan_LIPASE_SER,superfamily_SSF53474" - no_errors tier1 768 0 414 180 30.3 NA NA NA 344551 TCGA-AB-2905 AML12 3 133782432 133782432 G A SNP ACAD11 NM_032169.4 human genbank 54_36p -1 validated intronic c.1622-1340 e14-1340 0 - - - no_errors tier2 737 2 0.27 480 169 26.04 NA NA NA 344551 TCGA-AB-2905 AML12 3 137054156 137054156 C T SNP - - - - - - - - - - - - - - - tier3 2374 2 0.08 1406 683 32.68 NA NA NA 344551 TCGA-AB-2905 AML12 3 138408895 138408895 T C SNP - - - - - - - - - - - - - - - tier3 1354 1 0.07 692 330 32.29 NA NA NA 344551 TCGA-AB-2905 AML12 3 142761810 142761810 T C SNP RASA2 NM_006506.2 human genbank 54_36p 1 reviewed intronic c.863+283 e9+283 0.001 - - - no_errors tier3 690 4 0.58 557 219 28.19 NA NA NA 344551 TCGA-AB-2905 AML12 3 155585310 155585310 A T SNP GPR149 NM_001038705.1 human genbank 54_36p -1 provisional intronic c.1623+36212 e3+36212 0.001 - - - no_errors tier3 1519 1 0.07 1021 473 31.66 NA NA NA 344551 TCGA-AB-2905 AML12 3 159302639 159302639 T C SNP SHOX2 NM_003030.3 human genbank 54_36p -1 reviewed intronic c.168+522 e1+522 1 - - - no_errors tier2 1398 3 0.21 924 446 32.53 NA NA NA 344551 TCGA-AB-2905 AML12 3 163977359 163977359 A C SNP - - - - - - - - - - - - - - - tier3 536 0 0 363 184 33.64 NA NA NA 344551 TCGA-AB-2905 AML12 3 166732768 166732768 C T SNP - - - - - - - - - - - - - - - tier3 840 0 0 663 295 30.76 NA NA NA 344551 TCGA-AB-2905 AML12 3 168053097 168053097 A T SNP ENSG00000185790 ENST00000331839 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41027 NULL 0 - - - no_coding_region:pseudogene tier3 1086 1 0.09 652 293 30.97 NA NA NA 344551 TCGA-AB-2905 AML12 3 191993988 191993988 C G SNP LOC100130481 XM_001726752.1 human genbank 54_36p 1 model intronic c.608-16297 e6-16297 0.27 - - - no_errors tier3 785 0 0 463 191 29.2 NA NA NA 344551 TCGA-AB-2905 AML12 4 18022446 18022446 A G SNP - - - - - - - - - - - - - - - tier3 2958 5 0.17 1266 561 30.71 NA NA NA 344551 TCGA-AB-2905 AML12 4 30307137 30307137 A T SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25006 NULL 0 - - - no_errors tier3 1303 1 0.08 751 309 29.15 NA NA NA 344551 TCGA-AB-2905 AML12 4 31270458 31270458 G A SNP - - - - - - - - - - - - - - - tier3 796 0 0 451 215 32.28 NA NA NA 344551 TCGA-AB-2905 AML12 4 34212163 34212163 G T SNP LOC727819 XM_001125877.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-8793 NULL 0 - - - no_errors tier3 793 2 0.25 526 253 32.48 NA NA NA 344551 TCGA-AB-2905 AML12 4 38187783 38187783 A G SNP ENSG00000211560 ENST00000390134 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*1632 NULL 0.001 - - - no_errors tier3 1968 1 0.05 1002 451 31.04 NA NA NA 344551 TCGA-AB-2905 AML12 4 41125911 41125911 T G SNP LIMCH1 NM_014988.1 human genbank 54_36p 1 validated intronic c.97-65399 e2-65399 0.788 - - - no_errors tier2 1469 1 0.07 738 344 31.65 NA NA NA 344551 TCGA-AB-2905 AML12 4 42669318 42669318 T C SNP GRXCR1 NM_001080476.1 human genbank 54_36p 1 inferred intronic c.627+9410 e2+9410 0 - - - no_errors tier3 672 1 0.15 522 274 34.42 NA NA NA 344551 TCGA-AB-2905 AML12 4 43462705 43462705 C A SNP - - - - - - - - - - - - - - - tier3 1171 5 0.43 801 325 28.86 NA NA NA 344551 TCGA-AB-2905 AML12 4 43787432 43787432 G C SNP - - - - - - - - - - - - - - - tier3 580 1 0.17 485 238 32.87 NA NA NA 344551 TCGA-AB-2905 AML12 4 70818434 70818434 G A SNP CSN1S1 NM_001890.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14429 NULL 0.001 - - - no_errors tier3 1212 7 0.57 962 386 28.64 NA NA NA 344551 TCGA-AB-2905 AML12 4 85264030 85264030 C G SNP - - - - - - - - - - - - - - - tier3 588 12 2 728 373 33.88 NA NA NA 344551 TCGA-AB-2905 AML12 4 88640095 88640095 G A SNP SPARCL1 NM_004684.1 human genbank 54_36p -1 validated intronic c.1-334 e1-334 0.044 - - - no_errors tier3 1469 0 0 1093 468 29.98 NA NA NA 344551 TCGA-AB-2905 AML12 4 95120048 95120048 T C SNP - - - - - - - - - - - - - - - tier3 890 0 0 621 273 30.47 NA NA NA 344551 TCGA-AB-2905 AML12 4 100911881 100911881 T A SNP DAPP1 ENST00000296414 human ensembl 54_36p 1 known 5_prime_flanking_region c.-45213 NULL 0.008 - - - no_errors tier3 540 0 0 551 238 30.16 NA NA NA 344551 TCGA-AB-2905 AML12 4 108173229 108173229 C T SNP DKK2 NM_014421.2 human genbank 54_36p -1 reviewed intronic c.222+2747 e1+2747 0.014 - - - no_errors tier3 917 0 0 635 281 30.64 NA NA NA 344551 TCGA-AB-2905 AML12 4 122201273 122201273 A G SNP C4orf31 NM_024574.3 human genbank 54_36p -1 validated intronic c.1+11325 e0+11325 0.253 - - - no_errors tier3 688 0 0 350 168 32.43 NA NA NA 344551 TCGA-AB-2905 AML12 4 128090070 128090070 T A SNP - - - - - - - - - - - - - - - tier3 1151 0 0 815 378 31.66 NA NA NA 344551 TCGA-AB-2905 AML12 4 135006281 135006281 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 4 136239164 136239164 T C SNP LOC729551 XM_001130594.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*1018 NULL 0.001 - - - no_errors tier3 759 0 0 703 215 23.42 NA NA NA 344551 TCGA-AB-2905 AML12 4 147276823 147276823 A G SNP LSM6 NM_007080.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46701 NULL 0.001 - - - no_errors tier3 1184 8 0.67 610 261 29.97 NA NA NA 344551 TCGA-AB-2905 AML12 4 153752456 153752456 T G SNP TMEM154 NM_152680.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*16692 NULL 0.002 - - - no_errors tier3 1602 1 0.06 995 409 28.93 NA NA NA 344551 TCGA-AB-2905 AML12 4 155677932 155677932 C T SNP PLRG1 NM_002669.2 human genbank 54_36p -1 provisional missense c.1441 p.E481K 1 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 1182 4 0.34 688 328 32.28 NA NA NA 344551 TCGA-AB-2905 AML12 4 166751336 166751336 T C SNP - - - - - - - - - - - - - - - tier3 1120 10 0.88 795 331 29.4 NA NA NA 344551 TCGA-AB-2905 AML12 4 173645778 173645778 T C SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.553+139363 e4+139363 0 - - - no_errors tier3 650 0 0 516 172 24.96 NA NA NA 344551 TCGA-AB-2905 AML12 4 185117520 185117520 C G SNP STOX2 NM_020225.1 human genbank 54_36p 1 provisional intronic c.167-41952 e2-41952 0.014 - - - no_errors tier3 618 0 0 339 118 25.82 NA NA NA 344551 TCGA-AB-2905 AML12 4 186250361 186250361 C T SNP ENSG00000222556 ENST00000410624 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19004 NULL 0.001 - - - no_errors tier3 371 0 0 208 106 33.76 NA NA NA 344551 TCGA-AB-2905 AML12 4 188407031 188407031 G A SNP - - - - - - - - - - - - - - - tier2 801 3 0.37 635 263 29.25 NA NA NA 344551 TCGA-AB-2905 AML12 4 189546172 189546172 T C SNP LOC152663 XM_087499.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-38000 NULL 0.992 - - - pseudogene tier3 1342 1 0.07 711 316 30.77 NA NA NA 344551 TCGA-AB-2905 AML12 4 189710566 189710566 C T SNP - - - - - - - - - - - - - - - tier3 287 1 0.35 336 144 30 NA NA NA 344551 TCGA-AB-2905 AML12 5 4534246 4534246 T C SNP - - - - - - - - - - - - - - - tier2 1074 1 0.09 819 402 32.9 NA NA NA 344551 TCGA-AB-2905 AML12 5 9882399 9882399 A G SNP LOC100134212 XM_001714259.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*25643 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 789 0 0 606 219 26.55 NA NA NA 344551 TCGA-AB-2905 AML12 5 10284224 10284224 C T SNP FAM173B NM_199133.2 human genbank 54_36p -1 validated intronic c.496-3465 e5-3465 0.019 - - - no_errors tier3 1023 3 0.29 510 246 32.5 NA NA NA 344551 TCGA-AB-2905 AML12 5 11631195 11631196 - T INS CTNND2 NM_001332.2 human genbank 54_36p -1 validated intronic c.175-13028_175-13027 e3-13027 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 5 16484517 16484517 A T SNP FAM134B NM_001034850.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*43333 NULL 0.003 - - - no_errors tier3 609 3 0.49 313 143 31.36 NA NA NA 344551 TCGA-AB-2905 AML12 5 21585471 21585471 A G SNP LOC100132788 XM_001722155.1 human genbank 54_36p 1 model intronic c.124+47779 e1+47779 0.01 - - - no_errors tier3 906 0 0 784 207 20.89 NA NA NA 344551 TCGA-AB-2905 AML12 5 22581023 22581023 G C SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-39793 e1-39793 0.01 - - - no_errors tier3 785 2 0.25 550 258 31.93 NA NA NA 344551 TCGA-AB-2905 AML12 5 25277881 25277881 A T SNP LOC100133786 XM_001716394.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*26916 NULL 0.998 - - - no_start_codon:pseudogene:no_stop_codon tier2 1088 1 0.09 552 263 32.27 NA NA NA 344551 TCGA-AB-2905 AML12 5 29076636 29076636 C T SNP - - - - - - - - - - - - - - - tier3 569 4 0.7 380 165 30.22 NA NA NA 344551 TCGA-AB-2905 AML12 5 66595758 66595758 A G SNP - - - - - - - - - - - - - - - tier2 2104 0 0 1201 605 33.48 NA NA NA 344551 TCGA-AB-2905 AML12 5 71517915 71517915 G T SNP MAP1B NM_005909.3 human genbank 54_36p 1 validated intronic c.370-282 e4-282 0.029 - - - no_errors tier3 1559 3 0.19 703 331 32.01 NA NA NA 344551 TCGA-AB-2905 AML12 5 79581859 79581859 C T SNP SERINC5 NM_178276.4 human genbank 54_36p -1 validated intronic c.27+5612 e1+5612 0 - - - no_errors tier3 1548 12 0.77 785 349 30.75 NA NA NA 344551 TCGA-AB-2905 AML12 5 83211965 83211965 T A SNP - - - - - - - - - - - - - - - tier2 206 0 0 190 93 32.86 NA NA NA 344551 TCGA-AB-2905 AML12 5 87729608 87729608 G A SNP ENSG00000206958 ENST00000384231 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*15128 NULL 0.136 - - - no_errors tier2 695 1 0.14 304 132 30.28 NA NA NA 344551 TCGA-AB-2905 AML12 5 92816665 92816665 G C SNP - - - - - - - - - - - - - - - tier3 1000 6 0.6 623 290 31.73 NA NA NA 344551 TCGA-AB-2905 AML12 5 99140687 99140687 G A SNP - - - - - - - - - - - - - - - tier3 443 0 0 461 137 22.91 NA NA NA 344551 TCGA-AB-2905 AML12 5 101016546 101016546 C T SNP - - - - - - - - - - - - - - - tier3 883 0 0 527 229 30.29 NA NA NA 344551 TCGA-AB-2905 AML12 5 105268966 105268966 T A SNP ENSG00000201790 ENST00000364920 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17628 NULL 0.003 - - - no_errors tier2 804 3 0.37 781 334 29.96 NA NA NA 344551 TCGA-AB-2905 AML12 5 105703687 105703687 C T SNP - - - - - - - - - - - - - - - tier3 508 0 0 377 162 30.06 NA NA NA 344551 TCGA-AB-2905 AML12 5 110358685 110358685 G A SNP - - - - - - - - - - - - - - - tier3 1003 2 0.2 1071 469 30.43 NA NA NA 344551 TCGA-AB-2905 AML12 5 116192440 116192440 C T SNP - - - - - - - - - - - - - - - tier2 263 0 0 229 83 26.6 NA NA NA 344551 TCGA-AB-2905 AML12 5 116344440 116344440 C G SNP - - - - - - - - - - - - - - - tier3 891 1 0.11 553 218 28.27 NA NA NA 344551 TCGA-AB-2905 AML12 5 120420980 120420980 C A SNP ENSG00000208998 ENST00000386263 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*26130 NULL 0 - - - pseudogene tier3 2240 2 0.09 1336 627 31.83 NA NA NA 344551 TCGA-AB-2905 AML12 5 125302232 125302232 C A SNP - - - - - - - - - - - - - - - tier3 737 0 0 604 252 29.37 NA NA NA 344551 TCGA-AB-2905 AML12 5 132962209 132962209 G C SNP FSTL4 NM_015082.1 human genbank 54_36p -1 validated intronic c.126+5239 e1+5239 0.001 - - - no_errors tier3 887 0 0 466 229 32.95 NA NA NA 344551 TCGA-AB-2905 AML12 5 137852266 137852266 G A SNP EGR1 NM_001964.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*20597 NULL 0.101 - - - no_errors tier3 1425 5 0.35 520 194 27.17 NA NA NA 344551 TCGA-AB-2905 AML12 5 148150119 148150119 C T SNP ADRB2 NM_000024.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36469 NULL 0.002 - - - no_errors tier3 1054 1 0.09 554 295 34.67 NA NA NA 344551 TCGA-AB-2905 AML12 5 149338005 149338005 T C SNP SLC26A2 NM_000112.3 human genbank 54_36p 1 reviewed silent c.597 p.N199 0.008 NULL "HMMPfam_STAS,superfamily_STAS,HMMPfam_Sulfate_transp,PatternScan_SLC26A" - no_errors tier1 1500 0 675 303 30.98 NA NA NA 344551 TCGA-AB-2905 AML12 5 150920232 150920232 G A SNP FAT2 NM_001447.2 human genbank 54_36p -1 reviewed intronic c.3574+2847 e2+2847 0 - - - no_errors tier3 915 1 0.11 454 188 29.24 NA NA NA 344551 TCGA-AB-2905 AML12 5 160150963 160150963 G C SNP ATP10B NM_025153.2 human genbank 54_36p -1 validated intronic c.1-5575 e1-5575 0.001 - - - no_errors tier3 2157 0 0 961 436 31.19 NA NA NA 344551 TCGA-AB-2905 AML12 5 163831957 163831957 T G SNP - - - - - - - - - - - - - - - tier3 850 1 0.12 450 189 29.58 NA NA NA 344551 TCGA-AB-2905 AML12 5 167354473 167354473 T A SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.1186+1708 e5+1708 0 - - - no_errors tier3 1310 2 0.15 1067 457 29.95 NA NA NA 344551 TCGA-AB-2905 AML12 5 168422609 168422609 C T SNP SLIT3 NM_003062.2 human genbank 54_36p -1 validated intronic c.413+130452 e4+130452 0 - - - no_errors tier3 937 3 0.32 498 253 33.64 NA NA NA 344551 TCGA-AB-2905 AML12 5 172179115 172179115 G A SNP DUSP1 NM_004417.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-48554 NULL 0 - - - no_errors tier3 1851 1 0.05 1245 467 27.25 NA NA NA 344551 TCGA-AB-2905 AML12 5 174093014 174093014 C T SNP MSX2 NM_002449.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*3822 NULL 1 - - - no_errors tier2 2117 18 0.84 378 162 29.94 NA NA NA 344551 TCGA-AB-2905 AML12 6 3274382 3274382 C T SNP SLC22A23 NM_021945.1 human genbank 54_36p -1 validated intronic c.71-5147 e2-5147 0.001 - - - no_errors tier3 1758 0 0 886 356 28.64 NA NA NA 344551 TCGA-AB-2905 AML12 6 8174246 8174246 G A SNP - - - - - - - - - - - - - - - tier3 1007 0 0 774 368 32.22 NA NA NA 344551 TCGA-AB-2905 AML12 6 21224462 21224462 C T SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated intronic c.1299+7789 e11+7789 0 - - - no_errors tier3 1521 2 0.13 1132 484 29.95 NA NA NA 344551 TCGA-AB-2905 AML12 6 65865110 65865110 C T SNP LOC727977 XM_001126270.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-29514 NULL 0.079 - - - no_errors tier3 483 0 0 519 200 27.82 NA NA NA 344551 TCGA-AB-2905 AML12 6 92987974 92987974 T C SNP - - - - - - - - - - - - - - - tier3 775 0 0 792 319 28.69 NA NA NA 344551 TCGA-AB-2905 AML12 6 94380928 94380928 C A SNP - - - - - - - - - - - - - - - tier3 701 1 0.14 577 222 27.75 NA NA NA 344551 TCGA-AB-2905 AML12 6 95363443 95363443 C T SNP - - - - - - - - - - - - - - - tier3 546 0 0 430 164 27.56 NA NA NA 344551 TCGA-AB-2905 AML12 6 116928255 116928255 G A SNP BET3L ENST00000368602 human ensembl 54_36p -1 known intronic c.426+82 e4+82 0 - - - no_errors tier3 199 0 0 243 101 29.36 NA NA NA 344551 TCGA-AB-2905 AML12 6 118646009 118646009 A C SNP SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated intronic c.350-17356 e3-17356 0.011 - - - no_errors tier3 741 0 0 545 249 31.36 NA NA NA 344551 TCGA-AB-2905 AML12 6 118774461 118774461 C G SNP SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*32353 NULL 0.001 - - - no_errors tier3 1052 0 0 799 374 31.88 NA NA NA 344551 TCGA-AB-2905 AML12 6 121955894 121955894 A G SNP ENSG00000222659 ENST00000410727 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12528 NULL 0.994 - - - no_errors tier2 2273 1 0.04 1480 834 36.03 NA NA NA 344551 TCGA-AB-2905 AML12 6 132333075 132333075 T A SNP LOC100131774 XM_001717693.1 human genbank 54_36p 1 model intronic c.787+18988 e2+18988 0.001 - - - no_errors tier3 521 0 0 351 159 31.12 NA NA NA 344551 TCGA-AB-2905 AML12 6 138376930 138376930 G C SNP ENSG00000219463 ENST00000403415 human ensembl 54_36p 1 known 3_prime_flanking_region c.*17953 NULL 0 - - - no_coding_region:pseudogene tier3 1923 2 0.1 1121 434 27.89 NA NA NA 344551 TCGA-AB-2905 AML12 6 139593445 139593445 G - DEL HECA NM_016217.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*53510 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 6 158731161 158731161 G C SNP TULP4 NM_020245.1 human genbank 54_36p 1 validated intronic c.253-22924 e2-22924 0 - - - no_errors tier3 693 0 0 591 299 33.6 NA NA NA 344551 TCGA-AB-2905 AML12 6 161892001 161892001 C T SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.934-1976 e9-1976 0.001 - - - no_errors tier3 2746 1 0.04 1894 766 28.79 NA NA NA 344551 TCGA-AB-2905 AML12 6 168184756 168184756 C T SNP KIF25 NM_030615.3 human genbank 54_36p 1 reviewed intronic c.647-742 e6-742 0.001 - - - no_errors tier3 521 2 0.38 268 127 32.15 NA NA NA 344551 TCGA-AB-2905 AML12 7 2730040 2730040 C T SNP LOC100134041 XM_001720931.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-8975 NULL 0.006 - - - pseudogene:no_stop_codon tier3 717 1 0.14 260 122 31.94 NA NA NA 344551 TCGA-AB-2905 AML12 7 9615893 9615893 G A SNP PER4 NR_002790.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-24532 NULL 0.001 - - - pseudogene tier3 798 7 0.87 368 174 32.1 NA NA NA 344551 TCGA-AB-2905 AML12 7 29437777 29437777 C G SNP CHN2 NM_004067.1 human genbank 54_36p 1 reviewed intronic c.576+30808 e6+30808 0 - - - no_errors tier3 989 0 0 544 261 32.42 NA NA NA 344551 TCGA-AB-2905 AML12 7 34495541 34495541 C T SNP ENSG00000197085 ENST00000357959 human ensembl 54_36p -1 known intronic c.189-71732 e4-71732 0.004 - - - no_errors tier3 2825 7 0.25 2118 1086 33.87 NA NA NA 344551 TCGA-AB-2905 AML12 7 42751484 42751484 G A SNP LOC100134743 XM_001726727.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*8068 NULL 0 - - - no_start_codon:no_stop_codon tier3 1411 8 0.56 1005 400 28.47 NA NA NA 344551 TCGA-AB-2905 AML12 7 51835107 51835107 G A SNP - - - - - - - - - - - - - - - tier3 410 0 0 374 135 26.52 NA NA NA 344551 TCGA-AB-2905 AML12 7 52465103 52465103 G A SNP - - - - - - - - - - - - - - - tier3 699 0 0 546 299 35.38 NA NA NA 344551 TCGA-AB-2905 AML12 7 67864465 67864465 G T SNP ENSG00000222428 ENST00000410496 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-37495 NULL 0.005 - - - no_errors tier3 241 1 0.41 164 63 27.75 NA NA NA 344551 TCGA-AB-2905 AML12 7 70760090 70760090 G T SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.1081-8242 e7-8242 0.002 - - - no_errors tier2 2385 10 0.42 1494 683 31.36 NA NA NA 344551 TCGA-AB-2905 AML12 7 78835326 78835326 T C SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.301+84946 e1+84946 0.044 - - - no_errors tier3 902 1 0.11 890 460 34.05 NA NA NA 344551 TCGA-AB-2905 AML12 7 88138328 88138328 C T SNP ENSG00000211518 ENST00000390184 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*30451 NULL 0 - - - no_errors tier3 909 2 0.22 723 321 30.72 NA NA NA 344551 TCGA-AB-2905 AML12 7 95048711 95048711 T G SNP ASB4 NM_016116.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*43704 NULL 0 - - - no_errors tier3 1065 1 0.09 687 325 32.08 NA NA NA 344551 TCGA-AB-2905 AML12 7 118574542 118574542 G A SNP - - - - - - - - - - - - - - - tier3 737 0 0 597 212 26.17 NA NA NA 344551 TCGA-AB-2905 AML12 7 119109305 119109305 T C SNP - - - - - - - - - - - - - - - tier3 1042 3 0.29 815 371 31.28 NA NA NA 344551 TCGA-AB-2905 AML12 7 119479263 119479263 G A SNP ENSG00000194647 ENST00000350695 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45872 NULL 0.032 - - - no_errors tier2 393 2 0.51 232 120 34.09 NA NA NA 344551 TCGA-AB-2905 AML12 7 120213557 120213557 G A SNP KCND2 NM_012281.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*38409 NULL 0.003 - - - no_errors tier3 1631 2 0.12 1745 731 29.51 NA NA NA 344551 TCGA-AB-2905 AML12 7 121779850 121779850 C A SNP CADPS2 NM_017954.2 human genbank 54_36p -1 validated intronic c.3505-6879 e28-6879 0 - - - no_errors tier3 983 0 0 750 309 29.18 NA NA NA 344551 TCGA-AB-2905 AML12 7 127366497 127366497 G A SNP SND1 NM_014390.2 human genbank 54_36p 1 validated intronic c.1669+9879 e15+9879 0.001 - - - no_errors tier3 2312 2 0.09 1302 524 28.68 NA NA NA 344551 TCGA-AB-2905 AML12 7 129632066 129632066 T G SNP TMEM209 NM_032842.3 human genbank 54_36p -1 validated intronic c.3+383 e1+383 0 - - - no_errors tier2 649 2 0.31 443 207 31.85 NA NA NA 344551 TCGA-AB-2905 AML12 7 138296839 138296839 T A SNP KIAA1549 NM_020910.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42078 NULL 0 - - - no_errors tier3 1314 2 0.15 739 272 26.82 NA NA NA 344551 TCGA-AB-2905 AML12 7 152332275 152332275 G A SNP - - - - - - - - - - - - - - - tier2 1060 0 0 609 321 34.44 NA NA NA 344551 TCGA-AB-2905 AML12 7 157539734 157539734 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1723+27017 e11+27017 0 - - - no_errors tier3 1762 0 0 779 447 36.46 NA NA NA 344551 TCGA-AB-2905 AML12 7 157836885 157836885 G A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.164-34500 e3-34500 0.001 - - - no_errors tier2 360 0 0 171 76 30.77 NA NA NA 344551 TCGA-AB-2905 AML12 8 2945408 2945408 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.6954-3442 e48-3442 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 339 0 0 254 164 39.23 NA NA NA 344551 TCGA-AB-2905 AML12 8 2987460 2987460 C - DEL CSMD1 NM_033225.4 human genbank 54_36p -1 validated frame_shift_del c.6179 p.N2061fs 0.975 NULL "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,superfamily_Complement control module/SCR domain" - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 8 13829662 13829662 G A SNP - - - - - - - - - - - - - - - tier3 630 0 0 455 223 32.89 NA NA NA 344551 TCGA-AB-2905 AML12 8 14754649 14754649 T A SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.40-297843 e2-297843 0.02 - - - no_errors tier3 966 3 0.31 1112 530 32.28 NA NA NA 344551 TCGA-AB-2905 AML12 8 14784451 14784451 C G SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.40-327645 e2-327645 0.001 - - - no_errors tier3 1183 1 0.08 894 373 29.39 NA NA NA 344551 TCGA-AB-2905 AML12 8 18096760 18096760 G A SNP NAT1 NM_000662.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27077 NULL 0.004 - - - no_errors tier3 1236 1 0.08 744 390 34.39 NA NA NA 344551 TCGA-AB-2905 AML12 8 26507555 26507555 T C SNP DPYSL2 NM_001386.4 human genbank 54_36p 1 validated intronic c.313+10139 e3+10139 0 - - - no_errors tier3 1591 0 0 778 331 29.82 NA NA NA 344551 TCGA-AB-2905 AML12 8 26507578 26507578 G C SNP DPYSL2 NM_001386.4 human genbank 54_36p 1 validated intronic c.313+10162 e3+10162 0.003 - - - no_errors tier2 1542 0 0 773 329 29.85 NA NA NA 344551 TCGA-AB-2905 AML12 8 34237282 34237282 A G SNP - - - - - - - - - - - - - - - tier2 590 0 0 462 182 28.17 NA NA NA 344551 TCGA-AB-2905 AML12 8 36346779 36346779 T C SNP - - - - - - - - - - - - - - - tier3 1026 2 0.19 899 408 31.19 NA NA NA 344551 TCGA-AB-2905 AML12 8 42647819 42647819 A C SNP CHRNB3 NM_000749.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-24028 NULL 0.021 - - - no_errors tier3 990 1 0.1 532 223 29.5 NA NA NA 344551 TCGA-AB-2905 AML12 8 55945006 55945006 G A SNP - - - - - - - - - - - - - - - tier2 1416 1 0.07 1041 400 27.76 NA NA NA 344551 TCGA-AB-2905 AML12 8 76293948 76293948 A C SNP - - - - - - - - - - - - - - - tier3 1386 1 0.07 1225 489 28.5 NA NA NA 344551 TCGA-AB-2905 AML12 8 77509553 77509553 G A SNP - - - - - - - - - - - - - - - tier2 1426 2 0.14 932 398 29.92 NA NA NA 344551 TCGA-AB-2905 AML12 8 85778323 85778323 G T SNP RALYL NM_001100391.1 human genbank 54_36p 1 validated intronic c.296-71046 e3-71046 0.002 - - - no_errors tier3 414 0 0 415 171 29.13 NA NA NA 344551 TCGA-AB-2905 AML12 8 88457864 88457864 A G SNP CNBD1 NM_173538.2 human genbank 54_36p 1 provisional intronic c.1304-6100 e11-6100 0.046 - - - no_errors tier3 940 1 0.11 708 337 32.25 NA NA NA 344551 TCGA-AB-2905 AML12 8 104430932 104430933 - AT INS CTHRC1 NM_138455.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-22129 NULL 0.002:0.006 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 8 108189139 108189139 A G SNP - - - - - - - - - - - - - - - tier3 751 2 0.27 536 228 29.8 NA NA NA 344551 TCGA-AB-2905 AML12 8 109367516 109367516 C A SNP EIF3E NM_001568.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-37409 NULL 0.008 - - - no_errors tier3 834 0 0 574 196 25.45 NA NA NA 344551 TCGA-AB-2905 AML12 8 113324885 113324885 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.10402+914 e65+914 0 - - - no_errors tier3 824 1 0.12 654 289 30.65 NA NA NA 344551 TCGA-AB-2905 AML12 8 115686530 115686530 C T SNP - - - - - - - - - - - - - - - tier3 959 1 0.1 604 311 33.99 NA NA NA 344551 TCGA-AB-2905 AML12 8 125241507 125241507 C T SNP FER1L6 NM_001039112.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*40295 NULL 0 - - - no_errors tier3 1524 0 0 753 399 34.61 NA NA NA 344551 TCGA-AB-2905 AML12 8 133495024 133495024 T C SNP KCNQ3 NM_004519.2 human genbank 54_36p -1 reviewed intronic c.386+66552 e1+66552 0 - - - no_errors tier2 1950 4 0.2 949 454 32.34 NA NA NA 344551 TCGA-AB-2905 AML12 8 139573620 139573620 G A SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.1+4476 e0+4476 0 - - - no_errors tier3 2028 2 0.1 633 256 28.76 NA NA NA 344551 TCGA-AB-2905 AML12 8 142557705 142557705 G A SNP FLJ43860 NM_207414.2 human genbank 54_36p -1 validated intronic c.1242+196 e10+196 0.005 - - - pseudogene tier3 262 0 0 336 175 34.11 NA NA NA 344551 TCGA-AB-2905 AML12 9 3593693 3593693 A G SNP - - - - - - - - - - - - - - - tier2 481 0 0 591 308 34.26 NA NA NA 344551 TCGA-AB-2905 AML12 9 9657396 9657396 G A SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1+67137 e0+67137 0 - - - no_errors tier3 1095 0 0 677 275 28.86 NA NA NA 344551 TCGA-AB-2905 AML12 9 14993246 14993246 G T SNP LOC389705 NR_003920.1 human genbank 54_36p 1 validated intronic c.NULL NULL 0 - - - pseudogene tier3 409 2 0.49 441 233 34.52 NA NA NA 344551 TCGA-AB-2905 AML12 9 18531139 18531139 C T SNP ADAMTSL1 NM_001040272.4 human genbank 54_36p 1 validated intronic c.237+7849 e3+7849 0 - - - no_errors tier3 1999 3 0.15 1257 575 31.37 NA NA NA 344551 TCGA-AB-2905 AML12 9 22026435 22026435 A G SNP CDKN2BAS NR_003529.3 human genbank 54_36p 1 validated intronic c.NULL NULL 0.003 - - - no_errors tier3 1062 0 0 682 308 31.11 NA NA NA 344551 TCGA-AB-2905 AML12 9 22887472 22887472 C T SNP - - - - - - - - - - - - - - - tier3 680 0 0 532 226 29.82 NA NA NA 344551 TCGA-AB-2905 AML12 9 23421604 23421604 G A SNP LOC100131398 XM_001716436.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-29694 NULL 0.998 - - - no_start_codon:pseudogene tier2 1097 1 0.09 684 139 16.89 NA NA NA 344551 TCGA-AB-2905 AML12 9 25881677 25881677 C T SNP - - - - - - - - - - - - - - - tier2 1155 2 0.17 606 320 34.45 NA NA NA 344551 TCGA-AB-2905 AML12 9 26424921 26424921 A C SNP - - - - - - - - - - - - - - - tier3 1074 0 0 1074 382 26.24 NA NA NA 344551 TCGA-AB-2905 AML12 9 29244309 29244309 C G SNP ENSG00000217213 ENST00000406421 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-29244309 NULL 0.137 - - - no_coding_region:pseudogene tier3 1067 0 0 592 220 27.09 NA NA NA 344551 TCGA-AB-2905 AML12 9 30678950 30678950 G A SNP ENSG00000220009 ENST00000405723 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17361 NULL 0.097 - - - no_coding_region:pseudogene tier2 444 0 0 334 130 28.02 NA NA NA 344551 TCGA-AB-2905 AML12 9 34562737 34562737 G A SNP CNTFR NM_001842.3 human genbank 54_36p -1 reviewed intronic c.1-3758 e1-3758 0 - - - no_errors tier3 2258 7 0.31 713 307 30.1 NA NA NA 344551 TCGA-AB-2905 AML12 9 36889849 36889849 C T SNP PAX5 NM_016734.1 human genbank 54_36p -1 reviewed intronic c.911-17747 e8-17747 0.008 - - - no_errors tier2 1782 5 0.28 903 382 29.73 NA NA NA 344551 TCGA-AB-2905 AML12 9 37636250 37636250 C T SNP SHB ENST00000401811 human ensembl 54_36p -1 known intronic c.894+46889 e3+46889 0.001 - - - no_errors tier3 1333 1 0.07 650 290 30.85 NA NA NA 344551 TCGA-AB-2905 AML12 9 85255999 85255999 T C SNP FRMD3 NM_174938.4 human genbank 54_36p -1 validated intronic c.148-61556 e2-61556 0.005 - - - no_errors tier3 872 1 0.11 455 206 31.12 NA NA NA 344551 TCGA-AB-2905 AML12 9 94698049 94698049 A G SNP ZNF484 NM_031486.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-20917 NULL 0 - - - no_errors tier3 503 2 0.4 264 154 36.84 NA NA NA 344551 TCGA-AB-2905 AML12 9 96354955 96354955 A G SNP FBP2 NM_003837.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*6086 NULL 0 - - - no_errors tier3 331 1 0.3 124 48 27.91 NA NA NA 344551 TCGA-AB-2905 AML12 9 103922250 103922250 C A SNP - - - - - - - - - - - - - - - tier3 646 0 0 700 323 31.54 NA NA NA 344551 TCGA-AB-2905 AML12 9 110025416 110025416 C G SNP - - - - - - - - - - - - - - - tier3 884 1 0.11 617 268 30.25 NA NA NA 344551 TCGA-AB-2905 AML12 9 121937589 121937589 G A SNP - - - - - - - - - - - - - - - tier2 1832 8 0.43 765 340 30.77 NA NA NA 344551 TCGA-AB-2905 AML12 9 125393486 125393486 G T SNP DENND1A NM_020946.1 human genbank 54_36p -1 validated intronic c.766-8116 e12-8116 0 - - - no_errors tier3 1294 2 0.15 636 301 32.12 NA NA NA 344551 TCGA-AB-2905 AML12 9 128430253 128430253 C T SNP LMX1B NM_002316.2 human genbank 54_36p 1 validated intronic c.257+12584 e2+12584 0.026 - - - no_errors tier2 1042 0 0 293 150 33.86 NA NA NA 344551 TCGA-AB-2905 AML12 10 9971185 9971185 G A SNP - - - - - - - - - - - - - - - tier3 822 2 0.24 606 280 31.6 NA NA NA 344551 TCGA-AB-2905 AML12 10 10557997 10557997 G A SNP - - - - - - - - - - - - - - - tier3 715 2 0.28 401 198 33.06 NA NA NA 344551 TCGA-AB-2905 AML12 10 13625307 13625307 C T SNP PRPF18 NM_003675.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-43786 NULL 0.001 - - - no_errors tier3 1033 1 0.1 348 161 31.63 NA NA NA 344551 TCGA-AB-2905 AML12 10 21422599 21422599 T C SNP NEBL NM_213569.2 human genbank 54_36p -1 validated intronic c.165-73463 e3-73463 0 - - - no_errors tier3 1653 0 0 1106 521 32 NA NA NA 344551 TCGA-AB-2905 AML12 10 25677059 25677059 C T SNP GPR158 NM_020752.2 human genbank 54_36p 1 validated intronic c.1009-47787 e3-47787 0.024 - - - no_errors tier3 1644 2 0.12 824 370 30.94 NA NA NA 344551 TCGA-AB-2905 AML12 10 27520846 27520846 G A SNP YME1L1 NM_139312.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37701 NULL 0 - - - no_errors tier3 896 2 0.22 570 196 25.59 NA NA NA 344551 TCGA-AB-2905 AML12 10 31400807 31400807 A G SNP ZNF438 ENST00000375311 human ensembl 54_36p -1 known 5_prime_flanking_region c.-222776 NULL 0 - - - no_errors tier2 1303 3 0.23 759 323 29.82 NA NA NA 344551 TCGA-AB-2905 AML12 10 31755532 31755532 C A SNP ZEB1 NM_030751.1 human genbank 54_36p 1 validated intronic c.59-34440 e2-34440 0.472 - - - no_errors tier2 1132 1 0.09 575 273 32.19 NA NA NA 344551 TCGA-AB-2905 AML12 10 34602770 34602770 C T SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional intronic c.3186-3937 e22-3937 0.042 - - - no_errors tier3 773 0 0 622 322 34.11 NA NA NA 344551 TCGA-AB-2905 AML12 10 50304649 50304649 G A SNP LOC100128032 XM_001719050.1 human genbank 54_36p 1 model intronic c.27+7087 e1+7087 0 - - - no_errors tier2 1937 4 0.21 1143 496 30.24 NA NA NA 344551 TCGA-AB-2905 AML12 10 55145508 55145508 C T SNP - - - - - - - - - - - - - - - tier3 611 0 0 478 197 29.14 NA NA NA 344551 TCGA-AB-2905 AML12 10 60720285 60720285 C T SNP FAM13C NM_198215.2 human genbank 54_36p -1 validated intronic c.508-7072 e6-7072 0 - - - no_errors tier3 1182 1 0.08 758 316 29.42 NA NA NA 344551 TCGA-AB-2905 AML12 10 82603853 82603853 G C SNP - - - - - - - - - - - - - - - tier3 604 0 0 571 260 31.18 NA NA NA 344551 TCGA-AB-2905 AML12 10 84893340 84893340 T C SNP - - - - - - - - - - - - - - - tier3 956 0 0 795 352 30.58 NA NA NA 344551 TCGA-AB-2905 AML12 10 86981083 86981083 T C SNP - - - - - - - - - - - - - - - tier3 1510 1 0.07 744 367 33 NA NA NA 344551 TCGA-AB-2905 AML12 10 88595223 88595223 G A SNP BMPR1A NM_004329.2 human genbank 54_36p 1 reviewed intronic c.1+6507 e0+6507 0 - - - no_errors tier3 2360 1 0.04 1567 707 31.01 NA NA NA 344551 TCGA-AB-2905 AML12 10 100806967 100806967 G A SNP HPSE2 NM_021828.3 human genbank 54_36p -1 validated intronic c.610+87018 e3+87018 0 - - - no_errors tier3 392 0 0 441 190 30.11 NA NA NA 344551 TCGA-AB-2905 AML12 10 107713081 107713082 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 10 120677378 120677378 G A SNP LOC729666 XR_015620.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*4216 NULL 0.246 - - - pseudogene tier2 1212 0 0 797 378 32.17 NA NA NA 344551 TCGA-AB-2905 AML12 10 128001862 128001863 - T INS ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed intronic c.186+7108_186+7107 e2+7108 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 10 132077137 132077137 C G SNP - - - - - - - - - - - - - - - tier3 648 0 0 279 117 29.55 NA NA NA 344551 TCGA-AB-2905 AML12 10 134102560 134102560 C T SNP LRRC27 ENST00000368613 human ensembl 54_36p 1 known intronic c.1593-6450 e11-6450 0 - - - no_errors tier2 272 1 0.37 115 65 36.11 NA NA NA 344551 TCGA-AB-2905 AML12 11 1042862 1042862 C T SNP MUC6 NM_005961.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16207 NULL 0 - - - no_errors tier3 305 0 0 135 84 38.36 NA NA NA 344551 TCGA-AB-2905 AML12 11 12618026 12618026 C A SNP TEAD1 NM_021961.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-124375 NULL 0.003 - - - no_errors tier2 227 0 0 56 26 31.71 NA NA NA 344551 TCGA-AB-2905 AML12 11 13224851 13224851 C T SNP ARNTL NM_001030272.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-107581 NULL 0 - - - no_errors tier3 1526 1 0.07 670 280 29.35 NA NA NA 344551 TCGA-AB-2905 AML12 11 15554926 15554926 T A SNP - - - - - - - - - - - - - - - tier3 2584 32 1.22 1123 460 28.99 NA NA NA 344551 TCGA-AB-2905 AML12 11 29919725 29919725 C T SNP - - - - - - - - - - - - - - - tier3 655 2 0.3 470 194 29.22 NA NA NA 344551 TCGA-AB-2905 AML12 11 32374498 32374499 - TCGGGGCTAC INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1130_1129 p.T377fs 0.991:0.888 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 11 38793090 38793090 T A SNP LOC100133559 XM_001719391.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-18685 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 965 0 0 815 367 31.02 NA NA NA 344551 TCGA-AB-2905 AML12 11 46862048 46862048 G A SNP LRP4 NM_002334.2 human genbank 54_36p -1 validated silent c.2562 p.I854 1 "HMMPfam_Ldl_recept_b,HMMSmart_SM00135,superfamily_YWTD domain" "HMMPfam_Ldl_recept_b,HMMSmart_SM00135,PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin,superfamily_YWTD domain" - no_errors tier1 1651 0 826 348 29.57 NA NA NA 344551 TCGA-AB-2905 AML12 11 57645687 57645687 G A SNP OR9Q1 NM_001005212.2 human genbank 54_36p 1 provisional intronic c.1-57792 e1-57792 0.001 - - - no_errors tier3 1437 2 0.14 813 365 30.96 NA NA NA 344551 TCGA-AB-2905 AML12 11 58704284 58704284 G A SNP DTX4 NM_015177.1 human genbank 54_36p 1 validated intronic c.212-1504 e2-1504 0.204 - - - no_errors tier3 1321 0 0 517 221 29.95 NA NA NA 344551 TCGA-AB-2905 AML12 11 71989673 71989673 C T SNP PDE2A NM_002599.1 human genbank 54_36p -1 validated intronic c.324-3362 e5-3362 0.145 - - - no_errors tier3 70 0 0 44 25 36.23 NA NA NA 344551 TCGA-AB-2905 AML12 11 79859135 79859135 C T SNP - - - - - - - - - - - - - - - tier3 622 0 0 534 233 30.38 NA NA NA 344551 TCGA-AB-2905 AML12 11 83458580 83458580 C G SNP DLG2 NM_001364.1 human genbank 54_36p -1 reviewed intronic c.435-10405 e6-10405 0.019 - - - no_errors tier3 1877 1 0.05 1483 658 30.73 NA NA NA 344551 TCGA-AB-2905 AML12 11 96272671 96272671 C T SNP - - - - - - - - - - - - - - - tier3 614 1 0.16 499 220 30.6 NA NA NA 344551 TCGA-AB-2905 AML12 11 99081436 99081436 G A SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.56-114049 e2-114049 0 - - - no_errors tier2 652 0 0 611 263 30.09 NA NA NA 344551 TCGA-AB-2905 AML12 11 103692496 103692496 C T SNP - - - - - - - - - - - - - - - tier3 932 2 0.21 477 172 26.5 NA NA NA 344551 TCGA-AB-2905 AML12 11 114163975 114163975 A G SNP - - - - - - - - - - - - - - - tier3 2071 6 0.29 1025 502 32.83 NA NA NA 344551 TCGA-AB-2905 AML12 11 130970698 130970698 A T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.82+224705 e1+224705 0 - - - no_errors tier3 2246 7 0.31 977 456 31.8 NA NA NA 344551 TCGA-AB-2905 AML12 11 131716418 131716418 G A SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*6168 NULL 0 - - - no_errors tier3 2112 6 0.28 1314 597 31.21 NA NA NA 344551 TCGA-AB-2905 AML12 11 133108319 133108319 C T SNP - - - - - - - - - - - - - - - tier3 1253 2 0.16 338 173 33.86 NA NA NA 344551 TCGA-AB-2905 AML12 12 15448957 15448957 A G SNP PTPRO NM_030667.2 human genbank 54_36p 1 reviewed intronic c.76-79218 e2-79218 0.053 - - - no_errors tier3 662 1 0.15 427 173 28.83 NA NA NA 344551 TCGA-AB-2905 AML12 12 32421790 32421790 G A SNP BICD1 NM_001714.1 human genbank 54_36p 1 reviewed missense c.2890 p.A964T 0.995 NULL HMMPfam_BicD - no_errors tier1 758 2 0.26 430 211 32.87 NA NA NA 344551 TCGA-AB-2905 AML12 12 32443257 32443257 G T SNP ENSG00000207176 ENST00000384447 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2909 NULL 0.003 - - - no_errors tier2 705 3 0.42 462 266 36.54 NA NA NA 344551 TCGA-AB-2905 AML12 12 44113509 44113509 C T SNP ENSG00000213660 ENST00000395478 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-11337 NULL 0.004 - - - no_coding_region:pseudogene tier3 1298 1 0.08 690 305 30.59 NA NA NA 344551 TCGA-AB-2905 AML12 12 50119998 50119998 C T SNP SLC4A8 NM_001039960.1 human genbank 54_36p 1 validated intronic c.49-761 e2-761 0.006 - - - no_errors tier3 1257 0 0 756 302 28.54 NA NA NA 344551 TCGA-AB-2905 AML12 12 52616444 52616444 G A SNP HOXC10 NM_017409.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48867 NULL 1 - - - no_errors tier2 938 0 0 373 126 25.25 NA NA NA 344551 TCGA-AB-2905 AML12 12 60394943 60394943 C T SNP FAM19A2 NM_178539.3 human genbank 54_36p -1 reviewed intronic c.385-4478 e4-4478 0 - - - no_errors tier3 1238 1 0.08 927 393 29.75 NA NA NA 344551 TCGA-AB-2905 AML12 12 61273627 61273627 C T SNP MON2 NM_015026.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*831 NULL 0.412 - - - no_errors tier2 462 0 0 371 160 30.13 NA NA NA 344551 TCGA-AB-2905 AML12 12 79352245 79352245 G T SNP - - - - - - - - - - - - - - - tier3 612 1 0.16 411 183 30.76 NA NA NA 344551 TCGA-AB-2905 AML12 12 85319524 85319524 A T SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+33541 e0+33541 0.015 - - - no_errors tier3 320 0 0 203 110 35.14 NA NA NA 344551 TCGA-AB-2905 AML12 12 86520499 86520499 C T SNP - - - - - - - - - - - - - - - tier3 1419 3 0.21 1126 462 29.06 NA NA NA 344551 TCGA-AB-2905 AML12 12 90817774 90817774 C T SNP - - - - - - - - - - - - - - - tier3 796 3 0.38 560 228 28.93 NA NA NA 344551 TCGA-AB-2905 AML12 12 93670919 93670919 C T SNP - - - - - - - - - - - - - - - tier3 1073 2 0.19 655 285 30.29 NA NA NA 344551 TCGA-AB-2905 AML12 12 96424220 96424220 A G SNP MIRN1251 ENST00000408552 human ensembl 54_36p 1 known 3_prime_flanking_region c.*14333 NULL 0.001 - - - no_errors tier3 336 1 0.3 224 113 33.53 NA NA NA 344551 TCGA-AB-2905 AML12 12 97131587 97131587 C T SNP - - - - - - - - - - - - - - - tier3 1800 0 0 1864 784 29.53 NA NA NA 344551 TCGA-AB-2905 AML12 12 98007986 98007986 C T SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.2527-5054 e16-5054 0.019 - - - no_errors tier3 772 1 0.13 573 221 27.76 NA NA NA 344551 TCGA-AB-2905 AML12 12 102190556 102190556 T C SNP LOC728545 XM_001127727.1 human genbank 54_36p -1 model intronic c.78+1207 e1+1207 0.001 - - - no_errors tier3 1322 0 0 829 334 28.67 NA NA NA 344551 TCGA-AB-2905 AML12 12 102930346 102930346 G A SNP GLT8D2 NM_031302.3 human genbank 54_36p -1 provisional intronic c.112+2575 e2+2575 0.009 - - - no_errors tier3 990 0 0 536 196 26.78 NA NA NA 344551 TCGA-AB-2905 AML12 12 103466731 103466731 A G SNP CHST11 NM_018413.4 human genbank 54_36p 1 provisional intronic c.119-53083 e2-53083 0 - - - no_errors tier3 1329 0 0 550 248 31.08 NA NA NA 344551 TCGA-AB-2905 AML12 12 104643412 104643412 C A SNP - - - - - - - - - - - - - - - tier3 1998 7 0.35 934 373 28.5 NA NA NA 344551 TCGA-AB-2905 AML12 12 116154185 116154185 C T SNP NOS1 NM_000620.2 human genbank 54_36p -1 validated missense c.3370 p.E1124K 1 "HMMPfam_FAD_binding_1,superfamily_Riboflavin synthase domain-like" "HMMPfam_NAD_binding_1,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_FAD_binding_1,HMMPfam_NO_synthase,PatternScan_NOS,superfamily_Nitric oxide (NO) synthase oxygenase domain,HMMPfam_Flavodoxin_1,superfamily_Riboflavin synthase domain-like,superfamily_Flavoproteins,superfamily_Ferredoxin reductase-like C-terminal NADP-linked domain" - no_errors tier1 1929 1 0.05 735 370 33.45 NA NA NA 344551 TCGA-AB-2905 AML12 12 120147084 120147084 A C SNP P2RX4 NM_002560.2 human genbank 54_36p 1 reviewed intronic c.524+1855 e5+1855 0.229 - - - no_errors tier3 1293 5 0.38 525 235 30.88 NA NA NA 344551 TCGA-AB-2905 AML12 12 128473856 128473856 C T SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1116-85541 e4-85541 0.001 - - - no_errors tier3 1098 0 0 616 287 31.78 NA NA NA 344551 TCGA-AB-2905 AML12 12 128545817 128545817 T G SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1115+35740 e3+35740 0.001 - - - no_errors tier2 1400 2 0.14 837 487 36.78 NA NA NA 344551 TCGA-AB-2905 AML12 13 26367947 26367947 C T SNP ENSG00000218019 ENST00000406275 human ensembl 54_36p 1 known 5_prime_flanking_region c.-9552 NULL 0.005 - - - no_coding_region:pseudogene tier3 876 1 0.11 502 260 33.85 NA NA NA 344551 TCGA-AB-2905 AML12 13 31278731 31278731 T A SNP RXFP2 NM_130806.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*4189 NULL 0.004 - - - no_errors tier3 1731 0 0 811 376 31.65 NA NA NA 344551 TCGA-AB-2905 AML12 13 33408467 33408467 G A SNP RFC3 NM_181558.3 human genbank 54_36p 1 reviewed intronic c.880-29757 e9-29757 0 - - - no_errors tier2 679 6 0.88 686 338 33.01 NA NA NA 344551 TCGA-AB-2905 AML12 13 33643794 33643794 G A SNP - - - - - - - - - - - - - - - tier2 1703 3 0.18 1327 573 30.14 NA NA NA 344551 TCGA-AB-2905 AML12 13 38469976 38469976 C A SNP NHLRC3 NM_001012754.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40801 NULL 0.986 - - - no_errors tier2 506 1 0.2 385 168 30.38 NA NA NA 344551 TCGA-AB-2905 AML12 13 46554312 46554312 C T SNP - - - - - - - - - - - - - - - tier2 880 0 0 788 348 30.61 NA NA NA 344551 TCGA-AB-2905 AML12 13 52915342 52915342 G A SNP - - - - - - - - - - - - - - - tier2 860 0 0 481 200 29.37 NA NA NA 344551 TCGA-AB-2905 AML12 13 59884654 59884654 T G SNP TDRD3 ENST00000196169 human ensembl 54_36p 1 known intronic c.1+15509 e0+15509 0 - - - no_errors tier3 608 0 0 473 189 28.55 NA NA NA 344551 TCGA-AB-2905 AML12 13 61493786 61493786 A T SNP - - - - - - - - - - - - - - - tier3 808 0 0 362 157 30.25 NA NA NA 344551 TCGA-AB-2905 AML12 13 65328243 65328243 A - DEL ENSG00000221685 ENST00000408758 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8063 NULL 0.007 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 13 68038546 68038546 G A SNP - - - - - - - - - - - - - - - tier3 696 0 0 327 145 30.72 NA NA NA 344551 TCGA-AB-2905 AML12 13 71747285 71747285 G A SNP - - - - - - - - - - - - - - - tier2 629 0 0 485 215 30.54 NA NA NA 344551 TCGA-AB-2905 AML12 13 74161286 74161286 C T SNP - - - - - - - - - - - - - - - tier3 939 3 0.32 767 342 30.81 NA NA NA 344551 TCGA-AB-2905 AML12 13 75165627 75165627 C T SNP LMO7 NM_005358.5 human genbank 54_36p 1 reviewed intronic c.226-19692 e3-19692 0.001 - - - no_errors tier3 634 1 0.16 416 168 28.57 NA NA NA 344551 TCGA-AB-2905 AML12 13 89531587 89531587 T C SNP - - - - - - - - - - - - - - - tier3 605 1 0.16 348 177 33.71 NA NA NA 344551 TCGA-AB-2905 AML12 13 90297761 90297761 A G SNP - - - - - - - - - - - - - - - tier3 266 0 0 194 66 25.29 NA NA NA 344551 TCGA-AB-2905 AML12 13 106455128 106455128 A T SNP - - - - - - - - - - - - - - - tier3 388 0 0 325 156 32.37 NA NA NA 344551 TCGA-AB-2905 AML12 13 108743013 108743013 C G SNP - - - - - - - - - - - - - - - tier3 980 2 0.2 625 258 29.15 NA NA NA 344551 TCGA-AB-2905 AML12 14 19480317 19480317 G A SNP OR4K15 NM_001005486.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-33201 NULL 0 - - - no_errors tier3 1187 1 0.08 916 205 18.29 NA NA NA 344551 TCGA-AB-2905 AML12 14 20983037 20983037 T C SNP CHD8 NM_020920.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-13222 NULL 0.019 - - - no_errors tier3 1259 0 0 726 347 32.22 NA NA NA 344551 TCGA-AB-2905 AML12 14 21114408 21114408 G A SNP SALL2 NM_005407.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-39513 NULL 0 - - - no_errors tier3 1150 1 0.09 729 322 30.64 NA NA NA 344551 TCGA-AB-2905 AML12 14 23827267 23827267 C T SNP TGM1 NM_000359.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25869 NULL 0.013 - - - no_errors tier3 902 3 0.33 439 186 29.67 NA NA NA 344551 TCGA-AB-2905 AML12 14 28373510 28373510 C T SNP C14orf23 ENST00000399387 human ensembl 54_36p 1 known 3_prime_flanking_region c.*42292 NULL 0 - - - no_errors tier3 706 5 0.7 537 232 30.17 NA NA NA 344551 TCGA-AB-2905 AML12 14 41557034 41557034 G A SNP - - - - - - - - - - - - - - - tier3 973 1 0.1 567 242 29.91 NA NA NA 344551 TCGA-AB-2905 AML12 14 42554999 42554999 T A SNP - - - - - - - - - - - - - - - tier3 582 1 0.17 389 179 31.46 NA NA NA 344551 TCGA-AB-2905 AML12 14 62440915 62440915 G T SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed intronic c.1369+45689 e7+45689 0.024 - - - no_errors tier3 1414 1 0.07 1069 519 32.64 NA NA NA 344551 TCGA-AB-2905 AML12 14 74433131 74433131 G T SNP DLST NM_001933.3 human genbank 54_36p 1 validated intronic c.771-1694 e11-1694 0.802 - - - no_errors tier2 821 1 0.12 485 234 32.5 NA NA NA 344551 TCGA-AB-2905 AML12 14 75302285 75302285 A G SNP TTLL5 NM_015072.3 human genbank 54_36p 1 validated silent c.1836 p.R612 0.056 NULL "HMMPfam_TTL,superfamily_Glutathione synthetase ATP-binding domain-like" - no_errors tier1 936 1 0.11 705 313 30.75 NA NA NA 344551 TCGA-AB-2905 AML12 14 82042253 82042253 G A SNP ENSG00000210376 ENST00000387641 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*43969 NULL 0.011 - - - pseudogene tier3 1089 0 0 712 297 29.38 NA NA NA 344551 TCGA-AB-2905 AML12 14 87302023 87302023 C T SNP - - - - - - - - - - - - - - - tier3 1899 1 0.05 876 428 32.82 NA NA NA 344551 TCGA-AB-2905 AML12 14 94350495 94350495 G A SNP GSC NM_173849.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-44390 NULL 0 - - - no_errors tier3 743 0 0 403 194 32.44 NA NA NA 344551 TCGA-AB-2905 AML12 14 96971346 96971346 G A SNP LOC730217 XM_001132986.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-22083 NULL 0 - - - no_errors tier3 2030 5 0.25 1031 429 29.38 NA NA NA 344551 TCGA-AB-2905 AML12 14 98770569 98770569 G A SNP BCL11B NM_138576.1 human genbank 54_36p -1 reviewed intronic c.428-2922 e3-2922 0 - - - no_errors tier2 1954 1 0.05 758 299 28.23 NA NA NA 344551 TCGA-AB-2905 AML12 15 23817243 23817243 G C SNP ENSG00000206187 ENST00000383019 human ensembl 54_36p 1 known intronic c.396+4982 e2+4982 0.017 - - - no_errors tier3 1093 1 0.09 624 294 32.03 NA NA NA 344551 TCGA-AB-2905 AML12 15 27776929 27776929 T A SNP ENSG00000212769 ENST00000391458 human ensembl 54_36p 1 known 5_prime_flanking_region c.-33179 NULL 0 - - - no_coding_region:pseudogene tier3 710 0 0 552 258 31.81 NA NA NA 344551 TCGA-AB-2905 AML12 15 27803659 27803659 G A SNP TJP1 NM_003257.3 human genbank 54_36p -1 validated intronic c.2412+2216 e18+2216 0.001 - - - no_errors tier3 1292 0 0 853 394 31.6 NA NA NA 344551 TCGA-AB-2905 AML12 15 29157582 29157582 G A SNP TRPM1 NM_002420.4 human genbank 54_36p -1 reviewed intronic c.1-1103 e1-1103 0 - - - no_errors tier3 2160 0 0 1034 473 31.37 NA NA NA 344551 TCGA-AB-2905 AML12 15 32730053 32730053 A T SNP - - - - - - - - - - - - - - - tier3 550 0 0 612 133 17.85 NA NA NA 344551 TCGA-AB-2905 AML12 15 33854769 33854769 G C SNP - - - - - - - - - - - - - - - tier3 611 0 0 534 219 29.08 NA NA NA 344551 TCGA-AB-2905 AML12 15 33858385 33858385 C T SNP - - - - - - - - - - - - - - - tier3 738 0 0 738 314 29.82 NA NA NA 344551 TCGA-AB-2905 AML12 15 38078729 38078729 A C SNP EIF2AK4 NM_001013703.2 human genbank 54_36p 1 validated intronic c.2922+452 e20+452 0.002 - - - no_errors tier3 1171 2 0.17 860 422 32.87 NA NA NA 344551 TCGA-AB-2905 AML12 15 49488943 49488943 G A SNP DMXL2 NM_015263.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*39530 NULL 0.001 - - - no_errors tier3 666 0 0 479 222 31.62 NA NA NA 344551 TCGA-AB-2905 AML12 15 57155571 57155571 C T SNP RNF111 NM_017610.6 human genbank 54_36p 1 reviewed nonsense c.1813 p.Q605* 1 NULL "HMMSmart_SM00184,HMMPfam_zf-C3HC4,superfamily_RING/U-box" - no_errors tier1 941 0 523 220 29.53 NA NA NA 344551 TCGA-AB-2905 AML12 15 58649242 58649242 C T SNP RORA NM_134260.3 human genbank 54_36p -1 reviewed intronic c.138-11445 e2-11445 0.991 - - - no_errors tier3 1043 0 0 571 260 31.29 NA NA NA 344551 TCGA-AB-2905 AML12 15 68855792 68855792 C G SNP UACA NM_018003.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-12992 NULL 0.002 - - - no_errors tier3 1228 6 0.49 611 284 31.73 NA NA NA 344551 TCGA-AB-2905 AML12 15 70336820 70336820 G T SNP PARP6 NM_020214.2 human genbank 54_36p -1 provisional missense c.922 p.R308S 0.993 NULL "HMMPfam_PARP,superfamily_ADP-ribosylation" - no_errors tier1 1316 10 0.75 725 332 31.41 NA NA NA 344551 TCGA-AB-2905 AML12 15 88928994 88928994 T A SNP CRTC3 NM_022769.1 human genbank 54_36p 1 validated intronic c.232-8878 e3-8878 0.52 - - - no_errors tier3 965 0 0 548 303 35.44 NA NA NA 344551 TCGA-AB-2905 AML12 15 90634892 90634892 C A SNP ENSG00000213443 ENST00000394218 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*3978 NULL 0.011 - - - no_coding_region:pseudogene tier3 1508 2 0.13 729 338 31.65 NA NA NA 344551 TCGA-AB-2905 AML12 15 91489345 91489345 T C SNP - - - - - - - - - - - - - - - tier3 1813 1 0.06 1180 495 29.53 NA NA NA 344551 TCGA-AB-2905 AML12 16 329942 329942 A C SNP AXIN1 NM_003502.2 human genbank 54_36p -1 reviewed intronic c.878+6207 e1+6207 0.001 - - - no_errors tier3 1136 9 0.79 470 227 32.57 NA NA NA 344551 TCGA-AB-2905 AML12 16 4898889 4898889 G A SNP PPL NM_002705.4 human genbank 54_36p -1 reviewed intronic c.162+1963 e2+1963 0 - - - no_errors tier3 1700 1 0.06 654 209 24.22 NA NA NA 344551 TCGA-AB-2905 AML12 16 5313865 5313865 G A SNP ENSG00000215086 ENST00000399556 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41933 NULL 0 - - - no_coding_region:pseudogene tier3 1397 0 0 605 275 31.25 NA NA NA 344551 TCGA-AB-2905 AML12 16 6122246 6122246 C A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+112252 e0+112252 0 - - - no_errors tier3 1536 9 0.58 1422 577 28.86 NA NA NA 344551 TCGA-AB-2905 AML12 16 9831881 9831881 T C SNP GRIN2A NM_000833.3 human genbank 54_36p -1 reviewed intronic c.1778-871 e8-871 0.002 - - - no_errors tier3 1162 3 0.26 618 229 26.88 NA NA NA 344551 TCGA-AB-2905 AML12 16 12966367 12966367 G A SNP - - - - - - - - - - - - - - - tier3 1192 3 0.25 700 236 25.16 NA NA NA 344551 TCGA-AB-2905 AML12 16 20116892 20116892 T G SNP LOC100131046 XR_037711.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*39327 NULL 0.003 - - - pseudogene tier3 381 0 0 325 157 32.51 NA NA NA 344551 TCGA-AB-2905 AML12 16 22843493 22843493 G A SNP HS3ST2 NM_006043.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*9109 NULL 0.002 - - - no_errors tier3 1596 0 0 1100 558 33.59 NA NA NA 344551 TCGA-AB-2905 AML12 16 25008383 25008383 C T SNP LCMT1 NM_016309.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22323 NULL 0.001 - - - no_errors tier3 572 0 0 475 181 27.47 NA NA NA 344551 TCGA-AB-2905 AML12 16 47404508 47404508 G A SNP - - - - - - - - - - - - - - - tier3 710 2 0.28 491 207 29.66 NA NA NA 344551 TCGA-AB-2905 AML12 16 48287858 48287858 C T SNP ZNF423 NM_015069.2 human genbank 54_36p -1 reviewed intronic c.277+34325 e3+34325 0.101 - - - no_errors tier3 1110 2 0.18 492 207 29.61 NA NA NA 344551 TCGA-AB-2905 AML12 16 53887242 53887242 A G SNP IRX6 NM_024335.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29263 NULL 1 - - - no_errors tier2 2410 1 0.04 1218 527 30.2 NA NA NA 344551 TCGA-AB-2905 AML12 16 60625510 60625510 C A SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.1+1975 e0+1975 0.001 - - - no_errors tier3 609 1 0.16 332 126 27.51 NA NA NA 344551 TCGA-AB-2905 AML12 16 62891601 62891601 A - DEL LOC729217 XR_015483.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-34051 NULL 0.08 - - - pseudogene tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 16 63086679 63086679 A T SNP - - - - - - - - - - - - - - - tier3 448 0 0 398 197 33.11 NA NA NA 344551 TCGA-AB-2905 AML12 16 72196567 72196567 C T SNP - - - - - - - - - - - - - - - tier3 1243 2 0.16 609 275 31.04 NA NA NA 344551 TCGA-AB-2905 AML12 16 73324157 73324157 G A SNP FA2H NM_024306.3 human genbank 54_36p -1 validated intronic c.364-5372 e3-5372 0.001 - - - no_errors tier3 1187 0 0 567 235 29.23 NA NA NA 344551 TCGA-AB-2905 AML12 16 77989229 77989229 C A SNP - - - - - - - - - - - - - - - tier3 1719 1 0.06 1162 603 34.13 NA NA NA 344551 TCGA-AB-2905 AML12 17 779500 779500 C A SNP NXN NM_022463.3 human genbank 54_36p -1 validated intronic c.360+49809 e1+49809 0 - - - no_errors tier3 1978 2 0.1 491 214 30.31 NA NA NA 344551 TCGA-AB-2905 AML12 17 3445553 3445553 C T SNP TRPV1 ENST00000174621 human ensembl 54_36p -1 known intronic c.1+1408 e0+1408 0.009 - - - no_errors tier3 1848 6 0.32 846 411 32.64 NA NA NA 344551 TCGA-AB-2905 AML12 17 6317323 6317323 A C SNP PITPNM3 NM_031220.3 human genbank 54_36p -1 validated intronic c.1259-452 e11-452 0 - - - no_errors tier2 675 1 0.15 213 78 26.8 NA NA NA 344551 TCGA-AB-2905 AML12 17 11667277 11667277 T A SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed intronic c.9246+201 e48+201 0.117 - - - no_errors tier3 1296 0 0 691 329 32.22 NA NA NA 344551 TCGA-AB-2905 AML12 17 21443323 21443323 G C SNP ENSG00000212719 ENST00000391411 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47789 NULL 0 - - - no_errors tier3 1092 2 0.18 880 398 31.12 NA NA NA 344551 TCGA-AB-2905 AML12 17 32384219 32384219 T C SNP AATF NM_012138.3 human genbank 54_36p 1 reviewed intronic c.284-80 e3-80 0 - - - no_errors tier3 788 2 0.25 404 209 34.04 NA NA NA 344551 TCGA-AB-2905 AML12 17 47971574 47971574 G A SNP - - - - - - - - - - - - - - - tier3 450 2 0.44 355 150 29.7 NA NA NA 344551 TCGA-AB-2905 AML12 17 48127441 48127441 C A SNP - - - - - - - - - - - - - - - tier2 1347 1 0.07 857 383 30.86 NA NA NA 344551 TCGA-AB-2905 AML12 17 51398311 51398311 A G SNP - - - - - - - - - - - - - - - tier2 2304 2 0.09 1198 546 31.31 NA NA NA 344551 TCGA-AB-2905 AML12 17 63955039 63955039 A G SNP WIPI1 NM_017983.5 human genbank 54_36p -1 validated intronic c.334-2714 e4-2714 0.002 - - - no_errors tier3 567 2 0.35 323 138 29.93 NA NA NA 344551 TCGA-AB-2905 AML12 17 66553801 66553801 G T SNP ENSG00000211252 ENST00000388517 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-38984 NULL 0.041 - - - pseudogene tier3 1074 2 0.19 565 242 29.99 NA NA NA 344551 TCGA-AB-2905 AML12 17 70142320 70142320 G A SNP RAB37 NM_175738.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37001 NULL 0 - - - no_errors tier3 1878 4 0.21 1048 405 27.85 NA NA NA 344551 TCGA-AB-2905 AML12 17 76705471 76705471 C T SNP AATK NM_001080395.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*1326 NULL 0.001 - - - no_errors tier3 119 3 2.46 58 38 39.58 NA NA NA 344551 TCGA-AB-2905 AML12 18 5546173 5546173 T G SNP EPB41L3 ENST00000400111 human ensembl 54_36p -1 known intronic c.266-67013 e2-67013 0.001 - - - no_start_codon:no_stop_codon tier3 843 0 0 422 176 29.38 NA NA NA 344551 TCGA-AB-2905 AML12 18 5553032 5553032 C T SNP EPB41L3 ENST00000400111 human ensembl 54_36p -1 known intronic c.265+67344 e1+67344 0.004 - - - no_start_codon:no_stop_codon tier3 1171 3 0.26 600 284 32.13 NA NA NA 344551 TCGA-AB-2905 AML12 18 12762176 12762176 G A SNP PTPN2 NM_002828.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*22101 NULL 0.228 - - - no_errors tier3 734 3 0.41 469 211 31.03 NA NA NA 344551 TCGA-AB-2905 AML12 18 22985203 22985204 TA - DEL CHST9 NM_031422.3 human genbank 54_36p -1 validated intronic c.1-8337_8338 e1-8336 0.009:0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 18 30059675 30059675 G A SNP LOC730045 XM_001714795.1 human genbank 54_36p -1 model intronic c.99-782 e2-782 0.001 - - - no_errors tier2 330 1 0.3 265 121 31.35 NA NA NA 344551 TCGA-AB-2905 AML12 18 39051383 39051383 C A SNP - - - - - - - - - - - - - - - tier3 915 2 0.22 733 276 27.33 NA NA NA 344551 TCGA-AB-2905 AML12 18 43310440 43310440 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 18 48007703 48007703 A T SNP - - - - - - - - - - - - - - - tier3 1138 1 0.09 701 328 31.88 NA NA NA 344551 TCGA-AB-2905 AML12 18 49571844 49571844 C A SNP - - - - - - - - - - - - - - - tier3 2176 0 0 1314 535 28.84 NA NA NA 344551 TCGA-AB-2905 AML12 18 64622037 64622037 C T SNP CCDC102B NM_001093729.1 human genbank 54_36p 1 validated intronic c.1-32929 e1-32929 0.016 - - - no_errors tier3 747 3 0.4 675 290 30.02 NA NA NA 344551 TCGA-AB-2905 AML12 18 70775074 70775074 G A SNP ZNF407 NM_017757.2 human genbank 54_36p 1 provisional intronic c.5428+13438 e7+13438 0.998 - - - no_errors tier2 969 1 0.1 601 250 29.38 NA NA NA 344551 TCGA-AB-2905 AML12 18 70955201 70955201 A C SNP C18orf33 XM_001714254.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-8005 NULL 0.008 - - - no_errors tier3 775 0 0 429 204 32.23 NA NA NA 344551 TCGA-AB-2905 AML12 18 71880614 71880614 C T SNP - - - - - - - - - - - - - - - tier2 917 1 0.11 348 162 31.76 NA NA NA 344551 TCGA-AB-2905 AML12 19 1367826 1367826 A T SNP DAZAP1 NM_018959.2 human genbank 54_36p 1 reviewed intronic c.30-673 e2-673 0.006 - - - no_errors tier3 1674 2 0.12 628 194 23.57 NA NA NA 344551 TCGA-AB-2905 AML12 19 3882715 3882715 C T SNP ITGB1BP3 NM_170678.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-1955 NULL 0 - - - no_errors tier2 1182 0 0 505 247 32.85 NA NA NA 344551 TCGA-AB-2905 AML12 19 10053553 10053553 T C SNP C19orf66 ENST00000253110 human ensembl 54_36p 1 known intronic c.18+174 e1+174 0.002 - - - no_start_codon tier3 5163 7 0.14 1976 938 32.16 NA NA NA 344551 TCGA-AB-2905 AML12 19 15914042 15914042 C A SNP CYP4F11 NM_021187.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7824 NULL 0 - - - no_errors tier3 2200 4 0.18 1784 779 30.38 NA NA NA 344551 TCGA-AB-2905 AML12 19 37995988 37995988 G A SNP TDRD12 ENST00000311695 human ensembl 54_36p 1 known intronic c.3049-442 e25-442 0 - - - no_stop_codon tier2 1785 3 0.17 606 302 33.26 NA NA NA 344551 TCGA-AB-2905 AML12 19 47264055 47264056 CT - DEL GRIK5 NM_002088.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2293 NULL 0.739:0.749 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 344551 TCGA-AB-2905 AML12 19 52687146 52687146 C T SNP NAPA NM_003827.2 human genbank 54_36p -1 reviewed missense c.604 p.A202T 1 superfamily_TPR-like "HMMPfam_NSF,superfamily_TPR-like" - no_errors tier1 1045 3 0.29 566 207 26.64 NA NA NA 344551 TCGA-AB-2905 AML12 20 77153 77153 G A SNP DEFB127 NM_139074.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-9033 NULL 0 - - - no_errors tier3 1668 1 0.06 981 421 30.03 NA NA NA 344551 TCGA-AB-2905 AML12 20 30639673 30639673 G A SNP uc002wxy.2 ENST00000375670 human ensembl 54_36p 1 known intronic c.1+654 e0+654 0.012 - - - no_errors tier2 1315 1 0.08 396 157 28.34 NA NA NA 344551 TCGA-AB-2905 AML12 20 44758136 44758136 C A SNP SLC13A3 NM_022829.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-44669 NULL 0.793 - - - no_errors tier3 3183 3 0.09 873 407 31.77 NA NA NA 344551 TCGA-AB-2905 AML12 20 46833536 46833536 G A SNP PREX1 NM_020820.3 human genbank 54_36p -1 reviewed intronic c.220-35712 e2-35712 0.005 - - - no_errors tier3 3065 7 0.23 1347 618 31.37 NA NA NA 344551 TCGA-AB-2905 AML12 20 52088682 52088682 G A SNP BCAS1 NM_003657.2 human genbank 54_36p -1 reviewed intronic c.143-9764 e3-9764 0.001 - - - no_errors tier3 1069 1 0.09 818 335 28.95 NA NA NA 344551 TCGA-AB-2905 AML12 20 52642964 52642964 T C SNP DOK5 NM_018431.3 human genbank 54_36p 1 reviewed intronic c.599+1213 e5+1213 0.001 - - - no_errors tier2 470 0 0 392 205 34.34 NA NA NA 344551 TCGA-AB-2905 AML12 20 54358856 54358856 G A SNP CSTF1 NM_001033521.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45160 NULL 0.001 - - - no_errors tier3 744 4 0.53 483 229 32.16 NA NA NA 344551 TCGA-AB-2905 AML12 20 57447767 57447767 C T SNP LOC645605 XM_001716708.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*21302 NULL 0.005 - - - no_errors tier3 1736 0 0 840 316 27.29 NA NA NA 344551 TCGA-AB-2905 AML12 20 61149696 61149696 C T SNP C20orf51 XR_040056.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier2 1007 4 0.39 1038 477 31.46 NA NA NA 344551 TCGA-AB-2905 AML12 20 61509008 61509008 G T SNP KCNQ2 NM_172107.4 human genbank 54_36p -1 reviewed silent c.2052 p.G684 1 NULL "HMMPfam_Ion_trans,HMMPfam_KCNQ_channel,superfamily_Voltage-gated potassium channels" - no_errors tier1 163 0 84 42 33.33 NA NA NA 344551 TCGA-AB-2905 AML12 21 14178425 14178425 G A SNP uc002yjf.1 ENST00000359319 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35869 NULL 0 - - - no_coding_region:pseudogene tier3 175 0 0 64 19 22.89 NA NA NA 344551 TCGA-AB-2905 AML12 21 17381344 17381344 G C SNP - - - - - - - - - - - - - - - tier3 855 0 0 789 303 27.75 NA NA NA 344551 TCGA-AB-2905 AML12 21 17590842 17590842 G A SNP - - - - - - - - - - - - - - - tier2 588 0 0 776 374 32.49 NA NA NA 344551 TCGA-AB-2905 AML12 21 25988020 25988020 G A SNP JAM2 NM_021219.2 human genbank 54_36p 1 reviewed missense c.323 p.R108H 0.994 "HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726" "HMMSmart_IGc2,HMMSmart_IG,HMMPfam_V-set,HMMPfam_ig,superfamily_SSF48726" - no_errors tier1 1121 1 0.09 710 357 33.46 NA NA NA 344551 TCGA-AB-2905 AML12 21 28547804 28547804 A C SNP - - - - - - - - - - - - - - - tier3 1177 4 0.34 741 374 33.51 NA NA NA 344551 TCGA-AB-2905 AML12 21 37532350 37532350 G C SNP DSCR3 NM_006052.1 human genbank 54_36p -1 reviewed intronic c.351+281 e3+281 0.024 - - - no_errors tier3 1284 1 0.08 772 329 29.88 NA NA NA 344551 TCGA-AB-2905 AML12 21 38618049 38618049 C T SNP LOC100131955 XM_001715532.1 human genbank 54_36p 1 model intronic c.64-8663 e2-8663 0.001 - - - no_errors tier3 2029 2 0.1 1006 452 31 NA NA NA 344551 TCGA-AB-2905 AML12 21 39018974 39018974 C T SNP - - - - - - - - - - - - - - - tier3 4106 0 0 2527 1094 30.2 NA NA NA 344551 TCGA-AB-2905 AML12 21 40690271 40690271 G A SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.509-27229 e4-27229 0 - - - no_errors tier2 872 3 0.34 610 272 30.84 NA NA NA 344551 TCGA-AB-2905 AML12 21 44147885 44147885 G A SNP AGPAT3 NM_020132.1 human genbank 54_36p 1 reviewed intronic c.1-381 e1-381 0.001 - - - no_errors tier3 603 0 0 273 110 28.72 NA NA NA 344551 TCGA-AB-2905 AML12 21 45721727 45721727 G A SNP COL18A1 NM_030582.3 human genbank 54_36p 1 reviewed intronic c.1469-26 e6-26 0.007 - - - no_errors tier3 874 3 0.34 308 136 30.63 NA NA NA 344551 TCGA-AB-2905 AML12 22 18599185 18599185 C T SNP RTN4R NM_023004.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*10049 NULL 0.477 - - - no_errors tier2 286 0 0 125 49 28.16 NA NA NA 344551 TCGA-AB-2905 AML12 22 24169273 24169273 G T SNP LRP5L ENST00000402785 human ensembl 54_36p -1 known 5_prime_flanking_region c.-83214 NULL 0 - - - no_errors tier2 447 1 0.22 319 153 32.42 NA NA NA 344551 TCGA-AB-2905 AML12 22 38142467 38142467 G A SNP MAP3K7IP1 NM_006116.2 human genbank 54_36p 1 reviewed intronic c.325-275 e4-275 0 - - - no_errors tier3 1493 0 0 658 280 29.76 NA NA NA 344551 TCGA-AB-2905 AML12 22 43551854 43551854 G T SNP LOC553158 NM_181334.3 human genbank 54_36p 1 reviewed intronic c.38-9147 e2-9147 0.005 - - - no_errors tier3 1139 7 0.61 692 309 30.87 NA NA NA 344551 TCGA-AB-2905 AML12 22 44306193 44306193 G A SNP FBLN1 NM_006486.2 human genbank 54_36p 1 reviewed intronic c.544+325 e5+325 0 - - - no_errors tier3 1152 1 0.09 378 183 32.62 NA NA NA 529205 TCGA-AB-2906 AML49 Y 4737456 4737456 C T SNP ENSG00000217045 ENST00000404516 human ensembl 54_36p -1 known 5_prime_flanking_region c.-6567 NULL 0.014 - - - no_coding_region:pseudogene tier3 728 0 0 69 461 86.82 NA NA NA 529205 TCGA-AB-2906 AML49 X 6651804 6651804 T A SNP - - - - - - - - - - - - - - - tier3 1264 2 0.16 364 678 65.07 NA NA NA 529205 TCGA-AB-2906 AML49 Y 19979267 19979267 A G SNP ENSG00000219205 ENST00000404818 human ensembl 54_36p 1 known 3_prime_flanking_region c.*29444 NULL 0 - - - no_coding_region:pseudogene tier3 1081 3 0.28 197 910 82.2 NA NA NA 529205 TCGA-AB-2906 AML49 X 21298534 21298534 G T SNP CNKSR2 NM_014927.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-4403 NULL 0.028 - - - no_errors tier3 405 1 0.25 64 312 82.98 NA NA NA 529205 TCGA-AB-2906 AML49 X 30141548 30141548 G A SNP MAGEB1 NM_002363.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36984 NULL 0.002 - - - no_errors tier3 352 0 0 46 284 86.06 NA NA NA 529205 TCGA-AB-2906 AML49 X 47061447 47061447 C A SNP ENSG00000218737 ENST00000404256 human ensembl 54_36p -1 known 5_prime_flanking_region c.-42714 NULL 0.032 - - - no_coding_region:pseudogene tier2 1002 1 0.1 161 578 77.79 NA NA NA 529205 TCGA-AB-2906 AML49 X 86214315 86214315 A T SNP - - - - - - - - - - - - - - - tier3 333 0 0 56 303 84.4 NA NA NA 529205 TCGA-AB-2906 AML49 X 93431807 93431807 A G SNP LOC643371 XM_001726980.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-29510 NULL 0.031 - - - no_errors tier3 1038 0 0 387 529 57.75 NA NA NA 529205 TCGA-AB-2906 AML49 X 112190866 112190866 T C SNP - - - - - - - - - - - - - - - tier3 849 0 0 121 717 85.05 NA NA NA 529205 TCGA-AB-2906 AML49 X 126153091 126153091 G T SNP - - - - - - - - - - - - - - - tier3 417 0 0 161 208 56.37 NA NA NA 529205 TCGA-AB-2906 AML49 X 142921274 142921274 T A SNP - - - - - - - - - - - - - - - tier3 638 0 0 66 454 87.31 NA NA NA 529205 TCGA-AB-2906 AML49 1 1833141 1833141 C G SNP GNB1 NM_002074.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-86389 NULL 0.002 - - - no_errors tier3 59 1 1.67 26 14 34.15 NA NA NA 529205 TCGA-AB-2906 AML49 1 16219641 16219641 A G SNP CLCNKA NM_004070.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2061 NULL 0.001 - - - no_errors tier3 217 0 0 236 119 33.52 NA NA NA 529205 TCGA-AB-2906 AML49 1 22625076 22625076 T C SNP ZBTB40 NM_001083621.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-63953 NULL 0.003 - - - no_errors tier2 854 0 0 475 360 43.11 NA NA NA 529205 TCGA-AB-2906 AML49 1 35142783 35142783 G A SNP DLGAP3 NM_001080418.1 human genbank 54_36p -1 provisional silent c.789 p.S263 0.929 NULL HMMPfam_GKAP - no_errors tier1 1820 1 0.05 1242 884 41.58 NA NA NA 529205 TCGA-AB-2906 AML49 1 36604644 36604644 G C SNP STK40 NM_032017.1 human genbank 54_36p -1 provisional intronic c.1+1392 e0+1392 0.061 - - - no_errors tier2 690 0 0 377 270 41.67 NA NA NA 529205 TCGA-AB-2906 AML49 1 38075726 38075726 T C SNP MTF1 NM_005955.2 human genbank 54_36p -1 reviewed intronic c.779+1158 e3+1158 0 - - - no_errors tier3 1537 2 0.13 793 498 38.52 NA NA NA 529205 TCGA-AB-2906 AML49 1 38573433 38573433 G C SNP - - - - - - - - - - - - - - - tier2 1346 0 0 760 560 42.36 NA NA NA 529205 TCGA-AB-2906 AML49 1 46221720 46221720 G A SNP MAST2 NM_015112.2 human genbank 54_36p 1 validated intronic c.593-14263 e6-14263 0.008 - - - no_errors tier3 1146 0 0 1088 760 41.06 NA NA NA 529205 TCGA-AB-2906 AML49 1 52219113 52219113 A C SNP RAB3B NM_002867.2 human genbank 54_36p -1 provisional intronic c.1-3736 e1-3736 0.04 - - - no_errors tier3 112 0 0 31 40 56.34 NA NA NA 529205 TCGA-AB-2906 AML49 1 53715205 53715205 G T SNP FLJ40434 NR_002314.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-37571 NULL 0 - - - pseudogene tier3 463 1 0.22 235 169 41.83 NA NA NA 529205 TCGA-AB-2906 AML49 1 63107033 63107033 T C SNP ENSG00000216534 ENST00000403241 human ensembl 54_36p 1 known 5_prime_flanking_region c.-36406 NULL 0 - - - no_coding_region:pseudogene tier3 984 0 0 510 395 43.65 NA NA NA 529205 TCGA-AB-2906 AML49 1 63935292 63935292 A G SNP PGM1 NM_002633.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*37358 NULL 0 - - - no_errors tier3 1147 0 0 555 458 45.17 NA NA NA 529205 TCGA-AB-2906 AML49 1 74149427 74149427 A G SNP - - - - - - - - - - - - - - - tier3 827 0 0 576 329 36.35 NA NA NA 529205 TCGA-AB-2906 AML49 1 81824581 81824581 G A SNP LPHN2 ENST00000370725 human ensembl 54_36p 1 known intronic c.1+5328 e0+5328 0.022 - - - no_errors tier3 1142 2 0.17 859 389 31.05 NA NA NA 529205 TCGA-AB-2906 AML49 1 85355943 85355943 T C SNP WDR63 NM_145172.3 human genbank 54_36p 1 validated intronic c.1787-57 e16-57 0.133 - - - no_errors tier3 1139 1 0.09 764 517 40.33 NA NA NA 529205 TCGA-AB-2906 AML49 1 106390401 106390401 A G SNP LOC126987 XR_016153.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*34356 NULL 0.005 - - - no_errors tier3 2545 1 0.04 1197 847 41.44 NA NA NA 529205 TCGA-AB-2906 AML49 1 108530261 108530262 GT - DEL SLC25A24 NM_013386.3 human genbank 54_36p -1 validated intronic c.184-163_184-162 e2-162 0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 1 149952860 149952860 G A SNP TNRC4 NM_007185.3 human genbank 54_36p -1 reviewed intronic c.228+834 e2+834 0.004 - - - no_errors tier3 1304 0 0 655 421 39.09 NA NA NA 529205 TCGA-AB-2906 AML49 1 154909179 154909179 G A SNP NES NM_006617.1 human genbank 54_36p -1 reviewed silent c.1425 p.S475 0 NULL "HMMPfam_Filament,PatternScan_IF" - no_errors tier1 178 2 1.11 170 145 46.03 NA NA NA 529205 TCGA-AB-2906 AML49 1 159079266 159079266 C A SNP CD244 NM_016382.2 human genbank 54_36p -1 validated intronic c.62-951 e2-951 0 - - - no_errors tier3 1195 2 0.17 650 402 38.07 NA NA NA 529205 TCGA-AB-2906 AML49 1 163541177 163541177 G T SNP LMX1A NM_177398.1 human genbank 54_36p -1 provisional intronic c.263+47760 e2+47760 0.009 - - - no_errors tier3 861 0 0 753 356 32.1 NA NA NA 529205 TCGA-AB-2906 AML49 1 188279538 188279538 A C SNP - - - - - - - - - - - - - - - tier3 2169 1 0.05 969 451 31.72 NA NA NA 529205 TCGA-AB-2906 AML49 1 194955324 194955324 G A SNP CFH NM_000186.3 human genbank 54_36p 1 reviewed intronic c.1696+3802 e11+3802 0.002 - - - no_errors tier3 707 2 0.28 345 234 40.28 NA NA NA 529205 TCGA-AB-2906 AML49 1 216054878 216054878 T A SNP SPATA17 NM_138796.2 human genbank 54_36p 1 provisional intronic c.1005+13063 e9+13063 0.002 - - - no_errors tier3 1574 0 0 871 315 26.54 NA NA NA 529205 TCGA-AB-2906 AML49 1 216500788 216500788 T A SNP RRP15 NM_016052.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-24494 NULL 0.625 - - - no_errors tier2 2202 0 0 802 626 43.84 NA NA NA 529205 TCGA-AB-2906 AML49 1 216652121 216652121 T A SNP TGFB2 NM_003238.1 human genbank 54_36p 1 validated intronic c.510+6824 e2+6824 0.007 - - - no_errors tier3 1139 0 0 732 516 41.35 NA NA NA 529205 TCGA-AB-2906 AML49 1 217890250 217890250 C T SNP LOC728518 XM_001127626.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-25537 NULL 0 - - - no_errors tier2 3113 5 0.16 1829 1394 43.17 NA NA NA 529205 TCGA-AB-2906 AML49 1 223874885 223874885 C T SNP ENAH NM_001008493.1 human genbank 54_36p -1 validated intronic c.5+32126 e1+32126 0.001 - - - no_errors tier3 1219 0 0 759 490 39.23 NA NA NA 529205 TCGA-AB-2906 AML49 1 228960613 228960613 G A SNP CAPN9 NM_006615.2 human genbank 54_36p 1 reviewed intronic c.284-1268 e3-1268 0.002 - - - no_errors tier3 2172 0 0 976 624 38.98 NA NA NA 529205 TCGA-AB-2906 AML49 1 230715316 230715316 G A SNP SIPA1L2 NM_020808.3 human genbank 54_36p -1 validated intronic c.1483+910 e1+910 0.014 - - - no_errors tier3 1335 1 0.07 727 604 45.31 NA NA NA 529205 TCGA-AB-2906 AML49 1 234643399 234643399 A C SNP EDARADD NM_145861.3 human genbank 54_36p 1 reviewed intronic c.121-784 e3-784 0.001 - - - no_errors tier3 590 0 0 282 199 41.29 NA NA NA 529205 TCGA-AB-2906 AML49 1 238283604 238283604 C T SNP FMN2 NM_020066.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38000 NULL 0.001 - - - no_errors tier3 1913 1 0.05 1242 497 28.58 NA NA NA 529205 TCGA-AB-2906 AML49 1 238579417 238579418 - A INS FMN2 NM_020066.4 human genbank 54_36p 1 validated intronic c.5195-6322_5195-6321 e14-6321 0.024:0.148 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 1 240599671 240599671 G A SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.1-21504 e1-21504 0.002 - - - no_errors tier3 2795 0 0 1253 951 43.13 NA NA NA 529205 TCGA-AB-2906 AML49 1 243663814 243663814 C T SNP KIF26B NM_018012.3 human genbank 54_36p 1 provisional intronic c.1166+14144 e4+14144 0.278 - - - no_errors tier3 2270 3 0.13 1095 789 41.79 NA NA NA 529205 TCGA-AB-2906 AML49 1 245698098 245698098 T C SNP OR2W5 NM_001004698.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-22955 NULL 0.224 - - - no_errors tier3 1181 0 0 527 373 41.35 NA NA NA 529205 TCGA-AB-2906 AML49 2 1875734 1875734 A C SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.2027-668 e10-668 0 - - - no_errors tier3 309 0 0 315 216 40.68 NA NA NA 529205 TCGA-AB-2906 AML49 2 4284312 4284312 A T SNP ENSG00000215960 ENST00000401141 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*30329 NULL 0.097 - - - no_errors tier3 1002 0 0 630 401 38.89 NA NA NA 529205 TCGA-AB-2906 AML49 2 13319186 13319186 G A SNP - - - - - - - - - - - - - - - tier3 1471 1 0.07 601 483 44.43 NA NA NA 529205 TCGA-AB-2906 AML49 2 14154731 14154731 A G SNP - - - - - - - - - - - - - - - tier3 1554 0 0 739 469 38.82 NA NA NA 529205 TCGA-AB-2906 AML49 2 14154745 14154745 A C SNP - - - - - - - - - - - - - - - tier3 1414 0 0 684 452 39.79 NA NA NA 529205 TCGA-AB-2906 AML49 2 19472442 19472442 C T SNP - - - - - - - - - - - - - - - tier3 1575 2 0.13 675 375 35.68 NA NA NA 529205 TCGA-AB-2906 AML49 2 22455530 22455530 G C SNP ENSG00000206882 ENST00000384155 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40150 NULL 0.001 - - - no_errors tier3 2548 0 0 1276 990 43.63 NA NA NA 529205 TCGA-AB-2906 AML49 2 29644577 29644577 T C SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.953-36091 e4-36091 1 - - - no_errors tier2 1026 2 0.19 761 537 41.37 NA NA NA 529205 TCGA-AB-2906 AML49 2 36928661 36928661 G C SNP STRN NM_003162.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*1442 NULL 0.012 - - - no_errors tier3 910 0 0 454 307 40.29 NA NA NA 529205 TCGA-AB-2906 AML49 2 39415020 39415020 A C SNP MAP4K3 NM_003618.2 human genbank 54_36p -1 reviewed intronic c.415-801 e7-801 0.024 - - - no_errors tier3 1061 0 0 744 358 32.46 NA NA NA 529205 TCGA-AB-2906 AML49 2 50202608 50202608 T G SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.3547-30472 e18-30472 0.099 - - - no_errors tier3 1366 0 0 671 379 36.06 NA NA NA 529205 TCGA-AB-2906 AML49 2 52243829 52243829 C G SNP - - - - - - - - - - - - - - - tier3 1316 0 0 633 412 39.43 NA NA NA 529205 TCGA-AB-2906 AML49 2 53618095 53618095 C G SNP ASB3 ENST00000406053 human ensembl 54_36p -1 known intronic c.1323-3569 e10-3569 0.001 - - - no_errors tier3 1320 0 0 897 418 31.76 NA NA NA 529205 TCGA-AB-2906 AML49 2 67697561 67697561 T C SNP - - - - - - - - - - - - - - - tier2 1084 0 0 675 505 42.72 NA NA NA 529205 TCGA-AB-2906 AML49 2 71896486 71896486 G A SNP - - - - - - - - - - - - - - - tier3 2365 3 0.13 1494 1118 42.8 NA NA NA 529205 TCGA-AB-2906 AML49 2 75493864 75493864 C T SNP ENSG00000208916 ENST00000386181 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*5617 NULL 0.002 - - - pseudogene tier3 2134 1 0.05 801 525 39.56 NA NA NA 529205 TCGA-AB-2906 AML49 2 78486791 78486791 A G SNP ENSG00000214429 ENST00000398312 human ensembl 54_36p -1 known 3_prime_flanking_region c.*6631 NULL 0 - - - no_errors tier3 951 1 0.1 531 446 45.51 NA NA NA 529205 TCGA-AB-2906 AML49 2 81008834 81008834 T G SNP - - - - - - - - - - - - - - - tier3 800 0 0 399 259 39.36 NA NA NA 529205 TCGA-AB-2906 AML49 2 81307563 81307563 A G SNP - - - - - - - - - - - - - - - tier3 444 0 0 209 91 30.33 NA NA NA 529205 TCGA-AB-2906 AML49 2 82251731 82251731 G A SNP - - - - - - - - - - - - - - - tier3 1409 0 0 626 453 41.98 NA NA NA 529205 TCGA-AB-2906 AML49 2 111177281 111177281 A G SNP BUB1 NM_004336.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25238 NULL 0.052 - - - no_errors tier3 837 0 0 627 438 41.13 NA NA NA 529205 TCGA-AB-2906 AML49 2 111713759 111713759 C T SNP LOC100128130 XM_001722090.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-1202 NULL 0.001 - - - no_errors tier3 673 0 0 355 212 37.39 NA NA NA 529205 TCGA-AB-2906 AML49 2 114104192 114104192 G A SNP RABL2A NM_007082.3 human genbank 54_36p 1 reviewed intronic c.107+1432 e1+1432 0 - - - no_errors tier3 498 0 0 155 119 43.43 NA NA NA 529205 TCGA-AB-2906 AML49 2 114586776 114586776 G A SNP - - - - - - - - - - - - - - - tier3 979 1 0.1 627 477 43.21 NA NA NA 529205 TCGA-AB-2906 AML49 2 128292089 128292089 T A SNP WDR33 NM_018383.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-47064 NULL 0.007 - - - no_errors tier3 1245 2 0.16 443 331 42.76 NA NA NA 529205 TCGA-AB-2906 AML49 2 135298485 135298485 G T SNP ACMSD NM_138326.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14238 NULL 0.004 - - - no_errors tier2 1254 0 0 720 342 32.17 NA NA NA 529205 TCGA-AB-2906 AML49 2 145395660 145395660 C A SNP - - - - - - - - - - - - - - - tier3 1175 2 0.17 803 565 41.24 NA NA NA 529205 TCGA-AB-2906 AML49 2 151592653 151592653 C T SNP ENSG00000222031 ENST00000409243 human ensembl 54_36p -1 known intronic c.213+5916 e3+5916 0.009 - - - no_errors tier3 694 1 0.14 596 433 42.04 NA NA NA 529205 TCGA-AB-2906 AML49 2 157585382 157585382 C T SNP - - - - - - - - - - - - - - - tier2 1176 0 0 665 510 43.4 NA NA NA 529205 TCGA-AB-2906 AML49 2 162118032 162118032 G A SNP KRT18P46 XM_001720115.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-26796 NULL 0.016 - - - pseudogene tier3 1246 0 0 802 605 43 NA NA NA 529205 TCGA-AB-2906 AML49 2 167324418 167324418 G A SNP - - - - - - - - - - - - - - - tier3 1393 1 0.07 837 615 42.36 NA NA NA 529205 TCGA-AB-2906 AML49 2 175487180 175487180 G C SNP CHN1 NM_001025201.2 human genbank 54_36p -1 reviewed intronic c.260+852 e5+852 0.002 - - - no_errors tier3 1709 0 0 1002 692 40.83 NA NA NA 529205 TCGA-AB-2906 AML49 2 182854395 182854395 C T SNP PDE1A NM_005019.1 human genbank 54_36p -1 validated intronic c.102-17009 e2-17009 0.008 - - - no_errors tier3 1915 1 0.05 1077 773 41.78 NA NA NA 529205 TCGA-AB-2906 AML49 2 184620302 184620302 C T SNP - - - - - - - - - - - - - - - tier3 907 0 0 631 415 39.67 NA NA NA 529205 TCGA-AB-2906 AML49 2 186000510 186000510 G A SNP - - - - - - - - - - - - - - - tier3 1190 1 0.08 599 412 40.71 NA NA NA 529205 TCGA-AB-2906 AML49 2 189529890 189529890 G A SNP COL3A1 NM_000090.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17571 NULL 0 - - - no_errors tier3 830 1 0.12 242 152 38.58 NA NA NA 529205 TCGA-AB-2906 AML49 2 190084383 190084383 C G SNP SLC40A1 NM_014585.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*50466 NULL 0.188 - - - no_errors tier3 2346 3 0.13 1408 949 40.21 NA NA NA 529205 TCGA-AB-2906 AML49 2 193221159 193221159 T C SNP - - - - - - - - - - - - - - - tier3 1205 2 0.17 576 439 43.25 NA NA NA 529205 TCGA-AB-2906 AML49 2 199596399 199596399 C G SNP - - - - - - - - - - - - - - - tier2 1395 0 0 764 451 37.06 NA NA NA 529205 TCGA-AB-2906 AML49 2 202468487 202468487 T G SNP ALS2CR7 ENST00000409505 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*4625 NULL 0.098 - - - no_errors tier3 986 0 0 549 270 32.93 NA NA NA 529205 TCGA-AB-2906 AML49 2 205116539 205116539 C T SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated 5_prime_flanking_region c.-2429 NULL 0 - - - no_errors tier3 430 0 0 315 147 31.82 NA NA NA 529205 TCGA-AB-2906 AML49 2 205305217 205305217 C T SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated intronic c.222+45967 e2+45967 0 - - - no_errors tier3 1846 1 0.05 1393 546 28.13 NA NA NA 529205 TCGA-AB-2906 AML49 2 221695242 221695242 C T SNP - - - - - - - - - - - - - - - tier2 662 1 0.15 430 265 38.13 NA NA NA 529205 TCGA-AB-2906 AML49 2 222701963 222701963 C G SNP - - - - - - - - - - - - - - - tier3 1384 0 0 644 436 40.37 NA NA NA 529205 TCGA-AB-2906 AML49 2 222780668 222780668 T C SNP PAX3 NM_181459.4 human genbank 54_36p -1 reviewed intronic c.1174-5515 e8-5515 0 - - - no_errors tier3 1399 0 0 782 604 43.55 NA NA NA 529205 TCGA-AB-2906 AML49 2 223849422 223849422 A G SNP ENSG00000222485 ENST00000410553 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27666 NULL 0.009 - - - no_errors tier3 1011 4 0.39 467 323 40.89 NA NA NA 529205 TCGA-AB-2906 AML49 2 228304708 228304708 C A SNP SLC19A3 NM_025243.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-29430 NULL 0.002 - - - no_errors tier3 855 0 0 362 287 44.15 NA NA NA 529205 TCGA-AB-2906 AML49 2 229734538 229734538 C T SNP PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.124-5614 e2-5614 0 - - - no_errors tier3 895 1 0.11 631 350 35.68 NA NA NA 529205 TCGA-AB-2906 AML49 2 230134088 230134088 C G SNP DNER NM_139072.3 human genbank 54_36p -1 validated intronic c.848-14036 e5-14036 0 - - - no_errors tier3 1311 0 0 879 615 41.11 NA NA NA 529205 TCGA-AB-2906 AML49 2 238680319 238680319 G T SNP ESPNL NM_194312.2 human genbank 54_36p 1 validated intronic c.673-852 e4-852 0 - - - no_errors tier3 213 1 0.47 242 154 38.89 NA NA NA 529205 TCGA-AB-2906 AML49 2 240690909 240690909 T C SNP ENSG00000213048 ENST00000391990 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6283 NULL 0.017 - - - no_coding_region:pseudogene tier3 1004 0 0 868 590 40.33 NA NA NA 529205 TCGA-AB-2906 AML49 3 1243904 1243904 C A SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.183-598 e3-598 0.865 - - - no_errors tier3 1035 3 0.29 602 240 28.5 NA NA NA 529205 TCGA-AB-2906 AML49 3 5877196 5877196 T C SNP - - - - - - - - - - - - - - - tier3 1724 0 0 728 473 39.35 NA NA NA 529205 TCGA-AB-2906 AML49 3 6577495 6577495 T C SNP - - - - - - - - - - - - - - - tier3 1436 1 0.07 611 372 37.8 NA NA NA 529205 TCGA-AB-2906 AML49 3 10524729 10524729 G A SNP ATP2B2 ENST00000397077 human ensembl 54_36p -1 known intronic c.1+25994 e0+25994 0 - - - no_errors tier3 392 1 0.25 201 174 46.4 NA NA NA 529205 TCGA-AB-2906 AML49 3 10661955 10661955 A C SNP ATP2B2 ENST00000397077 human ensembl 54_36p -1 known intronic c.1-25309 e1-25309 0 - - - no_errors tier3 1398 2 0.14 722 515 41.57 NA NA NA 529205 TCGA-AB-2906 AML49 3 13674330 13674330 G A SNP FBLN2 ENST00000295761 human ensembl 54_36p 1 known 3_prime_flanking_region c.*19910 NULL 0.015 - - - no_errors tier2 478 0 0 333 167 33.4 NA NA NA 529205 TCGA-AB-2906 AML49 3 25320188 25320188 G A SNP RARB ENST00000404969 human ensembl 54_36p 1 known intronic c.178+129118 e1+129118 0.03 - - - no_errors tier3 1593 0 0 714 560 43.92 NA NA NA 529205 TCGA-AB-2906 AML49 3 29202488 29202488 G C SNP - - - - - - - - - - - - - - - tier3 1488 0 0 1299 586 31.04 NA NA NA 529205 TCGA-AB-2906 AML49 3 32779614 32779614 T C SNP CNOT10 NM_015442.1 human genbank 54_36p 1 provisional intronic c.1840+255 e15+255 0.001 - - - no_errors tier3 388 0 0 260 212 44.92 NA NA NA 529205 TCGA-AB-2906 AML49 3 34616122 34616122 T A SNP - - - - - - - - - - - - - - - tier3 2620 0 0 1305 1044 44.39 NA NA NA 529205 TCGA-AB-2906 AML49 3 45275720 45275720 C A SNP TMEM158 NM_015444.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33197 NULL 0.003 - - - no_errors tier3 1858 1 0.05 817 629 43.5 NA NA NA 529205 TCGA-AB-2906 AML49 3 45971992 45971992 C G SNP FYCO1 NM_024513.2 human genbank 54_36p -1 validated intronic c.3800-103 e13-103 0.002 - - - no_errors tier3 568 0 0 380 273 41.81 NA NA NA 529205 TCGA-AB-2906 AML49 3 52800504 52800504 C T SNP ITIH1 NM_002215.2 human genbank 54_36p 1 validated intronic c.2495-69 e21-69 0.799 - - - no_errors tier3 549 0 0 367 322 46.6 NA NA NA 529205 TCGA-AB-2906 AML49 3 57106759 57106759 G C SNP IL17RD NM_017563.3 human genbank 54_36p -1 validated nonsense c.1916 p.S639* 0.998 NULL HMMPfam_SEFIR - no_errors tier1 452 0 354 242 40.6 NA NA NA 529205 TCGA-AB-2906 AML49 3 61709633 61709633 C G SNP PTPRG NM_002841.3 human genbank 54_36p 1 reviewed missense c.127 p.H43D 1 NULL "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_Carb_anhydrase,superfamily_Carbonic anhydrase,HMMSmart_SM00404,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 941 0 464 352 43.03 NA NA NA 529205 TCGA-AB-2906 AML49 3 63391851 63391851 A T SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-12311 NULL 0.001 - - - no_errors tier3 1155 2 0.17 767 540 41.32 NA NA NA 529205 TCGA-AB-2906 AML49 3 64614565 64614565 T C SNP ADAMTS9 NM_182920.1 human genbank 54_36p -1 reviewed intronic c.1316+504 e8+504 0.006 - - - no_errors tier3 665 1 0.15 394 253 39.1 NA NA NA 529205 TCGA-AB-2906 AML49 3 67255057 67255057 A T SNP - - - - - - - - - - - - - - - tier2 1395 0 0 920 572 38.34 NA NA NA 529205 TCGA-AB-2906 AML49 3 73860062 73860062 A T SNP - - - - - - - - - - - - - - - tier3 2548 0 0 734 560 43.21 NA NA NA 529205 TCGA-AB-2906 AML49 3 74101737 74101737 A T SNP ENSG00000211033 ENST00000388298 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9969 NULL 0.001 - - - pseudogene tier3 1325 0 0 857 556 39.35 NA NA NA 529205 TCGA-AB-2906 AML49 3 76657301 76657301 A G SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-572554 e2-572554 0.011 - - - no_stop_codon:overly_large_intron tier2 925 0 0 461 287 38.37 NA NA NA 529205 TCGA-AB-2906 AML49 3 77169107 77169107 A T SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-60748 e2-60748 0.003 - - - no_stop_codon:overly_large_intron tier3 1408 1 0.07 532 385 41.94 NA NA NA 529205 TCGA-AB-2906 AML49 3 79722353 79722353 C T SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-602 NULL 0 - - - no_errors tier3 952 0 0 592 361 37.88 NA NA NA 529205 TCGA-AB-2906 AML49 3 81763070 81763070 C T SNP GBE1 NM_000158.3 human genbank 54_36p -1 reviewed intronic c.992+11552 e7+11552 0.346 - - - no_errors tier3 920 0 0 729 295 28.72 NA NA NA 529205 TCGA-AB-2906 AML49 3 85195839 85195839 T C SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+104330 e1+104330 0.294 - - - no_errors tier2 1312 1 0.08 682 500 42.27 NA NA NA 529205 TCGA-AB-2906 AML49 3 86723924 86723924 G A SNP - - - - - - - - - - - - - - - tier2 1221 0 0 592 406 40.68 NA NA NA 529205 TCGA-AB-2906 AML49 3 111394988 111394988 G A SNP - - - - - - - - - - - - - - - tier3 1475 1 0.07 721 558 43.59 NA NA NA 529205 TCGA-AB-2906 AML49 3 111991671 111991671 G T SNP - - - - - - - - - - - - - - - tier3 498 0 0 397 209 34.49 NA NA NA 529205 TCGA-AB-2906 AML49 3 112811077 112811077 A G SNP CD96 NM_198196.4 human genbank 54_36p 1 reviewed intronic c.1228+2748 e9+2748 0.027 - - - no_errors tier3 975 0 0 475 401 45.78 NA NA NA 529205 TCGA-AB-2906 AML49 3 117111527 117111527 C T SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.515-57373 e4-57373 0.002 - - - no_errors tier3 2140 1 0.05 1206 902 42.77 NA NA NA 529205 TCGA-AB-2906 AML49 3 117764616 117764616 C T SNP ENSG00000209192 ENST00000386457 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19531 NULL 0.148 - - - pseudogene tier3 1475 2 0.14 923 366 28.39 NA NA NA 529205 TCGA-AB-2906 AML49 3 124727538 124727538 G A SNP PTPLB NM_198402.3 human genbank 54_36p -1 provisional intronic c.381+2385 e4+2385 0.001 - - - no_errors tier3 1415 1 0.07 1159 445 27.71 NA NA NA 529205 TCGA-AB-2906 AML49 3 124727539 124727539 C A SNP PTPLB NM_198402.3 human genbank 54_36p -1 provisional intronic c.381+2384 e4+2384 0.001 - - - no_errors tier3 1435 0 0 1179 441 27.22 NA NA NA 529205 TCGA-AB-2906 AML49 3 126005324 126005324 T - DEL ITGB5 NM_002213.3 human genbank 54_36p -1 provisional intronic c.1263+5235 e9+5235 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 3 128700271 128700271 T A SNP - - - - - - - - - - - - - - - tier3 593 2 0.34 374 267 41.59 NA NA NA 529205 TCGA-AB-2906 AML49 3 130254905 130254905 T C SNP GP9 NM_000174.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8368 NULL 0 - - - no_errors tier2 943 0 0 448 339 43.07 NA NA NA 529205 TCGA-AB-2906 AML49 3 131437743 131437743 C A SNP LOC100131335 XM_001717966.1 human genbank 54_36p 1 model intronic c.711+988 e12+988 0 - - - no_errors tier3 1906 0 0 1250 636 33.72 NA NA NA 529205 TCGA-AB-2906 AML49 3 136355761 136355761 C T SNP EPHB1 NM_004441.3 human genbank 54_36p 1 reviewed nonsense c.1375 p.Q459* 1 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III" "HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),PatternScan_EGF_2,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 1302 0 698 600 46.08 NA NA NA 529205 TCGA-AB-2906 AML49 3 138238637 138238637 C T SNP IL20RB NM_144717.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*26882 NULL 0.998 - - - no_errors tier2 1293 0 0 713 395 35.62 NA NA NA 529205 TCGA-AB-2906 AML49 3 143154278 143154278 T C SNP TFDP2 NM_006286.3 human genbank 54_36p -1 provisional intronic c.978-50 e10-50 0 - - - no_errors tier3 547 1 0.18 385 250 39.37 NA NA NA 529205 TCGA-AB-2906 AML49 3 143760312 143760312 C T SNP ATR NM_001184.3 human genbank 54_36p -1 reviewed splice_region c.1733-4 e8-4 0.015 - - - no_errors tier3 1092 0 0 756 493 39.47 NA NA NA 529205 TCGA-AB-2906 AML49 3 147085393 147085393 A - DEL ENSG00000222350 ENST00000410418 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-12371 NULL 0.003 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 3 158555471 158555471 C - DEL VEPH1 NM_024621.1 human genbank 54_36p -1 provisional intronic c.1735+8376 e8+8376 0.021 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 3 164538093 164538093 A C SNP - - - - - - - - - - - - - - - tier2 573 0 0 440 303 40.78 NA NA NA 529205 TCGA-AB-2906 AML49 3 165463366 165463366 A G SNP - - - - - - - - - - - - - - - tier3 832 0 0 435 325 42.71 NA NA NA 529205 TCGA-AB-2906 AML49 3 166236407 166236407 A C SNP SI NM_001041.2 human genbank 54_36p -1 validated intronic c.2515+464 e21+464 0.012 - - - no_errors tier3 852 0 0 500 379 43.12 NA NA NA 529205 TCGA-AB-2906 AML49 3 167062516 167062516 G A SNP BCHE NM_000055.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31001 NULL 0 - - - no_errors tier3 814 0 0 452 238 34.49 NA NA NA 529205 TCGA-AB-2906 AML49 3 188420628 188420628 C T SNP MASP1 NM_001879.1 human genbank 54_36p -1 reviewed silent c.2025 p.K675 0.93 "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases" "PatternScan_ASX_HYDROXYL,HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMPfam_Trypsin,HMMSmart_SM00020,HMMSmart_SM00179,superfamily_Trypsin-like serine proteases,PatternScan_EGF_2,superfamily_Complement control module/SCR domain,PatternScan_EGF_CA,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER,superfamily_EGF/Laminin" - no_errors tier1 1566 0 993 770 43.68 NA NA NA 529205 TCGA-AB-2906 AML49 3 188750545 188750545 C T SNP - - - - - - - - - - - - - - - tier3 1893 1 0.05 1010 853 45.79 NA NA NA 529205 TCGA-AB-2906 AML49 3 192197875 192197875 G A SNP - - - - - - - - - - - - - - - tier3 1953 0 0 1173 645 35.48 NA NA NA 529205 TCGA-AB-2906 AML49 3 194587837 194587837 T C SNP ATP13A5 NM_198505.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-8629 NULL 0.011 - - - no_errors tier2 1252 1 0.08 837 422 33.44 NA NA NA 529205 TCGA-AB-2906 AML49 3 195067659 195067659 G A SNP - - - - - - - - - - - - - - - tier3 681 1 0.15 398 231 36.67 NA NA NA 529205 TCGA-AB-2906 AML49 4 4421483 4421483 A G SNP uc003ghz.1 ENST00000327590 human ensembl 54_36p 1 known intronic c.1-16618 e1-16618 0.001 - - - no_errors tier3 773 1 0.13 341 253 42.52 NA NA NA 529205 TCGA-AB-2906 AML49 4 9433921 9433921 G T SNP ENSG00000209883 ENST00000387148 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30338 NULL 0.002 - - - pseudogene tier3 1633 0 0 737 541 42.3 NA NA NA 529205 TCGA-AB-2906 AML49 4 10373294 10373294 T C SNP - - - - - - - - - - - - - - - tier3 1141 1 0.09 757 531 41.19 NA NA NA 529205 TCGA-AB-2906 AML49 4 16079531 16079531 A G SNP LDB2 NM_001290.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*33833 NULL 0.009 - - - no_errors tier3 944 1 0.11 339 245 41.88 NA NA NA 529205 TCGA-AB-2906 AML49 4 16847491 16847491 T C SNP - - - - - - - - - - - - - - - tier3 1643 0 0 1025 442 30.13 NA NA NA 529205 TCGA-AB-2906 AML49 4 17242726 17242726 T C SNP LAP3 NM_015907.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*24416 NULL 0.012 - - - no_errors tier2 1883 1 0.05 681 402 37.08 NA NA NA 529205 TCGA-AB-2906 AML49 4 19937216 19937216 G C SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.395+57614 e4+57614 0 - - - no_errors tier3 698 0 0 306 225 42.21 NA NA NA 529205 TCGA-AB-2906 AML49 4 25335708 25335708 A G SNP ENSG00000210018 ENST00000387283 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-6981 NULL 0.005 - - - pseudogene tier3 1535 0 0 1241 902 42.09 NA NA NA 529205 TCGA-AB-2906 AML49 4 25936888 25936888 T C SNP RBPJ NM_005349.2 human genbank 54_36p 1 validated intronic c.59+5353 e1+5353 0.015 - - - no_errors tier2 597 0 0 346 238 40.75 NA NA NA 529205 TCGA-AB-2906 AML49 4 28741830 28741830 A T SNP - - - - - - - - - - - - - - - tier3 1550 0 0 552 359 39.32 NA NA NA 529205 TCGA-AB-2906 AML49 4 32002588 32002588 G T SNP - - - - - - - - - - - - - - - tier2 1597 1 0.06 880 448 33.71 NA NA NA 529205 TCGA-AB-2906 AML49 4 32739652 32739652 C A SNP LOC642305 XR_042368.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-49890 NULL 0 - - - pseudogene tier2 1276 0 0 974 414 29.83 NA NA NA 529205 TCGA-AB-2906 AML49 4 33294303 33294303 G A SNP - - - - - - - - - - - - - - - tier3 718 1 0.14 336 269 44.46 NA NA NA 529205 TCGA-AB-2906 AML49 4 36908525 36908525 G A SNP ENSG00000215243 ENST00000389006 human ensembl 54_36p 1 known 5_prime_flanking_region c.-125918 NULL 0.997 - - - no_start_codon:no_stop_codon tier2 1240 1 0.08 492 335 40.46 NA NA NA 529205 TCGA-AB-2906 AML49 4 40522424 40522424 C T SNP APBB2 NM_173075.4 human genbank 54_36p -1 validated intronic c.1747+237 e10+237 0 - - - no_errors tier3 607 1 0.16 404 250 38.23 NA NA NA 529205 TCGA-AB-2906 AML49 4 41412193 41412193 T C SNP LOC100128654 XM_001716720.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22814 NULL 0.506 - - - no_errors tier2 1376 1 0.07 610 362 37.24 NA NA NA 529205 TCGA-AB-2906 AML49 4 46477461 46477461 C T SNP COX7B2 NM_130902.2 human genbank 54_36p -1 validated intronic c.1-45446 e1-45446 0 - - - no_errors tier3 1363 0 0 622 425 40.55 NA NA NA 529205 TCGA-AB-2906 AML49 4 47537800 47537800 G A SNP CORIN NM_006587.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3077 NULL 0.06 - - - no_errors tier2 730 1 0.14 464 316 40.46 NA NA NA 529205 TCGA-AB-2906 AML49 4 48761422 48761422 C A SNP FLJ21511 NM_025087.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*2758 NULL 0 - - - no_errors tier3 1519 0 0 860 755 46.72 NA NA NA 529205 TCGA-AB-2906 AML49 4 54955515 54955515 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 4 62053928 62053928 C T SNP LPHN3 NM_015236.4 human genbank 54_36p 1 reviewed intronic c.55+8267 e1+8267 0 - - - no_errors tier3 579 0 0 255 162 38.85 NA NA NA 529205 TCGA-AB-2906 AML49 4 65901446 65901446 C G SNP EPHA5 NM_004439.5 human genbank 54_36p -1 reviewed intronic c.2237-30 e13-30 0.001 - - - no_errors tier3 981 0 0 637 318 33.3 NA NA NA 529205 TCGA-AB-2906 AML49 4 66125340 66125340 A T SNP EPHA5 NM_004439.5 human genbank 54_36p -1 reviewed intronic c.910+24614 e3+24614 0.006 - - - no_errors tier3 1208 2 0.17 656 292 30.8 NA NA NA 529205 TCGA-AB-2906 AML49 4 66671126 66671126 C T SNP - - - - - - - - - - - - - - - tier3 1494 0 0 738 582 44.06 NA NA NA 529205 TCGA-AB-2906 AML49 4 71099228 71099228 G A SNP ODAM NM_017855.3 human genbank 54_36p 1 validated intronic c.423+296 e5+296 0 - - - no_errors tier3 1578 0 0 926 645 41.06 NA NA NA 529205 TCGA-AB-2906 AML49 4 73545107 73545107 T C SNP ADAMTS3 NM_014243.1 human genbank 54_36p -1 reviewed intronic c.505-45555 e4-45555 0.002 - - - no_errors tier3 598 0 0 371 188 33.63 NA NA NA 529205 TCGA-AB-2906 AML49 4 92777973 92777973 A T SNP - - - - - - - - - - - - - - - tier3 1030 0 0 523 244 31.81 NA NA NA 529205 TCGA-AB-2906 AML49 4 99291253 99291253 G A SNP C4orf37 NM_174952.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-7929 NULL 0 - - - no_errors tier2 928 0 0 526 324 38.07 NA NA NA 529205 TCGA-AB-2906 AML49 4 105368483 105368483 G A SNP - - - - - - - - - - - - - - - tier3 1833 0 0 1203 495 29.13 NA NA NA 529205 TCGA-AB-2906 AML49 4 117083637 117083637 A G SNP - - - - - - - - - - - - - - - tier2 811 0 0 438 257 36.98 NA NA NA 529205 TCGA-AB-2906 AML49 4 117843264 117843264 C A SNP - - - - - - - - - - - - - - - tier3 934 1 0.11 449 345 43.45 NA NA NA 529205 TCGA-AB-2906 AML49 4 126033460 126033460 T C SNP - - - - - - - - - - - - - - - tier3 682 0 0 405 275 40.38 NA NA NA 529205 TCGA-AB-2906 AML49 4 127589505 127589505 G A SNP - - - - - - - - - - - - - - - tier3 1188 0 0 607 441 42.08 NA NA NA 529205 TCGA-AB-2906 AML49 4 132313922 132313922 A G SNP - - - - - - - - - - - - - - - tier3 725 1 0.14 484 430 47.05 NA NA NA 529205 TCGA-AB-2906 AML49 4 133127590 133127590 C T SNP LOC646187 XR_016991.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-9225 NULL 0.001 - - - no_errors tier3 965 0 0 427 329 43.46 NA NA NA 529205 TCGA-AB-2906 AML49 4 137229396 137229396 A G SNP - - - - - - - - - - - - - - - tier3 1029 0 0 604 446 42.48 NA NA NA 529205 TCGA-AB-2906 AML49 4 147790123 147790123 T A SNP POU4F2 NM_004575.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*8713 NULL 0 - - - no_errors tier3 2022 1 0.05 905 607 40.09 NA NA NA 529205 TCGA-AB-2906 AML49 4 152905372 152905372 G A SNP PET112L NM_004564.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-3788 NULL 1 - - - no_errors tier3 978 0 0 514 250 32.68 NA NA NA 529205 TCGA-AB-2906 AML49 4 153854485 153854485 T C SNP TMEM154 NM_152680.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-33950 NULL 0.001 - - - no_errors tier2 1362 1 0.07 426 327 43.43 NA NA NA 529205 TCGA-AB-2906 AML49 4 160996769 160996769 G A SNP - - - - - - - - - - - - - - - tier3 575 0 0 284 180 38.79 NA NA NA 529205 TCGA-AB-2906 AML49 4 162800688 162800688 C T SNP FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.728-3592 e6-3592 0.002 - - - no_errors tier3 971 0 0 565 389 40.73 NA NA NA 529205 TCGA-AB-2906 AML49 4 172984494 172984494 A T SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.138+12050 e1+12050 0.041 - - - no_errors tier3 1164 0 0 480 362 42.99 NA NA NA 529205 TCGA-AB-2906 AML49 4 173115098 173115098 A G SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.138+142654 e1+142654 0 - - - no_errors tier3 689 0 0 498 341 40.64 NA NA NA 529205 TCGA-AB-2906 AML49 4 177065189 177065189 T C SNP GPM6A NM_005277.3 human genbank 54_36p -1 validated intronic c.1-94795 e1-94795 0 - - - no_errors tier3 2329 1 0.04 1064 788 42.5 NA NA NA 529205 TCGA-AB-2906 AML49 4 178987434 178987434 T - DEL LOC285501 NM_001085490.1 human genbank 54_36p 1 predicted intronic c.1+96807 e0+96807 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 4 182496358 182496358 G A SNP - - - - - - - - - - - - - - - tier3 1840 0 0 832 591 41.5 NA NA NA 529205 TCGA-AB-2906 AML49 4 182910997 182910997 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 4 183023990 183023990 C T SNP LOC728191 XM_001126817.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-35870 NULL 0.41 - - - no_errors tier3 2151 0 0 1231 739 37.51 NA NA NA 529205 TCGA-AB-2906 AML49 4 187336085 187336085 G A SNP KLKB1 NM_000892.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-50259 NULL 0.019 - - - no_errors tier3 1279 0 0 443 500 52.97 NA NA NA 529205 TCGA-AB-2906 AML49 4 190205924 190205924 G C SNP - - - - - - - - - - - - - - - tier3 915 0 0 671 291 30.25 NA NA NA 529205 TCGA-AB-2906 AML49 5 2645059 2645059 G C SNP LOC100133292 XM_001715713.1 human genbank 54_36p -1 model missense c.227 p.T76R 0.065 NULL NULL - no_errors tier1 1188 0 517 374 41.93 NA NA NA 529205 TCGA-AB-2906 AML49 5 2776008 2776008 G A SNP C5orf38 NM_178569.2 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-29371 NULL 0.001 - - - no_errors tier3 655 0 0 336 279 45.37 NA NA NA 529205 TCGA-AB-2906 AML49 5 2871766 2871766 T G SNP ENSG00000215233 ENST00000399855 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30120 NULL 0 - - - no_coding_region:pseudogene tier3 618 0 0 363 290 44.41 NA NA NA 529205 TCGA-AB-2906 AML49 5 5095620 5095620 G C SNP ENSG00000215231 ENST00000399853 human ensembl 54_36p 1 known intronic c.132+3709 e2+3709 0 - - - no_errors tier3 2055 2 0.1 1138 803 41.33 NA NA NA 529205 TCGA-AB-2906 AML49 5 8325881 8325881 C T SNP - - - - - - - - - - - - - - - tier3 2302 0 0 1158 977 45.7 NA NA NA 529205 TCGA-AB-2906 AML49 5 15726124 15726124 G T SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.127+56943 e2+56943 0.023 - - - no_errors tier3 536 1 0.19 363 160 30.59 NA NA NA 529205 TCGA-AB-2906 AML49 5 16716174 16716174 C A SNP MYO10 NM_012334.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*3627 NULL 0.002 - - - no_errors tier2 1256 3 0.24 907 649 41.68 NA NA NA 529205 TCGA-AB-2906 AML49 5 18071197 18071198 TT - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 5 22062145 22062145 G A SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.232-50894 e2-50894 0 - - - no_errors tier3 1290 2 0.15 537 449 45.54 NA NA NA 529205 TCGA-AB-2906 AML49 5 22348792 22348792 C T SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1+92331 e0+92331 0.002 - - - no_errors tier3 1045 1 0.1 385 261 40.4 NA NA NA 529205 TCGA-AB-2906 AML49 5 22545589 22545589 C T SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-4359 e1-4359 0.039 - - - no_errors tier3 1005 2 0.2 636 286 30.99 NA NA NA 529205 TCGA-AB-2906 AML49 5 22731514 22731514 A G SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1+157410 e0+157410 0.004 - - - no_errors tier2 620 0 0 348 206 37.12 NA NA NA 529205 TCGA-AB-2906 AML49 5 29385298 29385298 T C SNP - - - - - - - - - - - - - - - tier3 698 0 0 456 204 30.91 NA NA NA 529205 TCGA-AB-2906 AML49 5 39409530 39409530 A G SNP DAB2 NM_001343.2 human genbank 54_36p -1 validated intronic c.2313-246 e14-246 0.001 - - - no_errors tier3 882 0 0 602 368 37.94 NA NA NA 529205 TCGA-AB-2906 AML49 5 41685265 41685265 G A SNP - - - - - - - - - - - - - - - tier3 917 0 0 558 390 41.05 NA NA NA 529205 TCGA-AB-2906 AML49 5 53391004 53391004 T G SNP ARL15 NM_019087.2 human genbank 54_36p -1 validated intronic c.462+53785 e4+53785 0.012 - - - no_errors tier3 830 0 0 422 295 41.14 NA NA NA 529205 TCGA-AB-2906 AML49 5 55781015 55781015 G A SNP - - - - - - - - - - - - - - - tier3 903 2 0.22 616 460 42.75 NA NA NA 529205 TCGA-AB-2906 AML49 5 57754481 57754481 G C SNP PLK2 NM_006622.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*31686 NULL 0.013 - - - no_errors tier3 1333 0 0 653 498 43.23 NA NA NA 529205 TCGA-AB-2906 AML49 5 62430896 62430896 T A SNP - - - - - - - - - - - - - - - tier3 818 1 0.12 398 285 41.73 NA NA NA 529205 TCGA-AB-2906 AML49 5 66921795 66921795 G T SNP - - - - - - - - - - - - - - - tier2 1844 0 0 1279 850 39.91 NA NA NA 529205 TCGA-AB-2906 AML49 5 71645016 71645016 T A SNP MRPS27 NM_015084.2 human genbank 54_36p -1 reviewed intronic c.151+648 e2+648 0.012 - - - no_errors tier3 1288 0 0 908 658 42.02 NA NA NA 529205 TCGA-AB-2906 AML49 5 77151757 77151757 G T SNP TBCA NM_004607.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43920 NULL 0 - - - no_errors tier3 1155 0 0 588 401 40.55 NA NA NA 529205 TCGA-AB-2906 AML49 5 91593817 91593817 G A SNP - - - - - - - - - - - - - - - tier3 1214 0 0 540 347 39.08 NA NA NA 529205 TCGA-AB-2906 AML49 5 103096152 103096152 C A SNP - - - - - - - - - - - - - - - tier3 1040 0 0 430 205 32.28 NA NA NA 529205 TCGA-AB-2906 AML49 5 103209376 103209376 G A SNP - - - - - - - - - - - - - - - tier3 1850 0 0 1011 747 42.44 NA NA NA 529205 TCGA-AB-2906 AML49 5 109751468 109751468 C T SNP FLJ43080 XM_001719018.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*36983 NULL 0.024 - - - no_errors tier3 1185 0 0 619 448 41.99 NA NA NA 529205 TCGA-AB-2906 AML49 5 114594838 114594838 C T SNP PGGT1B NM_005023.3 human genbank 54_36p -1 validated intronic c.613-221 e6-221 0 - - - no_errors tier3 2632 2 0.08 1401 914 39.46 NA NA NA 529205 TCGA-AB-2906 AML49 5 121867587 121867587 C T SNP ENSG00000197462 ENST00000354541 human ensembl 54_36p -1 known 5_prime_flanking_region c.-25246 NULL 0.001 - - - no_errors tier3 1522 0 0 1040 642 38.1 NA NA NA 529205 TCGA-AB-2906 AML49 5 135053339 135053339 C T SNP - - - - - - - - - - - - - - - tier3 1116 0 0 692 495 41.67 NA NA NA 529205 TCGA-AB-2906 AML49 5 137571248 137571248 A G SNP CDC23 NM_004661.3 human genbank 54_36p -1 reviewed intronic c.235-976 e3-976 0.334 - - - no_errors tier3 658 1 0.15 448 331 42.49 NA NA NA 529205 TCGA-AB-2906 AML49 5 143134527 143134527 T C SNP HMHB1 NM_021182.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-37499 NULL 0 - - - no_errors tier2 1191 1 0.08 497 407 44.87 NA NA NA 529205 TCGA-AB-2906 AML49 5 144344364 144344364 A G SNP - - - - - - - - - - - - - - - tier3 2401 2 0.08 1101 907 45.17 NA NA NA 529205 TCGA-AB-2906 AML49 5 154681694 154681694 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 5 155251605 155251605 C T SNP ENSG00000200275 ENST00000363405 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46463 NULL 0 - - - no_errors tier3 596 0 0 325 232 41.65 NA NA NA 529205 TCGA-AB-2906 AML49 5 157661896 157661896 G A SNP - - - - - - - - - - - - - - - tier2 681 0 0 398 227 36.32 NA NA NA 529205 TCGA-AB-2906 AML49 5 158809596 158809596 G A SNP - - - - - - - - - - - - - - - tier3 2512 1 0.04 1269 998 44 NA NA NA 529205 TCGA-AB-2906 AML49 5 174373030 174373030 G A SNP ENSG00000204754 ENST00000377300 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17707 NULL 0 - - - no_errors tier3 759 3 0.39 571 486 45.55 NA NA NA 529205 TCGA-AB-2906 AML49 6 6411541 6411541 C T SNP - - - - - - - - - - - - - - - tier3 1376 0 0 850 590 40.97 NA NA NA 529205 TCGA-AB-2906 AML49 6 7334482 7334482 A T SNP CAGE1 NM_205864.2 human genbank 54_36p -1 validated 5_prime_untranslated_region c.-10355 NULL 0.021 - - - no_errors tier3 442 0 0 219 120 35.29 NA NA NA 529205 TCGA-AB-2906 AML49 6 10632755 10632755 T C SNP GCNT2 ENST00000409770 human ensembl 54_36p 1 known intronic c.1-2938 e1-2938 0.02 - - - no_errors tier3 921 0 0 484 386 44.32 NA NA NA 529205 TCGA-AB-2906 AML49 6 12614999 12614999 G A SNP LOC653232 XM_927555.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-7329 NULL 0 - - - pseudogene tier3 1519 0 0 736 511 40.98 NA NA NA 529205 TCGA-AB-2906 AML49 6 14737965 14737965 C G SNP ENSG00000206960 ENST00000384233 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16780 NULL 0 - - - no_errors tier3 942 0 0 451 248 35.48 NA NA NA 529205 TCGA-AB-2906 AML49 6 17312982 17312982 C G SNP ENSG00000209103 ENST00000386368 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*20247 NULL 0 - - - pseudogene tier3 322 0 0 239 185 43.53 NA NA NA 529205 TCGA-AB-2906 AML49 6 19759981 19759981 T A SNP ENSG00000200957 ENST00000364087 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9242 NULL 0.038 - - - no_errors tier3 1249 0 0 662 543 45.06 NA NA NA 529205 TCGA-AB-2906 AML49 6 21218046 21218046 C T SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated intronic c.1299+1373 e11+1373 0.005 - - - no_errors tier3 1383 0 0 969 389 28.62 NA NA NA 529205 TCGA-AB-2906 AML49 6 23194556 23194556 A C SNP ENSG00000218476 ENST00000404015 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16339 NULL 0.508 - - - no_coding_region:pseudogene tier2 1914 0 0 1308 934 41.64 NA NA NA 529205 TCGA-AB-2906 AML49 6 38640721 38640722 - T INS BTBD9 NM_001099272.1 human genbank 54_36p -1 validated intronic c.1154+12632_1154+12631 e5+12632 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 6 51399295 51399295 T C SNP ENSG00000212532 ENST00000391230 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38152 NULL 0.002 - - - no_errors tier3 1303 3 0.23 496 350 41.32 NA NA NA 529205 TCGA-AB-2906 AML49 6 63782631 63782631 T A SNP - - - - - - - - - - - - - - - tier3 893 1 0.11 307 216 41.3 NA NA NA 529205 TCGA-AB-2906 AML49 6 66728368 66728368 C T SNP - - - - - - - - - - - - - - - tier2 821 0 0 420 358 46.02 NA NA NA 529205 TCGA-AB-2906 AML49 6 71041165 71041165 G A SNP COL9A1 NM_001851.4 human genbank 54_36p -1 reviewed missense c.1007 p.S336F 0.948 HMMPfam_Collagen "HMMSmart_TSPN,HMMPfam_Collagen,superfamily_ConA_like_lec_gl" - no_errors tier1 1091 0 622 321 34.04 NA NA NA 529205 TCGA-AB-2906 AML49 6 74082409 74082410 - T INS C6orf221 NM_001017361.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46765 NULL 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 6 78097308 78097308 G A SNP - - - - - - - - - - - - - - - tier3 594 0 0 382 239 38.42 NA NA NA 529205 TCGA-AB-2906 AML49 6 78986517 78986517 A G SNP - - - - - - - - - - - - - - - tier3 883 0 0 362 225 38.33 NA NA NA 529205 TCGA-AB-2906 AML49 6 82218044 82218044 G A SNP - - - - - - - - - - - - - - - tier3 1382 2 0.14 920 635 40.84 NA NA NA 529205 TCGA-AB-2906 AML49 6 87098624 87098624 G C SNP - - - - - - - - - - - - - - - tier3 2068 0 0 1041 713 40.58 NA NA NA 529205 TCGA-AB-2906 AML49 6 89087988 89087988 C T SNP ENSG00000220267 ENST00000403258 human ensembl 54_36p -1 known 5_prime_flanking_region c.-44561 NULL 0.531 - - - no_coding_region:pseudogene tier3 1219 0 0 771 538 41.1 NA NA NA 529205 TCGA-AB-2906 AML49 6 95328814 95328814 A G SNP - - - - - - - - - - - - - - - tier3 1411 0 0 1228 862 41.22 NA NA NA 529205 TCGA-AB-2906 AML49 6 98370907 98370907 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 6 98453927 98453927 C T SNP - - - - - - - - - - - - - - - tier3 957 3 0.31 521 453 46.41 NA NA NA 529205 TCGA-AB-2906 AML49 6 99280934 99280934 A G SNP - - - - - - - - - - - - - - - tier2 1190 1 0.08 724 484 40.07 NA NA NA 529205 TCGA-AB-2906 AML49 6 103260047 103260047 G T SNP - - - - - - - - - - - - - - - tier3 1356 0 0 1051 603 36.44 NA NA NA 529205 TCGA-AB-2906 AML49 6 108136737 108136737 G T SNP SCML4 ENST00000369020 human ensembl 54_36p -1 known intronic c.974-829 e6-829 0 - - - no_errors tier3 1778 1 0.06 858 564 39.58 NA NA NA 529205 TCGA-AB-2906 AML49 6 116177294 116177294 C T SNP ENSG00000217019 ENST00000401765 human ensembl 54_36p -1 known 3_prime_flanking_region c.*27796 NULL 0.429 - - - no_coding_region:pseudogene tier3 1245 2 0.16 776 601 43.65 NA NA NA 529205 TCGA-AB-2906 AML49 6 118611042 118611042 C T SNP SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated intronic c.349+28566 e2+28566 0.007 - - - no_errors tier3 1842 3 0.16 1086 710 39.47 NA NA NA 529205 TCGA-AB-2906 AML49 6 122080015 122080015 C A SNP ENSG00000219135 ENST00000406913 human ensembl 54_36p -1 known 5_prime_flanking_region c.-36711 NULL 0.046 - - - no_coding_region:pseudogene tier3 1222 0 0 684 459 40.12 NA NA NA 529205 TCGA-AB-2906 AML49 6 126943576 126943576 A G SNP ENSG00000201613 ENST00000364743 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9550 NULL 0.258 - - - no_errors tier3 1824 0 0 1328 580 30.38 NA NA NA 529205 TCGA-AB-2906 AML49 6 128156453 128156453 G T SNP C6orf190 NM_001010923.1 human genbank 54_36p -1 validated intronic c.1758+19268 e4+19268 0.002 - - - no_errors tier3 1131 0 0 615 326 34.64 NA NA NA 529205 TCGA-AB-2906 AML49 6 132606647 132606647 G A SNP ENSG00000220956 ENST00000405500 human ensembl 54_36p 1 known 5_prime_flanking_region c.-28167 NULL 0.05 - - - no_coding_region:pseudogene tier3 869 1 0.11 567 258 31.27 NA NA NA 529205 TCGA-AB-2906 AML49 6 144014913 144014913 G T SNP PHACTR2 NM_014721.1 human genbank 54_36p 1 validated intronic c.13+43761 e1+43761 0.004 - - - no_errors tier3 1436 0 0 568 387 39.61 NA NA NA 529205 TCGA-AB-2906 AML49 6 148416741 148416741 G A SNP - - - - - - - - - - - - - - - tier3 2530 1 0.04 1464 1083 42.49 NA NA NA 529205 TCGA-AB-2906 AML49 6 152209317 152209317 G A SNP ESR1 NM_000125.3 human genbank 54_36p 1 reviewed intronic c.643+3702 e2+3702 0.889 - - - no_errors tier2 1926 2 0.1 936 667 41.61 NA NA NA 529205 TCGA-AB-2906 AML49 6 154870640 154870640 A G SNP CNKSR3 NM_173515.2 human genbank 54_36p -1 validated intronic c.52+2249 e1+2249 0.703 - - - no_errors tier3 1150 1 0.09 495 239 32.56 NA NA NA 529205 TCGA-AB-2906 AML49 6 158084276 158084276 C T SNP ENSG00000208440 ENST00000385705 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31166 NULL 0 - - - pseudogene tier2 1310 2 0.15 422 336 44.33 NA NA NA 529205 TCGA-AB-2906 AML49 7 2686645 2686645 C G SNP AMZ1 NM_133463.1 human genbank 54_36p 1 provisional intronic c.1+814 e0+814 0.007 - - - no_errors tier2 677 1 0.15 295 252 46.07 NA NA NA 529205 TCGA-AB-2906 AML49 7 11303458 11303458 C T SNP ENSG00000220166 ENST00000405055 human ensembl 54_36p -1 known 5_prime_flanking_region c.-38771 NULL 0 - - - no_coding_region:pseudogene tier3 1224 2 0.16 563 427 43.09 NA NA NA 529205 TCGA-AB-2906 AML49 7 14266125 14266125 C - DEL DGKB NM_004080.2 human genbank 54_36p -1 reviewed intronic c.2125+78540 e22+78540 0.526 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 7 17803475 17803475 C G SNP SNX13 NM_015132.4 human genbank 54_36p -1 reviewed intronic c.2514-388 e25-388 0.003 - - - no_errors tier2 1266 1 0.08 643 460 41.63 NA NA NA 529205 TCGA-AB-2906 AML49 7 22384695 22384695 C T SNP RAPGEF5 NM_012294.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-68531 NULL 0.437 - - - no_errors tier3 510 0 0 302 233 43.55 NA NA NA 529205 TCGA-AB-2906 AML49 7 27847637 27847637 G A SNP JAZF1 NM_175061.3 human genbank 54_36p -1 reviewed intronic c.386-626 e4-626 0 - - - no_errors tier3 1191 2 0.17 926 691 42.71 NA NA NA 529205 TCGA-AB-2906 AML49 7 30383371 30383371 A G SNP NOD1 NM_006092.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*48408 NULL 0.016 - - - no_errors tier3 1249 3 0.24 1210 835 40.79 NA NA NA 529205 TCGA-AB-2906 AML49 7 34849286 34849286 G T SNP NPSR1 NM_207173.1 human genbank 54_36p 1 reviewed intronic c.758-1747 e7-1747 0.003 - - - no_errors tier3 1662 0 0 1048 838 44.34 NA NA NA 529205 TCGA-AB-2906 AML49 7 42541397 42541397 A G SNP LOC100134560 XM_001718995.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-25822 NULL 0.03 - - - no_start_codon:pseudogene tier3 1260 1 0.08 666 489 42.34 NA NA NA 529205 TCGA-AB-2906 AML49 7 50223309 50223309 A G SNP LOC100134819 XM_001718961.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*37332 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1175 0 0 735 513 41.04 NA NA NA 529205 TCGA-AB-2906 AML49 7 50411953 50411953 A G SNP IKZF1 ENST00000331340 human ensembl 54_36p 1 known missense c.389 p.N130S 1 "PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 533 0 346 235 40.38 NA NA NA 529205 TCGA-AB-2906 AML49 7 54276580 54276580 C A SNP - - - - - - - - - - - - - - - tier3 898 1 0.11 545 395 41.93 NA NA NA 529205 TCGA-AB-2906 AML49 7 55280183 55280183 C T SNP EGFR NM_005228.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*39379 NULL 0.891 - - - no_errors tier3 810 0 0 447 262 36.95 NA NA NA 529205 TCGA-AB-2906 AML49 7 77762427 77762427 T C SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.1409-38593 e10-38593 0 - - - no_errors tier3 1858 0 0 1222 628 33.93 NA NA NA 529205 TCGA-AB-2906 AML49 7 78858094 78858094 C A SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.301+62178 e1+62178 0.003 - - - no_errors tier3 1176 1 0.08 903 414 31.39 NA NA NA 529205 TCGA-AB-2906 AML49 7 79028444 79028444 G T SNP - - - - - - - - - - - - - - - tier3 829 0 0 371 201 35.08 NA NA NA 529205 TCGA-AB-2906 AML49 7 81511143 81511143 C T SNP CACNA2D1 NM_000722.2 human genbank 54_36p -1 reviewed intronic c.880-5656 e11-5656 0 - - - no_errors tier2 1853 5 0.27 1289 589 31.33 NA NA NA 529205 TCGA-AB-2906 AML49 7 83777314 83777314 C T SNP - - - - - - - - - - - - - - - tier3 837 1 0.12 429 322 42.88 NA NA NA 529205 TCGA-AB-2906 AML49 7 90850061 90850061 C T SNP - - - - - - - - - - - - - - - tier3 1342 0 0 730 454 38.34 NA NA NA 529205 TCGA-AB-2906 AML49 7 94101411 94101411 T A SNP SGCE NM_001099401.1 human genbank 54_36p -1 reviewed intronic c.110-4322 e2-4322 0 - - - no_errors tier3 678 0 0 309 244 44.04 NA NA NA 529205 TCGA-AB-2906 AML49 7 96277318 96277318 A T SNP LOC402679 XR_041896.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-44413 NULL 0 - - - no_errors tier3 1497 0 0 1213 813 40.09 NA NA NA 529205 TCGA-AB-2906 AML49 7 107681622 107681622 A G SNP NRCAM NM_001037132.1 human genbank 54_36p -1 reviewed intronic c.1-13772 e1-13772 0 - - - no_errors tier2 1781 3 0.17 868 633 42 NA NA NA 529205 TCGA-AB-2906 AML49 7 115873155 115873155 C T SNP - - - - - - - - - - - - - - - tier3 1513 1 0.07 886 626 41.37 NA NA NA 529205 TCGA-AB-2906 AML49 7 122373857 122373857 G A SNP TAS2R16 NM_016945.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*48192 NULL 0.009 - - - no_errors tier3 474 0 0 298 184 38.17 NA NA NA 529205 TCGA-AB-2906 AML49 7 123091670 123091671 - T INS LMOD2 ENST00000332074 human ensembl 54_36p 1 known intronic c.NULL NULL 0.003:0.001 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 7 126068563 126068563 C A SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.1358-31775 e7-31775 0.067 - - - no_errors tier3 1382 0 0 784 370 32.06 NA NA NA 529205 TCGA-AB-2906 AML49 7 126653712 126653712 C A SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.510+16273 e1+16273 0.006 - - - no_errors tier3 868 0 0 474 230 32.67 NA NA NA 529205 TCGA-AB-2906 AML49 7 130790381 130790381 G A SNP MKLN1 NM_013255.1 human genbank 54_36p 1 validated intronic c.1526-8135 e13-8135 0.004 - - - no_errors tier3 1057 0 0 496 352 41.46 NA NA NA 529205 TCGA-AB-2906 AML49 7 137963279 137963279 T C SNP SVOPL NM_174959.1 human genbank 54_36p -1 validated intronic c.613+164 e6+164 0.001 - - - no_errors tier3 1434 0 0 608 441 41.96 NA NA NA 529205 TCGA-AB-2906 AML49 7 138227238 138227238 C T SNP KIAA1549 NM_020910.1 human genbank 54_36p -1 validated intronic c.3882+2390 e9+2390 0 - - - no_errors tier3 885 0 0 542 354 39.46 NA NA NA 529205 TCGA-AB-2906 AML49 7 139630878 139630878 C T SNP ENSG00000213232 ENST00000393023 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8140 NULL 0.018 - - - no_coding_region:pseudogene tier3 1199 0 0 489 353 41.92 NA NA NA 529205 TCGA-AB-2906 AML49 7 145577431 145577431 G A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.97+132433 e1+132433 0 - - - no_errors tier3 1315 2 0.15 591 475 44.52 NA NA NA 529205 TCGA-AB-2906 AML49 7 154517958 154517958 C A SNP uc003wlt.1 ENST00000395731 human ensembl 54_36p -1 known 5_prime_flanking_region c.-24012 NULL 0.002 - - - no_errors tier3 1056 0 0 358 285 44.25 NA NA NA 529205 TCGA-AB-2906 AML49 8 4536927 4536927 C - DEL CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.86-54439 e2-54439 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 8 10250881 10250881 C T SNP MSRA NM_012331.1 human genbank 54_36p 1 reviewed intronic c.543+35972 e5+35972 0 - - - no_errors tier3 1429 0 0 852 388 31.29 NA NA NA 529205 TCGA-AB-2906 AML49 8 12627703 12627703 A G SNP LONRF1 NM_152271.3 human genbank 54_36p -1 provisional silent c.2067 p.S689 0.951 "HMMPfam_LON,HMMSmart_SM00464" "HMMSmart_SM00184,HMMPfam_LON,HMMSmart_SM00464,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,HMMSmart_SM00028,superfamily_TPR-like,superfamily_RING/U-box" - no_errors tier1 988 2 0.2 640 469 42.25 NA NA NA 529205 TCGA-AB-2906 AML49 8 14349651 14349651 G T SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.234+106961 e2+106961 0.025 - - - no_errors tier2 1367 1 0.07 636 438 40.74 NA NA NA 529205 TCGA-AB-2906 AML49 8 25924714 25924714 G A SNP EBF2 NM_022659.2 human genbank 54_36p -1 validated intronic c.551+21804 e6+21804 0 - - - no_errors tier3 1311 2 0.15 493 353 41.73 NA NA NA 529205 TCGA-AB-2906 AML49 8 34348248 34348248 G A SNP RPL10AP3 ENST00000399893 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47546 NULL 1 - - - no_stop_codon tier2 1382 4 0.29 1388 602 30.24 NA NA NA 529205 TCGA-AB-2906 AML49 8 34852021 34852021 C A SNP LOC100133273 XR_039238.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*250 NULL 0.001 - - - pseudogene tier3 969 2 0.21 234 178 43.2 NA NA NA 529205 TCGA-AB-2906 AML49 8 39505072 39505072 T A SNP LOC100130964 XM_001724582.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-44962 NULL 0.008 - - - no_errors tier3 873 0 0 461 364 44.07 NA NA NA 529205 TCGA-AB-2906 AML49 8 40477711 40477711 T C SNP ZMAT4 NM_024645.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*31188 NULL 0 - - - no_errors tier3 1301 2 0.15 743 461 38.29 NA NA NA 529205 TCGA-AB-2906 AML49 8 69652270 69652270 G T SNP C8orf34 NM_052958.1 human genbank 54_36p 1 predicted intronic c.772+44332 e6+44332 0 - - - no_errors tier3 504 0 0 311 127 28.8 NA NA NA 529205 TCGA-AB-2906 AML49 8 70541599 70541599 G T SNP SULF1 NM_015170.1 human genbank 54_36p 1 validated 5_prime_untranslated_region c.-97166 NULL 1 - - - no_errors tier2 910 1 0.11 473 321 40.33 NA NA NA 529205 TCGA-AB-2906 AML49 8 84339755 84339755 T A SNP - - - - - - - - - - - - - - - tier3 1332 1 0.07 750 318 29.78 NA NA NA 529205 TCGA-AB-2906 AML49 8 84648035 84648035 G A SNP - - - - - - - - - - - - - - - tier3 1311 0 0 534 408 43.31 NA NA NA 529205 TCGA-AB-2906 AML49 8 89995874 89995874 A G SNP - - - - - - - - - - - - - - - tier3 1319 1 0.08 957 747 43.84 NA NA NA 529205 TCGA-AB-2906 AML49 8 93379623 93379623 G T SNP - - - - - - - - - - - - - - - tier3 2211 2 0.09 1728 797 31.56 NA NA NA 529205 TCGA-AB-2906 AML49 8 102945478 102945478 A G SNP NCALD NM_001040624.1 human genbank 54_36p -1 reviewed intronic c.1+23067 e0+23067 0 - - - no_errors tier3 2394 0 0 1359 1082 44.33 NA NA NA 529205 TCGA-AB-2906 AML49 8 106719629 106719629 C T SNP ZFPM2 NM_012082.3 human genbank 54_36p 1 reviewed intronic c.532+3868 e5+3868 0.006 - - - no_errors tier3 1661 0 0 916 603 39.67 NA NA NA 529205 TCGA-AB-2906 AML49 8 108499607 108499607 T C SNP ANGPT1 NM_001146.3 human genbank 54_36p -1 reviewed intronic c.298-71106 e2-71106 0 - - - no_errors tier3 1382 0 0 901 641 41.57 NA NA NA 529205 TCGA-AB-2906 AML49 8 109812515 109812515 T C SNP - - - - - - - - - - - - - - - tier3 1184 0 0 661 441 40.02 NA NA NA 529205 TCGA-AB-2906 AML49 8 112777941 112777941 G T SNP - - - - - - - - - - - - - - - tier3 471 0 0 237 123 34.17 NA NA NA 529205 TCGA-AB-2906 AML49 8 115206324 115206324 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 8 115566671 115566671 A G SNP - - - - - - - - - - - - - - - tier3 975 0 0 464 315 40.44 NA NA NA 529205 TCGA-AB-2906 AML49 8 132451499 132451499 G T SNP - - - - - - - - - - - - - - - tier3 1629 2 0.12 798 525 39.68 NA NA NA 529205 TCGA-AB-2906 AML49 8 136603122 136603122 G T SNP KHDRBS3 NM_006558.1 human genbank 54_36p 1 provisional intronic c.207+342 e2+342 0.001 - - - no_errors tier3 1093 0 0 558 389 41.08 NA NA NA 529205 TCGA-AB-2906 AML49 8 144285865 144285865 G A SNP LY6H NM_002347.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*25177 NULL 0.002 - - - no_errors tier2 854 1 0.12 312 258 45.1 NA NA NA 529205 TCGA-AB-2906 AML49 9 1271395 1271395 G T SNP ENSG00000218946 ENST00000407607 human ensembl 54_36p 1 known 5_prime_flanking_region c.-47269 NULL 0 - - - no_coding_region:pseudogene tier3 1081 0 0 917 159 14.76 NA NA NA 529205 TCGA-AB-2906 AML49 9 7593123 7593123 A - DEL LOC392285 XR_017134.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*4529 NULL 0.005 - - - pseudogene tier2 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 9 10112565 10112565 A T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-88775 e1-88775 0.044 - - - no_errors tier3 1295 0 0 704 365 34.14 NA NA NA 529205 TCGA-AB-2906 AML49 9 11694982 11694982 C A SNP - - - - - - - - - - - - - - - tier3 1034 0 0 686 501 42.21 NA NA NA 529205 TCGA-AB-2906 AML49 9 13363849 13363849 G A SNP FLJ41200 XM_379623.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*34495 NULL 0.272 - - - no_errors tier2 1011 0 0 577 398 40.82 NA NA NA 529205 TCGA-AB-2906 AML49 9 16357798 16357798 A T SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated 3_prime_flanking_region c.*51189 NULL 0.001 - - - no_errors tier3 906 0 0 458 344 42.89 NA NA NA 529205 TCGA-AB-2906 AML49 9 20388730 20388730 T C SNP MLLT3 NM_004529.2 human genbank 54_36p -1 validated intronic c.1125+14989 e5+14989 1 - - - no_errors tier2 782 0 0 505 364 41.89 NA NA NA 529205 TCGA-AB-2906 AML49 9 22104306 22104306 T C SNP CDKN2BAS NR_003529.3 human genbank 54_36p 1 validated intronic c.NULL NULL 0 - - - no_errors tier3 1017 1 0.1 695 300 30.15 NA NA NA 529205 TCGA-AB-2906 AML49 9 25434662 25434662 C T SNP - - - - - - - - - - - - - - - tier3 680 2 0.29 579 300 34.13 NA NA NA 529205 TCGA-AB-2906 AML49 9 25899885 25899885 T C SNP - - - - - - - - - - - - - - - tier3 2571 5 0.19 960 739 43.45 NA NA NA 529205 TCGA-AB-2906 AML49 9 28385583 28385583 G C SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1-22717 e1-22717 0 - - - no_errors tier2 1406 0 0 791 523 39.74 NA NA NA 529205 TCGA-AB-2906 AML49 9 31096196 31096196 A G SNP - - - - - - - - - - - - - - - tier3 1615 1 0.06 934 619 39.86 NA NA NA 529205 TCGA-AB-2906 AML49 9 46983496 46983496 A G SNP LOC100131538 XM_001719973.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*15061 NULL 0 - - - no_errors tier3 1367 0 0 798 216 21.22 NA NA NA 529205 TCGA-AB-2906 AML49 9 75898074 75898075 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 9 81841621 81841621 G T SNP - - - - - - - - - - - - - - - tier3 951 0 0 605 445 42.18 NA NA NA 529205 TCGA-AB-2906 AML49 9 84209028 84209028 T C SNP LOC442427 XR_037390.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*27596 NULL 0.005 - - - pseudogene tier3 872 0 0 632 284 30.97 NA NA NA 529205 TCGA-AB-2906 AML49 9 85099222 85099222 G A SNP FRMD3 NM_174938.4 human genbank 54_36p -1 validated intronic c.1071-3760 e13-3760 0.002 - - - no_errors tier3 1070 1 0.09 670 474 40.24 NA NA NA 529205 TCGA-AB-2906 AML49 9 89295063 89295063 G A SNP DAPK1 NM_004938.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8750 NULL 0 - - - no_errors tier3 771 0 0 401 241 37.54 NA NA NA 529205 TCGA-AB-2906 AML49 9 92533881 92533881 C T SNP ENSG00000187503 ENST00000339424 human ensembl 54_36p -1 known 3_prime_flanking_region c.*10747 NULL 0.013 - - - no_coding_region:pseudogene tier3 486 0 0 331 280 45.75 NA NA NA 529205 TCGA-AB-2906 AML49 9 112942066 112942066 C A SNP ENSG00000212409 ENST00000391107 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42552 NULL 0.006 - - - no_errors tier3 1303 0 0 803 525 39.5 NA NA NA 529205 TCGA-AB-2906 AML49 9 122211216 122211216 C T SNP CDK5RAP2 NM_018249.1 human genbank 54_36p -1 reviewed splice_region c.4604+10 e30+10 0 - - - no_errors tier2 722 1 0.14 518 411 44.24 NA NA NA 529205 TCGA-AB-2906 AML49 9 128145237 128145237 C T SNP FAM125B NM_033446.1 human genbank 54_36p 1 validated intronic c.204+2507 e2+2507 0.009 - - - no_errors tier3 614 0 0 452 195 30.09 NA NA NA 529205 TCGA-AB-2906 AML49 9 132100914 132100914 G A SNP - - - - - - - - - - - - - - - tier3 656 1 0.15 339 279 45.15 NA NA NA 529205 TCGA-AB-2906 AML49 10 2831690 2831690 G A SNP - - - - - - - - - - - - - - - tier2 1077 0 0 650 410 38.64 NA NA NA 529205 TCGA-AB-2906 AML49 10 4298318 4298318 A G SNP - - - - - - - - - - - - - - - tier3 846 0 0 559 406 42.07 NA NA NA 529205 TCGA-AB-2906 AML49 10 4498167 4498167 T A SNP LOC100128356 XM_001719204.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-25645 NULL 0.001 - - - no_errors tier3 1685 1 0.06 625 445 41.55 NA NA NA 529205 TCGA-AB-2906 AML49 10 14264563 14264563 T - DEL FRMD4A NM_018027.3 human genbank 54_36p -1 validated intronic c.45+147500 e1+147500 0.018 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 10 16910969 16910969 C T SNP CUBN NM_001081.3 human genbank 54_36p -1 reviewed silent c.10605 p.T3535 0.938 "HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain" "PatternScan_ASX_HYDROXYL,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 1390 5 0.36 747 596 44.35 NA NA NA 529205 TCGA-AB-2906 AML49 10 19235684 19235684 T C SNP ENSG00000217698 ENST00000401631 human ensembl 54_36p 1 known 5_prime_flanking_region c.-33752 NULL 0.016 - - - no_coding_region:pseudogene tier3 949 0 0 736 360 32.85 NA NA NA 529205 TCGA-AB-2906 AML49 10 26527277 26527277 G A SNP MYO3A NM_017433.4 human genbank 54_36p 1 reviewed intronic c.4546-2923 e31-2923 0 - - - no_errors tier3 1538 0 0 756 584 43.58 NA NA NA 529205 TCGA-AB-2906 AML49 10 37578082 37578082 C T SNP ENSG00000220479 ENST00000407974 human ensembl 54_36p 1 known intronic c.NULL NULL 0.029 - - - no_coding_region:pseudogene tier3 1575 1 0.06 566 403 41.59 NA NA NA 529205 TCGA-AB-2906 AML49 10 43052172 43052172 T - DEL RASGEF1A NM_145313.2 human genbank 54_36p -1 validated intronic c.1+30127 e0+30127 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 10 44936647 44936647 T C SNP LOC728509 XR_015300.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-45287 NULL 0.017 - - - pseudogene tier3 576 0 0 398 334 45.63 NA NA NA 529205 TCGA-AB-2906 AML49 10 55297756 55297756 G T SNP PCDH15 NM_033056.1 human genbank 54_36p -1 reviewed intronic c.3502-1133 e26-1133 0.001 - - - no_errors tier3 1589 1 0.06 1032 503 32.77 NA NA NA 529205 TCGA-AB-2906 AML49 10 55713007 55713007 T C SNP PCDH15 NM_033056.1 human genbank 54_36p -1 reviewed intronic c.876+34030 e7+34030 0.001 - - - no_errors tier3 1110 0 0 553 375 40.28 NA NA NA 529205 TCGA-AB-2906 AML49 10 62565087 62565087 G A SNP - - - - - - - - - - - - - - - tier3 1082 0 0 638 302 31.99 NA NA NA 529205 TCGA-AB-2906 AML49 10 62865367 62865367 T C SNP TMEM26 NM_178505.6 human genbank 54_36p -1 validated intronic c.270+567 e2+567 0 - - - no_errors tier2 1033 0 0 711 313 30.54 NA NA NA 529205 TCGA-AB-2906 AML49 10 66789936 66789936 T A SNP - - - - - - - - - - - - - - - tier2 1931 2 0.1 1037 527 33.65 NA NA NA 529205 TCGA-AB-2906 AML49 10 79904926 79904926 C A SNP LOC100132987 XM_001716093.1 human genbank 54_36p 1 model intronic c.1-50167 e1-50167 0.071 - - - no_errors tier3 1137 0 0 661 486 42.37 NA NA NA 529205 TCGA-AB-2906 AML49 10 79989210 79989210 A T SNP LOC100132987 XM_001716093.1 human genbank 54_36p 1 model intronic c.388-454 e4-454 0 - - - no_errors tier3 734 0 0 451 311 40.81 NA NA NA 529205 TCGA-AB-2906 AML49 10 107122534 107122534 T A SNP - - - - - - - - - - - - - - - tier3 1147 0 0 684 311 31.26 NA NA NA 529205 TCGA-AB-2906 AML49 10 107652852 107652852 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 10 122069136 122069136 A G SNP ENSG00000220842 ENST00000404812 human ensembl 54_36p -1 known 3_prime_flanking_region c.*35281 NULL 0 - - - no_coding_region:pseudogene tier3 1303 1 0.08 705 527 42.78 NA NA NA 529205 TCGA-AB-2906 AML49 10 133598203 133598203 C G SNP PPP2R2D NM_001003656.1 human genbank 54_36p 1 validated intronic c.1+154 e0+154 0.002 - - - no_errors tier3 440 0 0 311 269 46.38 NA NA NA 529205 TCGA-AB-2906 AML49 11 1844013 1844013 C T SNP - - - - - - - - - - - - - - - tier3 353 0 0 164 137 45.51 NA NA NA 529205 TCGA-AB-2906 AML49 11 7870224 7870224 C T SNP - - - - - - - - - - - - - - - tier3 1101 0 0 572 439 43.42 NA NA NA 529205 TCGA-AB-2906 AML49 11 11444571 11444571 C T SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated intronic c.236-17512 e2-17512 0.014 - - - no_errors tier3 526 0 0 290 228 44.02 NA NA NA 529205 TCGA-AB-2906 AML49 11 12439087 12439087 A T SNP PARVA NM_018222.3 human genbank 54_36p 1 provisional intronic c.137-12781 e2-12781 0.032 - - - no_errors tier3 1068 1 0.09 696 534 43.24 NA NA NA 529205 TCGA-AB-2906 AML49 11 14089249 14089249 G A SNP - - - - - - - - - - - - - - - tier3 1236 0 0 780 513 39.64 NA NA NA 529205 TCGA-AB-2906 AML49 11 16272131 16272131 G T SNP - - - - - - - - - - - - - - - tier3 1465 0 0 901 571 38.79 NA NA NA 529205 TCGA-AB-2906 AML49 11 19453453 19453453 C A SNP - - - - - - - - - - - - - - - tier3 1070 0 0 886 423 32.29 NA NA NA 529205 TCGA-AB-2906 AML49 11 20022972 20022972 C G SNP - - - - - - - - - - - - - - - tier3 1674 3 0.18 827 556 40.12 NA NA NA 529205 TCGA-AB-2906 AML49 11 31100485 31100485 G C SNP - - - - - - - - - - - - - - - tier2 1357 1 0.07 727 617 45.87 NA NA NA 529205 TCGA-AB-2906 AML49 11 33637810 33637810 C G SNP - - - - - - - - - - - - - - - tier3 584 3 0.51 394 319 44.74 NA NA NA 529205 TCGA-AB-2906 AML49 11 39033117 39033117 C T SNP - - - - - - - - - - - - - - - tier3 983 1 0.1 397 260 39.51 NA NA NA 529205 TCGA-AB-2906 AML49 11 43946111 43946111 G A SNP - - - - - - - - - - - - - - - tier3 1378 4 0.29 633 273 30.1 NA NA NA 529205 TCGA-AB-2906 AML49 11 71990401 71990401 G A SNP - - - - - - - - - - - - - - - tier2 64 0 0 37 17 31.48 NA NA NA 529205 TCGA-AB-2906 AML49 11 83762961 83762961 A G SNP - - - - - - - - - - - - - - - tier3 1967 1 0.05 1100 836 43.14 NA NA NA 529205 TCGA-AB-2906 AML49 11 86233121 86233121 C T SNP - - - - - - - - - - - - - - - tier3 2467 1 0.04 1569 1015 39.23 NA NA NA 529205 TCGA-AB-2906 AML49 11 88656520 88656520 C T SNP - - - - - - - - - - - - - - - tier3 1290 0 0 558 463 45.3 NA NA NA 529205 TCGA-AB-2906 AML49 11 102259791 102259791 C T SNP MMP3 NM_002422.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-40304 NULL 0 - - - no_errors tier3 1309 0 0 555 432 43.68 NA NA NA 529205 TCGA-AB-2906 AML49 11 103320731 103320731 C T SNP PDGFD NM_025208.4 human genbank 54_36p -1 reviewed intronic c.574-1143 e5-1143 0 - - - no_errors tier3 1201 0 0 675 511 43.09 NA NA NA 529205 TCGA-AB-2906 AML49 11 106558990 106558990 C T SNP LOC341230 XR_016383.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*5309 NULL 0.185 - - - pseudogene tier3 1838 5 0.27 914 618 40.31 NA NA NA 529205 TCGA-AB-2906 AML49 11 112463912 112463912 C T SNP LOC100128226 XM_001725905.1 human genbank 54_36p 1 model intronic c.181-1278 e2-1278 0.001 - - - no_errors tier3 1242 0 0 843 520 38.15 NA NA NA 529205 TCGA-AB-2906 AML49 11 112528022 112528022 G A SNP NCAM1 ENST00000404693 human ensembl 54_36p 1 known intronic c.1+18642 e0+18642 0 - - - no_errors tier3 1016 0 0 653 392 37.51 NA NA NA 529205 TCGA-AB-2906 AML49 11 112586922 112586922 G A SNP NCAM1 ENST00000404693 human ensembl 54_36p 1 known intronic c.562+2988 e4+2988 0.001 - - - no_errors tier3 820 0 0 723 546 43.03 NA NA NA 529205 TCGA-AB-2906 AML49 11 114572015 114572015 A G SNP CADM1 NM_014333.1 human genbank 54_36p -1 validated intronic c.1078+13489 e8+13489 0 - - - no_errors tier3 1883 2 0.11 684 506 42.49 NA NA NA 529205 TCGA-AB-2906 AML49 11 115994162 115994162 G A SNP - - - - - - - - - - - - - - - tier3 1298 1 0.08 569 323 36.21 NA NA NA 529205 TCGA-AB-2906 AML49 11 123060185 123060185 G A SNP SCN3B NM_001040151.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-30466 NULL 0 - - - no_errors tier3 2309 2 0.09 1743 1260 41.96 NA NA NA 529205 TCGA-AB-2906 AML49 11 123129267 123129267 A C SNP ZNF202 NM_003455.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22461 NULL 0.001 - - - no_errors tier3 1597 1 0.06 629 423 40.13 NA NA NA 529205 TCGA-AB-2906 AML49 11 125069035 125069035 T A SNP ACRV1 NM_001612.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-13150 NULL 0.001 - - - no_errors tier3 973 1 0.1 409 332 44.68 NA NA NA 529205 TCGA-AB-2906 AML49 11 131710591 131710591 C A SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*341 NULL 0 - - - no_errors tier3 936 0 0 613 589 48.92 NA NA NA 529205 TCGA-AB-2906 AML49 11 132486924 132486924 G A SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.62-168809 e2-168809 0.011 - - - no_errors tier3 1238 0 0 706 551 43.83 NA NA NA 529205 TCGA-AB-2906 AML49 11 133640440 133640440 A G SNP ACAD8 NM_014384.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*376 NULL 0 - - - no_errors tier3 477 0 0 293 215 42.32 NA NA NA 529205 TCGA-AB-2906 AML49 11 134365299 134365299 C T SNP - - - - - - - - - - - - - - - tier3 816 0 0 369 282 43.19 NA NA NA 529205 TCGA-AB-2906 AML49 12 2348654 2348654 T C SNP CACNA1C NM_000719.6 human genbank 54_36p 1 reviewed intronic c.478-79749 e4-79749 0 - - - no_errors tier3 1024 3 0.29 528 266 33.5 NA NA NA 529205 TCGA-AB-2906 AML49 12 4300878 4300878 T G SNP C12orf5 NM_020375.2 human genbank 54_36p 1 reviewed intronic c.32+148 e1+148 0.002 - - - no_errors tier2 473 2 0.42 236 164 41 NA NA NA 529205 TCGA-AB-2906 AML49 12 14563343 14563343 C A SNP PLBD1 NM_024829.5 human genbank 54_36p -1 validated intronic c.845-7431 e7-7431 0.002 - - - no_errors tier2 920 0 0 648 458 41.41 NA NA NA 529205 TCGA-AB-2906 AML49 12 38483209 38483209 C T SNP SLC2A13 NM_052885.3 human genbank 54_36p -1 validated intronic c.1388+26963 e7+26963 0.001 - - - no_errors tier3 1573 1 0.06 973 461 32.13 NA NA NA 529205 TCGA-AB-2906 AML49 12 52405125 52405125 G T SNP CALCOCO1 NM_020898.1 human genbank 54_36p -1 validated intronic c.156+13 e1+13 0.012 - - - no_errors tier3 782 1 0.13 354 251 41.42 NA NA NA 529205 TCGA-AB-2906 AML49 12 62512373 62512373 C G SNP SRGAP1 NM_020762.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-12491 NULL 0.002 - - - no_errors tier3 1377 0 0 544 336 38.14 NA NA NA 529205 TCGA-AB-2906 AML49 12 75373802 75373802 A T SNP OSBPL8 NM_020841.1 human genbank 54_36p -1 reviewed intronic c.79+3968 e2+3968 0.002 - - - no_errors tier3 1135 0 0 1000 638 38.95 NA NA NA 529205 TCGA-AB-2906 AML49 12 77070868 77070868 G T SNP NAV3 NM_014903.4 human genbank 54_36p 1 validated intronic c.4785+4038 e22+4038 0 - - - no_errors tier3 1234 0 0 526 338 39.12 NA NA NA 529205 TCGA-AB-2906 AML49 12 79004131 79004131 G A SNP - - - - - - - - - - - - - - - tier3 1751 0 0 837 470 35.96 NA NA NA 529205 TCGA-AB-2906 AML49 12 80260466 80260466 T C SNP PPFIA2 NM_003625.2 human genbank 54_36p -1 reviewed intronic c.2263-1348 e18-1348 0.002 - - - no_errors tier2 1319 1 0.08 660 338 33.83 NA NA NA 529205 TCGA-AB-2906 AML49 12 96408142 96408142 G A SNP MIRN1251 ENST00000408552 human ensembl 54_36p 1 known 5_prime_flanking_region c.-1676 NULL 0.005 - - - no_errors tier3 1160 1 0.09 687 451 39.6 NA NA NA 529205 TCGA-AB-2906 AML49 12 96719768 96719768 C T SNP LOC732096 XM_001720784.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-68568 NULL 0 - - - no_errors tier3 1721 4 0.23 953 695 42.12 NA NA NA 529205 TCGA-AB-2906 AML49 12 97090157 97090157 C T SNP - - - - - - - - - - - - - - - tier3 1396 1 0.07 1028 530 34.02 NA NA NA 529205 TCGA-AB-2906 AML49 12 97555217 97555217 C T SNP IKIP NM_153687.2 human genbank 54_36p -1 provisional intronic c.180-2895 e2-2895 0.002 - - - no_errors tier3 1147 1 0.09 467 402 46.26 NA NA NA 529205 TCGA-AB-2906 AML49 12 108258303 108258303 A G SNP FOXN4 NM_213596.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49315 NULL 0 - - - no_errors tier3 914 0 0 451 227 33.38 NA NA NA 529205 TCGA-AB-2906 AML49 12 124553530 124553530 C T SNP TMEM132B NM_052907.2 human genbank 54_36p 1 provisional intronic c.1092-16408 e4-16408 0.008 - - - no_errors tier3 1131 3 0.26 602 425 41.34 NA NA NA 529205 TCGA-AB-2906 AML49 12 126825902 126825902 C T SNP - - - - - - - - - - - - - - - tier3 2317 1 0.04 1114 534 32.36 NA NA NA 529205 TCGA-AB-2906 AML49 12 126898389 126898389 A G SNP - - - - - - - - - - - - - - - tier3 1754 0 0 736 541 42.36 NA NA NA 529205 TCGA-AB-2906 AML49 12 129687725 129687725 G A SNP - - - - - - - - - - - - - - - tier3 582 1 0.17 317 71 18.16 NA NA NA 529205 TCGA-AB-2906 AML49 13 18433453 18433454 - A INS ENSG00000218236 ENST00000405207 human ensembl 54_36p -1 known intronic c.NULL NULL 0.000:0.000 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 13 21195115 21195115 G C SNP FGF9 NM_002010.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*21541 NULL 0.001 - - - no_errors tier3 366 0 0 179 127 41.5 NA NA NA 529205 TCGA-AB-2906 AML49 13 27506255 27506256 - ATCATATTCATATTCTCTGAA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1801_1800 p.600in_frame_insFREYEYD 1.000:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 13 35248664 35248664 G A SNP DCLK1 NM_004734.3 human genbank 54_36p -1 validated intronic c.2133-1828 e17-1828 0.001 - - - no_errors tier3 1275 1 0.08 650 386 37.26 NA NA NA 529205 TCGA-AB-2906 AML49 13 39342879 39342879 A - DEL ENSG00000212553 ENST00000391251 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13515 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 13 40454315 40454315 C T SNP ELF1 NM_172373.1 human genbank 54_36p -1 reviewed 5_prime_untranslated_region c.-125 NULL 0.001 - - - no_errors tier3 1185 1 0.08 575 373 39.35 NA NA NA 529205 TCGA-AB-2906 AML49 13 44963708 44963708 T A SNP COG3 NM_031431.2 human genbank 54_36p 1 reviewed intronic c.1095+34 e10+34 0 - - - no_errors tier3 726 0 0 394 310 43.97 NA NA NA 529205 TCGA-AB-2906 AML49 13 53595012 53595012 C A SNP - - - - - - - - - - - - - - - tier3 1056 0 0 568 440 43.65 NA NA NA 529205 TCGA-AB-2906 AML49 13 55112339 55112339 A C SNP - - - - - - - - - - - - - - - tier3 1848 4 0.22 646 411 38.85 NA NA NA 529205 TCGA-AB-2906 AML49 13 56933323 56933323 G A SNP - - - - - - - - - - - - - - - tier3 1048 0 0 719 317 30.57 NA NA NA 529205 TCGA-AB-2906 AML49 13 56971042 56971042 T C SNP - - - - - - - - - - - - - - - tier3 976 0 0 551 398 41.89 NA NA NA 529205 TCGA-AB-2906 AML49 13 57841239 57841239 G T SNP - - - - - - - - - - - - - - - tier2 1222 1 0.08 557 348 38.45 NA NA NA 529205 TCGA-AB-2906 AML49 13 58716279 58716279 C A SNP - - - - - - - - - - - - - - - tier3 1153 0 0 726 286 28.26 NA NA NA 529205 TCGA-AB-2906 AML49 13 59625055 59625055 A G SNP DIAPH3 NM_001042517.1 human genbank 54_36p -1 validated intronic c.180+10667 e1+10667 0.003 - - - no_errors tier3 1890 1 0.05 905 668 42.44 NA NA NA 529205 TCGA-AB-2906 AML49 13 61108600 61108600 T - DEL ENSG00000209865 ENST00000387130 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*21527 NULL 0.15 - - - pseudogene tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 13 62861514 62861514 C A SNP - - - - - - - - - - - - - - - tier3 613 0 0 347 138 28.45 NA NA NA 529205 TCGA-AB-2906 AML49 13 63510693 63510693 A T SNP - - - - - - - - - - - - - - - tier2 458 1 0.22 288 199 40.78 NA NA NA 529205 TCGA-AB-2906 AML49 13 71249160 71249160 A G SNP DACH1 NM_080759.4 human genbank 54_36p -1 reviewed intronic c.854+88895 e1+88895 0.001 - - - no_errors tier3 1036 2 0.19 647 299 31.51 NA NA NA 529205 TCGA-AB-2906 AML49 13 78335367 78335367 C A SNP CCT5P2 ENST00000401918 human ensembl 54_36p 1 known 5_prime_flanking_region c.-45688 NULL 0 - - - no_coding_region:pseudogene tier3 716 1 0.14 525 357 40.48 NA NA NA 529205 TCGA-AB-2906 AML49 13 81375382 81375382 C T SNP - - - - - - - - - - - - - - - tier3 2095 0 0 880 575 39.46 NA NA NA 529205 TCGA-AB-2906 AML49 13 84571046 84571046 G A SNP - - - - - - - - - - - - - - - tier3 584 1 0.17 370 281 43.16 NA NA NA 529205 TCGA-AB-2906 AML49 13 84997518 84997518 C G SNP - - - - - - - - - - - - - - - tier3 951 0 0 569 410 41.71 NA NA NA 529205 TCGA-AB-2906 AML49 13 91789848 91789848 G A SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1561+194605 e7+194605 0 - - - no_errors tier3 1551 0 0 766 536 41.14 NA NA NA 529205 TCGA-AB-2906 AML49 13 93965061 93965061 C T SNP DCT NM_001922.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35551 NULL 0 - - - no_errors tier3 1985 1 0.05 1070 792 42.51 NA NA NA 529205 TCGA-AB-2906 AML49 13 96553670 96553670 C T SNP ENSG00000210327 ENST00000387592 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*45937 NULL 0 - - - pseudogene tier3 2550 0 0 1239 925 42.65 NA NA NA 529205 TCGA-AB-2906 AML49 13 97319041 97319041 C T SNP ENSG00000218920 ENST00000407957 human ensembl 54_36p 1 known 5_prime_flanking_region c.-32867 NULL 0 - - - no_coding_region:pseudogene tier3 644 1 0.15 408 268 39.59 NA NA NA 529205 TCGA-AB-2906 AML49 13 100774531 100774531 G A SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.799+21087 e6+21087 0.001 - - - no_errors tier3 882 1 0.11 599 247 29.16 NA NA NA 529205 TCGA-AB-2906 AML49 13 100844649 100844649 G A SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.291+886 e2+886 0 - - - no_errors tier3 1027 2 0.19 710 473 39.98 NA NA NA 529205 TCGA-AB-2906 AML49 13 101197761 101197761 G A SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.424-20600 e4-20600 0.001 - - - no_errors tier3 1321 1 0.08 649 270 29.35 NA NA NA 529205 TCGA-AB-2906 AML49 13 104149633 104149633 C T SNP - - - - - - - - - - - - - - - tier2 1304 0 0 803 346 30.11 NA NA NA 529205 TCGA-AB-2906 AML49 13 111954480 111954480 G A SNP - - - - - - - - - - - - - - - tier3 264 0 0 188 128 40.51 NA NA NA 529205 TCGA-AB-2906 AML49 14 25038617 25038617 C T SNP - - - - - - - - - - - - - - - tier3 2026 0 0 1178 856 42.06 NA NA NA 529205 TCGA-AB-2906 AML49 14 25776304 25776304 C T SNP ENSG00000213882 ENST00000396692 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*28979 NULL 0.001 - - - no_coding_region:pseudogene tier3 758 0 0 311 224 41.87 NA NA NA 529205 TCGA-AB-2906 AML49 14 25846117 25846117 C T SNP - - - - - - - - - - - - - - - tier3 1543 3 0.19 1168 918 44.01 NA NA NA 529205 TCGA-AB-2906 AML49 14 27012044 27012044 A G SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model intronic c.202-150857 e3-150857 0 - - - no_errors tier3 895 0 0 579 225 27.99 NA NA NA 529205 TCGA-AB-2906 AML49 14 27685712 27685712 G A SNP - - - - - - - - - - - - - - - tier3 704 0 0 370 261 41.36 NA NA NA 529205 TCGA-AB-2906 AML49 14 32625898 32625898 A G SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.51-128241 e2-128241 1 - - - no_errors tier2 1260 1 0.08 573 457 44.28 NA NA NA 529205 TCGA-AB-2906 AML49 14 35846597 35846597 T C SNP MBIP NM_016586.1 human genbank 54_36p -1 validated intronic c.888+452 e7+452 0 - - - no_errors tier3 1304 0 0 971 432 30.79 NA NA NA 529205 TCGA-AB-2906 AML49 14 37950492 37950492 G A SNP - - - - - - - - - - - - - - - tier2 1922 0 0 1119 783 41.17 NA NA NA 529205 TCGA-AB-2906 AML49 14 47029824 47029824 T A SNP MDGA2 ENST00000399232 human ensembl 54_36p -1 known intronic c.73+183646 e1+183646 0 - - - no_errors tier3 1198 1 0.08 723 518 41.64 NA NA NA 529205 TCGA-AB-2906 AML49 14 50360501 50360501 C T SNP NIN NM_020921.3 human genbank 54_36p -1 reviewed intronic c.1-1956 e1-1956 0.004 - - - no_errors tier2 1023 0 0 535 391 42.22 NA NA NA 529205 TCGA-AB-2906 AML49 14 58606215 58606215 C T SNP - - - - - - - - - - - - - - - tier3 1705 0 0 998 613 38 NA NA NA 529205 TCGA-AB-2906 AML49 14 76595432 76595432 G A SNP C14orf4 NM_024496.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31544 NULL 0 - - - no_errors tier3 598 1 0.17 356 256 41.76 NA NA NA 529205 TCGA-AB-2906 AML49 14 80711103 80711103 T C SNP ENSG00000210351 ENST00000387616 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-27441 NULL 0.02 - - - pseudogene tier3 605 2 0.33 353 230 39.45 NA NA NA 529205 TCGA-AB-2906 AML49 14 82042009 82042009 G T SNP ENSG00000210376 ENST00000387641 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*43725 NULL 0.021 - - - pseudogene tier3 794 0 0 592 395 39.98 NA NA NA 529205 TCGA-AB-2906 AML49 14 85571825 85571825 A G SNP LOC283584 XM_211108.1 human genbank 54_36p -1 model intronic c.233+18806 e3+18806 0 - - - no_errors tier3 836 4 0.48 437 316 41.97 NA NA NA 529205 TCGA-AB-2906 AML49 14 92509217 92509217 G A SNP ITPK1 NM_014216.1 human genbank 54_36p -1 validated intronic c.365-10270 e5-10270 0 - - - no_errors tier3 539 0 0 315 249 44.15 NA NA NA 529205 TCGA-AB-2906 AML49 14 96774926 96774926 G A SNP - - - - - - - - - - - - - - - tier3 1279 0 0 710 536 43.02 NA NA NA 529205 TCGA-AB-2906 AML49 14 96924919 96924919 A G SNP - - - - - - - - - - - - - - - tier3 737 1 0.12 512 365 38.06 NA NA NA 529205 TCGA-AB-2906 AML49 14 98116907 98116907 C T SNP - - - - - - - - - - - - - - - tier3 1179 0 0 544 362 39.96 NA NA NA 529205 TCGA-AB-2906 AML49 14 99882783 99882783 G A SNP WARS NM_004184.3 human genbank 54_36p -1 reviewed intronic c.826+53 e6+53 0.042 - - - no_errors tier3 528 0 0 298 176 37.13 NA NA NA 529205 TCGA-AB-2906 AML49 15 19803620 19803620 G C SNP RPS8P10 ENST00000398077 human ensembl 54_36p -1 known intronic c.NULL NULL 0.042 - - - no_coding_region:pseudogene tier3 1599 1 0.06 1558 281 15.26 NA NA NA 529205 TCGA-AB-2906 AML49 15 24364629 24364629 A G SNP GABRB3 NM_000814.4 human genbank 54_36p -1 reviewed intronic c.683-656 e7-656 0.001 - - - no_errors tier3 2124 0 0 1206 887 42.34 NA NA NA 529205 TCGA-AB-2906 AML49 15 25874379 25874379 G A SNP OCA2 NM_000275.2 human genbank 54_36p -1 reviewed intronic c.1785-423 e16-423 0.077 - - - no_errors tier3 834 4 0.48 393 226 36.45 NA NA NA 529205 TCGA-AB-2906 AML49 15 27591212 27591212 C T SNP - - - - - - - - - - - - - - - tier3 2571 1 0.04 1048 764 42.12 NA NA NA 529205 TCGA-AB-2906 AML49 15 31182290 31182290 A G SNP FMN1 NM_001103184.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-34913 NULL 0.007 - - - no_errors tier3 1439 0 0 756 573 43.12 NA NA NA 529205 TCGA-AB-2906 AML49 15 32399550 32399550 A G SNP SLC12A6 NM_133647.1 human genbank 54_36p -1 reviewed intronic c.271+16353 e1+16353 0.019 - - - no_errors tier3 901 0 0 603 422 41.13 NA NA NA 529205 TCGA-AB-2906 AML49 15 40394295 40394295 G A SNP GANC NM_198141.2 human genbank 54_36p 1 reviewed intronic c.1057+3959 e10+3959 0 - - - no_errors tier3 747 1 0.13 403 269 40.03 NA NA NA 529205 TCGA-AB-2906 AML49 15 41323740 41323740 C T SNP TGM5 NM_201631.2 human genbank 54_36p -1 validated intronic c.863-3260 e7-3260 0.004 - - - no_errors tier3 2302 1 0.04 955 625 39.56 NA NA NA 529205 TCGA-AB-2906 AML49 15 49408106 49408106 A G SNP CYP19A1 NM_000103.3 human genbank 54_36p -1 reviewed intronic c.1+9878 e0+9878 0.003 - - - no_errors tier3 972 1 0.1 491 324 39.75 NA NA NA 529205 TCGA-AB-2906 AML49 15 75434529 75434529 C T SNP - - - - - - - - - - - - - - - tier3 1860 0 0 1174 850 41.95 NA NA NA 529205 TCGA-AB-2906 AML49 15 82196144 82196144 A C SNP ADAMTSL3 NM_207517.2 human genbank 54_36p 1 validated intronic c.189+31880 e2+31880 0.456 - - - no_errors tier3 1531 0 0 738 533 41.94 NA NA NA 529205 TCGA-AB-2906 AML49 15 84371127 84371127 C T SNP - - - - - - - - - - - - - - - tier3 1811 2 0.11 669 490 42.24 NA NA NA 529205 TCGA-AB-2906 AML49 15 95678740 95678740 T C SNP ENSG00000208890 ENST00000386155 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18991 NULL 0.001 - - - pseudogene tier3 1875 0 0 1353 963 41.49 NA NA NA 529205 TCGA-AB-2906 AML49 15 95836802 95836802 A T SNP ENSG00000208887 ENST00000386152 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20317 NULL 0.808 - - - pseudogene tier2 2134 3 0.14 1187 913 43.46 NA NA NA 529205 TCGA-AB-2906 AML49 15 96548998 96548998 T G SNP - - - - - - - - - - - - - - - tier3 888 0 0 674 540 44.48 NA NA NA 529205 TCGA-AB-2906 AML49 15 98419387 98419387 C T SNP ADAMTS17 NM_139057.2 human genbank 54_36p -1 reviewed intronic c.2138-7605 e16-7605 0 - - - no_errors tier3 572 0 0 352 224 38.89 NA NA NA 529205 TCGA-AB-2906 AML49 16 7582349 7582349 C T SNP A2BP1 NM_145891.1 human genbank 54_36p 1 reviewed intronic c.529-3203 e5-3203 0 - - - no_errors tier3 920 0 0 489 331 40.32 NA NA NA 529205 TCGA-AB-2906 AML49 16 10623896 10623896 A T SNP EMP2 NM_001424.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-74921 NULL 0.262 - - - no_errors tier3 620 0 0 271 214 44.03 NA NA NA 529205 TCGA-AB-2906 AML49 16 14241929 14241929 C T SNP MKL2 NM_014048.3 human genbank 54_36p 1 validated intronic c.1079+87 e8+87 0 - - - no_errors tier3 1206 0 0 717 474 39.8 NA NA NA 529205 TCGA-AB-2906 AML49 16 46232202 46232202 C T SNP PHKB NM_000293.2 human genbank 54_36p 1 validated intronic c.1459-245 e15-245 0.679 - - - no_errors tier3 1437 0 0 871 619 41.54 NA NA NA 529205 TCGA-AB-2906 AML49 16 49524195 49524195 T C SNP - - - - - - - - - - - - - - - tier3 877 0 0 476 398 45.43 NA NA NA 529205 TCGA-AB-2906 AML49 16 50120931 50120931 G A SNP - - - - - - - - - - - - - - - tier3 1055 0 0 619 447 41.93 NA NA NA 529205 TCGA-AB-2906 AML49 16 50473437 50473437 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 16 51480455 51480455 A T SNP LOC390730 XR_016422.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-45770 NULL 0.063 - - - pseudogene tier3 1614 0 0 852 586 40.75 NA NA NA 529205 TCGA-AB-2906 AML49 16 52395415 52395415 G T SNP FTO NM_001080432.1 human genbank 54_36p 1 provisional intronic c.46-6138 e2-6138 0 - - - no_errors tier3 1336 1 0.07 1054 723 40.64 NA NA NA 529205 TCGA-AB-2906 AML49 16 60440265 60440265 C T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.667+8259 e3+8259 0.001 - - - no_errors tier3 1177 0 0 607 404 39.92 NA NA NA 529205 TCGA-AB-2906 AML49 16 60836635 60836635 A T SNP - - - - - - - - - - - - - - - tier3 838 0 0 578 335 36.69 NA NA NA 529205 TCGA-AB-2906 AML49 16 65415610 65415610 A G SNP NAE1 NM_003905.1 human genbank 54_36p -1 reviewed intronic c.250-606 e5-606 0.002 - - - no_errors tier2 721 0 0 309 259 45.6 NA NA NA 529205 TCGA-AB-2906 AML49 16 74972117 74972117 C T SNP CNTNAP4 NM_138994.3 human genbank 54_36p 1 validated intronic c.315+25208 e3+25208 0 - - - no_errors tier3 1082 0 0 570 443 43.73 NA NA NA 529205 TCGA-AB-2906 AML49 16 78034822 78034822 G A SNP - - - - - - - - - - - - - - - tier3 587 0 0 270 266 49.63 NA NA NA 529205 TCGA-AB-2906 AML49 17 2716555 2716555 G T SNP GARNL4 NM_015085.1 human genbank 54_36p 1 validated intronic c.81-38773 e3-38773 0 - - - no_errors tier3 421 1 0.24 224 165 42.42 NA NA NA 529205 TCGA-AB-2906 AML49 17 4886214 4886214 C T SNP ZFP3 NM_153018.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49310 NULL 0.009 - - - no_errors tier2 784 0 0 291 209 41.8 NA NA NA 529205 TCGA-AB-2906 AML49 17 7254079 7254079 C T SNP NLGN2 NM_020795.2 human genbank 54_36p 1 reviewed intronic c.457+1324 e1+1324 0 - - - no_errors tier2 578 0 0 348 322 48.06 NA NA NA 529205 TCGA-AB-2906 AML49 17 8050891 8050891 G A SNP AURKB NM_004217.2 human genbank 54_36p -1 validated missense c.439 p.R147W 0.999 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,PatternScan_N6_MTASE,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 806 1 0.12 319 278 46.33 NA NA NA 529205 TCGA-AB-2906 AML49 17 10178545 10178545 C T SNP MYH13 NM_003802.2 human genbank 54_36p -1 validated intronic c.2057-1312 e17-1312 0 - - - no_errors tier3 1172 2 0.17 799 310 27.88 NA NA NA 529205 TCGA-AB-2906 AML49 17 12067619 12067619 C G SNP - - - - - - - - - - - - - - - tier3 1130 4 0.35 485 318 39.6 NA NA NA 529205 TCGA-AB-2906 AML49 17 21915690 21915690 G T SNP ENSG00000222865 ENST00000410933 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29775 NULL 0 - - - no_errors tier3 972 0 0 882 397 30.97 NA NA NA 529205 TCGA-AB-2906 AML49 17 23860910 23860910 T A SNP FOXN1 NM_003593.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-14205 NULL 0.002 - - - no_errors tier3 286 0 0 191 171 46.85 NA NA NA 529205 TCGA-AB-2906 AML49 17 24389481 24389481 C A SNP SEZ6 NM_178860.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-32468 NULL 0.098 - - - no_errors tier2 853 0 0 343 328 48.88 NA NA NA 529205 TCGA-AB-2906 AML49 17 34135078 34135078 C T SNP MLLT6 NM_005937.3 human genbank 54_36p 1 validated intronic c.3241-258 e20-258 0 - - - no_errors tier3 498 0 0 356 266 42.77 NA NA NA 529205 TCGA-AB-2906 AML49 17 40192768 40192768 C T SNP ADAM11 NM_002390.4 human genbank 54_36p 1 reviewed missense c.214 p.R72C 1 HMMPfam_Pep_M12B_propep "HMMPfam_Reprolysin,HMMPfam_Disintegrin,HMMSmart_SM00050,superfamily_Blood coagulation inhibitor (disintegrin),HMMPfam_Pep_M12B_propep,HMMPfam_ADAM_CR,HMMSmart_SM00608,PatternScan_EGF_1,HMMPfam_EGF_2,PatternScan_DISINTEGRIN_1,superfamily_Metalloproteases (""zincins"") catalytic domain,superfamily_EGF/Laminin" - no_errors tier1 78 0 74 53 41.41 NA NA NA 529205 TCGA-AB-2906 AML49 17 47305939 47305940 - T INS CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.279+57409_279+57408 e3+57409 0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 17 47965993 47965993 C T SNP - - - - - - - - - - - - - - - tier3 795 0 0 422 210 33.23 NA NA NA 529205 TCGA-AB-2906 AML49 17 49717989 49717989 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 17 51663043 51663043 A G SNP ANKFN1 NM_153228.2 human genbank 54_36p 1 validated intronic c.62+2726 e2+2726 0.943 - - - no_errors tier2 1820 1 0.05 863 723 45.59 NA NA NA 529205 TCGA-AB-2906 AML49 17 56490218 56490218 T G SNP BCAS3 NM_001099432.1 human genbank 54_36p 1 validated intronic c.2075-16845 e20-16845 0.012 - - - no_errors tier3 718 1 0.14 365 234 39 NA NA NA 529205 TCGA-AB-2906 AML49 17 59605754 59605754 G T SNP TEX2 NM_018469.3 human genbank 54_36p -1 validated intronic c.2592+2663 e5+2663 0 - - - no_errors tier3 928 0 0 521 392 42.94 NA NA NA 529205 TCGA-AB-2906 AML49 17 67547919 67547919 G A SNP FLJ37644 XM_001126807.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*30962 NULL 0 - - - no_errors tier3 1746 1 0.06 534 329 38.08 NA NA NA 529205 TCGA-AB-2906 AML49 17 69596861 69596861 A T SNP - - - - - - - - - - - - - - - tier3 1080 0 0 729 613 45.24 NA NA NA 529205 TCGA-AB-2906 AML49 17 69613633 69613633 A C SNP - - - - - - - - - - - - - - - tier3 681 0 0 269 202 42.89 NA NA NA 529205 TCGA-AB-2906 AML49 17 76585631 76585631 C G SNP CHMP6 NM_024591.4 human genbank 54_36p 1 validated intronic c.415-25 e6-25 0.002 - - - no_errors tier3 360 0 0 220 148 40.22 NA NA NA 529205 TCGA-AB-2906 AML49 17 77652999 77652999 G A SNP CCDC57 NM_198082.2 human genbank 54_36p -1 validated missense c.2596 p.P866S 0 NULL NULL - no_errors tier1 154 0 109 84 43.3 NA NA NA 529205 TCGA-AB-2906 AML49 17 77686237 77686238 TG - DEL CCDC57 NM_198082.2 human genbank 54_36p -1 validated intronic c.2242-6476_2242-6475 e14-6475 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 18 6374938 6374938 G C SNP L3MBTL4 NM_173464.3 human genbank 54_36p -1 validated intronic c.1+29862 e0+29862 0.001 - - - no_errors tier3 1831 0 0 1529 678 30.72 NA NA NA 529205 TCGA-AB-2906 AML49 18 7019085 7019085 G A SNP LAMA1 NM_005559.2 human genbank 54_36p -1 validated intronic c.2274+2980 e16+2980 0 - - - no_errors tier3 858 0 0 371 141 27.54 NA NA NA 529205 TCGA-AB-2906 AML49 18 11603041 11603041 T C SNP LOC729602 XM_001717235.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*4177 NULL 0 - - - no_errors tier3 314 0 0 115 182 61.28 NA NA NA 529205 TCGA-AB-2906 AML49 18 12790346 12790346 T C SNP PTPN2 NM_002828.2 human genbank 54_36p -1 reviewed intronic c.1040+1623 e8+1623 0.002 - - - no_errors tier3 805 1 0.12 376 265 41.34 NA NA NA 529205 TCGA-AB-2906 AML49 18 21481618 21481618 G A SNP - - - - - - - - - - - - - - - tier2 2026 1 0.05 1085 784 41.95 NA NA NA 529205 TCGA-AB-2906 AML49 18 22048237 22048237 A T SNP TAF4B NM_005640.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-12659 NULL 0.002 - - - no_errors tier3 599 0 0 291 153 34.46 NA NA NA 529205 TCGA-AB-2906 AML49 18 24545548 24545548 G A SNP ENSG00000221268 ENST00000408341 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*45701 NULL 0 - - - no_errors tier3 1843 0 0 1039 771 42.57 NA NA NA 529205 TCGA-AB-2906 AML49 18 26219582 26219582 G A SNP - - - - - - - - - - - - - - - tier3 802 1 0.12 463 378 44.95 NA NA NA 529205 TCGA-AB-2906 AML49 18 29530177 29530177 A - DEL ASXL3 NM_030632.1 human genbank 54_36p 1 validated intronic c.879+12647 e8+12647 0.008 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 529205 TCGA-AB-2906 AML49 18 33864797 33864797 T A SNP - - - - - - - - - - - - - - - tier2 872 0 0 563 477 45.82 NA NA NA 529205 TCGA-AB-2906 AML49 18 43952982 43952982 C T SNP LOC100127909 XM_001721243.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37815 NULL 0.001 - - - no_errors tier2 1014 2 0.2 655 466 41.5 NA NA NA 529205 TCGA-AB-2906 AML49 18 56929943 56929943 C T SNP - - - - - - - - - - - - - - - tier3 1637 0 0 942 755 44.49 NA NA NA 529205 TCGA-AB-2906 AML49 18 61028562 61028562 C A SNP - - - - - - - - - - - - - - - tier3 360 0 0 267 78 22.61 NA NA NA 529205 TCGA-AB-2906 AML49 18 64295336 64295336 G A SNP - - - - - - - - - - - - - - - tier3 1327 0 0 663 456 40.75 NA NA NA 529205 TCGA-AB-2906 AML49 18 71697112 71697112 G A SNP - - - - - - - - - - - - - - - tier2 1035 0 0 429 275 39.01 NA NA NA 529205 TCGA-AB-2906 AML49 18 75115228 75115228 C T SNP ATP9B NM_198531.3 human genbank 54_36p 1 validated intronic c.1268+699 e12+699 0 - - - no_errors tier3 999 1 0.1 728 303 29.36 NA NA NA 529205 TCGA-AB-2906 AML49 18 75410708 75410708 C T SNP NFATC1 NM_172387.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*22143 NULL 0.001 - - - no_errors tier2 105 0 0 35 32 47.76 NA NA NA 529205 TCGA-AB-2906 AML49 19 324949 324949 C G SNP THEG NM_016585.3 human genbank 54_36p -1 reviewed missense c.494 p.C165S 0.051 NULL HMMSmart_SM00705 - no_errors tier1 373 0 166 99 37.36 NA NA NA 529205 TCGA-AB-2906 AML49 19 7022155 7022155 G C SNP ZNF557 NM_001044387.1 human genbank 54_36p 1 validated intronic c.1+491 e0+491 0.084 - - - no_errors tier3 697 2 0.29 247 184 42.69 NA NA NA 529205 TCGA-AB-2906 AML49 19 15730831 15730831 C T SNP OR10H5 NM_001004466.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-35028 NULL 0.001 - - - no_errors tier3 1427 0 0 825 469 36.22 NA NA NA 529205 TCGA-AB-2906 AML49 19 33435008 33435008 G A SNP LOC727780 XM_001125708.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*42194 NULL 0 - - - no_errors tier3 1419 1 0.07 874 714 44.93 NA NA NA 529205 TCGA-AB-2906 AML49 19 35591055 35591055 G T SNP ZNF536 NM_014717.1 human genbank 54_36p 1 provisional intronic c.1-35253 e1-35253 0 - - - no_errors tier3 1408 2 0.14 693 525 43.07 NA NA NA 529205 TCGA-AB-2906 AML49 19 37140971 37140971 C T SNP ENSG00000221504 ENST00000408577 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*31537 NULL 0 - - - no_errors tier3 1834 1 0.05 1042 729 41.14 NA NA NA 529205 TCGA-AB-2906 AML49 19 55113533 55113533 C G SNP IL4I1 NM_172374.1 human genbank 54_36p -1 reviewed intronic c.1+9230 e0+9230 0 - - - no_errors tier3 1358 0 0 559 364 39.44 NA NA NA 529205 TCGA-AB-2906 AML49 20 6822723 6822723 A G SNP - - - - - - - - - - - - - - - tier3 1428 0 0 704 669 48.73 NA NA NA 529205 TCGA-AB-2906 AML49 20 8352086 8352086 G A SNP PLCB1 NM_015192.2 human genbank 54_36p 1 reviewed intronic c.246+51989 e3+51989 0 - - - no_errors tier2 1095 0 0 643 462 41.81 NA NA NA 529205 TCGA-AB-2906 AML49 20 10532326 10532326 T C SNP C20orf94 NM_001009608.1 human genbank 54_36p 1 validated intronic c.405+1859 e5+1859 0.001 - - - no_errors tier2 1600 2 0.12 776 576 42.57 NA NA NA 529205 TCGA-AB-2906 AML49 20 10532330 10532330 G A SNP C20orf94 NM_001009608.1 human genbank 54_36p 1 validated intronic c.405+1863 e5+1863 0 - - - no_errors tier2 1607 1 0.06 773 568 42.2 NA NA NA 529205 TCGA-AB-2906 AML49 20 14313887 14313887 C G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.272-108238 e4-108238 0.969 - - - no_errors tier2 731 0 0 466 211 31.17 NA NA NA 529205 TCGA-AB-2906 AML49 20 14916372 14916372 T A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.419-242214 e6-242214 0.005 - - - no_errors tier3 1055 0 0 518 297 36.44 NA NA NA 529205 TCGA-AB-2906 AML49 20 15253468 15253468 T C SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.540+94761 e6+94761 0.089 - - - no_errors tier3 985 0 0 698 457 39.5 NA NA NA 529205 TCGA-AB-2906 AML49 20 37876168 37876168 G A SNP - - - - - - - - - - - - - - - tier3 1300 0 0 832 524 38.53 NA NA NA 529205 TCGA-AB-2906 AML49 20 50970760 50970760 C T SNP RPL36P1 ENST00000401403 human ensembl 54_36p 1 known 3_prime_flanking_region c.*30428 NULL 0 - - - no_coding_region:pseudogene tier3 1412 1 0.07 590 410 40.96 NA NA NA 529205 TCGA-AB-2906 AML49 20 59511843 59511843 G A SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.170-240171 e3-240171 0 - - - no_errors tier2 773 0 0 502 358 41.58 NA NA NA 529205 TCGA-AB-2906 AML49 20 60127165 60127165 C T SNP SS18L1 NM_198935.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25107 NULL 0 - - - no_errors tier2 418 0 0 251 202 44.59 NA NA NA 529205 TCGA-AB-2906 AML49 21 16638102 16638102 G A SNP C21orf34 NM_001005734.1 human genbank 54_36p 1 validated intronic c.272-47703 e3-47703 0 - - - no_errors tier2 1216 4 0.33 739 521 41.35 NA NA NA 529205 TCGA-AB-2906 AML49 21 17871510 17871510 C G SNP CXADR ENST00000400169 human ensembl 54_36p 1 known intronic c.1017+11710 e7+11710 0.004 - - - no_errors tier2 1595 0 0 780 585 42.86 NA NA NA 529205 TCGA-AB-2906 AML49 21 24026325 24026325 T C SNP - - - - - - - - - - - - - - - tier3 767 0 0 421 309 42.33 NA NA NA 529205 TCGA-AB-2906 AML49 21 25383812 25383812 C T SNP ENSG00000222567 ENST00000410635 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-11504 NULL 0.006 - - - no_errors tier3 760 1 0.13 454 291 38.96 NA NA NA 529205 TCGA-AB-2906 AML49 21 39167326 39167326 C T SNP ENSG00000220397 ENST00000401535 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21385 NULL 0 - - - no_coding_region:pseudogene tier3 1209 2 0.16 914 694 43.16 NA NA NA 529205 TCGA-AB-2906 AML49 22 18130589 18130589 G A SNP TBX1 NM_080647.1 human genbank 54_36p 1 reviewed intronic c.411-175 e3-175 0.249 - - - no_errors tier3 320 0 0 262 192 42.29 NA NA NA 529205 TCGA-AB-2906 AML49 22 32639164 32639164 T C SNP LARGE NM_004737.4 human genbank 54_36p -1 reviewed intronic c.1+6819 e0+6819 0.001 - - - no_errors tier3 1481 0 0 671 605 47.38 NA NA NA 529205 TCGA-AB-2906 AML49 22 33706098 33706098 C T SNP - - - - - - - - - - - - - - - tier3 1428 0 0 641 430 40.07 NA NA NA 529205 TCGA-AB-2906 AML49 22 36249727 36249727 C T SNP CARD10 NM_014550.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4574 NULL 0.001 - - - no_errors tier3 488 0 0 216 137 38.7 NA NA NA 529205 TCGA-AB-2906 AML49 22 37653691 37653691 T A SNP APOBEC3A NM_145699.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29952 NULL 0 - - - no_errors tier2 674 0 0 393 307 43.86 NA NA NA 529205 TCGA-AB-2906 AML49 22 42971101 42971101 G A SNP KIAA1644 NM_001099294.1 human genbank 54_36p -1 predicted 3_prime_untranslated_region c.*5797 NULL 0 - - - no_errors tier3 624 0 0 306 245 44.38 NA NA NA 440422 TCGA-AB-2907 AML29 X 1563044 1563044 C T SNP P2RY8 NM_178129.4 human genbank 54_36p -1 reviewed intronic c.1-17569 e1-17569 0.966 - - - no_errors tier3 56 0 0 47 14 22.58 NA NA NA 440422 TCGA-AB-2907 AML29 X 14437000 14437000 C T SNP GLRA2 NM_002063.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21101 NULL 0.001 - - - no_errors tier3 199 4 1.97 78 140 64.22 NA NA NA 440422 TCGA-AB-2907 AML29 Y 20331174 20331174 C G SNP JARID1D NM_004653.3 human genbank 54_36p -1 reviewed intronic c.2584-91 e19-91 0.004 - - - no_errors tier3 254 5 1.93 127 192 60.19 NA NA NA 440422 TCGA-AB-2907 AML29 X 22269549 22269549 C T SNP - - - - - - - - - - - - - - - tier3 50 0 0 39 68 63.55 NA NA NA 440422 TCGA-AB-2907 AML29 X 31432189 31432189 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.8390+3130 e56+3130 0.002 - - - no_errors tier3 178 0 0 315 107 25.36 NA NA NA 440422 TCGA-AB-2907 AML29 X 99370280 99370280 G A SNP - - - - - - - - - - - - - - - tier3 162 5 2.99 70 143 67.14 NA NA NA 440422 TCGA-AB-2907 AML29 X 118193908 118193908 C A SNP KIAA1210 NM_020721.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-25338 NULL 0 - - - no_errors tier3 46 2 4.17 31 50 61.73 NA NA NA 440422 TCGA-AB-2907 AML29 X 140934810 140934810 C T SNP - - - - - - - - - - - - - - - tier3 96 2 2.04 76 76 50 NA NA NA 440422 TCGA-AB-2907 AML29 X 144743175 144743175 A T SNP SLITRK2 NM_032539.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*29002 NULL 0.001 - - - no_errors tier3 81 0 0 172 55 24.23 NA NA NA 440422 TCGA-AB-2907 AML29 1 4041894 4041894 C T SNP - - - - - - - - - - - - - - - tier3 192 3 1.54 77 52 40.31 NA NA NA 440422 TCGA-AB-2907 AML29 1 6658768 6658768 T G SNP DNAJC11 NM_018198.3 human genbank 54_36p -1 validated intronic c.276+2273 e3+2273 0 - - - no_errors tier3 244 2 0.81 170 74 30.33 NA NA NA 440422 TCGA-AB-2907 AML29 1 17976735 17976735 G C SNP ACTL8 NM_030812.1 human genbank 54_36p 1 provisional intronic c.1+22149 e0+22149 0.002 - - - no_errors tier3 206 15 6.76 119 52 30.41 NA NA NA 440422 TCGA-AB-2907 AML29 1 35929564 35929564 G A SNP PSMB2 NM_002794.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49944 NULL 0.001 - - - no_errors tier3 610 5 0.81 108 57 34.55 NA NA NA 440422 TCGA-AB-2907 AML29 1 61030713 61030713 C A SNP ENSG00000213674 ENST00000395551 human ensembl 54_36p -1 known 5_prime_flanking_region c.-46033 NULL 0.001 - - - no_coding_region:pseudogene tier3 191 5 2.55 165 95 36.54 NA NA NA 440422 TCGA-AB-2907 AML29 1 68432309 68432309 G C SNP GPR177 NM_001002292.1 human genbank 54_36p -1 validated missense c.290 p.P97R 0.975 NULL HMMPfam_DUF1171 - no_errors tier1 274 5 1.79 198 88 30.66 NA NA NA 440422 TCGA-AB-2907 AML29 1 72941843 72941843 T A SNP ENSG00000212366 ENST00000391064 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14091 NULL 0.115 - - - no_errors tier3 108 2 1.82 258 112 30.19 NA NA NA 440422 TCGA-AB-2907 AML29 1 73389366 73389366 C T SNP ENSG00000216972 ENST00000402980 human ensembl 54_36p 1 known 3_prime_flanking_region c.*44818 NULL 0 - - - no_coding_region:pseudogene tier3 191 4 2.05 251 92 26.82 NA NA NA 440422 TCGA-AB-2907 AML29 1 79129986 79129986 G A SNP ELTD1 NM_022159.3 human genbank 54_36p -1 validated intronic c.1842-21 e14-21 0 - - - no_errors tier3 240 1 0.41 190 93 32.63 NA NA NA 440422 TCGA-AB-2907 AML29 1 79159068 79159068 G A SNP ELTD1 NM_022159.3 human genbank 54_36p -1 validated intronic c.1258-409 e10-409 0.108 - - - no_errors tier3 93 1 1.06 190 98 34.03 NA NA NA 440422 TCGA-AB-2907 AML29 1 80457059 80457059 G A SNP - - - - - - - - - - - - - - - tier3 57 0 0 180 74 29.13 NA NA NA 440422 TCGA-AB-2907 AML29 1 92838196 92838196 G A SNP EVI5 NM_005665.4 human genbank 54_36p -1 validated intronic c.2022+5256 e16+5256 0.001 - - - no_errors tier3 72 1 1.35 157 71 30.87 NA NA NA 440422 TCGA-AB-2907 AML29 1 100867771 100867771 T C SNP ENSG00000220882 ENST00000407102 human ensembl 54_36p 1 known 5_prime_flanking_region c.-22320 NULL 0.01 - - - no_coding_region:pseudogene tier3 268 4 1.47 284 135 32.22 NA NA NA 440422 TCGA-AB-2907 AML29 1 119248348 119248348 C T SNP TBX15 NM_152380.2 human genbank 54_36p -1 validated intronic c.609-5077 e6-5077 0.005 - - - no_errors tier3 360 1 0.28 373 172 31.5 NA NA NA 440422 TCGA-AB-2907 AML29 1 163269187 163269187 A G SNP ENSG00000212086 ENST00000390797 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49334 NULL 0.002 - - - no_errors tier3 139 2 1.42 223 114 33.83 NA NA NA 440422 TCGA-AB-2907 AML29 1 168548692 168548692 G T SNP - - - - - - - - - - - - - - - tier3 565 5 0.88 508 231 31.22 NA NA NA 440422 TCGA-AB-2907 AML29 1 178226884 178226884 G A SNP CEP350 NM_014810.4 human genbank 54_36p 1 reviewed intronic c.232+505 e3+505 0.025 - - - no_errors tier3 70 1 1.41 120 59 32.96 NA NA NA 440422 TCGA-AB-2907 AML29 1 179820840 179820840 C T SNP CACNA1E NM_000721.2 human genbank 54_36p 1 reviewed intronic c.951+4305 e6+4305 0.027 - - - no_errors tier3 269 1 0.37 194 98 33.56 NA NA NA 440422 TCGA-AB-2907 AML29 1 194542271 194542271 T C SNP KCNT2 NM_198503.2 human genbank 54_36p -1 validated intronic c.2484-1173 e22-1173 0 - - - no_errors tier3 289 5 1.7 162 81 33.2 NA NA NA 440422 TCGA-AB-2907 AML29 1 207586763 207586763 A G SNP - - - - - - - - - - - - - - - tier3 52 1 1.89 150 82 35.34 NA NA NA 440422 TCGA-AB-2907 AML29 1 214890081 214890081 T G SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.589+857 e3+857 0 - - - no_errors tier3 33 0 0 138 47 25.41 NA NA NA 440422 TCGA-AB-2907 AML29 1 215841074 215841074 G A SNP GPATCH2 NM_018040.2 human genbank 54_36p -1 provisional intronic c.1098+9212 e5+9212 0 - - - no_errors tier3 47 1 2.08 214 82 27.61 NA NA NA 440422 TCGA-AB-2907 AML29 1 226377694 226377694 A G SNP GJC2 NM_020435.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34389 NULL 0 - - - no_errors tier3 78 2 2.5 55 29 34.52 NA NA NA 440422 TCGA-AB-2907 AML29 1 227586846 227586846 C A SNP C1orf96 NM_145257.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42011 NULL 0.01 - - - no_errors tier3 192 0 0 320 87 21.32 NA NA NA 440422 TCGA-AB-2907 AML29 1 235707748 235707748 G A SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.1708+8638 e17+8638 0 - - - no_errors tier3 632 8 1.25 437 200 31.4 NA NA NA 440422 TCGA-AB-2907 AML29 1 243103838 243103838 A C SNP LOC100129656 XM_001717015.1 human genbank 54_36p 1 model intronic c.1009+8533 e3+8533 0.01 - - - no_errors tier3 147 2 1.34 113 56 33.14 NA NA NA 440422 TCGA-AB-2907 AML29 2 2216305 2216305 C T SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.1+50878 e0+50878 0 - - - no_errors tier3 162 1 0.61 100 34 25.37 NA NA NA 440422 TCGA-AB-2907 AML29 2 6705538 6705538 G A SNP LOC100133653 XR_037179.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - pseudogene tier3 190 3 1.55 142 67 32.06 NA NA NA 440422 TCGA-AB-2907 AML29 2 10832882 10832882 A G SNP ATP6V1C2 NM_001039362.1 human genbank 54_36p 1 reviewed intronic c.825+234 e9+234 0 - - - no_errors tier3 42 0 0 37 23 38.33 NA NA NA 440422 TCGA-AB-2907 AML29 2 14321680 14321680 C T SNP ENSG00000210748 ENST00000388013 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*10517 NULL 0.061 - - - pseudogene tier3 356 3 0.83 204 115 35.71 NA NA NA 440422 TCGA-AB-2907 AML29 2 15342601 15342601 C T SNP NBAS NM_015909.2 human genbank 54_36p -1 validated intronic c.5138+2047 e42+2047 0.418 - - - no_errors tier3 111 2 1.77 197 97 32.99 NA NA NA 440422 TCGA-AB-2907 AML29 2 23091355 23091355 C T SNP - - - - - - - - - - - - - - - tier3 420 11 2.55 376 166 30.57 NA NA NA 440422 TCGA-AB-2907 AML29 2 26285055 26285055 A T SNP HADHA NM_000182.4 human genbank 54_36p -1 reviewed intronic c.1085+1098 e11+1098 0.007 - - - no_errors tier3 154 0 0 216 36 14.29 NA NA NA 440422 TCGA-AB-2907 AML29 2 28096411 28096411 A G SNP BRE NM_004899.3 human genbank 54_36p 1 validated intronic c.301-5186 e4-5186 0.001 - - - no_errors tier3 266 3 1.12 307 124 28.77 NA NA NA 440422 TCGA-AB-2907 AML29 2 44134376 44134376 G A SNP ENSG00000219391 ENST00000403786 human ensembl 54_36p -1 known 3_prime_flanking_region c.*12161 NULL 0 - - - no_coding_region:pseudogene tier3 371 11 2.86 197 83 29.64 NA NA NA 440422 TCGA-AB-2907 AML29 2 49655458 49655458 C T SNP - - - - - - - - - - - - - - - tier3 39 1 2.44 146 72 32.58 NA NA NA 440422 TCGA-AB-2907 AML29 2 73109611 73109611 G A SNP SFXN5 NM_144579.2 human genbank 54_36p -1 validated intronic c.250-5760 e4-5760 0.011 - - - no_errors tier3 423 2 0.47 165 72 30.38 NA NA NA 440422 TCGA-AB-2907 AML29 2 79793006 79793006 G A SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.103-32015 e2-32015 0.002 - - - no_errors tier3 221 4 1.78 294 143 32.65 NA NA NA 440422 TCGA-AB-2907 AML29 2 82670196 82670196 G A SNP - - - - - - - - - - - - - - - tier3 40 0 0 187 76 28.79 NA NA NA 440422 TCGA-AB-2907 AML29 2 83166692 83166692 A G SNP - - - - - - - - - - - - - - - tier3 67 1 1.47 116 68 36.76 NA NA NA 440422 TCGA-AB-2907 AML29 2 114291139 114291139 C T SNP SLC35F5 NM_025181.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-60683 NULL 0 - - - no_errors tier3 625 18 2.8 477 210 30.52 NA NA NA 440422 TCGA-AB-2907 AML29 2 122310330 122310330 G A SNP LOC646179 XR_040904.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*39928 NULL 0.001 - - - no_errors tier3 102 3 2.86 147 64 30.33 NA NA NA 440422 TCGA-AB-2907 AML29 2 128971916 128971916 C T SNP LOC100130549 XR_039102.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*19404 NULL 0 - - - pseudogene tier3 57 0 0 51 32 38.55 NA NA NA 440422 TCGA-AB-2907 AML29 2 133778344 133778344 G C SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.70-1192 e2-1192 0 - - - no_errors tier3 56 3 5.08 125 57 31.32 NA NA NA 440422 TCGA-AB-2907 AML29 2 139495537 139495537 A G SNP - - - - - - - - - - - - - - - tier3 36 1 2.7 158 94 37.3 NA NA NA 440422 TCGA-AB-2907 AML29 2 140728230 140728230 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.13248-7029 e87-7029 0.087 - - - no_errors tier3 42 0 0 124 63 33.69 NA NA NA 440422 TCGA-AB-2907 AML29 2 143217115 143217115 T C SNP - - - - - - - - - - - - - - - tier3 196 2 1.01 142 58 29 NA NA NA 440422 TCGA-AB-2907 AML29 2 154551321 154551321 T A SNP GALNT13 NM_052917.2 human genbank 54_36p 1 validated intronic c.142+41923 e1+41923 0 - - - no_errors tier3 114 2 1.72 150 88 36.97 NA NA NA 440422 TCGA-AB-2907 AML29 2 177734394 177734394 A G SNP ENSG00000201102 ENST00000364232 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33563 NULL 0.001 - - - no_errors tier3 78 4 4.88 142 66 31.73 NA NA NA 440422 TCGA-AB-2907 AML29 2 179355792 179355792 T C SNP TTN NM_133379.3 human genbank 54_36p -1 reviewed missense c.3086 p.Y1029C 1 "HMMPfam_I-set,superfamily_SSF48726" "PatternScan_THIOL_PROTEASE_HIS,PatternScan_IG_MHC,HMMSmart_IGc2,HMMSmart_IG,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,superfamily_SSF48726" - no_errors tier1 225 2 0.88 183 71 27.95 NA NA NA 440422 TCGA-AB-2907 AML29 2 180223141 180223142 - A INS ZNF385B NM_152520.1 human genbank 54_36p -1 validated intronic c.254-105201_254-105200 e2-105200 0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 2 183439321 183439321 T C SNP FRZB NM_001463.2 human genbank 54_36p -1 validated missense c.205 p.I69V 1 "superfamily_Frizzled cysteine-rich domain,HMMPfam_Fz,HMMSmart_SM00063" "superfamily_Frizzled cysteine-rich domain,superfamily_TIMP-like,HMMPfam_NTR,HMMSmart_SM00643,HMMPfam_Fz,HMMSmart_SM00063" - no_errors tier1 744 7 0.93 205 92 30.87 NA NA NA 440422 TCGA-AB-2907 AML29 2 188649869 188649869 A C SNP - - - - - - - - - - - - - - - tier3 149 1 0.67 296 141 32.27 NA NA NA 440422 TCGA-AB-2907 AML29 2 189353275 189353275 T A SNP DIRC1 NM_052952.2 human genbank 54_36p -1 validated intronic c.1+9560 e0+9560 0.604 - - - no_errors tier3 56 1 1.75 178 80 30.89 NA NA NA 440422 TCGA-AB-2907 AML29 2 189448897 189448897 C T SNP - - - - - - - - - - - - - - - tier3 155 0 0 212 42 16.54 NA NA NA 440422 TCGA-AB-2907 AML29 2 192014927 192014927 G A SNP MYO1B NM_012223.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*17996 NULL 0 - - - no_errors tier3 186 1 0.53 88 45 33.83 NA NA NA 440422 TCGA-AB-2907 AML29 2 195743803 195743803 C G SNP - - - - - - - - - - - - - - - tier3 202 1 0.49 204 121 37.23 NA NA NA 440422 TCGA-AB-2907 AML29 2 197198370 197198370 A G SNP HECW2 NM_020760.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-191978 NULL 0.003 - - - no_errors tier3 125 1 0.79 183 75 29.07 NA NA NA 440422 TCGA-AB-2907 AML29 2 202109171 202109171 C T SNP ALS2CR11 NM_152525.4 human genbank 54_36p -1 validated missense c.1324 p.V442M 0 NULL NULL - no_errors tier1 277 4 1.42 266 149 35.65 NA NA NA 440422 TCGA-AB-2907 AML29 2 211040902 211040902 T C SNP LANCL1 NM_006055.1 human genbank 54_36p -1 reviewed intronic c.199+4026 e2+4026 0 - - - no_errors tier3 75 1 1.32 196 93 32.07 NA NA NA 440422 TCGA-AB-2907 AML29 2 211899433 211899433 T C SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*57152 NULL 0 - - - no_errors tier3 92 2 2.13 199 87 30.42 NA NA NA 440422 TCGA-AB-2907 AML29 2 214423727 214423727 C T SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1071-11727 e11-11727 0 - - - no_errors tier3 108 0 0 256 59 18.73 NA NA NA 440422 TCGA-AB-2907 AML29 2 229773908 229773908 C T SNP PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.124-44984 e2-44984 0.001 - - - no_errors tier3 436 6 1.36 272 120 30.46 NA NA NA 440422 TCGA-AB-2907 AML29 2 235001049 235001049 G C SNP LOC727890 XM_001714076.1 human genbank 54_36p 1 model intronic c.93-10020 e2-10020 0.001 - - - no_errors tier3 156 5 3.09 174 122 41.08 NA NA NA 440422 TCGA-AB-2907 AML29 3 11492058 11492058 G C SNP ATG7 NM_006395.2 human genbank 54_36p 1 validated intronic c.2079+48658 e17+48658 0 - - - no_errors tier3 235 6 2.49 106 53 33.33 NA NA NA 440422 TCGA-AB-2907 AML29 3 12025514 12025514 C A SNP SYN2 ENST00000341648 human ensembl 54_36p 1 known intronic c.170+4086 e2+4086 0.001 - - - no_errors tier3 269 5 1.82 196 110 35.95 NA NA NA 440422 TCGA-AB-2907 AML29 3 15280195 15280195 A C SNP SH3BP5 NM_004844.2 human genbank 54_36p -1 validated intronic c.496-1395 e5-1395 0.001 - - - no_errors tier3 343 1 0.29 261 106 28.88 NA NA NA 440422 TCGA-AB-2907 AML29 3 21638046 21638046 T G SNP ZNF385D NM_024697.1 human genbank 54_36p -1 provisional intronic c.165+43336 e2+43336 0 - - - no_errors tier3 301 8 2.54 196 98 33.11 NA NA NA 440422 TCGA-AB-2907 AML29 3 26205996 26205996 G A SNP LOC645101 XR_016793.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-26821 NULL 0 - - - no_errors tier3 288 2 0.69 325 153 31.94 NA NA NA 440422 TCGA-AB-2907 AML29 3 34052981 34052981 C T SNP - - - - - - - - - - - - - - - tier3 178 0 0 197 110 35.26 NA NA NA 440422 TCGA-AB-2907 AML29 3 35065109 35065109 G T SNP - - - - - - - - - - - - - - - tier3 51 2 3.77 127 56 30.43 NA NA NA 440422 TCGA-AB-2907 AML29 3 35071638 35071638 C T SNP - - - - - - - - - - - - - - - tier3 95 0 0 194 80 28.99 NA NA NA 440422 TCGA-AB-2907 AML29 3 43132760 43132760 C T SNP C3orf39 NM_032806.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-34833 NULL 0.002 - - - no_errors tier3 435 0 0 78 55 41.35 NA NA NA 440422 TCGA-AB-2907 AML29 3 54341138 54341138 C T SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.321+11513 e3+11513 0.018 - - - no_errors tier3 162 2 1.22 239 100 29.5 NA NA NA 440422 TCGA-AB-2907 AML29 3 55783744 55783744 G A SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2565-39758 e14-39758 0.002 - - - no_errors tier3 159 6 3.64 127 60 32.09 NA NA NA 440422 TCGA-AB-2907 AML29 3 59140363 59140363 A G SNP - - - - - - - - - - - - - - - tier3 234 5 2.08 211 88 29.43 NA NA NA 440422 TCGA-AB-2907 AML29 3 63472269 63472269 C T SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated intronic c.149+30597 e2+30597 0.018 - - - no_errors tier3 303 7 2.24 271 114 29.46 NA NA NA 440422 TCGA-AB-2907 AML29 3 73560728 73560728 T C SNP PDZRN3 NM_015009.1 human genbank 54_36p -1 provisional intronic c.919-24492 e4-24492 0.013 - - - no_errors tier3 69 1 1.41 158 59 27.19 NA NA NA 440422 TCGA-AB-2907 AML29 3 77739362 77739362 A C SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.3137-277 e21-277 0.692 - - - no_errors tier3 82 0 0 120 38 24.05 NA NA NA 440422 TCGA-AB-2907 AML29 3 79276678 79276678 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-19299 e2-19299 0 - - - no_errors tier3 79 0 0 187 99 34.62 NA NA NA 440422 TCGA-AB-2907 AML29 3 88353340 88353340 A G SNP ENSG00000212026 ENST00000390737 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-14994 NULL 0.002 - - - no_errors tier3 159 2 1.24 271 101 27.15 NA NA NA 440422 TCGA-AB-2907 AML29 3 95305125 95305125 G A SNP NSUN3 NM_022072.3 human genbank 54_36p 1 provisional intronic c.743+8437 e5+8437 0 - - - no_errors tier3 33 1 2.94 106 63 37.28 NA NA NA 440422 TCGA-AB-2907 AML29 3 104627931 104627931 G T SNP - - - - - - - - - - - - - - - tier3 42 1 2.33 150 72 32.43 NA NA NA 440422 TCGA-AB-2907 AML29 3 115365210 115365210 A G SNP DRD3 NM_000796.3 human genbank 54_36p -1 reviewed intronic c.271-3806 e2-3806 0.003 - - - no_errors tier3 122 3 2.38 165 83 33.47 NA NA NA 440422 TCGA-AB-2907 AML29 3 118151798 118151798 A T SNP ENSG00000200372 ENST00000363502 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14851 NULL 0.001 - - - no_errors tier3 38 0 0 163 90 35.57 NA NA NA 440422 TCGA-AB-2907 AML29 3 118489780 118489780 G C SNP - - - - - - - - - - - - - - - tier3 62 1 1.59 151 68 31.05 NA NA NA 440422 TCGA-AB-2907 AML29 3 123253523 123253523 G A SNP CD86 NM_175862.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3504 NULL 0.003 - - - no_errors tier3 132 3 2.22 128 82 38.86 NA NA NA 440422 TCGA-AB-2907 AML29 3 126569406 126569406 T A SNP ZNF148 NM_021964.2 human genbank 54_36p -1 validated intronic c.1+7230 e0+7230 0 - - - no_errors tier3 128 4 3.03 109 38 25.85 NA NA NA 440422 TCGA-AB-2907 AML29 3 141666358 141666358 C T SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.1223-1784 e8-1784 0 - - - no_errors tier3 65 2 2.99 132 48 26.37 NA NA NA 440422 TCGA-AB-2907 AML29 3 144763522 144763522 C T SNP SLC9A9 NM_173653.2 human genbank 54_36p -1 validated intronic c.1001-9540 e9-9540 0.001 - - - no_errors tier3 321 6 1.83 312 123 28.28 NA NA NA 440422 TCGA-AB-2907 AML29 3 149947301 149947301 A T SNP AGTR1 NM_000685.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*4709 NULL 0.004 - - - no_errors tier3 211 4 1.86 218 107 32.92 NA NA NA 440422 TCGA-AB-2907 AML29 3 150390201 150390201 A G SNP CP NM_000096.3 human genbank 54_36p -1 reviewed intronic c.1714-1522 e10-1522 0.015 - - - no_errors tier3 73 1 1.35 185 69 27.17 NA NA NA 440422 TCGA-AB-2907 AML29 3 158965696 158965696 G A SNP - - - - - - - - - - - - - - - tier3 93 0 0 349 49 12.31 NA NA NA 440422 TCGA-AB-2907 AML29 3 160099424 160099424 C T SNP - - - - - - - - - - - - - - - tier3 89 1 1.1 258 63 19.63 NA NA NA 440422 TCGA-AB-2907 AML29 3 160477737 160477737 G A SNP SCHIP1 NM_014575.2 human genbank 54_36p 1 provisional intronic c.63+3371 e1+3371 0.001 - - - no_errors tier3 81 0 0 216 117 35.14 NA NA NA 440422 TCGA-AB-2907 AML29 3 167588847 167588847 A G SNP - - - - - - - - - - - - - - - tier3 126 5 3.82 266 109 29.07 NA NA NA 440422 TCGA-AB-2907 AML29 3 168692131 168692131 T C SNP WDR49 NM_178824.3 human genbank 54_36p -1 provisional intronic c.1975+8504 e13+8504 0.001 - - - no_errors tier3 181 3 1.63 289 112 27.93 NA NA NA 440422 TCGA-AB-2907 AML29 3 179453602 179453602 G A SNP - - - - - - - - - - - - - - - tier3 43 0 0 208 88 29.63 NA NA NA 440422 TCGA-AB-2907 AML29 3 183447665 183447665 C T SNP - - - - - - - - - - - - - - - tier3 243 1 0.41 267 114 29.92 NA NA NA 440422 TCGA-AB-2907 AML29 3 184689608 184689608 T C SNP KLHL6 NM_130446.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*2801 NULL 0 - - - no_errors tier3 68 1 1.45 75 35 31.82 NA NA NA 440422 TCGA-AB-2907 AML29 3 190228764 190228764 T C SNP - - - - - - - - - - - - - - - tier3 643 7 1.08 307 165 34.96 NA NA NA 440422 TCGA-AB-2907 AML29 4 12680314 12680314 A G SNP - - - - - - - - - - - - - - - tier3 279 3 1.06 197 93 32.07 NA NA NA 440422 TCGA-AB-2907 AML29 4 14719735 14719735 A G SNP LOC100129903 XM_001721453.1 human genbank 54_36p -1 model intronic c.1-91132 e1-91132 0 - - - no_errors tier3 135 3 2.17 142 83 36.73 NA NA NA 440422 TCGA-AB-2907 AML29 4 19238330 19238330 G A SNP - - - - - - - - - - - - - - - tier3 189 5 2.56 269 113 29.58 NA NA NA 440422 TCGA-AB-2907 AML29 4 22843850 22843850 G A SNP - - - - - - - - - - - - - - - tier3 202 0 0 270 121 30.95 NA NA NA 440422 TCGA-AB-2907 AML29 4 47958601 47958601 A G SNP TEC NM_003215.2 human genbank 54_36p -1 reviewed intronic c.1+7925 e0+7925 0.005 - - - no_errors tier3 31 1 3.12 77 51 39.84 NA NA NA 440422 TCGA-AB-2907 AML29 4 53690257 53690257 A G SNP SCFD2 NM_152540.3 human genbank 54_36p -1 validated intronic c.1561+16000 e5+16000 0.987 - - - no_errors tier3 53 0 0 148 95 39.09 NA NA NA 440422 TCGA-AB-2907 AML29 4 59890519 59890519 G A SNP - - - - - - - - - - - - - - - tier3 170 4 2.3 251 137 35.22 NA NA NA 440422 TCGA-AB-2907 AML29 4 61855189 61855189 C A SNP - - - - - - - - - - - - - - - tier3 122 0 0 301 100 24.94 NA NA NA 440422 TCGA-AB-2907 AML29 4 68338197 68338197 C A SNP GNRHR NM_000406.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-35549 NULL 0 - - - no_errors tier3 156 4 2.5 189 83 30.51 NA NA NA 440422 TCGA-AB-2907 AML29 4 71118402 71118402 G A SNP CSN3 NM_005212.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26724 NULL 0.002 - - - no_errors tier3 225 6 2.6 243 123 33.61 NA NA NA 440422 TCGA-AB-2907 AML29 4 71392232 71392232 C T SNP LOC100129410 XM_001714842.1 human genbank 54_36p -1 model intronic c.101-10167 e2-10167 0.002 - - - no_errors tier3 134 5 3.6 275 152 35.51 NA NA NA 440422 TCGA-AB-2907 AML29 4 85652770 85652770 C T SNP NKX6-1 NM_006168.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14365 NULL 0.011 - - - no_errors tier3 208 4 1.89 240 121 33.33 NA NA NA 440422 TCGA-AB-2907 AML29 4 89849041 89849041 G A SNP NAP1L5 NM_153757.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11113 NULL 0.002 - - - no_errors tier3 203 2 0.98 110 58 34.52 NA NA NA 440422 TCGA-AB-2907 AML29 4 90998840 90998840 A G SNP MMRN1 NM_007351.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36306 NULL 0.002 - - - no_errors tier3 38 0 0 84 55 39.57 NA NA NA 440422 TCGA-AB-2907 AML29 4 99892405 99892405 T C SNP ENSG00000174991 ENST00000309260 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*10933 NULL 0 - - - no_coding_region:pseudogene tier3 35 1 2.78 98 62 38.75 NA NA NA 440422 TCGA-AB-2907 AML29 4 102067894 102067894 A C SNP - - - - - - - - - - - - - - - tier3 62 1 1.59 190 98 34.03 NA NA NA 440422 TCGA-AB-2907 AML29 4 105423173 105423173 C T SNP - - - - - - - - - - - - - - - tier3 112 2 1.75 177 90 33.46 NA NA NA 440422 TCGA-AB-2907 AML29 4 116016741 116016741 A - DEL NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.1537-5186 e6-5186 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 4 124750621 124750621 T C SNP - - - - - - - - - - - - - - - tier3 157 4 2.48 280 136 32.61 NA NA NA 440422 TCGA-AB-2907 AML29 4 137415642 137415642 A G SNP - - - - - - - - - - - - - - - tier3 208 4 1.89 207 78 27.37 NA NA NA 440422 TCGA-AB-2907 AML29 4 147784943 147784943 G T SNP POU4F2 NM_004575.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*3533 NULL 0 - - - no_errors tier3 52 0 0 142 39 21.55 NA NA NA 440422 TCGA-AB-2907 AML29 4 148207118 148207118 C T SNP - - - - - - - - - - - - - - - tier3 172 2 1.15 272 128 32 NA NA NA 440422 TCGA-AB-2907 AML29 4 150081900 150081900 A T SNP - - - - - - - - - - - - - - - tier3 47 0 0 254 113 30.62 NA NA NA 440422 TCGA-AB-2907 AML29 4 155968543 155968543 C T SNP RBM46 NM_144979.3 human genbank 54_36p 1 validated silent c.1476 p.S492 1 NULL "HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928" - no_errors tier1 341 1 0.29 167 89 34.5 NA NA NA 440422 TCGA-AB-2907 AML29 4 181240369 181240369 T C SNP - - - - - - - - - - - - - - - tier3 79 2 2.47 137 67 32.84 NA NA NA 440422 TCGA-AB-2907 AML29 4 183182567 183182567 G T SNP - - - - - - - - - - - - - - - tier3 33 0 0 73 46 38.66 NA NA NA 440422 TCGA-AB-2907 AML29 5 2028223 2028223 G A SNP - - - - - - - - - - - - - - - tier3 292 6 2.01 105 78 42.62 NA NA NA 440422 TCGA-AB-2907 AML29 5 4008295 4008295 A G SNP - - - - - - - - - - - - - - - tier3 98 0 0 270 74 21.51 NA NA NA 440422 TCGA-AB-2907 AML29 5 5669578 5669578 G T SNP - - - - - - - - - - - - - - - tier3 72 1 1.37 90 42 31.82 NA NA NA 440422 TCGA-AB-2907 AML29 5 20116093 20116093 G T SNP - - - - - - - - - - - - - - - tier3 55 0 0 212 89 29.57 NA NA NA 440422 TCGA-AB-2907 AML29 5 20626534 20626534 A G SNP - - - - - - - - - - - - - - - tier3 415 0 0 439 121 21.61 NA NA NA 440422 TCGA-AB-2907 AML29 5 29787585 29787585 C T SNP - - - - - - - - - - - - - - - tier3 31 0 0 78 51 39.23 NA NA NA 440422 TCGA-AB-2907 AML29 5 42593136 42593136 T C SNP GHR NM_000163.2 human genbank 54_36p 1 reviewed intronic c.1-8587 e1-8587 0.029 - - - no_errors tier3 415 7 1.65 305 171 35.92 NA NA NA 440422 TCGA-AB-2907 AML29 5 45261121 45261121 A G SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*36659 NULL 0.001 - - - no_errors tier3 56 0 0 97 42 30.22 NA NA NA 440422 TCGA-AB-2907 AML29 5 67367556 67367556 G A SNP - - - - - - - - - - - - - - - tier3 193 2 1.03 147 75 33.63 NA NA NA 440422 TCGA-AB-2907 AML29 5 72658700 72658700 C T SNP - - - - - - - - - - - - - - - tier3 261 6 2.25 166 77 31.69 NA NA NA 440422 TCGA-AB-2907 AML29 5 85311398 85311398 G C SNP - - - - - - - - - - - - - - - tier3 110 1 0.9 154 77 33.33 NA NA NA 440422 TCGA-AB-2907 AML29 5 93822215 93822215 C T SNP uc003kko.1 ENST00000312498 human ensembl 54_36p -1 known intronic c.1091+1633 e6+1633 0.008 - - - no_start_codon tier3 86 0 0 373 116 23.67 NA NA NA 440422 TCGA-AB-2907 AML29 5 111038450 111038450 C A SNP ENSG00000209164 ENST00000386429 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*45038 NULL 0 - - - pseudogene tier3 102 1 0.97 337 163 32.53 NA NA NA 440422 TCGA-AB-2907 AML29 5 111579441 111579441 T C SNP EPB41L4A NM_022140.3 human genbank 54_36p -1 validated intronic c.1088-5863 e13-5863 0.006 - - - no_errors tier3 141 5 3.42 269 126 31.9 NA NA NA 440422 TCGA-AB-2907 AML29 5 112322837 112322837 A G SNP DCP2 NM_152624.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17693 NULL 0.035 - - - no_errors tier3 61 1 1.61 97 52 34.9 NA NA NA 440422 TCGA-AB-2907 AML29 5 117655738 117655738 G A SNP - - - - - - - - - - - - - - - tier3 347 2 0.57 205 94 31.44 NA NA NA 440422 TCGA-AB-2907 AML29 5 120562109 120562109 C G SNP - - - - - - - - - - - - - - - tier3 218 7 3.1 264 131 33.08 NA NA NA 440422 TCGA-AB-2907 AML29 5 124401476 124401476 T A SNP - - - - - - - - - - - - - - - tier3 277 0 0 502 74 12.85 NA NA NA 440422 TCGA-AB-2907 AML29 5 134891601 134891601 C A SNP CXCL14 NM_004887.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*43841 NULL 0.001 - - - no_errors tier3 345 4 1.15 114 50 30.49 NA NA NA 440422 TCGA-AB-2907 AML29 5 140413003 140413003 C A SNP PCDHB1 NM_013340.2 human genbank 54_36p 1 reviewed silent c.1764 p.T588 1 "HMMPfam_Cadherin,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 240 2 0.82 136 66 32.67 NA NA NA 440422 TCGA-AB-2907 AML29 5 143487287 143487287 A G SNP KCTD16 NM_020768.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-79184 NULL 0.003 - - - no_errors tier3 56 2 3.45 103 39 27.46 NA NA NA 440422 TCGA-AB-2907 AML29 5 147955935 147955935 A G SNP HTR4 NM_001040173.4 human genbank 54_36p -1 reviewed intronic c.26+40810 e1+40810 0 - - - no_errors tier3 180 1 0.55 194 101 34.24 NA NA NA 440422 TCGA-AB-2907 AML29 5 158857256 158857256 G T SNP - - - - - - - - - - - - - - - tier3 908 7 0.76 334 179 34.82 NA NA NA 440422 TCGA-AB-2907 AML29 5 166613960 166613960 T A SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known 5_prime_flanking_region c.-30461 NULL 0.561 - - - no_errors tier3 360 1 0.28 330 44 11.76 NA NA NA 440422 TCGA-AB-2907 AML29 5 173096862 173096862 G T SNP LOC729170 XM_001129548.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*49884 NULL 0.007 - - - no_errors tier3 178 3 1.66 121 58 32.4 NA NA NA 440422 TCGA-AB-2907 AML29 5 174714399 174714399 T C SNP - - - - - - - - - - - - - - - tier3 187 2 1.06 237 127 34.89 NA NA NA 440422 TCGA-AB-2907 AML29 5 180479322 180479322 T - DEL OR2V2 NM_206880.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-35227 NULL 0.03 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 6 4601332 4601332 G A SNP LOC442153 XR_016425.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-32765 NULL 0.009 - - - pseudogene tier3 46 0 0 130 86 39.81 NA NA NA 440422 TCGA-AB-2907 AML29 6 5681228 5681228 C T SNP FARS2 NM_006567.3 human genbank 54_36p 1 reviewed intronic c.1218-35295 e6-35295 0.031 - - - no_errors tier3 148 1 0.67 187 102 34.93 NA NA NA 440422 TCGA-AB-2907 AML29 6 8183620 8183620 G A SNP - - - - - - - - - - - - - - - tier3 136 0 0 176 79 30.98 NA NA NA 440422 TCGA-AB-2907 AML29 6 13184730 13184730 A C SNP PHACTR1 NM_030948.1 human genbank 54_36p 1 validated intronic c.415+22983 e3+22983 0 - - - no_errors tier3 279 10 3.45 266 135 33.67 NA NA NA 440422 TCGA-AB-2907 AML29 6 14723871 14723871 C T SNP ENSG00000206960 ENST00000384233 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-30874 NULL 0 - - - no_errors tier3 246 1 0.4 278 115 29.11 NA NA NA 440422 TCGA-AB-2907 AML29 6 35108001 35108001 G A SNP ANKS1A NM_015245.2 human genbank 54_36p 1 validated intronic c.2010+14187 e11+14187 0.012 - - - no_errors tier3 103 0 0 119 56 32 NA NA NA 440422 TCGA-AB-2907 AML29 6 45488262 45488262 T G SNP RUNX2 NM_001024630.2 human genbank 54_36p 1 reviewed intronic c.263-10046 e3-10046 0 - - - no_errors tier3 43 1 2.27 79 29 26.85 NA NA NA 440422 TCGA-AB-2907 AML29 6 45752338 45752338 G A SNP ENSG00000210937 ENST00000388202 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*30440 NULL 0 - - - pseudogene tier3 98 2 2 89 38 29.92 NA NA NA 440422 TCGA-AB-2907 AML29 6 46298840 46298840 G C SNP RCAN2 NM_005822.2 human genbank 54_36p -1 validated missense c.591 p.N197K 1 NULL HMMPfam_Calcipressin - no_errors tier1 258 2 0.77 218 63 22.26 NA NA NA 440422 TCGA-AB-2907 AML29 6 46495378 46495378 T C SNP RCAN2 ENST00000306764 human ensembl 54_36p -1 known intronic c.225+37070 e1+37070 0 - - - no_errors tier3 76 2 2.56 84 38 31.15 NA NA NA 440422 TCGA-AB-2907 AML29 6 51136891 51136891 A G SNP ENSG00000210990 ENST00000388255 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48200 NULL 0.191 - - - pseudogene tier3 58 1 1.69 158 84 34.71 NA NA NA 440422 TCGA-AB-2907 AML29 6 58030275 58030275 C T SNP - - - - - - - - - - - - - - - tier3 246 2 0.81 147 68 31.63 NA NA NA 440422 TCGA-AB-2907 AML29 6 73565220 73565220 C T SNP KCNQ5 NM_019842.2 human genbank 54_36p 1 reviewed intronic c.398+176184 e1+176184 0.001 - - - no_errors tier3 106 3 2.75 222 136 37.88 NA NA NA 440422 TCGA-AB-2907 AML29 6 74582006 74582006 T C SNP CD109 NM_133493.3 human genbank 54_36p 1 validated intronic c.3911+439 e30+439 0 - - - no_errors tier3 38 0 0 173 55 24.12 NA NA NA 440422 TCGA-AB-2907 AML29 6 88647030 88647030 G C SNP ENSG00000211983 ENST00000390694 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32961 NULL 0 - - - no_errors tier3 125 0 0 204 71 25.82 NA NA NA 440422 TCGA-AB-2907 AML29 6 88712435 88712435 A G SNP - - - - - - - - - - - - - - - tier3 381 12 3.05 314 145 31.52 NA NA NA 440422 TCGA-AB-2907 AML29 6 103497637 103497637 T C SNP - - - - - - - - - - - - - - - tier3 85 1 1.15 152 70 31.25 NA NA NA 440422 TCGA-AB-2907 AML29 6 110577350 110577350 G T SNP WASF1 NM_001024934.1 human genbank 54_36p -1 reviewed intronic c.1-21825 e1-21825 0 - - - no_errors tier3 220 9 3.93 199 99 33.22 NA NA NA 440422 TCGA-AB-2907 AML29 6 113688557 113688557 G A SNP ENSG00000216904 ENST00000402732 human ensembl 54_36p 1 known 3_prime_flanking_region c.*36590 NULL 0 - - - no_coding_region:pseudogene tier3 298 0 0 256 131 33.85 NA NA NA 440422 TCGA-AB-2907 AML29 6 122796369 122796369 A G SNP PKIB NM_181794.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-284270 NULL 0.005 - - - no_errors tier3 74 0 0 216 98 31.21 NA NA NA 440422 TCGA-AB-2907 AML29 6 123426552 123426552 C T SNP RLBP1L2 NM_001010852.2 human genbank 54_36p 1 provisional missense c.931 p.R311C 1 NULL "HMMPfam_CRAL_TRIO,HMMSmart_SM00516,superfamily_CRAL/TRIO domain,PatternScan_SUGAR_TRANSPORT_1,HMMPfam_CRAL_TRIO_N,superfamily_CRAL/TRIO N-terminal domain" - no_errors tier1 327 3 0.91 471 143 23.18 NA NA NA 440422 TCGA-AB-2907 AML29 6 137535065 137535065 G T SNP IL22RA2 NM_052962.2 human genbank 54_36p -1 reviewed intronic c.1+1178 e0+1178 0.007 - - - no_errors tier3 128 0 0 323 42 11.41 NA NA NA 440422 TCGA-AB-2907 AML29 6 146865867 146865867 C T SNP RAB32 NM_006834.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-40834 NULL 0 - - - no_errors tier3 328 3 0.91 200 98 32.89 NA NA NA 440422 TCGA-AB-2907 AML29 6 148779531 148779531 G A SNP SASH1 NM_015278.3 human genbank 54_36p 1 validated intronic c.286-23482 e3-23482 0 - - - no_errors tier3 193 0 0 145 79 35.11 NA NA NA 440422 TCGA-AB-2907 AML29 6 149361049 149361049 C T SNP UST NM_005715.2 human genbank 54_36p 1 validated intronic c.682-20919 e6-20919 0.998 - - - no_errors tier3 84 0 0 131 60 31.41 NA NA NA 440422 TCGA-AB-2907 AML29 6 154255675 154255675 G A SNP ENSG00000217085 ENST00000403971 human ensembl 54_36p -1 known 3_prime_flanking_region c.*45586 NULL 0.055 - - - no_coding_region:pseudogene tier3 77 1 1.27 163 84 33.87 NA NA NA 440422 TCGA-AB-2907 AML29 6 155580677 155580677 G A SNP TIAM2 NM_012454.2 human genbank 54_36p 1 reviewed intronic c.3168+6544 e12+6544 0.001 - - - no_errors tier3 37 1 2.56 122 74 37.76 NA NA NA 440422 TCGA-AB-2907 AML29 6 164508468 164508468 G A SNP LOC728275 XM_001127046.2 human genbank 54_36p 1 model intronic c.545-169523 e3-169523 0.001 - - - no_errors tier3 207 5 2.36 253 121 32.18 NA NA NA 440422 TCGA-AB-2907 AML29 6 165634428 165634428 G A SNP C6orf118 NM_144980.3 human genbank 54_36p -1 validated intronic c.754-463 e3-463 0 - - - no_errors tier3 571 0 0 199 74 27.11 NA NA NA 440422 TCGA-AB-2907 AML29 7 3963062 3963062 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.1151-2027 e8-2027 0 - - - no_errors tier3 48 1 2.04 39 20 33.9 NA NA NA 440422 TCGA-AB-2907 AML29 7 8946918 8946918 G C SNP ENSG00000220953 ENST00000402957 human ensembl 54_36p 1 known 3_prime_flanking_region c.*1394 NULL 1 - - - no_coding_region:pseudogene tier3 47 1 2.08 170 72 29.75 NA NA NA 440422 TCGA-AB-2907 AML29 7 9992935 9992935 T A SNP LOC340268 XR_041608.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.009 - - - no_errors tier3 101 1 0.98 158 69 30.4 NA NA NA 440422 TCGA-AB-2907 AML29 7 10660381 10660381 T C SNP LOC100131472 XM_001722341.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-48451 NULL 0.001 - - - no_errors tier3 153 2 1.29 337 152 31.08 NA NA NA 440422 TCGA-AB-2907 AML29 7 13653073 13653073 C T SNP - - - - - - - - - - - - - - - tier3 99 0 0 221 94 29.75 NA NA NA 440422 TCGA-AB-2907 AML29 7 25443523 25443523 A G SNP LOC100134549 XM_001724842.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*11033 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 81 1 1.2 185 93 33.45 NA NA NA 440422 TCGA-AB-2907 AML29 7 39397912 39397912 C T SNP POU6F2 NM_007252.2 human genbank 54_36p 1 validated intronic c.886-14812 e6-14812 0 - - - no_errors tier3 137 0 0 191 76 28.36 NA NA NA 440422 TCGA-AB-2907 AML29 7 63244866 63244866 C T SNP ENSG00000209045 ENST00000386310 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36508 NULL 0 - - - pseudogene tier3 273 4 1.44 129 56 30.27 NA NA NA 440422 TCGA-AB-2907 AML29 7 84500906 84500906 A T SNP SEMA3D NM_152754.2 human genbank 54_36p -1 validated intronic c.1191+3235 e10+3235 0.001 - - - no_errors tier3 36 0 0 143 68 32.08 NA NA NA 440422 TCGA-AB-2907 AML29 7 85711627 85711627 C T SNP - - - - - - - - - - - - - - - tier3 602 10 1.63 229 125 35.01 NA NA NA 440422 TCGA-AB-2907 AML29 7 88496312 88496312 A T SNP ZNF804B NM_181646.2 human genbank 54_36p 1 provisional intronic c.109-189093 e2-189093 0.167 - - - no_errors tier3 145 1 0.68 212 100 32.05 NA NA NA 440422 TCGA-AB-2907 AML29 7 102490106 102490106 C T SNP FBXL13 NM_145032.1 human genbank 54_36p -1 validated intronic c.1-6676 e1-6676 0.357 - - - no_errors tier3 116 3 2.52 123 52 29.55 NA NA NA 440422 TCGA-AB-2907 AML29 7 107377608 107377608 C T SNP LAMB1 NM_002291.2 human genbank 54_36p -1 reviewed intronic c.3391+1299 e23+1299 0.227 - - - no_errors tier3 49 0 0 130 47 26.55 NA NA NA 440422 TCGA-AB-2907 AML29 7 116048564 116048564 G C SNP - - - - - - - - - - - - - - - tier3 194 4 2.02 227 109 32.44 NA NA NA 440422 TCGA-AB-2907 AML29 7 118824451 118824451 G T SNP - - - - - - - - - - - - - - - tier3 54 0 0 90 36 28.57 NA NA NA 440422 TCGA-AB-2907 AML29 7 119112172 119112172 C G SNP - - - - - - - - - - - - - - - tier3 35 0 0 191 106 35.57 NA NA NA 440422 TCGA-AB-2907 AML29 7 124252841 124252841 G A SNP POT1 NM_015450.1 human genbank 54_36p -1 reviewed intronic c.1687-194 e14-194 0.037 - - - no_errors tier3 48 0 0 209 82 28.08 NA NA NA 440422 TCGA-AB-2907 AML29 7 131132530 131132530 C G SNP ENSG00000172400 ENST00000305171 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43210 NULL 0.028 - - - no_coding_region:pseudogene tier3 117 0 0 203 87 29.79 NA NA NA 440422 TCGA-AB-2907 AML29 7 135163553 135163553 G A SNP ENSG00000222219 ENST00000410287 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30156 NULL 0 - - - no_errors tier3 148 4 2.63 111 41 26.97 NA NA NA 440422 TCGA-AB-2907 AML29 7 154399039 154399039 C T SNP PAXIP1 NM_007349.3 human genbank 54_36p -1 reviewed intronic c.439-65 e6-65 0 - - - no_errors tier3 108 1 0.92 160 69 30 NA NA NA 440422 TCGA-AB-2907 AML29 7 155465999 155465999 C T SNP LOC389602 XM_001721557.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*15642 NULL 0 - - - no_errors tier3 59 1 1.67 61 20 24.69 NA NA NA 440422 TCGA-AB-2907 AML29 8 3152527 3152527 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.3954+97 e26+97 0.002 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 254 3 1.16 358 228 38.84 NA NA NA 440422 TCGA-AB-2907 AML29 8 3444726 3444726 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1100+13480 e9+13480 0.023 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 436 3 0.68 297 136 31.34 NA NA NA 440422 TCGA-AB-2907 AML29 8 12729858 12729858 T C SNP - - - - - - - - - - - - - - - tier3 97 2 2.02 180 75 29.41 NA NA NA 440422 TCGA-AB-2907 AML29 8 18577276 18577276 T C SNP PSD3 NM_015310.3 human genbank 54_36p -1 validated intronic c.2173-19801 e10-19801 0 - - - no_errors tier3 271 2 0.73 195 86 30.6 NA NA NA 440422 TCGA-AB-2907 AML29 8 21238727 21238727 G T SNP - - - - - - - - - - - - - - - tier3 32 0 0 146 81 35.68 NA NA NA 440422 TCGA-AB-2907 AML29 8 27113397 27113397 A C SNP STMN4 NM_030795.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*36883 NULL 0.027 - - - no_errors tier3 149 4 2.61 203 120 37.15 NA NA NA 440422 TCGA-AB-2907 AML29 8 27460130 27460130 A G SNP EPHX2 NM_001979.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*2174 NULL 0 - - - no_errors tier3 87 3 3.33 128 67 34.36 NA NA NA 440422 TCGA-AB-2907 AML29 8 28233351 28233351 C T SNP PNOC NM_006228.3 human genbank 54_36p 1 validated intronic c.1+2599 e0+2599 0 - - - no_errors tier3 131 4 2.96 205 95 31.67 NA NA NA 440422 TCGA-AB-2907 AML29 8 35379721 35379721 A T SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.104-146631 e2-146631 0 - - - no_errors tier3 400 7 1.72 267 124 31.71 NA NA NA 440422 TCGA-AB-2907 AML29 8 35534389 35534389 C T SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.307+7819 e2+7819 0.184 - - - no_errors tier3 151 2 1.31 156 80 33.76 NA NA NA 440422 TCGA-AB-2907 AML29 8 63718718 63718718 C T SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.273+53811 e3+53811 0.001 - - - no_errors tier3 342 6 1.72 204 119 36.84 NA NA NA 440422 TCGA-AB-2907 AML29 8 81781338 81781338 T C SNP ZNF704 NM_001033723.1 human genbank 54_36p -1 provisional intronic c.222-13441 e2-13441 0 - - - no_errors tier3 191 2 1.04 191 113 37.05 NA NA NA 440422 TCGA-AB-2907 AML29 8 94670483 94670483 T A SNP - - - - - - - - - - - - - - - tier3 297 2 0.67 332 115 25.73 NA NA NA 440422 TCGA-AB-2907 AML29 8 96247563 96247563 C T SNP PLEKHF2 NM_024613.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*11365 NULL 0 - - - no_errors tier3 315 3 0.94 147 84 36.36 NA NA NA 440422 TCGA-AB-2907 AML29 8 110868002 110868002 T C SNP - - - - - - - - - - - - - - - tier3 177 1 0.56 232 109 31.96 NA NA NA 440422 TCGA-AB-2907 AML29 8 113586200 113586200 T C SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.4896-818 e30-818 0 - - - no_errors tier3 164 3 1.8 309 151 32.83 NA NA NA 440422 TCGA-AB-2907 AML29 8 113978783 113978783 G C SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1633+24249 e10+24249 0 - - - no_errors tier3 82 1 1.2 242 120 33.06 NA NA NA 440422 TCGA-AB-2907 AML29 8 117705811 117705811 G A SNP EIF3H NM_003756.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*20615 NULL 0 - - - no_errors tier3 158 2 1.25 232 119 33.9 NA NA NA 440422 TCGA-AB-2907 AML29 8 118453987 118453987 T G SNP - - - - - - - - - - - - - - - tier3 229 4 1.72 203 139 40.64 NA NA NA 440422 TCGA-AB-2907 AML29 8 135371595 135371595 G A SNP - - - - - - - - - - - - - - - tier3 30 1 3.23 129 53 29.12 NA NA NA 440422 TCGA-AB-2907 AML29 8 136051580 136051580 G A SNP ENSG00000213624 ENST00000395315 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8776 NULL 0 - - - no_coding_region:pseudogene tier3 411 8 1.91 279 135 32.61 NA NA NA 440422 TCGA-AB-2907 AML29 8 137045912 137045912 G A SNP - - - - - - - - - - - - - - - tier3 213 5 2.29 173 69 28.51 NA NA NA 440422 TCGA-AB-2907 AML29 8 142873328 142873328 G A SNP - - - - - - - - - - - - - - - tier3 117 4 3.31 89 49 35.51 NA NA NA 440422 TCGA-AB-2907 AML29 9 23943159 23943159 C T SNP LOC100133655 XM_001716507.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-2011 NULL 0 - - - no_start_codon:pseudogene tier3 125 4 3.08 188 79 29.37 NA NA NA 440422 TCGA-AB-2907 AML29 9 75764615 75764615 A T SNP - - - - - - - - - - - - - - - tier3 39 2 4.88 102 47 31.54 NA NA NA 440422 TCGA-AB-2907 AML29 9 77177438 77177438 C T SNP ENSG00000220707 ENST00000404903 human ensembl 54_36p -1 known 3_prime_flanking_region c.*29192 NULL 0 - - - no_coding_region:pseudogene tier3 354 4 1.12 301 132 30.41 NA NA NA 440422 TCGA-AB-2907 AML29 9 82761694 82761694 G C SNP - - - - - - - - - - - - - - - tier3 42 0 0 148 78 34.51 NA NA NA 440422 TCGA-AB-2907 AML29 9 85224828 85224828 C G SNP FRMD3 NM_174938.4 human genbank 54_36p -1 validated intronic c.148-30385 e2-30385 0.107 - - - no_errors tier3 415 1 0.24 378 129 25.29 NA NA NA 440422 TCGA-AB-2907 AML29 9 97113062 97113062 C T SNP FANCC NM_000136.2 human genbank 54_36p -1 reviewed intronic c.1+6567 e0+6567 0.001 - - - no_errors tier3 172 1 0.58 86 49 36.03 NA NA NA 440422 TCGA-AB-2907 AML29 9 104659218 104659218 C A SNP - - - - - - - - - - - - - - - tier3 93 3 3.12 287 132 31.5 NA NA NA 440422 TCGA-AB-2907 AML29 9 105332960 105332960 C T SNP - - - - - - - - - - - - - - - tier3 221 5 2.21 248 108 30.34 NA NA NA 440422 TCGA-AB-2907 AML29 9 107403451 107403451 G T SNP FKTN NM_001079802.1 human genbank 54_36p 1 reviewed splice_site c.369+1 e3+1 1 - - - no_errors tier1 162 1 0.61 314 102 24.52 NA NA NA 440422 TCGA-AB-2907 AML29 9 108976999 108976999 G A SNP ENSG00000214180 ENST00000397723 human ensembl 54_36p -1 known 5_prime_flanking_region c.-3749 NULL 0 - - - no_coding_region:pseudogene tier3 121 0 0 103 53 33.76 NA NA NA 440422 TCGA-AB-2907 AML29 10 701181 701181 C T SNP DIP2C NM_014974.2 human genbank 54_36p -1 reviewed intronic c.85+24253 e1+24253 0.009 - - - no_errors tier3 31 0 0 93 29 23.77 NA NA NA 440422 TCGA-AB-2907 AML29 10 13319597 13319597 C T SNP UCMA NM_145314.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-3333 NULL 0.673 - - - no_errors tier3 301 5 1.63 161 62 27.8 NA NA NA 440422 TCGA-AB-2907 AML29 10 13325759 13325759 C T SNP UCMA NM_145314.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-9495 NULL 0.001 - - - no_errors tier3 114 1 0.87 102 30 22.39 NA NA NA 440422 TCGA-AB-2907 AML29 10 14245554 14245554 A C SNP FRMD4A NM_018027.3 human genbank 54_36p -1 validated intronic c.45+166509 e1+166509 0 - - - no_errors tier3 946 6 0.63 400 218 35.28 NA NA NA 440422 TCGA-AB-2907 AML29 10 19498932 19498932 G A SNP LOC729195 XM_001129637.2 human genbank 54_36p 1 model intronic c.750+4187 e5+4187 0.022 - - - no_errors tier3 271 4 1.45 337 169 33.4 NA NA NA 440422 TCGA-AB-2907 AML29 10 24070194 24070194 G C SNP KIAA1217 NM_001098500.1 human genbank 54_36p 1 validated intronic c.1+46025 e0+46025 0.001 - - - no_errors tier3 237 7 2.87 198 110 35.6 NA NA NA 440422 TCGA-AB-2907 AML29 10 24253699 24253699 C G SNP KIAA1217 NM_001098500.1 human genbank 54_36p 1 validated intronic c.1-82461 e1-82461 0.003 - - - no_errors tier3 188 2 1.05 266 119 30.91 NA NA NA 440422 TCGA-AB-2907 AML29 10 32491810 32491810 C G SNP LOC439953 XR_017375.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*25234 NULL 0 - - - pseudogene tier3 281 5 1.75 171 96 35.96 NA NA NA 440422 TCGA-AB-2907 AML29 10 42240282 42240282 G A SNP CCNYL2 XM_374787.1 human genbank 54_36p -1 model intronic c.1032+499 e9+499 0.009 - - - no_errors tier3 139 0 0 102 48 32 NA NA NA 440422 TCGA-AB-2907 AML29 10 48049363 48049363 G A SNP GDF10 NM_004962.2 human genbank 54_36p -1 reviewed missense c.529 p.L177F 0.005 NULL "HMMPfam_TGF_beta,HMMSmart_SM00204,PatternScan_TGF_BETA_1,superfamily_Cystine-knot cytokines" - no_errors tier1 85 1 1.16 30 24 44.44 NA NA NA 440422 TCGA-AB-2907 AML29 10 49311649 49311649 C G SNP MAPK8 NM_139047.2 human genbank 54_36p 1 reviewed intronic c.1139-1284 e11-1284 0 - - - no_errors tier3 224 3 1.32 159 76 32.34 NA NA NA 440422 TCGA-AB-2907 AML29 10 64995334 64995334 C T SNP REEP3 NM_001001330.1 human genbank 54_36p 1 provisional intronic c.33-770 e2-770 0.003 - - - no_errors tier3 141 2 1.39 262 136 34 NA NA NA 440422 TCGA-AB-2907 AML29 10 78579212 78579212 T A SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.809-28400 e6-28400 0.001 - - - no_errors tier3 174 3 1.69 261 124 32.12 NA NA NA 440422 TCGA-AB-2907 AML29 10 79438483 79438483 C A SNP POLR3A NM_007055.2 human genbank 54_36p -1 validated intronic c.1909+818 e14+818 0 - - - no_errors tier3 379 4 1.04 217 98 31.11 NA NA NA 440422 TCGA-AB-2907 AML29 10 79699378 79699378 G A SNP - - - - - - - - - - - - - - - tier3 247 3 1.2 231 111 32.46 NA NA NA 440422 TCGA-AB-2907 AML29 10 83996744 83996744 T A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.824-111731 e2-111731 0 - - - no_errors tier3 562 5 0.88 415 204 32.96 NA NA NA 440422 TCGA-AB-2907 AML29 10 86547181 86547181 G A SNP - - - - - - - - - - - - - - - tier3 192 6 3.03 188 75 28.41 NA NA NA 440422 TCGA-AB-2907 AML29 10 91910088 91910088 C T SNP ENSG00000222451 ENST00000410519 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*3300 NULL 0.176 - - - no_errors tier3 262 2 0.76 259 116 30.93 NA NA NA 440422 TCGA-AB-2907 AML29 10 98309744 98309744 A G SNP TM9SF3 NM_020123.3 human genbank 54_36p -1 validated intronic c.583-261 e5-261 0 - - - no_errors tier3 89 2 2.2 107 61 36.31 NA NA NA 440422 TCGA-AB-2907 AML29 10 123944307 123944307 C T SNP TACC2 NM_206862.2 human genbank 54_36p 1 reviewed intronic c.5835-238 e7-238 0 - - - no_errors tier3 219 2 0.9 151 85 35.71 NA NA NA 440422 TCGA-AB-2907 AML29 10 128666901 128666901 T C SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.171+659 e3+659 0.006 - - - no_errors tier3 317 2 0.63 258 122 32.02 NA NA NA 440422 TCGA-AB-2907 AML29 11 12710604 12710604 T A SNP TEAD1 NM_021961.4 human genbank 54_36p 1 validated intronic c.1-31698 e1-31698 0.005 - - - no_errors tier3 141 2 1.4 224 97 30.22 NA NA NA 440422 TCGA-AB-2907 AML29 11 15123706 15123706 T A SNP INSC NM_001031853.3 human genbank 54_36p 1 provisional intronic c.97-3546 e2-3546 0.001 - - - no_errors tier3 211 4 1.86 168 78 31.71 NA NA NA 440422 TCGA-AB-2907 AML29 11 39587068 39587068 T C SNP - - - - - - - - - - - - - - - tier3 85 3 3.41 201 56 21.79 NA NA NA 440422 TCGA-AB-2907 AML29 11 42038937 42038937 G A SNP - - - - - - - - - - - - - - - tier3 36 1 2.7 138 67 32.68 NA NA NA 440422 TCGA-AB-2907 AML29 11 49898603 49898603 C T SNP OR4C13 NM_001001955.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-31948 NULL 1 - - - no_errors tier3 279 2 0.71 185 95 33.93 NA NA NA 440422 TCGA-AB-2907 AML29 11 50071560 50071560 T C SNP - - - - - - - - - - - - - - - tier3 121 2 1.63 108 48 30.77 NA NA NA 440422 TCGA-AB-2907 AML29 11 76019251 76019251 A T SNP LRRC32 NM_005512.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*29045 NULL 0 - - - no_errors tier3 116 0 0 84 32 27.59 NA NA NA 440422 TCGA-AB-2907 AML29 11 76409602 76409602 G A SNP ACER3 NM_018367.5 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*583 NULL 0 - - - no_errors tier3 395 7 1.74 194 122 38.49 NA NA NA 440422 TCGA-AB-2907 AML29 11 78200790 78200790 C T SNP ODZ4 NM_001098816.2 human genbank 54_36p -1 validated intronic c.1+25 e0+25 0 - - - no_errors tier3 674 15 2.18 234 98 29.43 NA NA NA 440422 TCGA-AB-2907 AML29 11 78463065 78463065 G A SNP ODZ4 ENST00000278550 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4428 NULL 0.002 - - - no_errors tier3 181 0 0 79 33 29.2 NA NA NA 440422 TCGA-AB-2907 AML29 11 87459092 87459092 G A SNP ENSG00000206690 ENST00000383963 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13719 NULL 0.011 - - - no_errors tier3 113 0 0 296 142 32.35 NA NA NA 440422 TCGA-AB-2907 AML29 11 92350425 92350425 C T SNP MTNR1B NM_005959.3 human genbank 54_36p 1 reviewed intronic c.224-3836 e2-3836 0 - - - no_errors tier3 149 2 1.32 114 48 29.45 NA NA NA 440422 TCGA-AB-2907 AML29 11 103849443 103849443 C A SNP - - - - - - - - - - - - - - - tier3 371 6 1.59 357 165 31.55 NA NA NA 440422 TCGA-AB-2907 AML29 11 104735771 104735771 G A SNP ENSG00000211026 ENST00000388291 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-6868 NULL 0 - - - pseudogene tier3 168 1 0.59 220 97 30.5 NA NA NA 440422 TCGA-AB-2907 AML29 11 105500924 105500924 G T SNP KBTBD3 NM_152433.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-65890 NULL 0.001 - - - no_errors tier3 106 0 0 240 72 23 NA NA NA 440422 TCGA-AB-2907 AML29 11 108494336 108494336 C T SNP ENSG00000200613 ENST00000363743 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*2479 NULL 0 - - - no_errors tier3 85 3 3.41 114 49 29.88 NA NA NA 440422 TCGA-AB-2907 AML29 11 110651106 110651106 G A SNP C11orf53 NM_198498.1 human genbank 54_36p 1 predicted intronic c.1-6227 e1-6227 0 - - - no_errors tier3 60 2 3.23 126 52 29.21 NA NA NA 440422 TCGA-AB-2907 AML29 11 120687805 120687805 A G SNP SC5DL NM_001024956.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*4374 NULL 0.001 - - - no_errors tier3 162 0 0 321 42 11.57 NA NA NA 440422 TCGA-AB-2907 AML29 11 126840240 126840240 G T SNP - - - - - - - - - - - - - - - tier3 103 2 1.9 143 65 31.25 NA NA NA 440422 TCGA-AB-2907 AML29 11 128756559 128756559 A - DEL BARX2 NM_003658.4 human genbank 54_36p 1 reviewed intronic c.187+5232 e1+5232 0.002 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 11 128946996 128946996 C T SNP - - - - - - - - - - - - - - - tier3 380 2 0.52 240 90 27.27 NA NA NA 440422 TCGA-AB-2907 AML29 11 131838122 131838122 C T SNP OPCML NM_002545.1 human genbank 54_36p -1 reviewed intronic c.527-25659 e4-25659 0.026 - - - no_errors tier3 275 1 0.36 226 88 27.94 NA NA NA 440422 TCGA-AB-2907 AML29 12 1448612 1448612 C T SNP ERC1 NM_178040.2 human genbank 54_36p 1 reviewed intronic c.3214-20908 e18-20908 0.001 - - - no_errors tier3 324 1 0.31 184 113 38.05 NA NA NA 440422 TCGA-AB-2907 AML29 12 14089532 14089532 G A SNP - - - - - - - - - - - - - - - tier3 40 1 2.44 191 76 28.36 NA NA NA 440422 TCGA-AB-2907 AML29 12 14101419 14101419 C A SNP - - - - - - - - - - - - - - - tier3 199 5 2.45 235 139 37.17 NA NA NA 440422 TCGA-AB-2907 AML29 12 20256136 20256136 A G SNP - - - - - - - - - - - - - - - tier3 214 0 0 283 88 23.66 NA NA NA 440422 TCGA-AB-2907 AML29 12 23624997 23624997 A T SNP SOX5 NM_006940.4 human genbank 54_36p -1 reviewed intronic c.1165-4958 e10-4958 0.007 - - - no_errors tier3 150 3 1.96 248 120 32.61 NA NA NA 440422 TCGA-AB-2907 AML29 12 36843154 36843154 G A SNP ENSG00000199843 ENST00000362973 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1503 NULL 0 - - - no_errors tier3 603 4 0.66 185 52 21.85 NA NA NA 440422 TCGA-AB-2907 AML29 12 55133361 55133361 G A SNP MIP NM_012064.2 human genbank 54_36p -1 validated intronic c.526-158 e3-158 0 - - - no_errors tier3 120 2 1.64 76 26 25.49 NA NA NA 440422 TCGA-AB-2907 AML29 12 87104499 87104499 T C SNP TMTC3 NM_181783.3 human genbank 54_36p 1 validated intronic c.1433-2252 e10-2252 0 - - - no_errors tier3 110 1 0.89 231 81 25.96 NA NA NA 440422 TCGA-AB-2907 AML29 12 97290662 97290662 T G SNP ENSG00000201296 ENST00000364426 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*45145 NULL 0 - - - no_errors tier3 291 2 0.68 270 152 36.02 NA NA NA 440422 TCGA-AB-2907 AML29 12 112819940 112819940 C T SNP RBM19 NM_016196.2 human genbank 54_36p -1 provisional intronic c.2558+17217 e21+17217 0.001 - - - no_errors tier3 304 6 1.94 198 86 30.18 NA NA NA 440422 TCGA-AB-2907 AML29 12 116619303 116619303 C T SNP KSR2 NM_173598.4 human genbank 54_36p -1 validated intronic c.624-29457 e3-29457 0 - - - no_errors tier3 224 0 0 221 94 29.65 NA NA NA 440422 TCGA-AB-2907 AML29 12 117829971 117829971 C G SNP ENSG00000201042 ENST00000364172 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19219 NULL 0 - - - no_errors tier3 153 2 1.29 245 106 30.2 NA NA NA 440422 TCGA-AB-2907 AML29 12 118720390 118720390 C T SNP CIT NM_007174.1 human genbank 54_36p -1 validated intronic c.1295+5003 e9+5003 0.001 - - - no_errors tier3 834 11 1.3 440 231 34.43 NA NA NA 440422 TCGA-AB-2907 AML29 12 124004770 124004770 G A SNP DHX37 NM_032656.2 human genbank 54_36p -1 reviewed intronic c.2454-60 e19-60 0 - - - no_errors tier3 88 1 1.12 48 12 20 NA NA NA 440422 TCGA-AB-2907 AML29 12 125520889 125520889 G A SNP ENSG00000214043 ENST00000397346 human ensembl 54_36p 1 known intronic c.516-271 e6-271 0.028 - - - no_errors tier3 70 0 0 196 85 30.25 NA NA NA 440422 TCGA-AB-2907 AML29 12 125561786 125561786 A G SNP LOC100128554 XM_001719470.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*45535 NULL 0.012 - - - no_errors tier3 229 6 2.54 172 101 37 NA NA NA 440422 TCGA-AB-2907 AML29 12 128833962 128833962 C T SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.80-82766 e2-82766 0 - - - no_errors tier3 63 1 1.56 145 62 29.81 NA NA NA 440422 TCGA-AB-2907 AML29 12 129893077 129893077 T A SNP STX2 NM_194356.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3480 NULL 0.03 - - - no_errors tier3 37 0 0 30 20 40 NA NA NA 440422 TCGA-AB-2907 AML29 13 53147420 53147420 C T SNP - - - - - - - - - - - - - - - tier3 171 1 0.58 222 92 29.21 NA NA NA 440422 TCGA-AB-2907 AML29 13 53163301 53163301 G T SNP - - - - - - - - - - - - - - - tier3 58 3 4.92 176 76 30.16 NA NA NA 440422 TCGA-AB-2907 AML29 13 57033986 57033986 T A SNP - - - - - - - - - - - - - - - tier3 72 3 4 167 76 31.28 NA NA NA 440422 TCGA-AB-2907 AML29 13 58720067 58720067 A G SNP - - - - - - - - - - - - - - - tier3 36 0 0 155 94 37.75 NA NA NA 440422 TCGA-AB-2907 AML29 13 62459901 62459901 G T SNP - - - - - - - - - - - - - - - tier3 59 0 0 159 80 33.47 NA NA NA 440422 TCGA-AB-2907 AML29 13 65737674 65737674 G T SNP ENSG00000219045 ENST00000404591 human ensembl 54_36p 1 known 5_prime_flanking_region c.-3456 NULL 0.376 - - - no_coding_region:pseudogene tier3 269 1 0.37 194 110 36.18 NA NA NA 440422 TCGA-AB-2907 AML29 13 72582277 72582277 C T SNP ENSG00000118928 ENST00000237789 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9153 NULL 0 - - - no_coding_region:pseudogene tier3 137 0 0 142 84 36.84 NA NA NA 440422 TCGA-AB-2907 AML29 13 83077080 83077080 C G SNP - - - - - - - - - - - - - - - tier3 79 0 0 157 33 17.28 NA NA NA 440422 TCGA-AB-2907 AML29 13 89847992 89847992 C G SNP - - - - - - - - - - - - - - - tier3 478 11 2.25 275 124 31 NA NA NA 440422 TCGA-AB-2907 AML29 13 95654212 95654212 G A SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+112388 e1+112388 0.009 - - - no_errors tier3 41 0 0 169 80 32.13 NA NA NA 440422 TCGA-AB-2907 AML29 13 100771104 100771104 T G SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.799+24514 e6+24514 0.001 - - - no_errors tier3 69 0 0 125 56 30.94 NA NA NA 440422 TCGA-AB-2907 AML29 13 100849695 100849695 C T SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.1-178 e1-178 0 - - - no_errors tier3 53 1 1.82 215 102 32.18 NA NA NA 440422 TCGA-AB-2907 AML29 13 103745651 103745651 T A SNP - - - - - - - - - - - - - - - tier3 56 0 0 130 59 31.22 NA NA NA 440422 TCGA-AB-2907 AML29 13 113654871 113654871 G T SNP FAM70B NM_182614.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-3025 NULL 0.004 - - - no_errors tier3 157 6 3.68 54 26 32.5 NA NA NA 440422 TCGA-AB-2907 AML29 14 26381575 26381575 C A SNP - - - - - - - - - - - - - - - tier3 213 1 0.47 206 80 27.97 NA NA NA 440422 TCGA-AB-2907 AML29 14 26569281 26569281 T C SNP - - - - - - - - - - - - - - - tier3 32 0 0 51 19 27.14 NA NA NA 440422 TCGA-AB-2907 AML29 14 31839603 31839603 C T SNP AKAP6 NM_004274.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-132848 NULL 0 - - - no_errors tier3 172 2 1.15 180 106 37.06 NA NA NA 440422 TCGA-AB-2907 AML29 14 37656351 37656351 G A SNP LOC729122 XM_001129370.1 human genbank 54_36p -1 model intronic c.1-26238 e1-26238 0.752 - - - no_errors tier3 190 1 0.52 241 84 25.77 NA NA NA 440422 TCGA-AB-2907 AML29 14 43493462 43493462 G T SNP - - - - - - - - - - - - - - - tier3 106 0 0 197 92 31.83 NA NA NA 440422 TCGA-AB-2907 AML29 14 48489123 48489123 C T SNP - - - - - - - - - - - - - - - tier3 137 1 0.72 220 140 38.89 NA NA NA 440422 TCGA-AB-2907 AML29 14 55331825 55331825 C T SNP ENSG00000177350 ENST00000313768 human ensembl 54_36p 1 known 3_prime_flanking_region c.*28607 NULL 0.087 - - - no_errors tier3 226 2 0.88 216 43 16.54 NA NA NA 440422 TCGA-AB-2907 AML29 14 58852599 58852599 A G SNP DAAM1 NM_014992.1 human genbank 54_36p 1 reviewed intronic c.345+777 e3+777 0 - - - no_errors tier3 265 10 3.64 324 174 34.87 NA NA NA 440422 TCGA-AB-2907 AML29 14 64898818 64898818 A G SNP FUT8 NM_178155.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-199217 NULL 0.009 - - - no_errors tier3 215 3 1.38 235 99 29.64 NA NA NA 440422 TCGA-AB-2907 AML29 14 75111292 75111292 A G SNP FLVCR2 NM_017791.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3777 NULL 0.107 - - - no_errors tier3 43 1 2.27 66 40 37.74 NA NA NA 440422 TCGA-AB-2907 AML29 14 78240733 78240733 T C SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.103-4580 e2-4580 0 - - - no_errors tier3 221 3 1.34 226 88 28.03 NA NA NA 440422 TCGA-AB-2907 AML29 14 82687825 82687825 C T SNP - - - - - - - - - - - - - - - tier3 148 2 1.33 193 91 31.82 NA NA NA 440422 TCGA-AB-2907 AML29 14 86938767 86938767 G T SNP - - - - - - - - - - - - - - - tier3 457 2 0.43 240 129 34.96 NA NA NA 440422 TCGA-AB-2907 AML29 14 98219463 98219463 A G SNP C14orf177 NM_182560.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-32819 NULL 0.001 - - - no_errors tier3 81 2 2.41 120 54 31.03 NA NA NA 440422 TCGA-AB-2907 AML29 14 101117396 101117396 C A SNP DIO3OS NR_002770.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-25630 NULL 0.947 - - - no_errors tier3 122 1 0.81 132 51 27.87 NA NA NA 440422 TCGA-AB-2907 AML29 15 24647976 24647976 G T SNP GABRB3 ENST00000383015 human ensembl 54_36p -1 known intronic c.201-35322 e2-35322 0.135 - - - no_errors tier3 295 4 1.33 114 51 30.91 NA NA NA 440422 TCGA-AB-2907 AML29 15 35210038 35210038 G C SNP MEIS2 NM_170675.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31079 NULL 0.001 - - - no_errors tier3 250 6 2.33 177 79 30.62 NA NA NA 440422 TCGA-AB-2907 AML29 15 43965240 43965240 C A SNP - - - - - - - - - - - - - - - tier3 107 1 0.93 101 49 32.67 NA NA NA 440422 TCGA-AB-2907 AML29 15 52030056 52030056 A G SNP - - - - - - - - - - - - - - - tier3 65 1 1.52 129 67 34.18 NA NA NA 440422 TCGA-AB-2907 AML29 15 85203791 85203791 G A SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.3084-128431 e22-128431 0.001 - - - no_errors tier3 179 4 2.19 246 117 32.23 NA NA NA 440422 TCGA-AB-2907 AML29 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 50 1 1.92 49 22 30.99 NA NA NA 440422 TCGA-AB-2907 AML29 15 93236875 93236875 C T SNP LOC440311 XR_016779.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*35727 NULL 0 - - - pseudogene tier3 56 3 5.08 102 47 31.54 NA NA NA 440422 TCGA-AB-2907 AML29 16 7136653 7136653 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.27+94553 e1+94553 0 - - - no_errors tier3 158 0 0 229 65 22.11 NA NA NA 440422 TCGA-AB-2907 AML29 16 7147669 7147669 C T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.27+105569 e1+105569 0 - - - no_errors tier3 488 3 0.61 302 138 31.36 NA NA NA 440422 TCGA-AB-2907 AML29 16 7971172 7971172 G A SNP - - - - - - - - - - - - - - - tier3 134 1 0.74 225 88 28.03 NA NA NA 440422 TCGA-AB-2907 AML29 16 11385371 11385371 C G SNP LOC388210 XM_370934.1 human genbank 54_36p -1 model splice_region c.766-5 e6-5 0 - - - no_errors tier3 106 0 0 89 16 15.24 NA NA NA 440422 TCGA-AB-2907 AML29 16 16153620 16153620 C G SNP ABCC6 NM_001171.3 human genbank 54_36p -1 reviewed intronic c.4209-1490 e30-1490 0.003 - - - no_errors tier3 66 0 0 91 49 35 NA NA NA 440422 TCGA-AB-2907 AML29 16 17086764 17086764 G A SNP XYLT1 NM_022166.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*23289 NULL 0.001 - - - no_errors tier3 307 3 0.97 178 85 32.32 NA NA NA 440422 TCGA-AB-2907 AML29 16 24465382 24465383 - T INS RBBP6 NM_006910.4 human genbank 54_36p 1 reviewed intronic c.266+298_266+297 e2+298 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 16 47748131 47748131 G A SNP - - - - - - - - - - - - - - - tier3 441 2 0.45 263 156 37.23 NA NA NA 440422 TCGA-AB-2907 AML29 16 50571267 50571267 C T SNP LOC388276 XR_041360.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*46498 NULL 0 - - - no_errors tier3 248 5 1.97 253 130 33.94 NA NA NA 440422 TCGA-AB-2907 AML29 16 52703554 52703554 A G SNP FTO NM_001080432.1 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*226 NULL 0.001 - - - no_errors tier3 117 1 0.84 134 50 27.17 NA NA NA 440422 TCGA-AB-2907 AML29 16 58162346 58162346 C T SNP ENSG00000200062 ENST00000363192 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*30675 NULL 0.001 - - - no_errors tier3 60 1 1.64 149 92 38.17 NA NA NA 440422 TCGA-AB-2907 AML29 16 59985247 59985247 G C SNP - - - - - - - - - - - - - - - tier3 223 4 1.76 297 148 33.26 NA NA NA 440422 TCGA-AB-2907 AML29 16 63754698 63754698 C G SNP CDH11 NM_001797.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-158425 NULL 0.001 - - - no_errors tier3 205 0 0 297 130 30.3 NA NA NA 440422 TCGA-AB-2907 AML29 16 65116381 65116381 G T SNP TK2 NM_004614.3 human genbank 54_36p -1 validated intronic c.575+4017 e6+4017 0 - - - no_errors tier3 146 2 1.35 114 68 37.36 NA NA NA 440422 TCGA-AB-2907 AML29 16 76015567 76015567 C T SNP ADAMTS18 NM_199355.2 human genbank 54_36p -1 reviewed intronic c.495+7126 e3+7126 0 - - - no_errors tier3 236 5 2.07 145 50 25.64 NA NA NA 440422 TCGA-AB-2907 AML29 16 81327424 81327424 A T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.45+109181 e1+109181 0.005 - - - no_errors tier3 199 2 1 466 194 29.39 NA NA NA 440422 TCGA-AB-2907 AML29 17 1190823 1190824 AT - DEL ENSG00000209456 ENST00000386721 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-34294 NULL 0.000:0.001 - - - pseudogene tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 17 5718662 5718662 G A SNP - - - - - - - - - - - - - - - tier3 240 5 2.03 169 80 32.13 NA NA NA 440422 TCGA-AB-2907 AML29 17 14361435 14361435 G A SNP - - - - - - - - - - - - - - - tier3 253 3 1.16 252 127 33.51 NA NA NA 440422 TCGA-AB-2907 AML29 17 15923369 15923369 T A SNP NCOR1 NM_006311.2 human genbank 54_36p -1 reviewed intronic c.3501+634 e25+634 0 - - - no_errors tier3 82 0 0 112 67 37.43 NA NA NA 440422 TCGA-AB-2907 AML29 17 25716954 25716954 C - DEL CPD NM_001304.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13171 NULL 0.008 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 17 32905174 32905174 G A SNP TADA2L NM_001488.3 human genbank 54_36p 1 reviewed intronic c.1029-137 e13-137 0 - - - no_errors tier3 125 2 1.57 144 49 25.39 NA NA NA 440422 TCGA-AB-2907 AML29 17 44687752 44687752 G A SNP ENSG00000177369 ENST00000322227 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*2737 NULL 0.001 - - - no_errors tier3 199 2 1 73 44 37.61 NA NA NA 440422 TCGA-AB-2907 AML29 17 50868091 50868091 G A SNP MMD NM_012329.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14036 NULL 0.027 - - - no_errors tier3 81 1 1.22 84 41 32.8 NA NA NA 440422 TCGA-AB-2907 AML29 17 51077234 51077234 G T SNP - - - - - - - - - - - - - - - tier3 413 5 1.2 317 158 33.26 NA NA NA 440422 TCGA-AB-2907 AML29 17 55621158 55621158 T C SNP USP32 NM_032582.3 human genbank 54_36p -1 validated intronic c.3642+1548 e29+1548 0.076 - - - no_errors tier3 214 0 0 93 41 30.6 NA NA NA 440422 TCGA-AB-2907 AML29 17 57494203 57494203 A G SNP MED13 NM_005121.2 human genbank 54_36p -1 reviewed intronic c.301+1007 e2+1007 0.001 - - - no_errors tier3 59 0 0 74 42 36.21 NA NA NA 440422 TCGA-AB-2907 AML29 17 64360905 64360905 T C SNP ABCA8 NM_007168.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*14916 NULL 0.001 - - - no_errors tier3 284 4 1.39 278 128 31.45 NA NA NA 440422 TCGA-AB-2907 AML29 17 67270856 67270856 C T SNP - - - - - - - - - - - - - - - tier3 237 3 1.25 236 114 32.39 NA NA NA 440422 TCGA-AB-2907 AML29 17 68652501 68652501 C T SNP COG1 NM_018714.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48303 NULL 0.012 - - - no_errors tier3 296 2 0.67 199 89 30.9 NA NA NA 440422 TCGA-AB-2907 AML29 17 74301009 74301009 G C SNP CYTH1 NM_004762.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11109 NULL 0 - - - no_errors tier3 437 3 0.68 210 50 19.16 NA NA NA 440422 TCGA-AB-2907 AML29 18 27994904 27994904 T C SNP MEP1B NM_005925.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29128 NULL 0.005 - - - no_errors tier3 187 4 2.09 155 84 35.15 NA NA NA 440422 TCGA-AB-2907 AML29 18 29563800 29563800 G A SNP ASXL3 NM_030632.1 human genbank 54_36p 1 validated intronic c.880-2130 e9-2130 0 - - - no_errors tier3 620 3 0.48 327 192 36.92 NA NA NA 440422 TCGA-AB-2907 AML29 18 30905524 30905524 C T SNP MAPRE2 NM_014268.1 human genbank 54_36p 1 reviewed intronic c.250+1240 e2+1240 0.007 - - - no_errors tier3 43 1 2.27 133 57 30 NA NA NA 440422 TCGA-AB-2907 AML29 18 33240525 33240525 A C SNP BRUNOL4 NM_020180.1 human genbank 54_36p -1 reviewed intronic c.369+78961 e2+78961 0.002 - - - no_errors tier3 79 5 5.95 58 28 32.56 NA NA NA 440422 TCGA-AB-2907 AML29 18 43894167 43894167 G A SNP LOC100127909 XM_001721243.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*20626 NULL 0.001 - - - no_errors tier3 301 3 0.98 160 67 29.52 NA NA NA 440422 TCGA-AB-2907 AML29 18 48450539 48450539 G A SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.92-81883 e2-81883 0 - - - no_errors tier3 307 1 0.32 371 199 34.91 NA NA NA 440422 TCGA-AB-2907 AML29 18 50104673 50104673 G A SNP C18orf54 NM_173529.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36268 NULL 0.009 - - - no_errors tier3 93 1 1.06 184 88 32.35 NA NA NA 440422 TCGA-AB-2907 AML29 18 53327450 53327450 A G SNP ONECUT2 NM_004852.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*32497 NULL 0.025 - - - no_errors tier3 88 1 1.12 176 71 28.74 NA NA NA 440422 TCGA-AB-2907 AML29 18 60644429 60644429 T A SNP - - - - - - - - - - - - - - - tier3 332 9 2.64 329 161 32.79 NA NA NA 440422 TCGA-AB-2907 AML29 18 65540294 65540294 C A SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.600-16887 e6-16887 0 - - - no_errors tier3 38 0 0 145 58 28.57 NA NA NA 440422 TCGA-AB-2907 AML29 18 65568481 65568481 C T SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.739-7491 e7-7491 0.001 - - - no_errors tier3 68 1 1.45 115 56 32.75 NA NA NA 440422 TCGA-AB-2907 AML29 18 68126340 68126340 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 18 72709732 72709732 C G SNP ZNF236 NM_007345.3 human genbank 54_36p 1 validated missense c.461 p.A154G 0.953 "HMMPfam_zf-C2H2,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 308 2 0.65 154 71 31.14 NA NA NA 440422 TCGA-AB-2907 AML29 19 10526019 10526019 G T SNP KRI1 NM_023008.3 human genbank 54_36p -1 validated intronic c.1800-62 e19-62 0 - - - no_errors tier3 165 1 0.6 61 41 39.42 NA NA NA 440422 TCGA-AB-2907 AML29 19 34458519 34458519 C A SNP ENSG00000222848 ENST00000410916 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42387 NULL 0.001 - - - no_errors tier3 409 8 1.91 244 111 31.27 NA NA NA 440422 TCGA-AB-2907 AML29 19 38104399 38104399 G C SNP CCDC123 NM_032816.3 human genbank 54_36p -1 validated intronic c.1268+1786 e12+1786 0.014 - - - no_errors tier3 190 4 2.06 180 69 27.49 NA NA NA 440422 TCGA-AB-2907 AML29 19 57581279 57581279 C T SNP ZNF528 NM_032423.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-15800 NULL 0.029 - - - no_errors tier2 219 2 0.9 279 142 33.57 NA NA NA 440422 TCGA-AB-2907 AML29 19 61957699 61957699 C A SNP ZIM2 NM_015363.3 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*20169 NULL 0.009 - - - no_errors tier3 185 3 1.6 236 107 31.2 NA NA NA 440422 TCGA-AB-2907 AML29 19 63659414 63659414 G A SNP ZNF324B NM_207395.2 human genbank 54_36p 1 validated missense c.1291 p.G431S 0.719 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 207 6 2.82 54 21 28 NA NA NA 440422 TCGA-AB-2907 AML29 20 146954 146955 - T INS LOC100134244 XM_001717071.1 human genbank 54_36p -1 model intronic c.142+2150_142+2149 e2+2150 0.000:0.000 - - - no_start_codon:pseudogene:no_stop_codon tier3 NA NA NA NA NA NA NA NA NA 440422 TCGA-AB-2907 AML29 20 4806585 4806585 A G SNP SLC23A2 NM_005116.5 human genbank 54_36p -1 reviewed intronic c.825-3243 e8-3243 0 - - - no_errors tier3 133 4 2.92 208 89 29.77 NA NA NA 440422 TCGA-AB-2907 AML29 20 9813492 9813492 C T SNP PAK7 NM_020341.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-240516 NULL 0.01 - - - no_errors tier3 241 1 0.41 222 159 41.73 NA NA NA 440422 TCGA-AB-2907 AML29 20 10963968 10963968 A G SNP LOC100134329 XM_001713828.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-2164 NULL 0.998 - - - no_start_codon:no_stop_codon tier3 371 6 1.59 210 122 36.75 NA NA NA 440422 TCGA-AB-2907 AML29 20 13506535 13506535 T C SNP TASP1 NM_017714.2 human genbank 54_36p -1 reviewed intronic c.488+3009 e5+3009 0.059 - - - no_errors tier3 149 2 1.32 319 180 36 NA NA NA 440422 TCGA-AB-2907 AML29 20 20725902 20725902 G A SNP - - - - - - - - - - - - - - - tier3 142 3 2.07 136 70 33.98 NA NA NA 440422 TCGA-AB-2907 AML29 20 23615390 23615390 T C SNP CST4 NM_001899.2 human genbank 54_36p -1 reviewed intronic c.342+335 e2+335 0.003 - - - no_errors tier3 191 6 3.05 77 51 39.84 NA NA NA 440422 TCGA-AB-2907 AML29 20 30488419 30488419 C T SNP ASXL1 NM_015338.4 human genbank 54_36p 1 reviewed nonsense c.4243 p.R1415* 1 NULL NULL - no_errors tier1 86 0 35 19 35.19 NA NA NA 440422 TCGA-AB-2907 AML29 20 40556026 40556026 C T SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.1154-21410 e8-21410 0.004 - - - no_errors tier3 239 8 3.24 269 168 38.36 NA NA NA 440422 TCGA-AB-2907 AML29 20 46718391 46718391 T C SNP PREX1 NM_020820.3 human genbank 54_36p -1 reviewed intronic c.1666-2091 e15-2091 0 - - - no_errors tier3 210 3 1.41 158 103 39.46 NA NA NA 440422 TCGA-AB-2907 AML29 21 32009758 32009758 A T SNP SFRS15 NM_020706.1 human genbank 54_36p -1 reviewed intronic c.31-9217 e2-9217 0.002 - - - no_errors tier3 218 2 0.91 108 164 60.29 NA NA NA 440422 TCGA-AB-2907 AML29 21 35153747 35153747 T G SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed splice_site c.509-2 e5-2 1 - - - no_errors tier1 128 0 90 72 44.44 NA NA NA 440422 TCGA-AB-2907 AML29 22 28493401 28493401 C A SNP UCRC NM_013387.1 human genbank 54_36p 1 validated missense c.14 p.T5K 0.003 superfamily_Ubiquinol_cytC_Reductase_QCR9 "HMMPfam_UCR_UQCRX_QCR9,superfamily_Ubiquinol_cytC_Reductase_QCR9" - no_errors tier1 141 1 0.7 75 40 34.78 NA NA NA 440422 TCGA-AB-2907 AML29 22 38398294 38398294 G A SNP CACNA1I NM_021096.1 human genbank 54_36p 1 reviewed intronic c.4649+35 e27+35 0.001 - - - no_errors tier3 65 0 0 42 24 36.36 NA NA NA 440422 TCGA-AB-2907 AML29 22 41663494 41663494 T A SNP PACSIN2 NM_007229.2 human genbank 54_36p -1 provisional intronic c.1+9353 e0+9353 0 - - - no_errors tier3 496 4 0.8 117 69 37.1 NA NA NA 440422 TCGA-AB-2907 AML29 22 43780420 43780420 T A SNP PHF21B NM_138415.1 human genbank 54_36p -1 validated intronic c.120+2670 e2+2670 0 - - - no_errors tier3 35 1 2.78 45 26 36.62 NA NA NA 440422 TCGA-AB-2907 AML29 22 46607212 46607212 C T SNP - - - - - - - - - - - - - - - tier3 296 4 1.33 138 84 37.84 NA NA NA 100232 TCGA-AB-2908 MT 1872 1872 A G SNP ENSG00000210082 ENST00000387347 human ensembl 54_36p 1 known rna NULL NULL NULL - - - no_errors tier1 1354 17 1.24 2584 967 26.95 NA NA NA 100232 TCGA-AB-2908 MT 6721 6721 A G SNP MT-CO1 ENST00000361624 human ensembl 54_36p 1 known missense c.817 p.M273V NULL "HMMPfam_COX1,PatternScan_COX1_CUB,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^I-like" "HMMPfam_COX1,PatternScan_COX1_CUB,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^I-like" - no_stop_codon tier1 2661 39 1.44 5528 2014 26.54 NA NA NA 100232 TCGA-AB-2908 17 7517622 7517622 G A SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed nonsense c.949 p.Q317* 0.55 NULL "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 409 1 0.24 198 133 39.94 43 6 12.24 100232 TCGA-AB-2908 17 7519232 7519232 G C SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.423 p.C141W 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 185 2 1.07 152 49 24.02 17 43 71.67 100232 TCGA-AB-2908 13 20566654 20566654 G A SNP LOC338870 XR_016327.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 199 5 2.45 100 67 39.88 1 12 92.31 100232 TCGA-AB-2908 2 25310747 25310747 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2644 p.R882C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 99 4 3.88 91 65 41.67 37 39 51.32 100232 TCGA-AB-2908 1 26974278 26974278 G A SNP ARID1A NM_006015.4 human genbank 54_36p 1 reviewed missense c.4973 p.R1658Q 1 NULL "HMMPfam_ARID,HMMSmart_SM00501,superfamily_ARID-like" - no_errors tier1 204 6 2.86 150 98 39.36 64 62 49.21 100232 TCGA-AB-2908 8 27690517 27690517 G A SNP ESCO2 NM_001017420.2 human genbank 54_36p 1 reviewed missense c.773 p.R258K 0.001 NULL NULL - no_errors tier1 70 2 2.78 108 64 36.78 4 4 50 100232 TCGA-AB-2908 15 27788125 27788125 A G SNP TJP1 NM_003257.3 human genbank 54_36p -1 validated missense c.4780 p.S1594P 1 NULL "HMMPfam_ZU5,HMMSmart_SM00218,superfamily_SH3-domain,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_Guanylate_kin,HMMSmart_SM00072,HMMPfam_SH3_2,HMMPfam_Gua_kin_assoc_C,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 150 4 2.6 127 72 36.18 NA 100232 TCGA-AB-2908 17 35175680 35175680 G A SNP IKZF3 NM_012481.3 human genbank 54_36p -1 reviewed silent c.1419 p.C473 1 "PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 210 2 0.94 102 42 29.17 14 0 100232 TCGA-AB-2908 19 46322534 46322534 C T SNP CYP2F1 NM_000774.3 human genbank 54_36p 1 reviewed silent c.1035 p.A345 0.086 "HMMPfam_p450,superfamily_Cytochrome P450" "HMMPfam_p450,superfamily_Cytochrome P450,PatternScan_CYTOCHROME_P450" - no_errors tier1 126 2 1.56 60 24 28.24 NA 100232 TCGA-AB-2908 14 49187773 49187773 G T SNP POLE2 NM_002692.2 human genbank 54_36p -1 provisional silent c.1284 p.V428 1 HMMPfam_DNA_pol_E_B HMMPfam_DNA_pol_E_B - no_errors tier1 104 0 99 49 33.11 34 30 46.88 100232 TCGA-AB-2908 16 75081173 75081173 G A SNP CNTNAP4 NM_138994.3 human genbank 54_36p 1 validated missense c.1753 p.E585K 0.993 superfamily_Concanavalin A-like lectins/glucanases "HMMPfam_F5_F8_type_C,HMMSmart_SM00231,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMSmart_SM00282,superfamily_Fibrinogen C-terminal domain-like,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Galactose-binding domain-like,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2" - no_errors tier1 148 2 1.33 135 85 38.12 NA 100232 TCGA-AB-2908 7 86306304 86306304 G C SNP GRM3 NM_000840.2 human genbank 54_36p 1 reviewed missense c.1538 p.C513S 1 "HMMPfam_NCD3G,superfamily_Periplasmic binding protein-like I" "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_Periplasmic binding protein-like I" - no_errors tier1 155 5 3.12 106 72 39.78 NA 100232 TCGA-AB-2908 4 106384227 106384227 C T SNP TET2 ENST00000265149 human ensembl 54_36p 1 known nonsense c.52 p.R18* 1 NULL NULL - no_start_codon tier1 67 3 4.29 119 71 36.98 8 8 50 100232 TCGA-AB-2908 10 112351822 112351822 A G SNP SMC3 NM_005445.3 human genbank 54_36p 1 reviewed missense c.3001 p.I1001V 1 "HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain" - no_errors tier1 46 1 2.13 46 51 52.04 25 28 52.83 100232 TCGA-AB-2908 11 117290332 117290332 C T SNP TMPRSS13 NM_001077263.1 human genbank 54_36p -1 validated missense c.664 p.D222N 0.962 NULL "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,HMMSmart_SM00202,superfamily_SRCR-like,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER" - no_errors tier1 190 14 6.86 105 81 43.55 5 0 100232 TCGA-AB-2908 5 137755699 137755699 C - DEL JMJD1B NM_016604.3 human genbank 54_36p 1 validated frame_shift_del c.2479 p.Q827fs 1 NULL "HMMSmart_SM00558,HMMPfam_JmjC,superfamily_Clavaminate synthase-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 100232 TCGA-AB-2908 5 140202942 140202942 C A SNP PCDHA8 NM_018911.2 human genbank 54_36p 1 reviewed missense c.1852 p.P618T 0.001 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 36 0 7 29 80.56 NA 100232 TCGA-AB-2908 8 142550446 142550446 G T SNP FLJ43860 NM_207414.2 human genbank 54_36p -1 validated missense c.1897 p.Q633K 0.639 superfamily_ARM repeat "HMMPfam_HEAT,superfamily_ARM repeat" - pseudogene tier1 325 1 0.31 224 110 32.54 NA 100232 TCGA-AB-2908 5 146732949 146732949 C T SNP STK32A ENST00000306304 human ensembl 54_36p 1 known nonsense c.802 p.R268* 0.997 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 220 1 0.45 69 108 60.67 NA 100232 TCGA-AB-2908 1 158984926 158984926 A G SNP SLAMF7 NM_021181.3 human genbank 54_36p 1 provisional missense c.374 p.Y125C 0.922 "HMMPfam_V-set,superfamily_Immunoglobulin" "HMMPfam_V-set,superfamily_Immunoglobulin" - no_errors tier1 347 9 2.53 295 155 34.29 31 0 100232 TCGA-AB-2908 1 170692206 170692206 T - DEL C1orf105 NM_139240.2 human genbank 54_36p 1 predicted frame_shift_del c.227 p.L76fs 0.06 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 115225 TCGA-AB-2909 13 27506271 27506272 - ATTCTG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1785_1784 p.R595in_frame_insSRI 0.996:0.999 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 123804 TCGA-AB-2910 12 14510735 14510738 ACAA - DEL ATF7IP NM_018179.3 human genbank 54_36p 1 validated frame_shift_del c.2806_2809 p.N937fs 0.999:0.994:0.986:0.999 NULL "HMMPfam_fn3,superfamily_Fibronectin type III" - no_errors tier1 NA NA NA NA NA NA NA NA NA 123804 TCGA-AB-2910 13 27490642 27490642 C G SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835H 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 44 0 100 46 30.46 401 313 43.78 123804 TCGA-AB-2910 9 32323505 32323505 C T SNP LOC392301 XR_017331.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 89 6 6.32 280 168 36.84 53 0 123804 TCGA-AB-2910 20 36690993 36690993 T C SNP C20orf95 XM_293123.1 human genbank 54_36p 1 model missense c.409 p.S137P 0.003 NULL "HMMPfam_RhoGAP,HMMSmart_SM00324,superfamily_GTPase activation domain GAP" - no_errors tier1 320 6 1.84 399 189 31.98 NA 123804 TCGA-AB-2910 8 36785454 36785454 G A SNP KCNU1 NM_001031836.2 human genbank 54_36p 1 validated silent c.717 p.A239 1 "HMMPfam_Ion_trans,superfamily_SSF81324" "HMMPfam_BK_channel_a,HMMPfam_Ion_trans,superfamily_NAD(P)-bd,superfamily_SSF81324" - no_errors tier1 64 2 2.99 143 74 34.1 NA 123804 TCGA-AB-2910 21 37460160 37460160 C T SNP TTC3 NM_001001894.1 human genbank 54_36p 1 validated silent c.3774 p.S1258 0 "superfamily_Spectrin,superfamily_SSF48452" "HMMPfam_TPR_1,HMMSmart_RING,HMMPfam_zf-C3HC4,HMMSmart_TPR,superfamily_Spectrin,superfamily_SSF48452,superfamily_SSF57850" - no_errors tier1 37 2 5.13 89 54 37.24 29 47 61.84 123804 TCGA-AB-2910 19 47483358 47483358 G A SNP CIC NM_015125.3 human genbank 54_36p 1 validated missense c.499 p.G167R 1 NULL "HMMPfam_HMG_box,HMMSmart_HMG,superfamily_HMG-box" - no_errors tier1 30 1 3.23 91 37 28.91 47 67 58.26 123804 TCGA-AB-2910 11 73846174 73846174 T C SNP KCNE3 NM_005472.4 human genbank 54_36p -1 reviewed missense c.83 p.N28S 0.512 NULL NULL - no_errors tier1 38 1 2.56 77 34 30.09 20 16 44.44 123804 TCGA-AB-2910 16 82658861 82658861 C T SNP MBTPS1 NM_003791.2 human genbank 54_36p -1 reviewed missense c.2140 p.V714M 0.992 NULL "HMMPfam_Peptidase_S8,PatternScan_SUBTILASE_ASP,PatternScan_SUBTILASE_HIS,PatternScan_SUBTILASE_SER,superfamily_Pept_S8_S53" - no_errors tier1 29 1 3.33 84 53 38.41 39 26 40 123804 TCGA-AB-2910 12 105157456 105157456 G A SNP CKAP4 NM_006825.3 human genbank 54_36p -1 validated missense c.1285 p.R429C 0 NULL NULL - no_errors tier1 14 0 65 12 15.58 25 10 28.57 123804 TCGA-AB-2910 2 131391112 131391112 C T SNP LOC730032 XM_001132160.2 human genbank 54_36p 1 model silent c.3123 p.Y1041 0 NULL NULL - no_errors tier1 7 0 37 30 44.12 NA 123804 TCGA-AB-2910 5 132256676 132256676 T G SNP AFF4 NM_014423.3 human genbank 54_36p -1 validated missense c.2341 p.K781Q 1 HMMPfam_AF-4 HMMPfam_AF-4 - no_errors tier1 75 1 1.32 89 47 33.81 13 14 51.85 123804 TCGA-AB-2910 7 141075826 141075826 A T SNP WEE2 NM_001105558.1 human genbank 54_36p 1 validated missense c.1562 p.Q521L 0.043 NULL "PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 73 3 3.95 116 67 36.22 NA 123804 TCGA-AB-2910 X 152467453 152467453 G T SNP ATP2B3 NM_001001344.1 human genbank 54_36p 1 reviewed missense c.1285 p.V429F 1 "HMMPfam_E1-E2_ATPase,superfamily_Calcium ATPase transmembrane domain M" "HMMPfam_Cation_ATPase_N,HMMPfam_Hydrolase,HMMPfam_Cation_ATPase_C,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_Calcium ATPase transmembrane domain M" - no_errors tier1 58 3 4.92 175 105 37.1 NA 123804 TCGA-AB-2910 1 153254070 153254070 G A SNP ZBTB7B NM_015872.2 human genbank 54_36p 1 validated missense c.310 p.E104K 1 "HMMSmart_BTB,superfamily_BTB/POZ_fold,HMMPfam_BTB" "HMMSmart_BTB,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_BTB/POZ_fold,HMMPfam_BTB,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 24 0 172 98 36.16 133 134 50.19 242129 TCGA-AB-2911 11 66805867 66805867 A G SNP ADRBK1 NM_001619.3 human genbank 54_36p 1 reviewed splice_site c.827-2 e11-2 1 - - - no_errors tier1 8 0 33 7 17.5 144 90 242129 TCGA-AB-2911 X 101025404 101025407 CTTT - DEL ZMAT1 NM_001011657.1 human genbank 54_36p -1 validated frame_shift_del c.1651_1648 p.E550fs 0.192:0.427:0.556:0.570 NULL "HMMSmart_SM00451,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMPfam_zf-U1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 242129 TCGA-AB-2911 14 105305265 105305265 G A SNP IGHG3 ENST00000390550 human ensembl 54_36p -1 known nonsense c.1186 p.R396* 0.991 NULL "PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin" - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 8 0 50 57 53.27 3 0 242129 TCGA-AB-2911 3 109699627 109699627 C T SNP MYH15 NM_014981.1 human genbank 54_36p -1 validated missense c.640 p.A214T 1 "HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Myosin_head,HMMSmart_SM00242,HMMPfam_Myosin_tail_1,HMMPfam_Myosin_N,superfamily_Prefoldin,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 69 6 8 156 119 43.12 3 0 245450 TCGA-AB-2912 17 8138818 8138818 G A SNP SLC25A35 NM_201520.1 human genbank 54_36p -1 provisional silent c.33 p.C11 0.992 "superfamily_Mitoch_carrier,HMMPfam_Mito_carr" "superfamily_Mitoch_carrier,HMMPfam_Mito_carr" - no_errors tier1 68 0 95 58 37.91 4 100 245450 TCGA-AB-2912 2 25316812 25316812 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2185 p.R729W 1 "HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 19 0 27 26 49.06 15 10 40 245450 TCGA-AB-2912 20 33425414 33425414 C A SNP UQCC NM_018244.3 human genbank 54_36p -1 validated missense c.393 p.E131D 1 NULL HMMPfam_Ubiq_cyt_C_chap - no_errors tier1 112 4 3.45 99 67 40.36 17 8 32 245450 TCGA-AB-2912 8 33570685 33570685 C A SNP DUSP26 NM_024025.1 human genbank 54_36p -1 provisional missense c.344 p.G115V 1 "HMMPfam_DSPc,HMMSmart_SM00195,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_DSPc,PatternScan_TYR_PHOSPHATASE_1,HMMSmart_SM00195,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 106 0 155 78 33.33 NA 245450 TCGA-AB-2912 21 35174747 35174747 C T SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.485 p.R162K 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 49 2 3.92 36 22 37.93 230 215 48.31 245450 TCGA-AB-2912 8 36761105 36761105 C T SNP KCNU1 NM_001031836.2 human genbank 54_36p 1 validated nonsense c.19 p.R7* 0 NULL "HMMPfam_BK_channel_a,HMMPfam_Ion_trans,superfamily_NAD(P)-bd,superfamily_SSF81324" - no_errors tier1 112 1 0.88 157 73 31.74 NA 245450 TCGA-AB-2912 17 36933744 36933744 G C SNP KRT19 NM_002276.4 human genbank 54_36p -1 reviewed missense c.980 p.T327R 0.99 HMMPfam_Filament "superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF" - no_errors tier1 35 2 5.41 56 34 37.78 NA 245450 TCGA-AB-2912 21 43397525 43397525 G A SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.101 p.S34F 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 39 0 55 31 36.05 78 69 46.94 245450 TCGA-AB-2912 3 52147344 52147344 C T SNP WDR51A NM_015426.3 human genbank 54_36p -1 provisional missense c.694 p.V232M 0.999 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 121 2 1.63 131 108 45.19 13 12 48 245450 TCGA-AB-2912 4 55659711 55659711 C T SNP KDR NM_002253.2 human genbank 54_36p -1 validated silent c.2283 p.T761 0.682 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 84 0 95 52 35.37 NA 245450 TCGA-AB-2912 2 71507731 71507731 G A SNP ZNF638 NM_001014972.1 human genbank 54_36p 1 reviewed missense c.5224 p.D1742N 1 NULL "HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00451,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_RNA-binding domain RBD" - no_errors tier1 192 1 0.52 136 62 31.31 41 41 50 245450 TCGA-AB-2912 15 72323519 72323519 C T SNP CCDC33 NM_025055.3 human genbank 54_36p 1 validated silent c.162 p.S54 0.12 "HMMPfam_C2,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)" "HMMPfam_C2,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)" - no_errors tier1 159 0 229 32 12.21 NA 245450 TCGA-AB-2912 X 79714774 79714774 C T SNP LOC642546 XR_038841.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 58 4 6.45 21 65 75.58 14 0 245450 TCGA-AB-2912 X 83206679 83206679 G A SNP RPS6KA6 NM_014496.2 human genbank 54_36p -1 provisional missense c.2068 p.P690S 1 superfamily_Protein kinase-like (PK-like) "PatternScan_SERPIN,HMMSmart_SM00133,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,HMMPfam_Pkinase_C" - no_errors tier1 94 1 1.05 69 16 18.82 NA 245450 TCGA-AB-2912 10 112333981 112333981 G A SNP SMC3 NM_005445.3 human genbank 54_36p 1 reviewed missense c.1142 p.R381Q 1 "HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain" - no_errors tier1 102 2 1.92 120 64 34.78 51 34 40 245450 TCGA-AB-2912 3 123208591 123208591 C T SNP ILDR1 NM_175924.2 human genbank 54_36p -1 provisional missense c.166 p.V56M 0.997 "HMMSmart_IG,superfamily_SSF48726" "HMMSmart_IG,HMMPfam_LSR,superfamily_SSF48726" - no_errors tier1 122 2 1.61 153 98 39.04 1 100 245450 TCGA-AB-2912 10 128730879 128730879 T A SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known missense c.1948 p.F650I 1 NULL "HMMPfam_SH3_1,HMMSmart_SH3,superfamily_SH3,superfamily_Cytochrome_c" - no_errors tier1 138 0 107 71 39.89 3 10 76.92 245450 TCGA-AB-2912 12 130991817 130991817 A T SNP PUS1 NM_025215.1 human genbank 54_36p 1 validated missense c.572 p.N191I 1 "HMMPfam_PseudoU_synth_1,superfamily_Pseudouridine synthase" "HMMPfam_PseudoU_synth_1,superfamily_Pseudouridine synthase" - no_errors tier1 38 0 54 45 45.45 11 14 56 245450 TCGA-AB-2912 6 132189027 132189027 C T SNP LOC100128322 XR_039280.1 human genbank 54_36p -1 model rna NULL NULL 0.998 - - - pseudogene tier1 49 1 2 57 46 44.66 0 245450 TCGA-AB-2912 X 133339378 133339379 - A INS PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed frame_shift_ins c.65_66 p.N23fs 1.000:1.000 NULL "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger" - no_errors tier1 NA NA NA NA NA NA NA NA NA 245450 TCGA-AB-2912 8 136624127 136624127 C T SNP KHDRBS3 NM_006558.1 human genbank 54_36p 1 provisional missense c.256 p.R86C 1 "HMMSmart_SM00322,superfamily_Eukaryotic type KH-domain (KH-domain type I)" "HMMSmart_SM00322,superfamily_Eukaryotic type KH-domain (KH-domain type I)" - no_errors tier1 124 1 0.8 206 66 24.26 NA 245450 TCGA-AB-2912 1 154883956 154883956 C T SNP BCAN NM_021948.3 human genbank 54_36p 1 validated missense c.499 p.R167C 1 "HMMPfam_Xlink,HMMSmart_SM00445,superfamily_C-type lectin-like" "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin" - no_errors tier1 121 2 1.63 146 113 43.63 NA 245450 TCGA-AB-2912 2 165711731 165711731 C G SNP SCN3A NM_006922.1 human genbank 54_36p -1 reviewed missense c.1435 p.G479R 0.985 NULL "HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Ion_trans,HMMPfam_Na_trans_assoc,superfamily_SSF81324" - no_errors tier1 88 4 4.35 97 66 40.49 NA 245450 TCGA-AB-2912 1 242647552 242647552 C T SNP ADSS NM_001126.2 human genbank 54_36p -1 reviewed splice_site c.1070+1 e10+1 1 - - - no_errors tier1 92 0 87 41 32.03 8 3 27.27 255108 TCGA-AB-2913 3 10362072 10362072 G A SNP ATP2B2 NM_001001331.2 human genbank 54_36p -1 reviewed missense c.2699 p.T900M 1 superfamily_Calcium ATPase transmembrane domain M "HMMPfam_Cation_ATPase_N,HMMPfam_Hydrolase,HMMPfam_Cation_ATPase_C,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_Calcium ATPase transmembrane domain M" - no_errors tier1 375 14 3.6 125 77 38.12 NA 255108 TCGA-AB-2913 19 18513580 18513580 C T SNP FKBP8 NM_012181.3 human genbank 54_36p -1 reviewed silent c.201 p.E67 0.994 superfamily_SSF54534 "HMMPfam_FKBP_C,HMMPfam_TPR_1,superfamily_SSF48452,superfamily_SSF54534" - no_errors tier1 606 39 6.05 47 32 40 39 33 45.83 255108 TCGA-AB-2913 13 27506240 27506241 - AAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1816_1815 p.605in_frame_insSSDNEYFYVDFREYEYDLKWEF 1.000:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 255108 TCGA-AB-2913 16 30997770 30997770 C T SNP ZNF646 NM_014699.3 human genbank 54_36p 1 validated missense c.2624 p.A875V 0.122 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 385 49 11.24 43 38 45.78 3 7 70 255108 TCGA-AB-2913 11 32374378 32374378 C G SNP WT1 NM_024426.3 human genbank 54_36p -1 reviewed splice_site c.1249+1 e7+1 1 - - - no_errors tier1 150 18 10.71 8 69 89.61 5 100 255108 TCGA-AB-2913 17 37960014 37960014 A G SNP HSD17B1 NM_000413.2 human genbank 54_36p 1 validated missense c.605 p.E202G 0.008 superfamily_NAD(P)-binding Rossmann-fold domains "HMMPfam_adh_short,PatternScan_ADH_SHORT,superfamily_NAD(P)-binding Rossmann-fold domains" - no_errors tier1 160 13 7.47 36 40 51.28 10 3 23.08 255108 TCGA-AB-2913 19 45998824 45998824 G A SNP EGLN2 NM_053046.2 human genbank 54_36p 1 reviewed silent c.507 p.A169 0.001 NULL "HMMPfam_2OG-FeII_Oxy,HMMSmart_SM00702" - no_errors tier1 158 1 0.63 50 47 47.96 8 8 50 255108 TCGA-AB-2913 3 49698920 49698920 T G SNP MST1 NM_020998.3 human genbank 54_36p -1 validated splice_site c.806-2 e8-2 0.046 - - - no_errors tier1 66 2 2.94 29 12 29.27 0 255108 TCGA-AB-2913 16 51037488 51037488 A T SNP TOX3 NM_001080430.1 human genbank 54_36p -1 provisional silent c.825 p.G275 0.973 "HMMPfam_HMG_box,HMMSmart_HMG,superfamily_HMG-box" "HMMPfam_HMG_box,HMMSmart_HMG,superfamily_HMG-box" - no_errors tier1 364 10 2.67 224 152 40.11 NA 255108 TCGA-AB-2913 19 62603022 62603022 A G SNP ZNF548 NM_152909.2 human genbank 54_36p 1 provisional missense c.1555 p.T519A 0 NULL "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 549 33 5.65 278 200 41.41 13 16 55.17 255108 TCGA-AB-2913 3 64507612 64507612 A T SNP ADAMTS9 NM_182920.1 human genbank 54_36p -1 reviewed silent c.4926 p.I1642 1 "HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat" "HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_Reprolysin,HMMPfam_Pep_M12B_propep,HMMPfam_ADAM_spacer1,HMMPfam_GON,superfamily_Metalloproteases (""zincins"") catalytic domain" - no_errors tier1 130 5 3.6 150 148 49.5 NA 255108 TCGA-AB-2913 17 70302819 70302819 G A SNP TMEM104 NM_017728.3 human genbank 54_36p 1 validated silent c.501 p.V167 1 NULL HMMPfam_Aa_trans - no_errors tier1 604 35 5.46 126 117 47.37 12 13 52 255108 TCGA-AB-2913 5 73172319 73172319 C A SNP RGNEF NM_001080479.1 human genbank 54_36p 1 provisional missense c.1405 p.Q469K 0.99 NULL "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_PH,HMMSmart_SM00233,HMMPfam_C1_1,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,superfamily_PH domain-like,superfamily_Cysteine-rich domain" - no_errors tier1 118 5 4.07 76 66 45.21 NA 255108 TCGA-AB-2913 15 83202210 83202210 G A SNP ALPK3 NM_020778.4 human genbank 54_36p 1 validated silent c.3843 p.E1281 0.865 NULL "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_Alpha_kinase,HMMSmart_SM00811,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,superfamily_Immunoglobulin" - no_errors tier1 122 4 3.17 80 70 46.36 NA 255108 TCGA-AB-2913 15 98406586 98406586 G A SNP ADAMTS17 NM_139057.2 human genbank 54_36p -1 reviewed missense c.2590 p.R864W 0.986 "HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat" "HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_Reprolysin,HMMPfam_Pep_M12B_propep,HMMSmart_SM00608,PatternScan_ZINC_FINGER_C2H2_1,HMMPfam_ADAM_spacer1,HMMPfam_PLAC,superfamily_Metalloproteases (""zincins"") catalytic domain" - no_errors tier1 208 17 7.52 61 38 38.38 NA 255108 TCGA-AB-2913 X 123027969 123027969 T C SNP STAG2 NM_001042749.1 human genbank 54_36p 1 validated splice_site c.2265+2 e21+2 1 - - - no_errors tier1 63 2 3.08 11 64 85.33 100 100 255108 TCGA-AB-2913 8 145012319 145012319 C T SNP EPPK1 NM_031308.1 human genbank 54_36p -1 provisional missense c.7016 p.R2339Q 0.999 "HMMPfam_Plectin,HMMSmart_SM00250,superfamily_Plakin repeat" "HMMPfam_Plectin,HMMSmart_SM00250,superfamily_Plakin repeat" - no_stop_codon:bad_bp_length_for_coding_region tier1 113 0 36 6 13.95 1 0 255108 TCGA-AB-2913 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 258135 TCGA-AB-2914 17 4846516 4846516 C T SNP KIF1C NM_006612.4 human genbank 54_36p 1 provisional nonsense c.463 p.R155* 0.997 "HMMPfam_Kinesin,HMMSmart_KISc,superfamily_SSF52540" "HMMPfam_FHA,HMMSmart_FHA,HMMPfam_Kinesin,HMMSmart_KISc,superfamily_SMAD_FHA,PatternScan_KINESIN_MOTOR_DOMAIN1,superfamily_SSF52540" - no_errors tier1 118 9 7.09 78 59 42.75 4 1 20 258135 TCGA-AB-2914 11 5467416 5467416 G T SNP OR52D1 NM_001005163.1 human genbank 54_36p 1 provisional nonsense c.904 p.E302* 0.986 superfamily_Family A G protein-coupled receptor-like "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 98 1 1.01 220 65 22.57 NA 258135 TCGA-AB-2914 8 13401792 13401792 G A SNP DLC1 NM_182643.3 human genbank 54_36p -1 reviewed missense c.160 p.R54C 0.992 NULL "HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_START,HMMSmart_SM00234,superfamily_GTPase activation domain GAP,HMMPfam_SAM_2,superfamily_Bet v1-like" - no_errors tier1 100 2 1.96 144 109 42.91 NA 258135 TCGA-AB-2914 22 28269470 28269470 A C SNP THOC5 NM_001002877.1 human genbank 54_36p -1 validated missense c.302 p.L101R 1 HMMPfam_FimP HMMPfam_FimP - no_errors tier1 231 19 7.57 200 150 42.74 20 20 50 258135 TCGA-AB-2914 6 33499266 33499266 C T SNP SYNGAP1 NM_006772.2 human genbank 54_36p 1 validated silent c.57 p.Y19 1 HMMSmart_SM00233 "HMMPfam_C2,HMMSmart_SM00239,HMMSmart_SM00233,HMMPfam_RasGAP,HMMSmart_SM00323,PatternScan_RAS_GTPASE_ACTIV_1,superfamily_GTPase activation domain GAP,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_PH domain-like" - no_errors tier1 67 8 10.67 73 57 43.85 1 0 258135 TCGA-AB-2914 2 36958647 36958649 AGA - DEL STRN NM_003162.2 human genbank 54_36p -1 validated in_frame_del c.1214_1212 p.S405in_frame_del 0.997:1.000:0.996 NULL "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_Striatin,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 NA NA NA NA NA NA NA NA NA 258135 TCGA-AB-2914 17 41604391 41604392 - G INS KIAA1267 NM_015443.2 human genbank 54_36p -1 validated frame_shift_ins c.896_895 p.R299fs 1.000:1.000 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 258135 TCGA-AB-2914 11 48115300 48115300 C T SNP PTPRJ NM_002843.1 human genbank 54_36p 1 reviewed silent c.2043 p.D681 0 "HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" "HMMPfam_Y_phosphatase,HMMSmart_PTPc,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,PatternScan_TYR_PHOSPHATASE_1,superfamily_SSF52799" - no_errors tier1 55 1 1.79 108 80 42.55 22 9 29.03 258135 TCGA-AB-2914 7 50641535 50641535 G A SNP GRB10 NM_005311.2 human genbank 54_36p -1 reviewed missense c.1265 p.T422M 0.292 NULL "HMMPfam_RA,HMMSmart_SM00314,HMMPfam_SH2,HMMSmart_SM00252,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_BPS,superfamily_PH domain-like,superfamily_SH2 domain" - no_errors tier1 84 5 5.62 131 91 40.81 15 11 42.31 258135 TCGA-AB-2914 18 59456078 59456078 G A SNP SERPINB4 NM_002974.2 human genbank 54_36p -1 validated missense c.1028 p.A343V 1 "HMMPfam_Serpin,HMMSmart_SERPIN,superfamily_Prot_inh_serpin" "HMMPfam_Serpin,HMMSmart_SERPIN,PatternScan_SERPIN,superfamily_Prot_inh_serpin" - no_errors tier1 84 2 2.33 139 37 20.9 NA 258135 TCGA-AB-2914 X 64666340 64666340 C T SNP LAS1L NM_031206.3 human genbank 54_36p -1 provisional missense c.658 p.D220N 0.442 NULL HMMPfam_Las1 - no_errors tier1 185 7 3.63 147 106 41.73 68 0 258135 TCGA-AB-2914 12 70316623 70316623 T C SNP ZFC3H1 NM_144982.4 human genbank 54_36p -1 validated missense c.2014 p.I672V 0.832 NULL "HMMSmart_SM00386,HMMPfam_zf-C3H1,superfamily_Protein prenylyltransferase" - no_errors tier1 110 1 0.9 122 35 22.15 36 10 21.74 258135 TCGA-AB-2914 15 72254944 72254944 C T SNP ISLR NM_005545.3 human genbank 54_36p 1 validated missense c.692 p.A231V 0.299 "superfamily_SSF48726,superfamily_SSF52058" "HMMSmart_LRRNT,HMMPfam_LRRCT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMSmart_IGc2,HMMPfam_I-set,superfamily_SSF48726,superfamily_SSF52058" - no_errors tier1 15 0 35 12 25.53 NA 258135 TCGA-AB-2914 1 99544957 99544957 G A SNP LPPR4 NM_014839.3 human genbank 54_36p 1 reviewed missense c.2095 p.G699R 1 NULL "HMMPfam_PAP2,HMMSmart_SM00014,superfamily_Acid phosphatase/Vanadium-dependent haloperoxidase" - no_errors tier1 82 6 6.82 159 54 25.12 NA 258135 TCGA-AB-2914 10 106792824 106792824 G C SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed missense c.976 p.G326R 1 "HMMSmart_VPS10,superfamily_SSF110296" "HMMPfam_PKD,superfamily_PKD,HMMSmart_VPS10,superfamily_SSF110296" - no_errors tier1 102 4 3.77 118 111 48.26 NA 258135 TCGA-AB-2914 12 111372582 111372582 C T SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.215 p.A72V 1 "HMMPfam_SH2,HMMSmart_SM00252,superfamily_SH2 domain" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 37 3 7.5 103 37 26.24 31 5 13.89 258135 TCGA-AB-2914 11 112792868 112792868 G A SNP DRD2 NM_000795.3 human genbank 54_36p -1 reviewed silent c.459 p.T153 0.95 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 150 8 5.06 188 73 27.76 NA 258135 TCGA-AB-2914 11 118654085 118654085 G C SNP CBL NM_005188.2 human genbank 54_36p 1 reviewed splice_site c.1096-1 e8-1 1 - - - no_errors tier1 95 2 2.06 168 43 19.91 1 28 96.55 258135 TCGA-AB-2914 10 125516574 125516574 A - DEL CPXM2 NM_198148.2 human genbank 54_36p -1 validated frame_shift_del c.1384 p.L462fs 0.596 "HMMPfam_Peptidase_M14,HMMSmart_SM00631,superfamily_Zn-dependent exopeptidases" "HMMPfam_F5_F8_type_C,HMMSmart_SM00231,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMPfam_Peptidase_M14,HMMSmart_SM00631,PatternScan_CARBOXYPEPT_ZN_1,superfamily_Carboxypeptidase regulatory domain,superfamily_Galactose-binding domain-like,superfamily_Zn-dependent exopeptidases" - no_errors tier1 NA NA NA NA NA NA NA NA NA 258135 TCGA-AB-2914 1 226679386 226679386 C T SNP HIST3H3 NM_003493.2 human genbank 54_36p -1 reviewed silent c.264 p.S88 0.986 "HMMSmart_SM00428,HMMPfam_Histone,superfamily_Histone-fold" "HMMSmart_SM00428,PatternScan_HISTONE_H3_1,HMMPfam_Histone,superfamily_Histone-fold" - no_errors tier1 43 0 84 25 22.94 1 0 193139 TCGA-AB-2915 19 2167684 2167684 G C SNP DOT1L NM_032482.2 human genbank 54_36p 1 validated silent c.2328 p.P776 0.759 NULL "HMMPfam_DOT1,HMMPfam_AT_hook,HMMSmart_AT_hook,superfamily_SSF53335" - no_errors tier1 5 0 3 7 70 30 26 46.43 193139 TCGA-AB-2915 19 2940633 2940633 C G SNP TLE6 NM_024760.1 human genbank 54_36p 1 validated missense c.725 p.A242G 0.999 superfamily_WD40_like "HMMSmart_WD40,superfamily_WD40_like,PatternScan_WD_REPEATS_1" - no_errors tier1 24 0 86 48 34.78 NA 193139 TCGA-AB-2915 19 8921044 8921044 G A SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated silent c.27402 p.S9134 0 NULL "HMMPfam_SEA,HMMSmart_SM00200,PatternScan_ATPASE_ALPHA_BETA,superfamily_SEA domain" - no_errors tier1 137 4 2.84 133 100 42.74 NA 193139 TCGA-AB-2915 11 11271283 11271283 C T SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated missense c.1546 p.V516M 1 "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,superfamily_Ricin B-like lectins" "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,HMMPfam_Glycos_transf_2,superfamily_Ricin B-like lectins,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 36 0 119 92 43.4 2 0 193139 TCGA-AB-2915 1 17820946 17820946 G A SNP ARHGEF10L NM_018125.2 human genbank 54_36p 1 validated missense c.943 p.V315M 1 superfamily_DBL homology domain (DH-domain) "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),superfamily_WD40 repeat-like,superfamily_PH domain-like" - no_errors tier1 36 0 91 63 40.38 11 8 42.11 193139 TCGA-AB-2915 2 20017100 20017100 C T SNP WDR35 NM_001006657.1 human genbank 54_36p -1 reviewed missense c.1409 p.R470Q 0.996 superfamily_WD40 repeat-like "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" - no_errors tier1 71 2 2.74 179 151 45.62 13 0 193139 TCGA-AB-2915 13 27506260 27506261 - ATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCAG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1796_1795 p.599in_frame_insSGSSDNEYFYVDFREYE 1.000:0.999 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 193139 TCGA-AB-2915 17 49189919 49189919 G A SNP LOC645173 XR_017590.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 15 0 7 8 50 0 193139 TCGA-AB-2915 X 54351093 54351093 C T SNP WNK3 NM_020922.2 human genbank 54_36p -1 validated missense c.1076 p.R359Q 1 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,HMMPfam_Pkinase" - no_errors tier1 66 1 1.47 144 89 37.71 NA 193139 TCGA-AB-2915 3 58767162 58767162 G A SNP C3orf67 NM_198463.2 human genbank 54_36p -1 predicted missense c.1483 p.R495W 0.973 NULL NULL - no_errors tier1 49 3 5.66 183 123 39.81 NA 193139 TCGA-AB-2915 18 59385208 59385208 G A SNP SERPINB12 NM_080474.1 human genbank 54_36p 1 provisional missense c.1202 p.R401K 0.998 "HMMPfam_Serpin,HMMSmart_SERPIN,superfamily_Prot_inh_serpin" "HMMPfam_Serpin,HMMSmart_SERPIN,PatternScan_SERPIN,superfamily_Prot_inh_serpin" - no_errors tier1 156 3 1.88 223 175 43.53 NA 193139 TCGA-AB-2915 11 65095649 65095651 CCT - DEL SSSCA1 NM_006396.1 human genbank 54_36p 1 provisional in_frame_del c.468_470 p.L158in_frame_del 0.997:1.000:1.000 NULL HMMPfam_Auto_anti-p27 - no_errors tier1 NA NA NA NA NA NA NA NA NA 193139 TCGA-AB-2915 10 71553248 71553248 C A SNP AIFM2 NM_032797.4 human genbank 54_36p -1 reviewed silent c.213 p.V71 0.972 "HMMPfam_Pyr_redox_2,superfamily_FAD/NAD(P)-binding domain" "HMMPfam_Pyr_redox_2,superfamily_FAD/NAD(P)-binding domain" - no_errors tier1 37 1 2.63 77 58 42.96 7 3 30 193139 TCGA-AB-2915 4 85384395 85384395 G A SNP LOC152845 XR_038721.1 human genbank 54_36p 1 model rna NULL NULL 0.974 - - - pseudogene tier1 64 2 2.99 139 85 37.78 3 0 193139 TCGA-AB-2915 4 85384914 85384914 C T SNP LOC152845 XR_038721.1 human genbank 54_36p 1 model rna NULL NULL 1 - - - pseudogene tier1 91 0 173 132 43.28 NA 193139 TCGA-AB-2915 5 92629616 92629616 G T SNP LOC391811 XR_016127.2 human genbank 54_36p 1 model rna NULL NULL 0.999 - - - pseudogene tier1 37 0 173 120 40.27 15 0 193139 TCGA-AB-2915 6 94023922 94023922 T C SNP EPHA7 NM_004440.3 human genbank 54_36p -1 reviewed silent c.2151 p.G717 1 "HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)" "HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_Growth factor receptor domain,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),PatternScan_EGF_2,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 56 1 1.72 66 48 42.11 NA 193139 TCGA-AB-2915 2 98177383 98177384 - A INS VWA3B NM_144992.4 human genbank 54_36p 1 provisional frame_shift_ins c.1733_1734 p.I580fs 0.454:0.255 "HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like" "HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 193139 TCGA-AB-2915 X 102771563 102771563 G A SNP TCEAL1 NM_001006639.1 human genbank 54_36p 1 reviewed silent c.63 p.E21 0.807 HMMPfam_TFA HMMPfam_TFA - no_errors tier1 30 0 68 46 40 27 0 193139 TCGA-AB-2915 4 106858234 106858234 G A SNP GSTCD NM_001031720.2 human genbank 54_36p 1 validated silent c.15 p.K5 0.511 NULL "superfamily_Glutathione S-transferase (GST) C-terminal domain,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" - no_errors tier1 75 7 8.54 115 64 35.56 6 0 193139 TCGA-AB-2915 6 108608256 108608256 G T SNP NR2E1 NM_003269.3 human genbank 54_36p 1 validated missense c.679 p.V227F 1 "HMMPfam_Hormone_recep,HMMSmart_SM00430,superfamily_Nuclear receptor ligand-binding domain" "HMMPfam_Hormone_recep,HMMSmart_SM00430,HMMPfam_zf-C4,HMMSmart_SM00399,PatternScan_NUCLEAR_REC_DBD_1,superfamily_Nuclear receptor ligand-binding domain,superfamily_Glucocorticoid receptor-like (DNA-binding domain)" - no_errors tier1 56 0 72 46 38.98 NA 193139 TCGA-AB-2915 9 116435895 116435895 G A SNP C9orf91 NM_153045.3 human genbank 54_36p 1 validated silent c.501 p.L167 0.985 NULL NULL - no_errors tier1 33 0 59 55 48.25 12 12 50 193139 TCGA-AB-2915 3 139519691 139519691 G A SNP TXNDC6 NM_178130.2 human genbank 54_36p -1 provisional silent c.190 p.L64 1 superfamily_Thiordxn-like_fd "HMMPfam_NDK,HMMSmart_NDK,superfamily_NDK,superfamily_Thiordxn-like_fd,PatternScan_THIOREDOXIN_1" - no_errors tier1 46 4 8 98 88 46.81 NA 193139 TCGA-AB-2915 4 140490147 140490147 G A SNP NARG1 NM_057175.3 human genbank 54_36p 1 validated nonsense c.773 p.W258* 1 superfamily_TPR-like "HMMPfam_TPR_2,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 64 7 9.86 159 111 40.81 24 5 17.24 193139 TCGA-AB-2915 1 150545333 150545333 T A SNP FLG NM_002016.1 human genbank 54_36p -1 provisional missense c.8653 p.R2885W 0 HMMPfam_Filaggrin "PatternScan_S100_CABP,HMMPfam_Filaggrin,HMMPfam_S_100,PatternScan_EF_HAND_1,superfamily_SSF47473" - no_errors tier1 15 0 85 33 27.5 NA 193139 TCGA-AB-2915 5 170767325 170767325 A G SNP NPM1 NM_002520.1 human genbank 54_36p 1 validated missense c.788 p.K263R 1 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 60 0 40 44 52.38 99 85 46.2 193139 TCGA-AB-2915 1 180293709 180293709 A C SNP ZNF648 NM_001009992.1 human genbank 54_36p -1 provisional silent c.60 p.T20 0.151 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 51 1 1.92 93 121 56.28 0 193139 TCGA-AB-2915 2 210269249 210269249 C T SNP MAP2 NM_002374.1 human genbank 54_36p 1 reviewed silent c.4110 p.D1370 0.697 HMMPfam_MAP2_projctn "HMMPfam_Tubulin-binding,PatternScan_TAU_MAP,HMMPfam_MAP2_projctn,HMMPfam_RII_binding_1" - no_errors tier1 73 0 109 86 43.88 NA 290344 TCGA-AB-2916 MT 14767 14767 T C SNP MT-CYB ENST00000361789 human ensembl 54_36p 1 known missense c.20 p.I7T NULL superfamily_Transmembr_di-haem_cytochrome "HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome" - no_stop_codon:bad_bp_length_for_coding_region tier1 3010 22 0.72 1372 171 11 NA NA NA 290344 TCGA-AB-2916 8 2953569 2953569 G T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated missense c.6721 p.L2241I 1 NULL "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,superfamily_Complement control module/SCR domain" - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 115 2 1.71 113 86 42.79 NA 290344 TCGA-AB-2916 6 13314113 13314114 - G INS PHACTR1 NM_030948.1 human genbank 54_36p 1 validated frame_shift_ins c.752_753 p.P254fs 0.638:0.521 NULL "HMMPfam_RPEL,HMMSmart_SM00707" - no_errors tier1 NA NA NA NA NA NA NA NA NA 290344 TCGA-AB-2916 3 15661430 15661430 G A SNP BTD NM_000060.2 human genbank 54_36p 1 reviewed missense c.1063 p.D355N 0.003 NULL "HMMPfam_CN_hydrolase,superfamily_Carbon-nitrogen hydrolase" - no_errors tier1 97 2 2.02 105 61 36.31 15 5 25 290344 TCGA-AB-2916 2 25310747 25310747 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2644 p.R882C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 93 1 1.06 64 28 30.11 16 9 34.62 290344 TCGA-AB-2916 11 29989637 29989637 G A SNP KCNA4 NM_002233.2 human genbank 54_36p -1 reviewed missense c.1165 p.R389C 1 "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" "HMMSmart_SM00225,HMMPfam_K_tetra,HMMPfam_Ion_trans,superfamily_POZ domain,HMMPfam_K_channel_TID,superfamily_Voltage-gated potassium channels" - no_errors tier1 479 19 3.82 154 160 50.63 NA 290344 TCGA-AB-2916 7 48857942 48857942 G T SNP LOC100131447 XR_036885.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 72 1 1.37 141 39 21.55 NA 290344 TCGA-AB-2916 15 62473369 62473369 T C SNP TRIP4 NM_016213.3 human genbank 54_36p 1 validated splice_site c.271+2 e2+2 1 - - - no_errors tier1 128 2 1.53 121 69 35.94 7 100 290344 TCGA-AB-2916 10 104439667 104439667 G T SNP ARL3 NM_004311.2 human genbank 54_36p -1 reviewed missense c.288 p.D96E 1 "HMMSmart_ARF,HMMPfam_Arf,superfamily_SSF52540" "HMMSmart_ARF,PatternScan_ARF,HMMPfam_Arf,superfamily_SSF52540" - no_errors tier1 103 1 0.96 103 59 36.2 9 11 55 290344 TCGA-AB-2916 10 134521111 134521111 G A SNP C10orf92 ENST00000263170 human ensembl 54_36p -1 known silent c.30 p.S10 0.001 NULL NULL - no_errors tier1 34 1 2.78 8 15 65.22 NA 290344 TCGA-AB-2916 6 135552652 135552652 T C SNP MYB NM_005375.1 human genbank 54_36p 1 validated missense c.244 p.W82R 1 "HMMSmart_SM00717,superfamily_Homeodomain-like,HMMPfam_Myb_DNA-binding" "HMMSmart_SM00717,superfamily_Homeodomain-like,HMMPfam_Wos2,HMMPfam_Myb_DNA-binding,HMMPfam_Cmyb_C" - no_errors tier1 94 0 119 14 10.45 52 13 20 290344 TCGA-AB-2916 1 156567469 156567469 C T SNP CD1B NM_001764.2 human genbank 54_36p -1 reviewed silent c.69 p.Q23 0.003 NULL "HMMPfam_MHC_I,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_MHC antigen-recognition domain,superfamily_Immunoglobulin" - no_errors tier1 296 7 2.31 148 83 35.47 0 290344 TCGA-AB-2916 2 168705498 168705498 C T SNP STK39 NM_013233.2 human genbank 54_36p -1 reviewed silent c.645 p.A215 0.986 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 108 0 138 77 35.81 15 20 57.14 290344 TCGA-AB-2916 5 172677648 172677648 G A SNP STC2 NM_003714.2 human genbank 54_36p -1 reviewed silent c.717 p.H239 0.003 HMMPfam_Stanniocalcin HMMPfam_Stanniocalcin - no_errors tier1 38 1 2.56 24 19 43.18 NA 290344 TCGA-AB-2916 1 246822922 246822922 G T SNP OR2T10 NM_001004693.1 human genbank 54_36p -1 provisional nonsense c.771 p.Y257* 0 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 107 3 2.73 153 95 38 NA 303818 TCGA-AB-2917 1 1561654 1561654 G A SNP CDC2L2 NM_033529.2 human genbank 54_36p -1 reviewed nonsense c.1969 p.Q657* 0.978 NULL NULL - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 30 0 27 11 28.95 47 2 4.08 303818 TCGA-AB-2917 4 8639798 8639798 G A SNP GPR78 NM_080819.2 human genbank 54_36p 1 validated silent c.900 p.P300 1 superfamily_Family A G protein-coupled receptor-like "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 56 3 5.08 19 26 56.52 NA 303818 TCGA-AB-2917 19 9185994 9185994 T A SNP OR7D4 NM_001005191.1 human genbank 54_36p -1 provisional missense c.520 p.I174F 0 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 235 11 4.42 197 177 47.2 NA 303818 TCGA-AB-2917 12 25289478 25289478 T C SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.108 p.I36M 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 45 1 2.17 27 41 60.29 2 33 94.29 303818 TCGA-AB-2917 1 35023596 35023596 C T SNP GJB3 NM_001005752.1 human genbank 54_36p 1 reviewed nonsense c.646 p.R216* 0.009 NULL "HMMPfam_Connexin,HMMSmart_SM00037,PatternScan_CONNEXINS_1,PatternScan_CONNEXINS_2,HMMPfam_Connexin_CCC" - no_errors tier1 64 0 66 58 46.4 NA 303818 TCGA-AB-2917 18 40785905 40785905 G A SNP SETBP1 NM_015559.1 human genbank 54_36p 1 validated missense c.2440 p.D814N 1 NULL "HMMPfam_AT_hook,HMMSmart_AT_hook" - no_errors tier1 149 6 3.85 100 102 50.25 20 19 48.72 303818 TCGA-AB-2917 12 43696557 43696557 G A SNP DBX2 NM_001004329.2 human genbank 54_36p -1 validated missense c.799 p.R267W 0.001 NULL "HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like,PatternScan_HOMEOBOX_1" - no_errors tier1 182 5 2.66 81 131 61.5 NA 303818 TCGA-AB-2917 3 61703497 61703497 G A SNP LOC100128936 XM_001726108.1 human genbank 54_36p -1 model missense c.74 p.A25V 1 "HMMPfam_Ribosomal_L1,superfamily_Ribosomal protein L1" "HMMPfam_Ribosomal_L1,PatternScan_RIBOSOMAL_L1,superfamily_Ribosomal protein L1" - pseudogene tier1 114 3 2.56 105 92 46.7 1366 1 0.07 303818 TCGA-AB-2917 11 65077003 65077003 C T SNP LTBP3 NM_021070.1 human genbank 54_36p -1 validated missense c.1090 p.V364M 1 "HMMSmart_EGF_CA,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_SSF57196" "PatternScan_ASX_HYDROXYL,HMMSmart_EGF_CA,HMMPfam_TB,superfamily_Fibril-assoc,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_SSF57196" - no_errors tier1 200 7 3.35 61 45 42.45 19 12 38.71 303818 TCGA-AB-2917 X 70263942 70263942 C T SNP MED12 NM_005120.2 human genbank 54_36p 1 validated missense c.2881 p.R961W 1 NULL HMMPfam_Med12 - no_errors tier1 465 28 5.61 199 141 41.47 2 40 95.24 303818 TCGA-AB-2917 6 75880038 75880038 G A SNP COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed missense c.7840 p.P2614S 1 "HMMSmart_SM00210,superfamily_Concanavalin A-like lectins/glucanases" "HMMPfam_VWA,HMMSmart_SM00327,HMMSmart_SM00210,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Collagen,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_vWA-like" - no_errors tier1 180 8 4.23 134 99 42.49 NA 303818 TCGA-AB-2917 8 87311171 87311171 C T SNP SLC7A13 NM_138817.2 human genbank 54_36p -1 validated missense c.452 p.R151H 0.114 NULL HMMPfam_AA_permease - no_errors tier1 173 0 170 43 20.09 NA 303818 TCGA-AB-2917 X 96571382 96571382 C T SNP DIAPH2 NM_006729.4 human genbank 54_36p 1 reviewed missense c.3223 p.R1075W 1 NULL "HMMSmart_SM00498,HMMPfam_Drf_DAD,HMMPfam_Drf_FH3,HMMPfam_Drf_GBD,HMMPfam_FH2,superfamily_Formin homology 2 domain (FH2 domain)" - no_errors tier1 208 9 4.09 103 86 45.26 19 0 303818 TCGA-AB-2917 7 97774983 97774983 C T SNP BAIAP2L1 NM_018842.3 human genbank 54_36p -1 provisional missense c.1117 p.E373K 0.993 "HMMSmart_SH3,superfamily_SH3,HMMPfam_SH3_2" "HMMSmart_SH3,superfamily_SH3,HMMPfam_SH3_2,HMMPfam_IMD" - no_errors tier1 146 0 131 20 13.07 1 0 303818 TCGA-AB-2917 9 99124969 99124969 G A SNP KIAA1529 NM_020893.1 human genbank 54_36p 1 predicted missense c.1742 p.R581H 0.998 NULL NULL - no_errors tier1 130 1 0.76 128 30 18.4 3 2 40 303818 TCGA-AB-2917 2 166609962 166609962 C T SNP SCN1A NM_006920.4 human genbank 54_36p -1 validated missense c.1499 p.R500Q 1 NULL "HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Ion_trans,HMMPfam_Na_trans_assoc,PatternScan_RIBONUCLEASE_P,superfamily_SSF81324" - no_errors tier1 197 6 2.94 121 102 45.74 NA 303818 TCGA-AB-2917 1 184682217 184682217 C A SNP PDC NM_002597.3 human genbank 54_36p -1 reviewed missense c.177 p.R59S 0.996 "HMMPfam_Phosducin,superfamily_Thiordxn-like_fd" "HMMPfam_Phosducin,superfamily_Thiordxn-like_fd" - no_errors tier1 237 6 2.45 172 113 39.65 2 0 255421 TCGA-AB-2918 5 13894909 13894909 A G SNP DNAH5 NM_001369.2 human genbank 54_36p -1 validated silent c.5376 p.L1792 0.058 HMMPfam_DHC_N2 "HMMSmart_AAA,HMMPfam_Dynein_heavy,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin,superfamily_SSF52540" - no_errors tier1 131 24 15.48 127 104 44.64 NA 255421 TCGA-AB-2918 13 27506254 27506255 - ATCATATTCATATTCTCTGAA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1802_1801 p.602in_frame_insQRI*I*F 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 303642 TCGA-AB-2919 MT 12256 12256 T G SNP ENSG00000210184 ENST00000387449 human ensembl 54_36p 1 novel rna NULL NULL NULL - - - no_errors tier1 2884 26 0.89 1398 1350 48.56 NA NA NA 303642 TCGA-AB-2919 9 13214490 13214490 C T SNP MPDZ NM_003829.3 human genbank 54_36p -1 validated silent c.276 p.S92 0.705 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_L27_2,superfamily_L27 domain" - no_errors tier1 127 1 0.78 130 88 40.37 1 0 303642 TCGA-AB-2919 X 19943346 19943346 C T SNP MAP7D2 NM_152780.2 human genbank 54_36p -1 provisional silent c.1542 p.K514 0.996 HMMPfam_MAP7 HMMPfam_MAP7 - no_errors tier1 130 0 141 117 45.35 NA 303642 TCGA-AB-2919 22 21341172 21341172 C T SNP IGLV3-27 ENST00000390304 human ensembl 54_36p 1 known nonsense c.235 p.R79* 0.399 "HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" "HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" - no_stop_codon:bad_bp_length_for_coding_region tier1 25 1 3.85 27 34 55.74 20 0 303642 TCGA-AB-2919 2 25321690 25321690 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.1490 p.C497Y 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 23 0 17 26 60.47 15 49 76.56 303642 TCGA-AB-2919 11 32370133 32370133 G A SNP WT1 NM_024426.3 human genbank 54_36p -1 reviewed missense c.1393 p.H465Y 1 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 86 0 119 41 25.47 62 12 16.22 303642 TCGA-AB-2919 1 32910659 32910659 G A SNP RBBP4 NM_005610.1 human genbank 54_36p 1 reviewed missense c.988 p.E330K 1 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 153 0 110 20 15.38 68 20 22.73 303642 TCGA-AB-2919 3 33425280 33425280 G T SNP UBP1 NM_014517.1 human genbank 54_36p -1 validated missense c.833 p.P278H 1 NULL "HMMPfam_CP2,superfamily_SAM/Pointed domain" - no_errors tier1 218 2 0.9 169 155 47.4 36 23 38.98 303642 TCGA-AB-2919 13 36489471 36489471 G C SNP FAM48A NM_001014286.2 human genbank 54_36p -1 validated missense c.1903 p.L635V 1 NULL NULL - no_errors tier1 115 1 0.86 102 98 48.76 46 48 51.06 303642 TCGA-AB-2919 6 102622973 102622973 G A SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed missense c.2621 p.R874Q 1 NULL "HMMPfam_Lig_chan,HMMSmart_SM00079,HMMPfam_ANF_receptor,HMMPfam_Lig_chan-Glu_bd,superfamily_Periplasmic binding protein-like I,superfamily_Periplasmic binding protein-like II" - no_errors tier1 165 2 1.2 191 37 16.23 NA 303642 TCGA-AB-2919 1 109640989 109640989 G A SNP MYBPHL NM_001010985.2 human genbank 54_36p -1 validated silent c.669 p.N223 0.996 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,superfamily_Immunoglobulin" - no_errors tier1 120 0 82 85 49.42 NA 303642 TCGA-AB-2919 2 152027712 152027712 T A SNP RIF1 NM_018151.3 human genbank 54_36p 1 validated missense c.3432 p.H1144Q 0.057 superfamily_ARM repeat "superfamily_ARM repeat,PatternScan_ABC_TRANSPORTER_1" - no_errors tier1 60 1 1.64 69 79 52.67 33 35 51.47 303642 TCGA-AB-2919 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 303642 TCGA-AB-2919 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 43 0 64 49 42.98 34 38 52.78 325028 TCGA-AB-2920 17 3128252 3128252 C T SNP OR3A2 NM_002551.3 human genbank 54_36p -1 validated missense c.728 p.R243Q 0.004 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 69 0 175 24 11.88 NA 325028 TCGA-AB-2920 17 26586873 26586873 G A SNP NF1 NM_001042492.2 human genbank 54_36p 1 reviewed missense c.3827 p.R1276Q 1 "HMMPfam_RasGAP,HMMSmart_SM00323,superfamily_GTPase activation domain GAP" "HMMSmart_SM00516,HMMPfam_RasGAP,HMMSmart_SM00323,PatternScan_RAS_GTPASE_ACTIV_1,superfamily_GTPase activation domain GAP" - no_errors tier1 66 4 5.71 28 97 77.6 11 100 325028 TCGA-AB-2920 11 29990509 29990509 C T SNP KCNA4 NM_002233.2 human genbank 54_36p -1 reviewed missense c.293 p.R98Q 0.941 NULL "HMMSmart_SM00225,HMMPfam_K_tetra,HMMPfam_Ion_trans,superfamily_POZ domain,HMMPfam_K_channel_TID,superfamily_Voltage-gated potassium channels" - no_errors tier1 112 8 6.61 118 113 48.5 NA 325028 TCGA-AB-2920 6 30662408 30662408 G A SNP ABCF1 NM_001025091.1 human genbank 54_36p 1 reviewed missense c.1972 p.G658S 1 "HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_ABC_tran,HMMSmart_SM00382,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 238 19 7.39 281 199 40.95 22 36 62.07 325028 TCGA-AB-2920 6 30994596 30994596 G A SNP VARS2 NM_020442.3 human genbank 54_36p 1 provisional silent c.999 p.V333 0.615 "HMMPfam_tRNA-synt_1,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Nucleotidylyl transferase" "PatternScan_AA_TRNA_LIGASE_I,HMMPfam_tRNA-synt_1,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases,HMMPfam_Anticodon_1,superfamily_Nucleotidylyl transferase" - no_errors tier1 71 7 8.97 123 112 47.26 49 62 55.86 325028 TCGA-AB-2920 22 37864635 37864636 - GCTC INS CBX7 NM_175709.3 human genbank 54_36p -1 validated frame_shift_ins c.198_197 p.G68fs 0.981:0.999 NULL "HMMPfam_Chromo,HMMSmart_CHROMO,PatternScan_CHROMO_1,superfamily_Chromodomain-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 325028 TCGA-AB-2920 22 37864636 37864637 - GCTC INS CBX7 NM_175709.3 human genbank 54_36p -1 validated frame_shift_ins c.197_196 p.A66fs 0.999:1.000 NULL "HMMPfam_Chromo,HMMSmart_CHROMO,PatternScan_CHROMO_1,superfamily_Chromodomain-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 325028 TCGA-AB-2920 19 47101973 47101973 G A SNP ARHGEF1 NM_199002.3 human genbank 54_36p 1 reviewed missense c.2492 p.R831K 1 NULL "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMSmart_PH,HMMPfam_RGS-like,superfamily_Regulat_G_prot_signal_superfam,superfamily_SSF50729" - no_errors tier1 36 2 5.26 43 25 35.71 275 212 43.44 325028 TCGA-AB-2920 11 59016357 59016357 G T SNP ENSG00000204989 ENST00000378245 human ensembl 54_36p 1 known missense c.552 p.M184I 0 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,superfamily_SSF81321" - no_errors tier1 139 7 4.79 155 111 40.81 NA 325028 TCGA-AB-2920 2 95079067 95079067 C T SNP MAL NM_002371.2 human genbank 54_36p 1 reviewed silent c.276 p.H92 0.425 HMMPfam_MARVEL HMMPfam_MARVEL - no_errors tier1 20 2 9.09 46 36 43.37 15 0 325028 TCGA-AB-2920 9 110665699 110665699 G C SNP ACTL7A NM_006687.2 human genbank 54_36p 1 reviewed missense c.1276 p.G426R 1 "HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain" "HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain" - no_errors tier1 37 1 2.63 61 67 52.34 NA 325028 TCGA-AB-2920 9 139259932 139259932 G A SNP FAM166A NM_001001710.1 human genbank 54_36p -1 predicted missense c.251 p.P84L 0.99 NULL HMMPfam_DUF2475 - no_errors tier1 6 0 1 4 80 1 100 325028 TCGA-AB-2920 1 155141762 155141762 C T SNP PEAR1 NM_001080471.1 human genbank 54_36p 1 provisional missense c.229 p.R77C 0.994 HMMPfam_EMI "HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,HMMSmart_EGF,superfamily_Grow_fac_recept,HMMPfam_EMI,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2" - no_errors tier1 59 1 1.67 96 75 43.86 1 1 50 348685 TCGA-AB-2921 MT 651 651 A G SNP ENSG00000211459 ENST00000389680 human ensembl 54_36p 1 novel rna NULL NULL NULL - - - no_errors tier1 1957 73 3.57 551 524 48.16 NA NA NA 348685 TCGA-AB-2921 1 20313229 20313229 G A SNP PLA2G2D NM_012400.2 human genbank 54_36p -1 provisional missense c.403 p.R135W 0.037 "HMMPfam_Phospholip_A2_1,HMMSmart_PA2c,superfamily_PhospholipaseA2" "HMMPfam_Phospholip_A2_1,HMMSmart_PA2c,PatternScan_PA2_HIS,PatternScan_PA2_ASP,superfamily_PhospholipaseA2" - no_errors tier1 58 5 7.81 43 36 44.44 NA 348685 TCGA-AB-2921 2 21088951 21088951 C T SNP APOB NM_000384.2 human genbank 54_36p -1 reviewed missense c.4294 p.D1432N 0.542 NULL "HMMPfam_Vitellogenin_N,HMMSmart_SM00638,HMMPfam_DUF1081,HMMPfam_DUF1943,superfamily_Lipovitellin-phosvitin complex beta-sheet shell regions,superfamily_Lipovitellin-phosvitin complex superhelical domain" - no_errors tier1 198 4 1.97 139 87 37.83 NA 348685 TCGA-AB-2921 13 27506262 27506263 - CATATTCTCTGAAATCAACGTATC INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1794_1793 p.YDL599in_frame_insIR* 0.789:0.821 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 348685 TCGA-AB-2921 2 32316794 32316794 A G SNP NLRC4 NM_021209.3 human genbank 54_36p -1 validated missense c.2432 p.I811T 0.898 superfamily_RNI-like "HMMPfam_CARD,HMMPfam_NACHT,superfamily_DEATH domain,superfamily_RNI-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 177 4 2.21 95 63 38.65 15 9 37.5 348685 TCGA-AB-2921 19 52921252 52921252 C T SNP EHD2 NM_014601.3 human genbank 54_36p 1 reviewed missense c.874 p.R292C 1 NULL "HMMSmart_SM00027,HMMPfam_Dynamin_N,PatternScan_EF_HAND_1,superfamily_EF-hand,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 254 11 4.14 107 96 46.83 6 5 45.45 348685 TCGA-AB-2921 14 64476280 64476280 G C SNP GPX2 NM_002083.2 human genbank 54_36p -1 reviewed missense c.252 p.N84K 1 "HMMPfam_GSHPx,superfamily_Thioredoxin-like" "HMMPfam_GSHPx,PatternScan_GLUTATHIONE_PEROXID_2,superfamily_Thioredoxin-like" - pseudogene tier1 171 3 1.72 102 71 40.8 2 3 60 348685 TCGA-AB-2921 3 101856631 101856631 G A SNP GPR128 NM_032787.1 human genbank 54_36p 1 provisional missense c.1642 p.A548T 0.89 HMMPfam_7tm_2 "HMMPfam_GPS,HMMSmart_GPS,HMMPfam_7tm_2,PatternScan_G_PROTEIN_RECEP_F2_2" - no_errors tier1 164 3 1.8 90 71 43.29 NA 348685 TCGA-AB-2921 1 113924725 113924725 G A SNP MAGI3 NM_152900.1 human genbank 54_36p 1 validated missense c.472 p.V158M 1 "HMMPfam_Guanylate_kin,HMMSmart_GuKc,PatternScan_GUANYLATE_KINASE_1,superfamily_SSF52540" "HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ,HMMPfam_Guanylate_kin,HMMSmart_GuKc,PatternScan_GUANYLATE_KINASE_1,superfamily_SSF52540" - no_errors tier1 211 7 3.17 119 74 38.34 NA 348685 TCGA-AB-2921 4 120172000 120172000 G A SNP SYNPO2 NM_133477.1 human genbank 54_36p 1 validated silent c.2622 p.Q874 0.997 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like" - no_errors tier1 90 3 3.19 50 37 42.05 NA 348685 TCGA-AB-2921 X 152264227 152264227 A G SNP ZNF275 NM_001080485.2 human genbank 54_36p 1 validated silent c.255 p.L85 0 HMMSmart_SM00349 "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 96 3 2.97 81 63 43.15 6 100 405655 TCGA-AB-2922 19 18237111 18237112 - C INS KIAA1683 NM_025249.1 human genbank 54_36p -1 validated frame_shift_ins c.2239_2238 p.Q746fs 0.000:0.000 NULL "HMMPfam_IQ,HMMSmart_SM00015,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 NA NA NA NA NA NA NA NA NA 405655 TCGA-AB-2922 13 27506275 27506276 - AATCAACGTAGAAGTACTCATTATCTTCCGGGG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1781_1780 p.594in_frame_insSPEDNEYFYVD 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 405655 TCGA-AB-2922 8 36895547 36895547 G A SNP KCNU1 NM_001031836.2 human genbank 54_36p 1 validated missense c.2570 p.R857Q 0.781 NULL "HMMPfam_BK_channel_a,HMMPfam_Ion_trans,superfamily_NAD(P)-bd,superfamily_SSF81324" - no_errors tier1 140 15 9.68 138 92 39.83 NA NA NA 405655 TCGA-AB-2922 4 43595902 43595902 G A SNP ENSG00000124399 ENST00000244249 human ensembl 54_36p 1 known missense c.167 p.R56H 0.091 HMMPfam_NDUF_B4 HMMPfam_NDUF_B4 - no_start_codon tier1 57 6 9.52 68 55 44.72 NA NA NA 405655 TCGA-AB-2922 12 52937580 52937580 C T SNP CBX5 NM_012117.1 human genbank 54_36p -1 reviewed nonsense c.122 p.W41* 1 "HMMPfam_Chromo,HMMSmart_SM00298,PatternScan_CHROMO_1,superfamily_Chromo domain-like" "HMMPfam_Chromo,HMMSmart_SM00298,PatternScan_CHROMO_1,HMMPfam_Chromo_shadow,superfamily_Chromo domain-like,HMMSmart_SM00300" - no_errors tier1 65 13 16.67 90 71 44.1 NA NA NA 405655 TCGA-AB-2922 4 54575000 54575000 C T SNP CHIC2 NM_012110.2 human genbank 54_36p -1 reviewed missense c.374 p.R125K 1 HMMPfam_Erf4 HMMPfam_Erf4 - no_errors tier1 74 14 15.91 39 53 57.61 NA NA NA 405655 TCGA-AB-2922 11 62120701 62120701 T C SNP MTA2 NM_004739.2 human genbank 54_36p -1 reviewed missense c.866 p.D289G 1 "HMMSmart_SANT,HMMPfam_Myb_DNA-binding" "HMMPfam_GATA,HMMSmart_ZnF_GATA,PatternScan_GATA_ZN_FINGER_1,HMMPfam_ELM2,HMMSmart_SANT,HMMPfam_BAH,HMMSmart_BAH,HMMPfam_Myb_DNA-binding,superfamily_SSF57716" - no_errors tier1 283 36 11.21 161 108 40.15 NA NA NA 405655 TCGA-AB-2922 5 71531412 71531412 C A SNP MAP1B NM_005909.3 human genbank 54_36p 1 validated silent c.6474 p.T2158 0.567 NULL "HMMPfam_MAP1B_neuraxin,PatternScan_MAP1B_NEURAXIN" - no_errors tier1 102 11 9.73 94 89 48.63 NA NA NA 405655 TCGA-AB-2922 16 82585470 82585470 C T SNP NECAB2 NM_019065.2 human genbank 54_36p 1 provisional missense c.659 p.A220V 0.001 NULL "HMMSmart_EFh,HMMPfam_ABM,superfamily_Dimer_A_B_barrel,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_SSF47473" - no_errors tier1 40 2 4.76 51 48 48.48 NA NA NA 405655 TCGA-AB-2922 5 82868814 82868814 T C SNP VCAN NM_004385.1 human genbank 54_36p 1 validated silent c.4236 p.N1412 0.996 NULL "PatternScan_ASX_HYDROXYL,HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,HMMSmart_SM00179,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin" - no_errors tier1 103 18 14.88 77 92 54.44 NA NA NA 405655 TCGA-AB-2922 14 89721002 89721002 C A SNP KCNK13 NM_022054.2 human genbank 54_36p 1 reviewed missense c.1129 p.Q377K 0.625 NULL "HMMPfam_Ion_trans_2,superfamily_Voltage-gated potassium channels" - no_errors tier1 16 1 5.88 24 17 41.46 NA NA NA 405655 TCGA-AB-2922 4 126556077 126556077 G A SNP FAT4 NM_024582.4 human genbank 54_36p 1 validated missense c.6509 p.G2170E 1 "HMMPfam_Cadherin,superfamily_Cadherin" "PatternScan_ASX_HYDROXYL,HMMSmart_LamG,HMMSmart_EGF_CA,HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_EGF,HMMSmart_EGF,superfamily_ConA_like_lec_gl,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,superfamily_Cadherin,PatternScan_EGF_CA,superfamily_SSF57196" - no_errors tier1 44 0 41 24 36.92 NA NA NA 405655 TCGA-AB-2922 5 140413379 140413379 G A SNP PCDHB1 NM_013340.2 human genbank 54_36p 1 reviewed missense c.2140 p.V714I 0.032 NULL "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 82 11 11.83 71 57 44.53 NA NA NA 405655 TCGA-AB-2922 6 161055850 161055850 C T SNP PLG NM_000301.2 human genbank 54_36p 1 validated silent c.582 p.D194 0.917 "HMMPfam_Kringle,HMMSmart_KR,superfamily_Kringle-like" "HMMPfam_Kringle,HMMSmart_KR,HMMPfam_Trypsin,HMMSmart_Tryp_SPc,HMMPfam_PAN_1,HMMSmart_PAN_AP,superfamily_Pept_Ser_Cys,superfamily_Kringle-like,PatternScan_KRINGLE_1,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER,superfamily_SSF57414" - no_errors tier1 69 7 9.21 51 79 60.77 NA NA NA 405655 TCGA-AB-2922 5 172122401 172122402 - AG INS LOC401218 XR_042344.1 human genbank 54_36p -1 model rna NULL NULL 1.000:1.000 - - - pseudogene tier1 NA NA NA NA NA NA NA NA NA 405655 TCGA-AB-2922 1 233412089 233412089 T A SNP ARID4B NM_016374.5 human genbank 54_36p -1 reviewed missense c.2768 p.D923V 1 NULL "HMMPfam_ARID,HMMSmart_SM00501,superfamily_ARID-like,HMMSmart_SM00333,HMMPfam_RBB1NT" - no_errors tier1 109 7 6.03 58 72 55.38 NA NA NA 499862 TCGA-AB-2923 16 4875050 4875050 G A SNP PPL NM_002705.4 human genbank 54_36p -1 reviewed missense c.3607 p.R1203W 0.992 NULL "HMMPfam_Plectin,HMMSmart_SM00250,HMMSmart_SM00150,superfamily_Spectrin repeat,superfamily_Plakin repeat" - no_errors tier1 42 1 2.33 12 9 42.86 NA NA NA 499862 TCGA-AB-2923 6 7324007 7324007 G T SNP CAGE1 NM_205864.2 human genbank 54_36p -1 validated missense c.121 p.Q41K 0.001 NULL NULL - no_errors tier1 91 4 4.21 70 57 44.53 NA NA NA 499862 TCGA-AB-2923 X 15216005 15216005 G A SNP ASB11 NM_080873.1 human genbank 54_36p -1 reviewed missense c.766 p.R256C 0.006 "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" "HMMPfam_SOCS_box,HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" - no_errors tier1 30 2 6.25 27 8 22.22 NA NA NA 499862 TCGA-AB-2923 6 20210600 20210600 T - DEL MBOAT1 NM_001080480.1 human genbank 54_36p -1 provisional frame_shift_del c.1384 p.I462fs 0.993 NULL HMMPfam_MBOAT - no_errors tier1 NA NA NA NA NA NA NA NA NA 499862 TCGA-AB-2923 22 21377140 21377140 C G SNP IGLV3-22 ENST00000390307 human ensembl 54_36p 1 known missense c.178 p.Q60E 0.659 "HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" "HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" - no_stop_codon tier1 50 1 1.85 37 27 42.19 NA NA NA 499862 TCGA-AB-2923 6 28377655 28377655 A G SNP PGBD1 NM_032507.2 human genbank 54_36p 1 reviewed missense c.2045 p.N682S 0.978 NULL "HMMPfam_SCAN,HMMSmart_SCAN" - no_errors tier1 126 4 3.08 65 74 53.24 NA NA NA 499862 TCGA-AB-2923 6 34500485 34500485 C T SNP RPS10 NM_001014.3 human genbank 54_36p -1 reviewed silent c.261 p.P87 0.757 HMMPfam_S10_plectin HMMPfam_S10_plectin - no_errors tier1 40 0 28 24 46.15 NA NA NA 499862 TCGA-AB-2923 15 41697471 41697471 G A SNP STRC NM_153700.2 human genbank 54_36p -1 reviewed missense c.440 p.A147V 0.996 NULL NULL - no_errors tier1 61 0 45 14 23.73 NA NA NA 499862 TCGA-AB-2923 19 42310451 42310451 C T SNP ZNF420 NM_144689.3 human genbank 54_36p 1 provisional nonsense c.718 p.R240* 0.002 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 73 3 3.95 32 36 52.94 NA NA NA 499862 TCGA-AB-2923 19 45075876 45075876 C T SNP FCGBP NM_003890.2 human genbank 54_36p -1 validated missense c.9574 p.A3192T 0.014 "superfamily_Cysrich_TIL,HMMPfam_TIL" "HMMSmart_VWC,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_TIL_assoc,HMMSmart_FOLN,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 29 1 3.33 28 17 37.78 NA NA NA 499862 TCGA-AB-2923 11 55438204 55438204 A T SNP OR5W2 NM_001001960.1 human genbank 54_36p -1 provisional missense c.431 p.L144H 0.011 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 100 4 3.85 42 49 53.85 NA NA NA 499862 TCGA-AB-2923 6 56588852 56588852 C T SNP DST NM_001723.1 human genbank 54_36p -1 reviewed missense c.7372 p.E2458K 1 "HMMSmart_PLEC,superfamily_SSF75399" "HMMPfam_Plectin,HMMSmart_PLEC,HMMPfam_Spectrin,HMMSmart_SPEC,superfamily_Spectrin,superfamily_SSF75399" - no_errors tier1 65 3 4.29 43 26 37.14 NA NA NA 499862 TCGA-AB-2923 17 70303340 70303340 C T SNP TMEM104 NM_017728.3 human genbank 54_36p 1 validated nonsense c.610 p.R204* 0.969 NULL HMMPfam_Aa_trans - no_errors tier1 32 1 2.94 23 26 53.06 NA NA NA 499862 TCGA-AB-2923 8 87588410 87588410 A G SNP FAM82B NM_016033.2 human genbank 54_36p -1 validated silent c.177 p.A59 0.989 NULL superfamily_Prenyl_trans - no_errors tier1 87 1 1.14 43 46 51.69 NA NA NA 499862 TCGA-AB-2923 10 102038158 102038158 C T SNP PKD2L1 NM_016112.2 human genbank 54_36p -1 reviewed silent c.2403 p.T801 0 NULL "HMMPfam_PKD_channel,superfamily_Voltage-gated potassium channels" - no_errors tier1 79 3 3.66 50 41 45.05 NA NA NA 499862 TCGA-AB-2923 4 106376196 106376196 C T SNP TET2 NM_017628.1 human genbank 54_36p 1 validated nonsense c.1648 p.R550* 0.001 NULL NULL - no_errors tier1 118 4 3.25 71 49 40.5 NA NA NA 499862 TCGA-AB-2923 4 106377418 106377419 - A INS TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_ins c.2870_2871 p.Q958fs 1.000:0.960 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 499862 TCGA-AB-2923 1 115058052 115058052 T C SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.182 p.Q61R 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 97 2 2 73 14 16.09 NA NA NA 499862 TCGA-AB-2923 5 126702791 126702791 G T SNP MEGF10 NM_032446.2 human genbank 54_36p 1 validated missense c.197 p.W66L 1 HMMPfam_EMI "HMMPfam_Laminin_EGF,HMMSmart_SM00180,HMMSmart_SM00181,superfamily_Plant inhibitors of proteinases and amylases,HMMPfam_EMI,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_EGF/Laminin" - no_errors tier1 169 8 4.52 101 66 39.29 NA NA NA 499862 TCGA-AB-2923 3 142493844 142493844 T G SNP ACPL2 NM_001037172.1 human genbank 54_36p 1 validated missense c.550 p.Y184D 1 "HMMPfam_Acid_phosphat_A,superfamily_Phosphoglycerate mutase-like" "HMMPfam_Acid_phosphat_A,superfamily_Phosphoglycerate mutase-like" - no_errors tier1 82 0 40 25 38.46 NA NA NA 499862 TCGA-AB-2923 1 149773088 149773088 G A SNP CGN NM_020770.2 human genbank 54_36p 1 validated missense c.2756 p.R919Q 1 NULL HMMPfam_Myosin_tail_1 - no_errors tier1 44 1 2.22 25 22 46.81 NA NA NA 499862 TCGA-AB-2923 1 205851951 205851951 G A SNP CR1 NM_000651.3 human genbank 54_36p 1 reviewed missense c.6517 p.V2173M 0.019 "HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain" "HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain" - no_errors tier1 59 3 4.76 37 39 51.32 NA NA NA 499862 TCGA-AB-2923 2 219241639 219241639 G T SNP RNF25 NM_022453.2 human genbank 54_36p -1 reviewed missense c.49 p.P17T 1 HMMPfam_RWD "HMMSmart_SM00184,HMMPfam_RWD,HMMSmart_SM00591,superfamily_UBC-like,HMMPfam_zf-C3HC4,superfamily_RING/U-box" - no_errors tier1 74 0 54 39 41.94 NA NA NA 499862 TCGA-AB-2923 2 228388516 228388516 T A SNP CCL20 NM_004591.1 human genbank 54_36p 1 validated missense c.179 p.I60N 0.996 "PatternScan_SMALL_CYTOKINES_CC,HMMPfam_IL8,HMMSmart_SM00199,superfamily_Interleukin 8-like chemokines" "PatternScan_SMALL_CYTOKINES_CC,HMMPfam_IL8,HMMSmart_SM00199,superfamily_Interleukin 8-like chemokines" - no_errors tier1 73 3 3.95 42 35 45.45 NA NA NA 507202 TCGA-AB-2924 9 980602 980602 C G SNP DMRT3 NM_021240.2 human genbank 54_36p 1 validated missense c.1016 p.T339R 0.998 NULL "HMMPfam_DM,HMMSmart_DM,PatternScan_DM_1,superfamily_DM_DNA_bd,HMMPfam_DMA" - no_errors tier1 130 8 5.8 21 10 32.26 NA 507202 TCGA-AB-2924 19 8945715 8945715 C T SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated missense c.7100 p.S2367N 0 NULL "HMMPfam_SEA,HMMSmart_SM00200,PatternScan_ATPASE_ALPHA_BETA,superfamily_SEA domain" - no_errors tier1 530 42 7.34 144 96 40 NA 507202 TCGA-AB-2924 17 19032024 19032024 C T SNP SNORD3A ENST00000365494 human ensembl 54_36p 1 known rna NULL NULL 1 - - - no_errors tier1 379 21 5.25 76 14 15.38 50 7 12.28 507202 TCGA-AB-2924 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 96 15 13.51 34 22 38.6 311 249 44.46 507202 TCGA-AB-2924 5 34020284 34020284 C T SNP SLC45A2 NM_016180.2 human genbank 54_36p -1 reviewed silent c.162 p.A54 0.858 superfamily_MFS general substrate transporter superfamily_MFS general substrate transporter - no_errors tier1 139 11 7.28 39 34 45.95 NA 507202 TCGA-AB-2924 17 36192063 36192063 G A SNP KRT27 NM_181537.3 human genbank 54_36p -1 validated missense c.209 p.A70V 0 NULL HMMPfam_Filament - no_errors tier1 148 9 5.7 35 35 50 NA 507202 TCGA-AB-2924 5 54757513 54757513 A C SNP PPAP2A NM_176895.2 human genbank 54_36p -1 reviewed missense c.664 p.Y222D 1 "HMMPfam_PAP2,HMMSmart_SM00014,superfamily_Acid phosphatase/Vanadium-dependent haloperoxidase" "HMMPfam_PAP2,HMMSmart_SM00014,superfamily_Acid phosphatase/Vanadium-dependent haloperoxidase" - no_errors tier1 260 9 3.33 61 68 51.91 2 6 75 507202 TCGA-AB-2924 18 58648409 58648409 G C SNP PHLPP NM_194449.1 human genbank 54_36p 1 validated missense c.202 p.G68R 1 HMMPfam_PH "HMMPfam_LRR_1,HMMPfam_PH,HMMSmart_SM00332,superfamily_Protein serine/threonine phosphatase 2C catalytic domain,HMMSmart_SM00369,HMMPfam_PP2C,HMMSmart_SM00364,superfamily_L domain-like" - no_errors tier1 331 24 6.76 75 45 36.59 16 20 55.56 507202 TCGA-AB-2924 11 60802458 60802458 G - DEL VWCE NM_152718.2 human genbank 54_36p -1 validated frame_shift_del c.1391 p.V465fs 1 "HMMPfam_VWC,HMMSmart_SM00214,HMMSmart_SM00215" "PatternScan_ASX_HYDROXYL,HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMSmart_SM00179,HMMSmart_SM00181,HMMSmart_SM00215,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_EGF/Laminin" - no_errors tier1 NA NA NA NA NA NA NA NA NA 507202 TCGA-AB-2924 14 79739147 79739147 C T SNP DIO2 NM_001007023.4 human genbank 54_36p -1 reviewed missense c.568 p.A190T 1 HMMPfam_T4_deiodinase HMMPfam_T4_deiodinase - pseudogene tier1 113 13 10.24 30 32 50.79 1 0 507202 TCGA-AB-2924 16 79850793 79850793 T G SNP BCMO1 NM_017429.2 human genbank 54_36p 1 reviewed missense c.205 p.Y69D 0.938 HMMPfam_RPE65 HMMPfam_RPE65 - no_errors tier1 191 23 10.75 30 28 47.46 NA 507202 TCGA-AB-2924 5 170770151 170770152 - TGTA INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.862_863 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 375182 TCGA-AB-2925 8 3068744 3068744 G T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated missense c.4402 p.L1468I 1 NULL "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,superfamily_Complement control module/SCR domain" - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 74 2 2.63 37 33 47.14 NA 375182 TCGA-AB-2925 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 41 1 2.38 64 47 42.34 14 20 58.82 375182 TCGA-AB-2925 13 27506255 27506256 - ATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1801_1800 p.600in_frame_insNEYFYVDFREYEYD 1.000:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 375182 TCGA-AB-2925 6 29689157 29689157 C A SNP GABBR1 NM_001470.2 human genbank 54_36p -1 reviewed missense c.1408 p.A470S 1 "HMMPfam_ANF_receptor,superfamily_Periplasmic binding protein-like I" "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_ANF_receptor,superfamily_Complement control module/SCR domain,HMMPfam_7tm_3,superfamily_Periplasmic binding protein-like I" - no_errors tier1 82 2 2.38 100 75 42.86 35 39 52.7 375182 TCGA-AB-2925 13 33302083 33302083 A C SNP RFC3 NM_002915.3 human genbank 54_36p 1 reviewed missense c.502 p.T168P 1 "HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00382,superfamily_DNA polymerase III clamp loader subunits C-terminal domain,HMMPfam_RFC-E_C,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 60 0 64 22 25.58 43 3 6.52 375182 TCGA-AB-2925 7 43567983 43567983 C T SNP HECW1 NM_015052.3 human genbank 54_36p 1 validated missense c.4754 p.S1585L 0.985 "HMMPfam_HECT,HMMSmart_HECTc,superfamily_HECT" "HMMPfam_C2,HMMSmart_C2,HMMPfam_HECT,HMMSmart_HECTc,superfamily_HECT,HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,superfamily_C2_CaLB" - no_errors tier1 61 2 3.12 87 53 37.86 NA 375182 TCGA-AB-2925 2 68946310 68946310 A T SNP BMP10 NM_014482.1 human genbank 54_36p -1 reviewed missense c.1232 p.F411Y 1 "HMMPfam_TGF_beta,HMMSmart_TGFB,superfamily_SSF57501" "HMMPfam_TGFb_propeptide,HMMPfam_TGF_beta,HMMSmart_TGFB,PatternScan_TGF_BETA_1,superfamily_SSF57501" - no_errors tier1 91 1 1.09 101 62 38.04 NA 375182 TCGA-AB-2925 15 80361580 80361580 C T SNP FAM154B NM_001008226.1 human genbank 54_36p 1 predicted missense c.319 p.P107S 0.99 NULL NULL - no_errors tier1 58 1 1.67 57 46 44.66 NA 375182 TCGA-AB-2925 7 86253906 86253906 G A SNP GRM3 NM_000840.2 human genbank 54_36p 1 reviewed missense c.862 p.A288T 0.999 "HMMPfam_ANF_receptor,superfamily_Periplasmic binding protein-like I" "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_Periplasmic binding protein-like I" - no_errors tier1 7 0 13 19 59.38 NA 375182 TCGA-AB-2925 5 128379505 128379505 G A SNP SLC27A6 NM_001017372.1 human genbank 54_36p 1 reviewed missense c.998 p.R333H 0.465 "HMMPfam_AMP-binding,superfamily_SSF56801" "HMMPfam_AMP-binding,PatternScan_AMP_BINDING,superfamily_SSF56801" - no_errors tier1 171 3 1.71 89 56 38.62 2 100 375182 TCGA-AB-2925 3 129682841 129682841 G A SNP GATA2 NM_032638.1 human genbank 54_36p -1 reviewed missense c.1154 p.P385L 1 "HMMSmart_ZnF_GATA,superfamily_SSF57716" "HMMPfam_GATA,HMMSmart_ZnF_GATA,PatternScan_GATA_ZN_FINGER_1,superfamily_SSF57716" - no_errors tier1 54 0 54 41 43.16 11 93 89.42 375182 TCGA-AB-2925 9 140135748 140135748 G T SNP CACNA1B NM_000718.2 human genbank 54_36p 1 validated missense c.6496 p.G2166C 1 NULL "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels" - no_errors tier1 10 0 9 26 74.29 NA 375182 TCGA-AB-2925 1 151000425 151000425 T G SNP KPRP NM_001025231.1 human genbank 54_36p 1 provisional missense c.1737 p.F579L 0.976 NULL NULL - no_errors tier1 47 0 76 40 34.48 NA 375182 TCGA-AB-2925 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 375182 TCGA-AB-2925 2 179224470 179224470 C T SNP TTN ENST00000342992 human ensembl 54_36p -1 known missense c.2653 p.V885M 0.999 "superfamily_DH-domain,HMMPfam_PPAK" "superfamily_DH-domain,HMMSmart_IGc2,HMMSmart_IG,HMMPfam_fn3,HMMSmart_FN3,HMMPfam_PPAK,superfamily_FN_III-like,superfamily_ConA_like_lec_gl,superfamily_Man6php_recept,HMMPfam_I-set,HMMPfam_ig,PatternScan_FGGY_KINASES_1,superfamily_SSF48726" - no_stop_codon tier1 54 1 1.82 38 27 41.54 NA 375182 TCGA-AB-2925 1 195185236 195185236 C G SNP CFHR2 NM_005666.2 human genbank 54_36p 1 validated missense c.87 p.N29K 0.059 "HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain" "HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain" - no_errors tier1 107 3 2.73 97 46 32.17 0 387919 TCGA-AB-2926 12 840502 840502 A C SNP WNK1 NM_018979.2 human genbank 54_36p 1 validated missense c.1683 p.R561S 0.989 superfamily_Kinase_like "PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,HMMPfam_Pkinase" - no_errors tier1 120 7 5.47 64 41 38.32 NA NA NA 387919 TCGA-AB-2926 11 9970647 9970647 C T SNP SBF2 NM_030962.3 human genbank 54_36p -1 reviewed missense c.1187 p.R396H 1 "HMMPfam_dDENN,HMMSmart_SM00801" "HMMPfam_DENN,HMMSmart_SM00799,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_GRAM,HMMSmart_SM00568,HMMPfam_dDENN,HMMSmart_SM00801,HMMPfam_uDENN,HMMSmart_SM00800,HMMPfam_Myotub-related,superfamily_PH domain-like,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 89 5 5.26 61 56 47.46 NA NA NA 387919 TCGA-AB-2926 X 22928217 22928217 C T SNP DDX53 NM_182699.2 human genbank 54_36p 1 validated missense c.122 p.P41L 0.001 superfamily_SSF54791 "PatternScan_DEAD_ATP_HELICASE,HMMPfam_Helicase_C,HMMSmart_HELICc,HMMSmart_KH,HMMPfam_DEAD,HMMSmart_DEXDc,HMMPfam_KH_1,superfamily_SSF52540,superfamily_SSF54791" - no_errors tier1 74 5 6.33 40 35 46.67 NA NA NA 387919 TCGA-AB-2926 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 94 2 2.06 77 44 36.36 NA NA NA 387919 TCGA-AB-2926 1 32910659 32910659 G A SNP RBBP4 NM_005610.1 human genbank 54_36p 1 reviewed missense c.988 p.E330K 1 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 132 9 6.34 103 84 44.21 NA NA NA 387919 TCGA-AB-2926 22 37224035 37224035 C T SNP DDX17 NM_001098504.1 human genbank 54_36p -1 reviewed splice_site c.738+1 e5+1 1 - - - no_errors tier1 133 8 5.48 90 75 44.64 NA NA NA 387919 TCGA-AB-2926 1 40734107 40734107 A G SNP ZNF642 NM_198494.2 human genbank 54_36p 1 validated missense c.1370 p.H457R 0.957 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 109 15 12 45 55 55 NA NA NA 387919 TCGA-AB-2926 17 53763622 53763622 A G SNP MIRN142 ENST00000384835 human ensembl 54_36p -1 known rna NULL NULL 1 - - - no_errors tier1 61 2 3.12 48 30 37.97 NA NA NA 387919 TCGA-AB-2926 14 64005169 64005169 G A SNP AKAP5 NM_004857.3 human genbank 54_36p 1 reviewed missense c.304 p.E102K 0.265 HMMPfam_WSK "HMMPfam_WSK,HMMPfam_RII_binding_1" - no_errors tier1 54 5 8.33 35 22 38.6 NA NA NA 387919 TCGA-AB-2926 4 77162918 77162918 T C SNP CXCL10 NM_001565.2 human genbank 54_36p -1 reviewed silent c.138 p.E46 0.669 "HMMPfam_IL8,HMMSmart_SCY,superfamily_Chemokine_IL8,PatternScan_SMALL_CYTOKINES_CXC" "HMMPfam_IL8,HMMSmart_SCY,superfamily_Chemokine_IL8,PatternScan_SMALL_CYTOKINES_CXC" - no_errors tier1 213 25 10.29 106 84 44.21 NA NA NA 387919 TCGA-AB-2926 9 85707986 85707986 C T SNP KIF27 NM_017576.1 human genbank 54_36p -1 provisional missense c.1267 p.V423I 0.878 NULL "HMMPfam_Kinesin,HMMSmart_SM00129,PatternScan_KINESIN_MOTOR_DOMAIN1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 176 17 8.72 106 67 38.73 NA NA NA 387919 TCGA-AB-2926 1 94134956 94134956 C T SNP GCLM NM_002061.2 human genbank 54_36p -1 reviewed missense c.346 p.V116I 0.981 superfamily_NAD(P)-linked oxidoreductase "HMMPfam_Aldo_ket_red,superfamily_NAD(P)-linked oxidoreductase" - no_errors tier1 83 4 4.49 59 26 30.59 NA NA NA 387919 TCGA-AB-2926 1 153209534 153209535 - G INS SHC1 NM_183001.1 human genbank 54_36p -1 validated frame_shift_ins c.93_92 p.E32fs 1.000:1.000 NULL "HMMPfam_SH2,HMMSmart_SM00252,HMMPfam_PID,HMMSmart_SM00462,superfamily_PH domain-like,superfamily_SH2 domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 387919 TCGA-AB-2926 5 172677531 172677532 - C INS STC2 NM_003714.2 human genbank 54_36p -1 reviewed frame_shift_ins c.834_833 p.L279fs 0.011:0.001 NULL HMMPfam_Stanniocalcin - no_errors tier1 NA NA NA NA NA NA NA NA NA 387919 TCGA-AB-2926 2 187195324 187195324 T A SNP ITGAV NM_002210.1 human genbank 54_36p 1 reviewed nonsense c.330 p.Y110* 1 superfamily_Integrin alpha N-terminal domain "HMMPfam_Integrin_alpha,HMMPfam_FG-GAP,HMMSmart_SM00191,HMMPfam_Integrin_alpha2,PatternScan_INTEGRIN_ALPHA,superfamily_Integrin domains,superfamily_Integrin alpha N-terminal domain" - no_errors tier1 202 20 9.01 130 77 36.84 NA NA NA 387919 TCGA-AB-2926 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 81 5 5.81 50 55 51.89 NA NA NA 578179 TCGA-AB-2927 MT 9731 9731 T C SNP MT-CO3 ENST00000362079 human ensembl 54_36p 1 known missense c.524 p.L175P NULL "HMMPfam_COX3,superfamily_CytC_oxdse_III" "HMMPfam_COX3,superfamily_CytC_oxdse_III" - no_stop_codon:bad_bp_length_for_coding_region tier1 2658 72 2.62 348 1200 77.32 NA NA NA 578179 TCGA-AB-2927 MT 13370 13370 T C SNP MT-ND5 ENST00000361567 human ensembl 54_36p 1 known missense c.1033 p.S345P NULL HMMPfam_Oxidored_q1 "HMMPfam_Oxidored_q1_N,HMMPfam_Oxidored_q1,HMMPfam_NADH5_C" - no_errors tier1 1701 13 0.75 962 128 11.7 NA NA NA 578179 TCGA-AB-2927 MT 13763 13763 T C SNP MT-ND5 ENST00000361567 human ensembl 54_36p 1 known missense c.1426 p.S476P NULL HMMPfam_NADH5_C "HMMPfam_Oxidored_q1_N,HMMPfam_Oxidored_q1,HMMPfam_NADH5_C" - no_errors tier1 801 21 2.52 242 215 47.05 NA NA NA 578179 TCGA-AB-2927 1 19505127 19505127 C G SNP AKR7A2 NM_003689.2 human genbank 54_36p -1 validated missense c.890 p.R297P 0.998 superfamily_Aldo/ket_red "HMMPfam_Aldo_ket_red,superfamily_Aldo/ket_red" - no_errors tier1 56 0 10 13 56.52 22 13 37.14 578179 TCGA-AB-2927 X 23863381 23863381 C T SNP CXorf58 NM_152761.1 human genbank 54_36p 1 predicted nonsense c.703 p.R235* 0.77 NULL NULL - no_errors tier1 131 2 1.49 79 43 35.25 NA 578179 TCGA-AB-2927 6 26305375 26305375 T A SNP HIST1H3D ENST00000377831 human ensembl 54_36p -1 known nonsense c.484 p.R162* 1 NULL "HMMSmart_SM00414,PatternScan_HISTONE_H2A,HMMPfam_Histone,superfamily_Histone-fold" - no_errors tier1 18 0 21 11 34.38 61 38 38 578179 TCGA-AB-2927 14 29163175 29163175 G A SNP PRKD1 NM_002742.2 human genbank 54_36p -1 validated silent c.1839 p.I613 0.995 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMPfam_PH,HMMSmart_PH,HMMPfam_C1_1,HMMSmart_C1,PatternScan_ZF_DAG_PE_1,HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_SSF50729,superfamily_SSF57889" - no_errors tier1 104 2 1.87 135 100 42.55 1 0 578179 TCGA-AB-2927 20 30485895 30485895 G T SNP ASXL1 NM_015338.4 human genbank 54_36p 1 reviewed splice_site c.1720-1 e13-1 1 - - - no_errors tier1 16 0 39 20 33.9 14 23 62.16 578179 TCGA-AB-2927 21 30576841 30576841 G A SNP KRTAP24-1 NM_001085455.1 human genbank 54_36p -1 validated missense c.281 p.P94L 0.98 HMMPfam_PMG HMMPfam_PMG - no_errors tier1 78 4 4.88 121 69 36.32 NA 578179 TCGA-AB-2927 21 35153653 35153653 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed nonsense c.601 p.R201* 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 106 4 3.6 48 24 33.33 437 335 43.34 578179 TCGA-AB-2927 21 35174746 35174746 C A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.486 p.R162S 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 53 0 8 6 42.86 292 399 57.66 578179 TCGA-AB-2927 8 36899260 36899260 G A SNP KCNU1 NM_001031836.2 human genbank 54_36p 1 validated silent c.2691 p.T897 0.932 NULL "HMMPfam_BK_channel_a,HMMPfam_Ion_trans,superfamily_NAD(P)-bd,superfamily_SSF81324" - no_errors tier1 80 1 1.23 71 58 44.96 NA 578179 TCGA-AB-2927 X 37901198 37901198 C T SNP SRPX NM_006307.3 human genbank 54_36p -1 provisional silent c.984 p.T328 0.437 NULL "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_HYR,superfamily_Complement control module/SCR domain" - no_errors tier1 132 1 0.75 95 42 30.43 3 0 578179 TCGA-AB-2927 1 41256259 41256259 C T SNP SLFNL1 NM_144990.2 human genbank 54_36p -1 provisional missense c.592 p.D198N 0.971 NULL HMMPfam_AAA_4 - no_errors tier1 18 0 28 14 33.33 6 4 40 578179 TCGA-AB-2927 3 49911341 49911341 C T SNP MST1R NM_002447.2 human genbank 54_36p -1 validated missense c.1511 p.R504H 1 "HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain" "HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain,HMMPfam_PSI,HMMSmart_SM00220,HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00423,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),superfamily_E set domains,superfamily_Plexin repeat,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 22 1 4.35 17 9 34.62 8 3 27.27 578179 TCGA-AB-2927 18 51047117 51047118 - G INS TCF4 NM_001083962.1 human genbank 54_36p -1 reviewed frame_shift_ins c.1838_1837 p.Q613fs 1.000:1.000 "HMMPfam_HLH,HMMSmart_HLH,superfamily_HLH_basic" "HMMPfam_HLH,HMMSmart_HLH,superfamily_HLH_basic" - no_errors tier1 NA NA NA NA NA NA NA NA NA 578179 TCGA-AB-2927 11 55189860 55189860 G A SNP OR4C6 NM_001004704.1 human genbank 54_36p 1 provisional silent c.642 p.A214 0.001 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 113 4 3.39 121 79 39.5 2 0 578179 TCGA-AB-2927 11 61259672 61259672 C A SNP DAGLA NM_006133.1 human genbank 54_36p 1 validated silent c.1192 p.R398 1 "HMMPfam_Lipase_3,superfamily_SSF53474" "HMMPfam_Lipase_3,PatternScan_LIPASE_SER,superfamily_SSF53474" - no_errors tier1 24 0 18 4 17.39 1 3 75 578179 TCGA-AB-2927 17 70682466 70682467 - TA INS SUMO2 NM_006937.1 human genbank 54_36p -1 reviewed frame_shift_ins c.201_200 p.N68fs 1.000:1.000 "HMMPfam_ubiquitin,HMMSmart_SM00213,superfamily_Ubiquitin-like" "HMMPfam_ubiquitin,HMMSmart_SM00213,superfamily_Ubiquitin-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 578179 TCGA-AB-2927 13 72235718 72235718 T C SNP DIS3 NM_014953.1 human genbank 54_36p -1 validated missense c.1999 p.M667V 1 HMMPfam_RNB "HMMPfam_RNB,PatternScan_RIBONUCLEASE_II,HMMSmart_SM00670,superfamily_PIN domain-like" - no_errors tier1 54 0 85 50 37.04 15 6 28.57 578179 TCGA-AB-2927 16 74070660 74070660 C G SNP CHST6 NM_021615.4 human genbank 54_36p -1 provisional missense c.568 p.D190H 0.996 "HMMPfam_Sulfotransfer_1,superfamily_SSF52540" "HMMPfam_Sulfotransfer_1,superfamily_SSF52540" - no_errors tier1 16 0 9 4 30.77 NA 578179 TCGA-AB-2927 16 83463616 83463616 G A SNP CRISPLD2 NM_031476.3 human genbank 54_36p 1 validated splice_site c.981+1 e8+1 0.998 - - - no_errors tier1 93 0 99 56 36.13 2 0 578179 TCGA-AB-2927 15 90778526 90778526 C T SNP ST8SIA2 NM_006011.3 human genbank 54_36p 1 reviewed silent c.207 p.D69 1 NULL HMMPfam_Glyco_transf_29 - no_errors tier1 66 1 1.47 79 41 34.17 NA 578179 TCGA-AB-2927 14 91978270 91978270 G C SNP SLC24A4 NM_153646.2 human genbank 54_36p 1 validated missense c.427 p.G143R 1 HMMPfam_Na_Ca_ex HMMPfam_Na_Ca_ex - no_errors tier1 47 3 6 79 27 25.47 NA 578179 TCGA-AB-2927 14 101769807 101769807 G A SNP RAGE NM_014226.1 human genbank 54_36p -1 provisional silent c.663 p.P221 0.089 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 126 1 0.78 205 94 31.44 2 0 578179 TCGA-AB-2927 12 110369919 110369919 T A SNP SH2B3 NM_005475.2 human genbank 54_36p 1 validated missense c.1313 p.L438H 0.965 "HMMPfam_SH2,HMMSmart_SM00252,superfamily_SH2 domain" "HMMPfam_SH2,HMMSmart_SM00252,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Phe_ZIP,superfamily_Phenylalanine zipper,superfamily_PH domain-like,superfamily_SH2 domain" - no_errors tier1 37 0 17 19 52.78 57 44 43.56 578179 TCGA-AB-2927 9 121010841 121010841 G A SNP DBC1 NM_014618.2 human genbank 54_36p -1 validated silent c.1122 p.P374 1 NULL HMMSmart_SM00457 - no_errors tier1 95 1 1.04 131 72 35.47 NA 578179 TCGA-AB-2927 10 123960274 123960274 C T SNP TACC2 NM_206862.2 human genbank 54_36p 1 reviewed missense c.6344 p.T2115M 0.962 NULL HMMPfam_TACC - no_errors tier1 100 2 1.94 50 24 32.43 NA 578179 TCGA-AB-2927 2 179193024 179193024 A C SNP TTN ENST00000375038 human ensembl 54_36p -1 known missense c.34311 p.D11437E 1 "HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Concanavalin A-like lectins/glucanases,superfamily_WD40 repeat-like,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_PPAK,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Protein kinase-like (PK-like),superfamily_WD40 repeat-like,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,HMMPfam_Pkinase,PatternScan_FGGY_KINASES_1,PatternScan_PEROXIDASE_1,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" - no_errors tier1 109 3 2.68 70 33 32.04 3 0 578179 TCGA-AB-2927 1 201719493 201719493 C A SNP PRELP NM_002725.3 human genbank 54_36p 1 reviewed silent c.558 p.I186 1 "HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00364,superfamily_L domain-like" "HMMPfam_LRRNT,HMMSmart_SM00013,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00364,superfamily_L domain-like" - no_errors tier1 64 1 1.52 35 22 38.6 NA 605322 TCGA-AB-2928 19 22743930 22743930 C T SNP ZNF99 NM_001080409.1 human genbank 54_36p -1 provisional missense c.103 p.A35T 0.002 "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box" "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 87 16 15.24 85 70 44.59 0 605322 TCGA-AB-2928 2 25315569 25315569 T C SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2342 p.D781G 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 59 6 9.23 57 39 40.62 29 54 65.06 605322 TCGA-AB-2928 2 25324020 25324020 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed nonsense c.958 p.R320* 1 "HMMPfam_PWWP,HMMSmart_SM00293,superfamily_Tudor/PWWP/MBT" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 88 14 13.46 73 59 44.36 40 16 28.57 605322 TCGA-AB-2928 13 27490629 27490629 T C SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2516 p.D839G 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 171 11 5.98 130 43 24.02 171 59 25.65 605322 TCGA-AB-2928 1 50348217 50348217 G A SNP ELAVL4 ENST00000371821 human ensembl 54_36p 1 known silent c.18 p.L6 1 NULL "HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928" - no_errors tier1 262 36 12 121 126 50.2 NA 605322 TCGA-AB-2928 18 55254269 55254269 C T SNP CCBE1 NM_133459.1 human genbank 54_36p -1 provisional missense c.1072 p.G358R 1 NULL "PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMSmart_SM00181,HMMPfam_Collagen,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 116 21 15.22 118 84 41.38 NA 605322 TCGA-AB-2928 16 79738404 79738404 C T SNP PKD1L2 ENST00000299598 human ensembl 54_36p -1 known missense c.5192 p.R1731K 1 NULL "HMMPfam_GPS,HMMSmart_SM00303,PatternScan_CHANNEL_COLICIN,HMMPfam_PLAT,HMMSmart_SM00308,HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_Lipase/lipooxygenase domain (PLAT/LH2 domain),HMMPfam_PKD_channel,superfamily_C-type lectin-like" - no_errors tier1 248 38 13.15 78 62 44.29 NA 605322 TCGA-AB-2928 7 83430479 83430479 C T SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed missense c.1838 p.R613Q 0.991 "HMMSmart_IG,HMMPfam_ig,superfamily_SSF48726" "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema,HMMSmart_IG,HMMSmart_PSI,HMMPfam_ig,superfamily_Plexin-like_fold,superfamily_SSF48726" - no_errors tier1 190 10 4.98 138 34 19.65 NA 605322 TCGA-AB-2928 4 106158442 106158442 C - DEL TET2 NM_001127208.1 human genbank 58_37c 1 validated frame_shift_del c.3343 p.P1115fs 0.995 NULL NULL - no_errors tier1 253 30 11.81 253 89 34.9 24 9 37.5 605322 TCGA-AB-2928 4 106377891 106377891 C - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.3343 p.P1115fs 0.996 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 605322 TCGA-AB-2928 4 106377892 106377892 C - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.3344 p.P1115fs 1 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 605322 TCGA-AB-2928 4 106410226 106410226 A T SNP TET2 ENST00000265149 human ensembl 54_36p 1 known missense c.461 p.E154V 1 NULL NULL - no_start_codon tier1 152 21 11.86 181 118 39.46 19 19 50 605322 TCGA-AB-2928 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 94 11 10.48 102 63 37.72 26 38 59.38 415172 TCGA-AB-2929 19 6537144 6537144 G A SNP CD70 NM_001252.3 human genbank 54_36p -1 reviewed missense c.469 p.R157C 0.958 "HMMPfam_TNF,HMMSmart_SM00207,superfamily_TNF-like" "HMMPfam_TNF,HMMSmart_SM00207,PatternScan_TNF_1,superfamily_TNF-like" - no_errors tier1 83 8 8.7 151 74 32.89 11 9 45 415172 TCGA-AB-2929 10 7831225 7831225 C T SNP ITIH2 NM_002216.2 human genbank 54_36p 1 validated silent c.2763 p.N921 1 HMMPfam_ITI_HC_C "HMMPfam_VWA,HMMSmart_VWA,HMMSmart_VIT,HMMPfam_ITI_HC_C,HMMPfam_VIT,superfamily_SSF53300" - no_errors tier1 59 4 6.35 78 61 43.57 10 11 52.38 415172 TCGA-AB-2929 2 11717629 11717629 G A SNP NTSR2 NM_012344.3 human genbank 54_36p -1 reviewed missense c.980 p.A327V 0.001 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 47 0 71 26 26.26 NA 415172 TCGA-AB-2929 6 12233870 12233870 G A SNP HIVEP1 NM_002114.2 human genbank 54_36p 1 validated silent c.5856 p.S1952 0.006 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 41 1 2.38 50 30 37.5 10 6 37.5 415172 TCGA-AB-2929 11 18001042 18001042 C A SNP TPH1 NM_004179.1 human genbank 54_36p -1 provisional nonsense c.1039 p.G347* 1 "HMMPfam_Biopterin_H,superfamily_Aromatic aminoacid monoxygenases catalytic and oligomerization domains" "HMMPfam_ACT,PatternScan_BIOPTERIN_HYDROXYL,HMMPfam_Biopterin_H,superfamily_Aromatic aminoacid monoxygenases catalytic and oligomerization domains,superfamily_ACT-like" - no_errors tier1 83 3 3.49 94 60 38.96 1 1 50 415172 TCGA-AB-2929 11 19208937 19208937 A G SNP E2F8 NM_024680.2 human genbank 54_36p -1 validated missense c.1087 p.F363L 0 NULL "HMMPfam_E2F_TDP,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 89 5 5.21 101 77 42.31 4 2 33.33 415172 TCGA-AB-2929 12 25289551 25289551 C T SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.35 p.G12D 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 22 2 8 16 37 69.81 18 100 415172 TCGA-AB-2929 X 37820855 37820855 G A SNP SYTL5 NM_138780.1 human genbank 54_36p 1 provisional missense c.646 p.G216S 0.109 HMMPfam_RPH3A_effector "HMMPfam_C2,HMMSmart_C2,HMMPfam_RPH3A_effector,superfamily_C2_CaLB,superfamily_FYVE_PHD_ZnF" - no_errors tier1 84 4 4.55 131 77 36.84 NA 415172 TCGA-AB-2929 15 99245387 99245387 C T SNP ALDH1A3 NM_000693.2 human genbank 54_36p 1 reviewed missense c.292 p.R98W 0.96 "HMMPfam_Aldedh,superfamily_Aldehyde_DH/Histidinol_DH" "HMMPfam_Aldedh,PatternScan_ALDEHYDE_DEHYDR_CYS,PatternScan_ALDEHYDE_DEHYDR_GLU,superfamily_Aldehyde_DH/Histidinol_DH" - no_errors tier1 14 0 24 18 41.86 NA 415172 TCGA-AB-2929 X 105457450 105457450 G A SNP LOC644504 XM_001128075.1 human genbank 54_36p 1 model missense c.25 p.E9K 1 "HMMPfam_CHGN,superfamily_Nucleotide-diphospho-sugar transferases" "HMMPfam_CHGN,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 73 2 2.63 35 67 64.42 9 0 415172 TCGA-AB-2929 1 109821023 109821023 G A SNP SYPL2 NM_001040709.1 human genbank 54_36p 1 validated silent c.357 p.V119 1 HMMPfam_MARVEL HMMPfam_MARVEL - no_errors tier1 82 5 5.75 145 81 35.53 NA 415172 TCGA-AB-2929 9 116843181 116843181 G A SNP TNC NM_002160.2 human genbank 54_36p -1 validated missense c.5252 p.T1751I 0.001 "HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" "HMMPfam_Fibrinogen_C,HMMSmart_FBG,superfamily_Fibrinogen_a/b/g_C,HMMPfam_fn3,HMMSmart_FN3,HMMPfam_EGF,HMMSmart_EGF,superfamily_FN_III-like,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2" - no_errors tier1 97 2 2.02 173 116 40 16 10 38.46 415172 TCGA-AB-2929 11 123918146 123918146 G A SNP OR8B12 NM_001005195.1 human genbank 54_36p -1 provisional silent c.615 p.D205 0.006 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 68 0 133 38 22.09 NA 415172 TCGA-AB-2929 5 140773949 140773951 AGA - DEL PCDHGA10 NM_018913.2 human genbank 54_36p 1 reviewed in_frame_del c.1023_1025 p.E342in_frame_del 0.002:0.003:0.175 "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 415172 TCGA-AB-2929 5 149764445 149764445 G A SNP CD74 NM_001025159.1 human genbank 54_36p -1 validated missense c.616 p.P206S 0.002 "superfamily_Thyroglobulin type-1 domain,HMMPfam_MHCassoc_trimer,superfamily_Class II MHC-associated invariant chain ectoplasmic trimerization domain" "HMMPfam_Thyroglobulin_1,HMMSmart_SM00211,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin type-1 domain,HMMPfam_MHCassoc_trimer,superfamily_Class II MHC-associated invariant chain ectoplasmic trimerization domain,HMMPfam_MHC2-interact" - no_errors tier1 53 2 3.57 68 49 41.53 1915 2008 51.11 415172 TCGA-AB-2929 X 153958684 153958684 C T SNP BRCC3 NM_024332.1 human genbank 54_36p 1 reviewed nonsense c.241 p.R81* 1 "HMMPfam_Mov34,HMMSmart_SM00232,superfamily_JAB1/MPN domain" "HMMPfam_Mov34,HMMSmart_SM00232,superfamily_JAB1/MPN domain" - no_errors tier1 96 5 4.9 48 61 54.95 1 11 91.67 415172 TCGA-AB-2929 3 196875734 196875734 A G SNP ENSG00000214135 ENST00000397590 human ensembl 54_36p 1 known missense c.194 p.Y65C 1 "HMMPfam_FAD_binding_2,superfamily_SSF51905" "HMMPfam_FAD_binding_2,HMMPfam_Succ_DH_flav_C,superfamily_Succ_DH_flav_C,superfamily_SSF51905,superfamily_SSF56425" - no_start_codon:no_stop_codon tier1 8 0 15 7 31.82 4 0 415172 TCGA-AB-2929 2 197975079 197975079 T C SNP SF3B1 NM_012433.1 human genbank 54_36p -1 reviewed missense c.2098 p.K700E 1 "HMMPfam_HEAT,superfamily_ARM repeat" "HMMPfam_HEAT,HMMPfam_SF3b1,superfamily_ARM repeat" - no_errors tier1 44 0 57 57 49.57 291 258 46.99 617776 TCGA-AB-2930 12 5025095 5025095 C A SNP KCNA5 NM_002234.2 human genbank 54_36p 1 reviewed silent c.1521 p.T507 1 "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" "HMMSmart_SM00225,HMMPfam_K_tetra,HMMPfam_Ion_trans,superfamily_POZ domain,superfamily_Voltage-gated potassium channels" - no_errors tier1 31 2 6.06 22 18 45 1 2 66.67 617776 TCGA-AB-2930 11 7774959 7774960 - ATATGGTTACCAGGTAGATGC INS OR5P2 NM_153444.1 human genbank 54_36p -1 provisional in_frame_ins c.107_106 p.36in_frame_insCIYLVTI 0.149:0.139 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 NA NA NA NA NA NA NA NA NA 617776 TCGA-AB-2930 19 20937274 20937275 - G INS KRT18P40 XR_017288.1 human genbank 54_36p 1 model rna NULL NULL 0.997:1.000 - - - pseudogene tier1 NA NA NA NA NA NA NA NA NA 617776 TCGA-AB-2930 13 27506273 27506274 - GAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTACC INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1783_1782 p.594in_frame_insGTGSSDNEYFYVDF 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 617776 TCGA-AB-2930 11 32374517 32374518 - A INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1111_1110 p.V370fs 1.000:0.986 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 617776 TCGA-AB-2930 11 32374521 32374522 - C INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1107_1106 p.R370fs 0.458:0.832 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 617776 TCGA-AB-2930 4 35825560 35825563 CTTA - DEL ARAP2 NM_015230.2 human genbank 54_36p -1 reviewed splice_site_del c.3199+2_3199+1 e17+2 0.990:0.994:0.996:1.000 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 617776 TCGA-AB-2930 1 47387010 47387010 G A SNP CYP4A22 NM_001010969.2 human genbank 54_36p 1 reviewed missense c.1514 p.R505H 0.934 "HMMPfam_p450,superfamily_Cytochrome P450" "HMMPfam_p450,superfamily_Cytochrome P450,PatternScan_CYTOCHROME_P450" - no_errors tier1 76 4 5 36 41 53.25 NA 617776 TCGA-AB-2930 X 54973336 54973336 G A SNP TRO NM_001039705.1 human genbank 54_36p 1 reviewed missense c.3454 p.A1152T 0.002 NULL HMMPfam_MAGE - no_errors tier1 34 2 5.56 47 28 37.33 3 100 617776 TCGA-AB-2930 19 61425905 61425905 T C SNP ZSCAN5A NM_024303.1 human genbank 54_36p -1 provisional silent c.606 p.L202 0.014 NULL "HMMPfam_SCAN,HMMSmart_SCAN,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 68 6 8.11 56 56 50 6 6 50 617776 TCGA-AB-2930 11 66395519 66395519 G A SNP PC NM_000920.3 human genbank 54_36p -1 reviewed silent c.330 p.N110 0.244 "HMMPfam_CPSase_L_chain,superfamily_PreATP-grasp-like" "HMMPfam_Biotin_lipoyl,HMMPfam_HMGL-like,PatternScan_BIOTIN,HMMPfam_PYC_OADA,HMMPfam_CPSase_L_D2,HMMPfam_CPSase_L_chain,HMMPfam_Biotin_carb_C,superfamily_Hybrid_motif,superfamily_Rudmnt_hyb_motif,superfamily_PreATP-grasp-like,superfamily_SSF51569,superfamily_SSF56059,superfamily_SSF89000" - no_errors tier1 20 1 4.76 4 6 60 2 100 617776 TCGA-AB-2930 10 82029970 82029970 C T SNP MAT1A NM_000429.2 human genbank 54_36p -1 reviewed missense c.488 p.R163Q 0.977 "HMMPfam_S-AdoMet_synt_M,superfamily_S-AdoMet_synt" "HMMPfam_S-AdoMet_synt_N,HMMPfam_S-AdoMet_synt_M,HMMPfam_S-AdoMet_synt_C,PatternScan_ADOMET_SYNTHETASE_1,PatternScan_ADOMET_SYNTHETASE_2,superfamily_S-AdoMet_synt" - no_errors tier1 67 7 9.09 33 54 62.07 NA 617776 TCGA-AB-2930 6 159867366 159867367 - TT INS LOC642738 XR_017625.2 human genbank 54_36p -1 model rna NULL NULL 1.000:1.000 - - - pseudogene tier1 NA NA NA NA NA NA NA NA NA 632729 TCGA-AB-2931 MT 913 913 T C SNP ENSG00000211459 ENST00000389680 human ensembl 54_36p 1 novel rna NULL NULL NULL - - - no_errors tier1 1758 146 7.66 37 632 94.47 NA NA NA 632729 TCGA-AB-2931 19 6658203 6658203 C T SNP C3 NM_000064.2 human genbank 54_36p -1 reviewed missense c.2129 p.R710Q 0.942 "HMMPfam_ANATO,HMMSmart_SM00104,PatternScan_ANAPHYLATOXIN_1,superfamily_Anaphylotoxins (complement system)" "HMMPfam_ANATO,HMMSmart_SM00104,PatternScan_ANAPHYLATOXIN_1,HMMPfam_A2M,HMMPfam_A2M_N,superfamily_Terpenoid cyclases/Protein prenyltransferases,superfamily_TIMP-like,HMMPfam_A2M_recep,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_N_2,HMMPfam_A2M_comp,superfamily_Anaphylotoxins (complement system),HMMPfam_NTR,HMMSmart_SM00643,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN" - no_errors tier1 88 2 2.22 21 19 47.5 NA 632729 TCGA-AB-2931 1 16214717 16214717 C T SNP HSPB7 NM_014424.4 human genbank 54_36p -1 validated missense c.458 p.R153H 0.906 "HMMPfam_HSP20,superfamily_HSP20-like chaperones" "HMMPfam_HSP20,superfamily_HSP20-like chaperones" - no_errors tier1 124 4 3.12 20 34 62.96 NA 632729 TCGA-AB-2931 2 25310747 25310747 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2644 p.R882C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 106 4 3.64 23 20 46.51 41 50 54.95 632729 TCGA-AB-2931 13 27506219 27506220 - AAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGCCCTG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1837_1836 p.612in_frame_insQGFYVDFREYEYDLKWEFPRENLEF 1.000:1.000 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 632729 TCGA-AB-2931 21 44845000 44845000 C T SNP KRTAP10-7 NM_198689.2 human genbank 54_36p 1 validated silent c.51 p.S17 0.002 NULL HMMPfam_Keratin_B2 - no_errors tier1 109 6 5.17 49 35 41.67 NA 632729 TCGA-AB-2931 5 56813496 56813496 A G SNP ACTBL2 NM_001017992.2 human genbank 54_36p -1 validated missense c.796 p.S266P 1 "HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain" "HMMPfam_Actin,HMMSmart_SM00268,PatternScan_ACTINS_ACT_LIKE,PatternScan_ACTINS_1,PatternScan_ACTINS_2,superfamily_Actin-like ATPase domain" - no_errors tier1 150 3 1.96 65 63 49.22 NA 632729 TCGA-AB-2931 19 61013186 61013186 T G SNP NLRP11 NM_145007.3 human genbank 54_36p -1 validated missense c.602 p.E201A 0.072 HMMPfam_NACHT "PatternScan_CU2_MONOOXYGENASE_1,HMMSmart_SM00368,HMMPfam_PAAD_DAPIN,HMMPfam_NACHT,superfamily_DEATH domain,superfamily_RNI-like" - no_errors tier1 167 14 7.73 74 56 43.08 NA 632729 TCGA-AB-2931 7 107618963 107618963 G A SNP NRCAM NM_001037132.1 human genbank 54_36p -1 reviewed missense c.1904 p.A635V 1 superfamily_Immunoglobulin "PatternScan_IG_MHC,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 63 2 3.08 53 31 36.9 NA 632729 TCGA-AB-2931 8 139766733 139766733 G A SNP COL22A1 NM_152888.1 human genbank 54_36p -1 validated missense c.2867 p.A956V 0.108 HMMPfam_Collagen "HMMPfam_VWA,HMMSmart_SM00327,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases,superfamily_vWA-like" - no_errors tier1 48 0 29 4 12.12 NA 632729 TCGA-AB-2931 7 142670742 142670742 C T SNP GSTK1 NM_015917.1 human genbank 54_36p 1 reviewed missense c.14 p.P5L 0.419 superfamily_Thioredoxin-like "HMMPfam_DSBA,superfamily_Thioredoxin-like" - no_errors tier1 69 0 30 43 58.9 115 117 50.21 632729 TCGA-AB-2931 6 152779761 152779761 C T SNP SYNE1 NM_182961.2 human genbank 54_36p -1 reviewed missense c.5504 p.R1835H 0.024 superfamily_Spectrin repeat "PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_Spectrin,HMMPfam_KASH,superfamily_Calponin-homology domain CH-domain,HMMSmart_SM00150,superfamily_Spectrin repeat" - no_errors tier1 303 9 2.88 119 115 49.15 1 0 632729 TCGA-AB-2931 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 635258 TCGA-AB-2932 11 20915949 20915949 C A SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed silent c.1039 p.R347 0.995 HMMSmart_SM00214 "PatternScan_ASX_HYDROXYL,HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMSmart_SM00282,HMMSmart_SM00179,HMMSmart_SM00210,HMMSmart_SM00181,HMMSmart_SM00215,superfamily_Concanavalin A-like lectins/glucanases,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 220 11 4.76 201 60 22.99 NA 635258 TCGA-AB-2932 18 27354841 27354841 T G SNP DSG2 NM_001943.3 human genbank 54_36p 1 reviewed silent c.294 p.P98 0.573 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,superfamily_Cadherin" - no_errors tier1 68 2 2.78 33 32 49.23 NA 635258 TCGA-AB-2932 9 33907176 33907178 GAG - DEL UBE2R2 NM_017811.3 human genbank 54_36p 1 reviewed in_frame_del c.658_660 p.E223in_frame_del 1.000:1.000:1.000 NULL "HMMPfam_UQ_con,HMMSmart_SM00212,PatternScan_UBIQUITIN_CONJUGAT_1,superfamily_UBC-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 635258 TCGA-AB-2932 3 39203923 39203923 C T SNP XIRP1 NM_194293.2 human genbank 54_36p -1 provisional missense c.2018 p.R673H 0 NULL HMMPfam_Xin - no_errors tier1 53 3 5.36 21 7 25 NA 635258 TCGA-AB-2932 3 47140156 47140157 - C INS SETD2 ENST00000409792 human ensembl 54_36p -1 known frame_shift_ins c.974_973 p.E325fs 1.000:1.000 NULL "HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain,HMMPfam_SET,HMMSmart_SM00317,HMMSmart_SM00508,HMMSmart_SM00570,superfamily_Ferritin-like,HMMPfam_SRI_2,PatternScan_ADH_IRON_1,superfamily_SET domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 635258 TCGA-AB-2932 1 115060267 115060267 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.38 p.G13D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 99 8 7.41 68 35 33.98 27 7 20.59 635258 TCGA-AB-2932 5 145524130 145524130 G C SNP LARS NM_020117.9 human genbank 54_36p -1 reviewed missense c.530 p.A177G 1 superfamily_Nucleotidylyl transferase "PatternScan_AA_TRNA_LIGASE_I,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases,HMMPfam_Anticodon_1,HMMPfam_tRNA-synt_1g,superfamily_Nucleotidylyl transferase" - no_errors tier1 92 8 8 67 45 40.18 21 23 52.27 635258 TCGA-AB-2932 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 470690 TCGA-AB-2933 21 35174748 35174748 T C SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.484 p.R162G 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 48 12 20 10 14 58.33 119 162 57.65 470690 TCGA-AB-2933 2 113327591 113327592 - G INS ENSG00000163098 ENST00000295249 human ensembl 54_36p 1 known frame_shift_ins c.93_94 p.L33fs 0.994:0.999 "HMMPfam_BIR,HMMSmart_BIR,superfamily_SSF57924" "HMMPfam_BIR,HMMSmart_BIR,superfamily_SSF57924" - no_errors tier1 NA NA NA NA NA NA NA NA NA 723101 TCGA-AB-2934 MT 15651 15651 G A SNP MT-CYB ENST00000361789 human ensembl 54_36p 1 known missense c.904 p.A302T NULL "HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C" "HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome" - no_stop_codon:bad_bp_length_for_coding_region tier1 3556 95 2.58 3813 714 15.61 NA NA NA 723101 TCGA-AB-2934 2 25316790 25316790 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2207 p.R736H 1 "HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 47 6 11.32 34 26 41.27 25 31 55.36 723101 TCGA-AB-2934 2 25318080 25318080 C A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.1937 p.G646V 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 30 1 3.23 60 36 37.5 27 14 34.15 723101 TCGA-AB-2934 13 27506257 27506258 - CATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTTAGGAGCCGGTCC INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1799_1798 p.600in_frame_insGTGS*DNEYFYVDFREYEY 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 723101 TCGA-AB-2934 X 40912334 40912335 - CG INS USP9X NM_001039590.2 human genbank 54_36p 1 reviewed frame_shift_ins c.2555_2556 p.V853fs 1.000:1.000 NULL "HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_Cysteine proteinases" - no_errors tier1 NA NA NA NA NA NA NA NA NA 723101 TCGA-AB-2934 9 68791992 68791992 A G SNP LOC100132672 XR_038504.1 human genbank 54_36p 1 model rna NULL NULL 0.998 - - - pseudogene tier1 24 0 121 27 18 NA 723101 TCGA-AB-2934 12 84897866 84897866 G T SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated missense c.769 p.L257I 1 HMMPfam_Glyco_transf_54 HMMPfam_Glyco_transf_54 - no_errors tier1 37 3 7.5 72 65 46.76 NA 723101 TCGA-AB-2934 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 69 2 2.82 59 51 46.36 93 82 46.86 723101 TCGA-AB-2934 X 104537558 104537558 C T SNP KCTD9P2 ENST00000313275 human ensembl 54_36p 1 known silent c.354 p.H118 1 "HMMSmart_BTB,HMMPfam_K_tetra,superfamily_BTB/POZ_fold" "HMMSmart_BTB,HMMPfam_K_tetra,superfamily_BTB/POZ_fold" - no_errors tier1 59 6 9.23 15 107 87.7 8 0 723101 TCGA-AB-2934 9 115225484 115225484 A G SNP C9orf43 NM_152786.1 human genbank 54_36p 1 predicted missense c.541 p.T181A 0 NULL NULL - no_errors tier1 101 8 7.34 120 106 46.09 NA 723101 TCGA-AB-2934 11 118536561 118536561 A G SNP ABCG4 NM_022169.1 human genbank 54_36p 1 reviewed missense c.1700 p.Y567C 1 HMMPfam_ABC2_membrane "HMMPfam_ABC_tran,HMMSmart_SM00382,HMMPfam_ABC2_membrane,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 86 3 3.33 135 66 32.84 NA 723101 TCGA-AB-2934 7 150280827 150280827 T G SNP KCNH2 NM_000238.2 human genbank 54_36p -1 reviewed silent c.1176 p.A392 0.899 NULL "HMMPfam_cNMP_binding,HMMSmart_SM00100,HMMSmart_SM00086,HMMPfam_Ion_trans,HMMPfam_PAS,superfamily_cAMP-binding domain-like,superfamily_PYP-like sensor domain (PAS domain),superfamily_Voltage-gated potassium channels" - no_errors tier1 42 3 6.67 43 41 47.67 1 1 50 723101 TCGA-AB-2934 2 172119343 172119343 G T SNP CYBRD1 ENST00000375252 human ensembl 54_36p 1 known missense c.412 p.D138Y 0.981 NULL "HMMPfam_Cytochrom_B561,PatternScan_SPASE_I_1" - no_errors tier1 66 9 12 130 109 45.23 63 29 31.52 729805 TCGA-AB-2935 MT 7622 7622 T C SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known silent c.36 p.A12 NULL "HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 2128 3 0.14 3464 518 12.9 NA NA NA 729805 TCGA-AB-2935 17 7518263 7518263 C T SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.743 p.R248Q 1 "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 254 5 1.93 321 283 46.47 14 79 84.95 729805 TCGA-AB-2935 20 19904215 19904215 C T SNP RIN2 NM_018993.2 human genbank 54_36p 1 reviewed missense c.1546 p.R516C 0.801 NULL "HMMPfam_RA,HMMSmart_SM00314,HMMPfam_VPS9,HMMSmart_SM00167,superfamily_VPS9 domain (Pfam 02204),superfamily_SH2 domain" - no_errors tier1 67 0 198 78 28.26 6 6 50 729805 TCGA-AB-2935 15 26062848 26062848 G T SNP HERC2 NM_004667.4 human genbank 54_36p -1 validated missense c.11269 p.L3757M 0.998 NULL "HMMPfam_RCC1,PatternScan_RCC1_2,HMMPfam_ZZ,HMMSmart_SM00291,PatternScan_ZF_ZZ_1,HMMPfam_HECT,HMMSmart_SM00119,superfamily_Hect E3 ligase catalytic domain,HMMPfam_Cyt-b5,superfamily_Cytochrome b5-like heme/steroid binding domain,HMMSmart_SM00706,superfamily_Galactose-binding domain-like,superfamily_RCC1/BLIP-II,HMMPfam_MIB_HERC2,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 109 0 185 71 27.73 24 14 36.84 729805 TCGA-AB-2935 11 26620060 26620060 G C SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated missense c.2183 p.G728A 0.983 HMMPfam_DUF590 HMMPfam_DUF590 - no_errors tier1 283 0 364 144 28.24 NA 729805 TCGA-AB-2935 1 35023379 35023379 C G SNP GJB3 NM_001005752.1 human genbank 54_36p 1 reviewed missense c.429 p.F143L 0.072 HMMPfam_Connexin_CCC "HMMPfam_Connexin,HMMSmart_SM00037,PatternScan_CONNEXINS_1,PatternScan_CONNEXINS_2,HMMPfam_Connexin_CCC" - no_errors tier1 264 2 0.75 396 148 26.81 1 100 729805 TCGA-AB-2935 13 38350970 38350970 C T SNP FREM2 NM_207361.4 human genbank 54_36p 1 reviewed silent c.8862 p.D2954 1 NULL "HMMPfam_Calx-beta,HMMSmart_SM00237" - no_errors tier1 184 1 0.54 208 75 26.41 NA 729805 TCGA-AB-2935 4 43107115 43107115 G A SNP LOC441013 XR_016299.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 113 1 0.88 209 79 27.34 NA 729805 TCGA-AB-2935 10 45258945 45258945 C T SNP ALOX5 NM_000698.2 human genbank 54_36p 1 reviewed silent c.1527 p.F509 0.944 "HMMPfam_Lipoxygenase,superfamily_Lipoxygenase" "HMMPfam_PLAT,HMMSmart_LH2,superfamily_Lipase_LipOase,HMMPfam_Lipoxygenase,PatternScan_LIPOXYGENASE_2,PatternScan_LIPOXYGENASE_1,superfamily_Lipoxygenase" - no_errors tier1 36 0 124 45 26.32 30 15 32.61 729805 TCGA-AB-2935 19 49625375 49625375 G C SNP ZNF229 NM_014518.2 human genbank 54_36p -1 validated missense c.1421 p.S474C 0.205 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 206 0 276 135 32.61 4 2 33.33 729805 TCGA-AB-2935 3 49871771 49871771 C T SNP CAMKV NM_024046.3 human genbank 54_36p -1 validated missense c.1490 p.R497K 0.693 NULL "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" - no_errors tier1 82 0 137 58 29.29 NA 729805 TCGA-AB-2935 10 94956679 94956679 G A SNP LOC387703 XR_016730.2 human genbank 54_36p -1 model rna NULL NULL 0.943 - - - pseudogene tier1 201 3 1.46 410 277 39.86 NA 729805 TCGA-AB-2935 X 119271326 119271326 A C SNP ZBTB33 NM_006777.3 human genbank 54_36p 1 validated missense c.28 p.T10P 1 superfamily_POZ domain "HMMSmart_SM00225,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_POZ domain,HMMPfam_BTB,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 122 2 1.61 47 63 57.27 1 19 95 766126 TCGA-AB-2936 MT 9554 9554 G A SNP MT-CO3 ENST00000362079 human ensembl 54_36p 1 known nonsense c.347 p.W116* NULL "HMMPfam_COX3,superfamily_CytC_oxdse_III" "HMMPfam_COX3,superfamily_CytC_oxdse_III" - no_stop_codon:bad_bp_length_for_coding_region tier1 6797 88 1.27 321 82 20.3 NA NA NA 766126 TCGA-AB-2936 19 8669551 8669551 G A SNP MGC33407 NM_178525.3 human genbank 54_36p -1 validated silent c.501 p.F167 1 "HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain" "PatternScan_N6_MTASE,HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain" - no_errors tier1 171 3 1.71 21 18 46.15 NA 766126 TCGA-AB-2936 19 9949363 9949363 C T SNP COL5A3 NM_015719.3 human genbank 54_36p -1 reviewed silent c.3033 p.E1011 1 NULL "HMMPfam_COLFI,HMMSmart_SM00038,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2" - no_errors tier1 1196 27 2.19 80 68 45.95 NA 766126 TCGA-AB-2936 21 35093477 35093477 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed nonsense c.958 p.R320* 1 NULL "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 218 1 0.45 30 11 26.83 701 275 28.12 766126 TCGA-AB-2936 7 40201173 40201173 G T SNP C7orf10 NM_024728.1 human genbank 54_36p 1 predicted missense c.383 p.C128F 1 "HMMPfam_CoA_transf_3,superfamily_CoA-Trfase_fam_III" "HMMPfam_CoA_transf_3,superfamily_CoA-Trfase_fam_III" - no_errors tier1 562 18 3.05 70 30 29.7 NA 766126 TCGA-AB-2936 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 339 9 2.55 28 18 39.13 162 154 48.73 766126 TCGA-AB-2936 X 101282737 101282737 C A SNP TCEAL6 NM_001006938.2 human genbank 54_36p -1 validated nonsense c.223 p.E75* 0.009 HMMPfam_TFA HMMPfam_TFA - no_errors tier1 339 10 2.86 82 61 42.36 1 0 766126 TCGA-AB-2936 X 101511581 101511581 G A SNP NXF2B NM_001099686.1 human genbank 54_36p -1 inferred silent c.192 p.S64 0 NULL "HMMPfam_NTF2,HMMPfam_TAP_C,HMMSmart_TAP_C,superfamily_UBA_like,HMMPfam_Tap-RNA_bind,superfamily_SSF52058,superfamily_SSF54427,superfamily_SSF54928" - no_errors tier1 186 1 0.53 11 8 42.11 NA 766126 TCGA-AB-2936 5 110738461 110738461 C T SNP CAMK4 NM_001744.3 human genbank 54_36p 1 reviewed silent c.255 p.I85 0.982 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 703 10 1.38 70 69 49.64 16 0 766126 TCGA-AB-2936 7 129136160 129136160 C T SNP NRF1 NM_001040110.1 human genbank 54_36p 1 reviewed missense c.616 p.R206W 1 HMMPfam_Nrf1_DNA-bind "HMMPfam_Nrf1_DNA-bind,HMMPfam_Nrf1_activ_bdg" - no_errors tier1 723 20 2.68 90 47 33.81 20 26 56.52 766126 TCGA-AB-2936 1 239979605 239979605 G C SNP WDR64 NM_144625.3 human genbank 54_36p 1 validated silent c.858 p.L286 0.03 superfamily_WD40 repeat-like "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" - no_errors tier1 856 7 0.81 82 58 41.43 NA 514066 TCGA-AB-2937 MT 11462 11462 A G SNP MT-ND4 ENST00000361381 human ensembl 54_36p 1 known silent c.702 p.V234 NULL HMMPfam_Oxidored_q1 "HMMPfam_Oxidored_q5_N,HMMPfam_Oxidored_q1" - no_stop_codon:bad_bp_length_for_coding_region tier1 1213 16 1.3 2519 360 12.47 NA NA NA 514066 TCGA-AB-2937 NT_113923 88049 88050 G A SNP ENSG00000216522 ENST00000402757 human ensembl 54_36p -1 known splice_site c.733-1 e6-1 NULL - - - no_errors tier1 73 2 2.67 21 18 46.15 NA NA NA 514066 TCGA-AB-2937 17 11495324 11495324 C T SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed missense c.2311 p.R771C 0.002 HMMPfam_DHC_N1 "HMMSmart_SM00382,HMMPfam_Dynein_heavy,PatternScan_CPSASE_2,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 148 4 2.63 31 29 48.33 NA 514066 TCGA-AB-2937 6 32009522 32009522 C T SNP C2 NM_000063.4 human genbank 54_36p 1 reviewed missense c.599 p.T200M 0.933 "HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain" "HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Trypsin,HMMSmart_SM00020,HMMPfam_VWA,HMMSmart_SM00327,superfamily_Trypsin-like serine proteases,superfamily_Complement control module/SCR domain,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER,superfamily_vWA-like" - no_errors tier1 99 2 1.98 15 22 59.46 5 0 514066 TCGA-AB-2937 6 47789760 47789760 C T SNP GPR115 NM_153838.3 human genbank 54_36p 1 validated nonsense c.820 p.Q274* 0.042 NULL HMMPfam_7tm_2 - no_errors tier1 156 7 4.29 36 24 40 NA 514066 TCGA-AB-2937 4 55294078 55294078 A T SNP KIT NM_000222.2 human genbank 54_36p 1 reviewed missense c.2447 p.D816V 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 54 2 3.57 35 28 44.44 44 49 52.69 514066 TCGA-AB-2937 7 70768465 70768465 G A SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed nonsense c.1214 p.W405* 1 superfamily_Nucleotide-diphospho-sugar transferases "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,HMMPfam_Glycos_transf_2,superfamily_Ricin B-like lectins,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 259 9 3.36 49 36 42.35 NA 514066 TCGA-AB-2937 17 75936028 75936028 G C SNP RNF213 NM_020914.3 human genbank 54_36p 1 validated missense c.3517 p.V1173L 1 NULL "HMMSmart_SM00184,HMMSmart_SM00382,HMMPfam_zf-C3HC4,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_RING/U-box" - no_errors tier1 65 2 2.99 22 10 31.25 40 31 43.66 514066 TCGA-AB-2937 8 77926663 77926663 G C SNP ZFHX4 NM_024721.3 human genbank 54_36p 1 validated missense c.4816 p.D1606H 0.99 NULL "HMMPfam_Homeobox,HMMSmart_SM00389,HMMSmart_SM00451,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Homeodomain-like,HMMSmart_SM00355,PatternScan_HOMEOBOX_1,PatternScan_SOMATOTROPIN_2,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 290 5 1.69 73 51 41.13 NA 514066 TCGA-AB-2937 9 85781728 85781729 - T INS HNRNPK NM_002140.3 human genbank 54_36p -1 reviewed splice_site_ins c.213+1_213+1 e3+1 1.000:1.000 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 514066 TCGA-AB-2937 9 85781729 85781730 - TA INS HNRNPK NM_002140.3 human genbank 54_36p -1 reviewed frame_shift_ins c.214_213 p.N72fs 1.000:1.000 "HMMSmart_SM00322,HMMPfam_KH_1,superfamily_Eukaryotic type KH-domain (KH-domain type I)" "HMMSmart_SM00322,HMMPfam_ROKNT,HMMPfam_KH_1,superfamily_Eukaryotic type KH-domain (KH-domain type I)" - no_errors tier1 NA NA NA NA NA NA NA NA NA 514066 TCGA-AB-2937 13 100075849 100075849 G A SNP TMTC4 NM_032813.1 human genbank 54_36p -1 validated missense c.1777 p.R593W 1 "HMMPfam_TPR_1,HMMSmart_SM00028,superfamily_TPR-like" "HMMPfam_TPR_1,HMMPfam_TPR_2,HMMPfam_DUF1736,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 282 17 5.69 65 42 39.25 9 9 50 514066 TCGA-AB-2937 4 106374923 106374923 C - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.375 p.F125fs 0.6 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 514066 TCGA-AB-2937 7 142670736 142670736 C A SNP GSTK1 NM_015917.1 human genbank 54_36p 1 reviewed missense c.8 p.P3H 0.294 superfamily_Thioredoxin-like "HMMPfam_DSBA,superfamily_Thioredoxin-like" - no_errors tier1 103 2 1.9 24 21 46.67 156 103 39.77 530962 TCGA-AB-2938 7 5908853 5908853 C T SNP C7orf28A NM_015622.5 human genbank 54_36p 1 validated silent c.474 p.D158 1 HMMPfam_DUF2049 HMMPfam_DUF2049 - no_errors tier1 37 0 72 20 21.74 13 1 7.14 530962 TCGA-AB-2938 17 7514728 7514728 G - DEL TP53 NM_000546.4 human genbank 54_36p -1 reviewed frame_shift_del c.1024 p.R342fs 0.397 "HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 NA NA NA NA NA NA NA NA NA 530962 TCGA-AB-2938 17 7519119 7519119 T C SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.536 p.H179R 0.999 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 65 0 62 91 59.09 28 160 85.11 530962 TCGA-AB-2938 19 8275962 8275962 C G SNP CD320 NM_016579.2 human genbank 54_36p -1 validated missense c.221 p.C74S 0.974 "HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich" "HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich" - no_errors tier1 35 0 21 29 58 11 45 80.36 530962 TCGA-AB-2938 19 11317305 11317305 C G SNP TMEM205 ENST00000222124 human ensembl 54_36p -1 known splice_site c.1-1 e1-1 0.166 - - - no_errors tier1 115 0 214 25 10.42 46 10 17.86 530962 TCGA-AB-2938 8 12997037 12997037 G A SNP DLC1 NM_182643.3 human genbank 54_36p -1 reviewed missense c.3256 p.R1086C 1 superfamily_GTPase activation domain GAP "HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_START,HMMSmart_SM00234,superfamily_GTPase activation domain GAP,HMMPfam_SAM_2,superfamily_Bet v1-like" - no_errors tier1 107 0 51 26 33.77 109 95 46.34 530962 TCGA-AB-2938 13 18649444 18649444 G T SNP TUBA3C NM_006001.1 human genbank 54_36p -1 reviewed missense c.679 p.L227I 1 "HMMPfam_Tubulin,superfamily_Tubulin nucleotide-binding domain-like" "HMMPfam_Tubulin,superfamily_Tubulin C-terminal domain-like,PatternScan_TUBULIN,HMMPfam_Tubulin_C,superfamily_Tubulin nucleotide-binding domain-like" - no_errors tier1 58 0 50 13 20.63 NA 530962 TCGA-AB-2938 2 25324035 25324035 T - DEL DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed frame_shift_del c.943 p.M315fs 1 "HMMPfam_PWWP,HMMSmart_SM00293,superfamily_Tudor/PWWP/MBT" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 NA NA NA NA NA NA NA NA NA 530962 TCGA-AB-2938 6 30995886 30995886 G A SNP VARS2 NM_020442.3 human genbank 54_36p 1 provisional missense c.1207 p.E403K 0.997 "HMMPfam_tRNA-synt_1,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Nucleotidylyl transferase" "PatternScan_AA_TRNA_LIGASE_I,HMMPfam_tRNA-synt_1,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases,HMMPfam_Anticodon_1,superfamily_Nucleotidylyl transferase" - no_errors tier1 75 0 56 19 25.33 13 4 23.53 530962 TCGA-AB-2938 15 42482414 42482414 G A SNP CASC4 NM_138423.2 human genbank 54_36p 1 reviewed silent c.1110 p.P370 1 NULL NULL - no_errors tier1 53 0 67 32 31.68 11 22 66.67 530962 TCGA-AB-2938 6 43331348 43331348 G T SNP TTBK1 NM_032538.1 human genbank 54_36p 1 validated missense c.723 p.K241N 1 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)" "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 97 0 38 10 20.83 NA 530962 TCGA-AB-2938 6 58554097 58554097 G T SNP LOC727842 XR_015140.2 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 93 0 69 27 27.84 NA 530962 TCGA-AB-2938 19 59099782 59099782 C T SNP PRKCG NM_002739.3 human genbank 54_36p 1 reviewed missense c.1738 p.R580W 0.993 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMPfam_C2,HMMSmart_C2,HMMSmart_S_TK_X,HMMPfam_C1_1,HMMSmart_C1,PatternScan_ZF_DAG_PE_1,HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_C2_CaLB,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,HMMPfam_Pkinase_C,superfamily_SSF57889" - no_errors tier1 115 0 74 19 20.43 NA 530962 TCGA-AB-2938 16 66469944 66469944 C T SNP EDC4 NM_014329.3 human genbank 54_36p 1 validated missense c.1093 p.P365S 1 "HMMSmart_SM00320,superfamily_WD40 repeat-like" "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" - no_errors tier1 125 0 52 15 22.39 74 45 37.82 530962 TCGA-AB-2938 3 76069431 76069431 G A SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known missense c.97 p.G33R 0.742 NULL "HMMSmart_IGc2,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,superfamily_SSF48726" - no_stop_codon:overly_large_intron tier1 161 0 291 59 16.86 NA 530962 TCGA-AB-2938 14 79341275 79341275 A G SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed missense c.2873 p.E958G 0.998 NULL "PatternScan_ASX_HYDROXYL,HMMSmart_LamG,HMMSmart_4.1m,HMMPfam_EGF,HMMSmart_EGF,superfamily_ConA_like_lec_gl,HMMPfam_Laminin_G_2" - no_errors tier1 236 1 0.42 194 88 31.21 2 0 530962 TCGA-AB-2938 11 116569108 116569108 A G SNP SIDT2 NM_001040455.1 human genbank 54_36p 1 validated missense c.2135 p.N712S 1 NULL NULL - no_errors tier1 44 0 40 13 24.07 60 24 28.57 530962 TCGA-AB-2938 11 123917988 123917988 T C SNP OR8B12 NM_001005195.1 human genbank 54_36p -1 provisional missense c.773 p.Y258C 0.223 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 67 0 96 27 21.77 NA 530962 TCGA-AB-2938 9 137854321 137854321 T C SNP CAMSAP1 NM_015447.3 human genbank 54_36p -1 validated silent c.1173 p.P391 0 NULL "superfamily_PRC-barrel domain,HMMPfam_DUF1781" - no_errors tier1 22 0 37 14 26.92 13 4 23.53 530962 TCGA-AB-2938 3 139957479 139957479 C T SNP PIK3CB NM_006219.1 human genbank 54_36p -1 provisional missense c.204 p.M68I 1 "HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B" "HMMPfam_PI3K_rbd,HMMSmart_PI3K_rbd,HMMPfam_PI3_PI4_kinase,HMMSmart_PI3Kc,HMMPfam_PI3Ka,HMMSmart_PI3Ka,HMMPfam_PI3K_C2,HMMSmart_PI3K_C2,HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B,superfamily_C2_CaLB,superfamily_Kinase_like,superfamily_ARM-type_fold,PatternScan_PI3_4_KINASE_1,PatternScan_PI3_4_KINASE_2,superfamily_SSF54236" - no_errors tier1 78 0 104 40 27.59 106 103 49.28 530962 TCGA-AB-2938 4 147026748 147026748 G - DEL ZNF827 NM_178835.3 human genbank 54_36p -1 validated frame_shift_del c.1279 p.Q427fs 1 superfamily_SSF57667 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 NA NA NA NA NA NA NA NA NA 530962 TCGA-AB-2938 7 148088455 148088455 G T SNP CUL1 NM_003592.2 human genbank 54_36p 1 validated missense c.723 p.E241D 0.997 "HMMPfam_Cullin,superfamily_Cullin repeat" "HMMPfam_Cullin,PatternScan_CULLIN_1,HMMSmart_SM00182,superfamily_Cullin homology domain,superfamily_Cullin repeat,HMMPfam_Cullin_Nedd8,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 53 0 49 27 35.53 14 11 44 530962 TCGA-AB-2938 1 154980220 154980220 C T SNP HDGF NM_004494.1 human genbank 54_36p -1 reviewed silent c.564 p.E188 0.286 NULL "HMMPfam_PWWP,HMMSmart_PWWP,superfamily_SSF63748" - no_errors tier1 254 0 110 32 22.07 268 330 55.18 530962 TCGA-AB-2938 4 186781669 186781669 G A SNP SORBS2 NM_021069.1 human genbank 54_36p -1 reviewed silent c.1896 p.S632 0.811 NULL "HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_Sorb,HMMSmart_SM00459,PatternScan_ZINC_FINGER_C2H2_1" - no_errors tier1 42 0 38 14 26.92 0 767969 TCGA-AB-2939 MT 7655 7655 T C SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known silent c.69 p.F23 NULL "HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 4863 43 0.87 1793 746 29.13 NA NA NA 767969 TCGA-AB-2939 MT 9968 9968 T C SNP MT-CO3 ENST00000362079 human ensembl 54_36p 1 known missense c.761 p.V254A NULL "HMMPfam_COX3,superfamily_CytC_oxdse_III" "HMMPfam_COX3,superfamily_CytC_oxdse_III" - no_stop_codon:bad_bp_length_for_coding_region tier1 7147 145 1.97 1641 2713 61.67 NA NA NA 767969 TCGA-AB-2939 16 3059298 3059299 - G INS IL32 NM_001012631.1 human genbank 54_36p 1 reviewed frame_shift_ins c.508_509 p.D172fs 0.001:0.001 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 767969 TCGA-AB-2939 11 11355462 11355462 G A SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated missense c.820 p.R274W 0.981 "HMMPfam_Glycos_transf_2,superfamily_Nucleotide-diphospho-sugar transferases" "HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,HMMPfam_Glycos_transf_2,superfamily_Ricin B-like lectins,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 96 1 1.03 178 153 45.81 NA 767969 TCGA-AB-2939 7 12610771 12610771 A C SNP SCIN ENST00000297029 human ensembl 54_36p 1 known silent c.624 p.L208 0.066 "HMMSmart_SM00262,HMMPfam_Gelsolin,superfamily_Actin depolymerizing proteins" "HMMSmart_SM00262,HMMPfam_Gelsolin,superfamily_Actin depolymerizing proteins,superfamily_C-terminal gelsolin-like domain of Sec23/24" - no_errors tier1 94 0 158 126 43.75 1 100 767969 TCGA-AB-2939 12 25647538 25647538 G A SNP ENSG00000209624 ENST00000386889 human ensembl 54_36p -1 novel rna NULL NULL 0.013 - - - pseudogene tier1 156 7 4.27 134 108 43.72 NA 767969 TCGA-AB-2939 13 27543084 27543085 TG - DEL LOC100133684 XM_001716774.1 human genbank 54_36p -1 model frame_shift_del c.1040_1039 p.T347fs 0.000:0.000 NULL NULL - no_start_codon:pseudogene:no_stop_codon tier1 NA NA NA NA NA NA NA NA NA 767969 TCGA-AB-2939 11 33529297 33529297 C A SNP C11orf41 NM_012194.1 human genbank 54_36p 1 validated missense c.2764 p.Q922K 1 NULL NULL - no_errors tier1 178 8 4.23 92 91 49.46 NA 767969 TCGA-AB-2939 X 34059994 34059994 G A SNP FAM47A NM_203408.2 human genbank 54_36p -1 predicted missense c.323 p.S108F 0.038 NULL NULL - no_errors tier1 41 0 10 118 91.47 NA 767969 TCGA-AB-2939 3 45798633 45798633 G A SNP SLC6A20 NM_020208.3 human genbank 54_36p -1 reviewed missense c.208 p.R70W 1 HMMPfam_SNF "HMMPfam_SNF,PatternScan_NA_NEUROTRAN_SYMP_1,PatternScan_NA_NEUROTRAN_SYMP_2" - no_errors tier1 92 2 2.11 90 71 43.03 NA 767969 TCGA-AB-2939 12 47711634 47711634 A T SNP MLL2 NM_003482.3 human genbank 54_36p -1 validated missense c.13121 p.L4374Q 0.599 NULL "HMMPfam_HMG_box,HMMSmart_SM00398,HMMPfam_SET,HMMSmart_SM00317,HMMSmart_SM00184,HMMSmart_SM00249,HMMSmart_SM00508,HMMPfam_FYRN,HMMPfam_FYRC,PatternScan_RECOMBINASES_2,superfamily_HMG-box,superfamily_FYVE/PHD zinc finger,HMMSmart_SM00542,HMMSmart_SM00541,PatternScan_ZF_PHD_1,HMMPfam_PHD,superfamily_SET domain" - no_errors tier1 25 1 3.85 49 47 48.96 66 75 53.19 767969 TCGA-AB-2939 X 48519332 48519332 C G SNP LOC648603 XR_038238.1 human genbank 54_36p -1 model rna NULL NULL 0 - - - pseudogene tier1 98 6 5.71 5 191 95.98 5 5 50 767969 TCGA-AB-2939 12 51383390 51383390 C T SNP KRT77 NM_175078.2 human genbank 54_36p -1 validated silent c.96 p.P32 0 NULL "HMMPfam_Filament,PatternScan_IF" - no_errors tier1 179 4 2.17 105 74 41.34 NA 767969 TCGA-AB-2939 4 54059577 54059577 G A SNP LNX1 NM_032622.1 human genbank 54_36p -1 reviewed silent c.678 p.D226 1 "HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ" "HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ" - no_errors tier1 200 5 2.44 187 144 42.86 NA 767969 TCGA-AB-2939 4 55294078 55294078 A T SNP KIT NM_000222.2 human genbank 54_36p 1 reviewed missense c.2447 p.D816V 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 65 0 57 70 55.12 731 747 50.54 767969 TCGA-AB-2939 19 56786070 56786071 - CACCTG INS LOC100132800 XM_001724852.1 human genbank 54_36p 1 model in_frame_ins c.45_46 p.17in_frame_insHL 0.099:0.155 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 767969 TCGA-AB-2939 17 62504938 62504938 C A SNP HELZ NM_014877.3 human genbank 54_36p -1 validated missense c.5721 p.R1907S 0.998 NULL "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,HMMPfam_PAM2,superfamily_SSF52540,superfamily_SSF90229" - no_errors tier1 23 1 4 36 44 54.32 15 27 62.79 767969 TCGA-AB-2939 6 84291097 84291097 C T SNP PRSS35 NM_153362.1 human genbank 54_36p 1 provisional silent c.1218 p.N406 1 NULL "HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER" - no_errors tier1 90 1 1.1 154 128 45.07 NA 767969 TCGA-AB-2939 1 148522482 148522482 C A SNP C1orf51 NM_144697.2 human genbank 54_36p 1 predicted missense c.181 p.P61T 0.959 NULL NULL - no_errors tier1 283 3 1.05 334 268 44.37 NA 767969 TCGA-AB-2939 1 165228637 165228637 T C SNP MAEL NM_032858.1 human genbank 54_36p 1 validated missense c.416 p.I139T 1 HMMPfam_DUF1898 "superfamily_HMG-box,HMMPfam_DUF1898" - no_errors tier1 94 3 3.09 111 124 51.45 3 100 767969 TCGA-AB-2939 3 166216448 166216448 A G SNP SI NM_001041.2 human genbank 54_36p -1 validated missense c.3874 p.Y1292H 1 "HMMPfam_Glyco_hydro_31,superfamily_(Trans)glycosidases" "HMMPfam_Glyco_hydro_31,PatternScan_GLYCOSYL_HYDROL_F31_1,PatternScan_GLYCOSYL_HYDROL_F31_2,HMMPfam_Trefoil,HMMSmart_SM00018,superfamily_Trefoil,superfamily_(Trans)glycosidases,PatternScan_P_TREFOIL" - no_errors tier1 80 1 1.23 100 78 43.58 NA 767969 TCGA-AB-2939 2 230619146 230619146 G A SNP SLC16A14 NM_152527.3 human genbank 54_36p -1 provisional nonsense c.940 p.R314* 0.701 "HMMPfam_MFS_1,superfamily_MFS general substrate transporter" "HMMPfam_MFS_1,superfamily_MFS general substrate transporter" - no_errors tier1 135 3 2.16 116 67 36.41 11 7 38.89 593890 TCGA-AB-2940 17 7169461 7169461 C T SNP NEURL4 NM_032442.1 human genbank 54_36p -1 validated silent c.1422 p.G474 1 NULL "HMMPfam_Neuralized,HMMSmart_SM00588" - no_errors tier1 57 6 9.52 26 8 23.53 32 6 15.79 593890 TCGA-AB-2940 19 38484235 38484236 - CCA INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_ins c.926_925 p.309in_frame_insV 1.000:1.000 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 593890 TCGA-AB-2940 19 38485093 38485093 G - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_del c.68 p.P23fs 0.998 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 593890 TCGA-AB-2940 1 147939842 147939843 - C INS LOC729135 XR_039107.1 human genbank 54_36p -1 model rna NULL NULL 0.009:0.013 - - - pseudogene tier1 NA NA NA NA NA NA NA NA NA 593890 TCGA-AB-2940 7 151505094 151505094 C A SNP MLL3 NM_170606.2 human genbank 54_36p -1 reviewed nonsense c.8377 p.E2793* 0.943 NULL "PatternScan_HMGI_Y,HMMPfam_HMG_box,HMMSmart_SM00398,HMMPfam_SET,HMMSmart_SM00317,HMMSmart_SM00184,HMMSmart_SM00249,HMMSmart_SM00508,HMMPfam_FYRN,HMMPfam_FYRC,superfamily_FYVE/PHD zinc finger,HMMPfam_AT_hook,HMMSmart_SM00542,HMMSmart_SM00541,PatternScan_ZF_PHD_1,HMMPfam_PHD,PatternScan_ATPASE_ALPHA_BETA,superfamily_SET domain" - no_errors tier1 226 7 2.99 96 21 17.95 44 8 15.38 794178 TCGA-AB-2941 MT 13692 13692 A G SNP MT-ND5 ENST00000361567 human ensembl 54_36p 1 known missense c.1355 p.N452S NULL HMMPfam_NADH5_C "HMMPfam_Oxidored_q1_N,HMMPfam_Oxidored_q1,HMMPfam_NADH5_C" - no_errors tier1 1061 61 5.31 36 215 84.65 NA NA NA 794178 TCGA-AB-2941 17 7518990 7518990 A C SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.584 p.I195S 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 430 27 5.86 53 15 22.06 4 91 95.79 794178 TCGA-AB-2941 14 18961212 18961213 TG - DEL uc001vvs.1 ENST00000383038 human ensembl 54_36p -1 known frame_shift_del c.233_232 p.Q78fs 0.000:0.000 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 794178 TCGA-AB-2941 1 31917764 31917764 C T SNP COL16A1 ENST00000373668 human ensembl 54_36p -1 known nonsense c.2780 p.W927* 0.002 NULL "HMMSmart_TSPN,HMMPfam_Collagen,superfamily_ConA_like_lec_gl" - no_errors tier1 120 4 3.2 41 20 32.79 NA 794178 TCGA-AB-2941 21 32989378 32989378 T C SNP SYNJ1 NM_003895.2 human genbank 54_36p -1 validated missense c.565 p.I189V 1 HMMPfam_Syja_N "HMMSmart_SM00128,HMMPfam_Syja_N,HMMPfam_Exo_endo_phos,superfamily_DNase I-like,HMMPfam_DUF1866,superfamily_RNA-binding domain RBD" - no_errors tier1 262 32 10.77 52 35 39.77 20 27 57.45 794178 TCGA-AB-2941 7 62670184 62670184 G A SNP TNRC18 XM_376618.5 human genbank 54_36p -1 model missense c.1855 p.R619W 1 NULL NULL - pseudogene tier1 92 6 6.12 36 16 30.77 NA 794178 TCGA-AB-2941 X 102751098 102751098 A G SNP TCEAL3 NM_001006933.1 human genbank 54_36p 1 reviewed silent c.450 p.Q150 1 HMMPfam_TFA HMMPfam_TFA - no_errors tier1 206 8 3.67 120 38 24.05 14 0 794178 TCGA-AB-2941 6 123080792 123080792 C T SNP PKIB NM_032471.4 human genbank 54_36p 1 reviewed missense c.154 p.L52F 0.042 HMMPfam_PKI HMMPfam_PKI - no_errors tier1 143 4 2.72 61 32 34.41 NA 794178 TCGA-AB-2941 7 127456409 127456409 G A SNP LRRC4 NM_022143.4 human genbank 54_36p -1 validated silent c.1521 p.P507 0.948 NULL "HMMPfam_LRRNT,HMMSmart_SM00013,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 155 19 10.86 14 18 56.25 2 42 95.45 794178 TCGA-AB-2941 3 199332028 199332028 C T SNP LOC728247 XR_015241.2 human genbank 54_36p 1 model rna NULL NULL 0.431 - - - pseudogene tier1 69 1 1.43 30 11 26.83 NA 595704 TCGA-AB-2942 13 27506258 27506259 - TATTCATATTCTCTGAAATCAACG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1798_1797 p.DLKW599in_frame_insR* 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA NA NA 595704 TCGA-AB-2942 3 128878804 128878805 - C INS ABTB1 NM_172027.2 human genbank 54_36p 1 reviewed frame_shift_ins c.747_748 p.E251fs 1.000:1.000 NULL "HMMSmart_SM00225,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,superfamily_POZ domain,HMMPfam_BTB" - no_errors tier1 NA NA NA NA NA NA NA NA NA 806794 TCGA-AB-2943 MT 4598 4598 T C SNP MT-ND2 ENST00000361453 human ensembl 54_36p 1 known missense c.128 p.V43A NULL HMMPfam_Oxidored_q1 "HMMPfam_Oxidored_q1,HMMPfam_NADH_dehy_S2_C" - no_stop_codon:bad_bp_length_for_coding_region tier1 1171 9 0.75 633 302 32.06 NA NA NA 806794 TCGA-AB-2943 17 7517846 7517846 G A SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.817 p.R273C 0.797 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 98 7 6.54 46 144 74.61 17 137 88.96 806794 TCGA-AB-2943 10 12194961 12194961 T G SNP DHTKD1 NM_018706.5 human genbank 54_36p 1 validated silent c.2211 p.V737 0.112 "HMMPfam_Transket_pyr,superfamily_Thiamin diphosphate-binding fold (THDP-binding)" "HMMPfam_E1_dh,HMMPfam_Transket_pyr,superfamily_Thiamin diphosphate-binding fold (THDP-binding)" - no_errors tier1 183 0 161 52 24.19 19 7 26.92 806794 TCGA-AB-2943 1 12807570 12807570 C T SNP PRAMEF11 XM_001714837.1 human genbank 54_36p -1 model missense c.1358 p.R453H 0.033 NULL NULL - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 44 0 61 17 21.79 NA 806794 TCGA-AB-2943 1 21905663 21905663 C A SNP USP48 NM_032236.1 human genbank 54_36p -1 reviewed nonsense c.2095 p.E699* 1 NULL "HMMPfam_UCH,PatternScan_UCH_2_2,superfamily_Cysteine proteinases,superfamily_Ubiquitin-like" - no_errors tier1 120 0 146 165 52.72 56 53 48.62 806794 TCGA-AB-2943 13 27899448 27899448 G C SNP FLT1 NM_002019.3 human genbank 54_36p -1 validated silent c.1284 p.P428 0.997 superfamily_Immunoglobulin "HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_SM00220,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_Immunoglobulin" - no_errors tier1 70 0 109 34 23.61 2 0 806794 TCGA-AB-2943 6 34730508 34730508 T C SNP C6orf106 NM_024294.4 human genbank 54_36p -1 validated missense c.185 p.Y62C 1 superfamily_UBA-like superfamily_UBA-like - no_errors tier1 56 1 1.75 145 68 31.78 65 24 26.97 806794 TCGA-AB-2943 1 39780077 39780077 G C SNP LOC728448 NR_003929.2 human genbank 54_36p -1 validated rna NULL NULL 1 - - - pseudogene tier1 129 0 132 125 47.89 9 49 83.05 806794 TCGA-AB-2943 22 40330018 40330018 G T SNP PPPDE2 NM_015704.1 human genbank 54_36p -1 provisional missense c.266 p.S89Y 1 HMMPfam_DUF862 HMMPfam_DUF862 - no_errors tier1 57 1 1.72 97 25 20.16 179 28 13.53 806794 TCGA-AB-2943 10 51694780 51694780 C T SNP LOC728532 XR_015428.2 human genbank 54_36p 1 model rna NULL NULL 1 - - - pseudogene tier1 53 0 134 71 34.63 47 0 806794 TCGA-AB-2943 3 54905879 54905879 C A SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed nonsense c.2310 p.Y770* 1 NULL "HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Cache_1,HMMPfam_VWA_N,superfamily_vWA-like" - no_errors tier1 77 2 2.53 169 80 31.87 NA 806794 TCGA-AB-2943 19 62494825 62494825 A T SNP ZNF460 NM_006635.3 human genbank 54_36p 1 validated missense c.1104 p.Q368H 0.012 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 40 0 90 34 27.2 30 20 40 806794 TCGA-AB-2943 3 62553353 62553353 C T SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed missense c.1436 p.R479Q 0.998 HMMPfam_C2 "HMMPfam_C2,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_DUF1041,superfamily_PH domain-like" - no_errors tier1 107 0 161 38 19 NA 806794 TCGA-AB-2943 3 64060325 64060325 G A SNP PRICKLE2 NM_198859.3 human genbank 54_36p -1 validated silent c.1977 p.G659 0.036 NULL "HMMPfam_LIM,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,HMMPfam_PET,superfamily_SSF57716" - no_errors tier1 35 0 86 31 25.83 NA 806794 TCGA-AB-2943 3 89611262 89611262 G A SNP EPHA3 NM_005233.5 human genbank 54_36p 1 reviewed missense c.2872 p.V958M 0.994 "HMMSmart_SM00454,superfamily_SAM/Pointed domain,HMMPfam_SAM_2" "HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),HMMPfam_SAM_2,PatternScan_EGF_2,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 65 0 104 39 26.9 NA 806794 TCGA-AB-2943 14 94034210 94034210 C T SNP SERPINA12 NM_173850.2 human genbank 54_36p -1 provisional missense c.278 p.S93N 0.049 "HMMPfam_Serpin,HMMSmart_SERPIN,superfamily_Prot_inh_serpin" "HMMPfam_Serpin,HMMSmart_SERPIN,PatternScan_SERPIN,superfamily_Prot_inh_serpin" - no_errors tier1 112 0 162 72 30.64 NA 806794 TCGA-AB-2943 8 104137290 104137290 G T SNP ATP6V1C1 NM_001695.4 human genbank 54_36p 1 reviewed missense c.591 p.W197C 1 HMMPfam_V-ATPase_C HMMPfam_V-ATPase_C - no_errors tier1 54 0 149 70 31.82 43 41 48.81 806794 TCGA-AB-2943 10 104965961 104965961 A G SNP LOC401648 XR_017482.1 human genbank 54_36p 1 model rna NULL NULL 0.999 - - - pseudogene tier1 25 2 7.41 25 15 37.5 33 1 2.94 806794 TCGA-AB-2943 3 185003759 185003759 C T SNP YEATS2 NM_018023.3 human genbank 54_36p 1 provisional missense c.3524 p.S1175F 1 NULL HMMPfam_YEATS - no_errors tier1 92 0 103 43 28.86 27 4 12.9 708512 TCGA-AB-2945 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 184 12 6 15 21 58.33 NA NA NA 708512 TCGA-AB-2945 13 27490640 27490640 A T SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2505 p.D835E 0.991 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 119 6 4.55 40 10 20 NA NA NA 708512 TCGA-AB-2945 5 33673537 33673537 C T SNP ADAMTS12 NM_030955.2 human genbank 54_36p -1 reviewed missense c.1790 p.R597H 0.082 HMMSmart_SM00209 "HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_Reprolysin,HMMPfam_Pep_M12B_propep,HMMPfam_ADAM_spacer1,superfamily_Metalloproteases (""zincins"") catalytic domain" - no_errors tier1 122 10 7.52 98 43 30.5 NA NA NA 708512 TCGA-AB-2945 4 55294078 55294078 A T SNP KIT NM_000222.2 human genbank 54_36p 1 reviewed missense c.2447 p.D816V 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 74 4 5 23 29 55.77 NA NA NA 708512 TCGA-AB-2945 11 58705933 58705933 G A SNP DTX4 NM_015177.1 human genbank 54_36p 1 validated silent c.357 p.K119 1 "HMMPfam_WWE,HMMSmart_SM00678" "HMMSmart_SM00184,HMMPfam_WWE,HMMSmart_SM00678,HMMPfam_zf-C3HC4,superfamily_RING/U-box" - no_errors tier1 178 11 5.79 25 20 44.44 NA NA NA 708512 TCGA-AB-2945 11 64786408 64786412 AATTG - DEL POLA2 NM_002689.2 human genbank 54_36p 1 provisional frame_shift_del c.69_73 p.I24fs 0.000:0.000:0.000:0.004:0.836 HMMPfam_Pol_alpha_B_N "HMMPfam_DNA_pol_E_B,HMMPfam_Pol_alpha_B_N" - no_errors tier1 NA NA NA NA NA NA NA NA NA 708512 TCGA-AB-2945 16 80590579 80590579 C T SNP SDR42E1 NM_145168.2 human genbank 54_36p -1 validated missense c.820 p.G274S 1 "HMMPfam_3Beta_HSD,superfamily_NAD(P)-bd" "HMMPfam_3Beta_HSD,superfamily_NAD(P)-bd" - no_errors tier1 101 9 8.04 32 23 41.82 NA NA NA 708512 TCGA-AB-2945 6 88820400 88820400 G A SNP SPACA1 NM_030960.2 human genbank 54_36p 1 reviewed missense c.226 p.V76I 0.426 NULL NULL - no_errors tier1 94 4 4.08 57 20 25.97 NA NA NA 708512 TCGA-AB-2945 11 104515003 104515003 C T SNP CARD18 NM_021571.2 human genbank 54_36p -1 validated missense c.20 p.R7H 0 "HMMPfam_CARD,HMMSmart_CARD,superfamily_DEATH_like" "HMMPfam_CARD,HMMSmart_CARD,superfamily_DEATH_like" - no_errors tier1 170 22 11.34 76 65 45.77 NA NA NA 708512 TCGA-AB-2945 10 124447259 124447259 C G SNP C10orf120 NM_001010912.1 human genbank 54_36p -1 predicted missense c.988 p.A330P 0 NULL NULL - no_errors tier1 171 10 5.41 68 41 37.61 NA NA NA 708512 TCGA-AB-2945 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA NA 708512 TCGA-AB-2945 2 203753406 203753406 T C SNP NBEAL1 NM_001099273.1 human genbank 54_36p 1 validated missense c.2564 p.M855T 1 "HMMPfam_Beach,superfamily_BEACH domain" "HMMPfam_Beach,superfamily_BEACH domain,HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40,superfamily_PH domain-like" - no_errors tier1 81 4 4.71 46 26 36.11 NA NA NA 708512 TCGA-AB-2945 2 208821357 208821357 C T SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.395 p.R132H 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 70 2 2.7 33 14 29.17 NA NA NA 866660 TCGA-AB-2946 5 7920321 7920321 A G SNP FASTKD3 NM_024091.2 human genbank 54_36p -1 validated silent c.876 p.S292 0.982 NULL "HMMPfam_FAST_1,HMMPfam_FAST_2,HMMPfam_RAP" - no_errors tier1 68 5 6.76 103 26 20.16 10 0 866660 TCGA-AB-2946 22 48663765 48663765 G C SNP ZBED4 NM_014838.2 human genbank 54_36p 1 validated missense c.451 p.D151H 1 "HMMPfam_zf-BED,HMMSmart_SM00614" "HMMPfam_zf-BED,HMMSmart_SM00614,HMMPfam_hATC" - no_errors tier1 64 1 1.52 102 18 15 53 8 13.11 866660 TCGA-AB-2946 17 53317640 53317640 G A SNP CUEDC1 NM_017949.1 human genbank 54_36p -1 provisional silent c.285 p.S95 0.809 NULL "HMMPfam_CUE,HMMSmart_SM00546,superfamily_UBA-like" - no_errors tier1 8 0 21 19 47.5 2 4 66.67 868442 TCGA-AB-2947 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 53 14 20.9 47 32 40 NA NA 868442 TCGA-AB-2947 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 59 30 33.71 37 32 45.71 NA NA 868442 TCGA-AB-2947 16 73002259 73002259 T C SNP CLEC18B ENST00000268492 human ensembl 54_36p -1 known missense c.17 p.D6G 0 NULL "HMMPfam_Lectin_C,superfamily_C-type lectin-like,PatternScan_C_TYPE_LECTIN_1" - no_start_codon tier1 25 1 3.85 28 4 12.5 NA NA NA 868442 TCGA-AB-2947 9 140190562 140190562 C G SNP ENSG00000159247 ENST00000290377 human ensembl 54_36p 1 known silent c.360 p.V120 1 "HMMPfam_Tubulin,superfamily_Tubulin nucleotide-binding domain-like" "HMMPfam_Tubulin,superfamily_Tubulin C-terminal domain-like,PatternScan_TUBULIN,HMMPfam_Tubulin_C,superfamily_Tubulin nucleotide-binding domain-like" - no_start_codon tier1 7 0 8 1 11.11 NA NA NA 868442 TCGA-AB-2947 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA NA 914247 TCGA-AB-2948 MT 8706 8706 T C SNP MT-ATP6 ENST00000361899 human ensembl 54_36p 1 known missense c.179 p.M60T NULL HMMPfam_ATP-synt_A "HMMPfam_ATP-synt_A,PatternScan_ATPASE_A,superfamily_ATPase_F0_A" - no_errors tier1 5205 72 1.36 2476 273 9.87 NA NA NA 914247 TCGA-AB-2948 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 75 15 16.3 32 28 46.67 178 146 44.92 914247 TCGA-AB-2948 2 100549450 100549451 - C INS PDCL3 NM_024065.4 human genbank 54_36p 1 validated frame_shift_ins c.60_61 p.K22fs 0.997:1.000 "HMMPfam_Phosducin,superfamily_Thiordxn-like_fd" "HMMPfam_Phosducin,superfamily_Thiordxn-like_fd" - no_errors tier1 NA NA NA NA NA NA NA NA NA 740266 TCGA-AB-2949 9 2642945 2642945 C G SNP VLDLR NM_003383.1 human genbank 54_36p 1 validated missense c.2582 p.P861R 1 NULL "HMMPfam_Ldl_recept_b,HMMSmart_SM00135,PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin,superfamily_YWTD domain" - no_errors tier1 76 1 1.3 53 53 50 1 0 740266 TCGA-AB-2949 12 6571844 6571844 C T SNP CHD4 NM_001273.2 human genbank 54_36p -1 reviewed missense c.2924 p.R975H 1 HMMPfam_SNF2_N "HMMPfam_SNF2_N,HMMPfam_Chromo,HMMSmart_SM00298,PatternScan_CHROMO_1,HMMPfam_Helicase_C,HMMSmart_SM00490,HMMSmart_SM00249,PatternScan_DEAH_ATP_HELICASE,HMMPfam_DUF1086,HMMPfam_DUF1087,superfamily_FYVE/PHD zinc finger,HMMPfam_CHDCT2,HMMPfam_CHDNT,HMMSmart_SM00487,superfamily_Chromo domain-like,PatternScan_ZF_PHD_1,HMMPfam_PHD,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 198 8 3.86 146 54 26.87 175 67 27.69 740266 TCGA-AB-2949 15 18727164 18727164 G C SNP LOC646090 XR_017120.2 human genbank 54_36p -1 model rna NULL NULL 0.961 - - - pseudogene tier1 276 7 2.44 53 26 32.91 NA 740266 TCGA-AB-2949 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 112 8 6.67 26 21 44.68 45 60 57.14 740266 TCGA-AB-2949 17 27334134 27334135 CT - DEL SUZ12 NM_015355.2 human genbank 54_36p 1 reviewed frame_shift_del c.921_922 p.L308fs 0.998:0.998 NULL "PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,HMMPfam_VEFS-Box" - no_errors tier1 NA NA NA NA NA NA NA NA NA 740266 TCGA-AB-2949 17 29638754 29638754 C T SNP CCL11 NM_002986.2 human genbank 54_36p 1 reviewed missense c.226 p.P76S 0.992 "HMMPfam_IL8,HMMSmart_SM00199,superfamily_Interleukin 8-like chemokines" "PatternScan_SMALL_CYTOKINES_CC,HMMPfam_IL8,HMMSmart_SM00199,superfamily_Interleukin 8-like chemokines" - no_errors tier1 53 1 1.82 49 36 42.35 NA 740266 TCGA-AB-2949 21 35093494 35093495 AG - DEL RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed frame_shift_del c.941_940 p.S314fs 1.000:1.000 NULL "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 NA NA NA NA NA NA NA NA NA 740266 TCGA-AB-2949 20 45697745 45697745 A - DEL NCOA3 NM_181659.2 human genbank 54_36p 1 reviewed frame_shift_del c.1385 p.N462fs 0.984 NULL "HMMSmart_SM00091,HMMPfam_HLH,HMMSmart_SM00353,superfamily_Nuclear receptor coactivator interlocking domain,HMMPfam_DUF1518,superfamily_HLH helix-loop-helix DNA-binding domain,HMMPfam_PAS,HMMPfam_Nuc_rec_co-act,HMMPfam_SRC-1,superfamily_PYP-like sensor domain (PAS domain)" - no_errors tier1 NA NA NA NA NA NA NA NA NA 740266 TCGA-AB-2949 14 78245493 78245493 A G SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed missense c.283 p.M95V 0.998 "HMMSmart_LamG,superfamily_ConA_like_lec_gl" "PatternScan_ASX_HYDROXYL,HMMSmart_LamG,HMMSmart_4.1m,HMMPfam_EGF,HMMSmart_EGF,superfamily_ConA_like_lec_gl,HMMPfam_Laminin_G_2" - no_errors tier1 115 2 1.71 50 26 33.77 NA 740266 TCGA-AB-2949 2 84951165 84951165 G T SNP LOC129293 NM_001080824.1 human genbank 54_36p -1 predicted missense c.364 p.R122S 0.997 NULL NULL - no_errors tier1 65 2 2.99 23 22 48.89 NA 740266 TCGA-AB-2949 5 100250084 100250084 T C SNP ST8SIA4 NM_005668.4 human genbank 54_36p -1 reviewed missense c.365 p.H122R 0.997 HMMPfam_Glyco_transf_29 HMMPfam_Glyco_transf_29 - no_errors tier1 56 2 3.33 33 27 45 30 25 45.45 740266 TCGA-AB-2949 12 120563336 120563336 A G SNP ORAI1 NM_032790.3 human genbank 54_36p 1 reviewed missense c.316 p.M106V 0.997 HMMPfam_DUF1650 HMMPfam_DUF1650 - no_errors tier1 129 3 2.24 52 22 29.73 107 64 37.43 740266 TCGA-AB-2949 5 151764747 151764747 G A SNP NMUR2 NM_020167.4 human genbank 54_36p -1 reviewed missense c.121 p.R41C 0.866 superfamily_Family A G protein-coupled receptor-like "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 88 3 3.26 57 24 29.27 NA 740266 TCGA-AB-2949 3 199040920 199040920 G A SNP LRCH3 NM_032773.2 human genbank 54_36p 1 provisional missense c.866 p.R289K 1 superfamily_SSF52058 "HMMPfam_LRR_1,superfamily_Calponin-homology,superfamily_SSF52058" - no_errors tier1 109 2 1.79 65 58 46.77 14 18 56.25 740266 TCGA-AB-2949 2 208821357 208821357 C T SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.395 p.R132H 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 86 6 6.52 32 25 43.86 37 23 38.33 740266 TCGA-AB-2949 2 220213566 220213566 G A SNP SLC4A3 NM_201574.3 human genbank 54_36p 1 validated splice_site c.3528+1 e20+1 1 - - - no_errors tier1 110 1 0.89 52 9 14.75 0 740266 TCGA-AB-2949 2 228705007 228705007 G A SNP SPHKAP NM_030623.1 human genbank 54_36p -1 validated missense c.71 p.P24L 0 NULL HMMPfam_AKAP_110 - no_errors tier1 85 1 1.16 54 32 37.21 NA 750152 TCGA-AB-2950 15 39833933 39833934 TG - DEL MGA NM_001080541.1 human genbank 54_36p 1 provisional frame_shift_del c.7162_7163 p.V2389fs 0.094:0.101 NULL "HMMPfam_HLH,HMMSmart_SM00353,HMMPfam_T-box,HMMSmart_SM00425,superfamily_p53-like transcription factors,superfamily_HLH helix-loop-helix DNA-binding domain,PatternScan_TBOX_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 750152 TCGA-AB-2950 21 39955062 39955062 G A SNP B3GALT5 NM_006057.1 human genbank 54_36p 1 reviewed missense c.706 p.V236I 0.292 HMMPfam_Galactosyl_T HMMPfam_Galactosyl_T - no_errors tier1 134 5 3.52 303 216 41.62 NA 750152 TCGA-AB-2950 19 45100137 45100137 C T SNP FCGBP NM_003890.2 human genbank 54_36p -1 validated silent c.4542 p.A1514 0.937 HMMPfam_C8 "HMMSmart_VWC,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_TIL_assoc,HMMSmart_FOLN,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 68 2 2.86 42 80 65.57 1 0 750152 TCGA-AB-2950 15 47235040 47235040 A C SNP COPS2 NM_004236.1 human genbank 54_36p -1 validated missense c.28 p.C10G 1 NULL "HMMPfam_PCI,HMMSmart_SM00088,HMMSmart_SM00753,superfamily_""Winged helix"" DNA-binding domain,superfamily_TPR-like" - no_errors tier1 59 2 3.28 76 48 38.71 46 33 41.77 750152 TCGA-AB-2950 2 48789650 48789650 G A SNP LHCGR NM_000233.3 human genbank 54_36p -1 reviewed silent c.621 p.N207 0.019 superfamily_L domain-like "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_L domain-like,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 137 3 2.14 259 175 40.14 NA 750152 TCGA-AB-2950 19 52114941 52114941 C T SNP GRLF1 NM_004491.4 human genbank 54_36p 1 reviewed missense c.1169 p.A390V 0.998 HMMSmart_SM00441 "HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_FF,HMMSmart_SM00441,superfamily_GTPase activation domain GAP,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 95 6 5.94 76 90 53.89 17 35 67.31 750152 TCGA-AB-2950 11 64384284 64384284 C T SNP EHD1 NM_006795.2 human genbank 54_36p -1 reviewed silent c.603 p.S201 0.208 "HMMPfam_Dynamin_N,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00027,HMMPfam_Dynamin_N,PatternScan_EF_HAND_1,superfamily_EF-hand,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 35 1 2.78 68 30 30.61 58 34 36.96 750152 TCGA-AB-2950 10 87397062 87397062 G T SNP GRID1 NM_017551.2 human genbank 54_36p -1 reviewed nonsense c.2070 p.Y690* 1 "HMMPfam_Lig_chan,HMMSmart_SM00079,superfamily_Periplasmic binding protein-like II" "HMMPfam_Lig_chan,HMMSmart_SM00079,HMMPfam_ANF_receptor,PatternScan_ALDEHYDE_DEHYDR_GLU,HMMPfam_Lig_chan-Glu_bd,superfamily_Periplasmic binding protein-like I,superfamily_Periplasmic binding protein-like II" - no_errors tier1 147 3 1.95 209 70 25.09 NA 750152 TCGA-AB-2950 2 111258841 111258841 C T SNP ACOXL NM_001105516.2 human genbank 54_36p 1 validated missense c.137 p.A46V 0.187 superfamily_Acyl-CoA dehydrogenase NM domain-like "HMMPfam_Acyl-CoA_dh_1,HMMPfam_Acyl-CoA_dh_M,superfamily_Acyl-CoA dehydrogenase C-terminal domain-like,superfamily_Acyl-CoA dehydrogenase NM domain-like" - no_errors tier1 79 2 2.44 93 70 42.94 NA 750152 TCGA-AB-2950 10 112350880 112350880 T C SNP SMC3 NM_005445.3 human genbank 54_36p 1 reviewed splice_site c.2644+2 e23+2 0.991 - - - no_errors tier1 31 2 5.71 26 24 48 1 56 98.25 750152 TCGA-AB-2950 4 123422329 123422329 C G SNP KIAA1109 NM_015312.2 human genbank 54_36p 1 validated missense c.8987 p.S2996C 1 NULL "PatternScan_ASP_PROTEASE,HMMPfam_FSA_C" - no_errors tier1 69 1 1.43 52 50 49.02 20 24 54.55 750152 TCGA-AB-2950 X 135600449 135600449 C - DEL ARHGEF6 NM_004840.2 human genbank 54_36p -1 reviewed frame_shift_del c.1171 p.E391fs 1 "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain)" "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_PH,HMMSmart_SM00233,superfamily_Calponin-homology domain CH-domain,superfamily_PH domain-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 750152 TCGA-AB-2950 3 176647790 176647790 G A SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated silent c.1170 p.L390 0.953 "superfamily_Transferrin receptor ectodomain apical domain,superfamily_Zn-dependent exopeptidases" "superfamily_Transferrin receptor ectodomain C-terminal domain,PatternScan_GLYCOSYL_HYDROL_F5,superfamily_Transferrin receptor ectodomain apical domain,superfamily_Zn-dependent exopeptidases" - no_errors tier1 68 0 59 44 42.72 1 0 809653 TCGA-AB-2952 9 3818379 3818379 G A SNP GLIS3 NM_001042413.1 human genbank 54_36p -1 reviewed missense c.2686 p.L896F 0.997 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 157 9 5.42 132 86 39.27 NA 809653 TCGA-AB-2952 17 7517806 7517806 T C SNP TP53 NM_000546.4 human genbank 54_36p -1 reviewed missense c.857 p.E286G 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD" - no_errors tier1 276 28 9.21 38 175 81.78 24 228 90.12 809653 TCGA-AB-2952 17 8017594 8017595 - GGA INS ENSG00000200463 ENST00000363593 human ensembl 54_36p -1 novel rna NULL NULL 0.688:0.440 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 809653 TCGA-AB-2952 8 27978130 27978130 C T SNP C8orf80 NM_001010906.1 human genbank 54_36p -1 predicted missense c.749 p.R250H 0.973 superfamily_P-loop containing nucleoside triphosphate hydrolases superfamily_P-loop containing nucleoside triphosphate hydrolases - no_errors tier1 176 6 3.3 110 24 17.91 3 0 809653 TCGA-AB-2952 19 38484735 38484736 CC - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_del c.426_425 p.R142fs 0.999:1.000 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 809653 TCGA-AB-2952 22 42317297 42317297 G T SNP EFCAB6 NM_022785.2 human genbank 54_36p -1 validated missense c.3022 p.L1008M 0.478 superfamily_EF-hand "HMMSmart_SM00054,HMMPfam_DUF1880,PatternScan_EF_HAND_1,superfamily_EF-hand" - no_errors tier1 227 3 1.3 240 70 22.36 NA 809653 TCGA-AB-2952 19 45594838 45594838 T C SNP PRX NM_181882.2 human genbank 54_36p -1 reviewed missense c.1261 p.K421E 0.996 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like" - no_errors tier1 74 8 9.64 63 50 43.86 3 3 50 809653 TCGA-AB-2952 12 67516784 67516784 A C SNP MDM2 NM_002392.1 human genbank 54_36p 1 reviewed missense c.906 p.E302D 1 NULL "HMMPfam_zf-RanBP,PatternScan_ZF_RANBP2_1,HMMPfam_SWIB,superfamily_SWIB/MDM2 domain,superfamily_RING/U-box" - no_errors tier1 153 1 0.65 236 60 20.2 25 0 809653 TCGA-AB-2952 15 71522583 71522583 G A SNP C15orf60 NM_001042367.1 human genbank 54_36p 1 predicted missense c.4 p.A2T 0.997 NULL NULL - no_errors tier1 84 5 5.62 63 51 44.74 NA 809653 TCGA-AB-2952 1 115060270 115060270 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.35 p.G12D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 207 1 0.48 266 35 11.55 43 10 18.18 809653 TCGA-AB-2952 11 116806856 116806856 G A SNP DSCAML1 NM_020693.2 human genbank 54_36p -1 provisional silent c.5658 p.H1886 1 NULL "HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 453 59 11.52 56 52 47.71 1 0 809653 TCGA-AB-2952 1 117464866 117464866 C T SNP TRIM45 NM_025188.1 human genbank 54_36p -1 reviewed missense c.481 p.A161T 1 "HMMPfam_zf-B_box,HMMSmart_SM00336" "HMMPfam_zf-B_box,HMMSmart_SM00336,HMMSmart_SM00557,HMMSmart_SM00184,HMMSmart_SM00502,superfamily_E set domains,HMMPfam_Filamin,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,superfamily_RING/U-box" - no_errors tier1 195 16 7.58 232 182 43.44 7 4 36.36 809653 TCGA-AB-2952 11 120207797 120207797 C T SNP GRIK4 NM_014619.2 human genbank 54_36p 1 reviewed missense c.538 p.R180W 1 "HMMPfam_ANF_receptor,superfamily_SSF53822" "HMMPfam_Lig_chan,HMMSmart_PBPe,HMMPfam_ANF_receptor,HMMPfam_Lig_chan-Glu_bd,superfamily_SSF53822,superfamily_SSF53850" - no_errors tier1 64 1 1.54 63 13 16.88 NA 809653 TCGA-AB-2952 X 135941370 135941370 C T SNP GPR101 NM_054021.1 human genbank 54_36p -1 provisional missense c.130 p.A44T 0.001 superfamily_Family A G protein-coupled receptor-like "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 497 36 6.72 53 38 41.3 NA 809653 TCGA-AB-2952 1 166139804 166139804 T A SNP ADCY10 NM_018417.3 human genbank 54_36p -1 validated missense c.198 p.R66S 1 "HMMPfam_Guanylate_cyc,superfamily_Adenylyl and guanylyl cyclase catalytic domain" "HMMPfam_Guanylate_cyc,superfamily_Adenylyl and guanylyl cyclase catalytic domain,superfamily_TPR-like" - no_errors tier1 236 16 6.35 158 109 40.07 NA 809653 TCGA-AB-2952 4 187821731 187821731 C G SNP FAT1 NM_005245.3 human genbank 54_36p -1 reviewed missense c.3296 p.R1099P 0.989 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Cadherin-like" "PatternScan_ASX_HYDROXYL,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Cadherin-like,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 119 8 6.3 108 70 39.11 NA 862507 TCGA-AB-2954 11 1018705 1018705 A G SNP MUC6 NM_005961.2 human genbank 54_36p -1 validated missense c.1532 p.L511P 0.902 "HMMPfam_VWD,HMMSmart_SM00216" "HMMPfam_VWD,HMMSmart_SM00216,superfamily_Serine proterase inhibitors,HMMSmart_SM00041,HMMSmart_SM00215,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 8 0 1 4 80 NA 869922 TCGA-AB-2955 MT 7920 7920 G A SNP MT-CO2 ENST00000361739 human ensembl 54_36p 1 known missense c.334 p.D112N NULL "HMMPfam_COX2,superfamily_Cupredoxins" "PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region" - no_errors tier1 7626 378 4.72 3790 1965 33.92 NA NA NA 869922 TCGA-AB-2955 6 4002321 4002321 C G SNP PRPF4B NM_003913.4 human genbank 54_36p 1 reviewed silent c.2634 p.T878 0.859 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" - no_errors tier1 164 15 8.38 42 35 45.45 38 45 53.57 869922 TCGA-AB-2955 1 6559262 6559262 A G SNP TAS1R1 NM_138697.2 human genbank 54_36p 1 reviewed silent c.1461 p.G487 0.016 superfamily_Periplasmic binding protein-like I "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_Periplasmic binding protein-like I" - no_errors tier1 175 9 4.89 31 25 43.86 NA 869922 TCGA-AB-2955 2 15333344 15333344 T C SNP NBAS NM_015909.2 human genbank 54_36p -1 validated silent c.5439 p.A1813 0.222 NULL "superfamily_WD40 repeat-like,HMMPfam_Sec39,PatternScan_RIBOSOMAL_S14" - no_errors tier1 242 17 6.56 67 44 39.29 28 17 37.78 869922 TCGA-AB-2955 14 22944694 22944694 G C SNP MYH6 NM_002471.2 human genbank 54_36p -1 validated nonsense c.327 p.Y109* 1 "HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Myosin_head,HMMSmart_SM00242,HMMPfam_Myosin_tail_1,HMMPfam_Myosin_N,superfamily_Prefoldin,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 668 52 7.21 71 67 48.2 NA 869922 TCGA-AB-2955 19 24080696 24080696 C G SNP ZNF254 NM_203282.2 human genbank 54_36p 1 validated missense c.145 p.L49V 0.994 "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352)" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 108 4 3.57 30 18 37.5 10 6 35.29 869922 TCGA-AB-2955 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 233 21 8.24 50 34 40 34 40 53.33 869922 TCGA-AB-2955 15 28880384 28880384 G T SNP ENSG00000103832 ENST00000220188 human ensembl 54_36p 1 known missense c.790 p.A264S 0.951 NULL NULL - no_stop_codon tier1 368 27 6.84 33 33 50 2 0 869922 TCGA-AB-2955 17 31332517 31332517 G A SNP CCL16 NM_004590.2 human genbank 54_36p -1 reviewed missense c.53 p.T18I 0.001 NULL "PatternScan_SMALL_CYTOKINES_CC,HMMPfam_IL8,HMMSmart_SCY,superfamily_Chemokine_IL8" - no_errors tier1 931 89 8.72 95 95 49.48 NA 869922 TCGA-AB-2955 X 34060095 34060095 G A SNP FAM47A NM_203408.2 human genbank 54_36p -1 predicted silent c.222 p.D74 0.004 NULL NULL - no_errors tier1 146 17 10.43 40 35 46.05 NA 869922 TCGA-AB-2955 17 37387413 37387413 C T SNP DNAJC7 NM_003315.1 human genbank 54_36p -1 provisional missense c.1340 p.G447D 1 superfamily_Chaperone J-domain "HMMPfam_TPR_1,HMMPfam_DnaJ,HMMSmart_SM00271,superfamily_Chaperone J-domain,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 340 16 4.48 50 29 36.25 41 23 35.94 869922 TCGA-AB-2955 19 38484244 38484245 - GCT INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_ins c.917_916 p.306in_frame_insQ 1.000:1.000 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 869922 TCGA-AB-2955 19 38485024 38485024 G - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_del c.137 p.P46fs 1 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 869922 TCGA-AB-2955 15 40160574 40160574 G A SNP PLA2G4D NM_178034.3 human genbank 54_36p -1 validated missense c.1007 p.T336I 0.864 "HMMPfam_PLA2_B,HMMSmart_SM00022,superfamily_FabD/lysophospholipase-like" "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_PLA2_B,HMMSmart_SM00022,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FabD/lysophospholipase-like" - no_errors tier1 170 7 3.95 21 17 44.74 NA 869922 TCGA-AB-2955 3 48583702 48583702 G A SNP COL7A1 NM_000094.3 human genbank 54_36p -1 reviewed missense c.7082 p.A2361V 1 HMMPfam_Collagen "HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Kunitz_BPTI,PatternScan_BPTI_KUNITZ_1,superfamily_BPTI-like,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Collagen,superfamily_Fibronectin type III,superfamily_vWA-like" - no_errors tier1 276 19 6.44 46 28 37.84 NA 869922 TCGA-AB-2955 12 51171752 51171752 T C SNP LOC100129218 XM_001718439.1 human genbank 54_36p 1 model missense c.997 p.F333L 1 NULL NULL - no_errors tier1 217 19 8.05 21 26 55.32 NA 869922 TCGA-AB-2955 X 86659948 86659948 T C SNP KLHL4 NM_057162.4 human genbank 54_36p 1 reviewed silent c.396 p.D132 0.948 NULL "HMMSmart_SM00225,HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain,superfamily_POZ domain,HMMPfam_BACK,HMMPfam_BTB" - no_errors tier1 112 9 7.44 18 25 58.14 NA 869922 TCGA-AB-2955 3 129685499 129685499 G T SNP GATA2 NM_032638.1 human genbank 54_36p -1 reviewed missense c.911 p.P304H 1 "HMMPfam_GATA,HMMSmart_ZnF_GATA,PatternScan_GATA_ZN_FINGER_1,superfamily_SSF57716" "HMMPfam_GATA,HMMSmart_ZnF_GATA,PatternScan_GATA_ZN_FINGER_1,superfamily_SSF57716" - no_errors tier1 82 3 3.53 12 7 36.84 6 12 66.67 869922 TCGA-AB-2955 5 140147758 140147758 G A SNP PCDHA1 NM_018900.2 human genbank 54_36p 1 reviewed missense c.1699 p.A567T 0.018 superfamily_Cadherin-like "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 128 13 9.22 16 10 37.04 NA 869922 TCGA-AB-2955 5 140595772 140595772 T C SNP PCDHB18 ENST00000274705 human ensembl 54_36p 1 known missense c.1303 p.Y435H 0.998 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 83 6 6.74 9 7 43.75 NA 869922 TCGA-AB-2955 4 152243488 152243488 C T SNP RPS3A NM_001006.3 human genbank 54_36p 1 reviewed missense c.370 p.H124Y 1 HMMPfam_Ribosomal_S3Ae "HMMPfam_Ribosomal_S3Ae,PatternScan_RIBOSOMAL_S3AE" - no_errors tier1 405 32 7.32 83 60 41.96 173 174 50 869922 TCGA-AB-2955 1 152810583 152810583 G A SNP CHRNB2 NM_000748.2 human genbank 54_36p 1 reviewed silent c.660 p.T220 0.999 "HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like" "HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore,HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like,PatternScan_NEUROTR_ION_CHANNEL" - no_errors tier1 255 24 8.57 17 17 48.57 NA 923966 TCGA-AB-2956 12 532735 532735 C T SNP B4GALNT3 NM_173593.3 human genbank 54_36p 1 validated missense c.1385 p.T462I 0.003 NULL "HMMPfam_PA14,HMMSmart_SM00758,superfamily_Nucleotide-diphospho-sugar transferases" - no_errors tier1 33 2 5.71 4 6 60 3 0 923966 TCGA-AB-2956 4 46667971 46667971 G A SNP GABRA4 NM_000809.2 human genbank 54_36p -1 reviewed missense c.760 p.R254W 1 "HMMPfam_Neur_chan_LBD,superfamily_Neur_chan_LBD" "HMMPfam_Neur_chan_memb,superfamily_Neu_channel_TM,HMMPfam_Neur_chan_LBD,superfamily_Neur_chan_LBD,PatternScan_NEUROTR_ION_CHANNEL" - no_errors tier1 84 5 5.62 50 15 23.08 NA 923966 TCGA-AB-2956 10 89258179 89258179 C T SNP MINPP1 NM_004897.3 human genbank 54_36p 1 validated silent c.744 p.H248 0.978 "HMMPfam_Acid_phosphat_A,superfamily_Phosphoglycerate mutase-like" "HMMPfam_Acid_phosphat_A,PatternScan_ER_TARGET,superfamily_Phosphoglycerate mutase-like" - no_errors tier1 70 5 6.67 27 6 18.18 9 12 57.14 923966 TCGA-AB-2956 5 121814707 121814707 G A SNP SNCAIP NM_005460.2 human genbank 54_36p 1 reviewed missense c.2266 p.E756K 1 NULL "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" - no_errors tier1 45 2 4.26 24 23 48.94 NA 944281 TCGA-AB-2957 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 75 14 15.73 29 24 45.28 NA NA 944281 TCGA-AB-2957 11 31043202 31043202 G A SNP uc001msu.1 ENST00000342355 human ensembl 54_36p -1 known silent c.1230 p.H410 0.454 superfamily_RicinB_like superfamily_RicinB_like - no_errors tier1 44 2 4.26 28 23 45.1 NA NA NA 944281 TCGA-AB-2957 3 151867361 151867361 C T SNP C3orf44 NM_152394.3 human genbank 54_36p -1 validated missense c.1631 p.R544H 0.548 NULL NULL - no_errors tier1 51 3 5.36 64 46 41.82 NA NA NA 972783 TCGA-AB-2959 2 1436476 1436476 C A SNP TPO NM_000547.4 human genbank 54_36p 1 reviewed missense c.486 p.D162E 0.965 "HMMPfam_An_peroxidase,superfamily_Heme-dependent peroxidases" "PatternScan_ASX_HYDROXYL,HMMPfam_Sushi,HMMSmart_SM00032,HMMSmart_SM00179,HMMPfam_An_peroxidase,HMMSmart_SM00181,superfamily_Heme-dependent peroxidases,PatternScan_EGF_2,HMMPfam_EGF_CA,superfamily_Complement control module/SCR domain,PatternScan_EGF_CA,PatternScan_PEROXIDASE_1,superfamily_EGF/Laminin" - no_errors tier1 28 0 10 8 44.44 NA 972783 TCGA-AB-2959 17 1787436 1787436 C T SNP RTN4RL1 NM_178568.2 human genbank 54_36p -1 validated missense c.430 p.V144I 1 "HMMSmart_SM00369,superfamily_L domain-like" "HMMPfam_LRRNT,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like" - no_errors tier1 23 0 18 10 34.48 NA 972783 TCGA-AB-2959 11 9057523 9057523 G A SNP SCUBE2 NM_020974.1 human genbank 54_36p -1 provisional silent c.366 p.D122 1 "HMMSmart_SM00179,HMMSmart_SM00181,PatternScan_EGF_2,superfamily_EGF/Laminin" "PatternScan_ASX_HYDROXYL,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Growth factor receptor domain,HMMPfam_GCC2_GCC3,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 153 0 36 23 38.98 NA 972783 TCGA-AB-2959 20 18245128 18245128 T G SNP ZNF133 NM_001083330.1 human genbank 54_36p 1 validated missense c.1630 p.S544A 0.98 superfamily_SSF57667 "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 125 1 0.79 26 20 43.48 1 100 972783 TCGA-AB-2959 2 21088903 21088903 C T SNP APOB NM_000384.2 human genbank 54_36p -1 reviewed missense c.4342 p.V1448I 0.001 NULL "HMMPfam_Vitellogenin_N,HMMSmart_SM00638,HMMPfam_DUF1081,HMMPfam_DUF1943,superfamily_Lipovitellin-phosvitin complex beta-sheet shell regions,superfamily_Lipovitellin-phosvitin complex superhelical domain" - no_errors tier1 207 3 1.42 68 49 41.88 NA 972783 TCGA-AB-2959 14 22656548 22656548 C A SNP CEBPE NM_001805.2 human genbank 54_36p -1 reviewed silent c.834 p.G278 0.996 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 92 0 32 36 52.94 NA 972783 TCGA-AB-2959 14 24171052 24171052 G A SNP GZMB NM_004131.4 human genbank 54_36p -1 reviewed missense c.452 p.A151V 0 "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases" "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER" - no_errors tier1 70 0 17 18 50 16 3 15.79 972783 TCGA-AB-2959 1 24305101 24305101 G A SNP MYOM3 NM_152372.3 human genbank 54_36p -1 validated silent c.456 p.R152 0.929 superfamily_Immunoglobulin "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,PatternScan_EF_HAND_1,superfamily_Immunoglobulin" - no_errors tier1 46 0 22 10 31.25 NA 972783 TCGA-AB-2959 13 24568652 24568652 C G SNP PABPC3 NM_030979.2 human genbank 54_36p 1 validated missense c.316 p.L106V 0.998 "HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00361,superfamily_RNA-binding domain RBD" "HMMPfam_RRM_1,HMMSmart_SM00360,HMMPfam_PABP,HMMSmart_SM00517,superfamily_PABC (PABP) domain,HMMSmart_SM00361,superfamily_RNA-binding domain RBD" - no_errors tier1 105 1 0.94 57 10 14.93 NA 972783 TCGA-AB-2959 8 25192027 25192027 G A SNP DOCK5 NM_024940.6 human genbank 54_36p 1 validated missense c.250 p.E84K 0.981 NULL "HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain" - no_errors tier1 90 0 33 22 40 8 8 50 972783 TCGA-AB-2959 13 27778869 27778869 A G SNP FLT1 NM_002019.3 human genbank 54_36p -1 validated missense c.3761 p.M1254T 0.733 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_SM00220,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_Immunoglobulin" - no_errors tier1 113 2 1.74 43 43 50 NA 972783 TCGA-AB-2959 13 32236670 32236670 A G SNP PDS5B NM_015032.2 human genbank 54_36p 1 validated missense c.3562 p.T1188A 0.987 NULL "HMMPfam_HEAT,superfamily_ARM repeat,HMMPfam_AT_hook" - no_errors tier1 159 1 0.62 52 10 16.13 71 24 25.26 972783 TCGA-AB-2959 21 35153652 35153652 C T SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.602 p.R201Q 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 102 0 6 40 86.96 9 825 97.4 972783 TCGA-AB-2959 15 38703884 38703884 G C SNP CASC5 NM_170589.3 human genbank 54_36p 1 validated missense c.4208 p.G1403A 0.044 NULL NULL - no_errors tier1 99 1 1 21 18 46.15 30 12 28.57 972783 TCGA-AB-2959 1 44233906 44233906 C A SNP CCDC24 NM_152499.1 human genbank 54_36p 1 provisional missense c.599 p.A200E 0.002 NULL NULL - no_errors tier1 43 0 16 8 33.33 1 100 972783 TCGA-AB-2959 12 48643666 48643666 T C SNP AQP5 NM_001651.2 human genbank 54_36p 1 reviewed missense c.488 p.L163P 0.991 "HMMPfam_MIP,superfamily_MIP" "HMMPfam_MIP,PatternScan_MIP,superfamily_MIP" - no_errors tier1 21 1 4.55 4 4 50 NA 972783 TCGA-AB-2959 16 55389922 55389922 C A SNP NUP93 NM_014669.3 human genbank 54_36p 1 validated missense c.331 p.L111M 1 NULL HMMPfam_Nic96 - no_errors tier1 189 0 68 9 11.69 25 8 24.24 972783 TCGA-AB-2959 8 56529812 56529812 G A SNP LOC100133234 XR_038021.1 human genbank 54_36p -1 model rna NULL NULL 1 - - - pseudogene tier1 26 0 12 4 25 1 0 972783 TCGA-AB-2959 8 70907326 70907326 C T SNP SLCO5A1 NM_030958.1 human genbank 54_36p -1 reviewed missense c.137 p.C46Y 0.999 NULL "HMMSmart_KAZAL,HMMPfam_OATP,HMMPfam_Kazal_2,superfamily_MFS_gen_substrate_transporter,superfamily_SSF100895" - no_errors tier1 45 0 18 13 41.94 15 12 44.44 972783 TCGA-AB-2959 6 73024680 73024680 C T SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated missense c.2902 p.R968C 1 NULL "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FYVE/PHD zinc finger,PatternScan_GLYCOSYL_HYDROL_F1_1" - no_errors tier1 93 0 20 7 25.93 NA 972783 TCGA-AB-2959 4 85384652 85384652 G A SNP LOC152845 XR_038721.1 human genbank 54_36p 1 model rna NULL NULL 1 - - - pseudogene tier1 113 0 24 20 45.45 1 0 972783 TCGA-AB-2959 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 75 1 1.32 22 16 42.11 82 80 49.08 972783 TCGA-AB-2959 11 92729775 92729775 G A SNP CCDC67 NM_181645.3 human genbank 54_36p 1 validated missense c.215 p.R72Q 0.999 NULL NULL - no_errors tier1 151 1 0.65 24 20 45.45 NA 972783 TCGA-AB-2959 10 95781506 95781506 T C SNP PLCE1 NM_016341.3 human genbank 54_36p 1 validated missense c.713 p.M238T 0.287 NULL "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RA,HMMSmart_SM00314,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand" - no_errors tier1 187 3 1.56 54 31 36.47 NA 972783 TCGA-AB-2959 10 115347805 115347805 G T SNP NRAP NM_198060.3 human genbank 54_36p -1 validated missense c.4245 p.D1415E 1 HMMSmart_SM00227 "HMMPfam_Nebulin,HMMSmart_SM00227,HMMPfam_LIM,HMMSmart_SM00132,PatternScan_LIM_DOMAIN_1,superfamily_Glucocorticoid receptor-like (DNA-binding domain)" - no_errors tier1 68 2 2.86 32 14 30.43 NA 972783 TCGA-AB-2959 X 119271528 119271528 T A SNP ZBTB33 NM_006777.3 human genbank 54_36p 1 validated missense c.230 p.I77N 1 "HMMSmart_SM00225,superfamily_POZ domain,HMMPfam_BTB" "HMMSmart_SM00225,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_POZ domain,HMMPfam_BTB,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 83 3 3.45 6 27 81.82 6 28 82.35 972783 TCGA-AB-2959 X 133375518 133375518 G T SNP PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed splice_site c.586-1 e6-1 1 - - - no_errors tier1 64 0 12 22 64.71 0 972783 TCGA-AB-2959 2 170626130 170626130 C T SNP UBR3 NM_172070.3 human genbank 54_36p 1 validated silent c.1509 p.C503 1 NULL "HMMPfam_zf-C3HC4,superfamily_RING/U-box" - no_errors tier1 135 2 1.45 26 10 27.78 14 14 50 972783 TCGA-AB-2959 1 195657028 195657028 G A SNP CRB1 NM_201253.1 human genbank 54_36p 1 reviewed missense c.1447 p.A483T 0.005 superfamily_Concanavalin A-like lectins/glucanases "PatternScan_ASX_HYDROXYL,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_EGF/Laminin" - no_errors tier1 182 2 1.08 48 17 26.15 NA 123172 TCGA-AB-2963 AML03 Y 3289605 3289605 G A SNP LOC100130181 XM_001713805.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-27302 NULL 0.022 - - - no_start_codon:pseudogene:no_stop_codon tier3 255 16 5.9 24 338 93.37 0 0 NA 123172 TCGA-AB-2963 AML03 Y 12734623 12734623 C T SNP - - - - - - - - - - - - - - - tier2 187 7 3.59 41 319 88.61 0 0 NA 123172 TCGA-AB-2963 AML03 X 13775680 13775680 A C SNP GPM6B NM_001001994.1 human genbank 54_36p -1 validated intronic c.5-61832 e2-61832 0.355 - - - no_errors tier2 182 2 1.09 21 285 93.14 0 0 NA 123172 TCGA-AB-2963 AML03 Y 20118635 20118635 A G SNP BCORL2 ENST00000400605 human ensembl 54_36p -1 known intronic c.1+5671 e0+5671 1 - - - no_errors tier2 1093 22 1.97 94 1279 93.09 0 0 NA 123172 TCGA-AB-2963 AML03 X 29239085 29239085 G T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.362+27830 e2+27830 0 - - - no_errors tier3 367 15 3.93 49 493 90.96 0 0 NA 123172 TCGA-AB-2963 AML03 X 32415292 32415292 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.2623-2155 e21-2155 0 - - - no_errors tier3 117 8 6.4 7 207 96.73 0 0 NA 123172 TCGA-AB-2963 AML03 X 32895895 32895895 T C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.93+52282 e2+52282 0 - - - no_errors tier2 207 15 6.76 37 597 94.16 0 0 NA 123172 TCGA-AB-2963 AML03 X 44776587 44776587 G T SNP UTX NM_021140.2 human genbank 54_36p 1 validated intronic c.565-2533 e7-2533 0 - - - no_errors tier3 335 19 5.35 18 270 93.75 0 0 0 123172 TCGA-AB-2963 AML03 X 46323703 46323703 C T SNP CHST7 NM_019886.2 human genbank 54_36p 1 reviewed intronic c.1461+3901 e1+3901 0 - - - no_errors tier3 525 21 3.85 21 432 95.36 0 3 100 123172 TCGA-AB-2963 AML03 X 53443342 53443342 A T SNP SMC1A NM_006306.2 human genbank 54_36p -1 reviewed missense c.2456 p.I819N 1 "HMMPfam_SMC_N,superfamily_SSF52540" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540" - no_errors tier1 508 4 0.78 292 353 54.73 71 114 61.62 123172 TCGA-AB-2963 AML03 X 93384098 93384098 G A SNP - - - - - - - - - - - - - - - tier3 587 41 6.52 51 890 94.58 0 0 NA 123172 TCGA-AB-2963 AML03 X 96895053 96895053 C T SNP - - - - - - - - - - - - - - - tier3 139 6 4.14 20 437 95.62 0 0 NA 123172 TCGA-AB-2963 AML03 X 108405221 108405221 C A SNP - - - - - - - - - - - - - - - tier3 984 12 1.2 384 335 46.59 0 0 NA 123172 TCGA-AB-2963 AML03 X 132236640 132236640 G A SNP ENSG00000202199 ENST00000365329 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36130 NULL 0.685 - - - no_errors tier3 393 22 5.3 26 478 94.84 0 0 NA 123172 TCGA-AB-2963 AML03 1 7955156 7955156 C - DEL PARK7 NM_007262.1 human genbank 54_36p 1 reviewed intronic c.322+1546 e4+1546 0.01 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 1 11353844 11353844 G A SNP LOC100130707 XM_001713657.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-34316 NULL 0.004 - - - no_start_codon:pseudogene:no_stop_codon tier3 1944 51 2.55 303 247 44.83 0 0 NA 123172 TCGA-AB-2963 AML03 1 18545172 18545172 G A SNP IGSF21 NM_032880.2 human genbank 54_36p 1 provisional intronic c.424+11081 e4+11081 0 - - - no_errors tier3 300 3 0.98 132 90 40.54 0 0 0 123172 TCGA-AB-2963 AML03 1 22788115 22788115 G A SNP EPHA8 NM_020526.1 human genbank 54_36p 1 reviewed missense c.1144 p.G382S 0.859 "HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" "HMMPfam_Ephrin_lbd,HMMSmart_EPH_lbd,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SAM,HMMPfam_fn3,HMMSmart_FN3,PatternScan_PROTEIN_KINASE_TYR,superfamily_FN_III-like,superfamily_Gal_bind_like,superfamily_SAM_homology,superfamily_Kinase_like,PatternScan_EGF_2,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 1114 46 3.96 486 391 44.58 NA 123172 TCGA-AB-2963 AML03 1 29829614 29829614 C A SNP - - - - - - - - - - - - - - - tier3 774 33 4.09 319 256 44.44 0 0 NA 123172 TCGA-AB-2963 AML03 1 38279463 38279463 G A SNP FHL3 NM_004468.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41792 NULL 0.001 - - - no_errors tier2 1388 34 2.38 293 255 46.53 0 0 NA 123172 TCGA-AB-2963 AML03 1 42221824 42221824 A T SNP - - - - - - - - - - - - - - - tier3 1358 47 3.34 1048 889 45.9 0 0 NA 123172 TCGA-AB-2963 AML03 1 48127770 48127770 C G SNP LOC388630 XM_371250.2 human genbank 54_36p -1 model intronic c.1297-87892 e4-87892 0.002 - - - no_errors tier2 529 29 5.19 180 159 46.9 0 0 NA 123172 TCGA-AB-2963 AML03 1 49772623 49772623 G A SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.282+162949 e3+162949 0.003 - - - no_errors tier3 528 11 2.04 447 336 42.86 0 0 NA 123172 TCGA-AB-2963 AML03 1 54945453 54945453 G A SNP C1orf175 NM_001039464.2 human genbank 54_36p 1 validated intronic c.3658+655 e20+655 0.207 - - - no_errors tier3 1044 4 0.38 547 165 23.14 2 0 0 123172 TCGA-AB-2963 AML03 1 55799384 55799384 T C SNP - - - - - - - - - - - - - - - tier3 628 24 3.68 757 692 47.76 0 0 NA 123172 TCGA-AB-2963 AML03 1 57231018 57231018 C A SNP C8B NM_000066.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-26809 NULL 0.022 - - - no_errors tier2 491 20 3.91 333 263 44.13 0 0 NA 123172 TCGA-AB-2963 AML03 1 73117191 73117191 G T SNP - - - - - - - - - - - - - - - tier3 547 3 0.55 290 214 42.46 0 0 NA 123172 TCGA-AB-2963 AML03 1 93082134 93082134 C T SNP FAM69A ENST00000370310 human ensembl 54_36p -1 known silent c.681 p.V227 1 NULL NULL - no_errors tier1 664 15 2.21 694 528 43.14 3 1 25 123172 TCGA-AB-2963 AML03 1 95617708 95617708 G A SNP - - - - - - - - - - - - - - - tier2 533 6 1.11 734 550 42.83 0 0 NA 123172 TCGA-AB-2963 AML03 1 105984804 105984804 C A SNP - - - - - - - - - - - - - - - tier3 289 3 1.03 251 168 40.1 0 0 NA 123172 TCGA-AB-2963 AML03 1 155282905 155282905 C T SNP ARHGEF11 NM_198236.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2159 NULL 0.006 - - - no_errors tier3 383 14 3.52 139 112 44.62 0 0 NA 123172 TCGA-AB-2963 AML03 1 161691271 161691271 C T SNP ENSG00000218131 ENST00000401780 human ensembl 54_36p -1 known 5_prime_flanking_region c.-31693 NULL 0 - - - no_coding_region:pseudogene tier3 775 9 1.15 437 241 35.55 0 0 NA 123172 TCGA-AB-2963 AML03 1 162293864 162293864 G A SNP - - - - - - - - - - - - - - - tier3 690 14 1.98 409 390 48.81 0 0 NA 123172 TCGA-AB-2963 AML03 1 171327962 171327962 A G SNP TNFSF18 NM_005092.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-41237 NULL 0.04 - - - no_errors tier3 353 12 3.28 534 436 44.9 0 0 NA 123172 TCGA-AB-2963 AML03 1 180294095 180294095 G C SNP ZNF648 NM_001009992.1 human genbank 54_36p -1 provisional intronic c.1-264 e1-264 0.008 - - - no_errors tier2 686 26 3.65 321 289 47.3 0 0 NA 123172 TCGA-AB-2963 AML03 1 184611861 184611861 T C SNP C1orf27 ENST00000287859 human ensembl 54_36p 1 known intronic c.1+132 e0+132 0 - - - no_errors tier2 176 6 3.28 196 200 50.51 0 0 0 123172 TCGA-AB-2963 AML03 1 190120830 190120830 T C SNP - - - - - - - - - - - - - - - tier3 131 2 1.5 198 171 46.34 0 2 100 123172 TCGA-AB-2963 AML03 1 195737411 195737411 G A SNP CRB1 NM_201253.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*23779 NULL 0 - - - no_errors tier2 75 1 1.32 85 59 40.97 0 0 NA 123172 TCGA-AB-2963 AML03 1 208533618 208533618 A G SNP LOC100131961 XR_036984.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - pseudogene tier3 686 2 0.29 522 388 42.64 0 0 NA 123172 TCGA-AB-2963 AML03 1 208540718 208540718 C T SNP LOC100131961 XR_036984.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.997 - - - pseudogene tier2 475 15 3.06 477 400 45.61 0 0 NA 123172 TCGA-AB-2963 AML03 1 213028655 213028655 T A SNP - - - - - - - - - - - - - - - tier3 1496 29 1.89 790 586 42.56 0 0 NA 123172 TCGA-AB-2963 AML03 1 216643588 216643588 C T SNP TGFB2 NM_003238.1 human genbank 54_36p 1 validated intronic c.347-1546 e2-1546 0.042 - - - no_errors tier3 1812 61 3.25 1207 200 14.21 0 0 NA 123172 TCGA-AB-2963 AML03 1 217480030 217480030 G A SNP ENSG00000220015 ENST00000406758 human ensembl 54_36p -1 known 5_prime_flanking_region c.-39498 NULL 0.558 - - - no_coding_region:pseudogene tier2 432 23 5.05 446 371 45.41 0 0 NA 123172 TCGA-AB-2963 AML03 1 217951683 217951683 G T SNP ENSG00000222688 ENST00000410756 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48251 NULL 0 - - - no_errors tier3 618 12 1.9 352 295 45.6 0 0 NA 123172 TCGA-AB-2963 AML03 1 219803093 219803093 C T SNP ENSG00000216641 ENST00000404741 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12485 NULL 0.009 - - - no_coding_region:pseudogene tier3 469 36 7.13 472 393 45.43 0 0 NA 123172 TCGA-AB-2963 AML03 1 234869254 234869254 C G SNP ACTN2 NM_001103.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47343 NULL 0.004 - - - no_errors tier3 481 20 3.97 526 450 46.11 0 0 NA 123172 TCGA-AB-2963 AML03 1 245175636 245175636 C T SNP ZNF695 ENST00000366504 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*86 NULL 0 - - - no_errors tier3 750 1 0.13 355 124 25.89 7 0 0 123172 TCGA-AB-2963 AML03 2 3855901 3855901 G A SNP - - - - - - - - - - - - - - - tier3 741 13 1.72 585 534 47.72 0 0 NA 123172 TCGA-AB-2963 AML03 2 4484930 4484930 G T SNP - - - - - - - - - - - - - - - tier3 422 7 1.63 752 128 14.55 0 0 NA 123172 TCGA-AB-2963 AML03 2 12035572 12035572 G A SNP LOC729992 XR_038318.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-45479 NULL 0.001 - - - pseudogene tier3 1286 14 1.08 1022 365 26.3 0 0 NA 123172 TCGA-AB-2963 AML03 2 12124977 12124977 C T SNP LOC729992 XR_038318.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*42954 NULL 0.002 - - - pseudogene tier3 2009 77 3.68 1023 770 42.92 0 0 NA 123172 TCGA-AB-2963 AML03 2 17801849 17801849 C T SNP GEN1 NM_182625.1 human genbank 54_36p 1 validated intronic c.1-2828 e1-2828 0.015 - - - no_errors tier3 61 0 0 82 45 35.43 8 1 11.11 123172 TCGA-AB-2963 AML03 2 22272903 22272903 C T SNP ENSG00000219751 ENST00000393411 human ensembl 54_36p 1 known 3_prime_flanking_region c.*6213 NULL 0 - - - no_coding_region:pseudogene tier3 515 19 3.56 381 307 44.62 0 0 NA 123172 TCGA-AB-2963 AML03 2 31429056 31429056 C T SNP XDH NM_000379.3 human genbank 54_36p -1 reviewed intronic c.2632-2463 e25-2463 0.221 - - - no_errors tier3 304 10 3.18 153 116 43.12 0 0 NA 123172 TCGA-AB-2963 AML03 2 34326394 34326394 G T SNP - - - - - - - - - - - - - - - tier3 589 9 1.51 607 434 41.69 0 0 NA 123172 TCGA-AB-2963 AML03 2 39098931 39098931 T C SNP SOS1 NM_005633.3 human genbank 54_36p -1 reviewed intronic c.1859-3440 e11-3440 0 - - - no_errors tier3 262 12 4.33 495 393 44.26 0 0 0 123172 TCGA-AB-2963 AML03 2 51893677 51893677 A G SNP ENSG00000218271 ENST00000401794 human ensembl 54_36p -1 known 5_prime_flanking_region c.-37633 NULL 0.001 - - - no_coding_region:pseudogene tier3 1148 5 0.43 451 443 49.55 0 0 NA 123172 TCGA-AB-2963 AML03 2 53194588 53194588 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 2 55825652 55825652 C T SNP - - - - - - - - - - - - - - - tier3 305 3 0.97 345 288 45.43 0 0 NA 123172 TCGA-AB-2963 AML03 2 61245535 61245535 A G SNP AHSA2 NM_152392.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-19830 NULL 0.011 - - - no_errors tier3 2099 47 2.19 633 514 44.81 0 0 NA 123172 TCGA-AB-2963 AML03 2 70238938 70238938 A C SNP C2orf42 NM_017880.1 human genbank 54_36p -1 predicted intronic c.1516+2323 e7+2323 0.445 - - - no_errors tier2 284 3 1.05 286 87 23.32 0 3 100 123172 TCGA-AB-2963 AML03 2 71444154 71444154 G T SNP ZNF638 NM_001014972.1 human genbank 54_36p 1 reviewed intronic c.1418+325 e3+325 0 - - - no_errors tier3 98 1 1.01 221 277 55.62 0 2 100 123172 TCGA-AB-2963 AML03 2 75225048 75225048 T C SNP TACR1 NM_001058.3 human genbank 54_36p -1 reviewed intronic c.390-23646 e2-23646 0.336 - - - no_errors tier3 1002 13 1.28 706 652 47.94 0 0 NA 123172 TCGA-AB-2963 AML03 2 76907536 76907536 C G SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1555-77986 e3-77986 0.006 - - - no_errors tier3 851 4 0.47 978 311 24.13 0 0 NA 123172 TCGA-AB-2963 AML03 2 78519868 78519868 A G SNP ENSG00000214429 ENST00000398312 human ensembl 54_36p -1 known intronic c.1-26058 e1-26058 0 - - - no_errors tier3 210 3 1.4 426 354 45.33 0 0 NA 123172 TCGA-AB-2963 AML03 2 91123611 91123611 A G SNP ENSG00000219041 ENST00000405516 human ensembl 54_36p 1 known intronic c.300+80498 e1+80498 0 - - - no_start_codon:no_stop_codon tier3 1476 37 2.44 1188 119 9.09 0 0 NA 123172 TCGA-AB-2963 AML03 2 104180720 104180720 G A SNP - - - - - - - - - - - - - - - tier3 444 18 3.89 464 343 42.5 0 0 NA 123172 TCGA-AB-2963 AML03 2 104394716 104394716 C T SNP - - - - - - - - - - - - - - - tier3 1035 18 1.71 540 527 49.34 0 0 NA 123172 TCGA-AB-2963 AML03 2 111457123 111457123 C T SNP ACOXL NM_001105516.2 human genbank 54_36p 1 validated intronic c.1150-4033 e13-4033 0.001 - - - no_errors tier3 1174 21 1.75 523 424 44.68 0 0 NA 123172 TCGA-AB-2963 AML03 2 115910038 115910038 A C SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.272-63518 e4-63518 0.002 - - - no_errors tier3 585 12 2.01 226 227 50.11 0 0 NA 123172 TCGA-AB-2963 AML03 2 125411671 125411671 G T SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*23336 NULL 0.002 - - - no_errors tier3 2850 149 4.96 1493 1308 46.68 0 0 NA 123172 TCGA-AB-2963 AML03 2 127204609 127204609 G C SNP ENSG00000206963 ENST00000384236 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27621 NULL 0.004 - - - no_errors tier3 404 9 2.16 474 414 46.62 0 0 NA 123172 TCGA-AB-2963 AML03 2 127668401 127668401 G T SNP CYP27C1 NM_001001665.3 human genbank 54_36p -1 reviewed intronic c.720-488 e5-488 0 - - - no_errors tier3 195 1 0.51 259 198 43.33 0 0 NA 123172 TCGA-AB-2963 AML03 2 128581156 128581156 T C SNP UGCGL1 NM_020120.1 human genbank 54_36p 1 validated intronic c.278-826 e4-826 0.005 - - - no_errors tier3 102 0 0 137 111 44.76 0 0 0 123172 TCGA-AB-2963 AML03 2 133937241 133937241 G A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.69+54258 e1+54258 1 - - - no_errors tier2 300 12 3.85 413 354 46.09 0 0 NA 123172 TCGA-AB-2963 AML03 2 137697345 137697345 C T SNP THSD7B NM_001080427.1 human genbank 54_36p 1 provisional intronic c.1631-7739 e7-7739 0 - - - no_errors tier3 2100 47 2.19 978 847 46.36 0 0 NA 123172 TCGA-AB-2963 AML03 2 138217252 138217252 T C SNP ENSG00000222394 ENST00000410462 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*27770 NULL 0 - - - no_errors tier3 516 13 2.45 410 301 42.33 0 0 NA 123172 TCGA-AB-2963 AML03 2 140964963 140964963 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.9120+1684 e57+1684 0.001 - - - no_errors tier3 923 27 2.84 492 405 45.15 0 0 NA 123172 TCGA-AB-2963 AML03 2 155011069 155011069 C G SNP GALNT13 NM_052917.2 human genbank 54_36p 1 validated intronic c.1531-4100 e11-4100 0 - - - no_errors tier3 176 4 2.21 379 344 47.51 0 0 NA 123172 TCGA-AB-2963 AML03 2 159322859 159322859 G A SNP DAPL1 NM_001017920.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37272 NULL 0.02 - - - no_errors tier3 1952 65 3.22 612 499 44.91 0 0 NA 123172 TCGA-AB-2963 AML03 2 159655011 159655011 C A SNP TANC1 NM_033394.1 human genbank 54_36p 1 validated intronic c.62-7384 e2-7384 0 - - - no_errors tier3 975 24 2.4 533 418 43.86 0 0 NA 123172 TCGA-AB-2963 AML03 2 161652011 161652011 C G SNP TANK NM_004180.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-92409 NULL 0.001 - - - no_errors tier3 641 36 5.3 683 536 43.86 0 0 NA 123172 TCGA-AB-2963 AML03 2 163394219 163394219 A G SNP KCNH7 NM_033272.2 human genbank 54_36p -1 reviewed intronic c.307+7074 e2+7074 0 - - - no_errors tier3 652 17 2.54 517 373 41.86 0 0 NA 123172 TCGA-AB-2963 AML03 2 165590951 165590951 G T SNP - - - - - - - - - - - - - - - tier3 720 16 2.17 491 448 47.71 0 0 NA 123172 TCGA-AB-2963 AML03 2 172275222 172275222 G - DEL DYNC1I2 NM_001378.1 human genbank 54_36p 1 provisional intronic c.336-2301 e5-2301 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 2 174179555 174179555 G A SNP - - - - - - - - - - - - - - - tier3 2454 38 1.52 818 583 41.58 0 0 NA 123172 TCGA-AB-2963 AML03 2 176132037 176132037 G A SNP - - - - - - - - - - - - - - - tier3 783 15 1.88 539 422 43.91 0 0 NA 123172 TCGA-AB-2963 AML03 2 177247331 177247331 C T SNP LOC375295 XM_374020.1 human genbank 54_36p -1 model intronic c.636+5658 e4+5658 0 - - - no_errors tier3 189 3 1.55 249 239 48.98 0 0 NA 123172 TCGA-AB-2963 AML03 2 178262835 178262835 C A SNP PDE11A NM_016953.1 human genbank 54_36p -1 reviewed intronic c.2345+7471 e15+7471 0 - - - no_errors tier3 1117 19 1.67 593 490 45.24 0 0 NA 123172 TCGA-AB-2963 AML03 2 182031396 182031396 A G SNP ITGA4 NM_000885.4 human genbank 54_36p 1 reviewed intronic c.319+107 e2+107 0.001 - - - no_errors tier3 318 11 3.32 319 246 43.54 4 4 50 123172 TCGA-AB-2963 AML03 2 189670461 189670461 C A SNP COL5A2 NM_000393.3 human genbank 54_36p -1 reviewed intronic c.403-160 e6-160 0.001 - - - no_errors tier3 352 5 1.39 365 258 41.41 0 0 NA 123172 TCGA-AB-2963 AML03 2 196213362 196213362 C T SNP SLC39A10 NM_020342.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-39650 NULL 0 - - - no_errors tier3 666 28 4.01 439 309 41.31 0 0 NA 123172 TCGA-AB-2963 AML03 2 199439884 199439884 G A SNP - - - - - - - - - - - - - - - tier3 465 11 2.31 280 232 45.31 0 0 NA 123172 TCGA-AB-2963 AML03 2 203613328 203613332 CATGC - DEL LOC100129743 XM_001724736.1 human genbank 54_36p 1 model frame_shift_del c.253_257 p.A86fs 0.952:0.949:0.939:0.920:0.925 NULL "HMMPfam_Ribosomal_L30,superfamily_Ribosomal protein L30p/L7e,PatternScan_RIBOSOMAL_L30" - pseudogene tier1 NA NA NA NA NA NA NA 123172 TCGA-AB-2963 AML03 2 204933892 204933892 C A SNP - - - - - - - - - - - - - - - tier3 1288 12 0.92 792 560 41.39 0 0 NA 123172 TCGA-AB-2963 AML03 2 212289763 212289763 G C SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.884-3145 e8-3145 0 - - - no_errors tier3 787 12 1.5 694 536 43.51 0 0 NA 123172 TCGA-AB-2963 AML03 2 212435412 212435412 G A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.422-74283 e4-74283 0.005 - - - no_errors tier2 305 12 3.77 295 221 42.83 0 0 NA 123172 TCGA-AB-2963 AML03 2 212814804 212814804 G C SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.83-116931 e2-116931 0.001 - - - no_errors tier3 81 0 0 261 48 15.48 0 0 NA 123172 TCGA-AB-2963 AML03 2 238150673 238150673 G A SNP RAB17 NM_022449.2 human genbank 54_36p -1 provisional missense c.401 p.T134M 0.991 "HMMSmart_RAB,HMMPfam_Ras,superfamily_SSF52540" "HMMSmart_RAB,HMMPfam_Ras,superfamily_SSF52540" - no_errors tier1 1061 33 3.01 295 257 46.47 NA 123172 TCGA-AB-2963 AML03 3 438376 438376 A G SNP CHL1 NM_006614.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*15982 NULL 0.005 - - - no_errors tier3 713 25 3.39 491 355 41.96 0 0 NA 123172 TCGA-AB-2963 AML03 3 2044985 2044985 G A SNP - - - - - - - - - - - - - - - tier3 761 16 2.06 587 126 17.67 0 0 NA 123172 TCGA-AB-2963 AML03 3 2886859 2886859 C A SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.652+3226 e5+3226 0 - - - no_errors tier2 1712 44 2.5 516 422 44.99 0 0 NA 123172 TCGA-AB-2963 AML03 3 2888603 2888603 C T SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.652+4970 e5+4970 0.008 - - - no_errors tier3 254 11 4.14 142 133 48.36 0 0 NA 123172 TCGA-AB-2963 AML03 3 10713280 10713280 C T SNP ATP2B2 ENST00000397077 human ensembl 54_36p -1 known intronic c.1+11320 e0+11320 0 - - - no_errors tier3 2567 109 4.06 502 413 44.94 0 0 NA 123172 TCGA-AB-2963 AML03 3 21803329 21803329 C T SNP ZNF385D NM_024697.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-35917 NULL 0.999 - - - no_errors tier2 593 6 1 295 217 42.38 0 0 NA 123172 TCGA-AB-2963 AML03 3 27043413 27043413 G A SNP - - - - - - - - - - - - - - - tier3 892 20 2.18 703 553 43.99 0 0 NA 123172 TCGA-AB-2963 AML03 3 29411767 29411767 T A SNP RBMS3 NM_001003793.1 human genbank 54_36p 1 reviewed intronic c.76-39471 e2-39471 0.002 - - - no_errors tier3 910 27 2.88 360 353 49.51 0 0 NA 123172 TCGA-AB-2963 AML03 3 31120388 31120388 T A SNP - - - - - - - - - - - - - - - tier3 2282 2 0.09 1190 378 24.08 0 0 NA 123172 TCGA-AB-2963 AML03 3 35317594 35317594 C T SNP ENSG00000212442 ENST00000391140 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-44152 NULL 0.002 - - - no_errors tier3 653 4 0.61 443 328 42.49 0 0 NA 123172 TCGA-AB-2963 AML03 3 39200300 39200300 C A SNP XIRP1 NM_194293.2 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*109 NULL 0.028 - - - no_errors tier3 683 33 4.58 327 258 43.95 0 0 NA 123172 TCGA-AB-2963 AML03 3 39687915 39687915 C T SNP - - - - - - - - - - - - - - - tier3 691 7 1 742 530 41.67 0 0 NA 123172 TCGA-AB-2963 AML03 3 40249180 40249180 T C SNP MYRIP NM_015460.2 human genbank 54_36p 1 validated intronic c.1906-1174 e11-1174 0 - - - no_errors tier3 726 8 1.09 565 484 46.1 0 3 100 123172 TCGA-AB-2963 AML03 3 54985848 54985848 C T SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.2556+6937 e29+6937 0.009 - - - no_errors tier3 273 13 4.55 153 134 46.69 0 0 0 123172 TCGA-AB-2963 AML03 3 65032118 65032118 G A SNP - - - - - - - - - - - - - - - tier3 620 13 2.05 328 247 42.96 0 0 NA 123172 TCGA-AB-2963 AML03 3 75483319 75483319 T A SNP LOC339879 XM_291054.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-47203 NULL 0.122 - - - pseudogene tier3 1328 31 2.27 366 352 48.89 0 0 NA 123172 TCGA-AB-2963 AML03 3 76962183 76962183 G A SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-267672 e2-267672 0 - - - no_stop_codon:overly_large_intron tier2 1286 23 1.75 556 429 43.51 0 0 NA 123172 TCGA-AB-2963 AML03 3 77660634 77660634 C T SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.934+5891 e6+5891 0.035 - - - no_errors tier2 144 0 0 222 162 41.97 0 0 NA 123172 TCGA-AB-2963 AML03 3 78523328 78523328 T A SNP - - - - - - - - - - - - - - - tier2 1013 15 1.46 644 151 18.99 0 0 NA 123172 TCGA-AB-2963 AML03 3 86440519 86440519 G A SNP - - - - - - - - - - - - - - - tier3 502 3 0.59 719 182 20.2 0 0 NA 123172 TCGA-AB-2963 AML03 3 87244095 87244095 T C SNP - - - - - - - - - - - - - - - tier3 130 3 2.26 245 169 40.82 0 0 NA 123172 TCGA-AB-2963 AML03 3 100739392 100739392 A T SNP - - - - - - - - - - - - - - - tier3 680 45 6.19 533 500 48.26 0 0 NA 123172 TCGA-AB-2963 AML03 3 104313394 104313394 A G SNP ENSG00000201922 ENST00000365052 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48100 NULL 0.074 - - - no_errors tier3 366 13 3.42 394 363 47.89 0 0 NA 123172 TCGA-AB-2963 AML03 3 106467145 106467145 C G SNP - - - - - - - - - - - - - - - tier3 93 6 6.06 146 104 41.6 0 0 NA 123172 TCGA-AB-2963 AML03 3 107609661 107609661 G A SNP LOC728784 XM_001128470.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23441 NULL 0.001 - - - no_errors tier3 379 6 1.55 321 266 45.16 0 0 NA 123172 TCGA-AB-2963 AML03 3 120070570 120070570 A G SNP IGSF11 NM_001015887.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*33487 NULL 0.001 - - - no_errors tier3 423 10 2.3 305 254 45.44 0 0 NA 123172 TCGA-AB-2963 AML03 3 120380102 120380102 G A SNP UPK1B NM_006952.3 human genbank 54_36p 1 reviewed intronic c.1+4927 e0+4927 0.003 - - - no_errors tier3 1602 23 1.42 731 634 46.41 3 0 0 123172 TCGA-AB-2963 AML03 3 123322701 123322701 C T SNP CD86 NM_175862.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*1630 NULL 0.002 - - - no_errors tier3 1226 15 1.21 670 224 25.06 2 0 0 123172 TCGA-AB-2963 AML03 3 124588700 124588700 A C SNP ADCY5 NM_183357.1 human genbank 54_36p -1 validated intronic c.1135-34582 e2-34582 0 - - - no_errors tier3 728 20 2.67 305 267 46.6 0 0 NA 123172 TCGA-AB-2963 AML03 3 139201471 139201471 G A SNP CLDN18 NM_001002026.2 human genbank 54_36p 1 validated intronic c.220+851 e1+851 0.003 - - - no_errors tier3 88 1 1.11 97 95 49.48 0 0 NA 123172 TCGA-AB-2963 AML03 3 142454335 142454335 G A SNP ACPL2 NM_001037172.1 human genbank 54_36p 1 validated intronic c.1-7320 e1-7320 0.001 - - - no_errors tier3 1452 18 1.22 512 411 44.29 0 0 0 123172 TCGA-AB-2963 AML03 3 187288574 187288574 C T SNP ETV5 NM_004454.2 human genbank 54_36p -1 validated intronic c.233-6916 e5-6916 0 - - - no_errors tier3 829 10 1.19 395 297 42.86 0 0 0 123172 TCGA-AB-2963 AML03 3 188885134 188885134 A G SNP SST NM_001048.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14361 NULL 0 - - - no_errors tier3 440 13 2.87 270 240 47.06 0 0 NA 123172 TCGA-AB-2963 AML03 3 192158456 192158456 C G SNP - - - - - - - - - - - - - - - tier3 72 1 1.37 131 115 46.75 0 0 NA 123172 TCGA-AB-2963 AML03 3 193239823 193239823 G A SNP - - - - - - - - - - - - - - - tier3 905 20 2.16 567 492 46.46 0 0 NA 123172 TCGA-AB-2963 AML03 3 196114167 196114167 A C SNP - - - - - - - - - - - - - - - tier3 1434 74 4.9 664 572 46.24 0 0 NA 123172 TCGA-AB-2963 AML03 4 10598163 10598163 G A SNP - - - - - - - - - - - - - - - tier3 976 38 3.74 610 194 24.1 0 0 NA 123172 TCGA-AB-2963 AML03 4 18877491 18877491 C T SNP - - - - - - - - - - - - - - - tier3 1534 61 3.81 383 379 49.74 0 0 NA 123172 TCGA-AB-2963 AML03 4 18944899 18944899 C A SNP - - - - - - - - - - - - - - - tier3 823 15 1.79 585 405 40.91 0 0 NA 123172 TCGA-AB-2963 AML03 4 23796785 23796785 G A SNP - - - - - - - - - - - - - - - tier3 756 5 0.66 423 277 39.57 0 0 NA 123172 TCGA-AB-2963 AML03 4 23984451 23984451 G T SNP ENSG00000222262 ENST00000410330 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*47446 NULL 0.022 - - - no_errors tier3 1424 18 1.25 526 102 16.24 0 0 NA 123172 TCGA-AB-2963 AML03 4 31040775 31040775 C A SNP - - - - - - - - - - - - - - - tier3 500 11 2.15 227 189 45.32 0 0 NA 123172 TCGA-AB-2963 AML03 4 31248271 31248271 C A SNP - - - - - - - - - - - - - - - tier3 297 0 0 205 188 47.84 0 0 NA 123172 TCGA-AB-2963 AML03 4 32342893 32342893 T C SNP - - - - - - - - - - - - - - - tier3 1348 2 0.15 979 332 25.32 0 0 NA 123172 TCGA-AB-2963 AML03 4 37123097 37123097 A G SNP KIAA1239 ENST00000309447 human ensembl 54_36p 1 known missense c.1358 p.N453S 1 "HMMSmart_SM00320,superfamily_WD40 repeat-like" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1" - no_start_codon tier1 569 8 1.39 264 237 47.31 NA 123172 TCGA-AB-2963 AML03 4 38984633 38984633 T C SNP RFC1 NM_002913.3 human genbank 54_36p -1 reviewed missense c.1969 p.T657A 1 "HMMSmart_AAA,HMMPfam_AAA,superfamily_SSF52540" "HMMPfam_BRCT,HMMSmart_BRCT,superfamily_BRCT,HMMSmart_AAA,HMMPfam_AAA,superfamily_Pol_clamp_load_C,HMMPfam_RFC1,superfamily_SSF52540" - no_errors tier1 1011 18 1.75 999 807 44.59 17 23 57.5 123172 TCGA-AB-2963 AML03 4 44028912 44028912 C T SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated intronic c.961+115425 e1+115425 0 - - - no_errors tier3 390 0 0 415 117 21.99 0 0 NA 123172 TCGA-AB-2963 AML03 4 54406354 54406354 G A SNP - - - - - - - - - - - - - - - tier3 594 20 3.26 1028 761 42.47 0 0 NA 123172 TCGA-AB-2963 AML03 4 61542561 61542561 C G SNP - - - - - - - - - - - - - - - tier3 516 5 0.96 509 391 43.44 0 0 NA 123172 TCGA-AB-2963 AML03 4 61941967 61941967 C G SNP ENSG00000205682 ENST00000381217 human ensembl 54_36p -1 known 3_prime_flanking_region c.*33715 NULL 0 - - - no_errors tier3 77 3 3.75 87 55 38.73 0 0 NA 123172 TCGA-AB-2963 AML03 4 67355471 67355471 A T SNP - - - - - - - - - - - - - - - tier3 507 11 2.12 259 220 45.83 0 0 NA 123172 TCGA-AB-2963 AML03 4 71221101 71221101 C T SNP C4orf35 NM_033122.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14245 NULL 0.001 - - - no_errors tier3 640 9 1.39 835 712 45.94 0 0 NA 123172 TCGA-AB-2963 AML03 4 71227127 71227127 A G SNP C4orf35 NM_033122.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-8219 NULL 0 - - - no_errors tier3 693 17 2.39 654 537 45.09 0 0 NA 123172 TCGA-AB-2963 AML03 4 84289126 84289126 T C SNP PLAC8 NM_016619.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41028 NULL 0.002 - - - no_errors tier3 450 24 5.03 452 109 19.4 0 0 NA 123172 TCGA-AB-2963 AML03 4 85413028 85413028 G T SNP ENSG00000200108 ENST00000363238 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*39088 NULL 0.005 - - - no_errors tier3 679 2 0.29 730 228 23.77 0 0 NA 123172 TCGA-AB-2963 AML03 4 92438880 92438880 G T SNP LOC728394 XM_001130638.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*20378 NULL 0.037 - - - no_errors tier3 625 7 1.11 686 611 47.07 0 0 NA 123172 TCGA-AB-2963 AML03 4 93324586 93324586 T C SNP ENSG00000214910 ENST00000399219 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-424 NULL 0.014 - - - no_coding_region:pseudogene tier3 196 4 2 760 634 45.45 0 0 NA 123172 TCGA-AB-2963 AML03 4 104572163 104572163 G T SNP ENSG00000221522 ENST00000408595 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9361 NULL 0.003 - - - no_errors tier3 1106 8 0.72 1049 966 47.94 0 0 NA 123172 TCGA-AB-2963 AML03 4 112162433 112162433 G T SNP - - - - - - - - - - - - - - - tier3 570 7 1.21 327 228 41.08 0 0 NA 123172 TCGA-AB-2963 AML03 4 112989617 112989617 G A SNP - - - - - - - - - - - - - - - tier2 174 3 1.68 213 144 40.34 0 0 NA 123172 TCGA-AB-2963 AML03 4 118237960 118237960 C T SNP TRAM1L1 NM_152402.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11963 NULL 0 - - - no_errors tier3 254 6 2.31 224 206 47.91 0 0 NA 123172 TCGA-AB-2963 AML03 4 136665718 136665718 T A SNP - - - - - - - - - - - - - - - tier3 939 17 1.78 366 395 51.91 0 0 NA 123172 TCGA-AB-2963 AML03 4 138680241 138680241 A G SNP PCDH18 NM_019035.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7549 NULL 0 - - - no_errors tier3 251 6 2.33 213 175 45.1 0 0 NA 123172 TCGA-AB-2963 AML03 4 139754837 139754837 C G SNP ENSG00000196691 ENST00000357562 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8829 NULL 0.981 - - - no_coding_region:pseudogene tier3 570 3 0.52 429 371 46.38 0 0 NA 123172 TCGA-AB-2963 AML03 4 141913121 141913121 C A SNP TBC1D9 NM_015130.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16472 NULL 0 - - - no_errors tier3 635 7 1.09 333 298 47.23 0 0 NA 123172 TCGA-AB-2963 AML03 4 150288356 150288356 C T SNP - - - - - - - - - - - - - - - tier3 1012 7 0.69 457 326 41.63 0 0 NA 123172 TCGA-AB-2963 AML03 4 154105970 154105970 T A SNP FHDC1 NM_033393.2 human genbank 54_36p 1 validated intronic c.1100+393 e8+393 0.576 - - - no_errors tier3 321 3 0.92 324 347 51.71 0 0 NA 123172 TCGA-AB-2963 AML03 4 163152497 163152497 C A SNP FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.160+21730 e2+21730 0.005 - - - no_errors tier3 327 20 5.76 223 167 42.71 0 0 NA 123172 TCGA-AB-2963 AML03 4 188907678 188907678 A T SNP ENSG00000214607 ENST00000398655 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1358 NULL 0 - - - no_coding_region:pseudogene tier3 355 9 2.47 454 387 46.02 0 0 NA 123172 TCGA-AB-2963 AML03 5 960022 960022 C A SNP TRIP13 NM_004237.2 human genbank 54_36p 1 provisional intronic c.609-223 e7-223 0.004 - - - no_errors tier3 125 3 2.33 167 139 45.42 0 3 100 123172 TCGA-AB-2963 AML03 5 9197643 9197643 C T SNP SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.1482-7910 e11-7910 0.006 - - - no_errors tier3 990 0 0 625 191 23.38 0 0 NA 123172 TCGA-AB-2963 AML03 5 15761033 15761033 T A SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.127+91852 e2+91852 0 - - - no_errors tier3 810 17 2.05 627 584 48.15 0 0 NA 123172 TCGA-AB-2963 AML03 5 16270348 16270348 T A SNP MARCH11 NM_001102562.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-37664 NULL 0.028 - - - no_errors tier3 823 1 0.12 470 138 22.7 0 0 NA 123172 TCGA-AB-2963 AML03 5 20946298 20946298 T - DEL LOC100133741 XM_001714740.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*16817 NULL 0.345 - - - no_start_codon:pseudogene tier2 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 5 23740004 23740004 C T SNP - - - - - - - - - - - - - - - tier3 370 0 0 719 103 12.53 0 0 NA 123172 TCGA-AB-2963 AML03 5 24906566 24906566 C T SNP ENSG00000199911 ENST00000363041 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-39894 NULL 1 - - - no_errors tier2 451 14 3.01 418 311 42.6 0 0 NA 123172 TCGA-AB-2963 AML03 5 76329637 76329637 G A SNP AGGF1 NM_018046.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-32711 NULL 0 - - - no_errors tier3 560 8 1.41 291 214 42.38 0 1 100 123172 TCGA-AB-2963 AML03 5 80583725 80583725 G A SNP CKMT2 NM_001099735.1 human genbank 54_36p 1 reviewed intronic c.153-545 e2-545 0 - - - no_errors tier2 1325 70 5.02 598 455 43.17 2 0 0 123172 TCGA-AB-2963 AML03 5 83496744 83496744 G C SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.355+15223 e4+15223 0 - - - no_errors tier3 665 4 0.6 651 135 17.18 0 0 NA 123172 TCGA-AB-2963 AML03 5 84081487 84081487 A G SNP - - - - - - - - - - - - - - - tier3 161 1 0.61 166 144 46.45 0 0 NA 123172 TCGA-AB-2963 AML03 5 91271505 91271505 T C SNP - - - - - - - - - - - - - - - tier3 680 11 1.59 370 299 44.69 0 0 NA 123172 TCGA-AB-2963 AML03 5 92377047 92377047 C G SNP LOC391810 XM_001723772.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-46221 NULL 0.005 - - - pseudogene tier2 740 17 2.25 335 245 42.17 0 0 NA 123172 TCGA-AB-2963 AML03 5 93983155 93983155 G A SNP ANKRD32 ENST00000265140 human ensembl 54_36p 1 known intronic c.1+2929 e0+2929 0 - - - no_errors tier3 236 6 2.48 390 322 45.1 2 0 0 123172 TCGA-AB-2963 AML03 5 106275354 106275354 T C SNP - - - - - - - - - - - - - - - tier3 338 0 0 695 147 17.46 0 0 NA 123172 TCGA-AB-2963 AML03 5 111381668 111381669 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 5 113853899 113853899 A - DEL KCNN2 NM_021614.2 human genbank 54_36p 1 reviewed intronic c.1383-3100 e7-3100 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 5 116491277 116491277 C T SNP - - - - - - - - - - - - - - - tier3 782 15 1.88 660 495 42.86 0 0 NA 123172 TCGA-AB-2963 AML03 5 125316162 125316162 C T SNP - - - - - - - - - - - - - - - tier3 316 7 2.17 219 176 44.56 0 0 NA 123172 TCGA-AB-2963 AML03 5 137881160 137881160 A C SNP ETF1 NM_004730.2 human genbank 54_36p -1 validated missense c.391 p.F131V 1 "HMMPfam_eRF1_1,superfamily_N-terminal domain of eukaryotic peptide chain release factor subunit 1 ERF1" "HMMPfam_eRF1_1,HMMPfam_eRF1_2,HMMPfam_eRF1_3,superfamily_Translational machinery components,superfamily_L30e-like,superfamily_N-terminal domain of eukaryotic peptide chain release factor subunit 1 ERF1" - no_errors tier1 225 7 2.99 143 113 43.97 22 35 61.4 123172 TCGA-AB-2963 AML03 5 150181833 150181833 T C SNP MST150 NM_032947.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*26644 NULL 0.989 - - - no_errors tier2 60 3 4.76 147 149 50.17 0 0 NA 123172 TCGA-AB-2963 AML03 5 156127366 156127366 G C SNP ENSG00000199468 ENST00000362598 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46353 NULL 1 - - - no_errors tier2 495 21 4.05 418 384 47.7 0 0 NA 123172 TCGA-AB-2963 AML03 5 157783811 157783811 G T SNP - - - - - - - - - - - - - - - tier3 551 16 2.82 554 440 44.27 0 0 NA 123172 TCGA-AB-2963 AML03 5 170770152 170770153 - CCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 123172 TCGA-AB-2963 AML03 5 172677693 172677693 C T SNP STC2 NM_003714.2 human genbank 54_36p -1 reviewed silent c.672 p.E224 0.052 HMMPfam_Stanniocalcin HMMPfam_Stanniocalcin - no_errors tier1 547 12 2.15 143 131 47.81 NA 123172 TCGA-AB-2963 AML03 6 6167986 6167986 T C SNP F13A1 NM_000129.3 human genbank 54_36p -1 reviewed intronic c.974-583 e7-583 1 - - - no_errors tier2 1151 29 2.46 657 589 47.2 0 1 100 123172 TCGA-AB-2963 AML03 6 9084547 9084547 G A SNP LOC389365 XM_371797.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*48410 NULL 0 - - - no_errors tier3 1013 20 1.93 350 307 46.59 0 0 NA 123172 TCGA-AB-2963 AML03 6 10203027 10203027 G A SNP OFCC1 NM_153003.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-155508 NULL 0 - - - no_errors tier3 807 19 2.3 482 346 41.79 0 0 NA 123172 TCGA-AB-2963 AML03 6 13436862 13436862 C T SNP TBC1D7 ENST00000334971 human ensembl 54_36p -1 known intronic c.11-7549 e2-7549 0 - - - no_errors tier2 679 12 1.74 131 137 50.55 0 0 NA 123172 TCGA-AB-2963 AML03 6 20205615 20205615 T C SNP MBOAT1 NM_001080480.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*4881 NULL 0 - - - no_errors tier3 620 2 0.32 542 515 48.68 0 3 100 123172 TCGA-AB-2963 AML03 6 32243129 32243129 G A SNP EGFL8 NM_030652.2 human genbank 54_36p 1 validated missense c.626 p.R209H 0.574 NULL "PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,HMMPfam_EMI,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 2115 47 2.17 552 542 49.5 2 2 50 123172 TCGA-AB-2963 AML03 6 35651041 35651041 T C SNP FKBP5 NM_004117.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*549 NULL 0.001 - - - no_errors tier2 768 42 5.18 412 331 44.43 239 197 45.08 123172 TCGA-AB-2963 AML03 6 36312325 36312325 C T SNP PNPLA1 NM_173676.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-54830 NULL 0.005 - - - no_errors tier3 1471 76 4.9 507 340 40.09 0 0 NA 123172 TCGA-AB-2963 AML03 6 36829143 36829143 G C SNP CPNE5 NM_020939.1 human genbank 54_36p -1 reviewed intronic c.910-293 e14-293 0.005 - - - no_errors tier3 1328 17 1.26 506 383 43.08 1 0 0 123172 TCGA-AB-2963 AML03 6 42765657 42765657 A G SNP UBR2 NM_015255.1 human genbank 54_36p 1 provisional intronic c.5126+271 e46+271 0 - - - no_errors tier3 1702 28 1.62 504 455 47.4 3 2 40 123172 TCGA-AB-2963 AML03 6 50568624 50568624 C T SNP - - - - - - - - - - - - - - - tier3 699 28 3.85 997 708 41.45 0 0 NA 123172 TCGA-AB-2963 AML03 6 50717336 50717336 G A SNP - - - - - - - - - - - - - - - tier3 838 5 0.59 520 500 49.02 0 0 NA 123172 TCGA-AB-2963 AML03 6 54273945 54273945 G A SNP TINAG NM_014464.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7363 NULL 0 - - - no_errors tier3 1144 32 2.72 795 625 43.98 0 0 NA 123172 TCGA-AB-2963 AML03 6 55755727 55755727 T C SNP BMP5 NM_021073.2 human genbank 54_36p -1 reviewed intronic c.833-8727 e4-8727 0 - - - no_errors tier3 387 5 1.27 463 413 47.15 0 0 NA 123172 TCGA-AB-2963 AML03 6 74481174 74481174 C A SNP CD109 NM_133493.3 human genbank 54_36p 1 validated intronic c.248-8521 e3-8521 0 - - - no_errors tier3 440 7 1.57 443 348 43.99 0 0 NA 123172 TCGA-AB-2963 AML03 6 78576182 78576182 G A SNP ENSG00000214481 ENST00000398401 human ensembl 54_36p 1 known intronic c.775-19185 e4-19185 0 - - - no_stop_codon tier3 157 7 4.27 306 231 43.02 0 0 NA 123172 TCGA-AB-2963 AML03 6 79317874 79317874 A T SNP - - - - - - - - - - - - - - - tier3 1339 10 0.74 831 604 42.06 0 0 NA 123172 TCGA-AB-2963 AML03 6 82134996 82134996 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 6 90929454 90929454 C T SNP BACH2 NM_021813.2 human genbank 54_36p -1 validated intronic c.1+43555 e0+43555 0.024 - - - no_errors tier3 594 3 0.5 791 273 25.59 0 0 NA 123172 TCGA-AB-2963 AML03 6 93107027 93107028 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 6 94003699 94003699 C T SNP EPHA7 NM_004440.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*6166 NULL 0 - - - no_errors tier3 1016 31 2.96 469 309 39.72 0 0 NA 123172 TCGA-AB-2963 AML03 6 94108962 94108962 A C SNP EPHA7 NM_004440.3 human genbank 54_36p -1 reviewed intronic c.1324+14194 e5+14194 1 - - - no_errors tier2 264 13 4.69 354 306 46.36 0 0 NA 123172 TCGA-AB-2963 AML03 6 102761107 102761107 C T SNP - - - - - - - - - - - - - - - tier2 319 7 2.15 330 218 39.78 0 0 NA 123172 TCGA-AB-2963 AML03 6 109604481 109604481 T C SNP FLJ37396 XM_001722396.1 human genbank 54_36p 1 model intronic c.78-7342 e2-7342 0.007 - - - no_errors tier3 594 48 7.47 555 432 43.77 5 2 28.57 123172 TCGA-AB-2963 AML03 6 116973170 116973170 A G SNP FAM26D NM_153036.2 human genbank 54_36p 1 validated intronic c.1+1442 e0+1442 0 - - - no_errors tier3 139 3 2.11 232 177 43.28 0 0 NA 123172 TCGA-AB-2963 AML03 6 128204803 128204803 G A SNP C6orf190 NM_001010923.1 human genbank 54_36p -1 validated intronic c.251-12031 e3-12031 0.003 - - - no_errors tier2 449 9 1.97 394 322 44.97 0 0 NA 123172 TCGA-AB-2963 AML03 6 139330299 139330299 C T SNP REPS1 NM_031922.1 human genbank 54_36p -1 validated intronic c.1-19556 e1-19556 0.008 - - - no_errors tier3 431 2 0.46 361 238 39.73 1 1 50 123172 TCGA-AB-2963 AML03 6 141999053 141999053 T C SNP ENSG00000218351 ENST00000401762 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-141999053 NULL 0.978 - - - no_coding_region:pseudogene tier2 505 10 1.94 495 369 42.66 0 0 NA 123172 TCGA-AB-2963 AML03 6 150261299 150261299 G A SNP LRP11 NM_032832.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-34450 NULL 0 - - - no_errors tier3 1393 21 1.48 493 384 43.74 0 0 NA 123172 TCGA-AB-2963 AML03 6 155441654 155441654 T C SNP TIAM2 NM_012454.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-50396 NULL 0.001 - - - no_errors tier3 411 6 1.44 328 323 49.62 0 0 NA 123172 TCGA-AB-2963 AML03 6 157051068 157051068 A G SNP ENSG00000220347 ENST00000402808 human ensembl 54_36p 1 known 3_prime_flanking_region c.*25805 NULL 0 - - - no_coding_region:pseudogene tier3 507 4 0.78 286 234 45 0 0 NA 123172 TCGA-AB-2963 AML03 6 166047137 166047137 T A SNP ENSG00000206681 ENST00000383954 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*4576 NULL 0 - - - no_errors tier3 448 20 4.27 177 153 46.36 0 0 NA 123172 TCGA-AB-2963 AML03 6 169001562 169001562 C T SNP - - - - - - - - - - - - - - - tier3 207 9 4.17 221 164 42.6 0 0 NA 123172 TCGA-AB-2963 AML03 6 169885156 169885156 C T SNP TCTE3 NM_174910.1 human genbank 54_36p -1 provisional missense c.431 p.R144H 0.993 HMMPfam_Tctex-1 HMMPfam_Tctex-1 - no_errors tier1 179 4 2.19 258 206 44.21 2 0 123172 TCGA-AB-2963 AML03 7 3783385 3783385 C T SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.714-44223 e5-44223 0.032 - - - no_errors tier3 795 15 1.85 689 472 40.58 0 0 NA 123172 TCGA-AB-2963 AML03 7 10082192 10082192 C T SNP LOC340268 XR_041608.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.385 - - - no_errors tier2 675 13 1.88 485 406 45.52 0 0 NA 123172 TCGA-AB-2963 AML03 7 13671482 13671482 G A SNP - - - - - - - - - - - - - - - tier3 1652 42 2.48 1079 922 46.03 0 0 NA 123172 TCGA-AB-2963 AML03 7 18425688 18425688 A G SNP - - - - - - - - - - - - - - - tier3 737 2 0.27 887 146 14.11 2 1 33.33 123172 TCGA-AB-2963 AML03 7 28402452 28402452 C T SNP CREB5 NM_182899.1 human genbank 54_36p 1 reviewed intronic c.1+96867 e0+96867 0 - - - no_errors tier3 1091 27 2.41 314 290 48.01 0 0 NA 123172 TCGA-AB-2963 AML03 7 30025299 30025299 G A SNP FKBP14 NM_017946.2 human genbank 54_36p -1 validated intronic c.350-35 e3-35 0.002 - - - no_errors tier3 203 1 0.49 141 101 41.74 0 0 NA 123172 TCGA-AB-2963 AML03 7 34669751 34669751 C T SNP NPSR1 NM_207173.1 human genbank 54_36p 1 reviewed intronic c.147+5055 e1+5055 0 - - - no_errors tier3 1809 13 0.71 652 548 45.59 0 0 NA 123172 TCGA-AB-2963 AML03 7 41386040 41386040 C T SNP - - - - - - - - - - - - - - - tier3 606 19 3.04 466 328 41.31 0 0 NA 123172 TCGA-AB-2963 AML03 7 45489837 45489837 G A SNP - - - - - - - - - - - - - - - tier2 677 52 7.13 851 669 43.96 0 0 NA 123172 TCGA-AB-2963 AML03 7 45873822 45873822 G A SNP IGFBP1 NM_000596.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20955 NULL 0 - - - no_errors tier3 509 27 5.02 580 495 46.05 0 0 NA 123172 TCGA-AB-2963 AML03 7 47196543 47196543 A T SNP - - - - - - - - - - - - - - - tier3 831 12 1.41 480 395 44.89 0 0 NA 123172 TCGA-AB-2963 AML03 7 49046223 49046223 G A SNP - - - - - - - - - - - - - - - tier3 546 14 2.5 539 447 45.33 0 0 NA 123172 TCGA-AB-2963 AML03 7 51883566 51883566 A G SNP - - - - - - - - - - - - - - - tier3 1128 38 3.26 527 453 46.18 0 0 NA 123172 TCGA-AB-2963 AML03 7 78441180 78441180 C T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.418+33162 e2+33162 0 - - - no_errors tier3 869 6 0.68 839 260 23.66 0 0 NA 123172 TCGA-AB-2963 AML03 7 82378805 82378805 C T SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.13301-2540 e8-2540 0.001 - - - no_errors tier3 386 1 0.26 548 127 18.81 0 0 NA 123172 TCGA-AB-2963 AML03 7 85067891 85067891 G A SNP - - - - - - - - - - - - - - - tier3 864 16 1.82 584 542 48.09 0 0 NA 123172 TCGA-AB-2963 AML03 7 93169237 93169237 G A SNP - - - - - - - - - - - - - - - tier3 363 11 2.93 351 308 46.74 0 0 NA 123172 TCGA-AB-2963 AML03 7 98279279 98279279 C T SNP TRRAP NM_003496.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37431 NULL 0.064 - - - no_errors tier2 870 27 3 181 137 42.95 0 0 NA 123172 TCGA-AB-2963 AML03 7 113755843 113755843 G A SNP ENSG00000218695 ENST00000401993 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31124 NULL 0.003 - - - no_coding_region:pseudogene tier3 232 10 4.13 133 129 49.24 0 0 NA 123172 TCGA-AB-2963 AML03 7 118822723 118822723 G A SNP - - - - - - - - - - - - - - - tier3 539 0 0 343 81 19.1 0 0 NA 123172 TCGA-AB-2963 AML03 7 127409892 127409892 T C SNP SND1 NM_014390.2 human genbank 54_36p 1 validated intronic c.1670-8344 e16-8344 0.002 - - - no_errors tier3 469 13 2.7 616 506 45.06 1 4 80 123172 TCGA-AB-2963 AML03 7 134068707 134068707 C T SNP CALD1 NM_033138.5 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-134318 NULL 0.001 - - - no_errors tier3 836 11 1.29 372 248 40 0 0 NA 123172 TCGA-AB-2963 AML03 7 144614653 144614653 G T SNP - - - - - - - - - - - - - - - tier3 392 5 1.26 502 419 45.49 0 0 NA 123172 TCGA-AB-2963 AML03 7 155013509 155013509 G A SNP CNPY1 NM_001103176.1 human genbank 54_36p -1 validated intronic c.1+5707 e0+5707 0.001 - - - no_errors tier3 1124 43 3.68 344 290 45.74 0 0 NA 123172 TCGA-AB-2963 AML03 7 156474493 156474493 C T SNP LOC645249 XM_928291.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21476 NULL 0 - - - no_errors tier3 1232 15 1.2 280 240 46.07 0 0 NA 123172 TCGA-AB-2963 AML03 8 3406731 3406731 A C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1347+13144 e11+13144 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 2845 4 0.14 996 247 19.87 0 0 NA 123172 TCGA-AB-2963 AML03 8 3417014 3417014 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1347+2861 e11+2861 0.005 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 663 10 1.49 580 448 43.54 0 0 NA 123172 TCGA-AB-2963 AML03 8 15596997 15596997 C T SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed intronic c.798+21281 e6+21281 0 - - - no_errors tier3 861 35 3.89 561 499 47.03 0 0 NA 123172 TCGA-AB-2963 AML03 8 16555309 16555309 C A SNP - - - - - - - - - - - - - - - tier3 303 8 2.56 304 219 41.87 0 0 NA 123172 TCGA-AB-2963 AML03 8 20590103 20590103 C T SNP - - - - - - - - - - - - - - - tier3 816 17 2.04 561 457 44.85 0 0 NA 123172 TCGA-AB-2963 AML03 8 29130398 29130398 A G SNP KIF13B NM_015254.3 human genbank 54_36p -1 validated intronic c.150-20763 e3-20763 0.012 - - - no_errors tier3 949 14 1.45 304 197 39.24 0 0 0 123172 TCGA-AB-2963 AML03 8 60709317 60709317 A T SNP - - - - - - - - - - - - - - - tier3 291 8 2.68 196 158 44.63 0 0 NA 123172 TCGA-AB-2963 AML03 8 64871891 64871891 G A SNP - - - - - - - - - - - - - - - tier2 665 34 4.86 659 594 47.41 0 0 NA 123172 TCGA-AB-2963 AML03 8 75653337 75653337 G C SNP FLJ39080 XM_499117.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-34321 NULL 0.004 - - - no_errors tier3 633 15 2.31 278 239 46.23 0 0 NA 123172 TCGA-AB-2963 AML03 8 79723551 79723551 A G SNP FAM164A NM_016010.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17388 NULL 0.006 - - - no_errors tier3 555 11 1.94 296 313 51.4 0 0 NA 123172 TCGA-AB-2963 AML03 8 81166666 81166666 T G SNP TPD52 NM_001025253.1 human genbank 54_36p -1 validated intronic c.20-27283 e2-27283 0 - - - no_errors tier3 1012 79 7.23 537 514 48.81 0 0 0 123172 TCGA-AB-2963 AML03 8 88151775 88151775 A C SNP CNBD1 NM_173538.2 human genbank 54_36p 1 provisional intronic c.431+130677 e4+130677 0.002 - - - no_errors tier3 234 4 1.67 314 252 44.52 0 0 NA 123172 TCGA-AB-2963 AML03 8 101173331 101173331 G T SNP RGS22 NM_015668.3 human genbank 54_36p -1 validated intronic c.117+1520 e3+1520 0.001 - - - no_errors tier3 1512 51 3.26 788 656 45.43 0 0 NA 123172 TCGA-AB-2963 AML03 8 103992506 103992506 G A SNP AZIN1 NM_015878.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-67450 NULL 0.022 - - - no_errors tier3 739 14 1.86 333 265 44.24 0 0 NA 123172 TCGA-AB-2963 AML03 8 110616283 110616283 C G SNP EBAG9 NM_004215.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15947 NULL 0.001 - - - no_errors tier2 268 0 0 248 160 39.22 0 0 NA 123172 TCGA-AB-2963 AML03 8 114448475 114448475 A G SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.179-52277 e2-52277 0 - - - no_errors tier3 134 0 0 160 106 39.85 0 0 NA 123172 TCGA-AB-2963 AML03 8 117286013 117286013 T C SNP - - - - - - - - - - - - - - - tier3 330 5 1.49 366 301 44.99 0 0 NA 123172 TCGA-AB-2963 AML03 8 118975924 118975924 C A SNP EXT1 NM_000127.2 human genbank 54_36p -1 reviewed intronic c.963-57303 e2-57303 0.002 - - - no_errors tier3 949 4 0.42 615 104 14.44 0 0 0 123172 TCGA-AB-2963 AML03 8 131327539 131327539 A G SNP ASAP1 NM_018482.2 human genbank 54_36p -1 validated intronic c.187-9117 e3-9117 0.002 - - - no_errors tier3 1878 33 1.73 822 675 45.09 0 0 0 123172 TCGA-AB-2963 AML03 8 132510955 132510955 G T SNP - - - - - - - - - - - - - - - tier2 1344 14 1.03 796 233 22.58 0 0 NA 123172 TCGA-AB-2963 AML03 8 138496897 138496897 T C SNP - - - - - - - - - - - - - - - tier3 1383 29 2.05 1328 1195 47.35 0 0 NA 123172 TCGA-AB-2963 AML03 9 4128323 4128323 G A SNP GLIS3 NM_001042413.1 human genbank 54_36p -1 reviewed intronic c.389-12382 e2-12382 0 - - - no_errors tier2 703 35 4.74 744 757 50.4 0 0 NA 123172 TCGA-AB-2963 AML03 9 4413309 4413309 C T SNP ENSG00000200941 ENST00000364071 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36802 NULL 0.001 - - - no_errors tier3 1628 5 0.31 1336 274 17 0 0 NA 123172 TCGA-AB-2963 AML03 9 7533568 7533568 A G SNP LOC392285 XR_017134.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-30693 NULL 0.001 - - - pseudogene tier3 1262 17 1.33 634 591 48.21 0 0 NA 123172 TCGA-AB-2963 AML03 9 10309805 10309805 A G SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1+21158 e0+21158 0.002 - - - no_errors tier3 691 12 1.71 788 227 22.36 0 0 NA 123172 TCGA-AB-2963 AML03 9 10731295 10731295 G T SNP ENSG00000219748 ENST00000401476 human ensembl 54_36p 1 known 5_prime_flanking_region c.-36062 NULL 0 - - - no_coding_region:pseudogene tier3 527 4 0.75 527 101 16.08 0 0 NA 123172 TCGA-AB-2963 AML03 9 18474039 18474039 G A SNP ADAMTSL1 NM_001040272.4 human genbank 54_36p 1 validated intronic c.63+9746 e1+9746 0.001 - - - no_errors tier3 1331 44 3.2 429 417 49.29 0 0 NA 123172 TCGA-AB-2963 AML03 9 18933314 18933314 G A SNP FAM154A NM_153707.1 human genbank 54_36p -1 predicted intronic c.219-1477 e3-1477 0 - - - no_errors tier3 1351 13 0.95 803 579 41.84 0 0 NA 123172 TCGA-AB-2963 AML03 9 20462825 20462825 C T SNP MLLT3 NM_004529.2 human genbank 54_36p -1 validated intronic c.194-16041 e3-16041 0.001 - - - no_errors tier3 785 9 1.13 792 165 17.22 0 0 NA 123172 TCGA-AB-2963 AML03 9 25322598 25322598 C T SNP - - - - - - - - - - - - - - - tier3 707 7 0.98 830 162 16.28 0 0 NA 123172 TCGA-AB-2963 AML03 9 25946386 25946386 A G SNP - - - - - - - - - - - - - - - tier3 215 7 3.15 172 150 46.58 0 0 NA 123172 TCGA-AB-2963 AML03 9 27844753 27844753 G A SNP - - - - - - - - - - - - - - - tier3 682 13 1.87 384 268 41.1 0 0 NA 123172 TCGA-AB-2963 AML03 9 28247654 28247654 G A SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1+37552 e0+37552 0.538 - - - no_errors tier3 894 3 0.33 799 298 27.14 0 0 NA 123172 TCGA-AB-2963 AML03 9 36765607 36765607 G T SNP - - - - - - - - - - - - - - - tier2 705 12 1.67 491 422 46.22 0 0 NA 123172 TCGA-AB-2963 AML03 9 44803354 44803354 G A SNP ENSG00000204814 ENST00000377547 human ensembl 54_36p 1 known 5_prime_flanking_region c.-5725 NULL 1 - - - no_errors tier2 1425 18 1.25 197 166 45.73 0 0 0 123172 TCGA-AB-2963 AML03 9 74505198 74505198 T C SNP TMC1 NM_138691.2 human genbank 54_36p 1 reviewed intronic c.237-56 e4-56 0.25 - - - no_errors tier3 654 6 0.91 484 396 45 0 0 NA 123172 TCGA-AB-2963 AML03 9 75803257 75803257 T C SNP - - - - - - - - - - - - - - - tier3 337 2 0.59 530 152 22.29 0 0 NA 123172 TCGA-AB-2963 AML03 9 80664985 80664985 G A SNP - - - - - - - - - - - - - - - tier3 1300 29 2.18 557 543 49.32 0 0 NA 123172 TCGA-AB-2963 AML03 9 88781528 88781528 G A SNP GAS1 NM_002048.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-30014 NULL 0 - - - no_errors tier3 858 5 0.58 642 204 24.09 0 0 NA 123172 TCGA-AB-2963 AML03 9 108073433 108073433 C T SNP - - - - - - - - - - - - - - - tier3 495 14 2.75 279 209 42.74 0 0 NA 123172 TCGA-AB-2963 AML03 9 108499711 108499711 G A SNP LOC644620 XM_001718226.1 human genbank 54_36p 1 model intronic c.160-199 e3-199 0 - - - no_errors tier3 1176 17 1.42 588 492 45.51 0 0 NA 123172 TCGA-AB-2963 AML03 9 116582261 116582261 C G SNP LOC100129633 XM_001718491.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-33964 NULL 0 - - - no_errors tier3 740 16 2.12 555 452 44.89 0 0 NA 123172 TCGA-AB-2963 AML03 9 125759487 125759487 G A SNP DENND1A NM_020946.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-27482 NULL 0 - - - no_errors tier3 727 51 6.56 471 342 42.01 0 0 NA 123172 TCGA-AB-2963 AML03 10 29566180 29566180 T C SNP - - - - - - - - - - - - - - - tier3 600 16 2.59 247 229 48.01 0 0 NA 123172 TCGA-AB-2963 AML03 10 42609323 42609323 C A SNP BMS1 NM_014753.3 human genbank 54_36p 1 reviewed silent c.1107 p.T369 0.98 superfamily_P-loop containing nucleoside triphosphate hydrolases "HMMPfam_DUF663,HMMPfam_AARP2CN,HMMSmart_SM00785,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1194 73 5.74 772 703 47.63 19 16 45.71 123172 TCGA-AB-2963 AML03 10 63706395 63706395 G A SNP RTKN2 NM_145307.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-8020 NULL 0 - - - no_errors tier3 608 27 4.25 441 328 42.65 0 0 0 123172 TCGA-AB-2963 AML03 10 64329388 64329388 C T SNP - - - - - - - - - - - - - - - tier3 1096 16 1.43 672 522 43.72 0 0 NA 123172 TCGA-AB-2963 AML03 10 70663896 70663896 G A SNP HKDC1 NM_025130.3 human genbank 54_36p 1 validated intronic c.495+1001 e4+1001 0 - - - no_errors tier3 718 10 1.37 153 159 50.8 0 0 NA 123172 TCGA-AB-2963 AML03 10 72723681 72723681 G A SNP UNC5B NM_170744.3 human genbank 54_36p 1 validated silent c.2160 p.T720 0.564 NULL "HMMPfam_Death,HMMSmart_SM00005,HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_ZU5,HMMSmart_SM00218,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_DEATH domain,HMMPfam_I-set,superfamily_Immunoglobulin" - no_errors tier1 598 10 1.63 176 167 48.55 1 100 123172 TCGA-AB-2963 AML03 10 77481149 77481149 G A SNP C10orf11 NM_032024.3 human genbank 54_36p 1 provisional intronic c.314+4082 e3+4082 1 - - - no_errors tier2 1029 6 0.58 508 155 23.31 1 5 83.33 123172 TCGA-AB-2963 AML03 10 83836128 83836128 A G SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.823+210229 e1+210229 0.165 - - - no_errors tier3 445 6 1.33 465 397 46.06 0 0 NA 123172 TCGA-AB-2963 AML03 10 85798975 85798975 A C SNP ENSG00000214578 ENST00000398614 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32187 NULL 0.249 - - - no_coding_region:pseudogene tier3 1181 16 1.34 458 388 45.81 0 0 NA 123172 TCGA-AB-2963 AML03 10 88622732 88622732 A G SNP BMPR1A NM_004329.2 human genbank 54_36p 1 reviewed intronic c.1-2872 e1-2872 0.002 - - - no_errors tier3 2883 34 1.16 895 208 18.82 0 0 NA 123172 TCGA-AB-2963 AML03 10 92958833 92958833 A T SNP PCGF5 ENST00000371687 human ensembl 54_36p 1 known intronic c.1-13593 e1-13593 0.192 - - - no_errors tier3 111 3 2.63 186 166 47.16 0 0 NA 123172 TCGA-AB-2963 AML03 10 103969884 103969884 C T SNP GBF1 NM_004193.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-38802 NULL 0.53 - - - no_errors tier2 689 6 0.86 273 211 43.6 0 0 NA 123172 TCGA-AB-2963 AML03 10 117959015 117959015 G A SNP GFRA1 NM_005264.1 human genbank 54_36p -1 reviewed intronic c.433+2118 e4+2118 0 - - - no_errors tier2 1130 68 5.67 611 521 46.02 0 0 NA 123172 TCGA-AB-2963 AML03 10 121925250 121925251 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 10 122953959 122953959 G A SNP LOC100129699 XM_001718711.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*16160 NULL 0.015 - - - no_errors tier3 1335 38 2.76 450 383 45.98 0 0 NA 123172 TCGA-AB-2963 AML03 10 128400453 128400453 T A SNP - - - - - - - - - - - - - - - tier3 1181 85 6.71 667 581 46.52 0 0 NA 123172 TCGA-AB-2963 AML03 10 128734368 128734368 A G SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.2138+2950 e21+2950 0.002 - - - no_errors tier3 321 14 4.18 326 337 50.75 0 0 NA 123172 TCGA-AB-2963 AML03 10 131820522 131820522 C T SNP GLRX3 NM_006541.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-4153 NULL 0.001 - - - no_errors tier3 471 11 2.25 221 189 45.43 0 0 NA 123172 TCGA-AB-2963 AML03 11 4491888 4491888 C T SNP OR52M1 NM_001004137.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-31109 NULL 0 - - - no_errors tier3 711 18 2.47 562 229 28.88 0 0 NA 123172 TCGA-AB-2963 AML03 11 5972419 5972419 C A SNP OR52L1 NM_001005173.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-7683 NULL 1 - - - no_errors tier2 502 5 0.99 182 143 43.87 0 0 NA 123172 TCGA-AB-2963 AML03 11 12226769 12226769 T A SNP MICAL2 NM_014632.2 human genbank 54_36p 1 provisional intronic c.2785-538 e20-538 1 - - - no_errors tier3 255 8 3.04 174 164 48.52 0 0 0 123172 TCGA-AB-2963 AML03 11 15087851 15087851 C A SNP INSC NM_001031853.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-2741 NULL 0.089 - - - no_errors tier3 1854 13 0.7 443 346 43.85 0 0 NA 123172 TCGA-AB-2963 AML03 11 17459110 17459110 C T SNP ABCC8 NM_000352.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4211 NULL 0.005 - - - no_errors tier3 1501 55 3.53 372 236 38.69 0 0 NA 123172 TCGA-AB-2963 AML03 11 20944646 20944646 A C SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1300+5964 e12+5964 0.035 - - - no_errors tier3 679 15 2.16 834 294 26.06 0 0 NA 123172 TCGA-AB-2963 AML03 11 26325452 26325452 C T SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated intronic c.46+15008 e1+15008 0.001 - - - no_errors tier3 397 3 0.75 376 300 44.38 0 0 NA 123172 TCGA-AB-2963 AML03 11 29130374 29130374 T C SNP - - - - - - - - - - - - - - - tier3 423 3 0.7 232 214 47.98 0 0 NA 123172 TCGA-AB-2963 AML03 11 38678621 38678621 G A SNP - - - - - - - - - - - - - - - tier3 409 7 1.68 361 268 42.61 0 0 NA 123172 TCGA-AB-2963 AML03 11 40316288 40316288 T C SNP LRRC4C NM_020929.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-221870 NULL 0 - - - no_errors tier2 553 8 1.42 498 387 43.73 0 0 NA 123172 TCGA-AB-2963 AML03 11 41812083 41812083 C T SNP - - - - - - - - - - - - - - - tier2 731 14 1.87 725 616 45.9 0 0 NA 123172 TCGA-AB-2963 AML03 11 71778272 71778272 C T SNP CLPB NM_030813.3 human genbank 54_36p -1 provisional intronic c.543-9196 e4-9196 0 - - - no_errors tier3 1095 30 2.66 743 587 44.14 0 0 0 123172 TCGA-AB-2963 AML03 11 73219015 73219015 C T SNP MRPL48 NM_016055.5 human genbank 54_36p 1 reviewed intronic c.201+4526 e4+4526 0.006 - - - no_errors tier3 1101 27 2.39 581 466 44.51 6 2 25 123172 TCGA-AB-2963 AML03 11 76885744 76885744 T A SNP PAK1 NM_002576.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-104531 NULL 0.002 - - - no_errors tier3 1984 13 0.65 1259 293 18.87 0 0 NA 123172 TCGA-AB-2963 AML03 11 78172688 78172688 G A SNP ODZ4 NM_001098816.2 human genbank 54_36p -1 validated intronic c.379+2903 e2+2903 0.029 - - - no_errors tier3 493 5 1 240 197 45.08 0 0 NA 123172 TCGA-AB-2963 AML03 11 91344775 91344775 G C SNP - - - - - - - - - - - - - - - tier2 1113 11 0.98 671 534 44.28 0 0 NA 123172 TCGA-AB-2963 AML03 11 93864058 93864058 A T SNP MRE11A NM_005591.3 human genbank 54_36p -1 reviewed intronic c.21-279 e2-279 0 - - - no_errors tier3 213 4 1.83 339 288 45.86 0 0 0 123172 TCGA-AB-2963 AML03 11 95478434 95478434 T C SNP MAML2 NM_032427.1 human genbank 54_36p -1 validated intronic c.514-12105 e2-12105 1 - - - no_errors tier2 665 14 2.06 351 265 43.02 0 0 NA 123172 TCGA-AB-2963 AML03 11 99849621 99849621 G A SNP - - - - - - - - - - - - - - - tier3 1392 23 1.62 620 470 43.08 0 0 NA 123172 TCGA-AB-2963 AML03 11 102079823 102079823 G A SNP MMP27 NM_022122.2 human genbank 54_36p -1 reviewed intronic c.341+655 e2+655 0.013 - - - no_errors tier3 1065 4 0.37 594 147 19.84 0 0 NA 123172 TCGA-AB-2963 AML03 11 115901875 115901875 C T SNP - - - - - - - - - - - - - - - tier3 781 49 5.88 745 523 41.18 0 0 NA 123172 TCGA-AB-2963 AML03 11 123879033 123879033 C T SNP OR8B12 NM_001005195.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*38795 NULL 0 - - - no_errors tier3 1152 4 0.34 1204 349 22.46 0 0 NA 123172 TCGA-AB-2963 AML03 11 124762046 124762046 C A SNP PKNOX2 NM_022062.2 human genbank 54_36p 1 validated intronic c.399+1218 e3+1218 0 - - - no_errors tier3 1231 32 2.53 546 456 45.46 0 0 NA 123172 TCGA-AB-2963 AML03 11 130737390 130737390 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8522 NULL 0 - - - no_errors tier3 1445 4 0.28 606 190 23.84 0 0 NA 123172 TCGA-AB-2963 AML03 12 3976324 3976324 C T SNP - - - - - - - - - - - - - - - tier3 1551 17 1.08 973 760 43.83 0 0 NA 123172 TCGA-AB-2963 AML03 12 5383042 5383042 G A SNP NTF3 NM_001102654.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28710 NULL 1 - - - no_errors tier2 626 8 1.26 224 165 42.42 0 0 NA 123172 TCGA-AB-2963 AML03 12 25527261 25527261 T - DEL IFLTD1 NM_152590.1 human genbank 54_36p -1 validated intronic c.1167-6600 e9-6600 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 12 30021611 30021611 C A SNP - - - - - - - - - - - - - - - tier3 1165 23 1.93 490 420 46.15 0 0 NA 123172 TCGA-AB-2963 AML03 12 42147761 42147761 C T SNP ADAMTS20 NM_025003.3 human genbank 54_36p -1 validated intronic c.1224-896 e9-896 0 - - - no_errors tier3 318 0 0 328 226 40.79 0 0 NA 123172 TCGA-AB-2963 AML03 12 43383502 43383502 A C SNP NELL2 NM_006159.1 human genbank 54_36p -1 reviewed intronic c.1318+274 e12+274 1 - - - no_errors tier2 320 2 0.62 479 404 45.7 0 0 0 123172 TCGA-AB-2963 AML03 12 45045818 45045818 T C SNP SLC38A2 NM_018976.4 human genbank 54_36p -1 validated intronic c.564-579 e7-579 0.003 - - - no_errors tier3 334 7 2.05 334 185 35.65 10 15 60 123172 TCGA-AB-2963 AML03 12 49250263 49250264 - T INS DIP2B NM_173602.2 human genbank 54_36p 1 validated intronic c.101-55763_101-55762 e2-55762 0.005:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 12 56923621 56923621 T C SNP - - - - - - - - - - - - - - - tier3 731 28 3.68 664 573 46.28 0 0 NA 123172 TCGA-AB-2963 AML03 12 66835038 66835038 G T SNP IFNG NM_000619.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*362 NULL 0 - - - no_errors tier3 662 49 6.88 418 333 44.34 0 0 NA 123172 TCGA-AB-2963 AML03 12 70034658 70034658 G A SNP TSPAN8 ENST00000393330 human ensembl 54_36p -1 known intronic c.1-71792 e1-71792 0.009 - - - no_errors tier3 795 17 2.09 601 550 47.78 0 0 NA 123172 TCGA-AB-2963 AML03 12 70197354 70197354 A G SNP LGR5 NM_003667.2 human genbank 54_36p 1 provisional intronic c.285-7099 e3-7099 0.387 - - - no_errors tier3 1948 57 2.84 1131 859 43.14 0 0 NA 123172 TCGA-AB-2963 AML03 12 80741588 80741588 G A SNP - - - - - - - - - - - - - - - tier3 469 7 1.47 661 626 48.56 0 0 NA 123172 TCGA-AB-2963 AML03 12 84062914 84062914 G A SNP LRRIQ1 NM_001079910.1 human genbank 54_36p 1 validated intronic c.4329+7036 e18+7036 0 - - - no_errors tier2 99 1 1 160 61 27.6 0 0 NA 123172 TCGA-AB-2963 AML03 12 103499736 103499736 G A SNP CHST11 NM_018413.4 human genbank 54_36p 1 provisional intronic c.119-20078 e2-20078 0.318 - - - no_errors tier3 1375 13 0.93 828 674 44.87 5 5 50 123172 TCGA-AB-2963 AML03 12 105522745 105522745 G A SNP RFX4 NM_213594.3 human genbank 54_36p 1 reviewed intronic c.44-3960 e2-3960 0.006 - - - no_errors tier3 947 30 3.07 328 266 44.63 0 0 NA 123172 TCGA-AB-2963 AML03 12 111411293 111411293 G C SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.1530 p.Q510H 1 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 538 10 1.82 830 162 16.33 38 3 7.32 123172 TCGA-AB-2963 AML03 12 113577704 113577704 C T SNP TBX3 NM_016569.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*16325 NULL 0.004 - - - no_errors tier3 1560 3 0.19 367 103 21.78 0 0 NA 123172 TCGA-AB-2963 AML03 12 114276873 114276873 T C SNP - - - - - - - - - - - - - - - tier3 3242 104 3.1 918 722 43.97 0 0 NA 123172 TCGA-AB-2963 AML03 12 114621622 114621622 G A SNP ENSG00000222458 ENST00000410526 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18284 NULL 0 - - - no_errors tier3 273 11 3.87 87 67 43.51 0 0 NA 123172 TCGA-AB-2963 AML03 12 125925608 125925608 C T SNP LOC121296 XR_016630.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*9634 NULL 0.002 - - - no_errors tier3 338 2 0.59 333 223 40.04 0 0 NA 123172 TCGA-AB-2963 AML03 12 126732752 126732752 C T SNP LOC644489 XM_932212.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-46297 NULL 0.004 - - - no_errors tier3 373 8 2.1 203 204 50.12 0 0 NA 123172 TCGA-AB-2963 AML03 12 126860015 126860015 T G SNP - - - - - - - - - - - - - - - tier2 831 23 2.69 367 349 48.74 0 0 NA 123172 TCGA-AB-2963 AML03 12 129000287 129000287 G A SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-46450 NULL 1 - - - no_errors tier3 913 4 0.44 655 108 14.14 0 0 NA 123172 TCGA-AB-2963 AML03 13 20099394 20099394 A G SNP IFT88 NM_175605.3 human genbank 54_36p 1 reviewed intronic c.1326+1406 e15+1406 0 - - - no_errors tier3 433 7 1.59 329 266 44.71 0 0 0 123172 TCGA-AB-2963 AML03 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 1451 4 0.27 887 142 13.8 324 77 19.15 123172 TCGA-AB-2963 AML03 13 33401809 33401809 C T SNP RFC3 NM_181558.3 human genbank 54_36p 1 reviewed intronic c.880-36415 e9-36415 0.019 - - - no_errors tier3 76 0 0 257 125 32.72 0 0 NA 123172 TCGA-AB-2963 AML03 13 37362763 37362763 G A SNP TRPC4 NM_016179.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-107293 NULL 0.001 - - - no_errors tier3 1015 17 1.65 592 446 42.97 0 0 NA 123172 TCGA-AB-2963 AML03 13 39691666 39691666 G A SNP ENSG00000207458 ENST00000384727 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7298 NULL 0.016 - - - no_errors tier3 2121 78 3.54 277 227 45.04 0 0 NA 123172 TCGA-AB-2963 AML03 13 41072634 41072634 C T SNP KIAA0564 NM_015058.1 human genbank 54_36p -1 validated intronic c.4986+4670 e40+4670 0 - - - no_errors tier3 1505 70 4.44 453 427 48.47 0 0 0 123172 TCGA-AB-2963 AML03 13 42917739 42917739 G T SNP ENOX1 NM_017993.1 human genbank 54_36p -1 validated intronic c.1-32615 e1-32615 0.013 - - - no_errors tier3 672 11 1.6 594 521 46.73 0 0 NA 123172 TCGA-AB-2963 AML03 13 45525666 45525666 C T SNP CPB2 NM_001872.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*84 NULL 0.003 - - - no_errors tier2 152 0 0 358 94 20.75 1 0 0 123172 TCGA-AB-2963 AML03 13 55081578 55081578 G A SNP - - - - - - - - - - - - - - - tier3 257 8 3.02 208 169 44.59 0 0 NA 123172 TCGA-AB-2963 AML03 13 56145684 56145684 G T SNP - - - - - - - - - - - - - - - tier3 234 3 1.26 235 211 47.31 0 0 NA 123172 TCGA-AB-2963 AML03 13 56464014 56464014 C T SNP - - - - - - - - - - - - - - - tier3 1960 49 2.43 737 579 43.96 0 0 NA 123172 TCGA-AB-2963 AML03 13 61860244 61860244 A G SNP - - - - - - - - - - - - - - - tier2 496 8 1.58 384 353 47.9 0 0 NA 123172 TCGA-AB-2963 AML03 13 76819588 76819588 G A SNP MYCBP2 NM_015057.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20791 NULL 0.046 - - - no_errors tier3 67 4 5.63 90 69 43.4 0 0 NA 123172 TCGA-AB-2963 AML03 13 80897722 80897722 T A SNP - - - - - - - - - - - - - - - tier3 680 27 3.81 491 449 47.77 0 0 NA 123172 TCGA-AB-2963 AML03 13 92751331 92751331 C T SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.160+73461 e1+73461 0 - - - no_errors tier3 1550 35 2.21 373 312 45.48 0 0 NA 123172 TCGA-AB-2963 AML03 13 96185838 96185838 C T SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.708-96907 e2-96907 0.001 - - - no_errors tier3 1906 19 0.99 637 598 48.34 2 0 0 123172 TCGA-AB-2963 AML03 13 100735025 100735025 C T SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.1048-654 e9-654 0 - - - no_errors tier3 1683 21 1.23 1023 386 27.4 0 0 NA 123172 TCGA-AB-2963 AML03 13 104940386 104940386 C - DEL DAOA NM_172370.3 human genbank 54_36p 1 reviewed frame_shift_del c.417 p.Q140fs 0 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA 123172 TCGA-AB-2963 AML03 13 112637291 112637291 A G SNP MCF2L ENST00000375608 human ensembl 54_36p 1 known intronic c.169+32605 e1+32605 0.002 - - - no_errors tier3 242 11 4.35 151 126 45.49 0 0 NA 123172 TCGA-AB-2963 AML03 14 22591494 22591494 G T SNP CDH24 NM_022478.3 human genbank 54_36p -1 validated intronic c.1363+28 e7+28 0 - - - no_errors tier3 472 15 3.08 152 127 45.52 0 0 0 123172 TCGA-AB-2963 AML03 14 25475004 25475004 C G SNP - - - - - - - - - - - - - - - tier3 470 5 1.05 304 175 36.38 0 0 NA 123172 TCGA-AB-2963 AML03 14 26633373 26633373 T G SNP - - - - - - - - - - - - - - - tier3 370 15 3.9 378 326 46.31 0 0 NA 123172 TCGA-AB-2963 AML03 14 32931430 32931430 T C SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.429+25205 e4+25205 0.008 - - - no_errors tier3 532 1 0.19 700 600 46.15 0 0 NA 123172 TCGA-AB-2963 AML03 14 35756949 35756949 C T SNP ENSG00000212071 ENST00000390782 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-21424 NULL 0.001 - - - no_errors tier3 1371 29 2.07 681 524 43.49 0 0 NA 123172 TCGA-AB-2963 AML03 14 40824170 40824170 C T SNP - - - - - - - - - - - - - - - tier2 179 4 2.17 276 200 42.02 0 0 NA 123172 TCGA-AB-2963 AML03 14 41492918 41492918 C T SNP LRFN5 NM_152447.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*49790 NULL 0 - - - no_errors tier3 301 6 1.95 383 272 41.53 0 0 NA 123172 TCGA-AB-2963 AML03 14 47502005 47502005 T C SNP - - - - - - - - - - - - - - - tier3 152 1 0.65 183 164 47.26 0 0 NA 123172 TCGA-AB-2963 AML03 14 48480479 48480479 C T SNP - - - - - - - - - - - - - - - tier3 484 11 2.22 431 430 49.94 0 0 NA 123172 TCGA-AB-2963 AML03 14 53068213 53068213 G A SNP FAM30A XM_001725525.1 human genbank 54_36p 1 model intronic c.1-4041 e1-4041 0.009 - - - no_start_codon:pseudogene:no_stop_codon tier3 852 18 2.06 378 285 42.92 1 0 0 123172 TCGA-AB-2963 AML03 14 57236097 57236097 C T SNP - - - - - - - - - - - - - - - tier3 710 6 0.84 625 501 44.49 0 0 NA 123172 TCGA-AB-2963 AML03 14 61958917 61958917 T C SNP - - - - - - - - - - - - - - - tier3 262 6 2.24 380 283 42.62 0 0 NA 123172 TCGA-AB-2963 AML03 14 64282285 64282285 C T SNP SPTB NM_001024858.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*3492 NULL 0 - - - no_errors tier2 155 5 3.12 109 71 39.44 0 0 NA 123172 TCGA-AB-2963 AML03 14 70832548 70832548 C T SNP C14orf56 XM_001718387.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-4658 NULL 0.286 - - - no_errors tier3 1013 23 2.21 483 378 43.9 0 0 NA 123172 TCGA-AB-2963 AML03 14 81899527 81899527 A G SNP - - - - - - - - - - - - - - - tier2 570 17 2.9 527 467 46.98 0 0 NA 123172 TCGA-AB-2963 AML03 14 82433842 82433842 C T SNP - - - - - - - - - - - - - - - tier3 888 36 3.9 851 655 43.49 0 0 NA 123172 TCGA-AB-2963 AML03 14 96880637 96880637 G A SNP - - - - - - - - - - - - - - - tier3 1368 25 1.79 371 331 47.08 0 0 NA 123172 TCGA-AB-2963 AML03 14 99343812 99343813 - T INS EML1 NM_001008707.1 human genbank 54_36p 1 reviewed intronic c.67+14179_67+14178 e1+14179 0.000:0.000 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 15 18822089 18822089 C T SNP LOC100132980 XM_001723267.1 human genbank 54_36p 1 model intronic c.170-2052 e3-2052 0 - - - no_errors tier3 694 4 0.57 418 104 19.92 0 0 NA 123172 TCGA-AB-2963 AML03 15 19110919 19110919 A G SNP LOC401805 XR_017148.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-16952 NULL 0 - - - pseudogene tier3 122 9 6.87 465 105 18.42 0 0 NA 123172 TCGA-AB-2963 AML03 15 22330464 22330464 G A SNP - - - - - - - - - - - - - - - tier3 370 5 1.33 234 247 51.35 0 0 NA 123172 TCGA-AB-2963 AML03 15 32156549 32156549 G A SNP PGBD4 NM_152595.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25476 NULL 0.003 - - - no_errors tier3 2025 66 3.15 496 418 45.73 0 2 100 123172 TCGA-AB-2963 AML03 15 50831396 50831396 G C SNP ONECUT1 NM_004498.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*5648 NULL 0.588 - - - no_errors tier2 1055 29 2.67 118 108 47.79 0 0 NA 123172 TCGA-AB-2963 AML03 15 63483466 63483466 C T SNP IGDCC4 NM_020962.1 human genbank 54_36p -1 provisional intronic c.564-1588 e4-1588 0.001 - - - no_errors tier3 776 32 3.95 236 187 44.1 0 0 NA 123172 TCGA-AB-2963 AML03 15 79491227 79491227 T C SNP TMC3 NM_001080532.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-37754 NULL 0 - - - no_errors tier3 196 6 2.96 248 182 42.23 0 0 NA 123172 TCGA-AB-2963 AML03 15 91224770 91224770 A G SNP CHD2 NM_001271.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20702 NULL 0.069 - - - no_errors tier3 854 16 1.84 180 188 50.95 0 0 NA 123172 TCGA-AB-2963 AML03 15 93915452 93915452 C T SNP - - - - - - - - - - - - - - - tier3 763 18 2.3 540 434 44.56 0 0 NA 123172 TCGA-AB-2963 AML03 15 94809437 94809437 C T SNP ENSG00000222617 ENST00000410685 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21383 NULL 0.001 - - - no_errors tier3 805 36 4.28 344 277 44.61 0 0 NA 123172 TCGA-AB-2963 AML03 15 95161690 95161690 A - DEL ENSG00000223120 ENST00000411188 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24613 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 15 96243759 96243759 C T SNP ENSG00000214422 ENST00000398302 human ensembl 54_36p -1 known 5_prime_flanking_region c.-25240 NULL 0.103 - - - no_stop_codon tier3 2846 87 2.96 513 391 43.11 0 0 NA 123172 TCGA-AB-2963 AML03 16 6238488 6238488 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-68509 e1-68509 0 - - - no_errors tier3 1150 29 2.46 523 404 43.58 0 0 NA 123172 TCGA-AB-2963 AML03 16 6254947 6254947 G C SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-52050 e1-52050 0 - - - no_errors tier3 2304 84 3.51 821 613 42.75 0 0 NA 123172 TCGA-AB-2963 AML03 16 7217735 7217735 C T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.27+175635 e1+175635 0 - - - no_errors tier3 359 6 1.64 222 186 45.37 0 0 NA 123172 TCGA-AB-2963 AML03 16 7265599 7265599 C T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.27+223499 e1+223499 0.042 - - - no_errors tier3 528 11 2.03 321 275 46.14 0 0 NA 123172 TCGA-AB-2963 AML03 16 7531431 7531431 G A SNP A2BP1 NM_145891.1 human genbank 54_36p 1 reviewed intronic c.330+23039 e2+23039 0 - - - no_errors tier3 1308 36 2.67 488 409 45.39 0 0 NA 123172 TCGA-AB-2963 AML03 16 8227461 8227461 G A SNP - - - - - - - - - - - - - - - tier3 1114 20 1.76 845 270 24.17 0 0 NA 123172 TCGA-AB-2963 AML03 16 18056296 18056296 C T SNP LOC728222 XM_001129009.1 human genbank 54_36p -1 model intronic c.20-82992 e2-82992 0.001 - - - no_errors tier3 526 7 1.31 230 176 43.35 0 0 NA 123172 TCGA-AB-2963 AML03 16 23133436 23133436 C T SNP SCNN1G NM_001039.3 human genbank 54_36p 1 validated intronic c.1494-98 e11-98 0 - - - no_errors tier3 1227 10 0.8 629 506 44.58 0 0 NA 123172 TCGA-AB-2963 AML03 16 34334444 34334444 G C SNP ENSG00000221532 ENST00000408605 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33920 NULL 0 - - - no_errors tier3 379 2 0.52 377 37 8.87 0 0 NA 123172 TCGA-AB-2963 AML03 16 46572785 46572785 G A SNP - - - - - - - - - - - - - - - tier3 1018 13 1.26 357 330 48.03 0 0 NA 123172 TCGA-AB-2963 AML03 16 49623663 49623663 C T SNP LOC728654 XM_001128037.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*3148 NULL 0.042 - - - no_errors tier3 669 7 1.03 371 316 46 0 0 NA 123172 TCGA-AB-2963 AML03 16 50038297 50038297 G C SNP - - - - - - - - - - - - - - - tier3 1986 35 1.73 935 875 48.29 0 0 NA 123172 TCGA-AB-2963 AML03 16 53114061 53114061 C T SNP - - - - - - - - - - - - - - - tier3 484 22 4.35 294 247 45.57 0 0 NA 123172 TCGA-AB-2963 AML03 16 57997843 57997843 C T SNP - - - - - - - - - - - - - - - tier3 575 13 2.21 494 346 41.19 0 0 NA 123172 TCGA-AB-2963 AML03 16 58168401 58168401 G A SNP ENSG00000200062 ENST00000363192 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36730 NULL 0.001 - - - no_errors tier2 412 7 1.67 281 242 46.27 0 0 NA 123172 TCGA-AB-2963 AML03 16 60313168 60313168 C T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.1536+5331 e8+5331 0 - - - no_errors tier3 1412 25 1.74 917 289 23.96 0 0 NA 123172 TCGA-AB-2963 AML03 16 67782490 67782490 A G SNP SNTB2 NM_006750.3 human genbank 54_36p 1 reviewed intronic c.580+3340 e1+3340 0.01 - - - no_errors tier3 581 7 1.19 289 85 22.73 1 0 0 123172 TCGA-AB-2963 AML03 16 69337985 69337985 G A SNP VAC14 NM_018052.3 human genbank 54_36p -1 validated intronic c.1372-2002 e13-2002 0.021 - - - no_errors tier3 609 39 6.02 137 108 44.08 0 0 0 123172 TCGA-AB-2963 AML03 16 71378635 71378635 C T SNP ZFHX3 NM_006885.3 human genbank 54_36p -1 validated missense c.11041 p.G3681S 1 NULL "HMMPfam_Homeobox,HMMSmart_SM00389,HMMSmart_SM00451,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Homeodomain-like,HMMSmart_SM00355,PatternScan_HOMEOBOX_1,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 1185 33 2.7 304 267 46.76 1 0 123172 TCGA-AB-2963 AML03 16 75512530 75512530 C T SNP - - - - - - - - - - - - - - - tier3 587 9 1.5 631 469 42.48 0 0 NA 123172 TCGA-AB-2963 AML03 16 78580369 78580369 G A SNP - - - - - - - - - - - - - - - tier3 1193 55 4.41 536 403 42.92 0 0 NA 123172 TCGA-AB-2963 AML03 16 82718208 82718208 A T SNP HSDL1 NM_031463.3 human genbank 54_36p -1 provisional intronic c.895-2374 e4-2374 0.009 - - - no_errors tier3 390 3 0.76 320 126 28.25 3 0 0 123172 TCGA-AB-2963 AML03 16 83274267 83274267 C G SNP USP10 NM_005153.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-16931 NULL 0 - - - no_errors tier3 160 9 5.33 138 107 43.5 0 0 NA 123172 TCGA-AB-2963 AML03 17 4071039 4071039 G A SNP ANKFY1 NM_016376.3 human genbank 54_36p -1 validated intronic c.323-3877 e4-3877 0 - - - no_errors tier3 763 12 1.55 355 323 47.64 2 4 66.67 123172 TCGA-AB-2963 AML03 17 11057137 11057137 T C SNP uc002gna.2 ENST00000409168 human ensembl 54_36p 1 known 5_prime_flanking_region c.-28328 NULL 0 - - - no_errors tier3 1201 27 2.2 505 394 43.83 0 0 NA 123172 TCGA-AB-2963 AML03 17 13141656 13141656 C G SNP - - - - - - - - - - - - - - - tier3 1094 48 4.18 499 432 46.3 0 0 NA 123172 TCGA-AB-2963 AML03 17 17885191 17885191 C T SNP C17orf39 NM_024052.4 human genbank 54_36p 1 validated intronic c.438+1250 e1+1250 0.029 - - - no_errors tier3 71 3 4.05 58 38 39.58 0 0 0 123172 TCGA-AB-2963 AML03 17 17984739 17984739 C G SNP MYO15A NM_016239.3 human genbank 54_36p 1 reviewed intronic c.5360+35 e19+35 0.024 - - - no_errors tier2 135 8 5.59 106 73 40.78 0 0 NA 123172 TCGA-AB-2963 AML03 17 38223906 38223906 T C SNP BECN1 NM_003766.3 human genbank 54_36p -1 validated missense c.542 p.Q181R 0.968 HMMPfam_APG6 HMMPfam_APG6 - no_errors tier1 1400 36 2.51 330 278 45.5 38 38 50 123172 TCGA-AB-2963 AML03 17 40581510 40581510 G C SNP HEXIM1 NM_006460.2 human genbank 54_36p 1 reviewed 5_prime_untranslated_region c.-831 NULL 0.69 - - - no_errors tier2 249 10 3.8 70 43 37.39 0 0 NA 123172 TCGA-AB-2963 AML03 17 43672036 43672036 T A SNP SKAP1 NM_003726.1 human genbank 54_36p -1 reviewed intronic c.281-50175 e5-50175 0.734 - - - no_errors tier2 1336 35 2.55 1261 1076 45.94 0 1 100 123172 TCGA-AB-2963 AML03 17 49167502 49167502 C T SNP LOC645173 XR_017590.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*21788 NULL 0 - - - pseudogene tier3 893 16 1.76 542 484 47.13 0 0 NA 123172 TCGA-AB-2963 AML03 17 53000528 53000528 C T SNP MSI2 NM_138962.2 human genbank 54_36p 1 reviewed intronic c.455-28700 e8-28700 0 - - - no_errors tier3 894 18 1.97 339 252 42.57 1 4 80 123172 TCGA-AB-2963 AML03 17 65363411 65363411 C A SNP - - - - - - - - - - - - - - - tier3 339 6 1.74 433 287 39.86 0 0 NA 123172 TCGA-AB-2963 AML03 18 7849121 7849121 G T SNP PTPRM NM_001105244.1 human genbank 54_36p 1 reviewed intronic c.197-28983 e3-28983 0.056 - - - no_errors tier3 479 13 2.64 771 524 40.43 0 0 NA 123172 TCGA-AB-2963 AML03 18 13606615 13606615 G A SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.182-4501 e3-4501 0.001 - - - no_errors tier3 331 4 1.19 163 162 49.69 0 2 100 123172 TCGA-AB-2963 AML03 18 18009846 18009846 T C SNP GATA6 NM_005257.3 human genbank 54_36p 1 validated intronic c.1136-1068 e2-1068 0.053 - - - no_errors tier3 186 7 3.63 113 94 45.41 0 0 NA 123172 TCGA-AB-2963 AML03 18 27104120 27104120 G A SNP DSG1 NM_001942.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48142 NULL 0.113 - - - no_errors tier3 502 11 2.14 400 322 44.54 0 0 NA 123172 TCGA-AB-2963 AML03 18 28473227 28473227 T C SNP KLHL14 NM_020805.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*35391 NULL 0.001 - - - no_errors tier3 219 1 0.45 298 104 25.68 0 0 NA 123172 TCGA-AB-2963 AML03 18 31076889 31076889 C A SNP ZNF397 NM_032347.1 human genbank 54_36p 1 provisional intronic c.414+43 e1+43 0 - - - no_errors tier2 417 8 1.88 285 233 44.98 5 0 0 123172 TCGA-AB-2963 AML03 18 32380509 32380509 C T SNP FHOD3 NM_025135.2 human genbank 54_36p 1 validated intronic c.512-29903 e6-29903 0.001 - - - no_errors tier3 389 10 2.49 411 295 41.67 0 0 NA 123172 TCGA-AB-2963 AML03 18 43817833 43817833 C T SNP ZBTB7C NM_001039360.1 human genbank 54_36p -1 validated intronic c.1208+2436 e1+2436 0 - - - no_errors tier2 984 85 7.94 491 347 41.36 0 0 NA 123172 TCGA-AB-2963 AML03 18 47720623 47720623 C T SNP - - - - - - - - - - - - - - - tier2 684 5 0.73 428 269 38.59 0 0 NA 123172 TCGA-AB-2963 AML03 18 47859214 47859214 C A SNP - - - - - - - - - - - - - - - tier3 891 17 1.87 510 370 42.05 0 0 NA 123172 TCGA-AB-2963 AML03 18 49444562 49444562 C A SNP - - - - - - - - - - - - - - - tier3 332 13 3.77 377 278 42.44 0 0 NA 123172 TCGA-AB-2963 AML03 18 58121860 58121860 A G SNP KIAA1468 NM_020854.3 human genbank 54_36p 1 validated intronic c.3531-1767 e29-1767 0 - - - no_errors tier3 831 11 1.3 359 302 45.62 2 2 50 123172 TCGA-AB-2963 AML03 18 58418985 58418985 G C SNP ZCCHC2 NM_017742.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*24193 NULL 0.001 - - - no_errors tier3 768 29 3.62 313 245 43.91 0 0 NA 123172 TCGA-AB-2963 AML03 18 58464757 58464757 T C SNP ENSG00000222223 ENST00000410291 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*3766 NULL 0.001 - - - no_errors tier2 612 35 5.4 368 340 48.02 0 0 NA 123172 TCGA-AB-2963 AML03 18 65134966 65134966 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 18 68759398 68759398 C T SNP - - - - - - - - - - - - - - - tier3 1087 7 0.64 444 392 46.83 0 0 NA 123172 TCGA-AB-2963 AML03 18 70781855 70781855 T C SNP ZNF407 NM_017757.2 human genbank 54_36p 1 provisional intronic c.5428+20219 e7+20219 0.029 - - - no_errors tier3 406 15 3.56 354 313 46.93 0 0 0 123172 TCGA-AB-2963 AML03 18 71800864 71800864 C G SNP - - - - - - - - - - - - - - - tier3 610 27 4.23 460 347 43 0 0 NA 123172 TCGA-AB-2963 AML03 18 72577254 72577254 C T SNP FLJ44881 XR_039919.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*45733 NULL 0 - - - no_errors tier3 935 0 0 810 325 28.58 0 0 NA 123172 TCGA-AB-2963 AML03 18 73643614 73643614 C T SNP - - - - - - - - - - - - - - - tier3 417 11 2.57 446 332 42.67 0 0 NA 123172 TCGA-AB-2963 AML03 19 34569752 34569752 C A SNP LOC284395 XM_378787.3 human genbank 54_36p -1 model 3_prime_flanking_region c.*25915 NULL 0 - - - no_errors tier3 703 15 2.08 212 198 48.29 0 0 NA 123172 TCGA-AB-2963 AML03 19 47656979 47656979 G - DEL LIPE NM_005357.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33838 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 19 56146705 56146705 C T SNP KLK5 NM_001077491.1 human genbank 54_36p -1 reviewed intronic c.73+948 e1+948 0 - - - no_errors tier3 3145 147 4.46 353 310 46.69 0 0 NA 123172 TCGA-AB-2963 AML03 19 58585653 58585653 T C SNP ZNF765 NM_001040185.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-7428 NULL 0.993 - - - no_errors tier2 546 16 2.84 264 182 40.62 1 0 0 123172 TCGA-AB-2963 AML03 19 60562989 60562989 G A SNP ENSG00000180043 ENST00000326479 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-60562989 NULL 0.015 - - - no_coding_region:pseudogene tier3 779 5 0.63 259 218 45.7 0 0 NA 123172 TCGA-AB-2963 AML03 19 61158758 61158758 G C SNP NLRP8 NM_176811.2 human genbank 54_36p 1 provisional missense c.1522 p.V508L 0.003 NULL "HMMSmart_SM00368,HMMPfam_PAAD_DAPIN,HMMPfam_NACHT,superfamily_DEATH domain,superfamily_RNI-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 559 11 1.92 379 332 46.56 NA 123172 TCGA-AB-2963 AML03 20 2059395 2059395 C G SNP STK35 NM_080836.2 human genbank 54_36p 1 reviewed intronic c.1206-13035 e3-13035 0.001 - - - no_errors tier3 820 11 1.32 408 327 44.49 3 3 50 123172 TCGA-AB-2963 AML03 20 13848956 13848956 A G SNP SEL1L2 NM_025229.1 human genbank 54_36p -1 validated intronic c.284-1187 e4-1187 0 - - - no_errors tier2 2258 47 2.04 758 540 41.6 0 0 NA 123172 TCGA-AB-2963 AML03 20 14257376 14257376 C T SNP FLRT3 NM_013281.2 human genbank 54_36p -1 reviewed intronic c.1-1172 e1-1172 0.995 - - - no_errors tier3 485 13 2.61 245 196 44.44 0 0 NA 123172 TCGA-AB-2963 AML03 20 15444814 15444814 T G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.645+16322 e8+16322 0 - - - no_errors tier2 247 12 4.6 278 193 40.98 0 0 NA 123172 TCGA-AB-2963 AML03 20 19380807 19380807 A - DEL SLC24A3 NM_020689.3 human genbank 54_36p 1 validated intronic c.272-63325 e3-63325 0.092 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 123172 TCGA-AB-2963 AML03 20 22966906 22966906 C T SNP CD93 NM_012072.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*45681 NULL 0.001 - - - no_errors tier2 355 6 1.65 191 146 43.32 0 0 NA 123172 TCGA-AB-2963 AML03 20 31219471 31219471 C A SNP C20orf70 ENST00000253362 human ensembl 54_36p 1 known intronic c.1-1127 e1-1127 0.986 - - - no_errors tier2 1101 9 0.81 427 301 41.29 0 0 NA 123172 TCGA-AB-2963 AML03 20 38700868 38700868 G T SNP MAFB NM_005461.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*49065 NULL 0.024 - - - no_errors tier3 8037 22 0.27 926 683 42.45 0 0 NA 123172 TCGA-AB-2963 AML03 20 40118986 40118986 G A SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*23947 NULL 0 - - - no_errors tier3 1693 48 2.75 607 508 45.48 0 0 NA 123172 TCGA-AB-2963 AML03 20 41984719 41984719 G A SNP TOX2 NM_001098797.1 human genbank 54_36p 1 validated intronic c.99+7675 e1+7675 0.839 - - - no_errors tier3 637 22 3.33 381 241 38.75 0 0 NA 123172 TCGA-AB-2963 AML03 20 46228207 46228207 G A SNP - - - - - - - - - - - - - - - tier3 1682 13 0.76 421 314 42.72 0 0 NA 123172 TCGA-AB-2963 AML03 20 56068169 56068169 A G SNP ENSG00000221385 ENST00000408458 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7749 NULL 0.001 - - - no_errors tier3 569 12 2.07 494 431 46.59 0 0 NA 123172 TCGA-AB-2963 AML03 20 59354038 59354038 C T SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.169+90650 e2+90650 0 - - - no_errors tier3 904 18 1.95 341 279 45 0 0 NA 123172 TCGA-AB-2963 AML03 21 25163967 25163967 C A SNP - - - - - - - - - - - - - - - tier3 316 1 0.32 291 209 41.63 0 0 NA 123172 TCGA-AB-2963 AML03 21 27641750 27641750 G T SNP EIF4A1P ENST00000407743 human ensembl 54_36p -1 known 3_prime_flanking_region c.*19454 NULL 0.001 - - - no_coding_region:pseudogene tier3 361 10 2.7 393 276 41.19 0 0 NA 123172 TCGA-AB-2963 AML03 21 35609766 35609766 G A SNP - - - - - - - - - - - - - - - tier3 1564 50 3.09 556 391 41.29 0 0 NA 123172 TCGA-AB-2963 AML03 21 40675874 40675874 G T SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.509-12832 e4-12832 0.001 - - - no_errors tier3 299 8 2.61 399 350 46.73 0 0 NA 123172 TCGA-AB-2963 AML03 21 44379750 44379750 C T SNP C21orf33 NM_004649.5 human genbank 54_36p 1 validated intronic c.195-620 e3-620 0.016 - - - no_errors tier3 514 4 0.77 271 311 53.25 2 2 50 123172 TCGA-AB-2963 AML03 21 44947085 44947085 C A SNP ENSG00000218195 ENST00000404288 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*44947085 NULL 0.123 - - - no_coding_region:pseudogene tier3 154 2 1.28 104 90 46.39 0 0 NA 123172 TCGA-AB-2963 AML03 22 21780056 21780056 C T SNP GNAZ NM_002073.2 human genbank 54_36p 1 reviewed intronic c.723+11451 e1+11451 0 - - - no_errors tier3 95 4 4.04 74 67 47.52 0 0 0 123172 TCGA-AB-2963 AML03 22 32408509 32408509 C T SNP LARGE NM_004737.4 human genbank 54_36p -1 reviewed intronic c.107-31855 e2-31855 0 - - - no_errors tier3 1294 11 0.84 434 395 47.65 0 0 NA 123172 TCGA-AB-2963 AML03 22 33426215 33426215 C T SNP - - - - - - - - - - - - - - - tier3 1105 70 5.96 705 607 46.23 0 0 NA 123172 TCGA-AB-2963 AML03 22 45587494 45587494 G A SNP TBC1D22A NM_014346.1 human genbank 54_36p 1 provisional intronic c.637+15313 e4+15313 0 - - - no_errors tier3 1091 48 4.2 778 648 45.41 1 0 0 831711 TCGA-AB-2964 AML04 X 2797089 2797089 C T SNP GYG2 NM_003918.1 human genbank 54_36p 1 validated intronic c.1132-6762 e9-6762 0 - - - no_errors tier3 844 5 0.59 639 376 37.01 1 0 0 831711 TCGA-AB-2964 AML04 X 3031841 3031841 G A SNP ARSF NM_004042.3 human genbank 54_36p 1 reviewed missense c.1141 p.V381I 1 "HMMPfam_Sulfatase,superfamily_Alkaline phosphatase-like" "HMMPfam_Sulfatase,PatternScan_SULFATASE_2,PatternScan_SULFATASE_1,superfamily_Alkaline phosphatase-like" - no_errors tier1 726 2 0.27 657 406 38.19 NA 831711 TCGA-AB-2964 AML04 X 5167771 5167771 G A SNP - - - - - - - - - - - - - - - tier3 958 6 0.62 913 561 38.06 0 0 NA 831711 TCGA-AB-2964 AML04 X 5247175 5247175 C T SNP ENSG00000218705 ENST00000407168 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12006 NULL 0 - - - no_coding_region:pseudogene tier3 1012 14 1.36 845 614 42.05 0 0 NA 831711 TCGA-AB-2964 AML04 X 5391871 5391871 G A SNP - - - - - - - - - - - - - - - tier3 1139 5 0.44 570 441 43.62 0 0 NA 831711 TCGA-AB-2964 AML04 X 7588282 7588282 C A SNP - - - - - - - - - - - - - - - tier3 390 2 0.51 550 442 44.47 0 0 NA 831711 TCGA-AB-2964 AML04 X 9860372 9860372 C T SNP SHROOM2 NM_001649.2 human genbank 54_36p 1 reviewed nonsense c.3049 p.R1017* 0.732 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_ASD2,HMMPfam_ASD1" - no_errors tier1 319 0 89 54 37.76 NA 831711 TCGA-AB-2964 AML04 X 11888782 11888782 G A SNP LOC100130046 XM_001721046.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*46274 NULL 0 - - - no_errors tier3 1356 0 0 1102 795 41.91 0 0 NA 831711 TCGA-AB-2964 AML04 X 15840606 15840606 T A SNP ENSG00000219733 ENST00000405554 human ensembl 54_36p 1 known 5_prime_flanking_region c.-4986 NULL 0.001 - - - no_coding_region:pseudogene tier3 1114 8 0.71 471 329 41.12 0 0 NA 831711 TCGA-AB-2964 AML04 X 18415073 18415073 T A SNP CDKL5 NM_001037343.1 human genbank 54_36p 1 reviewed intronic c.1-19903 e1-19903 0.121 - - - no_errors tier3 1018 5 0.49 1272 976 43.4 0 3 100 831711 TCGA-AB-2964 AML04 X 18974416 18974416 C T SNP GPR64 NM_001079858.1 human genbank 54_36p -1 validated intronic c.119-6153 e2-6153 0.002 - - - no_errors tier3 935 3 0.32 789 435 35.48 0 0 NA 831711 TCGA-AB-2964 AML04 X 20566044 20566044 G A SNP - - - - - - - - - - - - - - - tier3 618 0 0 577 354 38.02 0 0 NA 831711 TCGA-AB-2964 AML04 X 26399478 26399478 C A SNP ENSG00000218955 ENST00000402392 human ensembl 54_36p 1 known 5_prime_flanking_region c.-25496 NULL 0 - - - no_coding_region:pseudogene tier2 343 0 0 353 286 44.76 0 0 NA 831711 TCGA-AB-2964 AML04 X 33538469 33538469 G T SNP ENSG00000221404 ENST00000408477 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*380 NULL 0 - - - no_errors tier3 808 14 1.7 396 307 43.67 0 0 NA 831711 TCGA-AB-2964 AML04 X 38970823 38970823 G A SNP - - - - - - - - - - - - - - - tier3 1235 4 0.32 1161 779 40.11 0 0 NA 831711 TCGA-AB-2964 AML04 X 41876238 41876238 T G SNP ENSG00000218164 ENST00000406521 human ensembl 54_36p -1 known 5_prime_flanking_region c.-32868 NULL 0.042 - - - no_coding_region:pseudogene tier3 2043 5 0.24 2070 1488 41.79 0 0 NA 831711 TCGA-AB-2964 AML04 X 46770518 46770518 C T SNP PHF16 NM_001077445.1 human genbank 54_36p 1 reviewed intronic c.475+1258 e4+1258 0 - - - no_errors tier3 1189 7 0.59 827 646 43.8 0 0 0 831711 TCGA-AB-2964 AML04 X 53377989 53377989 A G SNP IQSEC2 ENST00000396435 human ensembl 54_36p -1 known 5_prime_flanking_region c.-10943 NULL 0.001 - - - no_errors tier2 885 2 0.23 380 292 43.39 0 0 NA 831711 TCGA-AB-2964 AML04 X 55533268 55533268 G A SNP USP51 NM_201286.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-1171 NULL 0.002 - - - no_errors tier3 208 1 0.48 260 161 38.24 0 0 NA 831711 TCGA-AB-2964 AML04 X 68023162 68023162 G A SNP EFNB1 NM_004429.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45940 NULL 0.028 - - - no_errors tier3 598 1 0.17 346 252 42.07 0 0 NA 831711 TCGA-AB-2964 AML04 X 69174640 69174640 C A SNP EDA NM_001399.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*2456 NULL 0.004 - - - no_errors tier3 502 1 0.2 612 480 43.92 0 0 NA 831711 TCGA-AB-2964 AML04 X 82602693 82602693 C T SNP POU3F4 NM_000307.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47296 NULL 0.009 - - - no_errors tier3 1479 4 0.27 697 509 42.17 0 0 NA 831711 TCGA-AB-2964 AML04 X 103678919 103678919 G A SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-111332 NULL 0 - - - no_errors tier3 2596 11 0.42 969 729 42.88 0 0 NA 831711 TCGA-AB-2964 AML04 X 104918243 104918243 G A SNP NRK ENST00000243300 human ensembl 54_36p 1 known 5_prime_flanking_region c.-35252 NULL 0 - - - no_errors tier3 941 3 0.32 273 221 44.74 0 0 NA 831711 TCGA-AB-2964 AML04 X 109145961 109145961 G A SNP TMEM164 NM_032227.2 human genbank 54_36p 1 provisional intronic c.390+11913 e1+11913 0 - - - no_errors tier3 1573 4 0.25 1258 998 44.24 6 0 0 831711 TCGA-AB-2964 AML04 X 109855018 109855018 G T SNP CHRDL1 NM_145234.1 human genbank 54_36p -1 reviewed intronic c.302-3607 e4-3607 0 - - - no_errors tier3 1518 3 0.2 1197 849 41.48 0 0 NA 831711 TCGA-AB-2964 AML04 X 110393663 110393663 C T SNP CAPN6 NM_014289.2 human genbank 54_36p -1 reviewed missense c.158 p.R53H 0.998 "HMMPfam_Peptidase_C2,HMMSmart_CysPc,superfamily_SSF54001" "HMMPfam_C2,HMMSmart_C2,PatternScan_THIOL_PROTEASE_CYS,PatternScan_THIOL_PROTEASE_HIS,PatternScan_THIOL_PROTEASE_ASN,HMMPfam_Peptidase_C2,HMMPfam_Calpain_III,HMMSmart_CysPc,HMMSmart_calpain_III,superfamily_Peptidase_C2,superfamily_C2_CaLB,superfamily_SSF54001" - no_errors tier1 1124 1 0.09 597 346 36.69 NA 831711 TCGA-AB-2964 AML04 X 110942071 110942071 C T SNP TRPC5 NM_012471.2 human genbank 54_36p -1 validated intronic c.1896+22734 e6+22734 0.009 - - - no_errors tier3 614 0 0 324 184 36.22 0 0 NA 831711 TCGA-AB-2964 AML04 X 121795071 121795071 C A SNP ENSG00000212321 ENST00000391019 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6889 NULL 0 - - - no_errors tier2 1011 2 0.2 1085 696 39.06 0 0 NA 831711 TCGA-AB-2964 AML04 X 123032722 123032722 C T SNP STAG2 NM_001042749.1 human genbank 54_36p 1 validated nonsense c.2401 p.Q801* 1 superfamily_ARM-type_fold "HMMPfam_STAG,superfamily_ARM-type_fold" - no_errors tier1 669 1 0.15 655 435 39.84 7 100 831711 TCGA-AB-2964 AML04 X 123786657 123786658 - A INS ODZ1 NM_014253.2 human genbank 54_36p -1 provisional intronic c.535+69168_535+69167 e3+69168 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 X 125014307 125014307 C T SNP - - - - - - - - - - - - - - - tier3 543 2 0.37 408 288 41.26 0 0 NA 831711 TCGA-AB-2964 AML04 X 127704622 127704622 C T SNP KRT18P44 XM_001719134.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*27173 NULL 0.008 - - - pseudogene tier3 1191 4 0.33 659 441 40.02 0 0 NA 831711 TCGA-AB-2964 AML04 X 127833444 127833444 A G SNP ENSG00000220383 ENST00000403093 human ensembl 54_36p -1 known 5_prime_flanking_region c.-32951 NULL 0 - - - no_coding_region:pseudogene tier3 1732 15 0.86 1617 1211 42.78 0 0 NA 831711 TCGA-AB-2964 AML04 X 128482282 128482282 C T SNP SMARCA1 NM_003069.3 human genbank 54_36p -1 reviewed intronic c.175-2177 e2-2177 0.002 - - - no_errors tier2 1166 6 0.51 408 310 43.18 0 0 NA 831711 TCGA-AB-2964 AML04 X 129048340 129048340 C T SNP ELF4 NM_001421.1 human genbank 54_36p -1 validated intronic c.1-5146 e1-5146 0.001 - - - no_errors tier2 608 4 0.65 173 165 48.82 0 7 100 831711 TCGA-AB-2964 AML04 X 131398721 131398721 T C SNP MBNL3 NM_018388.2 human genbank 54_36p -1 provisional intronic c.177+2423 e1+2423 0.958 - - - no_errors tier3 873 2 0.23 478 362 42.94 0 2 100 831711 TCGA-AB-2964 AML04 X 134255719 134255719 T C SNP ZNF75D NM_007131.2 human genbank 54_36p -1 validated missense c.14 p.E5G 0.003 NULL "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_SCAN,HMMSmart_SCAN,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 739 1 0.13 430 299 41.02 2 100 831711 TCGA-AB-2964 AML04 X 137654985 137654985 A T SNP FGF13 ENST00000370603 human ensembl 54_36p -1 known intronic c.236-36229 e3-36229 0 - - - no_errors tier3 955 4 0.42 834 518 38.31 0 0 NA 831711 TCGA-AB-2964 AML04 X 138049401 138049401 C T SNP - - - - - - - - - - - - - - - tier3 1880 7 0.37 1179 843 41.67 0 0 NA 831711 TCGA-AB-2964 AML04 X 144619036 144619036 G A SNP - - - - - - - - - - - - - - - tier3 558 5 0.89 714 450 38.66 0 0 NA 831711 TCGA-AB-2964 AML04 X 146306373 146306373 G C SNP - - - - - - - - - - - - - - - tier3 782 1 0.13 554 364 39.57 0 0 NA 831711 TCGA-AB-2964 AML04 X 148147451 148147451 A C SNP - - - - - - - - - - - - - - - tier3 1130 7 0.62 1182 897 43.12 0 0 NA 831711 TCGA-AB-2964 AML04 1 7644402 7644402 G A SNP CAMTA1 NM_015215.1 human genbank 54_36p 1 validated missense c.694 p.G232R 1 NULL "HMMPfam_IQ,HMMPfam_Ank,superfamily_Ankyrin repeat,HMMPfam_TIG,HMMPfam_CG-1,superfamily_E set domains,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 151 0 83 43 34.13 NA 831711 TCGA-AB-2964 AML04 1 20166197 20166197 C G SNP PLA2G2E NM_014589.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-43558 NULL 0.001 - - - no_errors tier3 1997 13 0.65 506 410 44.76 0 0 NA 831711 TCGA-AB-2964 AML04 1 20166198 20166198 A C SNP PLA2G2E NM_014589.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-43559 NULL 0.001 - - - no_errors tier3 1998 13 0.65 510 408 44.44 0 0 NA 831711 TCGA-AB-2964 AML04 1 21789979 21789979 G A SNP ALPL NM_000478.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*13251 NULL 0.001 - - - no_errors tier2 799 3 0.37 135 118 46.64 0 0 NA 831711 TCGA-AB-2964 AML04 1 22863277 22863277 G A SNP EPHB2 NM_004442.6 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46786 NULL 0.533 - - - no_errors tier2 463 1 0.22 232 203 46.67 0 0 NA 831711 TCGA-AB-2964 AML04 1 31671956 31671956 C T SNP SERINC2 NM_178865.3 human genbank 54_36p 1 validated intronic c.611-132 e6-132 0 - - - no_errors tier3 124 0 0 50 35 41.18 0 0 0 831711 TCGA-AB-2964 AML04 1 47869144 47869144 G - DEL ENSG00000221447 ENST00000408520 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9708 NULL 0.07 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 1 48767082 48767082 T C SNP ENSG00000220052 ENST00000401703 human ensembl 54_36p -1 known 5_prime_flanking_region c.-31087 NULL 0 - - - no_coding_region:pseudogene tier3 1788 4 0.22 1750 1375 43.94 0 0 NA 831711 TCGA-AB-2964 AML04 1 52632364 52632364 G A SNP ORC1L NM_004153.2 human genbank 54_36p -1 reviewed intronic c.722-301 e5-301 0 - - - no_errors tier3 1121 0 0 699 527 42.95 0 5 100 831711 TCGA-AB-2964 AML04 1 55684295 55684295 C A SNP - - - - - - - - - - - - - - - tier3 312 0 0 511 444 46.49 0 0 NA 831711 TCGA-AB-2964 AML04 1 56378390 56378390 T C SNP - - - - - - - - - - - - - - - tier3 1087 3 0.27 946 662 41.14 0 0 NA 831711 TCGA-AB-2964 AML04 1 60135951 60135951 G A SNP CYP2J2 NM_000775.2 human genbank 54_36p -1 reviewed intronic c.1330+3274 e8+3274 0.003 - - - no_errors tier3 645 0 0 500 395 44.13 0 0 NA 831711 TCGA-AB-2964 AML04 1 60919262 60919262 T C SNP - - - - - - - - - - - - - - - tier3 2091 6 0.29 506 390 43.53 0 0 NA 831711 TCGA-AB-2964 AML04 1 77230105 77230105 C T SNP ST6GALNAC5 NM_030965.1 human genbank 54_36p 1 provisional intronic c.262-52372 e3-52372 0.009 - - - no_errors tier2 1103 3 0.27 724 670 47.99 0 0 NA 831711 TCGA-AB-2964 AML04 1 79786004 79786004 G A SNP ADH5P2 ENST00000402790 human ensembl 54_36p 1 known 3_prime_flanking_region c.*25528 NULL 0.058 - - - no_coding_region:pseudogene tier3 464 9 1.9 203 130 38.92 0 0 NA 831711 TCGA-AB-2964 AML04 1 80890388 80890388 C T SNP - - - - - - - - - - - - - - - tier2 1057 5 0.47 487 445 47.75 0 0 NA 831711 TCGA-AB-2964 AML04 1 94924173 94924173 G A SNP ENSG00000217711 ENST00000404660 human ensembl 54_36p -1 known 5_prime_flanking_region c.-11868 NULL 0.004 - - - no_coding_region:pseudogene tier3 468 3 0.64 479 337 41.25 0 0 NA 831711 TCGA-AB-2964 AML04 1 97985192 97985192 G A SNP DPYD NM_000110.3 human genbank 54_36p -1 reviewed intronic c.234-6569 e4-6569 0 - - - no_errors tier3 722 1 0.14 293 177 37.58 0 0 0 831711 TCGA-AB-2964 AML04 1 110362786 110362786 C T SNP AHCYL1 NM_006621.4 human genbank 54_36p 1 validated silent c.1308 p.L436 0.942 "HMMPfam_AdoHcyase,HMMPfam_AdoHcyase_NAD,superfamily_NAD(P)-binding Rossmann-fold domains,superfamily_Formate/glycerate dehydrogenase catalytic domain-like" "HMMPfam_AdoHcyase,HMMPfam_AdoHcyase_NAD,superfamily_NAD(P)-binding Rossmann-fold domains,PatternScan_ADOHCYASE_1,PatternScan_ADOHCYASE_2,superfamily_Formate/glycerate dehydrogenase catalytic domain-like" - no_errors tier1 430 2 0.46 403 290 41.85 51 48 48.48 831711 TCGA-AB-2964 AML04 1 150648413 150648413 G A SNP CRNN NM_016190.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*281 NULL 0.002 - - - no_errors tier3 862 0 0 870 374 30.06 0 0 NA 831711 TCGA-AB-2964 AML04 1 151936649 151936649 C T SNP ILF2 NM_004515.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-26627 NULL 0.034 - - - no_errors tier3 194 0 0 90 74 45.12 0 0 NA 831711 TCGA-AB-2964 AML04 1 155194977 155194977 C T SNP ARHGEF11 NM_198236.2 human genbank 54_36p -1 reviewed intronic c.1502+181 e17+181 0 - - - no_errors tier3 666 2 0.3 650 472 41.99 0 2 100 831711 TCGA-AB-2964 AML04 1 170904263 170904263 A C SNP FASLG NM_000639.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*2484 NULL 0.002 - - - no_errors tier3 1170 1 0.09 860 694 44.6 0 0 NA 831711 TCGA-AB-2964 AML04 1 179955981 179955981 C T SNP CACNA1E NM_000721.2 human genbank 54_36p 1 reviewed missense c.1768 p.R590W 1 "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels" - no_errors tier1 589 2 0.34 334 236 41.33 NA 831711 TCGA-AB-2964 AML04 1 183924873 183924873 G C SNP HMCN1 NM_031935.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45662 NULL 0.015 - - - no_errors tier3 534 3 0.56 594 451 43.16 0 0 NA 831711 TCGA-AB-2964 AML04 1 186970693 186970693 T C SNP ENSG00000218573 ENST00000407161 human ensembl 54_36p 1 known 3_prime_flanking_region c.*39828 NULL 0.089 - - - no_coding_region:pseudogene tier3 508 0 0 436 302 40.92 0 0 NA 831711 TCGA-AB-2964 AML04 1 191521337 191521337 A G SNP CDC73 NM_024529.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*34872 NULL 0 - - - no_errors tier3 1066 5 0.47 967 676 41.14 0 0 NA 831711 TCGA-AB-2964 AML04 1 192018850 192018850 G A SNP ENSG00000219380 ENST00000407398 human ensembl 54_36p -1 known 5_prime_flanking_region c.-25830 NULL 0 - - - no_coding_region:pseudogene tier3 771 6 0.77 522 371 41.55 0 0 NA 831711 TCGA-AB-2964 AML04 1 201571073 201571073 T C SNP LOC730226 XM_001133046.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-44011 NULL 0.004 - - - no_errors tier3 869 0 0 131 110 45.64 0 0 NA 831711 TCGA-AB-2964 AML04 1 214623561 214623561 C T SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.652-18511 e3-18511 0.027 - - - no_errors tier3 1239 6 0.48 430 365 45.91 0 0 NA 831711 TCGA-AB-2964 AML04 1 228869202 228869202 G A SNP COG2 NM_007357.1 human genbank 54_36p 1 reviewed intronic c.486-1843 e6-1843 0.029 - - - no_errors tier3 646 6 0.92 433 250 36.55 0 0 0 831711 TCGA-AB-2964 AML04 1 235745054 235745054 A G SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.2822+3340 e24+3340 0 - - - no_errors tier3 836 0 0 926 656 41.47 0 0 NA 831711 TCGA-AB-2964 AML04 1 243609051 243609051 C T SNP KIF26B NM_018012.3 human genbank 54_36p 1 provisional intronic c.999+11759 e3+11759 0 - - - no_errors tier3 1168 2 0.17 708 399 36.04 0 0 NA 831711 TCGA-AB-2964 AML04 2 3883836 3883836 G A SNP - - - - - - - - - - - - - - - tier3 462 0 0 426 270 38.79 0 0 NA 831711 TCGA-AB-2964 AML04 2 9072613 9072613 C T SNP MBOAT2 NM_138799.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11419 NULL 0 - - - no_errors tier2 2085 12 0.57 380 243 38.88 0 0 NA 831711 TCGA-AB-2964 AML04 2 15471570 15471570 T C SNP NBAS NM_015909.2 human genbank 54_36p -1 validated intronic c.2937+1551 e25+1551 0.95 - - - no_errors tier2 1054 6 0.57 760 550 41.95 0 0 0 831711 TCGA-AB-2964 AML04 2 20433171 20433171 T G SNP PUM2 NM_015317.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-42569 NULL 0 - - - no_errors tier3 437 1 0.23 166 137 45.21 0 0 NA 831711 TCGA-AB-2964 AML04 2 31263076 31263076 C T SNP CAPN14 ENST00000403897 human ensembl 54_36p -1 known intronic c.1588-221 e15-221 0.006 - - - no_errors tier3 941 2 0.21 273 177 39.33 0 0 NA 831711 TCGA-AB-2964 AML04 2 31524192 31524192 A G SNP XDH NM_000379.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33156 NULL 0.001 - - - no_errors tier3 1093 2 0.18 740 453 37.97 0 0 NA 831711 TCGA-AB-2964 AML04 2 32849052 32849052 A G SNP TTC27 NM_017735.3 human genbank 54_36p 1 provisional intronic c.1681-7401 e14-7401 0.007 - - - no_errors tier3 999 6 0.6 687 463 40.23 0 0 0 831711 TCGA-AB-2964 AML04 2 43589037 43589037 A C SNP THADA NM_001083953.1 human genbank 54_36p -1 validated intronic c.3507+254 e22+254 0.001 - - - no_errors tier3 1265 13 1.02 1353 929 40.66 0 0 0 831711 TCGA-AB-2964 AML04 2 50461391 50461391 A T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.3364+84693 e16+84693 0.037 - - - no_errors tier3 1185 2 0.17 869 631 42.07 0 0 NA 831711 TCGA-AB-2964 AML04 2 51538151 51538151 G A SNP ENSG00000222692 ENST00000410760 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-22291 NULL 0.001 - - - no_errors tier3 1118 7 0.62 324 247 43.26 0 0 NA 831711 TCGA-AB-2964 AML04 2 59911564 59911564 C A SNP LOC100133826 XM_001719055.1 human genbank 54_36p -1 model intronic c.58+290 e1+290 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1381 11 0.79 757 540 41.63 0 0 NA 831711 TCGA-AB-2964 AML04 2 67139051 67139051 T A SNP - - - - - - - - - - - - - - - tier2 1501 2 0.13 654 535 45 0 0 NA 831711 TCGA-AB-2964 AML04 2 72231821 72231821 T A SNP CYP26B1 NM_019885.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3350 NULL 0.008 - - - no_errors tier3 638 2 0.31 171 104 37.82 0 0 NA 831711 TCGA-AB-2964 AML04 2 79427176 79427176 A T SNP CTNNA2 ENST00000409536 human ensembl 54_36p 1 known intronic c.1-27289 e1-27289 0 - - - no_errors tier3 1011 3 0.3 1075 839 43.77 0 0 NA 831711 TCGA-AB-2964 AML04 2 80436523 80436523 C T SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1060-37324 e7-37324 0.04 - - - no_errors tier2 960 5 0.52 465 266 36.39 0 0 NA 831711 TCGA-AB-2964 AML04 2 83669238 83669238 C T SNP - - - - - - - - - - - - - - - tier2 1124 6 0.53 727 586 44.63 0 0 NA 831711 TCGA-AB-2964 AML04 2 98229709 98229709 A T SNP VWA3B NM_144992.4 human genbank 54_36p 1 provisional intronic c.2674-3504 e19-3504 0.102 - - - no_errors tier3 575 1 0.17 317 204 39.16 0 0 NA 831711 TCGA-AB-2964 AML04 2 113511225 113511225 G A SNP IL1F8 NM_014438.3 human genbank 54_36p -1 reviewed intronic c.1-5411 e1-5411 0 - - - no_errors tier3 996 7 0.7 1267 950 42.83 0 0 NA 831711 TCGA-AB-2964 AML04 2 114640673 114640673 G A SNP - - - - - - - - - - - - - - - tier3 1075 3 0.28 601 422 41.21 0 0 NA 831711 TCGA-AB-2964 AML04 2 117151341 117151341 T A SNP - - - - - - - - - - - - - - - tier3 1424 8 0.56 933 660 41.38 0 0 NA 831711 TCGA-AB-2964 AML04 2 120793423 120793423 G A SNP INHBB NM_002193.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26812 NULL 0 - - - no_errors tier3 1036 3 0.29 351 247 41.3 0 0 NA 831711 TCGA-AB-2964 AML04 2 121253350 121253350 T C SNP GLI2 NM_005270.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-18017 NULL 0 - - - no_errors tier3 580 6 1.02 146 86 37.07 0 0 NA 831711 TCGA-AB-2964 AML04 2 122648037 122648037 G C SNP LOC728241 XM_001128741.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-30107 NULL 0.01 - - - no_errors tier3 608 9 1.46 774 628 44.76 0 0 NA 831711 TCGA-AB-2964 AML04 2 123183422 123183422 G A SNP - - - - - - - - - - - - - - - tier3 2090 10 0.48 1078 800 42.58 0 0 NA 831711 TCGA-AB-2964 AML04 2 126724390 126724390 T G SNP - - - - - - - - - - - - - - - tier2 1842 5 0.27 732 506 40.84 0 0 NA 831711 TCGA-AB-2964 AML04 2 139878590 139878590 G T SNP - - - - - - - - - - - - - - - tier3 949 12 1.25 180 107 37.28 0 0 NA 831711 TCGA-AB-2964 AML04 2 143709736 143709736 C G SNP ARHGAP15 NM_018460.3 human genbank 54_36p 1 validated intronic c.384+7029 e4+7029 0.003 - - - no_errors tier3 1357 9 0.66 591 471 44.27 1 2 66.67 831711 TCGA-AB-2964 AML04 2 145571508 145571508 A C SNP LOC730124 XM_001132529.1 human genbank 54_36p 1 model intronic c.126+74198 e1+74198 0 - - - no_errors tier3 1299 1 0.08 1007 716 41.48 0 0 NA 831711 TCGA-AB-2964 AML04 2 145928219 145928219 A G SNP - - - - - - - - - - - - - - - tier3 614 0 0 629 416 39.81 0 0 NA 831711 TCGA-AB-2964 AML04 2 150628560 150628560 G A SNP - - - - - - - - - - - - - - - tier3 1481 6 0.4 1574 1215 43.56 0 0 NA 831711 TCGA-AB-2964 AML04 2 154200108 154200108 C T SNP - - - - - - - - - - - - - - - tier3 405 1 0.25 170 98 36.43 0 0 NA 831711 TCGA-AB-2964 AML04 2 164418100 164418100 A C SNP - - - - - - - - - - - - - - - tier3 621 0 0 220 156 41.49 0 0 NA 831711 TCGA-AB-2964 AML04 2 170722679 170722679 G A SNP MYO3B NM_138995.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-20365 NULL 0 - - - no_errors tier3 652 4 0.61 238 163 40.45 0 0 NA 831711 TCGA-AB-2964 AML04 2 171228827 171228827 G A SNP ENSG00000213981 ENST00000397142 human ensembl 54_36p -1 known intronic c.535+4254 e4+4254 0.053 - - - no_stop_codon tier2 491 1 0.2 215 146 40.44 0 0 NA 831711 TCGA-AB-2964 AML04 2 176391875 176391875 T A SNP - - - - - - - - - - - - - - - tier3 1377 4 0.29 738 530 41.8 0 0 NA 831711 TCGA-AB-2964 AML04 2 178275791 178275791 T - DEL PDE11A NM_016953.1 human genbank 54_36p -1 reviewed intronic c.2154-1606 e14-1606 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 2 182521264 182521264 G A SNP PPP1R1C NM_001080545.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-37819 NULL 0 - - - no_errors tier3 932 4 0.43 342 226 39.72 0 0 NA 831711 TCGA-AB-2964 AML04 2 185955640 185955640 A T SNP - - - - - - - - - - - - - - - tier3 230 2 0.86 227 121 34.57 0 0 NA 831711 TCGA-AB-2964 AML04 2 197284297 197284297 G C SNP CCDC150 NM_001080539.1 human genbank 54_36p 1 provisional intronic c.1696-817 e16-817 0.54 - - - no_errors tier3 896 13 1.43 680 480 41.38 0 0 NA 831711 TCGA-AB-2964 AML04 2 199987915 199987915 T C SNP SATB2 NM_015265.2 human genbank 54_36p -1 validated intronic c.346+18391 e2+18391 0.003 - - - no_errors tier3 567 3 0.53 925 654 41.37 0 0 0 831711 TCGA-AB-2964 AML04 2 204806945 204806945 A T SNP - - - - - - - - - - - - - - - tier3 1619 17 1.04 442 293 39.81 0 0 NA 831711 TCGA-AB-2964 AML04 2 206472085 206472085 G A SNP ENSG00000201875 ENST00000365005 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1514 NULL 0.001 - - - no_errors tier3 790 5 0.63 1001 686 40.66 0 0 NA 831711 TCGA-AB-2964 AML04 2 210447142 210447142 C G SNP uc002vdl.1 ENST00000272845 human ensembl 54_36p 1 known intronic c.1371+1203 e9+1203 0.008 - - - no_start_codon tier3 553 3 0.54 632 553 46.67 0 0 NA 831711 TCGA-AB-2964 AML04 2 214268348 214268348 G A SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1071-167106 e11-167106 0 - - - no_errors tier3 1250 7 0.56 460 294 38.99 0 0 NA 831711 TCGA-AB-2964 AML04 2 218266831 218266831 C T SNP - - - - - - - - - - - - - - - tier3 839 1 0.12 531 359 40.34 0 0 NA 831711 TCGA-AB-2964 AML04 2 221719108 221719108 G A SNP - - - - - - - - - - - - - - - tier2 854 4 0.47 408 368 47.42 0 0 NA 831711 TCGA-AB-2964 AML04 2 222579476 222579476 A G SNP - - - - - - - - - - - - - - - tier3 898 6 0.66 1047 694 39.86 0 0 NA 831711 TCGA-AB-2964 AML04 2 226481938 226481938 A G SNP - - - - - - - - - - - - - - - tier3 287 0 0 140 99 41.42 0 0 NA 831711 TCGA-AB-2964 AML04 2 226775181 226775181 C G SNP - - - - - - - - - - - - - - - tier3 1098 8 0.72 871 631 42.01 0 0 NA 831711 TCGA-AB-2964 AML04 2 228797633 228797633 C T SNP SPHKAP NM_030623.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-43075 NULL 0.003 - - - no_errors tier2 641 2 0.31 961 748 43.74 0 0 NA 831711 TCGA-AB-2964 AML04 2 229016406 229016406 G A SNP - - - - - - - - - - - - - - - tier3 773 2 0.26 912 660 41.96 0 0 NA 831711 TCGA-AB-2964 AML04 2 231146624 231146624 C A SNP ENSG00000199791 ENST00000362921 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13460 NULL 1 - - - no_errors tier2 1106 5 0.45 1063 908 46.04 52 0 0 831711 TCGA-AB-2964 AML04 2 232789700 232789700 G A SNP DIS3L2 NM_152383.4 human genbank 54_36p 1 validated intronic c.1204+6341 e9+6341 0.026 - - - no_errors tier3 1299 12 0.92 865 656 43.1 0 0 0 831711 TCGA-AB-2964 AML04 2 235656842 235656842 A T SNP SH3BP4 NM_014521.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*29643 NULL 0 - - - no_errors tier3 944 0 0 370 238 39.14 0 0 NA 831711 TCGA-AB-2964 AML04 3 22864010 22864010 T C SNP - - - - - - - - - - - - - - - tier3 972 5 0.51 437 303 40.95 0 0 NA 831711 TCGA-AB-2964 AML04 3 28304297 28304297 G A SNP CMC1 NM_182523.1 human genbank 54_36p 1 provisional intronic c.109+24422 e2+24422 0.002 - - - no_errors tier3 332 1 0.3 46 11 19.3 1 7 87.5 831711 TCGA-AB-2964 AML04 3 52031790 52031790 C T SNP RPL29 NM_000992.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27273 NULL 0.997 - - - no_errors tier2 251 1 0.39 33 26 44.07 0 0 NA 831711 TCGA-AB-2964 AML04 3 55762137 55762137 G A SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2565-18151 e14-18151 0 - - - no_errors tier3 1047 5 0.47 858 1225 58.81 0 0 NA 831711 TCGA-AB-2964 AML04 3 58684167 58684167 A G SNP C3orf67 NM_198463.2 human genbank 54_36p -1 predicted 3_prime_flanking_region c.*19060 NULL 0 - - - no_errors tier3 482 2 0.41 319 177 35.69 0 0 NA 831711 TCGA-AB-2964 AML04 3 62365425 62365425 A T SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.3778-1525 e29-1525 1 - - - no_errors tier2 868 11 1.25 881 637 41.83 0 0 NA 831711 TCGA-AB-2964 AML04 3 69202009 69202009 C T SNP UBA3 NM_003968.3 human genbank 54_36p -1 reviewed intronic c.347+1367 e5+1367 0.004 - - - no_errors tier3 823 2 0.24 406 264 39.4 4 2 33.33 831711 TCGA-AB-2964 AML04 3 69860473 69860473 A G SNP MITF NM_198159.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-10966 NULL 0.016 - - - no_errors tier3 990 15 1.49 585 428 42.25 0 0 NA 831711 TCGA-AB-2964 AML04 3 71059078 71059078 G C SNP ENSG00000221382 ENST00000408455 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48445 NULL 0.001 - - - no_errors tier2 492 2 0.4 443 256 36.62 0 0 NA 831711 TCGA-AB-2964 AML04 3 74371597 74371597 T A SNP CNTN3 NM_020872.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*24645 NULL 0 - - - no_errors tier2 510 2 0.39 227 143 38.65 0 0 NA 831711 TCGA-AB-2964 AML04 3 76857808 76857808 C T SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-372047 e2-372047 0.001 - - - no_stop_codon:overly_large_intron tier3 780 21 2.62 616 472 43.38 0 0 NA 831711 TCGA-AB-2964 AML04 3 77149078 77149078 A G SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-80777 e2-80777 0.005 - - - no_stop_codon:overly_large_intron tier3 458 0 0 182 143 44 0 0 NA 831711 TCGA-AB-2964 AML04 3 78343006 78343006 G A SNP ENSG00000222574 ENST00000410642 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*49173 NULL 0.001 - - - no_errors tier3 668 2 0.3 487 352 41.95 0 0 NA 831711 TCGA-AB-2964 AML04 3 79154668 79154668 T C SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.173-83901 e3-83901 0.016 - - - no_errors tier2 681 0 0 187 136 41.98 0 0 NA 831711 TCGA-AB-2964 AML04 3 82710482 82710482 C T SNP - - - - - - - - - - - - - - - tier3 1059 4 0.38 310 189 37.88 0 0 NA 831711 TCGA-AB-2964 AML04 3 99593011 99593011 C G SNP OR5K3 NM_001005516.1 human genbank 54_36p 1 provisional missense c.812 p.P271R 0 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 559 2 0.36 381 342 47.24 NA 831711 TCGA-AB-2964 AML04 3 102127554 102127554 C T SNP ABI3BP NM_015429.3 human genbank 54_36p -1 validated intronic c.280+282 e2+282 0.004 - - - no_errors tier3 1297 2 0.15 709 440 38.26 0 0 NA 831711 TCGA-AB-2964 AML04 3 104087448 104087448 T C SNP - - - - - - - - - - - - - - - tier3 426 2 0.47 159 180 52.94 0 0 NA 831711 TCGA-AB-2964 AML04 3 104510152 104510152 A G SNP - - - - - - - - - - - - - - - tier3 642 5 0.77 494 307 38.33 0 0 NA 831711 TCGA-AB-2964 AML04 3 111194032 111194032 C G SNP - - - - - - - - - - - - - - - tier2 879 4 0.45 874 699 44.44 0 0 NA 831711 TCGA-AB-2964 AML04 3 137208350 137208350 C T SNP PPP2R3A NM_002718.3 human genbank 54_36p 1 reviewed intronic c.1995+3325 e1+3325 0.112 - - - no_errors tier3 874 7 0.79 677 409 37.63 0 0 NA 831711 TCGA-AB-2964 AML04 3 141158515 141158515 G A SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.109+21500 e1+21500 0 - - - no_errors tier3 977 2 0.2 842 534 38.7 0 0 NA 831711 TCGA-AB-2964 AML04 3 144361336 144361336 G T SNP ENSG00000181814 ENST00000316602 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16481 NULL 0.014 - - - no_coding_region:pseudogene tier3 645 5 0.77 416 297 41.6 0 0 NA 831711 TCGA-AB-2964 AML04 3 149162138 149162138 C T SNP - - - - - - - - - - - - - - - tier2 1425 7 0.49 766 530 40.83 0 0 NA 831711 TCGA-AB-2964 AML04 3 164872689 164872689 C T SNP - - - - - - - - - - - - - - - tier3 616 2 0.32 229 147 39.1 0 0 NA 831711 TCGA-AB-2964 AML04 3 170878356 170878356 C A SNP MDS1 NM_004991.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14502 NULL 0.031 - - - no_errors tier3 596 2 0.33 375 283 43.01 0 0 NA 831711 TCGA-AB-2964 AML04 3 175273930 175273930 T G SNP NLGN1 NM_014932.2 human genbank 54_36p 1 reviewed intronic c.647-201869 e3-201869 0.001 - - - no_errors tier3 625 3 0.48 498 325 39.49 0 2 100 831711 TCGA-AB-2964 AML04 3 175508004 175508004 G A SNP NLGN1 NM_014932.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*26217 NULL 0 - - - no_errors tier2 1656 7 0.42 884 620 41.17 0 0 NA 831711 TCGA-AB-2964 AML04 3 176939046 176939046 C G SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated intronic c.1990+1165 e12+1165 0.001 - - - no_errors tier3 423 1 0.24 242 107 30.57 0 0 NA 831711 TCGA-AB-2964 AML04 3 177763262 177763262 G A SNP - - - - - - - - - - - - - - - tier3 671 4 0.59 544 355 39.49 0 0 NA 831711 TCGA-AB-2964 AML04 3 182267097 182267097 T C SNP - - - - - - - - - - - - - - - tier2 1126 4 0.35 1672 1247 42.72 0 0 NA 831711 TCGA-AB-2964 AML04 3 191145464 191145464 G A SNP TP63 NM_003722.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*50479 NULL 0.068 - - - no_errors tier3 1325 3 0.23 1595 1126 41.37 0 0 NA 831711 TCGA-AB-2964 AML04 3 193569929 193569929 C T SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed intronic c.200-8908 e2-8908 0.005 - - - no_errors tier2 1207 5 0.41 1623 1182 42.11 0 0 NA 831711 TCGA-AB-2964 AML04 3 196160996 196160996 A T SNP - - - - - - - - - - - - - - - tier3 1020 3 0.29 552 415 42.92 0 0 NA 831711 TCGA-AB-2964 AML04 4 3710518 3710518 G A SNP ADRA2C NM_000683.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27614 NULL 0.045 - - - no_errors tier3 192 0 0 53 34 39.08 0 0 NA 831711 TCGA-AB-2964 AML04 4 6509331 6509331 C T SNP PPP2R2C NM_020416.3 human genbank 54_36p -1 reviewed intronic c.70+15457 e1+15457 0 - - - no_errors tier3 318 1 0.31 44 44 50 0 0 NA 831711 TCGA-AB-2964 AML04 4 11247388 11247388 T C SNP - - - - - - - - - - - - - - - tier3 1081 9 0.83 1194 844 41.39 0 0 NA 831711 TCGA-AB-2964 AML04 4 16064818 16064818 G A SNP LDB2 NM_001290.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*48546 NULL 0 - - - no_errors tier3 713 5 0.7 482 401 45.41 0 0 NA 831711 TCGA-AB-2964 AML04 4 16352213 16352213 T C SNP LDB2 NM_001290.1 human genbank 54_36p -1 validated intronic c.235+17666 e2+17666 0 - - - no_errors tier3 1389 3 0.22 1287 961 42.73 0 0 NA 831711 TCGA-AB-2964 AML04 4 16352214 16352214 C T SNP LDB2 NM_001290.1 human genbank 54_36p -1 validated intronic c.235+17665 e2+17665 0 - - - no_errors tier3 1384 2 0.14 1269 956 42.95 0 0 NA 831711 TCGA-AB-2964 AML04 4 16954096 16954096 T A SNP ENSG00000206780 ENST00000384053 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-22493 NULL 0.002 - - - no_errors tier3 1379 12 0.86 850 709 45.42 0 0 NA 831711 TCGA-AB-2964 AML04 4 18934019 18934019 G A SNP - - - - - - - - - - - - - - - tier3 795 5 0.62 1511 954 38.7 0 0 NA 831711 TCGA-AB-2964 AML04 4 19490372 19490372 G A SNP - - - - - - - - - - - - - - - tier3 1752 8 0.45 818 531 39.33 0 0 NA 831711 TCGA-AB-2964 AML04 4 23398105 23398105 C G SNP PPARGC1A NM_013261.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*8438 NULL 0 - - - no_errors tier3 739 1 0.14 856 640 42.78 0 0 NA 831711 TCGA-AB-2964 AML04 4 29713834 29713834 T C SNP - - - - - - - - - - - - - - - tier3 921 12 1.28 303 234 43.58 0 0 NA 831711 TCGA-AB-2964 AML04 4 42421398 42421398 C T SNP - - - - - - - - - - - - - - - tier2 561 2 0.36 648 539 45.33 0 0 NA 831711 TCGA-AB-2964 AML04 4 53111321 53111321 C A SNP USP46 NM_022832.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*47242 NULL 0 - - - no_errors tier3 1413 10 0.7 1343 1101 45.05 0 0 NA 831711 TCGA-AB-2964 AML04 4 58835309 58835309 G A SNP - - - - - - - - - - - - - - - tier3 683 4 0.58 509 338 39.91 0 0 NA 831711 TCGA-AB-2964 AML04 4 64149259 64149259 T G SNP - - - - - - - - - - - - - - - tier3 663 1 0.15 695 546 43.93 0 0 NA 831711 TCGA-AB-2964 AML04 4 69778352 69778352 G T SNP UGT2B10 NM_001075.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*47166 NULL 0 - - - no_errors tier3 198 2 1 129 53 29.12 0 0 NA 831711 TCGA-AB-2964 AML04 4 77634427 77634427 C A SNP SHROOM3 NM_020859.3 human genbank 54_36p 1 validated intronic c.165+58030 e1+58030 0.001 - - - no_errors tier3 682 9 1.3 568 353 38.29 0 0 NA 831711 TCGA-AB-2964 AML04 4 83705683 83705683 A C SNP FLJ12993 NM_001080506.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-60849 NULL 0 - - - no_errors tier3 400 2 0.5 313 199 38.87 0 0 NA 831711 TCGA-AB-2964 AML04 4 92216389 92216389 A G SNP - - - - - - - - - - - - - - - tier3 936 9 0.95 770 515 40.08 0 0 NA 831711 TCGA-AB-2964 AML04 4 104730348 104730348 A G SNP TACR3 NM_001059.1 human genbank 54_36p -1 reviewed silent c.1338 p.S446 0.958 NULL "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 489 2 0.41 996 667 40.08 NA 831711 TCGA-AB-2964 AML04 4 105416423 105416423 G A SNP - - - - - - - - - - - - - - - tier3 738 4 0.54 743 392 34.54 0 0 NA 831711 TCGA-AB-2964 AML04 4 106207540 106207540 A C SNP LOC643675 XR_041865.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.009 - - - no_errors tier3 626 4 0.63 807 669 45.33 0 0 NA 831711 TCGA-AB-2964 AML04 4 106377294 106377294 C T SNP TET2 NM_017628.1 human genbank 54_36p 1 validated nonsense c.2746 p.Q916* 0.006 NULL NULL - no_errors tier1 675 0 688 492 41.69 19 15 44.12 831711 TCGA-AB-2964 AML04 4 106416782 106416782 C T SNP TET2 ENST00000265149 human ensembl 54_36p 1 known missense c.2072 p.P691L 1 NULL NULL - no_start_codon tier1 317 6 1.86 781 602 43.5 17 11 39.29 831711 TCGA-AB-2964 AML04 4 114384226 114384226 G T SNP ANK2 NM_001148.1 human genbank 54_36p 1 reviewed intronic c.891+1412 e9+1412 0 - - - no_errors tier3 483 1 0.21 403 270 40.06 0 0 NA 831711 TCGA-AB-2964 AML04 4 128496367 128496367 C T SNP - - - - - - - - - - - - - - - tier3 1204 2 0.17 1128 749 39.86 0 0 NA 831711 TCGA-AB-2964 AML04 4 135030763 135030763 G A SNP - - - - - - - - - - - - - - - tier3 855 1 0.12 394 238 37.66 0 0 NA 831711 TCGA-AB-2964 AML04 4 150931236 150931236 T C SNP LOC285423 XR_041269.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.985 - - - no_errors tier2 983 2 0.2 635 363 36.3 0 0 NA 831711 TCGA-AB-2964 AML04 4 156057386 156057386 C G SNP LOC729902 XM_001131717.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*37542 NULL 0.204 - - - no_errors tier2 369 3 0.81 164 86 34.26 0 0 NA 831711 TCGA-AB-2964 AML04 4 163969074 163969074 G A SNP - - - - - - - - - - - - - - - tier3 1498 13 0.86 2070 1418 40.65 0 0 NA 831711 TCGA-AB-2964 AML04 4 164948766 164948766 A G SNP MARCH1 ENST00000274056 human ensembl 54_36p -1 known intronic c.111+45857 e1+45857 0.005 - - - no_errors tier3 1028 2 0.19 1254 790 38.61 0 0 NA 831711 TCGA-AB-2964 AML04 4 187868659 187868659 G A SNP FAT1 NM_005245.3 human genbank 54_36p -1 reviewed intronic c.1-666 e1-666 0.094 - - - no_errors tier3 468 2 0.43 62 20 24.39 0 0 NA 831711 TCGA-AB-2964 AML04 4 189122434 189122434 T C SNP ZFP42 NM_174900.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38522 NULL 0.001 - - - no_errors tier3 511 0 0 233 198 45.83 0 0 NA 831711 TCGA-AB-2964 AML04 5 2513674 2513674 C T SNP - - - - - - - - - - - - - - - tier3 1595 1 0.06 402 338 45.61 0 0 NA 831711 TCGA-AB-2964 AML04 5 3177905 3177905 C A SNP - - - - - - - - - - - - - - - tier2 396 1 0.25 122 104 46.02 0 0 NA 831711 TCGA-AB-2964 AML04 5 3912792 3912792 C T SNP - - - - - - - - - - - - - - - tier3 773 3 0.39 521 420 44.54 0 0 NA 831711 TCGA-AB-2964 AML04 5 25943147 25943147 G C SNP LOC100133558 XM_001716419.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*14221 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier2 615 1 0.16 182 110 37.67 0 0 NA 831711 TCGA-AB-2964 AML04 5 29858876 29858876 G A SNP - - - - - - - - - - - - - - - tier2 1278 5 0.39 1166 816 41.17 0 0 NA 831711 TCGA-AB-2964 AML04 5 30803538 30803538 A T SNP - - - - - - - - - - - - - - - tier3 807 1 0.12 669 460 40.74 0 0 NA 831711 TCGA-AB-2964 AML04 5 41214281 41214281 C T SNP C6 NM_000065.2 human genbank 54_36p -1 reviewed intronic c.928-1707 e7-1707 0.004 - - - no_errors tier3 694 2 0.29 386 250 39.25 0 0 NA 831711 TCGA-AB-2964 AML04 5 41501884 41501884 C T SNP PLCXD3 NM_001005473.2 human genbank 54_36p -1 validated intronic c.103+44399 e1+44399 0.022 - - - no_errors tier2 1074 2 0.19 583 379 39.36 0 0 NA 831711 TCGA-AB-2964 AML04 5 43264910 43264910 G A SNP MGC42105 NM_153361.2 human genbank 54_36p 1 provisional intronic c.1-16031 e1-16031 0 - - - no_errors tier2 665 0 0 658 401 37.87 0 0 NA 831711 TCGA-AB-2964 AML04 5 67010161 67010161 T C SNP - - - - - - - - - - - - - - - tier3 1425 9 0.62 1509 1083 41.75 0 0 NA 831711 TCGA-AB-2964 AML04 5 68151285 68151285 G A SNP - - - - - - - - - - - - - - - tier3 1466 0 0 1589 1141 41.79 0 0 NA 831711 TCGA-AB-2964 AML04 5 79319098 79319098 T - DEL MTX3 NM_001010891.3 human genbank 54_36p -1 validated intronic c.582-412 e7-412 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 5 87602683 87602683 A G SNP TMEM161B NM_153354.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-2387 NULL 0.014 - - - no_errors tier3 1064 3 0.28 295 243 45.17 2 5 71.43 831711 TCGA-AB-2964 AML04 5 92281742 92281742 A T SNP LOC391810 XM_001723772.1 human genbank 54_36p -1 model intronic c.715+1949 e5+1949 0 - - - pseudogene tier3 1194 0 0 1067 773 41.99 0 0 NA 831711 TCGA-AB-2964 AML04 5 101461842 101461842 C T SNP ENSG00000199786 ENST00000362916 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*32797 NULL 0 - - - no_errors tier3 639 4 0.62 1010 682 40.28 0 0 NA 831711 TCGA-AB-2964 AML04 5 105198421 105198421 G T SNP - - - - - - - - - - - - - - - tier3 810 4 0.49 451 315 41.12 0 0 NA 831711 TCGA-AB-2964 AML04 5 106110143 106110143 C A SNP - - - - - - - - - - - - - - - tier3 938 5 0.53 281 185 39.7 0 0 NA 831711 TCGA-AB-2964 AML04 5 106339464 106339464 G T SNP - - - - - - - - - - - - - - - tier3 864 5 0.58 1290 687 34.73 0 0 NA 831711 TCGA-AB-2964 AML04 5 108091849 108091849 T G SNP FER NM_005246.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-69934 NULL 0.001 - - - no_errors tier2 566 1 0.18 401 258 39.15 1 0 0 831711 TCGA-AB-2964 AML04 5 108476902 108476902 A T SNP FER NM_005246.2 human genbank 54_36p 1 reviewed intronic c.2048+12783 e15+12783 0.001 - - - no_errors tier3 3071 7 0.23 1438 999 40.98 0 0 NA 831711 TCGA-AB-2964 AML04 5 116436372 116436372 G T SNP - - - - - - - - - - - - - - - tier3 1063 0 0 473 392 45.32 0 0 NA 831711 TCGA-AB-2964 AML04 5 124918953 124918953 A G SNP - - - - - - - - - - - - - - - tier3 466 3 0.64 124 128 50.79 0 0 NA 831711 TCGA-AB-2964 AML04 5 126665150 126665150 C G SNP MEGF10 NM_032446.2 human genbank 54_36p 1 validated intronic c.1+1513 e0+1513 0.001 - - - no_errors tier3 526 1 0.19 441 253 36.46 0 0 NA 831711 TCGA-AB-2964 AML04 5 144706362 144706362 A G SNP - - - - - - - - - - - - - - - tier2 810 3 0.37 601 446 42.6 0 0 NA 831711 TCGA-AB-2964 AML04 5 146400336 146400336 C T SNP PPP2R2B NM_181676.1 human genbank 54_36p -1 reviewed intronic c.79+15085 e1+15085 0.001 - - - no_errors tier3 986 5 0.5 857 685 44.39 0 0 NA 831711 TCGA-AB-2964 AML04 5 151988190 151988190 G A SNP - - - - - - - - - - - - - - - tier3 1085 4 0.37 937 600 38.96 0 0 NA 831711 TCGA-AB-2964 AML04 5 152895821 152895821 G A SNP GRIA1 NM_000827.3 human genbank 54_36p 1 reviewed intronic c.220+42003 e2+42003 0 - - - no_errors tier3 3548 10 0.28 1176 962 44.97 0 0 NA 831711 TCGA-AB-2964 AML04 5 160742197 160742197 G A SNP GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed intronic c.541+28362 e5+28362 0 - - - no_errors tier3 1300 6 0.46 913 754 45.12 0 0 NA 831711 TCGA-AB-2964 AML04 5 167547409 167547409 G A SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.2570-2511 e16-2511 0 - - - no_errors tier2 516 7 1.34 293 199 40.37 0 0 NA 831711 TCGA-AB-2964 AML04 5 167930896 167930896 T C SNP PANK3 NM_024594.2 human genbank 54_36p -1 reviewed intronic c.29-2315 e2-2315 0.089 - - - no_errors tier3 452 2 0.44 124 81 39.51 2 0 0 831711 TCGA-AB-2964 AML04 5 170882212 170882212 C T SNP - - - - - - - - - - - - - - - tier3 1485 1 0.07 557 411 42.37 0 0 NA 831711 TCGA-AB-2964 AML04 5 172677558 172677558 G A SNP STC2 NM_003714.2 human genbank 54_36p -1 reviewed silent c.807 p.N269 0.153 HMMPfam_Stanniocalcin HMMPfam_Stanniocalcin - no_errors tier1 290 3 1.02 55 44 44.44 NA 831711 TCGA-AB-2964 AML04 5 175175561 175175561 C A SNP CPLX2 NM_006650.1 human genbank 54_36p 1 reviewed intronic c.1+6884 e0+6884 0 - - - no_errors tier3 839 2 0.24 545 387 41.52 0 0 NA 831711 TCGA-AB-2964 AML04 6 3494099 3494099 G A SNP LOC100133352 XM_001722160.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*34420 NULL 0 - - - no_start_codon:pseudogene tier3 1316 2 0.15 341 252 42.5 0 0 NA 831711 TCGA-AB-2964 AML04 6 5060971 5060971 A G SNP LYRM4 NM_020408.3 human genbank 54_36p -1 validated intronic c.208-6247 e3-6247 0.023 - - - no_errors tier3 550 2 0.36 144 105 42.17 0 1 100 831711 TCGA-AB-2964 AML04 6 12040825 12040825 A T SNP - - - - - - - - - - - - - - - tier2 808 1 0.12 482 370 43.43 0 0 NA 831711 TCGA-AB-2964 AML04 6 15272317 15272317 T G SNP ENSG00000210050 ENST00000387315 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16941 NULL 0.006 - - - pseudogene tier3 901 2 0.22 275 201 42.23 0 0 NA 831711 TCGA-AB-2964 AML04 6 15438976 15438976 A C SNP JARID2 NM_004973.2 human genbank 54_36p 1 reviewed intronic c.46-43351 e2-43351 0.261 - - - no_errors tier3 1758 5 0.28 943 731 43.67 5 6 54.55 831711 TCGA-AB-2964 AML04 6 16700866 16700866 T C SNP ATXN1 NM_000332.3 human genbank 54_36p -1 reviewed intronic c.1-6749 e1-6749 0.013 - - - no_errors tier3 1743 1 0.06 481 396 45.15 0 0 0 831711 TCGA-AB-2964 AML04 6 17208936 17208936 A G SNP FLJ23152 XM_376469.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-28470 NULL 0 - - - no_errors tier3 667 5 0.74 270 241 47.16 0 0 NA 831711 TCGA-AB-2964 AML04 6 17254500 17254500 T C SNP FLJ23152 XM_376469.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*15409 NULL 0.003 - - - no_errors tier3 578 6 1.02 520 391 42.87 0 0 NA 831711 TCGA-AB-2964 AML04 6 18841169 18841169 T - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 6 21637629 21637629 G A SNP - - - - - - - - - - - - - - - tier2 839 5 0.59 493 356 41.93 0 0 NA 831711 TCGA-AB-2964 AML04 6 22797025 22797025 A G SNP LOC389370 XM_374162.1 human genbank 54_36p -1 model intronic c.47-21778 e2-21778 1 - - - no_errors tier3 809 5 0.61 456 331 42.06 0 0 NA 831711 TCGA-AB-2964 AML04 6 25772238 25772238 A G SNP SCGN NM_006998.3 human genbank 54_36p 1 reviewed intronic c.247-912 e4-912 0.002 - - - no_errors tier3 509 5 0.97 304 182 37.45 0 0 NA 831711 TCGA-AB-2964 AML04 6 39086716 39086716 C A SNP DNAH8 NM_001371.2 human genbank 54_36p 1 validated intronic c.12721-1253 e86-1253 0.001 - - - no_errors tier3 1355 9 0.66 863 618 41.7 0 0 NA 831711 TCGA-AB-2964 AML04 6 39862308 39862308 G A SNP DAAM2 NM_015345.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-69749 NULL 0.01 - - - no_errors tier3 571 2 0.35 214 121 36.12 0 0 NA 831711 TCGA-AB-2964 AML04 6 51421143 51421143 G A SNP ENSG00000212532 ENST00000391230 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16304 NULL 0 - - - no_errors tier3 1423 5 0.35 475 357 42.91 0 0 NA 831711 TCGA-AB-2964 AML04 6 53572484 53572484 C T SNP KLHL31 NM_001003760.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*51871 NULL 0 - - - no_errors tier3 461 3 0.65 553 354 39.03 0 0 NA 831711 TCGA-AB-2964 AML04 6 62455990 62455990 A G SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.953-7066 e9-7066 0.001 - - - no_errors tier3 501 4 0.79 338 241 41.62 0 0 NA 831711 TCGA-AB-2964 AML04 6 79088438 79088438 C A SNP - - - - - - - - - - - - - - - tier3 730 6 0.82 594 395 39.94 0 0 NA 831711 TCGA-AB-2964 AML04 6 79230042 79230042 C A SNP - - - - - - - - - - - - - - - tier3 425 0 0 496 363 42.21 0 0 NA 831711 TCGA-AB-2964 AML04 6 82459795 82459795 T C SNP - - - - - - - - - - - - - - - tier2 605 8 1.31 558 388 41.01 0 0 NA 831711 TCGA-AB-2964 AML04 6 87607092 87607092 G A SNP LOC643962 XR_041993.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - no_errors tier3 1036 3 0.29 606 475 43.9 0 0 NA 831711 TCGA-AB-2964 AML04 6 96159761 96159761 T A SNP MANEA NM_024641.2 human genbank 54_36p 1 validated intronic c.731+261 e3+261 0.009 - - - no_errors tier3 243 2 0.82 59 40 40.4 0 0 0 831711 TCGA-AB-2964 AML04 6 96460079 96460079 A G SNP ENSG00000209248 ENST00000386513 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*32673 NULL 0 - - - pseudogene tier3 998 5 0.5 681 486 41.61 0 0 NA 831711 TCGA-AB-2964 AML04 6 100638760 100638760 T G SNP ENSG00000219257 ENST00000403835 human ensembl 54_36p -1 known 5_prime_flanking_region c.-32898 NULL 0.866 - - - no_coding_region:pseudogene tier2 786 7 0.88 682 408 37.43 0 0 NA 831711 TCGA-AB-2964 AML04 6 101447447 101447447 G C SNP ASCC3 NM_006828.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-24853 NULL 0 - - - no_errors tier3 448 0 0 511 347 40.44 0 0 NA 831711 TCGA-AB-2964 AML04 6 111302713 111302713 C G SNP AMD1 NM_001634.1 human genbank 54_36p 1 reviewed 5_prime_untranslated_region c.-289 NULL 1 - - - no_errors tier2 280 1 0.35 112 94 45.63 146 192 56.8 831711 TCGA-AB-2964 AML04 6 112537785 112537785 C T SNP LAMA4 NM_001105206.1 human genbank 54_36p -1 reviewed intronic c.5327-307 e38-307 0 - - - no_errors tier3 424 3 0.7 296 208 41.27 0 0 NA 831711 TCGA-AB-2964 AML04 6 114346811 114346811 G T SNP ENSG00000175967 ENST00000314481 human ensembl 54_36p 1 known intronic c.416-153 e3-153 0.192 - - - no_errors tier3 466 10 2.1 247 214 46.42 0 0 0 831711 TCGA-AB-2964 AML04 6 121916881 121916881 C T SNP ENSG00000201379 ENST00000364509 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-11410 NULL 0 - - - no_errors tier3 1106 11 0.98 922 620 40.18 0 0 NA 831711 TCGA-AB-2964 AML04 6 123021045 123021045 C T SNP PKIB NM_032471.4 human genbank 54_36p 1 reviewed intronic c.1+24834 e0+24834 0.001 - - - no_errors tier3 389 0 0 96 46 32.17 0 0 NA 831711 TCGA-AB-2964 AML04 6 132221486 132221486 T C SNP ENPP1 NM_006208.2 human genbank 54_36p 1 reviewed intronic c.560-15 e7-15 0.09 - - - no_errors tier3 579 0 0 359 282 43.99 0 0 NA 831711 TCGA-AB-2964 AML04 6 138810818 138810818 A G SNP NHSL1 ENST00000342260 human ensembl 54_36p -1 known intronic c.484-795 e4-795 0.01 - - - no_errors tier3 579 1 0.17 251 131 34.29 8 0 0 831711 TCGA-AB-2964 AML04 6 152750657 152750657 C T SNP SYNE1 NM_182961.2 human genbank 54_36p -1 reviewed intronic c.8178-448 e52-448 0 - - - no_errors tier3 920 5 0.54 332 204 37.99 0 0 NA 831711 TCGA-AB-2964 AML04 6 168595231 168595231 G A SNP SMOC2 NM_022138.1 human genbank 54_36p 1 provisional intronic c.84+10248 e1+10248 0.901 - - - no_errors tier3 1235 11 0.88 208 130 38.46 0 0 NA 831711 TCGA-AB-2964 AML04 6 168780243 168780243 C T SNP SMOC2 NM_022138.1 human genbank 54_36p 1 provisional intronic c.941-13043 e10-13043 0.005 - - - no_errors tier3 402 1 0.25 69 57 45.24 0 0 NA 831711 TCGA-AB-2964 AML04 7 12501973 12501973 G A SNP LOC100133035 XM_001716857.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-27437 NULL 0.001 - - - no_errors tier3 742 5 0.67 346 196 36.16 0 0 NA 831711 TCGA-AB-2964 AML04 7 12990467 12990467 C G SNP - - - - - - - - - - - - - - - tier3 675 2 0.3 368 257 41.05 0 0 NA 831711 TCGA-AB-2964 AML04 7 13660929 13660929 G A SNP - - - - - - - - - - - - - - - tier2 1054 5 0.47 235 147 38.48 0 0 NA 831711 TCGA-AB-2964 AML04 7 22959842 22959842 C G SNP FAM126A NM_032581.3 human genbank 54_36p -1 reviewed intronic c.991+6558 e9+6558 0.038 - - - no_errors tier3 699 2 0.28 142 117 45 0 3 100 831711 TCGA-AB-2964 AML04 7 27207807 27207807 A G SNP EVX1 NM_001989.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-41368 NULL 0.001 - - - no_errors tier3 342 0 0 56 28 33.33 0 0 NA 831711 TCGA-AB-2964 AML04 7 35295537 35295537 G A SNP TBX20 NM_001077653.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35781 NULL 0.001 - - - no_errors tier3 572 6 1.04 615 448 42.11 0 0 NA 831711 TCGA-AB-2964 AML04 7 42126546 42126546 G A SNP GLI3 NM_000168.5 human genbank 54_36p -1 reviewed intronic c.367+27804 e2+27804 1 - - - no_errors tier2 838 3 0.36 625 461 42.45 0 0 NA 831711 TCGA-AB-2964 AML04 7 45612833 45612833 A G SNP ADCY1 NM_021116.2 human genbank 54_36p 1 reviewed intronic c.790-3670 e3-3670 0.001 - - - no_errors tier3 875 4 0.46 96 59 38.06 0 0 NA 831711 TCGA-AB-2964 AML04 7 52610078 52610078 T C SNP - - - - - - - - - - - - - - - tier3 856 3 0.35 831 628 43.04 0 0 NA 831711 TCGA-AB-2964 AML04 7 54111027 54111027 C G SNP LOC100134574 XM_001726849.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*13791 NULL 0.027 - - - no_start_codon:pseudogene:no_stop_codon tier3 629 1 0.16 319 279 46.66 0 0 NA 831711 TCGA-AB-2964 AML04 7 70102464 70102464 G A SNP - - - - - - - - - - - - - - - tier3 2185 16 0.73 709 464 39.52 0 0 NA 831711 TCGA-AB-2964 AML04 7 73089974 73089974 G A SNP ELN NM_000501.2 human genbank 54_36p 1 reviewed silent c.165 p.A55 0.285 NULL "PatternScan_ENDONUCLEASE_III_2,PatternScan_HEXAPEP_TRANSFERASES" - no_errors tier1 226 0 64 28 30.43 NA 831711 TCGA-AB-2964 AML04 7 79416380 79416380 T C SNP ENSG00000206818 ENST00000384091 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36920 NULL 0.001 - - - no_errors tier3 2088 7 0.33 1253 954 43.23 0 0 NA 831711 TCGA-AB-2964 AML04 7 83390854 83390854 A C SNP ENSG00000222994 ENST00000411062 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3899 NULL 0.025 - - - no_errors tier3 523 0 0 139 168 54.72 0 0 NA 831711 TCGA-AB-2964 AML04 7 84641703 84641703 C T SNP - - - - - - - - - - - - - - - tier3 741 1 0.13 608 405 39.98 0 0 NA 831711 TCGA-AB-2964 AML04 7 93402111 93402111 T G SNP TFPI2 NM_006528.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-44185 NULL 0.001 - - - no_errors tier3 1183 3 0.25 952 685 41.84 0 0 NA 831711 TCGA-AB-2964 AML04 7 95028253 95028253 C T SNP ASB4 NM_016116.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*23246 NULL 0.02 - - - no_errors tier2 608 4 0.65 205 112 35.33 0 0 NA 831711 TCGA-AB-2964 AML04 7 104043068 104043068 T A SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed intronic c.446-121290 e2-121290 0.029 - - - no_errors tier3 1121 5 0.44 559 329 37.05 0 0 NA 831711 TCGA-AB-2964 AML04 7 110539760 110539760 T G SNP LRRN3 NM_001099658.1 human genbank 54_36p 1 validated intronic c.1-9947 e1-9947 0 - - - no_errors tier3 1045 4 0.38 1106 785 41.45 1 0 0 831711 TCGA-AB-2964 AML04 7 121695912 121695912 G A SNP LOC154860 XM_001726316.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37059 NULL 0 - - - no_errors tier3 2115 8 0.38 1332 857 39.1 0 0 NA 831711 TCGA-AB-2964 AML04 7 122372145 122372145 T C SNP TAS2R16 NM_016945.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*49904 NULL 0.073 - - - no_errors tier3 475 0 0 334 210 38.6 0 0 NA 831711 TCGA-AB-2964 AML04 7 124129676 124129676 A C SNP GPR37 NM_005302.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*44139 NULL 0 - - - no_errors tier3 530 6 1.12 710 485 40.59 0 0 NA 831711 TCGA-AB-2964 AML04 7 134716709 134716709 A G SNP CNOT4 NM_013316.1 human genbank 54_36p -1 validated intronic c.1618+12501 e9+12501 0.011 - - - no_errors tier3 1129 3 0.26 1583 1095 40.89 3 1 25 831711 TCGA-AB-2964 AML04 7 148646250 148646250 T C SNP ENSG00000218140 ENST00000406747 human ensembl 54_36p 1 known 5_prime_flanking_region c.-15798 NULL 0 - - - no_coding_region:pseudogene tier3 979 4 0.41 853 628 42.26 0 0 NA 831711 TCGA-AB-2964 AML04 7 149271012 149271013 - C INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 7 152224914 152224914 G A SNP ACTR3B NM_020445.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*42343 NULL 0.001 - - - no_errors tier3 593 2 0.34 182 134 42.41 0 1 100 831711 TCGA-AB-2964 AML04 7 152947902 152947902 C G SNP - - - - - - - - - - - - - - - tier3 530 0 0 958 737 43.46 0 0 NA 831711 TCGA-AB-2964 AML04 8 3113862 3113862 A C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.4157+15211 e27+15211 0.064 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 746 0 0 1044 915 46.71 0 0 NA 831711 TCGA-AB-2964 AML04 8 3310513 3310513 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1564+3129 e13+3129 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 831 5 0.6 1213 846 41.07 0 0 NA 831711 TCGA-AB-2964 AML04 8 3720106 3720106 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.819-121134 e6-121134 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 505 2 0.39 808 594 42.34 0 0 NA 831711 TCGA-AB-2964 AML04 8 3977700 3977700 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.416-100671 e4-100671 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 490 7 1.41 265 216 44.91 0 0 NA 831711 TCGA-AB-2964 AML04 8 5159302 5159302 C T SNP - - - - - - - - - - - - - - - tier2 793 6 0.75 181 165 47.69 0 0 NA 831711 TCGA-AB-2964 AML04 8 11466306 11466306 C T SNP LOC100128728 XM_001721450.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-11579 NULL 0 - - - no_errors tier3 188 1 0.53 65 30 31.58 1 0 0 831711 TCGA-AB-2964 AML04 8 13863139 13863139 G A SNP - - - - - - - - - - - - - - - tier3 597 2 0.33 404 307 43.18 0 0 NA 831711 TCGA-AB-2964 AML04 8 22584161 22584161 G C SNP BIN3 NM_018688.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-1652 NULL 0.002 - - - no_errors tier3 405 1 0.25 140 102 42.15 0 0 NA 831711 TCGA-AB-2964 AML04 8 34605307 34605307 G T SNP - - - - - - - - - - - - - - - tier2 837 9 1.06 756 559 42.51 0 0 NA 831711 TCGA-AB-2964 AML04 8 34728526 34728526 C T SNP - - - - - - - - - - - - - - - tier3 476 0 0 274 175 38.98 0 0 NA 831711 TCGA-AB-2964 AML04 8 35557944 35557944 T A SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.451+12643 e3+12643 0.066 - - - no_errors tier3 1191 2 0.17 837 571 40.55 0 0 NA 831711 TCGA-AB-2964 AML04 8 36450722 36450722 G T SNP - - - - - - - - - - - - - - - tier2 1660 3 0.18 1053 680 39.24 0 0 NA 831711 TCGA-AB-2964 AML04 8 38249178 38249178 C T SNP PPAPDC1B NM_001102559.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-3304 NULL 0.001 - - - no_errors tier2 483 0 0 307 246 44.48 22 11 33.33 831711 TCGA-AB-2964 AML04 8 50759941 50759941 G A SNP - - - - - - - - - - - - - - - tier3 891 1 0.11 1271 798 38.53 0 0 NA 831711 TCGA-AB-2964 AML04 8 52055557 52055557 A C SNP ENSG00000201316 ENST00000364446 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-34577 NULL 0.011 - - - no_errors tier3 1141 11 0.95 1377 1152 45.55 0 0 NA 831711 TCGA-AB-2964 AML04 8 64924187 64924187 A G SNP - - - - - - - - - - - - - - - tier3 1627 7 0.43 1430 1003 41.22 0 0 NA 831711 TCGA-AB-2964 AML04 8 68580898 68580898 G A SNP CPA6 NM_020361.1 human genbank 54_36p -1 validated intronic c.636+678 e6+678 0.003 - - - no_errors tier3 964 2 0.21 854 606 41.48 0 0 NA 831711 TCGA-AB-2964 AML04 8 83509243 83509243 G T SNP - - - - - - - - - - - - - - - tier3 278 1 0.36 30 19 38.78 0 0 NA 831711 TCGA-AB-2964 AML04 8 84261496 84261496 A T SNP - - - - - - - - - - - - - - - tier3 880 7 0.79 164 120 42.25 0 0 NA 831711 TCGA-AB-2964 AML04 8 84591873 84591873 C T SNP - - - - - - - - - - - - - - - tier3 530 3 0.56 464 263 36.18 0 0 NA 831711 TCGA-AB-2964 AML04 8 90846524 90846524 G A SNP RIPK2 NM_003821.5 human genbank 54_36p 1 reviewed intronic c.328-182 e3-182 0.001 - - - no_errors tier3 768 9 1.16 240 121 33.43 0 0 0 831711 TCGA-AB-2964 AML04 8 106241120 106241120 T C SNP - - - - - - - - - - - - - - - tier3 806 2 0.25 690 597 46.39 0 0 NA 831711 TCGA-AB-2964 AML04 8 107510128 107510128 G A SNP - - - - - - - - - - - - - - - tier3 920 6 0.65 1162 668 36.48 0 0 NA 831711 TCGA-AB-2964 AML04 8 115079106 115079106 A G SNP ENSG00000206719 ENST00000383992 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46703 NULL 0.02 - - - no_errors tier3 802 9 1.11 467 271 36.67 0 0 NA 831711 TCGA-AB-2964 AML04 8 115623342 115623342 C A SNP - - - - - - - - - - - - - - - tier3 638 0 0 216 135 38.35 0 0 NA 831711 TCGA-AB-2964 AML04 8 122675517 122675517 G T SNP HAS2AS NR_002835.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-45250 NULL 0 - - - no_errors tier2 1452 3 0.21 714 567 44.26 1 1 50 831711 TCGA-AB-2964 AML04 8 126686158 126686158 C A SNP - - - - - - - - - - - - - - - tier3 894 4 0.44 746 591 44.2 0 0 NA 831711 TCGA-AB-2964 AML04 8 130357616 130357616 C T SNP LOC728724 XM_001128934.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-35003 NULL 0 - - - no_errors tier3 1652 12 0.72 839 625 42.69 0 0 NA 831711 TCGA-AB-2964 AML04 8 130573134 130573134 C T SNP LOC100129525 XM_001725397.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*45933 NULL 0.342 - - - no_errors tier3 979 5 0.51 781 530 40.4 0 0 NA 831711 TCGA-AB-2964 AML04 8 142468539 142468539 G T SNP PTP4A3 NM_032611.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32984 NULL 0.001 - - - no_errors tier3 1197 2 0.17 20 13 39.39 0 0 NA 831711 TCGA-AB-2964 AML04 8 143047329 143047329 C T SNP ENSG00000221123 ENST00000408196 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22436 NULL 0.018 - - - no_errors tier3 716 3 0.42 384 209 35.13 0 0 NA 831711 TCGA-AB-2964 AML04 9 4504474 4504474 C T SNP SLC1A1 NM_004170.4 human genbank 54_36p 1 validated intronic c.91+23704 e1+23704 0 - - - no_errors tier3 1327 4 0.3 1447 1021 41.34 0 0 NA 831711 TCGA-AB-2964 AML04 9 11640015 11640015 G A SNP - - - - - - - - - - - - - - - tier3 594 3 0.5 748 516 40.82 0 0 NA 831711 TCGA-AB-2964 AML04 9 11868209 11868209 G A SNP - - - - - - - - - - - - - - - tier3 493 0 0 415 277 39.97 0 0 NA 831711 TCGA-AB-2964 AML04 9 13171725 13171725 G T SNP MPDZ NM_003829.3 human genbank 54_36p -1 validated intronic c.2649+1692 e18+1692 1 - - - no_errors tier2 740 0 0 967 512 34.62 0 0 NA 831711 TCGA-AB-2964 AML04 9 15264829 15264829 T C SNP TTC39B NM_152574.1 human genbank 54_36p -1 provisional intronic c.43-6883 e2-6883 0.001 - - - no_errors tier3 409 0 0 48 38 44.19 0 0 0 831711 TCGA-AB-2964 AML04 9 18108788 18108788 A T SNP - - - - - - - - - - - - - - - tier2 704 8 1.12 999 722 41.95 0 0 NA 831711 TCGA-AB-2964 AML04 9 20189433 20189433 C T SNP - - - - - - - - - - - - - - - tier2 974 6 0.61 584 402 40.77 0 0 NA 831711 TCGA-AB-2964 AML04 9 23896206 23896206 C G SNP LOC100133655 XM_001716507.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-48964 NULL 0 - - - no_start_codon:pseudogene tier3 1347 8 0.59 402 293 42.1 0 0 NA 831711 TCGA-AB-2964 AML04 9 24038848 24038848 C T SNP - - - - - - - - - - - - - - - tier3 2352 4 0.17 1977 1489 42.95 0 0 NA 831711 TCGA-AB-2964 AML04 9 27439109 27439109 T A SNP MOBKL2B NM_024761.3 human genbank 54_36p -1 reviewed intronic c.418+6022 e1+6022 0 - - - no_errors tier3 936 8 0.85 925 605 39.52 0 0 0 831711 TCGA-AB-2964 AML04 9 36699311 36699311 C T SNP MELK NM_014791.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*31977 NULL 0 - - - no_errors tier2 623 3 0.48 553 318 36.51 0 0 NA 831711 TCGA-AB-2964 AML04 9 76433335 76433335 G A SNP RORB NM_006914.3 human genbank 54_36p 1 reviewed intronic c.8-1683 e2-1683 0.012 - - - no_errors tier3 1321 5 0.38 344 165 32.42 0 0 NA 831711 TCGA-AB-2964 AML04 9 91779053 91779053 G A SNP - - - - - - - - - - - - - - - tier3 1039 9 0.86 1407 1079 43.39 0 0 NA 831711 TCGA-AB-2964 AML04 9 92238581 92238581 G C SNP LOC340515 XR_041526.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*25953 NULL 0.004 - - - no_errors tier2 869 0 0 458 294 39.1 0 0 NA 831711 TCGA-AB-2964 AML04 9 107200089 107200089 C A SNP SLC44A1 ENST00000374724 human ensembl 54_36p 1 known intronic c.1950+12485 e15+12485 0 - - - no_errors tier3 903 2 0.22 693 658 48.7 0 0 0 831711 TCGA-AB-2964 AML04 9 115090448 115090448 T C SNP PRPF4 NM_004697.3 human genbank 54_36p 1 provisional intronic c.1025+83 e10+83 0.749 - - - no_errors tier3 906 0 0 229 210 47.73 0 0 0 831711 TCGA-AB-2964 AML04 9 117909610 117909610 C A SNP PAPPA NM_002581.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46663 NULL 0.002 - - - no_errors tier3 767 3 0.39 1202 871 42 0 0 NA 831711 TCGA-AB-2964 AML04 9 119251061 119251062 - T INS ASTN2 NM_198187.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-34024 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 9 120098215 120098215 C T SNP - - - - - - - - - - - - - - - tier3 733 4 0.54 694 525 43.07 0 0 NA 831711 TCGA-AB-2964 AML04 9 120263202 120263202 C T SNP - - - - - - - - - - - - - - - tier3 1088 3 0.27 529 292 35.57 0 0 NA 831711 TCGA-AB-2964 AML04 9 123937046 123937046 C T SNP TTLL11 NM_194252.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41528 NULL 0 - - - no_errors tier3 497 1 0.2 181 133 42.36 0 0 NA 831711 TCGA-AB-2964 AML04 9 126454104 126454104 A G SNP NR6A1 NM_033334.3 human genbank 54_36p -1 reviewed intronic c.142+81304 e2+81304 0.005 - - - no_errors tier3 1176 6 0.51 1185 909 43.37 3 0 0 831711 TCGA-AB-2964 AML04 9 128230267 128230267 G A SNP FAM125B NM_033446.1 human genbank 54_36p 1 validated intronic c.757+6219 e7+6219 0 - - - no_errors tier3 849 2 0.23 180 122 40.4 1 3 75 831711 TCGA-AB-2964 AML04 9 131575987 131575987 C T SNP PTGES NM_004878.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20875 NULL 0.004 - - - no_errors tier3 292 2 0.68 84 69 45.1 0 0 NA 831711 TCGA-AB-2964 AML04 9 137082258 137082258 C T SNP OLFM1 NM_006334.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25116 NULL 0.008 - - - no_errors tier3 567 1 0.18 118 90 43.27 0 0 NA 831711 TCGA-AB-2964 AML04 9 138909812 138909812 G A SNP TRAF2 NM_021138.3 human genbank 54_36p 1 reviewed intronic c.1-3174 e1-3174 0.027 - - - no_errors tier3 244 4 1.61 67 54 44.63 0 0 0 831711 TCGA-AB-2964 AML04 10 4501848 4501848 G A SNP LOC100128356 XM_001719204.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-29326 NULL 0 - - - no_errors tier2 650 1 0.15 390 199 33.79 0 0 NA 831711 TCGA-AB-2964 AML04 10 4501849 4501849 C G SNP LOC100128356 XM_001719204.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-29327 NULL 0 - - - no_errors tier2 648 1 0.15 389 195 33.39 0 0 NA 831711 TCGA-AB-2964 AML04 10 7122810 7122810 A C SNP - - - - - - - - - - - - - - - tier3 653 2 0.3 574 408 41.42 0 0 NA 831711 TCGA-AB-2964 AML04 10 16378574 16378574 A G SNP - - - - - - - - - - - - - - - tier3 1061 4 0.38 707 439 38.27 0 0 NA 831711 TCGA-AB-2964 AML04 10 26502207 26502207 C T SNP MYO3A NM_017433.4 human genbank 54_36p 1 reviewed intronic c.3399-391 e28-391 0.035 - - - no_errors tier3 653 5 0.76 482 333 40.86 0 0 NA 831711 TCGA-AB-2964 AML04 10 33788682 33788682 G A SNP - - - - - - - - - - - - - - - tier3 972 0 0 475 403 45.9 0 0 NA 831711 TCGA-AB-2964 AML04 10 36397843 36397843 C A SNP - - - - - - - - - - - - - - - tier3 368 2 0.54 362 203 35.93 0 0 NA 831711 TCGA-AB-2964 AML04 10 36456624 36456624 G C SNP - - - - - - - - - - - - - - - tier3 534 6 1.11 258 210 44.78 0 0 NA 831711 TCGA-AB-2964 AML04 10 42269528 42269528 C T SNP CCNYL2 XM_374787.1 human genbank 54_36p -1 model intronic c.757+89 e5+89 0.049 - - - no_errors tier3 365 0 0 261 155 37.26 0 0 NA 831711 TCGA-AB-2964 AML04 10 44373095 44373095 G C SNP - - - - - - - - - - - - - - - tier3 682 3 0.44 691 470 40.48 0 0 NA 831711 TCGA-AB-2964 AML04 10 48153671 48153671 G T SNP ENSG00000221361 ENST00000408434 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*6433 NULL 0.125 - - - no_errors tier3 657 1 0.15 437 297 40.46 0 0 NA 831711 TCGA-AB-2964 AML04 10 56804084 56804084 G A SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1-207667 e1-207667 0 - - - no_errors tier3 682 2 0.29 728 571 43.96 0 0 NA 831711 TCGA-AB-2964 AML04 10 57610420 57610420 T A SNP - - - - - - - - - - - - - - - tier3 971 4 0.41 316 247 43.87 0 0 NA 831711 TCGA-AB-2964 AML04 10 58556893 58556893 T C SNP - - - - - - - - - - - - - - - tier3 1131 11 0.96 876 481 35.39 0 0 NA 831711 TCGA-AB-2964 AML04 10 63656429 63656429 C G SNP RTKN2 NM_145307.2 human genbank 54_36p -1 provisional intronic c.687-3332 e7-3332 0 - - - no_errors tier3 498 0 0 556 456 45.06 0 0 NA 831711 TCGA-AB-2964 AML04 10 73187974 73187974 A C SNP CDH23 NM_022124.4 human genbank 54_36p 1 reviewed intronic c.4845+16290 e37+16290 0 - - - no_errors tier3 306 3 0.96 38 31 44.29 4 0 0 831711 TCGA-AB-2964 AML04 10 80865782 80865782 C T SNP ZCCHC24 NM_153367.3 human genbank 54_36p -1 validated intronic c.247-3262 e2-3262 0.001 - - - no_errors tier3 218 0 0 119 93 43.87 0 0 0 831711 TCGA-AB-2964 AML04 10 81914940 81914940 T A SNP ANXA11 NM_001157.2 human genbank 54_36p -1 reviewed intronic c.858+880 e6+880 0.001 - - - no_errors tier3 297 3 1 110 73 39.89 6 0 0 831711 TCGA-AB-2964 AML04 10 83977802 83977802 A T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.824-130673 e2-130673 0 - - - no_errors tier2 1272 12 0.93 1103 965 46.66 0 0 NA 831711 TCGA-AB-2964 AML04 10 93388046 93388046 G A SNP PPP1R3C NM_005398.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-5340 NULL 0.086 - - - no_errors tier3 1502 3 0.2 533 347 39.39 0 0 NA 831711 TCGA-AB-2964 AML04 10 94382926 94382926 C A SNP KIF11 NM_004523.3 human genbank 54_36p 1 reviewed intronic c.1703-434 e14-434 0.001 - - - no_errors tier3 474 3 0.63 47 29 38.16 3 13 81.25 831711 TCGA-AB-2964 AML04 10 101274226 101274226 A T SNP NKX2-3 NM_145285.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-8653 NULL 0.747 - - - no_errors tier3 375 1 0.27 112 88 44 1 0 0 831711 TCGA-AB-2964 AML04 10 112513023 112513023 G T SNP ENSG00000203869 ENST00000369521 human ensembl 54_36p 1 known intronic c.192-17526 e2-17526 0 - - - no_stop_codon tier3 340 0 0 200 162 44.63 0 0 NA 831711 TCGA-AB-2964 AML04 10 116453871 116453871 G A SNP PPIAP19 XM_372328.1 human genbank 54_36p -1 model intronic c.142-13437 e2-13437 0.001 - - - pseudogene tier3 820 2 0.24 335 254 43.12 2 0 0 831711 TCGA-AB-2964 AML04 10 123175803 123175803 C T SNP ENSG00000222979 ENST00000411047 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*15099 NULL 0.006 - - - no_errors tier3 588 6 1.01 544 417 43.39 0 0 NA 831711 TCGA-AB-2964 AML04 10 129114870 129114870 C T SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.5049+605 e48+605 0.003 - - - no_errors tier3 383 1 0.26 151 102 40.32 0 0 0 831711 TCGA-AB-2964 AML04 10 129903384 129903384 C T SNP - - - - - - - - - - - - - - - tier2 367 1 0.27 139 118 45.91 0 0 NA 831711 TCGA-AB-2964 AML04 11 1228362 1228362 T C SNP MUC5B NM_002458.1 human genbank 54_36p 1 validated missense c.13685 p.V4562A 0 NULL "HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_VWD,HMMSmart_SM00216,superfamily_Serine proterase inhibitors,HMMSmart_SM00041,PatternScan_CTCK_1,HMMPfam_Cys_knot,HMMSmart_SM00215,superfamily_PMP inhibitors,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 NA NA NA NA NA NA NA 831711 TCGA-AB-2964 AML04 11 6246128 6246128 G A SNP CCKBR NM_176875.2 human genbank 54_36p 1 reviewed intronic c.152-1347 e2-1347 0.13 - - - no_errors tier2 895 0 0 240 150 38.46 0 0 NA 831711 TCGA-AB-2964 AML04 11 6772949 6772949 C T SNP OR6A2 NM_003696.2 human genbank 54_36p -1 provisional silent c.567 p.L189 0.006 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 1237 9 0.72 1422 1065 42.82 NA 831711 TCGA-AB-2964 AML04 11 8456533 8456533 T C SNP STK33 NM_030906.2 human genbank 54_36p -1 validated intronic c.1-3344 e1-3344 0.027 - - - no_errors tier3 440 1 0.23 246 160 39.31 0 0 NA 831711 TCGA-AB-2964 AML04 11 31746033 31746033 G A SNP ELP4 NM_019040.3 human genbank 54_36p 1 reviewed intronic c.1144-15484 e10-15484 0.115 - - - no_errors tier3 627 2 0.32 526 355 40.3 0 0 0 831711 TCGA-AB-2964 AML04 11 32410570 32410570 G A SNP WT1 NM_024426.3 human genbank 54_36p -1 reviewed intronic c.646+2252 e1+2252 0 - - - no_errors tier3 295 1 0.34 144 89 38.2 0 0 0 831711 TCGA-AB-2964 AML04 11 32415093 32415093 G C SNP WIT1 ENST00000395900 human ensembl 54_36p 1 known intronic c.1-874 e1-874 0.066 - - - no_errors tier3 273 0 0 120 90 42.86 2 4 66.67 831711 TCGA-AB-2964 AML04 11 33584359 33584359 A T SNP C11orf41 NM_012194.1 human genbank 54_36p 1 validated intronic c.4007-404 e13-404 0 - - - no_errors tier3 1264 2 0.16 1475 1016 40.77 0 0 0 831711 TCGA-AB-2964 AML04 11 40178541 40178541 G T SNP LRRC4C NM_020929.1 human genbank 54_36p -1 validated intronic c.1-84081 e1-84081 0.008 - - - no_errors tier3 1054 4 0.38 1214 717 37.09 0 0 NA 831711 TCGA-AB-2964 AML04 11 41251123 41251123 C T SNP LOC387753 XM_001724792.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*10042 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier2 866 3 0.34 764 497 39.41 0 0 NA 831711 TCGA-AB-2964 AML04 11 41398465 41398465 C T SNP - - - - - - - - - - - - - - - tier3 553 2 0.36 465 322 40.91 0 0 NA 831711 TCGA-AB-2964 AML04 11 70321759 70321759 G A SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.1780+437 e20+437 0 - - - no_errors tier3 475 2 0.42 112 47 29.56 0 0 NA 831711 TCGA-AB-2964 AML04 11 76701097 76701097 C T SNP GDPD4 NM_182833.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-27267 NULL 0.001 - - - no_errors tier3 525 0 0 224 134 37.43 0 0 NA 831711 TCGA-AB-2964 AML04 11 78036544 78036544 G A SNP ODZ4 NM_001098816.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*10207 NULL 0 - - - no_errors tier3 491 3 0.61 135 72 34.78 0 0 NA 831711 TCGA-AB-2964 AML04 11 79463319 79463319 C T SNP - - - - - - - - - - - - - - - tier3 1151 8 0.69 1567 990 38.7 0 0 NA 831711 TCGA-AB-2964 AML04 11 84494625 84494625 C T SNP DLG2 ENST00000376104 human ensembl 54_36p -1 known intronic c.357+5728 e4+5728 0.094 - - - no_errors tier3 1062 3 0.28 648 430 39.85 0 0 NA 831711 TCGA-AB-2964 AML04 11 85017412 85017412 G A SNP TMEM126B NM_018480.2 human genbank 54_36p 1 provisional intronic c.1+32 e0+32 0.001 - - - no_errors tier3 522 0 0 405 333 45.06 1 1 50 831711 TCGA-AB-2964 AML04 11 91464112 91464112 C T SNP - - - - - - - - - - - - - - - tier3 1168 5 0.43 1115 627 35.99 0 0 NA 831711 TCGA-AB-2964 AML04 11 103943471 103943471 A G SNP LOC643718 XM_931763.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*1336 NULL 0.003 - - - no_errors tier3 592 2 0.34 200 130 39.27 0 0 NA 831711 TCGA-AB-2964 AML04 11 104194450 104194450 G A SNP - - - - - - - - - - - - - - - tier3 958 2 0.21 1703 1345 44.08 0 1 100 831711 TCGA-AB-2964 AML04 11 106922100 106922100 A T SNP ALKBH8 NM_138775.2 human genbank 54_36p -1 validated intronic c.700+5644 e5+5644 0.001 - - - no_errors tier2 457 1 0.22 153 98 39.04 0 0 0 831711 TCGA-AB-2964 AML04 11 115890658 115890658 T G SNP - - - - - - - - - - - - - - - tier3 424 1 0.24 120 95 44.19 0 0 NA 831711 TCGA-AB-2964 AML04 11 117532019 117532019 T C SNP SCN4B NM_174934.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3421 NULL 0.306 - - - no_errors tier3 174 1 0.57 65 57 46.72 0 0 NA 831711 TCGA-AB-2964 AML04 11 127433279 127433279 G T SNP - - - - - - - - - - - - - - - tier3 1278 0 0 1710 1258 42.36 1 0 0 831711 TCGA-AB-2964 AML04 11 133548154 133548154 G C SNP NCAPD3 NM_015261.2 human genbank 54_36p -1 validated intronic c.3101+3258 e24+3258 0.931 - - - no_errors tier2 380 2 0.52 465 346 42.66 0 0 0 831711 TCGA-AB-2964 AML04 12 9052279 9052279 C T SNP KLRG1 NM_005810.3 human genbank 54_36p 1 reviewed intronic c.358-559 e4-559 0.009 - - - no_errors tier3 923 5 0.54 702 484 40.81 0 0 NA 831711 TCGA-AB-2964 AML04 12 13210124 13210124 G T SNP EMP1 ENST00000396301 human ensembl 54_36p 1 known intronic c.1+22969 e0+22969 0.048 - - - no_errors tier3 1377 6 0.43 419 320 43.24 0 0 NA 831711 TCGA-AB-2964 AML04 12 13476158 13476158 C T SNP ENSG00000201476 ENST00000364606 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8927 NULL 0.001 - - - no_errors tier3 1503 6 0.4 1851 1206 39.44 0 0 NA 831711 TCGA-AB-2964 AML04 12 15381692 15381692 G A SNP PTPRO NM_030667.2 human genbank 54_36p 1 reviewed intronic c.75+14690 e1+14690 0.029 - - - no_errors tier3 1034 4 0.39 450 374 45.33 0 0 NA 831711 TCGA-AB-2964 AML04 12 22436932 22436932 C T SNP - - - - - - - - - - - - - - - tier2 1284 3 0.23 467 339 42.06 0 0 NA 831711 TCGA-AB-2964 AML04 12 36764740 36764740 C T SNP - - - - - - - - - - - - - - - tier3 300 0 0 429 298 40.82 0 0 NA 831711 TCGA-AB-2964 AML04 12 47208926 47208926 C T SNP ENSG00000221171 ENST00000408244 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45738 NULL 0.005 - - - no_errors tier3 383 6 1.54 169 173 50.29 0 0 NA 831711 TCGA-AB-2964 AML04 12 51262836 51262836 G C SNP KRT74 NM_175053.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9008 NULL 0 - - - no_errors tier2 930 2 0.21 249 201 44.57 0 0 NA 831711 TCGA-AB-2964 AML04 12 56991529 56991529 A G SNP - - - - - - - - - - - - - - - tier3 710 3 0.42 684 532 43.75 0 0 NA 831711 TCGA-AB-2964 AML04 12 62966336 62966336 G C SNP C12orf56 NM_001099676.2 human genbank 54_36p -1 validated intronic c.634-229 e5-229 0.001 - - - no_errors tier3 808 8 0.98 571 427 42.7 0 0 NA 831711 TCGA-AB-2964 AML04 12 68396174 68396174 T C SNP BEST3 NM_032735.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-18329 NULL 0 - - - no_errors tier3 614 1 0.16 201 211 51.21 0 0 NA 831711 TCGA-AB-2964 AML04 12 69224759 69224759 G A SNP PTPRB NM_001109754.1 human genbank 54_36p -1 reviewed intronic c.5388-49 e22-49 0 - - - no_errors tier3 800 2 0.25 303 229 43.05 0 0 NA 831711 TCGA-AB-2964 AML04 12 73595032 73595032 T C SNP ENSG00000210718 ENST00000387983 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*38704 NULL 0 - - - pseudogene tier3 290 4 1.36 126 82 39.42 0 0 NA 831711 TCGA-AB-2964 AML04 12 76256601 76256601 C T SNP - - - - - - - - - - - - - - - tier3 561 1 0.18 278 190 40.6 0 0 NA 831711 TCGA-AB-2964 AML04 12 77980886 77980886 G A SNP SYT1 ENST00000261205 human ensembl 54_36p 1 known intronic c.1+15613 e0+15613 0.004 - - - no_errors tier3 1180 11 0.92 520 351 40.3 15 8 34.78 831711 TCGA-AB-2964 AML04 12 82050201 82050201 G A SNP TMTC2 NM_152588.1 human genbank 54_36p 1 provisional missense c.2413 p.A805T 1 "HMMPfam_TPR_1,HMMSmart_SM00028,superfamily_TPR-like" "HMMPfam_TPR_1,HMMPfam_TPR_2,HMMPfam_DUF1736,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 863 1 0.12 407 421 50.66 5 0 831711 TCGA-AB-2964 AML04 12 83749917 83749917 A T SNP SLC6A15 NM_182767.5 human genbank 54_36p -1 validated 3_prime_flanking_region c.*29625 NULL 0.004 - - - no_errors tier3 583 8 1.35 330 250 43.1 0 0 NA 831711 TCGA-AB-2964 AML04 12 93835487 93835487 A G SNP - - - - - - - - - - - - - - - tier2 468 0 0 187 124 39.87 0 0 NA 831711 TCGA-AB-2964 AML04 12 100876381 100876381 G C SNP ENSG00000211217 ENST00000388482 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30991 NULL 0.024 - - - pseudogene tier3 422 1 0.24 561 443 44.12 0 0 NA 831711 TCGA-AB-2964 AML04 12 107432934 107432934 G T SNP ISCU NM_014301.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49088 NULL 0 - - - no_errors tier2 269 8 2.88 182 98 35 0 0 NA 831711 TCGA-AB-2964 AML04 12 110059061 110059061 G A SNP CUX2 NM_015267.2 human genbank 54_36p 1 validated intronic c.64-77326 e2-77326 0.003 - - - no_errors tier2 1464 6 0.41 984 710 41.89 0 0 NA 831711 TCGA-AB-2964 AML04 12 110272146 110272146 G A SNP CUX2 NM_015267.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*1634 NULL 0.079 - - - no_errors tier2 286 1 0.35 99 83 45.6 0 0 NA 831711 TCGA-AB-2964 AML04 12 111772647 111772647 G T SNP RPH3A NM_014954.1 human genbank 54_36p 1 validated intronic c.218+2617 e2+2617 0.006 - - - no_errors tier3 2711 12 0.44 1100 854 43.71 0 0 NA 831711 TCGA-AB-2964 AML04 12 113625578 113625578 C T SNP TBX3 NM_016569.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20190 NULL 0.052 - - - no_errors tier3 1188 9 0.75 309 274 47 0 0 NA 831711 TCGA-AB-2964 AML04 12 114459604 114459604 G A SNP LOC100129020 XM_001716423.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37707 NULL 0.003 - - - no_errors tier3 1116 1 0.09 1267 805 38.83 0 0 NA 831711 TCGA-AB-2964 AML04 12 117474007 117474007 C T SNP - - - - - - - - - - - - - - - tier3 643 3 0.46 223 159 41.62 0 0 NA 831711 TCGA-AB-2964 AML04 12 127622739 127622739 C A SNP TMEM132C ENST00000315208 human ensembl 54_36p 1 known 5_prime_flanking_region c.-43942 NULL 0.869 - - - no_errors tier2 705 6 0.84 480 382 44.32 0 0 NA 831711 TCGA-AB-2964 AML04 12 127710006 127710006 C T SNP TMEM132C ENST00000315208 human ensembl 54_36p 1 known intronic c.154-9909 e2-9909 0.001 - - - no_errors tier3 445 2 0.45 588 389 39.82 0 0 NA 831711 TCGA-AB-2964 AML04 12 128136283 128136283 C A SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1444-1083 e6-1083 0 - - - no_errors tier2 216 4 1.82 145 97 40.08 0 0 NA 831711 TCGA-AB-2964 AML04 12 129095520 129095520 G A SNP ENSG00000214039 ENST00000397340 human ensembl 54_36p -1 known 5_prime_flanking_region c.-8117 NULL 0.001 - - - no_errors tier3 1020 5 0.49 349 204 36.82 0 0 NA 831711 TCGA-AB-2964 AML04 13 21110555 21110555 G C SNP LOC100128060 XM_001718205.1 human genbank 54_36p -1 model intronic c.1+1821 e0+1821 0.012 - - - pseudogene tier2 439 2 0.45 145 126 46.49 0 0 NA 831711 TCGA-AB-2964 AML04 13 39801787 39801787 T C SNP ENSG00000215483 ENST00000400432 human ensembl 54_36p -1 known 3_prime_flanking_region c.*20590 NULL 0.001 - - - no_errors tier3 838 1 0.12 425 318 42.74 0 0 NA 831711 TCGA-AB-2964 AML04 13 49983761 49983761 G T SNP LOC730194 XM_001132868.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*9791 NULL 0.002 - - - no_errors tier3 944 2 0.21 385 185 32.46 0 0 NA 831711 TCGA-AB-2964 AML04 13 54816989 54816989 G T SNP - - - - - - - - - - - - - - - tier2 3083 11 0.36 369 208 36.05 0 0 NA 831711 TCGA-AB-2964 AML04 13 54857807 54857807 G A SNP - - - - - - - - - - - - - - - tier3 1206 9 0.74 443 327 42.47 0 0 NA 831711 TCGA-AB-2964 AML04 13 55428564 55428564 C T SNP HNF4GP1 ENST00000403841 human ensembl 54_36p -1 known 3_prime_flanking_region c.*42792 NULL 0 - - - no_coding_region:pseudogene tier2 1352 7 0.52 636 383 37.51 0 0 NA 831711 TCGA-AB-2964 AML04 13 60762730 60762730 C T SNP - - - - - - - - - - - - - - - tier3 838 9 1.06 789 495 38.46 0 0 NA 831711 TCGA-AB-2964 AML04 13 60955486 60955486 A C SNP - - - - - - - - - - - - - - - tier3 1065 3 0.28 787 552 41.22 0 0 NA 831711 TCGA-AB-2964 AML04 13 63037166 63037166 G A SNP - - - - - - - - - - - - - - - tier3 164 2 1.2 86 61 41.5 0 0 NA 831711 TCGA-AB-2964 AML04 13 77716674 77716674 T C SNP - - - - - - - - - - - - - - - tier2 723 7 0.96 452 419 48.11 0 0 NA 831711 TCGA-AB-2964 AML04 13 80825358 80825358 G A SNP - - - - - - - - - - - - - - - tier3 799 12 1.48 351 236 40.2 0 0 NA 831711 TCGA-AB-2964 AML04 13 87143382 87143383 - T INS SLITRK5 NM_015567.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*14861 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 13 89372535 89372535 T C SNP - - - - - - - - - - - - - - - tier3 1718 20 1.15 666 565 45.82 0 0 NA 831711 TCGA-AB-2964 AML04 13 92359024 92359024 C A SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*42331 NULL 0 - - - no_errors tier3 981 10 1.01 887 619 41.1 0 0 NA 831711 TCGA-AB-2964 AML04 13 97867849 97867849 G A SNP FARP1 NM_005766.2 human genbank 54_36p 1 reviewed intronic c.1826+5560 e15+5560 0 - - - no_errors tier3 1465 8 0.54 403 290 41.79 0 0 NA 831711 TCGA-AB-2964 AML04 13 100407565 100407565 C A SNP - - - - - - - - - - - - - - - tier2 1582 4 0.25 1256 870 40.88 0 0 NA 831711 TCGA-AB-2964 AML04 13 110621485 110621485 A G SNP ARHGEF7 NM_145735.1 human genbank 54_36p 1 reviewed intronic c.252+17146 e2+17146 0.001 - - - no_errors tier3 1302 6 0.46 368 248 40.26 6 0 0 831711 TCGA-AB-2964 AML04 13 111705162 111705162 G A SNP ENSG00000200072 ENST00000363202 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-49231 NULL 0.012 - - - no_errors tier2 370 1 0.27 68 71 51.08 0 0 NA 831711 TCGA-AB-2964 AML04 14 20565620 20565620 G - DEL NDRG2 NM_201535.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4306 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 14 23065061 23065061 G T SNP ZFHX2 XM_001720095.1 human genbank 54_36p -1 model silent c.4332 p.G1444 0.892 NULL "HMMPfam_Homeobox,HMMSmart_SM00389,HMMSmart_SM00451,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Homeodomain-like,HMMSmart_SM00355,PatternScan_HOMEOBOX_1,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 1206 2 0.17 483 369 43.21 NA 831711 TCGA-AB-2964 AML04 14 24285060 24285060 G A SNP - - - - - - - - - - - - - - - tier3 1002 2 0.2 764 532 41.02 0 0 NA 831711 TCGA-AB-2964 AML04 14 28936484 28936484 T C SNP ENSG00000212061 ENST00000390772 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29384 NULL 0.015 - - - no_errors tier3 1013 7 0.69 470 356 43.1 0 0 NA 831711 TCGA-AB-2964 AML04 14 31630239 31630239 G A SNP ARHGAP5 NM_001030055.1 human genbank 54_36p 1 reviewed missense c.613 p.V205M 1 "HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_FF,HMMSmart_SM00441,superfamily_FF domain,superfamily_GTPase activation domain GAP,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1020 4 0.39 371 268 41.94 12 3 20 831711 TCGA-AB-2964 AML04 14 32851776 32851776 T A SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.347-54367 e4-54367 0 - - - no_errors tier2 1230 1 0.08 399 301 43 0 0 NA 831711 TCGA-AB-2964 AML04 14 36535701 36535701 C T SNP SLC25A21 NM_030631.2 human genbank 54_36p -1 provisional intronic c.71-121741 e2-121741 0.001 - - - no_errors tier2 1141 10 0.87 1127 824 42.19 0 0 NA 831711 TCGA-AB-2964 AML04 14 40131933 40131933 G A SNP - - - - - - - - - - - - - - - tier3 906 2 0.22 1076 853 44.17 0 0 NA 831711 TCGA-AB-2964 AML04 14 40389804 40389804 A T SNP - - - - - - - - - - - - - - - tier3 574 3 0.52 447 243 35.22 0 0 NA 831711 TCGA-AB-2964 AML04 14 41064948 41064948 C T SNP - - - - - - - - - - - - - - - tier3 309 1 0.32 91 59 39.33 0 0 NA 831711 TCGA-AB-2964 AML04 14 46597357 46597357 T C SNP MDGA2 NM_182830.1 human genbank 54_36p -1 validated intronic c.631+2845 e3+2845 0 - - - no_errors tier3 664 3 0.45 564 342 37.75 0 0 0 831711 TCGA-AB-2964 AML04 14 54966728 54966728 G A SNP TBPL2 NM_199047.2 human genbank 54_36p -1 validated intronic c.789-1283 e5-1283 0.019 - - - no_errors tier3 568 4 0.7 163 144 46.91 0 0 NA 831711 TCGA-AB-2964 AML04 14 60500244 60500244 T G SNP MNAT1 NM_002431.2 human genbank 54_36p 1 validated intronic c.810-4456 e8-4456 0.559 - - - no_errors tier3 371 2 0.53 293 218 42.66 0 0 0 831711 TCGA-AB-2964 AML04 14 61773892 61773892 C T SNP - - - - - - - - - - - - - - - tier3 484 2 0.41 377 243 39.13 0 0 NA 831711 TCGA-AB-2964 AML04 14 62252233 62252233 G A SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed intronic c.2020-7307 e11-7307 0 - - - no_errors tier3 514 4 0.77 250 108 30.08 0 0 NA 831711 TCGA-AB-2964 AML04 14 64445479 64445479 A G SNP CHURC1 NM_145165.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-5488 NULL 0.009 - - - no_errors tier3 1038 5 0.48 247 147 37.31 0 0 NA 831711 TCGA-AB-2964 AML04 14 75897492 75897492 C T SNP ESRRB NM_004452.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-77958 NULL 0 - - - no_errors tier3 369 2 0.54 107 78 42.16 0 0 NA 831711 TCGA-AB-2964 AML04 14 77686897 77686897 G C SNP ENSG00000199454 ENST00000362584 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*27002 NULL 0.715 - - - no_errors tier2 643 1 0.15 530 263 33.08 0 0 NA 831711 TCGA-AB-2964 AML04 14 82667882 82667882 A C SNP - - - - - - - - - - - - - - - tier3 332 1 0.3 442 334 43.04 0 0 NA 831711 TCGA-AB-2964 AML04 14 84932576 84932576 A C SNP - - - - - - - - - - - - - - - tier3 2045 3 0.15 1244 814 39.51 0 0 NA 831711 TCGA-AB-2964 AML04 14 86064593 86064593 A T SNP - - - - - - - - - - - - - - - tier3 433 1 0.23 348 280 44.59 0 0 NA 831711 TCGA-AB-2964 AML04 14 96162773 96162773 C T SNP ENSG00000223299 ENST00000411367 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*11511 NULL 0 - - - no_errors tier3 426 3 0.7 148 113 43.3 0 0 NA 831711 TCGA-AB-2964 AML04 14 97555988 97555988 T C SNP - - - - - - - - - - - - - - - tier3 1117 4 0.36 463 373 44.62 0 0 NA 831711 TCGA-AB-2964 AML04 15 19395647 19395647 G A SNP LOC440225 XR_042334.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.489 - - - pseudogene tier2 747 0 0 233 42 15.27 0 0 NA 831711 TCGA-AB-2964 AML04 15 23604961 23604961 A C SNP ATP10A NM_024490.3 human genbank 54_36p -1 reviewed intronic c.450-27498 e2-27498 0.001 - - - no_errors tier3 679 5 0.73 212 117 35.45 0 0 0 831711 TCGA-AB-2964 AML04 15 23677424 23677424 C A SNP ATP10A NM_024490.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-18088 NULL 0.005 - - - no_errors tier3 2123 13 0.61 885 626 41.4 0 0 NA 831711 TCGA-AB-2964 AML04 15 24625494 24625494 C A SNP GABRB3 ENST00000383015 human ensembl 54_36p -1 known intronic c.201-12840 e2-12840 0.018 - - - no_errors tier2 380 0 0 394 153 27.97 0 0 NA 831711 TCGA-AB-2964 AML04 15 27605569 27605569 A G SNP - - - - - - - - - - - - - - - tier3 1279 3 0.23 376 299 44.3 0 0 NA 831711 TCGA-AB-2964 AML04 15 34209867 34209867 G A SNP - - - - - - - - - - - - - - - tier3 681 0 0 425 268 38.67 0 0 NA 831711 TCGA-AB-2964 AML04 15 40070995 40070995 G A SNP PLA2G4E NM_001080490.1 human genbank 54_36p -1 provisional intronic c.1383+1232 e12+1232 0.097 - - - no_errors tier3 46 2 4.17 21 13 38.24 0 0 NA 831711 TCGA-AB-2964 AML04 15 42268153 42268153 A C SNP FRMD5 NM_032892.3 human genbank 54_36p -1 validated intronic c.102+6290 e1+6290 0 - - - no_errors tier3 698 0 0 294 223 43.13 0 0 NA 831711 TCGA-AB-2964 AML04 15 43388690 43388690 G C SNP SLC28A2 NM_004212.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*33687 NULL 0 - - - no_errors tier3 1858 20 1.06 262 145 35.63 0 0 NA 831711 TCGA-AB-2964 AML04 15 45023906 45023906 C T SNP - - - - - - - - - - - - - - - tier3 1393 4 0.29 602 360 37.42 0 0 NA 831711 TCGA-AB-2964 AML04 15 53570548 53570548 C T SNP DYX1C1 NM_130810.1 human genbank 54_36p -1 validated intronic c.405+65 e3+65 0 - - - no_errors tier3 1005 2 0.2 424 301 41.52 2 0 0 831711 TCGA-AB-2964 AML04 15 64097813 64097813 C T SNP MEGF11 NM_032445.2 human genbank 54_36p -1 validated intronic c.170-35933 e3-35933 0 - - - no_errors tier3 553 0 0 335 272 44.66 0 0 NA 831711 TCGA-AB-2964 AML04 15 65029288 65029288 C G SNP LOC729529 XM_001133761.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-7959 NULL 0.011 - - - no_errors tier2 737 3 0.41 222 156 41.27 0 0 NA 831711 TCGA-AB-2964 AML04 15 65255998 65255998 G A SNP SMAD3 NM_005902.1 human genbank 54_36p 1 validated intronic c.659-4635 e6-4635 0.981 - - - no_errors tier3 692 5 0.72 267 139 34.24 4 0 0 831711 TCGA-AB-2964 AML04 15 65558359 65558359 A T SNP IQCH NM_001031715.1 human genbank 54_36p 1 provisional intronic c.2799+3149 e18+3149 0 - - - no_errors tier3 1301 8 0.61 613 518 45.72 0 0 NA 831711 TCGA-AB-2964 AML04 15 66679078 66679078 C T SNP CORO2B NM_006091.3 human genbank 54_36p 1 validated intronic c.15+20408 e1+20408 0.001 - - - no_errors tier3 431 2 0.46 163 112 40.73 0 0 NA 831711 TCGA-AB-2964 AML04 15 83899998 83899998 G A SNP AKAP13 NM_006738.4 human genbank 54_36p 1 reviewed intronic c.662+11808 e4+11808 0.003 - - - no_errors tier3 747 0 0 656 429 39.54 0 4 100 831711 TCGA-AB-2964 AML04 15 85231173 85231173 A C SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.3084-101049 e22-101049 0.004 - - - no_errors tier3 767 0 0 951 668 41.23 0 0 NA 831711 TCGA-AB-2964 AML04 15 95727154 95727154 A G SNP ENSG00000208890 ENST00000386155 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29194 NULL 0.962 - - - pseudogene tier2 1834 9 0.49 1996 1447 41.87 0 0 NA 831711 TCGA-AB-2964 AML04 15 97800025 97800025 C T SNP - - - - - - - - - - - - - - - tier3 360 1 0.28 79 53 40.15 0 0 NA 831711 TCGA-AB-2964 AML04 15 99794074 99794074 G A SNP PCSK6 ENST00000348070 human ensembl 54_36p -1 known intronic c.400-4246 e4-4246 0 - - - no_errors tier3 385 1 0.26 201 155 43.54 0 0 NA 831711 TCGA-AB-2964 AML04 16 2703666 2703666 G C SNP PRSS27 NM_031948.3 human genbank 54_36p -1 validated silent c.543 p.L181 0.031 "HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys" "HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER" - no_errors tier1 294 0 77 61 44.2 3 0 831711 TCGA-AB-2964 AML04 16 5880365 5880365 G A SNP - - - - - - - - - - - - - - - tier3 682 10 1.45 325 196 37.62 0 0 NA 831711 TCGA-AB-2964 AML04 16 5918766 5918766 G C SNP - - - - - - - - - - - - - - - tier2 318 2 0.62 68 49 41.88 0 0 NA 831711 TCGA-AB-2964 AML04 16 6574725 6574725 C T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-69880 e1-69880 0 - - - no_errors tier3 988 3 0.3 835 666 44.34 0 0 NA 831711 TCGA-AB-2964 AML04 16 10721866 10721866 G A SNP NUBP1 NM_002484.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-23356 NULL 1 - - - no_errors tier2 183 0 0 63 52 44.83 0 0 NA 831711 TCGA-AB-2964 AML04 16 12058101 12058101 G A SNP SNX29 NM_001080530.2 human genbank 54_36p 1 provisional intronic c.1+4521 e0+4521 0.001 - - - no_errors tier3 332 2 0.6 130 73 35.78 2 0 0 831711 TCGA-AB-2964 AML04 16 34265668 34265668 C T SNP LOC100131688 XM_001718246.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-28120 NULL 0.999 - - - no_errors tier2 142 0 0 111 71 39.01 0 0 NA 831711 TCGA-AB-2964 AML04 16 45406157 45406157 A G SNP C16orf87 NM_001001436.2 human genbank 54_36p -1 predicted intronic c.164-4959 e3-4959 0.091 - - - no_errors tier3 1376 4 0.29 548 415 43.09 4 1 20 831711 TCGA-AB-2964 AML04 16 50342778 50342778 G A SNP - - - - - - - - - - - - - - - tier2 877 6 0.68 678 442 39.39 0 0 NA 831711 TCGA-AB-2964 AML04 16 51372690 51372690 G A SNP LOC100132440 XM_001719251.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-26033 NULL 0.001 - - - no_errors tier3 1021 8 0.78 695 592 45.96 0 0 NA 831711 TCGA-AB-2964 AML04 16 52949708 52949708 G A SNP LOC728792 XM_001719288.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*20979 NULL 0 - - - no_errors tier3 541 4 0.73 435 325 42.76 4 0 0 831711 TCGA-AB-2964 AML04 16 52952983 52952983 G T SNP LOC728792 XM_001719288.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*24254 NULL 0 - - - no_errors tier3 504 10 1.95 312 287 47.91 6 1 14.29 831711 TCGA-AB-2964 AML04 16 54217994 54217994 C T SNP SLC6A2 NM_001043.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30114 NULL 0 - - - no_errors tier3 828 1 0.12 975 729 42.76 0 0 NA 831711 TCGA-AB-2964 AML04 16 61416941 61416941 C T SNP ENSG00000223123 ENST00000411191 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*425 NULL 0 - - - no_errors tier2 452 3 0.66 390 237 37.8 0 0 NA 831711 TCGA-AB-2964 AML04 16 62031194 62031194 T G SNP - - - - - - - - - - - - - - - tier3 1193 3 0.25 1025 677 39.78 0 0 NA 831711 TCGA-AB-2964 AML04 16 72110139 72110139 G A SNP - - - - - - - - - - - - - - - tier3 869 8 0.91 1006 834 45.3 0 0 NA 831711 TCGA-AB-2964 AML04 16 74547790 74547790 G A SNP - - - - - - - - - - - - - - - tier3 732 2 0.27 588 389 39.78 0 0 NA 831711 TCGA-AB-2964 AML04 16 78825211 78825211 G A SNP LOC729847 XM_001131495.1 human genbank 54_36p -1 model intronic c.192-14947 e2-14947 0 - - - no_errors tier3 388 1 0.26 393 247 38.53 0 0 NA 831711 TCGA-AB-2964 AML04 16 78951288 78951288 T A SNP LOC729847 XM_001131495.1 human genbank 54_36p -1 model intronic c.191+132680 e1+132680 0.002 - - - no_errors tier3 936 5 0.53 891 683 43.39 0 0 NA 831711 TCGA-AB-2964 AML04 16 86356286 86356286 C G SNP KLHDC4 NM_017566.2 human genbank 54_36p -1 provisional intronic c.99+613 e1+613 0.001 - - - no_errors tier2 273 1 0.36 75 75 50 3 0 0 831711 TCGA-AB-2964 AML04 17 11657866 11657866 T A SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed intronic c.8707+3455 e45+3455 0 - - - no_errors tier2 1091 7 0.64 1181 776 39.63 0 0 NA 831711 TCGA-AB-2964 AML04 17 26848835 26848835 G T SNP RAB11FIP4 NM_032932.3 human genbank 54_36p 1 validated intronic c.337-19954 e4-19954 0.006 - - - no_errors tier3 2109 2 0.09 118 74 38.34 0 0 NA 831711 TCGA-AB-2964 AML04 17 35431191 35431191 C G SNP MED24 NM_014815.1 human genbank 54_36p -1 reviewed intronic c.2623+543 e22+543 0.647 - - - no_errors tier3 360 0 0 80 71 47.02 7 0 0 831711 TCGA-AB-2964 AML04 17 43672126 43672126 C G SNP SKAP1 NM_003726.1 human genbank 54_36p -1 reviewed intronic c.281-50265 e5-50265 0.004 - - - no_errors tier3 1469 4 0.27 2353 1514 39.12 9 0 0 831711 TCGA-AB-2964 AML04 17 44727761 44727761 T C SNP ZNF652 NM_014897.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*3013 NULL 0 - - - no_errors tier3 184 0 0 46 48 51.06 14 9 39.13 831711 TCGA-AB-2964 AML04 17 47279212 47279212 G T SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.279+84137 e3+84137 0 - - - no_errors tier3 495 0 0 726 497 40.6 0 0 NA 831711 TCGA-AB-2964 AML04 17 67284980 67284980 G A SNP - - - - - - - - - - - - - - - tier2 751 1 0.13 1015 680 40.07 0 0 NA 831711 TCGA-AB-2964 AML04 17 68449337 68449337 G A SNP SLC39A11 NM_139177.2 human genbank 54_36p -1 provisional intronic c.430+6149 e4+6149 0.001 - - - no_errors tier3 640 0 0 349 299 46.14 14 4 22.22 831711 TCGA-AB-2964 AML04 18 1763606 1763606 G A SNP LOC100134353 XM_001714570.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*7484 NULL 0.032 - - - no_start_codon:pseudogene:no_stop_codon tier3 445 0 0 177 85 32.44 0 0 NA 831711 TCGA-AB-2964 AML04 18 3511776 3511776 C T SNP DLGAP1 NM_004746.1 human genbank 54_36p -1 provisional intronic c.2479+12416 e7+12416 0.01 - - - no_errors tier3 762 2 0.26 400 286 41.69 0 0 NA 831711 TCGA-AB-2964 AML04 18 4262123 4262123 G A SNP LOC284215 XM_001127273.1 human genbank 54_36p 1 model intronic c.63+7222 e1+7222 0.001 - - - no_errors tier3 667 3 0.45 245 162 39.8 0 0 NA 831711 TCGA-AB-2964 AML04 18 7113551 7113551 G A SNP LAMA1 NM_005559.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5832 NULL 0 - - - no_errors tier3 566 4 0.7 217 135 38.35 0 0 NA 831711 TCGA-AB-2964 AML04 18 18588717 18588717 T C SNP - - - - - - - - - - - - - - - tier2 535 6 1.11 1081 776 41.79 0 0 NA 831711 TCGA-AB-2964 AML04 18 22064781 22064781 C T SNP TAF4B NM_005640.1 human genbank 54_36p 1 validated intronic c.343+3543 e1+3543 0 - - - no_errors tier3 303 18 5.59 221 131 37.11 0 0 0 831711 TCGA-AB-2964 AML04 18 26876505 26876505 C A SNP DSC3 NM_001941.3 human genbank 54_36p -1 reviewed intronic c.69+51 e1+51 0 - - - no_errors tier2 240 2 0.83 213 179 45.55 0 0 NA 831711 TCGA-AB-2964 AML04 18 32213594 32213594 G A SNP FHOD3 NM_025135.2 human genbank 54_36p 1 validated intronic c.337+6889 e3+6889 0 - - - no_errors tier2 1723 4 0.23 509 361 41.49 0 0 NA 831711 TCGA-AB-2964 AML04 18 33973055 33973055 A G SNP - - - - - - - - - - - - - - - tier3 1348 8 0.59 1021 741 42.03 0 0 NA 831711 TCGA-AB-2964 AML04 18 34682744 34682744 G A SNP - - - - - - - - - - - - - - - tier3 858 2 0.23 664 475 41.7 0 0 NA 831711 TCGA-AB-2964 AML04 18 39089569 39089569 T A SNP SYT4 NM_020783.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*14735 NULL 0 - - - no_errors tier3 1286 17 1.3 1212 883 42.13 0 0 NA 831711 TCGA-AB-2964 AML04 18 51371121 51371121 G C SNP TCF4 NM_001083962.1 human genbank 54_36p -1 reviewed intronic c.145+32388 e2+32388 1 - - - no_errors tier2 546 2 0.36 709 537 43.1 3 0 0 831711 TCGA-AB-2964 AML04 18 63971480 63971480 C T SNP - - - - - - - - - - - - - - - tier3 1269 8 0.63 1416 975 40.69 0 0 NA 831711 TCGA-AB-2964 AML04 18 64422477 64422477 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 831711 TCGA-AB-2964 AML04 18 67835625 67835625 C T SNP - - - - - - - - - - - - - - - tier3 1131 4 0.35 482 325 40.27 0 0 NA 831711 TCGA-AB-2964 AML04 18 68465764 68465764 C T SNP - - - - - - - - - - - - - - - tier3 894 4 0.45 332 226 40.5 0 0 NA 831711 TCGA-AB-2964 AML04 19 1229273 1229273 G A SNP C19orf24 NM_017914.3 human genbank 54_36p 1 validated intronic c.1-503 e1-503 0.071 - - - no_errors tier2 53 1 1.85 22 9 29.03 0 0 0 831711 TCGA-AB-2964 AML04 19 6042991 6042991 A G SNP RFX2 NM_000635.3 human genbank 54_36p -1 reviewed intronic c.1+18413 e0+18413 0.209 - - - no_errors tier2 475 5 1.04 115 55 32.35 9 14 60.87 831711 TCGA-AB-2964 AML04 19 13773283 13773283 A G SNP ZSWIM4 NM_023072.2 human genbank 54_36p 1 validated intronic c.355+1548 e2+1548 0.004 - - - no_errors tier3 222 1 0.45 46 27 36.99 2 0 0 831711 TCGA-AB-2964 AML04 19 18544931 18544931 G C SNP UBA52 NM_001033930.1 human genbank 54_36p 1 reviewed intronic c.1-172 e1-172 0.675 - - - no_errors tier2 452 1 0.22 131 97 42.54 0 0 0 831711 TCGA-AB-2964 AML04 19 33174097 33174097 G T SNP - - - - - - - - - - - - - - - tier3 193 0 0 79 53 40.15 0 0 NA 831711 TCGA-AB-2964 AML04 19 37583979 37583979 C T SNP DPY19L3 NM_207325.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-7021 NULL 0.002 - - - no_errors tier3 367 3 0.81 253 219 46.4 0 0 NA 831711 TCGA-AB-2964 AML04 19 41048861 41048861 C T SNP KIRREL2 NM_199180.5 human genbank 54_36p 1 validated intronic c.1792-38 e15-38 0 - - - no_errors tier2 288 0 0 68 63 48.09 0 0 NA 831711 TCGA-AB-2964 AML04 19 42593405 42593405 C T SNP ZNF569 NM_152484.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*1934 NULL 0.001 - - - no_errors tier2 1278 11 0.85 300 165 35.48 2 3 60 831711 TCGA-AB-2964 AML04 19 49263977 49263977 T A SNP ZNF223 NM_013361.4 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*707 NULL 0 - - - no_errors tier2 587 3 0.51 109 85 43.81 0 0 0 831711 TCGA-AB-2964 AML04 20 13505623 13505623 C T SNP TASP1 NM_017714.2 human genbank 54_36p -1 reviewed intronic c.488+3921 e5+3921 0.002 - - - no_errors tier3 1047 1 0.1 1035 731 41.37 0 1 100 831711 TCGA-AB-2964 AML04 20 15012650 15012650 T C SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.419-145936 e6-145936 0 - - - no_errors tier3 1176 7 0.59 589 541 47.88 0 0 NA 831711 TCGA-AB-2964 AML04 20 22818740 22818740 G A SNP CYB5P4 ENST00000404948 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4034 NULL 0.001 - - - no_coding_region:pseudogene tier3 2451 2 0.08 2226 1721 43.58 0 0 NA 831711 TCGA-AB-2964 AML04 20 37537266 37537266 C T SNP - - - - - - - - - - - - - - - tier3 461 0 0 683 473 40.92 0 0 NA 831711 TCGA-AB-2964 AML04 20 38518189 38518189 G T SNP - - - - - - - - - - - - - - - tier3 713 3 0.42 336 177 34.44 0 0 NA 831711 TCGA-AB-2964 AML04 20 57633164 57633164 G C SNP PHACTR3 NM_080672.3 human genbank 54_36p 1 reviewed intronic c.118+19582 e1+19582 0.217 - - - no_errors tier2 1230 5 0.4 152 76 33.33 0 0 NA 831711 TCGA-AB-2964 AML04 21 24675981 24675981 T C SNP uc002yli.1 ENST00000355181 human ensembl 54_36p 1 known 5_prime_flanking_region c.-46944 NULL 0.001 - - - no_coding_region:pseudogene tier3 1020 1 0.1 880 613 41.03 0 0 NA 831711 TCGA-AB-2964 AML04 21 27598617 27598617 C T SNP - - - - - - - - - - - - - - - tier3 800 3 0.37 837 643 43.42 0 0 NA 831711 TCGA-AB-2964 AML04 21 34103035 34103035 C G SNP ITSN1 NM_003024.1 human genbank 54_36p 1 reviewed intronic c.2320-2114 e20-2114 0.014 - - - no_errors tier2 568 0 0 209 168 44.44 0 2 100 831711 TCGA-AB-2964 AML04 21 35297673 35297673 G C SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed intronic c.58+45336 e1+45336 1 - - - no_errors tier3 654 0 0 387 305 43.95 17 26 60.47 831711 TCGA-AB-2964 AML04 21 42297031 42297031 C T SNP ZNF295 NM_001098402.1 human genbank 54_36p -1 validated intronic c.1-892 e1-892 0.009 - - - no_errors tier3 3087 8 0.26 484 304 38.58 0 4 100 831711 TCGA-AB-2964 AML04 21 43484354 43484354 C T SNP CRYAA NM_000394.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*18895 NULL 0 - - - no_errors tier3 702 4 0.57 124 79 38.92 0 0 NA 831711 TCGA-AB-2964 AML04 21 46076846 46076846 C T SNP PCBP3 ENST00000400314 human ensembl 54_36p 1 known intronic c.1-17457 e1-17457 0.079 - - - no_errors tier2 274 0 0 202 133 39.7 2 0 0 831711 TCGA-AB-2964 AML04 22 16911502 16911502 G A SNP PEX26 NM_017929.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29641 NULL 0 - - - no_errors tier2 736 6 0.81 159 138 46.31 0 0 NA 831711 TCGA-AB-2964 AML04 22 16920384 16920384 G C SNP PEX26 NM_017929.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20759 NULL 0 - - - no_errors tier3 448 1 0.22 156 129 45.26 0 0 NA 831711 TCGA-AB-2964 AML04 22 26295534 26295534 C A SNP - - - - - - - - - - - - - - - tier3 1294 7 0.54 306 244 44.36 0 0 NA 831711 TCGA-AB-2964 AML04 22 27123565 27123565 T C SNP TTC28 ENST00000397906 human ensembl 54_36p -1 known intronic c.382-90934 e3-90934 0 - - - no_errors tier2 1146 14 1.21 674 552 45.02 0 0 0 831711 TCGA-AB-2964 AML04 22 35880064 35880064 C G SNP IL2RB NM_000878.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-9906 NULL 0.003 - - - no_errors tier3 1613 3 0.19 317 268 45.73 0 0 NA 831711 TCGA-AB-2964 AML04 22 38822629 38822629 C A SNP TNRC6B NM_001024843.1 human genbank 54_36p 1 validated intronic c.1-20376 e1-20376 0 - - - no_errors tier3 5327 2 0.04 527 360 40.59 4 10 71.43 142074 TCGA-AB-2965 AML19 Y 21702259 21702259 T C SNP ENSG00000220870 ENST00000406184 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*21702259 NULL 0.001 - - - no_coding_region:pseudogene tier3 273 106 27.82 30 540 94.41 0 0 NA 142074 TCGA-AB-2965 AML19 X 124950804 124950804 G A SNP - - - - - - - - - - - - - - - tier3 75 24 24 5 84 94.38 0 0 NA 142074 TCGA-AB-2965 AML19 X 143600467 143600467 G A SNP - - - - - - - - - - - - - - - tier3 151 49 24.38 5 119 95.97 0 0 NA 142074 TCGA-AB-2965 AML19 1 84017501 84017501 A G SNP ENSG00000223231 ENST00000411299 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-14647 NULL 0.961 - - - no_errors tier3 262 33 11.15 102 107 50.95 0 0 NA 142074 TCGA-AB-2965 AML19 1 98190359 98190359 G A SNP DPYD NM_000110.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31293 NULL 0 - - - no_errors tier3 99 15 13.16 34 39 53.42 0 0 NA 142074 TCGA-AB-2965 AML19 1 104840685 104840685 T C SNP - - - - - - - - - - - - - - - tier3 90 24 21.05 24 35 59.32 0 0 NA 142074 TCGA-AB-2965 AML19 1 188334613 188334613 C T SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional missense c.1459 p.G487S 1 NULL "HMMPfam_MACPF,HMMSmart_SM00457" - no_errors tier1 382 58 13.18 308 275 47.09 NA 142074 TCGA-AB-2965 AML19 1 211122463 211122463 T C SNP FLVCR1 NM_014053.2 human genbank 54_36p 1 validated intronic c.1025-873 e4-873 0.026 - - - no_errors tier3 52 4 7.14 23 29 55.77 0 0 0 142074 TCGA-AB-2965 AML19 2 1461102 1461102 C T SNP TPO NM_000547.4 human genbank 54_36p 1 reviewed intronic c.1338+719 e7+719 0.001 - - - no_errors tier3 270 57 17.38 140 179 56.11 0 0 NA 142074 TCGA-AB-2965 AML19 2 4278636 4278636 C T SNP ENSG00000215960 ENST00000401141 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24653 NULL 0 - - - no_errors tier3 227 41 15.19 207 181 46.65 0 0 NA 142074 TCGA-AB-2965 AML19 2 15483298 15483298 C T SNP NBAS NM_015909.2 human genbank 54_36p -1 validated intronic c.2424-1255 e23-1255 0 - - - no_errors tier3 738 106 12.47 448 416 48.09 1 0 0 142074 TCGA-AB-2965 AML19 2 18862326 18862326 G T SNP - - - - - - - - - - - - - - - tier3 164 19 10.38 92 59 39.07 0 0 NA 142074 TCGA-AB-2965 AML19 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 NA NA NA NA NA NA 16 15 48.39 142074 TCGA-AB-2965 AML19 2 83033444 83033444 C G SNP - - - - - - - - - - - - - - - tier3 144 19 11.66 76 56 42.11 0 0 NA 142074 TCGA-AB-2965 AML19 2 117975852 117975852 C A SNP - - - - - - - - - - - - - - - tier3 225 37 14.12 167 106 38.83 0 0 NA 142074 TCGA-AB-2965 AML19 2 126601394 126601394 C T SNP - - - - - - - - - - - - - - - tier3 287 39 11.93 193 185 48.81 0 0 NA 142074 TCGA-AB-2965 AML19 2 131391188 131391188 G A SNP LOC730032 XM_001132160.2 human genbank 54_36p 1 model missense c.3199 p.A1067T 0 NULL NULL - no_errors tier1 93 14 13.08 99 110 52.63 NA 142074 TCGA-AB-2965 AML19 2 195938414 195938414 C T SNP - - - - - - - - - - - - - - - tier3 408 55 11.85 271 250 47.8 0 0 NA 142074 TCGA-AB-2965 AML19 3 37462853 37462853 C T SNP ITGA9 NM_002207.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6017 NULL 0.009 - - - no_errors tier3 321 62 16.15 139 121 46.54 0 0 NA 142074 TCGA-AB-2965 AML19 3 42530257 42530257 G A SNP VIPR1 NM_004624.3 human genbank 54_36p 1 validated missense c.91 p.A31T 0 superfamily_Hormone receptor domain (HRM Pfam 02793) "HMMPfam_7tm_2,HMMPfam_HRM,HMMSmart_SM00008,PatternScan_G_PROTEIN_RECEP_F2_1,PatternScan_G_PROTEIN_RECEP_F2_2,superfamily_Hormone receptor domain (HRM Pfam 02793),superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 342 48 12.24 87 115 56.93 NA 142074 TCGA-AB-2965 AML19 3 54543507 54543507 C T SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.545-28360 e6-28360 0.004 - - - no_errors tier3 424 78 15.51 235 203 46.35 0 0 NA 142074 TCGA-AB-2965 AML19 3 62923535 62923535 A C SNP LOC389127 XR_017671.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*35909 NULL 0 - - - pseudogene tier3 290 50 14.71 262 201 43.41 0 0 NA 142074 TCGA-AB-2965 AML19 3 131434060 131434060 G C SNP LOC100131335 XM_001717966.1 human genbank 54_36p 1 model intronic c.523-919 e10-919 0.013 - - - no_errors tier3 166 25 13.09 174 139 44.27 0 1 100 142074 TCGA-AB-2965 AML19 3 152230818 152230818 T C SNP - - - - - - - - - - - - - - - tier3 239 45 15.85 134 151 52.98 0 0 NA 142074 TCGA-AB-2965 AML19 3 181773263 181773263 A C SNP TTC14 NM_133462.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29481 NULL 0 - - - no_errors tier3 441 68 13.33 158 142 47.33 0 0 NA 142074 TCGA-AB-2965 AML19 4 4782195 4782195 C T SNP - - - - - - - - - - - - - - - tier3 175 50 22.22 104 108 50.7 0 0 NA 142074 TCGA-AB-2965 AML19 4 19358733 19358733 G C SNP - - - - - - - - - - - - - - - tier3 479 88 15.49 358 269 42.9 0 0 NA 142074 TCGA-AB-2965 AML19 4 19398752 19398752 A T SNP LOC645174 XR_017157.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-25699 NULL 0 - - - pseudogene tier3 48 9 15.52 21 23 52.27 0 0 NA 142074 TCGA-AB-2965 AML19 4 20254189 20254189 G C SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*24459 NULL 0 - - - no_errors tier3 493 60 10.81 162 126 43.75 0 0 NA 142074 TCGA-AB-2965 AML19 4 41468418 41468418 A G SNP PHOX2B NM_003924.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-23034 NULL 0.001 - - - no_errors tier3 187 33 14.93 91 91 50 0 0 NA 142074 TCGA-AB-2965 AML19 4 92933517 92933517 A T SNP - - - - - - - - - - - - - - - tier3 121 20 13.89 86 86 50 0 0 NA 142074 TCGA-AB-2965 AML19 4 96517302 96517302 C T SNP UNC5C NM_003728.2 human genbank 54_36p -1 reviewed intronic c.125-41497 e2-41497 0.001 - - - no_errors tier3 147 19 11.45 114 103 47.47 0 0 NA 142074 TCGA-AB-2965 AML19 4 96942887 96942887 C T SNP PDHA2 NM_005390.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37438 NULL 0.01 - - - no_errors tier3 93 11 10.48 47 48 50.53 0 0 NA 142074 TCGA-AB-2965 AML19 4 106400368 106400368 C - DEL TET2 ENST00000265149 human ensembl 54_36p 1 known frame_shift_del c.353 p.P118fs 1 NULL NULL - no_start_codon tier1 NA NA NA NA NA NA NA 142074 TCGA-AB-2965 AML19 4 116286660 116286660 C A SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-69019 NULL 0.024 - - - no_errors tier3 370 65 14.84 247 232 48.43 0 0 NA 142074 TCGA-AB-2965 AML19 4 123487977 123487977 A G SNP KIAA1109 NM_015312.2 human genbank 54_36p 1 validated intronic c.12872-150 e74-150 0.01 - - - no_errors tier3 276 46 14.24 194 162 45.51 4 7 63.64 142074 TCGA-AB-2965 AML19 4 137117541 137117541 A C SNP ENSG00000207322 ENST00000384592 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*18993 NULL 0.001 - - - no_errors tier3 38 3 7.32 33 28 45.9 0 0 NA 142074 TCGA-AB-2965 AML19 5 2361366 2361366 G T SNP - - - - - - - - - - - - - - - tier3 188 40 17.47 68 68 50 0 0 NA 142074 TCGA-AB-2965 AML19 5 14847593 14847593 C T SNP ANKH NM_054027.4 human genbank 54_36p -1 reviewed intronic c.97-25293 e2-25293 0 - - - no_errors tier3 362 53 12.74 246 181 42.39 0 0 NA 142074 TCGA-AB-2965 AML19 5 21792946 21792946 G C SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1634-1238 e10-1238 0.005 - - - no_errors tier3 423 78 15.57 255 232 47.44 0 0 NA 142074 TCGA-AB-2965 AML19 5 28302110 28302110 C T SNP - - - - - - - - - - - - - - - tier3 373 47 11.19 245 187 43.29 0 0 NA 142074 TCGA-AB-2965 AML19 5 116405307 116405307 C G SNP - - - - - - - - - - - - - - - tier3 167 45 21.23 46 46 50 0 0 NA 142074 TCGA-AB-2965 AML19 5 140129655 140129655 G A SNP PCDHA1 NM_018900.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-16405 NULL 0 - - - no_errors tier3 266 32 10.74 75 44 36.97 0 0 NA 142074 TCGA-AB-2965 AML19 5 154329272 154329272 T A SNP GEMIN5 NM_015465.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31386 NULL 0.016 - - - no_errors tier3 332 40 10.72 223 198 47.03 0 0 NA 142074 TCGA-AB-2965 AML19 5 161105377 161105377 G A SNP GABRA6 NM_000811.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*44020 NULL 0.001 - - - no_errors tier3 177 32 15.31 171 135 44.12 0 0 NA 142074 TCGA-AB-2965 AML19 5 168779764 168779764 A G SNP - - - - - - - - - - - - - - - tier3 296 47 13.66 262 272 50.94 0 0 NA 142074 TCGA-AB-2965 AML19 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 142074 TCGA-AB-2965 AML19 6 16556526 16556526 C T SNP ATXN1 NM_000332.3 human genbank 54_36p -1 reviewed intronic c.1+37656 e0+37656 0 - - - no_errors tier3 400 48 10.67 405 340 45.64 3 2 40 142074 TCGA-AB-2965 AML19 6 19796062 19796062 A T SNP ENSG00000200957 ENST00000364087 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45323 NULL 0.016 - - - no_errors tier3 359 44 10.89 208 190 47.74 0 0 NA 142074 TCGA-AB-2965 AML19 6 19802093 19802093 A T SNP - - - - - - - - - - - - - - - tier3 320 44 12.09 148 169 53.31 0 0 NA 142074 TCGA-AB-2965 AML19 6 89061632 89061632 C G SNP ENSG00000220267 ENST00000403258 human ensembl 54_36p -1 known 5_prime_flanking_region c.-18205 NULL 0 - - - no_coding_region:pseudogene tier3 337 49 12.66 231 161 41.07 1 0 0 142074 TCGA-AB-2965 AML19 6 95432783 95432783 C T SNP - - - - - - - - - - - - - - - tier3 112 21 15.67 101 73 41.71 0 0 NA 142074 TCGA-AB-2965 AML19 6 127276160 127276160 A C SNP - - - - - - - - - - - - - - - tier3 225 33 12.79 164 160 49.38 0 0 NA 142074 TCGA-AB-2965 AML19 6 148603930 148603930 A T SNP SASH1 ENST00000367469 human ensembl 54_36p 1 known 5_prime_flanking_region c.-31256 NULL 0 - - - no_errors tier3 123 17 12.14 39 30 43.48 0 0 NA 142074 TCGA-AB-2965 AML19 6 158411631 158411631 G A SNP SYNJ2 NM_003898.2 human genbank 54_36p 1 provisional intronic c.1940+938 e14+938 0.005 - - - no_errors tier3 291 48 14.08 115 88 43.35 0 0 NA 142074 TCGA-AB-2965 AML19 7 29848498 29848498 C T SNP WIPF3 NM_001080529.1 human genbank 54_36p 1 provisional intronic c.90+7543 e1+7543 0.003 - - - no_errors tier3 209 21 9.13 120 121 50 0 0 NA 142074 TCGA-AB-2965 AML19 7 79124553 79124553 T C SNP ENSG00000200786 ENST00000363916 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*3074 NULL 0.001 - - - no_errors tier3 60 13 17.81 15 51 77.27 0 0 NA 142074 TCGA-AB-2965 AML19 7 106284248 106284248 T C SNP PIK3CG NM_002649.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-10995 NULL 0.003 - - - no_errors tier3 367 68 15.56 121 125 50.81 0 0 NA 142074 TCGA-AB-2965 AML19 7 138774834 138774834 G A SNP LOC100129148 XM_001726722.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16236 NULL 0 - - - no_errors tier3 513 97 15.8 181 171 48.58 0 0 NA 142074 TCGA-AB-2965 AML19 7 155991455 155991455 G A SNP - - - - - - - - - - - - - - - tier3 367 49 11.78 165 152 47.95 0 0 NA 142074 TCGA-AB-2965 AML19 8 970193 970193 C T SNP C8orf68 XM_927505.1 human genbank 54_36p 1 model intronic c.71-104513 e3-104513 0 - - - no_errors tier3 574 102 15.07 123 156 55.91 0 0 NA 142074 TCGA-AB-2965 AML19 8 1055158 1055158 G C SNP C8orf68 XM_927505.1 human genbank 54_36p 1 model intronic c.71-19548 e3-19548 0 - - - no_errors tier3 216 39 15.23 178 137 43.49 0 0 NA 142074 TCGA-AB-2965 AML19 8 50569543 50569543 A G SNP - - - - - - - - - - - - - - - tier3 71 9 11.25 84 50 37.31 0 0 NA 142074 TCGA-AB-2965 AML19 8 56888021 56888021 C G SNP TGS1 NM_024831.6 human genbank 54_36p 1 validated intronic c.2361-132 e12-132 0 - - - no_errors tier3 85 21 19.63 49 35 41.67 6 7 53.85 142074 TCGA-AB-2965 AML19 8 76604832 76604832 G T SNP HNF4G ENST00000354370 human ensembl 54_36p 1 known intronic c.1-13769 e1-13769 0.005 - - - no_errors tier3 130 26 16.67 146 158 51.8 0 0 NA 142074 TCGA-AB-2965 AML19 8 85544981 85544981 T C SNP RALYL NM_001100391.1 human genbank 54_36p 1 validated intronic c.17-59108 e2-59108 0.014 - - - no_errors tier3 110 29 20.86 76 117 60.62 0 0 NA 142074 TCGA-AB-2965 AML19 8 101478545 101478545 G A SNP - - - - - - - - - - - - - - - tier3 187 30 13.82 104 92 46.94 0 0 NA 142074 TCGA-AB-2965 AML19 8 115434924 115434924 G T SNP - - - - - - - - - - - - - - - tier3 125 25 16.67 77 82 51.57 0 0 NA 142074 TCGA-AB-2965 AML19 8 132465082 132465082 C T SNP - - - - - - - - - - - - - - - tier3 395 59 13 219 207 48.59 0 0 NA 142074 TCGA-AB-2965 AML19 9 97400993 97400993 C T SNP - - - - - - - - - - - - - - - tier3 316 62 16.36 162 113 41.09 0 0 NA 142074 TCGA-AB-2965 AML19 9 125982148 125982148 A G SNP - - - - - - - - - - - - - - - tier3 122 21 14.69 70 93 57.06 0 0 NA 142074 TCGA-AB-2965 AML19 9 130544160 130544160 G A SNP ZER1 NM_006336.2 human genbank 54_36p -1 provisional intronic c.1576-219 e9-219 0 - - - no_errors tier3 288 52 15.12 112 101 47.42 6 4 40 142074 TCGA-AB-2965 AML19 10 2558357 2558357 G A SNP LOC727878 XM_001126639.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-24218 NULL 0.001 - - - no_errors tier3 95 10 9.43 44 45 50.56 0 0 NA 142074 TCGA-AB-2965 AML19 10 70493528 70493528 C T SNP SRGN NM_002727.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-24392 NULL 0.008 - - - no_errors tier3 406 70 14.61 189 146 43.58 1 1 50 142074 TCGA-AB-2965 AML19 10 70828539 70828539 G A SNP HK1 NM_033497.2 human genbank 54_36p 1 reviewed missense c.2570 p.R857H 0.888 "HMMPfam_Hexokinase_2,superfamily_SSF53067" "HMMPfam_Hexokinase_1,HMMPfam_Hexokinase_2,PatternScan_HEXOKINASES,superfamily_SSF53067" - no_errors tier1 557 119 17.47 190 183 48.93 32 27 45.76 142074 TCGA-AB-2965 AML19 10 127873311 127873311 C T SNP ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed intronic c.261-39447 e4-39447 0 - - - no_errors tier3 370 66 15.07 204 159 43.68 0 0 NA 142074 TCGA-AB-2965 AML19 10 132949431 132949431 A G SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated intronic c.671-734 e4-734 0.013 - - - no_errors tier3 239 39 14.03 98 95 49.22 0 0 NA 142074 TCGA-AB-2965 AML19 11 552159 552159 G T SNP RASSF7 NM_003475.1 human genbank 54_36p 1 validated missense c.205 p.A69S 0.996 "HMMPfam_RA,HMMSmart_SM00314" "HMMPfam_RA,HMMSmart_SM00314" - no_errors tier1 59 6 9.23 28 20 41.67 3 5 62.5 142074 TCGA-AB-2965 AML19 11 26757397 26757397 C T SNP - - - - - - - - - - - - - - - tier3 337 67 16.5 201 172 45.99 0 0 NA 142074 TCGA-AB-2965 AML19 11 43506785 43506785 G T SNP LOC100131381 XM_001717461.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-41747 NULL 0.005 - - - no_errors tier3 152 24 13.64 42 24 36.36 0 0 NA 142074 TCGA-AB-2965 AML19 11 132950844 132950844 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43415 NULL 0 - - - no_errors tier3 270 31 10.13 117 85 42.08 0 0 NA 142074 TCGA-AB-2965 AML19 13 21365751 21365751 G A SNP - - - - - - - - - - - - - - - tier3 341 68 16.63 147 151 50.5 0 0 NA 142074 TCGA-AB-2965 AML19 13 22065789 22065789 G C SNP - - - - - - - - - - - - - - - tier3 581 90 13.39 380 336 46.8 0 0 NA 142074 TCGA-AB-2965 AML19 13 27506338 27506339 - TTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1718_1717 p.574in_frame_insKPATDGTGDRLLR**VLLR*FQRK 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 142074 TCGA-AB-2965 AML19 13 64670444 64670444 T C SNP - - - - - - - - - - - - - - - tier3 172 33 16.1 112 97 46.41 0 0 NA 142074 TCGA-AB-2965 AML19 13 67860871 67860871 G C SNP - - - - - - - - - - - - - - - tier3 84 8 8.7 65 43 39.81 0 0 NA 142074 TCGA-AB-2965 AML19 13 92836143 92836143 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.160+158273 e1+158273 0 - - - no_errors tier3 247 25 9.16 138 101 42.26 0 0 NA 142074 TCGA-AB-2965 AML19 14 24839717 24839717 G A SNP ENSG00000179020 ENST00000323440 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33335 NULL 0.041 - - - no_coding_region:pseudogene tier3 456 104 18.54 286 285 49.91 0 0 NA 142074 TCGA-AB-2965 AML19 14 33292972 33292972 G A SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.813+18683 e7+18683 0 - - - no_errors tier3 283 44 13.46 148 139 48.43 0 0 NA 142074 TCGA-AB-2965 AML19 14 62821809 62821809 A C SNP RHOJ NM_020663.3 human genbank 54_36p 1 provisional intronic c.498+2122 e4+2122 0.003 - - - no_errors tier3 251 45 15.15 94 102 52.04 0 0 NA 142074 TCGA-AB-2965 AML19 14 100216933 100216933 C G SNP DLK1 NM_003836.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46226 NULL 0.007 - - - no_errors tier3 55 10 15.38 25 22 46.81 0 0 NA 142074 TCGA-AB-2965 AML19 15 25168203 25168203 G A SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.574+11422 e5+11422 0.004 - - - no_errors tier3 312 64 17.02 147 166 53.04 0 0 NA 142074 TCGA-AB-2965 AML19 15 27190646 27190646 C T SNP APBA2 NM_005503.1 human genbank 54_36p 1 reviewed intronic c.2038-2725 e11-2725 0 - - - no_errors tier3 167 34 16.83 44 29 39.73 0 0 NA 142074 TCGA-AB-2965 AML19 15 46491462 46491462 T C SNP FBN1 NM_000138.3 human genbank 54_36p -1 reviewed intronic c.8227-594 e65-594 0.012 - - - no_errors tier3 493 98 16.58 282 320 53.07 0 0 0 142074 TCGA-AB-2965 AML19 15 75198171 75198171 A T SNP SGK269 NM_024776.2 human genbank 54_36p -1 validated intronic c.4078-3455 e4-3455 0.037 - - - no_errors tier3 110 14 11.29 36 26 41.94 0 0 0 142074 TCGA-AB-2965 AML19 15 80317742 80317742 T C SNP EFTUD1 NM_024580.2 human genbank 54_36p -1 validated missense c.692 p.N231S 0.997 "HMMPfam_GTP_EFTU,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_EFG_C,HMMPfam_GTP_EFTU,HMMPfam_EFG_IV,superfamily_Translation proteins,superfamily_EF-G C-terminal domain-like,superfamily_Ribosomal protein S5 domain 2-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 376 59 13.56 191 197 50.77 8 11 57.89 142074 TCGA-AB-2965 AML19 16 30524020 30524020 G C SNP ZNF689 NM_138447.1 human genbank 54_36p -1 provisional missense c.569 p.S190C 0.705 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 386 61 13.62 126 96 43.24 2 6 75 142074 TCGA-AB-2965 AML19 16 86303443 86303443 G C SNP KLHDC4 NM_017566.2 human genbank 54_36p -1 provisional intronic c.836-893 e9-893 0 - - - no_errors tier3 159 17 9.6 108 96 46.83 2 0 0 142074 TCGA-AB-2965 AML19 17 61651963 61651963 G T SNP APOH NM_000042.2 human genbank 54_36p -1 reviewed intronic c.338+645 e3+645 0 - - - no_errors tier3 784 142 15.3 317 294 48.12 0 0 NA 142074 TCGA-AB-2965 AML19 18 2331447 2331447 T A SNP - - - - - - - - - - - - - - - tier3 436 80 15.44 313 297 48.69 0 0 NA 142074 TCGA-AB-2965 AML19 18 50244125 50244125 C A SNP - - - - - - - - - - - - - - - tier3 104 23 18.11 69 69 50 0 0 NA 142074 TCGA-AB-2965 AML19 18 71519923 71519923 C T SNP - - - - - - - - - - - - - - - tier3 356 85 19.27 223 208 48.26 0 0 NA 142074 TCGA-AB-2965 AML19 18 72747624 72747624 G A SNP ZNF236 NM_007345.3 human genbank 54_36p 1 validated intronic c.2291+1265 e13+1265 0 - - - no_errors tier3 572 64 10.03 248 226 47.68 0 2 100 142074 TCGA-AB-2965 AML19 19 33090925 33090925 C T SNP - - - - - - - - - - - - - - - tier3 280 31 9.94 83 68 45.03 0 3 100 142074 TCGA-AB-2965 AML19 20 7567513 7567513 A C SNP ENSG00000223193 ENST00000411261 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5015 NULL 0.624 - - - no_errors tier3 410 55 11.83 219 185 45.79 0 0 NA 142074 TCGA-AB-2965 AML19 20 37486623 37486623 G A SNP - - - - - - - - - - - - - - - tier3 289 61 17.43 145 160 52.46 0 0 NA 142074 TCGA-AB-2965 AML19 20 41002632 41002632 G A SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.89-54646 e2-54646 0 - - - no_errors tier3 774 129 14.24 394 361 47.81 0 0 NA 142074 TCGA-AB-2965 AML19 20 46272325 46272325 G A SNP - - - - - - - - - - - - - - - tier3 387 65 14.32 165 162 49.54 0 0 NA 142074 TCGA-AB-2965 AML19 20 51432700 51432700 A T SNP TSHZ2 NM_173485.4 human genbank 54_36p 1 validated intronic c.3105-104390 e3-104390 0 - - - no_errors tier3 315 70 18.09 192 144 42.86 0 0 NA 142074 TCGA-AB-2965 AML19 21 33675868 33675868 C T SNP IFNGR2 NM_005534.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-21852 NULL 0.002 - - - no_errors tier3 489 78 13.66 117 95 44.81 0 0 NA 142074 TCGA-AB-2965 AML19 21 36670227 36670227 T C SNP MORC3 NM_015358.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*763 NULL 0.996 - - - no_errors tier3 82 15 15.46 18 41 69.49 30 29 49.15 142074 TCGA-AB-2965 AML19 21 45612499 45612499 G A SNP COL18A1 NM_130445.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-37075 NULL 0.013 - - - no_errors tier3 114 30 20.69 59 51 46.36 0 0 NA 142074 TCGA-AB-2965 AML19 22 38424242 38424242 G T SNP CACNA1I NM_021096.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*11886 NULL 0.001 - - - no_errors tier3 96 16 14.16 55 46 45.54 0 0 NA 113971 TCGA-AB-2966 AML18 X 9114704 9114704 G A SNP FAM9B ENST00000380975 human ensembl 54_36p -1 known 5_prime_flanking_region c.-153677 NULL 0.007 - - - no_errors tier3 1558 5 0.32 485 368 42.99 0 0 NA 113971 TCGA-AB-2966 AML18 X 9163022 9163022 C G SNP - - - - - - - - - - - - - - - tier3 437 3 0.68 245 218 46.98 0 0 NA 113971 TCGA-AB-2966 AML18 X 10267500 10267500 G A SNP - - - - - - - - - - - - - - - tier3 805 26 3.13 356 280 44.03 0 0 NA 113971 TCGA-AB-2966 AML18 X 14478862 14478862 C A SNP GLRA2 NM_002063.1 human genbank 54_36p 1 validated intronic c.202+18447 e2+18447 0.001 - - - no_errors tier3 1819 26 1.41 621 551 47.01 0 0 NA 113971 TCGA-AB-2966 AML18 X 14529760 14529760 G A SNP GLRA2 NM_002063.1 human genbank 54_36p 1 validated intronic c.495-2598 e5-2598 0.022 - - - no_errors tier3 834 10 1.18 361 299 45.3 0 0 NA 113971 TCGA-AB-2966 AML18 X 14887641 14887641 G T SNP MOSPD2 NM_152581.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*39789 NULL 0.247 - - - no_errors tier3 355 3 0.84 365 294 44.61 0 0 NA 113971 TCGA-AB-2966 AML18 X 17602855 17602855 G A SNP NHS NM_198270.2 human genbank 54_36p 1 reviewed intronic c.566-12928 e2-12928 0.109 - - - no_errors tier3 864 3 0.35 334 268 44.37 0 0 NA 113971 TCGA-AB-2966 AML18 X 19575475 19575475 G A SNP SH3KBP1 NM_031892.2 human genbank 54_36p -1 validated intronic c.727-1961 e7-1961 0.026 - - - no_errors tier3 924 2 0.22 864 694 44.49 4 0 0 113971 TCGA-AB-2966 AML18 X 26155138 26155138 G A SNP MAGEB6 NM_173523.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*32030 NULL 0 - - - no_errors tier3 554 8 1.42 374 304 44.84 0 0 NA 113971 TCGA-AB-2966 AML18 X 29979406 29979406 C G SNP ENSG00000218702 ENST00000407256 human ensembl 54_36p -1 known 5_prime_flanking_region c.-33487 NULL 0 - - - no_coding_region:pseudogene tier3 644 0 0 557 441 44.06 0 0 NA 113971 TCGA-AB-2966 AML18 X 31045924 31045924 G T SNP DMD ENST00000378682 human ensembl 54_36p -1 known intronic c.10678-3187 e74-3187 0.001 - - - no_stop_codon tier3 561 0 0 551 490 47.07 0 0 NA 113971 TCGA-AB-2966 AML18 X 31798812 31798812 C A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.7098+4414 e48+4414 0 - - - no_errors tier3 214 0 0 233 157 40.26 0 0 NA 113971 TCGA-AB-2966 AML18 X 31804907 31804907 C T SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6913-1496 e48-1496 0 - - - no_errors tier3 448 2 0.44 162 98 37.69 0 0 NA 113971 TCGA-AB-2966 AML18 X 37251774 37251774 C T SNP FTHL19 XM_001714232.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*1874 NULL 0 - - - pseudogene tier3 405 12 2.87 247 240 49.28 0 0 NA 113971 TCGA-AB-2966 AML18 X 37685001 37685001 G A SNP ENSG00000220615 ENST00000405464 human ensembl 54_36p 1 known 5_prime_flanking_region c.-5080 NULL 0 - - - no_coding_region:pseudogene tier3 860 3 0.35 307 278 47.52 0 0 NA 113971 TCGA-AB-2966 AML18 X 39465573 39465573 C T SNP - - - - - - - - - - - - - - - tier3 1757 34 1.9 311 239 43.45 0 0 NA 113971 TCGA-AB-2966 AML18 X 39472475 39472475 C T SNP - - - - - - - - - - - - - - - tier3 862 3 0.35 290 224 43.33 0 0 NA 113971 TCGA-AB-2966 AML18 X 54202256 54202256 G T SNP FAM120C NM_017848.4 human genbank 54_36p -1 validated intronic c.946+272 e2+272 0 - - - no_errors tier3 911 10 1.08 399 326 44.97 0 0 0 113971 TCGA-AB-2966 AML18 X 55769536 55769536 C T SNP RRAGB NM_016656.4 human genbank 54_36p 1 validated intronic c.227-929 e4-929 0 - - - no_errors tier3 428 6 1.38 142 133 48.36 9 0 0 113971 TCGA-AB-2966 AML18 X 69646525 69646525 C T SNP TEX11 NM_001003811.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*19145 NULL 0.012 - - - no_errors tier3 762 1 0.13 302 250 45.21 0 0 NA 113971 TCGA-AB-2966 AML18 X 84592703 84592703 T C SNP - - - - - - - - - - - - - - - tier3 836 0 0 354 145 29.06 0 0 NA 113971 TCGA-AB-2966 AML18 X 90244099 90244099 C T SNP - - - - - - - - - - - - - - - tier3 748 7 0.93 286 239 45.44 0 0 NA 113971 TCGA-AB-2966 AML18 X 93303764 93303764 A C SNP ENSG00000202410 ENST00000365540 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-15896 NULL 0.003 - - - no_errors tier3 530 7 1.3 431 352 44.96 0 0 NA 113971 TCGA-AB-2966 AML18 X 93864312 93864312 A C SNP - - - - - - - - - - - - - - - tier3 1164 8 0.68 237 201 45.89 0 0 NA 113971 TCGA-AB-2966 AML18 X 96954876 96954876 C A SNP ERVWE2 ENST00000404461 human ensembl 54_36p 1 known 5_prime_flanking_region c.-34041 NULL 0.164 - - - no_coding_region:pseudogene tier3 392 0 0 305 226 42.48 0 0 NA 113971 TCGA-AB-2966 AML18 X 101802425 101802425 T A SNP ENSG00000220050 ENST00000405532 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44943 NULL 0.001 - - - no_coding_region:pseudogene tier3 249 0 0 455 309 40.34 0 0 NA 113971 TCGA-AB-2966 AML18 X 102923034 102923034 T C SNP PLP1 NM_000533.3 human genbank 54_36p 1 reviewed intronic c.5-4133 e2-4133 0.001 - - - no_errors tier3 419 1 0.24 649 518 44.39 0 0 NA 113971 TCGA-AB-2966 AML18 X 107698591 107698591 C T SNP COL4A5 NM_033380.3 human genbank 54_36p 1 reviewed intronic c.321+32 e5+32 0 - - - no_errors tier3 309 1 0.32 334 229 40.53 0 0 NA 113971 TCGA-AB-2966 AML18 X 110962930 110962930 A T SNP TRPC5 NM_012471.2 human genbank 54_36p -1 validated intronic c.1896+1875 e6+1875 0.058 - - - no_errors tier3 252 4 1.56 263 220 45.55 0 0 NA 113971 TCGA-AB-2966 AML18 X 118157100 118157100 G T SNP KIAA1210 NM_020721.1 human genbank 54_36p -1 validated intronic c.410+8364 e2+8364 0 - - - no_errors tier3 1058 0 0 412 359 46.56 0 0 NA 113971 TCGA-AB-2966 AML18 X 122984744 122984744 A T SNP STAG2 NM_001042749.1 human genbank 54_36p 1 validated intronic c.44+542 e1+542 0 - - - no_errors tier3 186 1 0.53 255 207 44.71 0 6 100 113971 TCGA-AB-2966 AML18 X 131527056 131527056 A T SNP ENSG00000206900 ENST00000384173 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14770 NULL 0.006 - - - no_errors tier3 730 3 0.41 282 221 43.68 0 0 NA 113971 TCGA-AB-2966 AML18 X 136589831 136589831 G C SNP ENSG00000208538 ENST00000385803 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-38835 NULL 0.044 - - - pseudogene tier3 343 5 1.44 392 300 43.17 0 0 NA 113971 TCGA-AB-2966 AML18 X 139530096 139530096 T C SNP - - - - - - - - - - - - - - - tier3 308 3 0.96 305 238 43.83 0 0 NA 113971 TCGA-AB-2966 AML18 X 140385415 140385415 G A SNP CXorf18 XR_040313.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-33100 NULL 0 - - - no_errors tier3 215 0 0 424 353 45.31 0 0 NA 113971 TCGA-AB-2966 AML18 X 141046314 141046314 C A SNP ENSG00000217283 ENST00000402189 human ensembl 54_36p -1 known 3_prime_flanking_region c.*17000 NULL 0.001 - - - no_coding_region:pseudogene tier3 870 9 1.02 400 275 40.68 0 0 NA 113971 TCGA-AB-2966 AML18 X 142586656 142586656 T C SNP SLITRK4 NM_173078.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-40066 NULL 0.009 - - - no_errors tier3 505 0 0 494 471 48.81 0 0 NA 113971 TCGA-AB-2966 AML18 X 142702544 142702544 C T SNP ENSG00000216543 ENST00000405023 human ensembl 54_36p 1 known 5_prime_flanking_region c.-14608 NULL 0.005 - - - no_coding_region:pseudogene tier3 318 3 0.93 145 127 46.35 0 0 NA 113971 TCGA-AB-2966 AML18 X 147962175 147962175 G T SNP LOC100132557 XM_001720865.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*15748 NULL 0.001 - - - no_errors tier3 184 0 0 279 224 44.53 0 0 NA 113971 TCGA-AB-2966 AML18 X 149108188 149108189 - T INS LOC389901 XM_001721068.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*41761 NULL 0.012:0.027 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 X 151954376 151954376 T C SNP PNMA3 NM_013364.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-21693 NULL 0.275 - - - no_errors tier3 54 1 1.82 69 58 45.67 0 0 NA 113971 TCGA-AB-2966 AML18 X 152434010 152434010 T C SNP ATP2B3 NM_001001344.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20890 NULL 0 - - - no_errors tier3 498 1 0.2 79 74 48.37 0 0 NA 113971 TCGA-AB-2966 AML18 X 152883350 152883350 G A SNP HCFC1 NM_005334.2 human genbank 54_36p -1 reviewed missense c.215 p.P72L 1 superfamily_Galactose oxidase central domain "HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Kelch_1,superfamily_Fibronectin type III,superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2" - no_errors tier1 173 2 1.14 133 115 46.18 25 112 81.75 113971 TCGA-AB-2966 AML18 1 4123754 4123754 G A SNP ENSG00000220404 ENST00000401749 human ensembl 54_36p -1 known 3_prime_flanking_region c.*11694 NULL 0 - - - no_coding_region:pseudogene tier3 82 1 1.2 79 83 51.23 0 0 NA 113971 TCGA-AB-2966 AML18 1 5622219 5622219 G A SNP - - - - - - - - - - - - - - - tier3 201 0 0 105 92 46.7 0 0 NA 113971 TCGA-AB-2966 AML18 1 9183631 9183631 C T SNP H6PD NM_004285.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-43950 NULL 0.002 - - - no_errors tier3 195 0 0 81 68 45.64 0 0 NA 113971 TCGA-AB-2966 AML18 1 17275146 17275146 C T SNP PADI2 NM_007365.2 human genbank 54_36p -1 reviewed intronic c.1311-241 e12-241 0 - - - no_errors tier3 403 2 0.49 236 216 47.68 0 0 NA 113971 TCGA-AB-2966 AML18 1 30406907 30406907 G A SNP - - - - - - - - - - - - - - - tier3 281 1 0.35 215 181 45.48 0 0 NA 113971 TCGA-AB-2966 AML18 1 30890199 30890199 A G SNP - - - - - - - - - - - - - - - tier3 504 1 0.2 272 197 41.83 0 0 NA 113971 TCGA-AB-2966 AML18 1 37109449 37109449 T C SNP GRIK3 NM_000831.3 human genbank 54_36p -1 reviewed intronic c.732+927 e4+927 0 - - - no_errors tier3 235 1 0.42 295 235 43.84 0 0 NA 113971 TCGA-AB-2966 AML18 1 38373523 38373523 C G SNP - - - - - - - - - - - - - - - tier3 269 0 0 235 141 37.5 0 0 NA 113971 TCGA-AB-2966 AML18 1 39200485 39200485 C T SNP RHBDL2 NM_017821.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43014 NULL 0 - - - no_errors tier3 986 1 0.1 284 208 42.28 0 0 NA 113971 TCGA-AB-2966 AML18 1 39801190 39801190 G C SNP PABPC4 NM_003819.1 human genbank 54_36p -1 reviewed intronic c.1621-515 e13-515 0.001 - - - no_errors tier3 205 2 0.97 353 297 45.69 4 5 55.56 113971 TCGA-AB-2966 AML18 1 42084854 42084854 T C SNP HIVEP3 NM_024503.1 human genbank 54_36p -1 validated intronic c.1+71817 e0+71817 0 - - - no_errors tier3 1063 5 0.47 281 213 42.94 0 0 NA 113971 TCGA-AB-2966 AML18 1 50252118 50252118 T A SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.34+9904 e1+9904 0.002 - - - no_errors tier3 363 0 0 491 373 43.17 0 0 NA 113971 TCGA-AB-2966 AML18 1 51469521 51469521 C T SNP ENSG00000210557 ENST00000387822 human ensembl 54_36p -1 novel rna NULL NULL 0 - - - pseudogene tier1 173 1 0.57 164 132 44.59 3 0 113971 TCGA-AB-2966 AML18 1 52076356 52076356 C T SNP NRD1 NM_002525.1 human genbank 54_36p -1 validated intronic c.631-476 e3-476 0.02 - - - no_errors tier3 969 2 0.21 273 236 46.37 4 6 60 113971 TCGA-AB-2966 AML18 1 56594441 56594441 G A SNP - - - - - - - - - - - - - - - tier3 484 1 0.21 378 297 44 0 0 NA 113971 TCGA-AB-2966 AML18 1 56601969 56601969 G A SNP - - - - - - - - - - - - - - - tier3 703 12 1.68 410 399 49.26 0 0 NA 113971 TCGA-AB-2966 AML18 1 70386823 70386823 C T SNP LRRC40 NM_017768.3 human genbank 54_36p -1 provisional silent c.1638 p.T546 0.095 "HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058" "HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058" - no_errors tier1 538 2 0.37 279 231 45.21 10 12 54.55 113971 TCGA-AB-2966 AML18 1 73619365 73619365 C T SNP - - - - - - - - - - - - - - - tier3 505 3 0.59 432 250 36.66 0 0 NA 113971 TCGA-AB-2966 AML18 1 85362134 85362134 T C SNP WDR63 NM_145172.3 human genbank 54_36p 1 validated intronic c.1982-258 e18-258 0.002 - - - no_errors tier3 588 4 0.67 336 348 50.73 0 0 NA 113971 TCGA-AB-2966 AML18 1 99353324 99353324 G T SNP LOC100129620 XM_001726877.1 human genbank 54_36p 1 model intronic c.10-28856 e2-28856 0.001 - - - no_errors tier3 1090 2 0.18 422 357 45.83 0 0 NA 113971 TCGA-AB-2966 AML18 1 102227814 102227814 C A SNP OLFM3 NM_058170.2 human genbank 54_36p -1 validated intronic c.69+7078 e1+7078 0 - - - no_errors tier3 668 7 1.04 288 238 45.25 0 0 NA 113971 TCGA-AB-2966 AML18 1 103336263 103336263 T C SNP COL11A1 NM_080629.3 human genbank 54_36p -1 reviewed intronic c.106+9954 e1+9954 0.003 - - - no_errors tier3 586 1 0.17 349 260 42.69 0 0 NA 113971 TCGA-AB-2966 AML18 1 103431184 103431184 C T SNP - - - - - - - - - - - - - - - tier3 425 1 0.23 186 104 35.86 0 0 NA 113971 TCGA-AB-2966 AML18 1 106240939 106240939 T C SNP LOC727839 XR_037066.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-5476 NULL 0.006 - - - pseudogene tier3 260 0 0 293 301 50.42 0 0 NA 113971 TCGA-AB-2966 AML18 1 108219007 108219007 T G SNP VAV3 NM_006113.1 human genbank 54_36p -1 reviewed intronic c.321+39 e2+39 0 - - - no_errors tier3 496 4 0.8 291 274 48.41 8 3 27.27 113971 TCGA-AB-2966 AML18 1 112006080 112006081 - T INS RAP1A NM_001010935.1 human genbank 54_36p 1 reviewed intronic c.1-29399_29398 e1-29398 0.005:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 1 146561869 146561870 AG - DEL LOC729086 XM_001129280.2 human genbank 54_36p 1 model 3_prime_untranslated_region c.*1389 NULL 0.013:0.010 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 1 152520682 152520682 A G SNP ATP8B2 NM_020452.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46218 NULL 0 - - - no_errors tier3 87 2 2.25 83 57 40.71 1 0 0 113971 TCGA-AB-2966 AML18 1 156252919 156252919 C T SNP KIRREL NM_018240.5 human genbank 54_36p 1 validated intronic c.1+22773 e0+22773 0 - - - no_errors tier3 1130 16 1.39 241 211 46.37 0 0 NA 113971 TCGA-AB-2966 AML18 1 175164606 175164606 G A SNP ASTN1 NM_004319.1 human genbank 54_36p -1 validated intronic c.2671+5305 e16+5305 0.006 - - - no_errors tier3 353 2 0.56 321 258 44.56 0 0 NA 113971 TCGA-AB-2966 AML18 1 178111873 178111873 G C SNP TOR1AIP2 NM_145034.2 human genbank 54_36p -1 provisional intronic c.1+1124 e0+1124 0.004 - - - no_errors tier3 533 1 0.19 151 148 49.5 2 1 33.33 113971 TCGA-AB-2966 AML18 1 180882643 180882643 C T SNP RGS8 NM_033345.1 human genbank 54_36p -1 reviewed silent c.447 p.T149 0.99 "HMMPfam_RGS,HMMSmart_RGS,superfamily_Regulat_G_prot_signal_superfam" "HMMPfam_RGS,HMMSmart_RGS,superfamily_Regulat_G_prot_signal_superfam" - no_errors tier1 246 9 3.52 232 144 38.2 NA 113971 TCGA-AB-2966 AML18 1 182901191 182901191 A T SNP EDEM3 NM_025191.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*28629 NULL 0.386 - - - no_errors tier3 630 7 1.1 203 188 47.96 0 0 NA 113971 TCGA-AB-2966 AML18 1 190729822 190729822 G A SNP ENSG00000221145 ENST00000408218 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2849 NULL 0.032 - - - no_errors tier3 84 0 0 88 41 31.78 0 0 NA 113971 TCGA-AB-2966 AML18 1 194264272 194264272 G T SNP - - - - - - - - - - - - - - - tier3 261 1 0.38 396 275 40.92 0 0 NA 113971 TCGA-AB-2966 AML18 1 195030458 195030458 G T SNP CFHR3 ENST00000367426 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*102 NULL 0 - - - no_errors tier3 60 0 0 10 94 90.38 0 0 NA 113971 TCGA-AB-2966 AML18 1 196774955 196774955 A G SNP ATP6V1G3 NM_133262.2 human genbank 54_36p -1 reviewed intronic c.82+1367 e1+1367 0.085 - - - no_errors tier3 632 2 0.31 517 371 41.78 0 0 NA 113971 TCGA-AB-2966 AML18 1 197175671 197175671 G C SNP LOC100131234 XM_001726746.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-40676 NULL 0 - - - no_errors tier3 669 2 0.3 549 460 45.54 2 4 66.67 113971 TCGA-AB-2966 AML18 1 199603188 199603188 C T SNP TNNT2 NM_000364.2 human genbank 54_36p -1 reviewed intronic c.199+334 e6+334 0 - - - no_errors tier3 201 0 0 286 189 39.79 0 0 NA 113971 TCGA-AB-2966 AML18 1 203596401 203596401 C A SNP NUAK2 NM_030952.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-39022 NULL 0 - - - no_errors tier3 447 1 0.22 194 166 46.11 0 0 NA 113971 TCGA-AB-2966 AML18 1 211653093 211653093 C T SNP LOC643330 XM_926662.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*15581 NULL 0.03 - - - no_errors tier3 597 1 0.17 408 360 46.88 0 0 NA 113971 TCGA-AB-2966 AML18 1 211919737 211919737 G A SNP - - - - - - - - - - - - - - - tier3 322 1 0.31 485 390 44.57 0 0 NA 113971 TCGA-AB-2966 AML18 1 212430337 212430337 A G SNP - - - - - - - - - - - - - - - tier3 209 2 0.95 222 175 44.08 0 0 NA 113971 TCGA-AB-2966 AML18 1 214867489 214867489 G A SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.589+23449 e3+23449 0.002 - - - no_errors tier3 329 0 0 311 204 39.53 0 0 NA 113971 TCGA-AB-2966 AML18 1 214883699 214883699 G T SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.589+7239 e3+7239 0.001 - - - no_errors tier3 825 0 0 731 500 40.58 0 0 NA 113971 TCGA-AB-2966 AML18 1 228973611 228973611 C T SNP CAPN9 NM_006615.2 human genbank 54_36p 1 reviewed intronic c.790-772 e7-772 0.01 - - - no_errors tier3 418 0 0 331 251 43.13 0 0 NA 113971 TCGA-AB-2966 AML18 1 230483792 230483792 C T SNP - - - - - - - - - - - - - - - tier3 559 1 0.18 371 350 48.48 0 0 NA 113971 TCGA-AB-2966 AML18 1 234266943 234266943 A G SNP NID1 NM_002508.2 human genbank 54_36p -1 reviewed intronic c.1285+1084 e5+1084 0 - - - no_errors tier3 299 1 0.33 149 140 48.44 0 0 NA 113971 TCGA-AB-2966 AML18 1 234885172 234885172 G T SNP ACTN2 NM_001103.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-31425 NULL 0.01 - - - no_errors tier3 867 3 0.34 243 202 45.39 0 0 NA 113971 TCGA-AB-2966 AML18 1 236636573 236636573 G C SNP - - - - - - - - - - - - - - - tier3 295 4 1.34 331 235 41.52 0 0 NA 113971 TCGA-AB-2966 AML18 1 239453753 239453753 G A SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.79-125068 e2-125068 0 - - - no_errors tier3 1248 0 0 412 336 44.92 0 0 NA 113971 TCGA-AB-2966 AML18 1 239946390 239946390 G - DEL WDR64 NM_144625.3 human genbank 54_36p 1 validated intronic c.184+4584 e2+4584 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 1 240723272 240723272 G A SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.1+30741 e0+30741 0 - - - no_errors tier3 509 2 0.39 463 321 40.79 0 0 NA 113971 TCGA-AB-2966 AML18 2 6629577 6629577 C A SNP LOC100133653 XR_037179.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*40836 NULL 0 - - - pseudogene tier3 866 0 0 530 428 44.58 0 0 NA 113971 TCGA-AB-2966 AML18 2 16990460 16990460 G A SNP - - - - - - - - - - - - - - - tier3 550 11 1.95 548 417 43.12 0 0 NA 113971 TCGA-AB-2966 AML18 2 17382946 17382946 G C SNP LOC388925 XR_016133.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-46877 NULL 0 - - - pseudogene tier3 499 2 0.4 319 300 48.47 0 0 NA 113971 TCGA-AB-2966 AML18 2 18692673 18692673 G A SNP - - - - - - - - - - - - - - - tier3 1082 4 0.37 623 566 47.6 0 0 NA 113971 TCGA-AB-2966 AML18 2 18978247 18978247 G A SNP LOC100134020 XM_001716611.1 human genbank 54_36p 1 model intronic c.648+13659 e2+13659 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 462 3 0.65 369 248 40.19 0 1 100 113971 TCGA-AB-2966 AML18 2 19605627 19605627 G A SNP - - - - - - - - - - - - - - - tier3 479 4 0.83 433 278 39.1 0 0 NA 113971 TCGA-AB-2966 AML18 2 22740300 22740300 C A SNP - - - - - - - - - - - - - - - tier3 407 0 0 317 332 51.16 0 0 NA 113971 TCGA-AB-2966 AML18 2 25320610 25320610 C - DEL DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed frame_shift_del c.1769 p.G590fs 1 superfamily_FYVE/PHD zinc finger "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 NA NA NA NA NA NA NA 113971 TCGA-AB-2966 AML18 2 25476792 25476792 G A SNP DTNB NM_021907.3 human genbank 54_36p -1 reviewed intronic c.1576-12058 e16-12058 0 - - - no_errors tier3 286 1 0.35 22 159 85.95 0 0 0 113971 TCGA-AB-2966 AML18 2 34194802 34194802 C T SNP - - - - - - - - - - - - - - - tier3 530 0 0 426 348 44.96 0 0 NA 113971 TCGA-AB-2966 AML18 2 41567907 41567907 A G SNP - - - - - - - - - - - - - - - tier3 504 1 0.2 370 252 40.45 0 0 NA 113971 TCGA-AB-2966 AML18 2 47469806 47469806 C T SNP MSH2 NM_000251.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-14029 NULL 0.068 - - - no_errors tier3 842 1 0.12 330 222 40.22 0 0 NA 113971 TCGA-AB-2966 AML18 2 50134499 50134499 G A SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.3719-267 e19-267 0.778 - - - no_errors tier3 168 5 2.89 231 154 40 0 0 NA 113971 TCGA-AB-2966 AML18 2 50217435 50217435 T C SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.3547-45299 e18-45299 0.113 - - - no_errors tier3 431 1 0.23 429 395 47.94 0 0 NA 113971 TCGA-AB-2966 AML18 2 60561597 60561597 T C SNP BCL11A NM_022893.3 human genbank 54_36p -1 reviewed intronic c.386-12125 e3-12125 0.001 - - - no_errors tier3 338 2 0.58 208 108 34.18 2 7 77.78 113971 TCGA-AB-2966 AML18 2 68036342 68036342 G A SNP - - - - - - - - - - - - - - - tier3 719 1 0.14 405 336 45.22 0 0 NA 113971 TCGA-AB-2966 AML18 2 85868758 85868758 G T SNP ATOH8 NM_032827.5 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*1234 NULL 0.103 - - - no_errors tier3 164 15 8.38 243 203 45.41 0 0 NA 113971 TCGA-AB-2966 AML18 2 86359214 86359214 T - DEL REEP1 NM_022912.2 human genbank 54_36p -1 validated intronic c.105+3590 e2+3590 0.045 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 2 101463971 101463971 C A SNP uc002tbb.1 ENST00000376826 human ensembl 54_36p -1 known 5_prime_flanking_region c.-75107 NULL 0 - - - no_errors tier3 91 0 0 163 158 49.07 0 0 NA 113971 TCGA-AB-2966 AML18 2 103654207 103654207 C T SNP LOC644265 XM_927443.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*47454 NULL 0.005 - - - no_errors tier3 173 0 0 159 123 43.62 0 0 NA 113971 TCGA-AB-2966 AML18 2 103827907 103827907 G C SNP - - - - - - - - - - - - - - - tier3 332 2 0.6 231 179 43.55 0 0 NA 113971 TCGA-AB-2966 AML18 2 114558112 114558112 C T SNP - - - - - - - - - - - - - - - tier3 301 2 0.66 303 239 44.1 0 0 NA 113971 TCGA-AB-2966 AML18 2 115185728 115185728 C T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+268843 e1+268843 0.002 - - - no_errors tier3 595 6 1 405 352 46.44 0 0 NA 113971 TCGA-AB-2966 AML18 2 115263344 115263344 G T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+346459 e1+346459 0 - - - no_errors tier3 312 5 1.58 324 218 40.15 0 0 NA 113971 TCGA-AB-2966 AML18 2 115719974 115719975 - T INS DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.61-63311_61-63310 e2-63310 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 2 116062568 116062568 C A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.441+62550 e5+62550 0.036 - - - no_errors tier3 637 0 0 434 322 42.59 0 0 NA 113971 TCGA-AB-2966 AML18 2 116134319 116134319 G T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.442-29414 e6-29414 0 - - - no_errors tier3 434 2 0.46 382 234 37.99 0 0 NA 113971 TCGA-AB-2966 AML18 2 121100271 121100271 C T SNP ENSG00000201006 ENST00000364136 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-25048 NULL 0.003 - - - no_errors tier3 219 0 0 156 144 48 0 0 NA 113971 TCGA-AB-2966 AML18 2 133112765 133112765 G C SNP GPR39 NM_001508.2 human genbank 54_36p 1 validated intronic c.857-6379 e2-6379 0.881 - - - no_errors tier3 927 4 0.43 420 333 44.22 0 0 NA 113971 TCGA-AB-2966 AML18 2 142001522 142001522 A T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.206-46950 e3-46950 0 - - - no_errors tier3 336 5 1.46 434 263 37.68 0 0 NA 113971 TCGA-AB-2966 AML18 2 142492219 142492219 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.82+112468 e1+112468 0.979 - - - no_errors tier3 744 1 0.13 784 619 44.12 0 0 NA 113971 TCGA-AB-2966 AML18 2 142915145 142915145 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 2 143338462 143338462 A G SNP KYNU NM_003937.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20945 NULL 0.006 - - - no_errors tier3 260 6 2.26 133 117 46.8 0 0 NA 113971 TCGA-AB-2966 AML18 2 146334937 146334937 G A SNP - - - - - - - - - - - - - - - tier3 194 0 0 148 96 39.34 0 0 NA 113971 TCGA-AB-2966 AML18 2 146370656 146370656 A G SNP - - - - - - - - - - - - - - - tier3 357 0 0 431 330 43.31 0 0 NA 113971 TCGA-AB-2966 AML18 2 146663439 146663439 G T SNP LOC100129653 XM_001717973.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-4895 NULL 0 - - - no_errors tier3 153 1 0.65 111 45 28.85 0 0 NA 113971 TCGA-AB-2966 AML18 2 147325455 147325455 C A SNP - - - - - - - - - - - - - - - tier3 262 4 1.5 213 124 36.8 0 0 NA 113971 TCGA-AB-2966 AML18 2 147485264 147485264 C A SNP - - - - - - - - - - - - - - - tier3 240 1 0.41 192 167 46.52 0 0 NA 113971 TCGA-AB-2966 AML18 2 151254989 151254989 A G SNP - - - - - - - - - - - - - - - tier3 274 2 0.72 442 416 48.48 0 0 NA 113971 TCGA-AB-2966 AML18 2 151684634 151684634 A T SNP - - - - - - - - - - - - - - - tier3 324 1 0.31 400 311 43.68 0 0 NA 113971 TCGA-AB-2966 AML18 2 152405423 152405423 T A SNP CACNB4 NM_000726.3 human genbank 54_36p -1 reviewed intronic c.1302+1240 e13+1240 0.013 - - - no_errors tier3 413 0 0 242 182 42.92 0 0 NA 113971 TCGA-AB-2966 AML18 2 158217329 158217329 C A SNP ACVR1C NM_145259.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23927 NULL 0.14 - - - no_errors tier3 404 0 0 378 221 36.89 0 0 NA 113971 TCGA-AB-2966 AML18 2 164304851 164304851 C T SNP FIGN NM_018086.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5168 NULL 0 - - - no_errors tier3 439 15 3.23 185 176 46.81 0 0 NA 113971 TCGA-AB-2966 AML18 2 167040296 167040296 A G SNP SCN7A NM_002976.2 human genbank 54_36p -1 validated intronic c.235-1196 e2-1196 0 - - - no_errors tier3 213 2 0.93 231 124 34.93 0 0 NA 113971 TCGA-AB-2966 AML18 2 168038023 168038023 A G SNP LOC643496 XR_041928.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 349 1 0.28 293 228 43.76 0 0 NA 113971 TCGA-AB-2966 AML18 2 175178850 175178850 C T SNP WIPF1 NM_001077269.1 human genbank 54_36p -1 reviewed intronic c.1-20265 e1-20265 0.063 - - - no_errors tier3 545 2 0.37 360 352 49.44 6 5 45.45 113971 TCGA-AB-2966 AML18 2 175423667 175423667 C G SNP CHN1 NM_001025201.2 human genbank 54_36p -1 reviewed intronic c.550-3736 e7-3736 0.005 - - - no_errors tier3 454 4 0.87 469 381 44.82 0 1 100 113971 TCGA-AB-2966 AML18 2 182101450 182101450 C G SNP ITGA4 NM_000885.4 human genbank 54_36p 1 reviewed intronic c.2431-1063 e23-1063 0 - - - no_errors tier3 179 1 0.56 304 232 43.28 28 65 69.89 113971 TCGA-AB-2966 AML18 2 182516261 182516261 T C SNP PPP1R1C NM_001080545.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-42822 NULL 0 - - - no_errors tier3 336 4 1.18 368 306 45.4 0 0 NA 113971 TCGA-AB-2966 AML18 2 187905912 187905912 C T SNP CALCRL NM_005795.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*13244 NULL 0.007 - - - no_errors tier3 586 11 1.83 203 198 49.38 0 0 NA 113971 TCGA-AB-2966 AML18 2 192215894 192215894 C T SNP OBFC2A NM_001031716.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-35692 NULL 0.001 - - - no_errors tier3 145 2 1.35 130 115 46.94 0 0 NA 113971 TCGA-AB-2966 AML18 2 194285304 194285304 C A SNP - - - - - - - - - - - - - - - tier3 286 1 0.35 216 134 38.29 0 0 NA 113971 TCGA-AB-2966 AML18 2 194680308 194680308 A T SNP - - - - - - - - - - - - - - - tier3 404 0 0 292 207 41.4 0 0 NA 113971 TCGA-AB-2966 AML18 2 196976715 196976715 C T SNP HECW2 NM_020760.1 human genbank 54_36p -1 provisional intronic c.292+29386 e1+29386 0.046 - - - no_errors tier3 452 0 0 669 556 45.35 0 0 NA 113971 TCGA-AB-2966 AML18 2 201241981 201241981 G A SNP AOX1 NM_001159.3 human genbank 54_36p 1 reviewed intronic c.3798+210 e33+210 0.054 - - - no_errors tier3 607 0 0 228 181 44.25 0 0 NA 113971 TCGA-AB-2966 AML18 2 202558846 202558846 C T SNP FZD7 NM_003507.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48770 NULL 0 - - - no_errors tier3 330 0 0 191 135 41.41 0 0 NA 113971 TCGA-AB-2966 AML18 2 203786450 203786450 G T SNP NBEAL1 NM_001099273.1 human genbank 54_36p 1 validated intronic c.3978-36 e28-36 0 - - - no_errors tier3 345 1 0.29 177 123 41 0 0 NA 113971 TCGA-AB-2966 AML18 2 210147712 210147712 T G SNP MAP2 NM_001039538.1 human genbank 54_36p 1 reviewed intronic c.1-5293 e1-5293 0.007 - - - no_errors tier3 232 1 0.43 127 129 50.39 0 0 NA 113971 TCGA-AB-2966 AML18 2 216692691 216692691 C T SNP XRCC5 NM_021141.3 human genbank 54_36p 1 reviewed intronic c.491+558 e5+558 0 - - - no_errors tier3 203 0 0 160 102 38.78 4 0 0 113971 TCGA-AB-2966 AML18 2 222876566 222876566 G A SNP CCDC140 NM_153038.1 human genbank 54_36p 1 validated intronic c.1-143 e1-143 0 - - - no_errors tier3 1029 2 0.19 133 89 40.09 0 0 NA 113971 TCGA-AB-2966 AML18 2 225072861 225072861 T A SNP LOC100131253 XR_039607.1 human genbank 54_36p -1 model rna NULL NULL 0.261 - - - pseudogene tier1 379 0 336 275 44.93 7 2 22.22 113971 TCGA-AB-2966 AML18 2 228727143 228727143 A G SNP SPHKAP NM_030623.1 human genbank 54_36p -1 validated intronic c.33-22098 e2-22098 0.001 - - - no_errors tier3 463 3 0.64 197 144 42.23 0 0 NA 113971 TCGA-AB-2966 AML18 3 528559 528559 G A SNP - - - - - - - - - - - - - - - tier3 281 2 0.71 292 247 45.74 0 0 NA 113971 TCGA-AB-2966 AML18 3 1555011 1555011 C A SNP - - - - - - - - - - - - - - - tier3 719 2 0.28 416 266 38.95 0 0 NA 113971 TCGA-AB-2966 AML18 3 10839478 10839478 T G SNP SLC6A11 NM_014229.1 human genbank 54_36p 1 provisional intronic c.533-509 e4-509 0 - - - no_errors tier3 580 1 0.17 351 294 45.51 0 0 NA 113971 TCGA-AB-2966 AML18 3 19878227 19878227 A G SNP EFHB NM_144715.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*17900 NULL 0 - - - no_errors tier3 562 4 0.7 371 333 47.03 0 0 NA 113971 TCGA-AB-2966 AML18 3 20860181 20860181 G A SNP - - - - - - - - - - - - - - - tier3 551 1 0.18 243 195 44.52 0 0 NA 113971 TCGA-AB-2966 AML18 3 25159937 25159937 G A SNP RARB ENST00000404969 human ensembl 54_36p 1 known 5_prime_flanking_region c.-30956 NULL 0 - - - no_errors tier3 236 1 0.42 315 262 45.41 0 0 NA 113971 TCGA-AB-2966 AML18 3 41116792 41116792 C G SNP - - - - - - - - - - - - - - - tier3 1405 4 0.28 403 336 45.34 0 0 NA 113971 TCGA-AB-2966 AML18 3 55043470 55043470 T C SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.2987+16086 e35+16086 0 - - - no_errors tier3 148 0 0 235 154 39.49 0 0 NA 113971 TCGA-AB-2966 AML18 3 55752705 55752705 T A SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2565-8719 e14-8719 0.001 - - - no_errors tier3 233 0 0 82 85 50.6 0 0 NA 113971 TCGA-AB-2966 AML18 3 59796113 59796113 C T SNP FHIT NM_002012.2 human genbank 54_36p -1 reviewed intronic c.349-83026 e5-83026 0 - - - no_errors tier3 576 2 0.35 503 412 45.03 0 3 100 113971 TCGA-AB-2966 AML18 3 62258529 62258529 C T SNP C3orf14 NM_020685.3 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-22658 NULL 0 - - - no_errors tier3 476 1 0.21 349 255 42.22 0 0 NA 113971 TCGA-AB-2966 AML18 3 75109433 75109433 A T SNP - - - - - - - - - - - - - - - tier3 757 3 0.39 353 248 41.26 0 0 NA 113971 TCGA-AB-2966 AML18 3 78038098 78038098 G A SNP - - - - - - - - - - - - - - - tier3 696 1 0.14 672 520 43.62 0 0 NA 113971 TCGA-AB-2966 AML18 3 78106416 78106416 C A SNP - - - - - - - - - - - - - - - tier3 123 0 0 160 92 36.51 0 0 NA 113971 TCGA-AB-2966 AML18 3 80229690 80229690 A C SNP - - - - - - - - - - - - - - - tier3 476 1 0.21 397 295 42.63 0 0 NA 113971 TCGA-AB-2966 AML18 3 82197975 82197975 C T SNP - - - - - - - - - - - - - - - tier3 831 4 0.48 444 331 42.71 0 0 NA 113971 TCGA-AB-2966 AML18 3 83568366 83568366 G C SNP - - - - - - - - - - - - - - - tier3 452 4 0.88 351 303 46.19 0 0 NA 113971 TCGA-AB-2966 AML18 3 84563824 84563824 A C SNP - - - - - - - - - - - - - - - tier3 542 1 0.18 455 368 44.66 0 0 NA 113971 TCGA-AB-2966 AML18 3 86763510 86763510 C A SNP - - - - - - - - - - - - - - - tier3 494 0 0 463 376 44.82 0 0 NA 113971 TCGA-AB-2966 AML18 3 89931208 89931208 A C SNP - - - - - - - - - - - - - - - tier3 382 8 2.05 278 253 47.65 0 0 NA 113971 TCGA-AB-2966 AML18 3 96182603 96182603 C T SNP WDR82P1 ENST00000332119 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43045 NULL 0.005 - - - no_coding_region:pseudogene tier3 100 0 0 144 120 45.45 0 0 NA 113971 TCGA-AB-2966 AML18 3 97322781 97322781 G C SNP ENSG00000221477 ENST00000408550 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*45570 NULL 0 - - - no_errors tier3 506 1 0.2 395 298 43 0 0 NA 113971 TCGA-AB-2966 AML18 3 97504671 97504671 C A SNP LOC644063 XR_016547.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-46223 NULL 0.966 - - - pseudogene tier3 228 0 0 218 138 38.76 0 0 NA 113971 TCGA-AB-2966 AML18 3 98172827 98172827 A T SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.451-16037 e3-16037 0.897 - - - no_errors tier3 511 1 0.2 246 234 48.75 0 0 NA 113971 TCGA-AB-2966 AML18 3 111520532 111520532 G A SNP - - - - - - - - - - - - - - - tier3 195 3 1.52 269 190 41.3 0 0 NA 113971 TCGA-AB-2966 AML18 3 117723311 117723311 G A SNP - - - - - - - - - - - - - - - tier3 747 1 0.13 314 231 42.31 0 0 NA 113971 TCGA-AB-2966 AML18 3 118783980 118783980 G C SNP ENSG00000206889 ENST00000384162 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*38132 NULL 0.003 - - - no_errors tier3 1523 3 0.2 484 372 43.46 0 0 NA 113971 TCGA-AB-2966 AML18 3 120128092 120128092 A G SNP IGSF11 NM_001015887.1 human genbank 54_36p -1 validated intronic c.425-299 e4-299 0.192 - - - no_errors tier3 386 0 0 277 164 37.1 0 0 NA 113971 TCGA-AB-2966 AML18 3 125648121 125648121 G A SNP KALRN NM_001024660.2 human genbank 54_36p 1 reviewed intronic c.3424-179 e21-179 0.002 - - - no_errors tier3 306 1 0.33 510 362 41.51 0 0 NA 113971 TCGA-AB-2966 AML18 3 141288715 141288715 C A SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.110-88768 e2-88768 0 - - - no_errors tier3 350 1 0.28 162 168 50.91 0 0 0 113971 TCGA-AB-2966 AML18 3 143769783 143769783 G A SNP ATR NM_001184.3 human genbank 54_36p -1 reviewed intronic c.60-97 e2-97 0.091 - - - no_errors tier3 350 9 2.5 197 149 43.06 0 3 100 113971 TCGA-AB-2966 AML18 3 144786564 144786564 G A SNP SLC9A9 NM_173653.2 human genbank 54_36p -1 validated intronic c.756-6309 e7-6309 0.002 - - - no_errors tier3 433 2 0.46 272 188 40.87 1 0 0 113971 TCGA-AB-2966 AML18 3 145064665 145064665 C T SNP LOC257039 XM_172230.1 human genbank 54_36p -1 model intronic c.250-6975 e2-6975 0.172 - - - no_errors tier3 475 1 0.21 316 259 45.04 0 0 NA 113971 TCGA-AB-2966 AML18 3 146493626 146493626 T A SNP - - - - - - - - - - - - - - - tier3 293 0 0 290 227 43.91 0 0 NA 113971 TCGA-AB-2966 AML18 3 148412442 148412442 C T SNP - - - - - - - - - - - - - - - tier3 419 0 0 184 148 44.58 0 0 NA 113971 TCGA-AB-2966 AML18 3 148492205 148492205 C T SNP ENSG00000214250 ENST00000327215 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*14476 NULL 0.023 - - - no_coding_region:pseudogene tier3 170 0 0 220 148 40.22 0 0 NA 113971 TCGA-AB-2966 AML18 3 150526240 150526240 G A SNP TM4SF18 NM_138786.2 human genbank 54_36p -1 provisional intronic c.268-741 e3-741 0.004 - - - no_errors tier3 639 23 3.47 308 278 47.36 0 0 NA 113971 TCGA-AB-2966 AML18 3 155798707 155798707 G A SNP - - - - - - - - - - - - - - - tier3 755 4 0.53 579 475 45.02 0 0 NA 113971 TCGA-AB-2966 AML18 3 155998628 155998628 A G SNP - - - - - - - - - - - - - - - tier3 249 1 0.4 287 216 42.86 0 0 NA 113971 TCGA-AB-2966 AML18 3 165269046 165269046 A G SNP - - - - - - - - - - - - - - - tier3 433 1 0.23 413 333 44.64 0 0 NA 113971 TCGA-AB-2966 AML18 3 165731068 165731068 G T SNP - - - - - - - - - - - - - - - tier3 459 2 0.43 310 206 39.92 0 0 NA 113971 TCGA-AB-2966 AML18 3 166467744 166467744 T C SNP - - - - - - - - - - - - - - - tier3 118 1 0.84 132 160 54.79 0 0 NA 113971 TCGA-AB-2966 AML18 3 173716077 173716077 T A SNP TNFSF10 NM_003810.2 human genbank 54_36p -1 reviewed intronic c.133-595 e2-595 0 - - - no_errors tier3 673 1 0.15 503 412 44.98 0 0 0 113971 TCGA-AB-2966 AML18 3 176472306 176472306 G A SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated intronic c.939+15293 e4+15293 0.003 - - - no_errors tier3 79 0 0 180 116 39.06 0 0 NA 113971 TCGA-AB-2966 AML18 3 182021321 182021321 C - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 3 187213827 187213827 C A SNP ETV5 NM_004454.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*35295 NULL 0 - - - no_errors tier3 669 1 0.15 609 441 42 0 0 NA 113971 TCGA-AB-2966 AML18 3 188874137 188874137 T C SNP SST NM_001048.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3364 NULL 0.061 - - - no_errors tier3 427 1 0.23 199 163 45.03 0 0 NA 113971 TCGA-AB-2966 AML18 3 190490298 190490298 A T SNP TPRG1 NM_198485.3 human genbank 54_36p 1 validated intronic c.480-20571 e4-20571 0 - - - no_errors tier3 3276 33 1 509 439 46.26 0 0 NA 113971 TCGA-AB-2966 AML18 3 190894064 190894064 C T SNP TP63 NM_003722.1 human genbank 54_36p 1 reviewed intronic c.63-44159 e2-44159 0.012 - - - no_errors tier3 500 8 1.57 315 217 40.79 0 0 NA 113971 TCGA-AB-2966 AML18 3 193797262 193797262 C G SNP FGF12 NM_004113.4 human genbank 54_36p -1 reviewed intronic c.13+130402 e1+130402 0 - - - no_errors tier3 712 1 0.14 464 335 41.93 0 0 NA 113971 TCGA-AB-2966 AML18 3 194829220 194829220 T C SNP OPA1 NM_130837.2 human genbank 54_36p 1 reviewed intronic c.789+2535 e7+2535 0 - - - no_errors tier3 182 0 0 190 169 47.08 5 3 37.5 113971 TCGA-AB-2966 AML18 3 196801467 196801467 C T SNP APOD NM_001647.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-13846 NULL 0.001 - - - no_errors tier3 454 0 0 291 182 38.48 0 0 NA 113971 TCGA-AB-2966 AML18 4 181783 181783 G A SNP LOC731542 XR_038695.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-34459 NULL 0 - - - pseudogene tier3 487 2 0.41 233 180 43.58 1 0 0 113971 TCGA-AB-2966 AML18 4 14514034 14514034 C T SNP - - - - - - - - - - - - - - - tier3 1412 12 0.84 687 483 41.28 0 0 NA 113971 TCGA-AB-2966 AML18 4 18807799 18807799 G A SNP ENSG00000209240 ENST00000386505 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15209 NULL 0.01 - - - pseudogene tier3 160 0 0 370 261 41.17 0 0 NA 113971 TCGA-AB-2966 AML18 4 19304651 19304651 C T SNP - - - - - - - - - - - - - - - tier3 1135 5 0.44 725 512 41.36 0 0 NA 113971 TCGA-AB-2966 AML18 4 19604811 19604811 T A SNP - - - - - - - - - - - - - - - tier3 221 0 0 123 96 43.84 0 0 NA 113971 TCGA-AB-2966 AML18 4 20144722 20144722 C T SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.1832+286 e18+286 0 - - - no_errors tier3 809 1 0.12 530 525 49.72 0 0 NA 113971 TCGA-AB-2966 AML18 4 20288100 20288100 A G SNP PACRGL NM_145048.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27103 NULL 0 - - - no_errors tier3 1024 5 0.49 458 388 45.86 0 0 NA 113971 TCGA-AB-2966 AML18 4 20318422 20318422 G A SNP PACRGL NM_145048.1 human genbank 54_36p 1 validated intronic c.208-102 e3-102 0.001 - - - no_errors tier3 409 1 0.24 560 390 41.05 0 0 0 113971 TCGA-AB-2966 AML18 4 21262132 21262132 G T SNP KCNIP4 NM_001035003.1 human genbank 54_36p -1 reviewed intronic c.88+45939 e1+45939 0 - - - no_errors tier3 824 0 0 491 325 39.78 0 0 NA 113971 TCGA-AB-2966 AML18 4 23497750 23497750 C T SNP PPARGC1A NM_013261.3 human genbank 54_36p -1 reviewed intronic c.55-2098 e2-2098 0 - - - no_errors tier3 892 3 0.34 571 464 44.83 0 0 NA 113971 TCGA-AB-2966 AML18 4 26130806 26130806 C T SNP CCKAR NM_000730.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29819 NULL 0 - - - no_errors tier3 273 10 3.52 214 74 25.69 0 0 NA 113971 TCGA-AB-2966 AML18 4 27874872 27874872 T C SNP - - - - - - - - - - - - - - - tier3 506 1 0.2 183 137 42.81 0 0 NA 113971 TCGA-AB-2966 AML18 4 28284232 28284233 - T INS ENSG00000210070 ENST00000387335 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-37687 NULL 0.003:0.003 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 4 30531716 30531716 T A SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3226+651 e3+651 0.001 - - - no_errors tier3 246 0 0 275 173 38.53 0 0 NA 113971 TCGA-AB-2966 AML18 4 31012529 31012529 A T SNP - - - - - - - - - - - - - - - tier3 297 0 0 159 123 43.62 0 0 NA 113971 TCGA-AB-2966 AML18 4 34154004 34154004 T A SNP - - - - - - - - - - - - - - - tier3 545 7 1.26 121 87 41.83 0 0 NA 113971 TCGA-AB-2966 AML18 4 35463086 35463086 A G SNP - - - - - - - - - - - - - - - tier3 400 7 1.72 216 153 41.35 0 0 NA 113971 TCGA-AB-2966 AML18 4 35571918 35571918 A T SNP - - - - - - - - - - - - - - - tier3 885 0 0 325 245 42.98 0 0 NA 113971 TCGA-AB-2966 AML18 4 36201225 36201225 C A SNP - - - - - - - - - - - - - - - tier3 805 1 0.12 509 349 40.68 0 0 NA 113971 TCGA-AB-2966 AML18 4 36231305 36231306 TG - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 4 43121110 43121110 T - DEL LOC441013 XR_016299.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-13399 NULL 0 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 4 44625036 44625036 A G SNP - - - - - - - - - - - - - - - tier3 476 42 8.11 451 327 42.03 0 0 NA 113971 TCGA-AB-2966 AML18 4 46123162 46123162 G A SNP GABRA2 NM_000807.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37682 NULL 0.002 - - - no_errors tier3 432 1 0.23 384 306 44.28 0 0 NA 113971 TCGA-AB-2966 AML18 4 52674150 52674150 G T SNP SPATA18 NM_145263.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*18340 NULL 0.004 - - - no_errors tier3 287 1 0.35 325 233 41.76 0 0 NA 113971 TCGA-AB-2966 AML18 4 65702559 65702559 G T SNP - - - - - - - - - - - - - - - tier3 211 0 0 271 190 41.21 0 0 NA 113971 TCGA-AB-2966 AML18 4 70188511 70188511 G A SNP UGT2B28 NM_053039.1 human genbank 54_36p 1 provisional intronic c.1002+1321 e3+1321 0.001 - - - no_errors tier3 120 1 0.83 121 113 47.88 0 5 100 113971 TCGA-AB-2966 AML18 4 70358974 70358974 C T SNP ENSG00000210783 ENST00000388048 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27632 NULL 0.982 - - - pseudogene tier3 298 4 1.32 486 391 44.53 0 0 0 113971 TCGA-AB-2966 AML18 4 71266885 71266885 C A SNP SMR3A NM_012390.3 human genbank 54_36p 1 validated intronic c.55-65 e2-65 0.001 - - - no_errors tier3 613 9 1.45 366 238 39.4 0 0 NA 113971 TCGA-AB-2966 AML18 4 79130561 79130561 G A SNP LOC391670 XR_016388.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-1570 NULL 0 - - - pseudogene tier3 257 1 0.39 209 142 40.46 0 0 NA 113971 TCGA-AB-2966 AML18 4 93761423 93761423 T A SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.244+30963 e2+30963 0 - - - no_errors tier3 501 4 0.79 431 319 42.53 0 0 NA 113971 TCGA-AB-2966 AML18 4 101346003 101346003 C G SNP DDIT4L NM_145244.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-15840 NULL 0.264 - - - no_errors tier3 249 1 0.4 190 145 43.28 0 0 NA 113971 TCGA-AB-2966 AML18 4 109419410 109419410 G C SNP LOC644993 XM_932570.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*22126 NULL 0.004 - - - no_errors tier3 618 1 0.16 381 290 43.22 0 0 NA 113971 TCGA-AB-2966 AML18 4 118933099 118933099 A G SNP - - - - - - - - - - - - - - - tier3 122 0 0 213 133 38.44 0 0 NA 113971 TCGA-AB-2966 AML18 4 135965400 135965400 G T SNP - - - - - - - - - - - - - - - tier3 359 1 0.28 263 174 39.82 0 0 NA 113971 TCGA-AB-2966 AML18 4 138222650 138222650 A G SNP LOC729578 XM_001130691.2 human genbank 54_36p -1 model intronic c.109+7515 e2+7515 0.005 - - - no_errors tier3 415 1 0.24 261 184 41.26 0 0 NA 113971 TCGA-AB-2966 AML18 4 138427269 138427269 G A SNP - - - - - - - - - - - - - - - tier3 438 3 0.68 446 408 47.78 0 0 NA 113971 TCGA-AB-2966 AML18 4 148658299 148658299 C A SNP EDNRA NM_001957.2 human genbank 54_36p 1 validated intronic c.421-2154 e2-2154 0 - - - no_errors tier3 561 0 0 286 254 46.95 0 0 NA 113971 TCGA-AB-2966 AML18 4 153068767 153068767 C A SNP ENSG00000208790 ENST00000386055 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*43326 NULL 0 - - - pseudogene tier3 612 2 0.33 293 268 47.77 0 0 0 113971 TCGA-AB-2966 AML18 4 163054990 163054990 A C SNP FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.409+6016 e3+6016 0.009 - - - no_errors tier3 190 1 0.52 134 113 45.75 0 0 NA 113971 TCGA-AB-2966 AML18 4 165177060 165177060 C A SNP - - - - - - - - - - - - - - - tier3 249 7 2.73 288 235 44.93 0 0 NA 113971 TCGA-AB-2966 AML18 4 165336389 165336389 T A SNP ANP32C NM_012403.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*1220 NULL 0.001 - - - no_errors tier3 299 0 0 220 178 44.72 0 0 NA 113971 TCGA-AB-2966 AML18 4 168359337 168359337 A T SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated intronic c.189+32374 e1+32374 0.043 - - - no_errors tier3 130 0 0 179 103 36.52 0 0 NA 113971 TCGA-AB-2966 AML18 4 174541405 174541405 G A SNP HMGB2 NM_002129.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-50030 NULL 0.045 - - - no_errors tier3 134 0 0 119 93 43.87 2 0 0 113971 TCGA-AB-2966 AML18 4 176958831 176958831 A T SNP GPM6A NM_005277.3 human genbank 54_36p -1 validated intronic c.37+11505 e1+11505 0 - - - no_errors tier3 536 6 1.11 343 228 39.93 0 0 NA 113971 TCGA-AB-2966 AML18 4 177661790 177661790 G T SNP - - - - - - - - - - - - - - - tier3 906 4 0.44 635 496 43.85 0 0 NA 113971 TCGA-AB-2966 AML18 4 178272125 178272125 G A SNP - - - - - - - - - - - - - - - tier3 273 1 0.36 194 212 52.22 0 0 NA 113971 TCGA-AB-2966 AML18 4 181289804 181289804 C A SNP - - - - - - - - - - - - - - - tier3 373 0 0 269 241 47.16 0 0 NA 113971 TCGA-AB-2966 AML18 4 182598743 182598743 G A SNP - - - - - - - - - - - - - - - tier3 408 2 0.49 319 196 38.06 0 0 NA 113971 TCGA-AB-2966 AML18 4 183556120 183556120 G T SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.511+51044 e2+51044 0 - - - no_errors tier3 322 2 0.62 231 172 42.68 0 0 NA 113971 TCGA-AB-2966 AML18 5 1390771 1390771 G A SNP CLPTM1L NM_030782.3 human genbank 54_36p -1 provisional intronic c.678+248 e5+248 0 - - - no_errors tier3 42 0 0 142 109 42.91 1 0 0 113971 TCGA-AB-2966 AML18 5 4279820 4279820 C T SNP - - - - - - - - - - - - - - - tier3 103 0 0 140 123 46.24 0 0 NA 113971 TCGA-AB-2966 AML18 5 7119282 7119282 A T SNP ENSG00000212258 ENST00000390956 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*18833 NULL 0.001 - - - no_errors tier3 223 0 0 781 677 46.4 0 0 NA 113971 TCGA-AB-2966 AML18 5 11426108 11426108 G C SNP CTNND2 NM_001332.2 human genbank 54_36p -1 validated intronic c.1178-8106 e8-8106 0.013 - - - no_errors tier3 224 2 0.88 284 248 46.44 0 0 NA 113971 TCGA-AB-2966 AML18 5 11784356 11784356 C T SNP CTNND2 NM_001332.2 human genbank 54_36p -1 validated intronic c.174+892 e2+892 0 - - - no_errors tier3 984 0 0 437 296 40.33 0 0 NA 113971 TCGA-AB-2966 AML18 5 12230620 12230620 C T SNP - - - - - - - - - - - - - - - tier3 136 0 0 307 256 45.47 0 0 NA 113971 TCGA-AB-2966 AML18 5 14730981 14730981 A G SNP FAM105B NM_138348.4 human genbank 54_36p 1 validated intronic c.230-809 e3-809 0.001 - - - no_errors tier3 243 0 0 138 96 41.03 0 0 0 113971 TCGA-AB-2966 AML18 5 18580015 18580015 T C SNP ENSG00000210087 ENST00000387352 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-3163 NULL 0.005 - - - pseudogene tier3 180 0 0 63 76 54.68 0 0 NA 113971 TCGA-AB-2966 AML18 5 18791466 18791466 G A SNP - - - - - - - - - - - - - - - tier3 203 1 0.49 151 117 43.66 0 0 NA 113971 TCGA-AB-2966 AML18 5 19918709 19918709 T A SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed intronic c.1-43601 e1-43601 0.001 - - - no_errors tier3 173 0 0 212 137 39.26 0 0 NA 113971 TCGA-AB-2966 AML18 5 26028744 26028744 C T SNP ENSG00000222560 ENST00000410628 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20011 NULL 0 - - - no_errors tier3 64 0 0 123 93 43.06 0 0 NA 113971 TCGA-AB-2966 AML18 5 26368780 26368780 G A SNP - - - - - - - - - - - - - - - tier3 384 0 0 109 79 42.02 0 0 NA 113971 TCGA-AB-2966 AML18 5 27410134 27410134 A T SNP - - - - - - - - - - - - - - - tier3 223 0 0 366 258 41.28 0 0 NA 113971 TCGA-AB-2966 AML18 5 29397036 29397036 C G SNP - - - - - - - - - - - - - - - tier3 267 0 0 322 243 43.01 0 0 NA 113971 TCGA-AB-2966 AML18 5 31083256 31083256 G A SNP LOC391774 XR_017200.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 520 1 0.19 432 308 41.62 0 0 NA 113971 TCGA-AB-2966 AML18 5 38050613 38050613 C A SNP - - - - - - - - - - - - - - - tier3 547 1 0.18 565 381 40.23 0 0 NA 113971 TCGA-AB-2966 AML18 5 39829825 39829825 T - DEL LOC285634 XR_017261.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-36378 NULL 0.003 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 5 51777233 51777233 T A SNP - - - - - - - - - - - - - - - tier3 397 21 5.02 269 222 45.21 0 0 NA 113971 TCGA-AB-2966 AML18 5 52659058 52659058 G A SNP - - - - - - - - - - - - - - - tier3 492 3 0.61 834 689 45.24 0 0 NA 113971 TCGA-AB-2966 AML18 5 53782631 53782631 C T SNP HSPB3 NM_006308.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-4746 NULL 0 - - - no_errors tier3 431 3 0.69 174 144 45.14 0 0 NA 113971 TCGA-AB-2966 AML18 5 55434473 55434473 T C SNP ANKRD55 NM_024669.1 human genbank 54_36p -1 validated intronic c.1631-303 e10-303 0 - - - no_errors tier3 121 0 0 113 111 49.55 0 0 NA 113971 TCGA-AB-2966 AML18 5 62913376 62913376 T C SNP ENSG00000201150 ENST00000364280 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22159 NULL 0 - - - no_errors tier3 134 0 0 122 94 43.12 0 0 NA 113971 TCGA-AB-2966 AML18 5 70835238 70835238 T A SNP BDP1 NM_018429.2 human genbank 54_36p 1 reviewed intronic c.2241+864 e15+864 0.16 - - - no_errors tier3 306 0 0 137 128 48.3 9 1 10 113971 TCGA-AB-2966 AML18 5 72209726 72209726 A T SNP TNPO1 NM_002270.3 human genbank 54_36p 1 reviewed intronic c.920+797 e9+797 0.001 - - - no_errors tier3 245 4 1.56 373 329 46.4 1 7 87.5 113971 TCGA-AB-2966 AML18 5 72278167 72278167 G A SNP FCHO2 NM_138782.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-9513 NULL 0.001 - - - no_errors tier3 630 4 0.63 167 117 41.2 0 0 NA 113971 TCGA-AB-2966 AML18 5 75745247 75745247 A G SNP IQGAP2 NM_006633.2 human genbank 54_36p 1 validated intronic c.46+10075 e1+10075 0.003 - - - no_errors tier3 388 2 0.51 160 121 43.06 3 3 50 113971 TCGA-AB-2966 AML18 5 75972058 75972058 G A SNP IQGAP2 NM_006633.2 human genbank 54_36p 1 validated intronic c.1924-456 e17-456 0 - - - no_errors tier3 351 2 0.56 258 226 46.5 0 2 100 113971 TCGA-AB-2966 AML18 5 78171342 78171342 A G SNP ARSB NM_000046.3 human genbank 54_36p -1 reviewed intronic c.1143-337 e6-337 0 - - - no_errors tier3 681 8 1.16 594 457 43.48 0 0 0 113971 TCGA-AB-2966 AML18 5 82852453 82852453 C A SNP VCAN NM_004385.1 human genbank 54_36p 1 validated missense c.2572 p.P858T 0.008 NULL "PatternScan_ASX_HYDROXYL,HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,HMMSmart_SM00179,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin" - no_errors tier1 808 3 0.37 312 257 45.09 NA 113971 TCGA-AB-2966 AML18 5 85235780 85235780 G A SNP - - - - - - - - - - - - - - - tier3 357 6 1.65 258 187 41.93 0 0 NA 113971 TCGA-AB-2966 AML18 5 85572432 85572432 G A SNP NBPF22P ENST00000380134 human ensembl 54_36p 1 known 5_prime_flanking_region c.-41908 NULL 0.001 - - - no_errors tier3 272 2 0.73 165 131 44.26 0 0 NA 113971 TCGA-AB-2966 AML18 5 89173566 89173566 G T SNP - - - - - - - - - - - - - - - tier3 297 1 0.33 249 171 40.71 0 0 NA 113971 TCGA-AB-2966 AML18 5 91232930 91232930 G A SNP - - - - - - - - - - - - - - - tier3 241 0 0 205 154 42.9 0 0 NA 113971 TCGA-AB-2966 AML18 5 94692315 94692315 C T SNP MCTP1 NM_024717.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-46280 NULL 0.015 - - - no_errors tier3 1144 3 0.26 611 472 43.58 0 0 NA 113971 TCGA-AB-2966 AML18 5 97350124 97350124 T C SNP - - - - - - - - - - - - - - - tier3 1364 1 0.07 219 169 43.44 0 0 NA 113971 TCGA-AB-2966 AML18 5 97986026 97986026 C T SNP ENSG00000223053 ENST00000411121 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*16675 NULL 0 - - - no_errors tier3 337 2 0.59 350 315 47.09 0 0 NA 113971 TCGA-AB-2966 AML18 5 106122215 106122215 G C SNP - - - - - - - - - - - - - - - tier3 104 0 0 153 124 44.77 0 0 NA 113971 TCGA-AB-2966 AML18 5 111188645 111188645 G C SNP - - - - - - - - - - - - - - - tier3 383 4 1.03 402 258 39.03 0 0 NA 113971 TCGA-AB-2966 AML18 5 114667005 114667005 C G SNP CCDC112 NM_001040440.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-6866 NULL 0.003 - - - no_errors tier3 244 2 0.81 156 165 51.4 0 0 NA 113971 TCGA-AB-2966 AML18 5 116550222 116550222 C A SNP - - - - - - - - - - - - - - - tier3 838 9 1.06 377 301 44.4 0 0 NA 113971 TCGA-AB-2966 AML18 5 116588930 116588930 G T SNP - - - - - - - - - - - - - - - tier3 246 1 0.4 205 134 39.53 0 0 NA 113971 TCGA-AB-2966 AML18 5 121208396 121208396 C A SNP FTMT NM_177478.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7162 NULL 0.003 - - - no_errors tier3 719 0 0 370 296 44.44 0 0 NA 113971 TCGA-AB-2966 AML18 5 122326319 122326319 G A SNP SNX24 NM_014035.2 human genbank 54_36p 1 validated intronic c.249+16566 e3+16566 0.001 - - - no_errors tier3 121 0 0 193 187 49.21 0 0 NA 113971 TCGA-AB-2966 AML18 5 125341317 125341317 T C SNP - - - - - - - - - - - - - - - tier3 253 2 0.78 237 198 45.41 0 0 NA 113971 TCGA-AB-2966 AML18 5 141217304 141217304 C T SNP PCDH1 NM_032420.3 human genbank 54_36p -1 reviewed intronic c.3100-84 e4-84 0 - - - no_errors tier3 353 1 0.28 146 123 45.72 0 0 NA 113971 TCGA-AB-2966 AML18 5 143590795 143590795 C T SNP KCTD16 NM_020768.3 human genbank 54_36p 1 validated intronic c.832+23493 e1+23493 0 - - - no_errors tier3 443 3 0.67 727 566 43.74 0 0 NA 113971 TCGA-AB-2966 AML18 5 152488964 152488964 C A SNP - - - - - - - - - - - - - - - tier3 765 1 0.13 711 556 43.88 0 0 NA 113971 TCGA-AB-2966 AML18 5 156469706 156469706 C T SNP HAVCR2 NM_032782.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-1134 NULL 0.004 - - - no_errors tier3 289 0 0 185 175 48.34 0 0 NA 113971 TCGA-AB-2966 AML18 5 159237124 159237124 T C SNP ADRA1B NM_000679.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-39367 NULL 0.006 - - - no_errors tier3 503 1 0.2 368 277 42.95 0 0 NA 113971 TCGA-AB-2966 AML18 5 160764182 160764183 - A INS GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed intronic c.541+6376_541+6375 e5+6376 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 5 164265266 164265266 G T SNP ENSG00000206845 ENST00000384118 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*29480 NULL 0.001 - - - no_errors tier3 497 1 0.2 342 221 39.25 0 0 NA 113971 TCGA-AB-2966 AML18 5 165053577 165053578 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 5 172539254 172539254 G C SNP LOC100128619 XM_001720411.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-34643 NULL 0.001 - - - no_errors tier3 634 1 0.16 353 300 45.94 0 0 NA 113971 TCGA-AB-2966 AML18 5 173490668 173490668 C T SNP HMP19 NM_015980.3 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*23554 NULL 0.004 - - - no_errors tier3 1307 3 0.23 904 586 39.17 0 0 NA 113971 TCGA-AB-2966 AML18 6 3739422 3739422 C T SNP C6orf145 NM_183373.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42658 NULL 0 - - - no_errors tier3 263 0 0 320 267 45.49 0 0 NA 113971 TCGA-AB-2966 AML18 6 10344732 10344732 G A SNP LOC442160 XR_042339.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22126 NULL 0 - - - pseudogene tier3 352 0 0 730 448 38.03 0 0 NA 113971 TCGA-AB-2966 AML18 6 12150286 12150286 G A SNP HIVEP1 NM_002114.2 human genbank 54_36p 1 validated intronic c.40+26399 e1+26399 0.002 - - - no_errors tier3 231 5 2.12 189 162 46.02 4 6 60 113971 TCGA-AB-2966 AML18 6 13064933 13064933 G A SNP PHACTR1 NM_030948.1 human genbank 54_36p 1 validated intronic c.251-96650 e3-96650 0.001 - - - no_errors tier3 245 0 0 183 139 43.17 0 0 NA 113971 TCGA-AB-2966 AML18 6 15692587 15692587 C T SNP DTNBP1 NM_032122.3 human genbank 54_36p -1 reviewed intronic c.511+8682 e7+8682 0.001 - - - no_errors tier3 150 1 0.66 387 287 42.52 6 3 33.33 113971 TCGA-AB-2966 AML18 6 18309605 18309605 C T SNP AOF1 NM_153042.3 human genbank 54_36p 1 validated intronic c.963+819 e9+819 0.108 - - - no_errors tier3 197 0 0 197 141 41.72 2 2 50 113971 TCGA-AB-2966 AML18 6 18875178 18875178 G T SNP - - - - - - - - - - - - - - - tier3 578 0 0 335 286 46.05 0 0 NA 113971 TCGA-AB-2966 AML18 6 18919272 18919272 A G SNP - - - - - - - - - - - - - - - tier3 257 2 0.77 124 110 47.01 0 0 NA 113971 TCGA-AB-2966 AML18 6 22621213 22621213 C T SNP - - - - - - - - - - - - - - - tier3 573 4 0.69 513 455 46.71 0 0 NA 113971 TCGA-AB-2966 AML18 6 40249371 40249371 T C SNP - - - - - - - - - - - - - - - tier3 795 19 2.33 190 192 50.26 0 0 NA 113971 TCGA-AB-2966 AML18 6 48421067 48421067 G A SNP - - - - - - - - - - - - - - - tier3 204 2 0.97 273 190 40.95 0 0 NA 113971 TCGA-AB-2966 AML18 6 50145801 50145801 G A SNP DEFB112 NM_001037498.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-21478 NULL 0 - - - no_errors tier3 1026 2 0.19 465 394 45.81 0 0 NA 113971 TCGA-AB-2966 AML18 6 51613835 51613835 A C SNP PKHD1 NM_138694.3 human genbank 54_36p -1 reviewed intronic c.11399-2122 e63-2122 0.076 - - - no_errors tier3 574 0 0 285 224 43.92 0 0 NA 113971 TCGA-AB-2966 AML18 6 63277462 63277462 A G SNP ENSG00000217067 ENST00000405686 human ensembl 54_36p 1 known 5_prime_flanking_region c.-37827 NULL 0.186 - - - no_coding_region:pseudogene tier3 162 2 1.22 181 152 45.51 0 0 NA 113971 TCGA-AB-2966 AML18 6 64819561 64819561 G A SNP - - - - - - - - - - - - - - - tier3 851 5 0.58 326 278 45.95 0 0 NA 113971 TCGA-AB-2966 AML18 6 65885837 65885837 T C SNP LOC727977 XM_001126270.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-8787 NULL 0.001 - - - no_errors tier3 804 3 0.37 465 409 46.8 0 0 NA 113971 TCGA-AB-2966 AML18 6 73109608 73109608 C T SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated intronic c.4366+9349 e29+9349 0 - - - no_errors tier3 1325 26 1.92 526 423 44.53 0 0 NA 113971 TCGA-AB-2966 AML18 6 77581939 77581939 C G SNP - - - - - - - - - - - - - - - tier3 369 5 1.34 330 273 45.27 0 0 NA 113971 TCGA-AB-2966 AML18 6 81608687 81608687 T A SNP - - - - - - - - - - - - - - - tier3 111 0 0 154 121 44 0 0 NA 113971 TCGA-AB-2966 AML18 6 83464874 83464874 A C SNP - - - - - - - - - - - - - - - tier3 306 0 0 430 358 45.32 0 0 NA 113971 TCGA-AB-2966 AML18 6 87480526 87480526 A T SNP ENSG00000218561 ENST00000407695 human ensembl 54_36p -1 known 3_prime_flanking_region c.*15619 NULL 0.047 - - - no_coding_region:pseudogene tier3 402 2 0.5 230 139 37.67 0 0 NA 113971 TCGA-AB-2966 AML18 6 93696542 93696542 A T SNP ENSG00000219387 ENST00000406040 human ensembl 54_36p -1 known 5_prime_flanking_region c.-41522 NULL 0.997 - - - no_coding_region:pseudogene tier3 352 1 0.28 242 225 47.97 0 0 NA 113971 TCGA-AB-2966 AML18 6 94095718 94095718 C T SNP EPHA7 NM_004440.3 human genbank 54_36p -1 reviewed intronic c.1324+27438 e5+27438 0 - - - no_errors tier3 363 2 0.55 264 221 45.57 0 0 NA 113971 TCGA-AB-2966 AML18 6 95700407 95700407 C T SNP - - - - - - - - - - - - - - - tier3 683 1 0.15 532 370 40.97 0 0 NA 113971 TCGA-AB-2966 AML18 6 96768239 96768239 C T SNP FUT9 NM_006581.3 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*9407 NULL 0 - - - no_errors tier3 183 0 0 336 255 43 0 0 NA 113971 TCGA-AB-2966 AML18 6 109574997 109574997 C T SNP C6orf182 NM_001083535.1 human genbank 54_36p 1 validated intronic c.340+164 e2+164 0 - - - no_errors tier3 223 0 0 130 104 44.44 0 1 100 113971 TCGA-AB-2966 AML18 6 111453673 111453673 G A SNP ENSG00000207431 ENST00000384700 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-17401 NULL 0.002 - - - no_errors tier3 457 8 1.72 122 121 49.79 13 4 23.53 113971 TCGA-AB-2966 AML18 6 111566156 111566156 G A SNP SLC16A10 NM_018593.4 human genbank 54_36p 1 validated intronic c.344-34435 e2-34435 0.014 - - - no_errors tier3 393 1 0.25 249 187 42.89 0 0 NA 113971 TCGA-AB-2966 AML18 6 112086765 112086765 A - DEL ENSG00000208826 ENST00000386091 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12442 NULL 0.007 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 6 113572009 113572009 G T SNP - - - - - - - - - - - - - - - tier3 411 1 0.24 428 266 38.33 0 0 NA 113971 TCGA-AB-2966 AML18 6 118423633 118423633 A - DEL SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated intronic c.173+87878 e1+87878 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 6 119952070 119952070 A G SNP LOC728727 XM_001128292.2 human genbank 54_36p 1 model intronic c.225+38811 e3+38811 0.002 - - - no_errors tier3 702 0 0 390 308 44.13 0 1 100 113971 TCGA-AB-2966 AML18 6 120312681 120312682 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 6 125569385 125569385 A G SNP TPD52L1 NM_003287.1 human genbank 54_36p 1 reviewed intronic c.20-13538 e2-13538 0 - - - no_errors tier3 239 1 0.42 276 185 40.13 0 0 NA 113971 TCGA-AB-2966 AML18 6 128406075 128406075 T C SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.2194+21521 e13+21521 0 - - - no_errors tier3 356 4 1.11 487 370 43.17 0 0 NA 113971 TCGA-AB-2966 AML18 6 145186954 145186954 A G SNP UTRN NM_007124.2 human genbank 54_36p 1 reviewed intronic c.9494+3107 e65+3107 0.001 - - - no_errors tier3 217 0 0 321 270 45.69 10 7 41.18 113971 TCGA-AB-2966 AML18 6 151119314 151119314 G A SNP PLEKHG1 NM_001029884.1 human genbank 54_36p 1 provisional intronic c.412-12153 e2-12153 0 - - - no_errors tier3 622 1 0.16 546 463 45.62 0 0 NA 113971 TCGA-AB-2966 AML18 6 158320535 158320535 C T SNP SYNJ2 NM_003898.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-2447 NULL 0.021 - - - no_errors tier3 112 0 0 90 62 40.79 0 0 NA 113971 TCGA-AB-2966 AML18 6 159850508 159850508 C T SNP LOC642738 XR_017625.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*16502 NULL 0.002 - - - pseudogene tier3 193 2 1.03 156 129 44.95 0 0 NA 113971 TCGA-AB-2966 AML18 6 162644133 162644133 T C SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.172-40346 e3-40346 0 - - - no_errors tier3 345 1 0.29 308 240 43.8 0 0 NA 113971 TCGA-AB-2966 AML18 7 1394556 1394556 G A SNP LOC100134474 XM_001715902.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-18612 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 90 3 3.23 46 46 49.46 0 0 NA 113971 TCGA-AB-2966 AML18 7 3732267 3732267 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.713+84004 e4+84004 0.001 - - - no_errors tier3 208 0 0 471 423 47.32 0 0 NA 113971 TCGA-AB-2966 AML18 7 4178229 4178229 G T SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.4801-2151 e33-2151 0 - - - no_errors tier3 86 0 0 99 99 50 0 0 NA 113971 TCGA-AB-2966 AML18 7 7444054 7444054 A G SNP COL28A1 NM_001037763.2 human genbank 54_36p -1 validated intronic c.1723-436 e21-436 0 - - - no_errors tier3 152 0 0 241 264 52.28 0 0 NA 113971 TCGA-AB-2966 AML18 7 15994105 15994105 C T SNP - - - - - - - - - - - - - - - tier3 546 1 0.18 543 427 43.98 0 0 NA 113971 TCGA-AB-2966 AML18 7 20709783 20709783 C T SNP ABCB5 NM_178559.4 human genbank 54_36p 1 validated intronic c.1003-1089 e8-1089 0 - - - no_errors tier3 345 1 0.29 298 188 38.68 0 0 NA 113971 TCGA-AB-2966 AML18 7 42080640 42080640 C T SNP GLI3 NM_000168.5 human genbank 54_36p -1 reviewed intronic c.473+2236 e3+2236 0.001 - - - no_errors tier3 412 7 1.67 533 492 47.95 0 0 NA 113971 TCGA-AB-2966 AML18 7 50151633 50151633 A G SNP LOC100130988 XM_001713888.1 human genbank 54_36p 1 model intronic c.965+103 e7+103 0 - - - no_errors tier3 368 0 0 301 216 41.7 0 0 NA 113971 TCGA-AB-2966 AML18 7 54570023 54570023 G C SNP VSTM2A NM_182546.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7895 NULL 0.381 - - - no_errors tier3 217 10 4.39 145 171 53.94 0 0 NA 113971 TCGA-AB-2966 AML18 7 57282890 57282890 C A SNP LOC642006 XM_001719189.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-31244 NULL 0 - - - pseudogene tier3 330 1 0.3 55 45 45 0 0 NA 113971 TCGA-AB-2966 AML18 7 66957287 66957287 G A SNP - - - - - - - - - - - - - - - tier3 1017 2 0.2 583 472 44.7 0 0 NA 113971 TCGA-AB-2966 AML18 7 70492886 70492886 G A SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.589+1563 e3+1563 0 - - - no_errors tier3 433 7 1.59 442 321 42.02 0 0 NA 113971 TCGA-AB-2966 AML18 7 77212712 77212712 G C SNP RSBN1L NM_198467.2 human genbank 54_36p 1 validated intronic c.704-3965 e3-3965 0.415 - - - no_errors tier3 809 4 0.49 298 215 41.91 4 2 33.33 113971 TCGA-AB-2966 AML18 7 80913004 80913005 - T INS LOC100128317 XM_001717593.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*26937 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 7 83656675 83656675 C G SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed intronic c.112+5052 e1+5052 0 - - - no_errors tier3 209 0 0 120 115 48.94 0 0 NA 113971 TCGA-AB-2966 AML18 7 99253693 99253693 G A SNP CYP3A43 NM_022820.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-9982 NULL 0 - - - no_errors tier3 469 2 0.42 195 177 47.58 0 0 NA 113971 TCGA-AB-2966 AML18 7 110078403 110078403 C T SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*12491 NULL 0 - - - no_errors tier3 280 0 0 346 261 43 0 0 NA 113971 TCGA-AB-2966 AML18 7 111862182 111862182 T C SNP IFRD1 NM_001007245.1 human genbank 54_36p 1 validated intronic c.1+11459 e0+11459 0.002 - - - no_errors tier3 743 20 2.62 342 267 43.84 3 0 0 113971 TCGA-AB-2966 AML18 7 112142222 112142222 C T SNP - - - - - - - - - - - - - - - tier3 623 5 0.8 481 361 42.77 0 0 NA 113971 TCGA-AB-2966 AML18 7 120444091 120444091 G T SNP C7orf58 NM_024913.1 human genbank 54_36p 1 validated intronic c.433+953 e2+953 0 - - - no_errors tier3 241 0 0 309 155 33.41 0 0 0 113971 TCGA-AB-2966 AML18 7 121776577 121776577 G C SNP CADPS2 NM_017954.2 human genbank 54_36p -1 validated intronic c.3505-3606 e28-3606 0.001 - - - no_errors tier3 64 3 4.48 186 116 38.41 0 0 NA 113971 TCGA-AB-2966 AML18 7 123092328 123092328 G T SNP LMOD2 ENST00000332074 human ensembl 54_36p 1 known intronic c.NULL NULL 0.001 - - - no_coding_region:pseudogene tier3 696 10 1.42 619 546 46.83 4 0 0 113971 TCGA-AB-2966 AML18 7 123855605 123855605 A G SNP LOC136157 NM_001085395.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-48056 NULL 0 - - - no_errors tier3 444 2 0.45 246 199 44.72 0 0 NA 113971 TCGA-AB-2966 AML18 7 124717839 124717839 T G SNP RPL31P39 ENST00000393325 human ensembl 54_36p -1 known 3_prime_flanking_region c.*9955 NULL 0.007 - - - no_coding_region:pseudogene tier3 983 3 0.3 457 378 45.27 0 0 NA 113971 TCGA-AB-2966 AML18 7 126562028 126562029 AA - DEL GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.511-28027_511-28026 e2-28026 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 7 132537799 132537799 C G SNP - - - - - - - - - - - - - - - tier3 390 1 0.26 239 167 40.83 0 0 NA 113971 TCGA-AB-2966 AML18 7 134740117 134740117 C T SNP CNOT4 NM_013316.1 human genbank 54_36p -1 validated intronic c.812+5697 e6+5697 0.988 - - - no_errors tier3 431 3 0.69 432 430 49.83 1 0 0 113971 TCGA-AB-2966 AML18 7 139475333 139475333 A G SNP JHDM1D NM_030647.1 human genbank 54_36p -1 provisional intronic c.559+429 e4+429 0.001 - - - no_errors tier3 320 0 0 221 171 43.62 0 0 0 113971 TCGA-AB-2966 AML18 7 142304276 142304276 G A SNP TRPV6 NM_018646.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-10893 NULL 0.001 - - - no_errors tier3 308 3 0.96 55 58 51.33 0 0 NA 113971 TCGA-AB-2966 AML18 7 147308189 147308189 C A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2383+2175 e15+2175 0.004 - - - no_errors tier3 136 1 0.73 164 110 40.15 0 0 NA 113971 TCGA-AB-2966 AML18 7 147530430 147530430 G A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.3011-14883 e19-14883 0 - - - no_errors tier3 2716 13 0.48 515 407 44.14 0 0 NA 113971 TCGA-AB-2966 AML18 7 150529544 150529544 T A SNP IQCA1L ENST00000340262 human ensembl 54_36p -1 known intronic c.646-1071 e5-1071 0.001 - - - no_errors tier3 244 1 0.41 168 126 42.71 0 0 NA 113971 TCGA-AB-2966 AML18 7 154007912 154007912 C T SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.628-52552 e6-52552 0 - - - no_errors tier3 412 1 0.24 320 259 44.58 0 0 NA 113971 TCGA-AB-2966 AML18 7 156916802 156916802 C T SNP DNAJB6 NM_058246.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*15249 NULL 0.001 - - - no_errors tier3 48 0 0 37 22 37.29 0 0 NA 113971 TCGA-AB-2966 AML18 8 1720643 1720643 G A SNP CLN8 NM_018941.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*4503 NULL 0.02 - - - no_errors tier3 326 0 0 357 314 46.8 5 0 0 113971 TCGA-AB-2966 AML18 8 3991960 3991960 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.416-114931 e4-114931 0.003 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 272 1 0.37 229 258 52.87 0 0 NA 113971 TCGA-AB-2966 AML18 8 4342758 4342758 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.303-77763 e3-77763 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 404 0 0 401 264 39.7 0 0 NA 113971 TCGA-AB-2966 AML18 8 5266385 5266385 G T SNP - - - - - - - - - - - - - - - tier3 323 28 7.98 264 232 46.77 0 0 NA 113971 TCGA-AB-2966 AML18 8 6045485 6045485 C T SNP - - - - - - - - - - - - - - - tier3 716 4 0.56 386 338 46.62 0 0 NA 113971 TCGA-AB-2966 AML18 8 8204952 8204952 G T SNP PRAGMIN NM_001080826.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*8134 NULL 0.002 - - - no_errors tier3 320 0 0 283 191 40.21 0 0 NA 113971 TCGA-AB-2966 AML18 8 11390192 11390192 C T SNP BLK NM_001715.2 human genbank 54_36p 1 validated intronic c.1+683 e0+683 0 - - - no_errors tier3 109 2 1.8 97 110 53.14 0 0 NA 113971 TCGA-AB-2966 AML18 8 14005650 14005650 G A SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.621-1271 e7-1271 0 - - - no_errors tier3 278 4 1.42 188 131 41.07 0 0 NA 113971 TCGA-AB-2966 AML18 8 15056230 15056230 A G SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.39+83235 e1+83235 0.027 - - - no_errors tier3 284 1 0.35 363 273 42.86 0 0 NA 113971 TCGA-AB-2966 AML18 8 20989494 20989494 G A SNP - - - - - - - - - - - - - - - tier3 638 0 0 389 304 43.87 0 0 NA 113971 TCGA-AB-2966 AML18 8 24356746 24356746 T C SNP ADAM7 NM_003817.2 human genbank 54_36p 1 validated intronic c.156+712 e2+712 0 - - - no_errors tier3 537 3 0.55 964 787 44.92 0 0 NA 113971 TCGA-AB-2966 AML18 8 26653517 26653517 G A SNP ADRA1A NM_033303.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*8507 NULL 0.002 - - - no_errors tier3 575 4 0.69 443 302 40.48 0 0 NA 113971 TCGA-AB-2966 AML18 8 26658916 26658916 G A SNP ADRA1A NM_033303.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*3108 NULL 0.001 - - - no_errors tier3 512 2 0.39 476 433 47.58 0 0 NA 113971 TCGA-AB-2966 AML18 8 32874427 32874427 C T SNP ENSG00000212407 ENST00000391105 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14126 NULL 0 - - - no_errors tier3 236 0 0 271 211 43.78 0 0 NA 113971 TCGA-AB-2966 AML18 8 35074566 35074566 C T SNP - - - - - - - - - - - - - - - tier3 883 0 0 371 258 40.82 0 0 NA 113971 TCGA-AB-2966 AML18 8 35395250 35395250 G C SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.104-131102 e2-131102 0.001 - - - no_errors tier3 213 2 0.93 123 114 48.1 0 0 NA 113971 TCGA-AB-2966 AML18 8 35600823 35600823 C T SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.555+28106 e4+28106 0.003 - - - no_errors tier3 118 0 0 111 68 37.99 0 0 NA 113971 TCGA-AB-2966 AML18 8 39548511 39548511 T C SNP ADAM18 NM_014237.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-12788 NULL 0.004 - - - no_errors tier3 482 1 0.21 290 213 42.35 0 0 NA 113971 TCGA-AB-2966 AML18 8 49146808 49146808 G A SNP UBE2V2 NM_003350.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*10867 NULL 0.006 - - - no_errors tier3 516 3 0.58 272 248 47.6 0 0 NA 113971 TCGA-AB-2966 AML18 8 50838998 50838998 C A SNP C8orf62 XR_016569.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22564 NULL 0 - - - pseudogene tier3 492 1 0.2 501 360 41.81 0 0 NA 113971 TCGA-AB-2966 AML18 8 51937072 51937072 A G SNP - - - - - - - - - - - - - - - tier3 588 12 2 417 344 45.2 0 0 NA 113971 TCGA-AB-2966 AML18 8 53517476 53517476 C T SNP ST18 NM_014682.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-228106 NULL 0 - - - no_errors tier3 729 1 0.14 724 579 44.37 0 4 100 113971 TCGA-AB-2966 AML18 8 57837461 57837461 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 8 60723712 60723712 C T SNP - - - - - - - - - - - - - - - tier3 318 2 0.62 411 339 45.14 0 0 NA 113971 TCGA-AB-2966 AML18 8 63622228 63622228 G A SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.55-32424 e2-32424 0.035 - - - no_errors tier3 492 1 0.2 359 236 39.66 0 0 NA 113971 TCGA-AB-2966 AML18 8 65610409 65610409 C T SNP BHLHE22 NM_152414.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45493 NULL 0 - - - no_errors tier3 732 2 0.27 433 306 41.35 0 0 NA 113971 TCGA-AB-2966 AML18 8 76542561 76542561 T - DEL HNF4G ENST00000354370 human ensembl 54_36p 1 known intronic c.1-22318 e1-22318 0.145 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 8 83618891 83618891 T C SNP - - - - - - - - - - - - - - - tier3 217 0 0 160 137 46.13 0 0 NA 113971 TCGA-AB-2966 AML18 8 84826122 84826122 G T SNP - - - - - - - - - - - - - - - tier3 359 0 0 142 125 46.64 0 0 NA 113971 TCGA-AB-2966 AML18 8 89812156 89812156 C T SNP - - - - - - - - - - - - - - - tier3 589 3 0.51 353 315 47.16 0 0 NA 113971 TCGA-AB-2966 AML18 8 94509199 94509199 C A SNP LOC100129242 XM_001717187.1 human genbank 54_36p -1 model intronic c.280-728 e4-728 0.002 - - - no_errors tier3 427 3 0.7 166 120 41.96 0 0 NA 113971 TCGA-AB-2966 AML18 8 95883961 95883961 T A SNP INTS8 NM_017864.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-20875 NULL 0.021 - - - no_errors tier3 444 2 0.45 267 225 45.64 0 0 NA 113971 TCGA-AB-2966 AML18 8 96679382 96679382 C T SNP ENSG00000202112 ENST00000365242 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1140 NULL 0 - - - no_errors tier3 163 0 0 30 20 40 0 0 NA 113971 TCGA-AB-2966 AML18 8 97632537 97632537 G A SNP SDC2 NM_002998.3 human genbank 54_36p 1 reviewed intronic c.61-42347 e2-42347 0 - - - no_errors tier3 155 1 0.64 396 323 44.92 0 0 NA 113971 TCGA-AB-2966 AML18 8 98896591 98896591 T A SNP LAPTM4B NM_018407.4 human genbank 54_36p 1 validated intronic c.485-141 e3-141 0 - - - no_errors tier3 369 1 0.27 153 107 41.15 0 0 0 113971 TCGA-AB-2966 AML18 8 101671110 101671110 G A SNP SNX31 NM_152628.3 human genbank 54_36p -1 validated intronic c.979-727 e11-727 0.001 - - - no_errors tier3 303 0 0 230 174 43.07 0 0 NA 113971 TCGA-AB-2966 AML18 8 102230757 102230757 G A SNP ZNF706 NM_001042510.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*50649 NULL 0 - - - no_errors tier3 471 1 0.21 326 235 41.89 0 0 NA 113971 TCGA-AB-2966 AML18 8 102315737 102315737 T G SNP ZNF706 NM_001042510.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-32592 NULL 0 - - - no_errors tier3 855 0 0 454 395 46.47 0 0 NA 113971 TCGA-AB-2966 AML18 8 102605251 102605251 C T SNP GRHL2 NM_024915.3 human genbank 54_36p 1 validated intronic c.21-19394 e2-19394 0.217 - - - no_errors tier3 580 0 0 345 233 40.31 0 0 NA 113971 TCGA-AB-2966 AML18 8 107494671 107494671 G A SNP - - - - - - - - - - - - - - - tier3 285 1 0.35 265 241 47.63 0 0 0 113971 TCGA-AB-2966 AML18 8 110819852 110819852 C A SNP GOLSYN NM_001099744.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-93788 NULL 0.399 - - - no_errors tier3 2216 6 0.27 849 605 41.61 0 0 NA 113971 TCGA-AB-2966 AML18 8 118727613 118727613 G C SNP - - - - - - - - - - - - - - - tier3 300 0 0 306 179 36.83 0 0 NA 113971 TCGA-AB-2966 AML18 8 132408122 132408122 C G SNP - - - - - - - - - - - - - - - tier3 1310 3 0.23 381 228 37.32 0 0 NA 113971 TCGA-AB-2966 AML18 8 135420897 135420897 T C SNP - - - - - - - - - - - - - - - tier3 327 0 0 298 248 45.42 0 0 NA 113971 TCGA-AB-2966 AML18 8 136162091 136162091 C T SNP - - - - - - - - - - - - - - - tier3 837 4 0.48 797 556 41.03 0 0 NA 113971 TCGA-AB-2966 AML18 8 136213004 136213004 G T SNP - - - - - - - - - - - - - - - tier3 664 5 0.75 373 319 46.1 0 0 NA 113971 TCGA-AB-2966 AML18 8 139936010 139936010 C T SNP COL22A1 NM_152888.1 human genbank 54_36p -1 validated intronic c.659-10427 e3-10427 0 - - - no_errors tier3 1339 11 0.81 685 627 47.75 0 0 NA 113971 TCGA-AB-2966 AML18 8 142931525 142931525 G A SNP - - - - - - - - - - - - - - - tier3 934 10 1.06 320 312 49.37 0 0 NA 113971 TCGA-AB-2966 AML18 9 887750 887750 A T SNP DMRT1 NM_021951.2 human genbank 54_36p 1 reviewed intronic c.822+3555 e3+3555 0.001 - - - no_errors tier3 308 2 0.64 182 160 46.78 0 0 NA 113971 TCGA-AB-2966 AML18 9 2811038 2811038 C T SNP KIAA0020 NM_014878.4 human genbank 54_36p -1 validated intronic c.1189-940 e12-940 0.06 - - - no_errors tier3 173 0 0 368 283 43.47 1 3 75 113971 TCGA-AB-2966 AML18 9 3045620 3045620 T C SNP - - - - - - - - - - - - - - - tier3 493 2 0.4 263 206 43.83 0 0 NA 113971 TCGA-AB-2966 AML18 9 6214590 6214590 T - DEL IL33 NM_033439.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17105 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 9 6610044 6610044 G A SNP GLDC NM_000170.2 human genbank 54_36p -1 validated intronic c.470+140 e3+140 0.003 - - - no_errors tier3 686 1 0.15 295 203 40.76 0 0 NA 113971 TCGA-AB-2966 AML18 9 9080586 9080586 C A SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-71851 e1-71851 0 - - - no_errors tier3 432 0 0 431 280 39.33 0 0 NA 113971 TCGA-AB-2966 AML18 9 9392125 9392125 C T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-4643 e1-4643 0.003 - - - no_errors tier3 514 3 0.58 329 176 34.85 0 0 NA 113971 TCGA-AB-2966 AML18 9 13568489 13568489 A C SNP - - - - - - - - - - - - - - - tier3 538 26 4.59 472 399 45.7 0 0 NA 113971 TCGA-AB-2966 AML18 9 15390945 15390945 A G SNP SNAPC3 NM_001039697.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21933 NULL 0.004 - - - no_errors tier3 392 2 0.51 180 122 40.26 0 0 0 113971 TCGA-AB-2966 AML18 9 19506072 19506072 T C SNP SLC24A2 NM_020344.1 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*79 NULL 0.856 - - - no_errors tier3 346 0 0 232 210 47.4 0 0 NA 113971 TCGA-AB-2966 AML18 9 23809607 23809607 G A SNP ELAVL2 NM_004432.2 human genbank 54_36p -1 validated intronic c.1+6197 e0+6197 0 - - - no_errors tier3 276 1 0.36 251 202 44.59 0 0 NA 113971 TCGA-AB-2966 AML18 9 24408949 24408949 C T SNP - - - - - - - - - - - - - - - tier3 106 0 0 104 98 48.51 0 0 NA 113971 TCGA-AB-2966 AML18 9 25101101 25101101 C T SNP ENSG00000222693 ENST00000410761 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-21952 NULL 0 - - - no_errors tier3 156 1 0.64 415 294 41.41 0 0 NA 113971 TCGA-AB-2966 AML18 9 26416176 26416176 G A SNP - - - - - - - - - - - - - - - tier3 363 0 0 262 267 50.47 0 0 NA 113971 TCGA-AB-2966 AML18 9 26563702 26563702 T C SNP - - - - - - - - - - - - - - - tier3 940 2 0.21 492 383 43.77 0 0 NA 113971 TCGA-AB-2966 AML18 9 29537078 29537078 C T SNP - - - - - - - - - - - - - - - tier3 357 4 1.11 299 209 41.14 0 0 NA 113971 TCGA-AB-2966 AML18 9 30569162 30569162 A G SNP ENSG00000219252 ENST00000404726 human ensembl 54_36p -1 known 5_prime_flanking_region c.-19599 NULL 0 - - - no_coding_region:pseudogene tier3 371 3 0.8 220 202 47.64 0 0 NA 113971 TCGA-AB-2966 AML18 9 31894938 31894938 G A SNP - - - - - - - - - - - - - - - tier3 531 0 0 390 394 50.19 0 0 NA 113971 TCGA-AB-2966 AML18 9 44807518 44807518 C T SNP ENSG00000204814 ENST00000377547 human ensembl 54_36p 1 known 5_prime_flanking_region c.-1561 NULL 0.035 - - - no_errors tier3 121 0 0 24 13 35.14 0 0 NA 113971 TCGA-AB-2966 AML18 9 71793133 71793133 C T SNP - - - - - - - - - - - - - - - tier3 980 4 0.41 428 379 46.96 0 0 NA 113971 TCGA-AB-2966 AML18 9 72647400 72647400 G A SNP TRPM3 NM_001007471.1 human genbank 54_36p -1 reviewed intronic c.801+339 e5+339 0 - - - no_errors tier3 280 0 0 268 196 42.06 0 0 NA 113971 TCGA-AB-2966 AML18 9 74732677 74732677 T C SNP ALDH1A1 NM_000689.3 human genbank 54_36p -1 reviewed intronic c.443-764 e5-764 0.001 - - - no_errors tier3 326 3 0.91 502 406 44.66 0 0 NA 113971 TCGA-AB-2966 AML18 9 84533860 84533860 T C SNP ENSG00000211245 ENST00000388510 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43970 NULL 0.001 - - - pseudogene tier3 699 1 0.14 402 362 47.32 0 0 NA 113971 TCGA-AB-2966 AML18 9 86438857 86438857 G A SNP NTRK2 NM_006180.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36627 NULL 0.004 - - - no_errors tier3 444 3 0.67 305 231 43.1 0 0 NA 113971 TCGA-AB-2966 AML18 9 88513923 88513923 C T SNP - - - - - - - - - - - - - - - tier3 502 0 0 236 191 44.73 0 0 NA 113971 TCGA-AB-2966 AML18 9 100544281 100544281 C T SNP ANKS6 NM_173551.3 human genbank 54_36p -1 provisional intronic c.2511+3381 e14+3381 0.007 - - - no_errors tier3 572 1 0.17 511 423 45.29 0 0 0 113971 TCGA-AB-2966 AML18 9 104758617 104758617 T C SNP CYLC2 NM_001340.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-38867 NULL 0.001 - - - no_errors tier3 563 1 0.18 589 467 44.18 0 0 NA 113971 TCGA-AB-2966 AML18 9 109302987 109302987 C T SNP KLF4 NM_004235.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11857 NULL 0.017 - - - no_errors tier3 118 0 0 86 82 48.81 0 0 NA 113971 TCGA-AB-2966 AML18 9 109610046 109610046 G A SNP ENSG00000222558 ENST00000410626 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-10097 NULL 0 - - - no_errors tier3 482 4 0.82 205 209 50.48 0 0 NA 113971 TCGA-AB-2966 AML18 9 111669741 111669741 G C SNP PALM2-AKAP2 NM_007203.3 human genbank 54_36p 1 validated intronic c.126+69 e2+69 0.983 - - - no_errors tier3 323 3 0.92 219 212 49.19 0 0 NA 113971 TCGA-AB-2966 AML18 9 114802341 114802341 G T SNP LOC169834 NM_001101338.1 human genbank 54_36p -1 validated intronic c.1-426 e1-426 0.01 - - - no_errors tier3 318 0 0 208 119 36.28 0 0 NA 113971 TCGA-AB-2966 AML18 9 121420928 121420928 C T SNP - - - - - - - - - - - - - - - tier3 807 1 0.12 343 241 40.57 0 0 NA 113971 TCGA-AB-2966 AML18 9 121704407 121704407 G T SNP ENSG00000222745 ENST00000410813 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*17252 NULL 0.149 - - - no_errors tier3 1478 33 2.18 524 402 43.41 0 0 NA 113971 TCGA-AB-2966 AML18 9 124475544 124475544 G A SNP OR1L3 NM_001005234.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1686 NULL 0 - - - no_errors tier3 706 1 0.14 936 746 44.25 0 0 NA 113971 TCGA-AB-2966 AML18 9 126053558 126053558 G A SNP NEK6 NM_014397.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-50507 NULL 0 - - - no_errors tier3 617 2 0.32 204 195 48.87 0 0 NA 113971 TCGA-AB-2966 AML18 9 126209238 126209238 C T SNP PSMB7 NM_002799.2 human genbank 54_36p -1 reviewed intronic c.396-1706 e5-1706 0.395 - - - no_errors tier3 615 2 0.32 134 132 49.44 0 0 0 113971 TCGA-AB-2966 AML18 9 128876645 128876645 A G SNP RALGPS1 NM_014636.1 human genbank 54_36p 1 provisional intronic c.610+5189 e7+5189 0.001 - - - no_errors tier3 414 6 1.43 361 312 46.29 0 0 NA 113971 TCGA-AB-2966 AML18 9 131993373 131993373 G T SNP FREQ NM_014286.1 human genbank 54_36p 1 reviewed intronic c.65-9685 e2-9685 0.003 - - - no_errors tier3 61 1 1.61 78 62 44.29 0 0 NA 113971 TCGA-AB-2966 AML18 9 132915561 132915561 G A SNP LAMC3 NM_006059.3 human genbank 54_36p 1 reviewed intronic c.1630+1223 e9+1223 0 - - - no_errors tier3 162 0 0 84 57 40.43 0 0 NA 113971 TCGA-AB-2966 AML18 10 2334280 2334280 C T SNP - - - - - - - - - - - - - - - tier3 462 2 0.43 283 227 44.51 0 0 NA 113971 TCGA-AB-2966 AML18 10 3039893 3039893 G T SNP - - - - - - - - - - - - - - - tier3 91 5 5.21 445 318 41.62 0 0 NA 113971 TCGA-AB-2966 AML18 10 3377470 3377470 T C SNP - - - - - - - - - - - - - - - tier3 781 2 0.26 287 247 46.25 0 0 NA 113971 TCGA-AB-2966 AML18 10 21556345 21556345 T C SNP ENSG00000218500 ENST00000401465 human ensembl 54_36p 1 known 5_prime_flanking_region c.-20342 NULL 0 - - - no_coding_region:pseudogene tier3 131 0 0 128 99 43.61 0 0 NA 113971 TCGA-AB-2966 AML18 10 26191263 26191263 C G SNP ENSG00000223019 ENST00000411087 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48411 NULL 0.001 - - - no_errors tier3 230 0 0 198 171 46.22 0 0 NA 113971 TCGA-AB-2966 AML18 10 28864562 28864562 C T SNP WAC NM_016628.3 human genbank 54_36p 1 reviewed silent c.144 p.D48 1 NULL "HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain" - no_errors tier1 358 9 2.45 343 298 46.42 102 111 52.11 113971 TCGA-AB-2966 AML18 10 29319425 29319425 A G SNP - - - - - - - - - - - - - - - tier3 704 16 2.22 269 231 46.2 0 0 NA 113971 TCGA-AB-2966 AML18 10 31809103 31809103 G A SNP ZEB1 NM_030751.1 human genbank 54_36p 1 validated intronic c.260-15611 e3-15611 0 - - - no_errors tier3 193 3 1.53 311 233 42.83 0 3 100 113971 TCGA-AB-2966 AML18 10 37478282 37478282 C T SNP ANKRD30A NM_052997.2 human genbank 54_36p 1 validated intronic c.1376-303 e10-303 0.001 - - - no_errors tier3 329 0 0 194 135 41.03 0 0 NA 113971 TCGA-AB-2966 AML18 10 38563581 38563581 C T SNP ENSG00000216557 ENST00000402645 human ensembl 54_36p 1 known 3_prime_flanking_region c.*47876 NULL 0.073 - - - no_coding_region:pseudogene tier3 40 1 2.44 53 35 39.77 0 0 NA 113971 TCGA-AB-2966 AML18 10 44601129 44601129 G A SNP ENSG00000220202 ENST00000407900 human ensembl 54_36p 1 known 5_prime_flanking_region c.-20768 NULL 0 - - - no_coding_region:pseudogene tier3 767 2 0.26 522 365 39.54 0 0 NA 113971 TCGA-AB-2966 AML18 10 48035731 48035731 G A SNP GDF2 NM_016204.1 human genbank 54_36p -1 reviewed intronic c.346+623 e1+623 0 - - - no_errors tier3 147 2 1.34 125 58 31.69 0 0 NA 113971 TCGA-AB-2966 AML18 10 52683566 52683566 A G SNP PRKG1 NM_006258.1 human genbank 54_36p 1 validated intronic c.478+100470 e2+100470 0.129 - - - no_errors tier3 330 3 0.9 297 221 42.66 0 0 0 113971 TCGA-AB-2966 AML18 10 59172136 59172136 G C SNP - - - - - - - - - - - - - - - tier3 503 0 0 526 423 44.57 0 0 NA 113971 TCGA-AB-2966 AML18 10 59695473 59695473 T C SNP IPMK NM_152230.3 human genbank 54_36p -1 provisional intronic c.190+1715 e1+1715 0.086 - - - no_errors tier3 125 0 0 247 217 46.77 2 0 0 113971 TCGA-AB-2966 AML18 10 72571262 72571262 G A SNP - - - - - - - - - - - - - - - tier3 241 1 0.41 135 115 45.82 0 0 NA 113971 TCGA-AB-2966 AML18 10 76180682 76180682 C T SNP ENSG00000213525 ENST00000394726 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-6211 NULL 0.011 - - - no_coding_region:pseudogene tier3 801 1 0.12 329 249 43.08 0 0 NA 113971 TCGA-AB-2966 AML18 10 84377098 84377098 A T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.954-111215 e3-111215 1 - - - no_errors tier3 614 7 1.13 282 259 47.7 0 0 NA 113971 TCGA-AB-2966 AML18 10 95983931 95983931 C A SNP PLCE1 NM_016341.3 human genbank 54_36p 1 validated missense c.2086 p.H696N 1 "HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF" "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RA,HMMSmart_SM00314,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand" - no_errors tier1 317 0 329 244 42.58 NA 113971 TCGA-AB-2966 AML18 10 97114189 97114189 G T SNP SORBS1 NM_001034954.1 human genbank 54_36p -1 validated intronic c.1955+3208 e20+3208 0 - - - no_errors tier3 465 5 1.06 277 157 36.18 0 0 0 113971 TCGA-AB-2966 AML18 10 102774372 102774372 C T SNP PDZD7 NM_024895.3 human genbank 54_36p -1 provisional intronic c.227-557 e2-557 0.002 - - - no_errors tier3 609 3 0.49 149 143 48.81 0 0 0 113971 TCGA-AB-2966 AML18 10 104073779 104073779 T C SNP GBF1 NM_004193.1 human genbank 54_36p 1 provisional intronic c.164-20019 e3-20019 0 - - - no_errors tier3 433 2 0.46 140 117 45.53 19 8 29.63 113971 TCGA-AB-2966 AML18 10 104479520 104479520 G A SNP SFXN2 NM_178858.4 human genbank 54_36p 1 validated silent c.558 p.A186 0.885 HMMPfam_Mtc HMMPfam_Mtc - no_errors tier1 207 0 179 165 47.41 4 2 33.33 113971 TCGA-AB-2966 AML18 10 106344833 106344833 G A SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46243 NULL 0 - - - no_errors tier3 650 2 0.31 418 332 44.15 0 0 NA 113971 TCGA-AB-2966 AML18 10 107439911 107439911 G A SNP ENSG00000218440 ENST00000402674 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4298 NULL 0 - - - no_coding_region:pseudogene tier3 588 2 0.34 421 357 45.83 0 0 NA 113971 TCGA-AB-2966 AML18 10 107653493 107653493 C G SNP - - - - - - - - - - - - - - - tier3 534 0 0 391 337 46.29 0 0 NA 113971 TCGA-AB-2966 AML18 10 108379945 108379945 C T SNP SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed intronic c.2476-809 e19-809 0 - - - no_errors tier3 697 3 0.43 351 260 42.55 0 0 NA 113971 TCGA-AB-2966 AML18 10 109202380 109202380 G T SNP ENSG00000200079 ENST00000363209 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8928 NULL 0 - - - no_errors tier3 1236 9 0.72 633 477 42.97 0 0 NA 113971 TCGA-AB-2966 AML18 10 110732147 110732147 C T SNP ENSG00000222436 ENST00000410504 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41089 NULL 0 - - - no_errors tier3 649 3 0.46 334 213 38.66 0 0 NA 113971 TCGA-AB-2966 AML18 10 119630807 119630807 C T SNP - - - - - - - - - - - - - - - tier3 161 0 0 135 91 38.89 0 0 NA 113971 TCGA-AB-2966 AML18 10 125221141 125221141 G A SNP - - - - - - - - - - - - - - - tier3 343 0 0 252 178 41.3 0 0 NA 113971 TCGA-AB-2966 AML18 10 126269462 126269462 G C SNP LHPP NM_022126.2 human genbank 54_36p 1 provisional intronic c.717-22361 e7-22361 0.002 - - - no_errors tier3 74 1 1.33 166 130 43.77 0 0 0 113971 TCGA-AB-2966 AML18 10 127737149 127737149 C A SNP ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed intronic c.1618+6216 e14+6216 0 - - - no_errors tier3 216 0 0 202 152 42.94 0 0 NA 113971 TCGA-AB-2966 AML18 10 133116441 133116441 A G SNP - - - - - - - - - - - - - - - tier3 231 0 0 155 93 37.5 0 0 NA 113971 TCGA-AB-2966 AML18 11 14141181 14141181 T C SNP SPON1 ENST00000310358 human ensembl 54_36p 1 known intronic c.822+27491 e7+27491 0 - - - no_errors tier3 753 12 1.56 343 257 42.83 1 0 0 113971 TCGA-AB-2966 AML18 11 16069534 16069534 C T SNP SOX6 NM_033326.1 human genbank 54_36p -1 reviewed intronic c.1101+4584 e8+4584 0 - - - no_errors tier3 363 1 0.27 317 341 51.75 0 0 NA 113971 TCGA-AB-2966 AML18 11 19778794 19778794 G T SNP NAV2 NM_182964.1 human genbank 54_36p 1 validated intronic c.268-31812 e2-31812 0.001 - - - no_errors tier3 349 12 3.3 193 145 42.4 0 0 NA 113971 TCGA-AB-2966 AML18 11 23092020 23092020 A T SNP - - - - - - - - - - - - - - - tier3 372 1 0.27 265 213 44.38 2 1 33.33 113971 TCGA-AB-2966 AML18 11 24627682 24627682 G T SNP LUZP2 NM_001009909.2 human genbank 54_36p 1 validated intronic c.63-79609 e2-79609 0.009 - - - no_errors tier3 595 0 0 244 171 41.2 0 0 NA 113971 TCGA-AB-2966 AML18 11 28447255 28447255 C T SNP - - - - - - - - - - - - - - - tier3 1073 1 0.09 406 274 40.29 0 2 100 113971 TCGA-AB-2966 AML18 11 31326721 31326721 C T SNP DCDC1 NM_181807.2 human genbank 54_36p -1 validated intronic c.1-13034 e1-13034 0 - - - no_errors tier3 172 1 0.58 403 265 39.43 0 0 NA 113971 TCGA-AB-2966 AML18 11 34564422 34564422 G A SNP EHF NM_012153.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-56332 NULL 0.002 - - - no_errors tier3 607 0 0 534 406 43.05 0 0 NA 113971 TCGA-AB-2966 AML18 11 36367478 36367478 A C SNP FLJ14213 NM_024841.3 human genbank 54_36p 1 provisional intronic c.1-11645 e1-11645 0.001 - - - no_errors tier3 406 0 0 239 201 45.68 0 4 100 113971 TCGA-AB-2966 AML18 11 39361888 39361888 T A SNP - - - - - - - - - - - - - - - tier3 347 3 0.85 411 261 38.78 0 0 NA 113971 TCGA-AB-2966 AML18 11 39729529 39729529 C A SNP ENSG00000209673 ENST00000386938 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-15548 NULL 0 - - - pseudogene tier3 563 2 0.35 266 158 37.18 0 0 NA 113971 TCGA-AB-2966 AML18 11 50248797 50248797 G A SNP ENSG00000164740 ENST00000338231 human ensembl 54_36p -1 known 5_prime_flanking_region c.-39495 NULL 0.004 - - - no_errors tier3 325 0 0 337 297 46.85 0 0 NA 113971 TCGA-AB-2966 AML18 11 55071096 55071096 T G SNP OR4C16 NM_001004701.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25084 NULL 0.02 - - - no_errors tier3 533 4 0.74 286 231 44.59 0 0 NA 113971 TCGA-AB-2966 AML18 11 55937876 55937876 G A SNP OR5R1 NM_001004744.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*3434 NULL 0 - - - no_errors tier3 393 2 0.5 292 220 42.88 0 0 NA 113971 TCGA-AB-2966 AML18 11 57818204 57818204 C T SNP OR10W1 NM_207374.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-26298 NULL 0.02 - - - no_errors tier3 221 1 0.45 442 372 45.59 0 0 NA 113971 TCGA-AB-2966 AML18 11 63123541 63123541 T G SNP PLA2G16 NM_007069.1 human genbank 54_36p -1 validated intronic c.16-1330 e2-1330 0.001 - - - no_errors tier3 303 2 0.65 293 260 46.76 0 0 NA 113971 TCGA-AB-2966 AML18 11 65240439 65240439 A T SNP KAT5 NM_182710.2 human genbank 54_36p 1 reviewed intronic c.1030-275 e9-275 0.001 - - - no_errors tier3 353 0 0 343 259 42.88 5 0 0 113971 TCGA-AB-2966 AML18 11 78044781 78044781 G A SNP ODZ4 NM_001098816.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1970 NULL 0.019 - - - no_errors tier3 295 11 3.59 214 191 47.16 0 0 NA 113971 TCGA-AB-2966 AML18 11 84398792 84398792 G A SNP DLG2 ENST00000376104 human ensembl 54_36p -1 known intronic c.357+101561 e4+101561 0 - - - no_errors tier3 532 2 0.37 576 453 43.98 0 0 NA 113971 TCGA-AB-2966 AML18 11 93648895 93648895 G A SNP FOLR4 NM_001080486.1 human genbank 54_36p 1 inferred 5_prime_flanking_region c.-29556 NULL 0 - - - no_errors tier3 681 0 0 526 390 42.58 0 0 NA 113971 TCGA-AB-2966 AML18 11 100715149 100715149 C A SNP - - - - - - - - - - - - - - - tier3 718 7 0.97 400 327 44.92 0 0 NA 113971 TCGA-AB-2966 AML18 11 104530445 104530445 G A SNP CARD18 NM_021571.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14782 NULL 0 - - - no_errors tier3 364 2 0.55 442 301 40.46 0 0 NA 113971 TCGA-AB-2966 AML18 11 106060328 106060328 G A SNP GUCY1A2 NM_000855.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*3157 NULL 0.001 - - - no_errors tier3 428 2 0.46 281 227 44.6 0 0 NA 113971 TCGA-AB-2966 AML18 11 113325246 113325246 C T SNP HTR3A NM_213621.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26012 NULL 0 - - - no_errors tier3 574 3 0.52 315 282 47.24 0 0 NA 113971 TCGA-AB-2966 AML18 11 118751824 118751824 G A SNP LOC100130353 XM_001719137.1 human genbank 54_36p 1 model missense c.227 p.R76Q 0.001 NULL NULL - no_errors tier1 92 1 1.08 84 58 40.85 NA 113971 TCGA-AB-2966 AML18 11 122921830 122921830 G A SNP GRAMD1B NM_020716.1 human genbank 54_36p 1 validated intronic c.23+19741 e1+19741 0.001 - - - no_errors tier3 217 0 0 262 208 44.16 0 0 NA 113971 TCGA-AB-2966 AML18 11 124606829 124606829 G T SNP PKNOX2 NM_022062.2 human genbank 54_36p 1 validated intronic c.1-3322 e1-3322 0.004 - - - no_errors tier3 434 1 0.23 396 245 38.16 0 0 NA 113971 TCGA-AB-2966 AML18 11 125334235 125334235 G C SNP CDON NM_016952.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1812 NULL 0 - - - no_errors tier3 427 1 0.23 297 252 45.82 0 0 NA 113971 TCGA-AB-2966 AML18 11 127181213 127181213 G A SNP - - - - - - - - - - - - - - - tier3 570 3 0.52 290 263 47.47 0 0 NA 113971 TCGA-AB-2966 AML18 11 128422310 128422310 G A SNP uc009zcp.1 ENST00000310343 human ensembl 54_36p -1 known intronic c.1-6196 e1-6196 0 - - - no_errors tier3 375 4 1.06 211 165 43.65 2 0 0 113971 TCGA-AB-2966 AML18 11 131899082 131899082 G A SNP OPCML NM_002545.1 human genbank 54_36p -1 reviewed intronic c.526+5083 e3+5083 0.866 - - - no_errors tier3 381 2 0.52 466 435 48.28 0 0 NA 113971 TCGA-AB-2966 AML18 11 132776891 132776891 T A SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+130478 e1+130478 0.016 - - - no_errors tier3 235 1 0.42 207 131 38.76 0 0 NA 113971 TCGA-AB-2966 AML18 12 12494601 12494601 C T SNP LOH12CR1 NM_058169.3 human genbank 54_36p 1 validated intronic c.360+14615 e3+14615 0 - - - no_errors tier3 228 0 0 220 185 45.68 1 6 85.71 113971 TCGA-AB-2966 AML18 12 17115644 17115644 G A SNP ENSG00000212358 ENST00000391056 human ensembl 54_36p -1 novel rna NULL NULL 0.001 - - - no_errors tier1 805 0 464 282 37.8 NA 113971 TCGA-AB-2966 AML18 12 25269829 25269829 C T SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.436 p.A146T 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 197 2 1.01 289 186 39.08 26 10 27.78 113971 TCGA-AB-2966 AML18 12 28094715 28094715 A C SNP - - - - - - - - - - - - - - - tier3 830 0 0 593 513 46.3 0 0 NA 113971 TCGA-AB-2966 AML18 12 29422689 29422689 C A SNP ERGIC2 NM_016570.2 human genbank 54_36p -1 validated intronic c.1+2626 e0+2626 0.001 - - - no_errors tier3 318 8 2.45 110 96 46.6 0 0 0 113971 TCGA-AB-2966 AML18 12 37804456 37804456 C T SNP - - - - - - - - - - - - - - - tier3 168 1 0.59 162 143 46.89 0 0 NA 113971 TCGA-AB-2966 AML18 12 41439162 41439162 C T SNP - - - - - - - - - - - - - - - tier3 345 0 0 248 177 41.26 0 0 NA 113971 TCGA-AB-2966 AML18 12 47936383 47936383 C T SNP PRPH NM_006262.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-38868 NULL 0.005 - - - no_errors tier3 304 3 0.97 207 173 45.53 0 0 0 113971 TCGA-AB-2966 AML18 12 56708150 56708150 A T SNP ENSG00000222210 ENST00000410278 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49827 NULL 0 - - - no_errors tier3 366 1 0.27 168 118 41.26 0 0 NA 113971 TCGA-AB-2966 AML18 12 57322213 57322213 C T SNP - - - - - - - - - - - - - - - tier3 338 2 0.59 263 349 56.93 0 0 NA 113971 TCGA-AB-2966 AML18 12 60326902 60326902 G A SNP - - - - - - - - - - - - - - - tier3 302 0 0 170 138 44.66 0 0 NA 113971 TCGA-AB-2966 AML18 12 63790458 63790458 G A SNP WIF1 NM_007191.3 human genbank 54_36p -1 reviewed intronic c.288+10006 e2+10006 0 - - - no_errors tier3 515 2 0.39 293 271 47.8 0 0 NA 113971 TCGA-AB-2966 AML18 12 76309190 76309190 A T SNP - - - - - - - - - - - - - - - tier3 541 0 0 449 315 41.18 0 0 NA 113971 TCGA-AB-2966 AML18 12 76325978 76325978 G A SNP - - - - - - - - - - - - - - - tier3 185 2 1.06 357 236 39.6 0 0 NA 113971 TCGA-AB-2966 AML18 12 83684582 83684582 C T SNP - - - - - - - - - - - - - - - tier3 551 2 0.36 278 195 41.23 0 0 NA 113971 TCGA-AB-2966 AML18 12 91671412 91671412 G C SNP PLEKHG7 NM_001004330.2 human genbank 54_36p 1 validated intronic c.316-585 e5-585 0.001 - - - no_errors tier3 453 20 4.23 248 205 45.25 0 0 NA 113971 TCGA-AB-2966 AML18 12 94275863 94275863 G A SNP MIRN331 ENST00000362302 human ensembl 54_36p 1 known 3_prime_flanking_region c.*49443 NULL 0.007 - - - no_errors tier3 362 5 1.36 322 283 46.78 0 0 NA 113971 TCGA-AB-2966 AML18 12 95428491 95428491 T G SNP C12orf55 XM_001715090.2 human genbank 54_36p 1 model intronic c.740-2404 e5-2404 0.023 - - - no_errors tier3 449 46 9.27 264 214 44.77 0 0 NA 113971 TCGA-AB-2966 AML18 12 97809706 97809706 C A SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.2779-59661 e18-59661 0.02 - - - no_errors tier3 195 1 0.51 159 100 38.61 0 0 NA 113971 TCGA-AB-2966 AML18 12 99484649 99484649 G A SNP GAS2L3 NM_174942.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-28165 NULL 0 - - - no_errors tier3 578 3 0.52 288 221 43.42 0 0 NA 113971 TCGA-AB-2966 AML18 12 102489638 102489638 A G SNP STAB2 NM_017564.9 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15747 NULL 0.195 - - - no_errors tier3 360 2 0.55 299 239 44.42 0 0 NA 113971 TCGA-AB-2966 AML18 12 103626493 103626493 G A SNP CHST11 NM_018413.4 human genbank 54_36p 1 provisional intronic c.205-48364 e3-48364 0 - - - no_errors tier3 222 2 0.89 136 108 43.9 7 10 58.82 113971 TCGA-AB-2966 AML18 12 121451175 121451175 A G SNP CLIP1 NM_002956.2 human genbank 54_36p -1 validated intronic c.1-20117 e1-20117 0 - - - no_errors tier3 255 0 0 212 177 45.38 1 0 0 113971 TCGA-AB-2966 AML18 12 123301140 123301140 C T SNP FAM101A NM_181709.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-61213 NULL 0.005 - - - no_errors tier3 428 0 0 247 207 45.59 0 0 NA 113971 TCGA-AB-2966 AML18 12 126518567 126518567 C T SNP - - - - - - - - - - - - - - - tier3 291 6 2.02 165 135 45 0 0 NA 113971 TCGA-AB-2966 AML18 12 126573964 126573964 C A SNP - - - - - - - - - - - - - - - tier3 278 2 0.71 242 206 45.98 0 0 NA 113971 TCGA-AB-2966 AML18 12 128415845 128415845 C A SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1116-27530 e4-27530 0.023 - - - no_errors tier3 235 1 0.42 157 107 40.53 0 0 NA 113971 TCGA-AB-2966 AML18 12 128545489 128545489 A G SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1115+36068 e3+36068 0 - - - no_errors tier3 640 9 1.38 565 395 41.06 0 0 NA 113971 TCGA-AB-2966 AML18 12 129010541 129010541 G A SNP - - - - - - - - - - - - - - - tier3 451 3 0.66 359 265 42.4 0 0 NA 113971 TCGA-AB-2966 AML18 12 129722330 129722330 G T SNP - - - - - - - - - - - - - - - tier3 248 1 0.4 268 182 40.35 0 0 NA 113971 TCGA-AB-2966 AML18 13 24641843 24641843 T G SNP FAM123A NM_152704.2 human genbank 54_36p -1 validated missense c.1915 p.I639L 1 NULL HMMPfam_WTX - no_errors tier1 222 2 0.89 250 207 45.3 NA 113971 TCGA-AB-2966 AML18 13 32662616 32662616 C T SNP STARD13 NM_178006.2 human genbank 54_36p -1 validated intronic c.170-22857 e2-22857 0 - - - no_errors tier3 330 0 0 173 130 42.76 0 0 NA 113971 TCGA-AB-2966 AML18 13 32970285 32970285 C T SNP - - - - - - - - - - - - - - - tier3 559 0 0 356 266 42.77 0 0 NA 113971 TCGA-AB-2966 AML18 13 34424060 34424060 T G SNP NBEA NM_015678.3 human genbank 54_36p 1 reviewed intronic c.294+8809 e1+8809 0.222 - - - no_errors tier3 266 1 0.37 224 163 42.12 0 0 NA 113971 TCGA-AB-2966 AML18 13 38966661 38966661 C T SNP LHFP NM_005780.2 human genbank 54_36p -1 reviewed intronic c.385+106308 e1+106308 0 - - - no_errors tier3 567 0 0 589 526 47.13 0 0 NA 113971 TCGA-AB-2966 AML18 13 42069630 42069630 G A SNP TNFSF11 NM_003701.3 human genbank 54_36p 1 reviewed intronic c.388-3258 e3-3258 0.004 - - - no_errors tier3 329 2 0.6 433 306 41.41 0 0 NA 113971 TCGA-AB-2966 AML18 13 47159844 47159844 G A SNP - - - - - - - - - - - - - - - tier3 778 0 0 566 467 45.16 0 0 NA 113971 TCGA-AB-2966 AML18 13 54006050 54006050 G A SNP LOC100128485 XM_001717043.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*11114 NULL 0.144 - - - no_errors tier3 386 0 0 465 405 46.5 0 0 NA 113971 TCGA-AB-2966 AML18 13 54058282 54058282 G T SNP - - - - - - - - - - - - - - - tier3 315 4 1.25 350 256 42.17 0 0 NA 113971 TCGA-AB-2966 AML18 13 57516801 57516801 T G SNP - - - - - - - - - - - - - - - tier3 140 2 1.4 200 210 51.22 0 0 NA 113971 TCGA-AB-2966 AML18 13 59318578 59318578 T G SNP DIAPH3 NM_001042517.1 human genbank 54_36p -1 validated intronic c.2738-6995 e23-6995 0.001 - - - no_errors tier3 684 1 0.15 308 223 42 2 0 0 113971 TCGA-AB-2966 AML18 13 60608088 60608088 G A SNP - - - - - - - - - - - - - - - tier3 1039 3 0.29 506 444 46.74 0 0 NA 113971 TCGA-AB-2966 AML18 13 67399489 67399489 A G SNP ENSG00000217316 ENST00000403455 human ensembl 54_36p 1 known 3_prime_flanking_region c.*24114 NULL 0.053 - - - no_coding_region:pseudogene tier3 191 2 1.04 181 150 45.32 0 0 NA 113971 TCGA-AB-2966 AML18 13 68035291 68035291 T C SNP - - - - - - - - - - - - - - - tier3 746 3 0.4 256 157 38.01 0 0 NA 113971 TCGA-AB-2966 AML18 13 72216364 72216364 A G SNP C13orf34 NM_024808.2 human genbank 54_36p 1 validated intronic c.455-280 e6-280 0 - - - no_errors tier3 843 18 2.09 288 245 45.88 1 1 50 113971 TCGA-AB-2966 AML18 13 75980390 75980390 C T SNP LOC100132423 XM_001717535.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-27276 NULL 0.002 - - - no_start_codon tier3 1490 13 0.86 545 401 42.39 0 0 NA 113971 TCGA-AB-2966 AML18 13 76183097 76183097 C T SNP - - - - - - - - - - - - - - - tier3 470 1 0.21 251 224 46.86 0 0 NA 113971 TCGA-AB-2966 AML18 13 78831479 78831479 A C SNP RBM26 NM_022118.3 human genbank 54_36p -1 validated intronic c.1529+232 e10+232 0.001 - - - no_errors tier3 323 3 0.92 357 291 44.84 3 2 40 113971 TCGA-AB-2966 AML18 13 80295959 80295959 C G SNP - - - - - - - - - - - - - - - tier3 472 0 0 584 395 40.27 0 1 100 113971 TCGA-AB-2966 AML18 13 80846480 80846480 T A SNP - - - - - - - - - - - - - - - tier3 205 1 0.49 189 140 42.55 0 0 NA 113971 TCGA-AB-2966 AML18 13 81693854 81693854 A T SNP - - - - - - - - - - - - - - - tier3 541 13 2.35 272 210 43.57 0 0 NA 113971 TCGA-AB-2966 AML18 13 82673407 82673407 C T SNP - - - - - - - - - - - - - - - tier3 330 10 2.94 182 166 47.7 0 0 NA 113971 TCGA-AB-2966 AML18 13 84632804 84632804 G A SNP - - - - - - - - - - - - - - - tier3 228 0 0 181 155 46.13 0 0 NA 113971 TCGA-AB-2966 AML18 13 86350444 86350444 A G SNP - - - - - - - - - - - - - - - tier3 412 0 0 235 216 47.89 0 0 NA 113971 TCGA-AB-2966 AML18 13 86403219 86403219 A G SNP - - - - - - - - - - - - - - - tier3 468 4 0.85 252 184 42.2 0 0 NA 113971 TCGA-AB-2966 AML18 13 87179856 87179856 T A SNP SLITRK5 NM_015567.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*51335 NULL 0 - - - no_errors tier3 154 2 1.28 166 134 44.67 0 0 NA 113971 TCGA-AB-2966 AML18 13 91789377 91789377 C T SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1561+194134 e7+194134 0.001 - - - no_errors tier3 207 1 0.48 224 170 43.15 0 0 NA 113971 TCGA-AB-2966 AML18 13 91958151 91958151 T C SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1562-358385 e8-358385 0.046 - - - no_errors tier3 127 0 0 140 112 44.44 0 0 NA 113971 TCGA-AB-2966 AML18 13 92089578 92089578 A T SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1562-226958 e8-226958 0.115 - - - no_errors tier3 627 2 0.32 184 149 44.74 0 0 NA 113971 TCGA-AB-2966 AML18 13 105256436 105256436 T A SNP - - - - - - - - - - - - - - - tier3 413 2 0.48 476 226 32.15 0 0 NA 113971 TCGA-AB-2966 AML18 13 105445871 105445871 T C SNP - - - - - - - - - - - - - - - tier3 391 4 1.01 191 215 52.83 0 0 NA 113971 TCGA-AB-2966 AML18 13 105599010 105599010 C T SNP ENSG00000222643 ENST00000410711 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*20172 NULL 0.001 - - - no_errors tier3 377 1 0.26 163 81 33.2 0 0 NA 113971 TCGA-AB-2966 AML18 13 106524384 106524384 C T SNP ENSG00000221316 ENST00000408389 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46998 NULL 0.001 - - - no_errors tier3 354 0 0 294 239 44.34 0 0 NA 113971 TCGA-AB-2966 AML18 13 112403261 112403261 G A SNP ATP11A NM_032189.2 human genbank 54_36p 1 reviewed intronic c.39+10491 e1+10491 0.008 - - - no_errors tier3 86 0 0 84 69 45.1 1 0 0 113971 TCGA-AB-2966 AML18 14 19836087 19836087 A G SNP TTC5 NM_138376.1 human genbank 54_36p -1 provisional intronic c.639+709 e5+709 0.002 - - - no_errors tier3 649 0 0 317 285 47.34 0 2 100 113971 TCGA-AB-2966 AML18 14 20120816 20120816 G A SNP RNASE9 NM_001001673.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-25748 NULL 0.006 - - - no_errors tier3 536 0 0 511 374 42.26 0 0 NA 113971 TCGA-AB-2966 AML18 14 24198455 24198455 T C SNP GZMB NM_004131.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25249 NULL 0.167 - - - no_errors tier3 784 2 0.25 367 275 42.77 0 0 NA 113971 TCGA-AB-2966 AML18 14 27847097 27847097 A G SNP ENSG00000197358 ENST00000355069 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*43003 NULL 0.262 - - - no_coding_region:pseudogene tier3 648 2 0.31 306 258 45.74 0 0 NA 113971 TCGA-AB-2966 AML18 14 34540646 34540646 G A SNP SRP54 NM_003136.2 human genbank 54_36p 1 provisional intronic c.255+669 e3+669 0.016 - - - no_errors tier3 871 3 0.34 306 171 35.85 9 3 25 113971 TCGA-AB-2966 AML18 14 36274670 36274670 C T SNP SLC25A21 NM_030631.2 human genbank 54_36p -1 provisional intronic c.204-1141 e4-1141 0.003 - - - no_errors tier3 293 4 1.35 303 260 46.1 0 0 NA 113971 TCGA-AB-2966 AML18 14 42386960 42386960 A G SNP - - - - - - - - - - - - - - - tier3 383 0 0 367 218 37.2 0 0 NA 113971 TCGA-AB-2966 AML18 14 43556622 43556622 T G SNP - - - - - - - - - - - - - - - tier3 668 1 0.15 505 416 45.17 0 0 NA 113971 TCGA-AB-2966 AML18 14 46674527 46674527 A C SNP MDGA2 NM_182830.1 human genbank 54_36p -1 validated intronic c.1-3728 e1-3728 0.328 - - - no_errors tier3 138 3 2.13 122 101 45.29 0 0 NA 113971 TCGA-AB-2966 AML18 14 54098487 54098487 A G SNP SAMD4A NM_015589.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-5901 NULL 0 - - - no_errors tier3 172 0 0 129 115 47.13 0 0 NA 113971 TCGA-AB-2966 AML18 14 54800991 54800991 C A SNP FBXO34 NM_017943.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-85871 NULL 0.007 - - - no_errors tier3 713 3 0.42 186 102 35.29 0 0 NA 113971 TCGA-AB-2966 AML18 14 62239704 62239704 C T SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*4275 NULL 0.002 - - - no_errors tier3 657 0 0 323 231 41.7 0 0 NA 113971 TCGA-AB-2966 AML18 14 67719225 67719225 G A SNP RAD51L1 NM_133509.4 human genbank 54_36p 1 reviewed intronic c.757-109129 e7-109129 0 - - - no_errors tier3 365 2 0.54 490 386 44.06 1 0 0 113971 TCGA-AB-2966 AML18 14 77986423 77986423 A G SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.1+46449 e0+46449 0.001 - - - no_errors tier3 262 1 0.38 284 177 38.39 1 0 0 113971 TCGA-AB-2966 AML18 14 78967267 78967267 A G SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2144-36050 e11-36050 0.001 - - - no_errors tier3 317 0 0 549 466 45.87 0 0 NA 113971 TCGA-AB-2966 AML18 14 79712864 79712864 G A SNP DIO2 ENST00000388841 human ensembl 54_36p -1 known 3_prime_flanking_region c.*26344 NULL 0.001 - - - no_errors tier3 205 1 0.48 204 156 43.33 0 0 NA 113971 TCGA-AB-2966 AML18 14 83350321 83350321 A G SNP - - - - - - - - - - - - - - - tier3 496 4 0.8 452 401 46.9 0 0 NA 113971 TCGA-AB-2966 AML18 14 84598051 84598051 G T SNP - - - - - - - - - - - - - - - tier3 641 8 1.23 488 281 36.49 0 0 NA 113971 TCGA-AB-2966 AML18 14 84631874 84631874 T G SNP - - - - - - - - - - - - - - - tier3 284 1 0.35 231 134 36.71 0 0 NA 113971 TCGA-AB-2966 AML18 14 87149389 87149389 C G SNP LOC730121 XM_001132513.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*21356 NULL 0.002 - - - no_errors tier3 955 5 0.52 657 554 45.71 0 0 NA 113971 TCGA-AB-2966 AML18 14 96592961 96592961 G A SNP - - - - - - - - - - - - - - - tier3 1059 2 0.19 362 288 44.31 0 0 NA 113971 TCGA-AB-2966 AML18 14 98709112 98709112 C G SNP BCL11B NM_138576.1 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*1129 NULL 0.035 - - - no_errors tier3 249 2 0.8 106 83 43.92 9 0 0 113971 TCGA-AB-2966 AML18 14 102698949 102698949 C G SNP TNFAIP2 NM_006291.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*27499 NULL 0.002 - - - no_errors tier3 139 0 0 114 75 39.68 0 0 NA 113971 TCGA-AB-2966 AML18 14 105138389 105138389 G A SNP IGHE ENST00000390541 human ensembl 54_36p -1 known missense c.514 p.P172S 0.106 "HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin" "PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin" - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 157 0 96 84 45.65 0 113971 TCGA-AB-2966 AML18 14 105705148 105705148 T A SNP ENSG00000221180 ENST00000408253 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29318 NULL 0 - - - no_errors tier3 306 0 0 264 253 48.75 0 0 0 113971 TCGA-AB-2966 AML18 15 27073830 27073830 G A SNP APBA2 NM_005503.1 human genbank 54_36p 1 reviewed intronic c.1-1418 e1-1418 0.003 - - - no_errors tier3 627 2 0.32 341 275 44.64 0 0 0 113971 TCGA-AB-2966 AML18 15 27545086 27545086 C T SNP - - - - - - - - - - - - - - - tier3 321 1 0.31 281 231 45.12 0 0 NA 113971 TCGA-AB-2966 AML18 15 29332431 29332431 C A SNP LOC283710 XM_211174.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22203 NULL 0.004 - - - no_errors tier3 59 0 0 88 62 41.33 0 0 NA 113971 TCGA-AB-2966 AML18 15 33939452 33939452 A T SNP - - - - - - - - - - - - - - - tier3 372 0 0 542 384 41.47 0 0 NA 113971 TCGA-AB-2966 AML18 15 39297410 39297410 G C SNP EXD1 NM_152596.2 human genbank 54_36p -1 provisional intronic c.29-766 e2-766 0.027 - - - no_errors tier3 760 3 0.39 218 158 42.02 0 0 NA 113971 TCGA-AB-2966 AML18 15 51201903 51201903 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 15 52176933 52176933 G T SNP UNC13C NM_001080534.1 human genbank 54_36p 1 provisional intronic c.2984-45574 e2-45574 0.003 - - - no_errors tier3 645 1 0.15 546 376 40.78 0 0 NA 113971 TCGA-AB-2966 AML18 15 55836918 55836918 C T SNP GCOM1 NM_001018090.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*42749 NULL 0 - - - no_errors tier3 536 3 0.56 354 380 51.77 0 0 NA 113971 TCGA-AB-2966 AML18 15 57303290 57303290 A G SNP MYO1E NM_004998.2 human genbank 54_36p -1 validated intronic c.778-608 e9-608 0 - - - no_errors tier3 572 7 1.21 534 374 41.19 0 1 100 113971 TCGA-AB-2966 AML18 15 60606366 60606366 A C SNP - - - - - - - - - - - - - - - tier3 247 0 0 433 386 47.13 0 0 NA 113971 TCGA-AB-2966 AML18 15 69869011 69869011 T G SNP LOC100132473 XM_001726777.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-33743 NULL 0.009 - - - no_errors tier3 608 3 0.49 423 354 45.56 0 0 NA 113971 TCGA-AB-2966 AML18 15 78457095 78457095 G A SNP ARNT2 NM_014862.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26818 NULL 0 - - - no_errors tier3 340 0 0 197 152 43.3 0 0 NA 113971 TCGA-AB-2966 AML18 15 78807657 78807657 C T SNP FAM108C1 NM_021214.1 human genbank 54_36p 1 validated intronic c.591-21252 e2-21252 0.003 - - - no_errors tier3 535 3 0.56 506 380 42.89 0 0 NA 113971 TCGA-AB-2966 AML18 15 82016262 82016262 G T SNP SH3GL3 NM_003027.3 human genbank 54_36p 1 validated intronic c.70-2747 e2-2747 0.004 - - - no_errors tier3 474 2 0.42 419 284 40.4 0 0 NA 113971 TCGA-AB-2966 AML18 15 84829045 84829045 G T SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.2418-38000 e17-38000 0 - - - no_errors tier3 762 5 0.65 798 533 40.02 0 0 NA 113971 TCGA-AB-2966 AML18 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 121 0 103 75 42.13 181 149 45.15 113971 TCGA-AB-2966 AML18 15 90801301 90801301 G A SNP ST8SIA2 NM_006011.3 human genbank 54_36p 1 reviewed intronic c.843-7033 e6-7033 0 - - - no_errors tier3 235 1 0.42 333 238 41.39 0 0 NA 113971 TCGA-AB-2966 AML18 15 91096872 91096872 A G SNP LOC728619 XM_001127935.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-43009 NULL 0.028 - - - no_errors tier3 451 3 0.66 224 181 44.69 0 0 NA 113971 TCGA-AB-2966 AML18 15 92583171 92583172 - T INS MCTP2 ENST00000357742 human ensembl 54_36p 1 known intronic c.1+6933_6934 e0+6933 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 15 94544754 94544754 C T SNP LOC100132798 XM_001721122.1 human genbank 54_36p -1 model intronic c.368-9127 e3-9127 0.008 - - - no_errors tier3 488 2 0.41 337 251 42.61 0 0 NA 113971 TCGA-AB-2966 AML18 16 4440471 4440471 G A SNP DNAJA3 NM_005147.1 human genbank 54_36p 1 validated silent c.1311 p.T437 0.515 NULL "HMMPfam_DnaJ_CXXCXGXG,superfamily_HSP_DnaJ_cys-rich,HMMPfam_DnaJ,HMMSmart_DnaJ,superfamily_DnaJ_N,HMMPfam_DnaJ_C,superfamily_HSP40_DnaJ_pep,PatternScan_DNAJ_1" - no_errors tier1 142 4 2.74 103 90 46.63 23 17 42.5 113971 TCGA-AB-2966 AML18 16 5006260 5006260 G A SNP SEC14L5 NM_014692.1 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*1288 NULL 0 - - - no_errors tier3 180 0 0 102 82 44.57 0 0 NA 113971 TCGA-AB-2966 AML18 16 6521415 6521415 C A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-123190 e1-123190 0 - - - no_errors tier3 379 0 0 319 225 41.28 0 0 NA 113971 TCGA-AB-2966 AML18 16 6798328 6798328 C T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+153676 e0+153676 0.006 - - - no_errors tier3 1678 4 0.24 534 479 47.29 0 0 NA 113971 TCGA-AB-2966 AML18 16 10648468 10648468 G A SNP TEKT5 NM_144674.1 human genbank 54_36p -1 provisional intronic c.1087-11192 e6-11192 0 - - - no_errors tier3 480 0 0 335 286 46.05 0 0 NA 113971 TCGA-AB-2966 AML18 16 16807203 16807203 C T SNP - - - - - - - - - - - - - - - tier3 1241 8 0.64 453 309 40.45 0 0 NA 113971 TCGA-AB-2966 AML18 16 18760480 18760480 A T SNP SMG1 NM_015092.4 human genbank 54_36p -1 reviewed missense c.6604 p.S2202T 1 "HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,superfamily_Protein kinase-like (PK-like)" "HMMPfam_HEAT,HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_FATC,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_2" - no_errors tier1 1003 15 1.47 265 281 51.09 38 29 43.28 113971 TCGA-AB-2966 AML18 16 26044020 26044020 G A SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.735-10414 e2-10414 0.001 - - - no_errors tier3 715 4 0.56 782 596 43.22 0 0 NA 113971 TCGA-AB-2966 AML18 16 49647306 49647306 C T SNP LOC728654 XM_001128037.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-17166 NULL 0 - - - no_errors tier3 918 0 0 279 277 49.73 0 0 NA 113971 TCGA-AB-2966 AML18 16 50721049 50721049 A G SNP - - - - - - - - - - - - - - - tier3 478 6 1.24 281 237 45.75 0 0 NA 113971 TCGA-AB-2966 AML18 16 51073699 51073699 G A SNP TOX3 NM_001080430.1 human genbank 54_36p -1 provisional intronic c.88-13712 e2-13712 0 - - - no_errors tier3 339 1 0.29 524 327 38.43 0 0 NA 113971 TCGA-AB-2966 AML18 16 52149260 52149260 G A SNP RPGRIP1L NM_015272.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*44229 NULL 0 - - - no_errors tier3 2835 2 0.07 177 155 46.69 0 0 NA 113971 TCGA-AB-2966 AML18 16 57017501 57017501 C T SNP NDRG4 NM_020465.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-61683 NULL 0.025 - - - no_errors tier3 1014 3 0.29 436 349 44.4 0 0 NA 113971 TCGA-AB-2966 AML18 16 61088506 61088506 C T SNP - - - - - - - - - - - - - - - tier3 900 1 0.11 296 227 43.4 0 0 NA 113971 TCGA-AB-2966 AML18 16 63128047 63128047 G A SNP - - - - - - - - - - - - - - - tier3 824 0 0 479 364 43.03 0 0 NA 113971 TCGA-AB-2966 AML18 16 63482454 63482454 C T SNP - - - - - - - - - - - - - - - tier3 779 4 0.51 390 291 42.73 0 0 NA 113971 TCGA-AB-2966 AML18 16 69297321 69297321 G A SNP VAC14 NM_018052.3 human genbank 54_36p -1 validated intronic c.1662-7106 e15-7106 0.001 - - - no_errors tier3 135 0 0 100 82 45.05 4 1 20 113971 TCGA-AB-2966 AML18 16 76490051 76490051 C T SNP VAT1L NM_020927.1 human genbank 54_36p 1 provisional intronic c.1077+13851 e7+13851 0.008 - - - no_errors tier3 148 0 0 74 61 45.19 0 0 NA 113971 TCGA-AB-2966 AML18 16 76502801 76502801 G T SNP VAT1L NM_020927.1 human genbank 54_36p 1 provisional intronic c.1077+26601 e7+26601 0 - - - no_errors tier3 254 7 2.68 290 199 40.7 0 0 NA 113971 TCGA-AB-2966 AML18 16 76732871 76732871 A G SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.410-22710 e5-22710 0.02 - - - no_errors tier3 101 0 0 176 116 39.73 0 0 0 113971 TCGA-AB-2966 AML18 16 79810242 79810242 C T SNP PKD1L2 NM_001076780.1 human genbank 54_36p -1 reviewed intronic c.301+934 e1+934 0.001 - - - no_errors tier3 567 4 0.7 285 243 45.94 0 0 NA 113971 TCGA-AB-2966 AML18 16 83220989 83220989 G A SNP COTL1 NM_021149.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11968 NULL 0.01 - - - no_errors tier3 701 0 0 222 150 40.32 0 0 NA 113971 TCGA-AB-2966 AML18 17 1310220 1310220 G A SNP CRK NM_016823.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4059 NULL 0.037 - - - no_errors tier3 540 0 0 128 66 34.02 0 0 NA 113971 TCGA-AB-2966 AML18 17 9011156 9011156 C A SNP NTN1 NM_004822.2 human genbank 54_36p 1 reviewed intronic c.1207+4113 e2+4113 0.998 - - - no_errors tier3 473 0 0 214 133 38.22 0 1 100 113971 TCGA-AB-2966 AML18 17 11146579 11146579 C T SNP uc002gna.2 ENST00000409168 human ensembl 54_36p 1 known intronic c.799+39011 e2+39011 0 - - - no_errors tier3 2022 11 0.54 513 371 41.97 0 0 NA 113971 TCGA-AB-2966 AML18 17 21928800 21928800 G A SNP ENSG00000222865 ENST00000410933 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16665 NULL 0.004 - - - no_errors tier3 176 2 1.12 243 204 45.64 0 0 NA 113971 TCGA-AB-2966 AML18 17 28604835 28604835 C T SNP ACCN1 NM_183377.4 human genbank 54_36p -1 reviewed intronic c.708+37704 e1+37704 0.016 - - - no_errors tier3 431 1 0.23 421 276 39.54 0 0 NA 113971 TCGA-AB-2966 AML18 17 36206129 36206129 G C SNP KRT28 NM_181535.3 human genbank 54_36p -1 validated intronic c.978+565 e5+565 0.036 - - - no_errors tier3 1085 1 0.09 262 214 44.96 0 0 NA 113971 TCGA-AB-2966 AML18 17 47870281 47870281 T C SNP - - - - - - - - - - - - - - - tier3 1027 4 0.39 572 518 47.44 0 0 NA 113971 TCGA-AB-2966 AML18 17 49105170 49105170 T C SNP - - - - - - - - - - - - - - - tier3 583 18 2.99 514 410 44.28 0 0 NA 113971 TCGA-AB-2966 AML18 17 58175308 58175308 A G SNP MARCH10 NM_001100875.1 human genbank 54_36p -1 validated intronic c.535+161 e4+161 0 - - - no_errors tier3 178 1 0.56 121 86 41.35 0 0 NA 113971 TCGA-AB-2966 AML18 17 59313896 59313896 C T SNP CSH1 ENST00000316193 human ensembl 54_36p -1 known intronic c.654-9465 e6-9465 0.033 - - - no_errors tier3 141 0 0 109 113 50.9 0 0 NA 113971 TCGA-AB-2966 AML18 17 67186132 67186132 T A SNP - - - - - - - - - - - - - - - tier3 669 0 0 512 377 42.41 0 0 NA 113971 TCGA-AB-2966 AML18 18 1356823 1356823 A T SNP C18orf2 ENST00000334697 human ensembl 54_36p -1 known 5_prime_flanking_region c.-93358 NULL 0.362 - - - no_errors tier3 494 1 0.2 306 245 44.46 0 0 NA 113971 TCGA-AB-2966 AML18 18 2463447 2463447 G A SNP LOC100133931 XM_001713654.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*4211 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 685 4 0.58 444 363 44.98 0 0 NA 113971 TCGA-AB-2966 AML18 18 3067421 3067421 C T SNP MYOM1 NM_003803.3 human genbank 54_36p -1 reviewed intronic c.4649-1662 e34-1662 0.003 - - - no_errors tier3 476 2 0.42 223 192 46.27 0 1 100 113971 TCGA-AB-2966 AML18 18 4481521 4481521 G A SNP - - - - - - - - - - - - - - - tier3 216 2 0.92 272 265 49.35 0 0 NA 113971 TCGA-AB-2966 AML18 18 5375045 5375045 G A SNP EPB41L3 NM_012307.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*9637 NULL 0 - - - no_errors tier3 485 6 1.22 368 270 42.19 0 0 NA 113971 TCGA-AB-2966 AML18 18 12714051 12714051 G A SNP PSMG2 NM_020232.3 human genbank 54_36p 1 provisional intronic c.582-447 e6-447 0 - - - no_errors tier3 383 0 0 204 221 52 15 4 21.05 113971 TCGA-AB-2966 AML18 18 17865691 17865691 C A SNP - - - - - - - - - - - - - - - tier3 527 0 0 305 196 39.04 0 0 NA 113971 TCGA-AB-2966 AML18 18 17926653 17926653 T C SNP ENSG00000221363 ENST00000408436 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*37909 NULL 0 - - - no_errors tier3 585 0 0 252 240 48.78 0 0 NA 113971 TCGA-AB-2966 AML18 18 32221288 32221288 G A SNP FHOD3 NM_025135.2 human genbank 54_36p 1 validated intronic c.337+14583 e3+14583 0.014 - - - no_errors tier3 439 0 0 442 175 28.36 0 0 NA 113971 TCGA-AB-2966 AML18 18 33723987 33723987 T C SNP - - - - - - - - - - - - - - - tier3 548 26 4.53 426 334 43.89 0 0 NA 113971 TCGA-AB-2966 AML18 18 38607088 38607088 G T SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional intronic c.427-29405 e5-29405 0.48 - - - no_errors tier3 318 3 0.93 217 138 38.87 0 0 NA 113971 TCGA-AB-2966 AML18 18 39812586 39812586 G C SNP - - - - - - - - - - - - - - - tier3 299 1 0.33 211 181 46.17 0 0 NA 113971 TCGA-AB-2966 AML18 18 45451928 45451928 G A SNP - - - - - - - - - - - - - - - tier3 256 4 1.53 197 175 46.79 0 0 NA 113971 TCGA-AB-2966 AML18 18 47782954 47782954 G A SNP - - - - - - - - - - - - - - - tier3 588 10 1.67 378 266 41.24 0 0 NA 113971 TCGA-AB-2966 AML18 18 52974910 52974910 C T SNP ENSG00000177529 ENST00000324097 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*8081 NULL 0 - - - no_coding_region:pseudogene tier3 832 3 0.36 356 272 43.17 0 0 NA 113971 TCGA-AB-2966 AML18 18 53287492 53287492 G A SNP ONECUT2 NM_004852.2 human genbank 54_36p 1 reviewed intronic c.1229-7175 e2-7175 0 - - - no_errors tier3 182 0 0 230 191 45.05 0 0 NA 113971 TCGA-AB-2966 AML18 18 57477637 57477637 G A SNP - - - - - - - - - - - - - - - tier3 545 14 2.5 311 283 47.48 0 0 NA 113971 TCGA-AB-2966 AML18 18 59923937 59923937 G A SNP C18orf20 ENST00000397982 human ensembl 54_36p -1 known intronic c.1-7083 e1-7083 0 - - - no_errors tier3 1395 3 0.21 340 306 47.37 0 0 NA 113971 TCGA-AB-2966 AML18 18 66199457 66199457 A C SNP ENSG00000214255 ENST00000397939 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48990 NULL 0.113 - - - no_coding_region:pseudogene tier3 167 0 0 126 128 50.39 0 0 NA 113971 TCGA-AB-2966 AML18 18 68044279 68044279 C T SNP - - - - - - - - - - - - - - - tier3 121 0 0 311 258 45.1 0 0 NA 113971 TCGA-AB-2966 AML18 18 74331662 74331662 G C SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-27539 NULL 0.003 - - - no_errors tier3 325 1 0.31 429 392 47.75 0 0 NA 113971 TCGA-AB-2966 AML18 19 7199686 7199686 C T SNP INSR NM_000208.2 human genbank 54_36p -1 reviewed intronic c.652+18670 e2+18670 0 - - - no_errors tier3 230 1 0.43 87 212 70.67 0 1 100 113971 TCGA-AB-2966 AML18 19 10009117 10009117 C T SNP COL5A3 NM_015719.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27056 NULL 0.001 - - - no_errors tier3 245 0 0 271 212 43.71 0 0 NA 113971 TCGA-AB-2966 AML18 19 16198261 16198261 C G SNP AP1M1 NM_032493.1 human genbank 54_36p 1 reviewed missense c.576 p.S192R 0.996 "HMMPfam_Adap_comp_sub,superfamily_Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor" "HMMPfam_Adap_comp_sub,superfamily_Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor,superfamily_SNARE-like,PatternScan_CLAT_ADAPTOR_M_1,PatternScan_CLAT_ADAPTOR_M_2" - no_errors tier1 35 0 77 70 47.62 24 17 41.46 113971 TCGA-AB-2966 AML18 19 22583241 22583241 C T SNP ZNF729 ENST00000357491 human ensembl 54_36p 1 known intronic c.2645-55666 e6-55666 0 - - - no_stop_codon tier3 657 35 5.04 184 166 47.03 0 0 0 113971 TCGA-AB-2966 AML18 19 33325918 33325918 C A SNP - - - - - - - - - - - - - - - tier3 1281 37 2.81 664 506 43.25 0 0 NA 113971 TCGA-AB-2966 AML18 19 34844602 34844602 G A SNP PLEKHF1 NM_024310.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-11985 NULL 0 - - - no_errors tier3 186 0 0 56 20 26.32 0 0 NA 113971 TCGA-AB-2966 AML18 19 40156116 40156116 A C SNP GRAMD1A NM_020895.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27107 NULL 0 - - - no_errors tier3 314 4 1.25 114 89 43.63 0 0 NA 113971 TCGA-AB-2966 AML18 19 43659957 43659957 G A SNP RYR1 NM_000540.2 human genbank 54_36p 1 reviewed intronic c.4294-233 e30-233 0.001 - - - no_errors tier3 395 0 0 331 268 44.74 0 0 NA 113971 TCGA-AB-2966 AML18 19 54215809 54215809 G A SNP CGB5 NM_033043.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23470 NULL 0 - - - no_errors tier3 240 0 0 44 29 39.73 2 0 0 113971 TCGA-AB-2966 AML18 19 56033444 56033444 C A SNP KLK1 NM_002257.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14628 NULL 0 - - - no_errors tier3 203 0 0 122 101 45.09 0 0 NA 113971 TCGA-AB-2966 AML18 20 3385344 3385344 A G SNP ATRN NM_139321.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-14411 NULL 0.124 - - - no_errors tier3 1039 7 0.67 184 156 45.88 0 0 NA 113971 TCGA-AB-2966 AML18 20 3632541 3632541 C T SNP SIGLEC1 NM_023068.3 human genbank 54_36p -1 reviewed missense c.904 p.V302I 0.657 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMPfam_C2-set_2,superfamily_Immunoglobulin" - no_errors tier1 143 0 160 96 37.07 NA 113971 TCGA-AB-2966 AML18 20 6301746 6301746 C T SNP - - - - - - - - - - - - - - - tier3 1029 0 0 441 308 41.01 0 0 NA 113971 TCGA-AB-2966 AML18 20 6411002 6411002 C G SNP - - - - - - - - - - - - - - - tier3 748 0 0 601 474 44.09 0 0 NA 113971 TCGA-AB-2966 AML18 20 14379336 14379336 A T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.272-42789 e4-42789 0.001 - - - no_errors tier3 274 1 0.36 207 165 44.35 0 0 NA 113971 TCGA-AB-2966 AML18 20 24269388 24269388 A C SNP - - - - - - - - - - - - - - - tier3 330 0 0 207 218 51.29 0 0 NA 113971 TCGA-AB-2966 AML18 20 24621463 24621463 G A SNP C20orf39 NM_024893.1 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*27323 NULL 0 - - - no_errors tier3 71 2 2.74 217 195 47.33 0 0 NA 113971 TCGA-AB-2966 AML18 20 32343765 32343765 T C SNP AHCY NM_000687.1 human genbank 54_36p -1 reviewed intronic c.445+60 e4+60 0.005 - - - no_errors tier3 97 1 1.02 51 34 40 0 0 0 113971 TCGA-AB-2966 AML18 20 33696428 33696428 C T SNP CPNE1 NM_003915.4 human genbank 54_36p -1 reviewed intronic c.1+8436 e0+8436 0 - - - no_errors tier3 539 7 1.28 215 183 45.86 1 2 66.67 113971 TCGA-AB-2966 AML18 20 53645877 53645877 C T SNP - - - - - - - - - - - - - - - tier3 308 2 0.65 336 241 41.77 0 0 NA 113971 TCGA-AB-2966 AML18 20 54694314 54694314 C T SNP ENSG00000221416 ENST00000408489 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33035 NULL 0.008 - - - no_errors tier3 554 1 0.18 228 166 41.92 0 0 NA 113971 TCGA-AB-2966 AML18 20 54757892 54757892 G A SNP PTMAP6 ENST00000403622 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47915 NULL 0.003 - - - no_coding_region:pseudogene tier3 579 0 0 131 126 49.03 0 0 NA 113971 TCGA-AB-2966 AML18 20 55263287 55263288 - A INS BMP7 NM_001719.2 human genbank 54_36p -1 reviewed intronic c.418+10880_418+10879 e1+10880 0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 20 56006956 56006956 G A SNP LOC100129869 XM_001723509.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-39154 NULL 0 - - - no_errors tier3 367 2 0.54 255 196 43.36 0 0 NA 113971 TCGA-AB-2966 AML18 20 56184023 56184023 C T SNP C20orf85 NM_178456.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*14739 NULL 0.002 - - - no_errors tier3 727 1 0.14 281 236 45.56 0 0 NA 113971 TCGA-AB-2966 AML18 20 56790664 56790664 A T SNP ENSG00000219697 ENST00000403982 human ensembl 54_36p -1 known intronic c.NULL NULL 0.002 - - - no_coding_region:pseudogene tier3 212 0 0 170 136 44.44 0 0 NA 113971 TCGA-AB-2966 AML18 21 9885112 9885112 A T SNP ENSG00000220964 ENST00000402565 human ensembl 54_36p 1 known 5_prime_flanking_region c.-8878 NULL 0.006 - - - no_coding_region:pseudogene tier3 205 0 0 321 74 18.73 0 0 NA 113971 TCGA-AB-2966 AML18 21 14980959 14980959 C T SNP LOC388813 XM_373925.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-43643 NULL 0 - - - no_errors tier3 445 2 0.45 408 324 44.26 0 0 NA 113971 TCGA-AB-2966 AML18 21 15123653 15123654 - TG INS ENSG00000217388 ENST00000404998 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-15123653 NULL 0.000:0.000 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 113971 TCGA-AB-2966 AML18 21 15551387 15551387 T C SNP - - - - - - - - - - - - - - - tier3 303 0 0 262 228 46.44 0 0 NA 113971 TCGA-AB-2966 AML18 21 16624674 16624674 C T SNP C21orf34 NM_001005734.1 human genbank 54_36p 1 validated intronic c.272-61131 e3-61131 0.07 - - - no_errors tier3 312 2 0.64 389 335 46.27 0 1 100 113971 TCGA-AB-2966 AML18 21 17725817 17725817 G A SNP ENSG00000209722 ENST00000386987 human ensembl 54_36p 1 novel rna NULL NULL 0 - - - pseudogene tier1 303 0 155 142 47.81 NA 113971 TCGA-AB-2966 AML18 21 19458309 19458309 C T SNP - - - - - - - - - - - - - - - tier3 1227 13 1.05 433 381 46.69 0 0 NA 113971 TCGA-AB-2966 AML18 21 20741067 20741067 G A SNP RPS3AP1 ENST00000338576 human ensembl 54_36p -1 known 5_prime_flanking_region c.-16122 NULL 0.005 - - - no_coding_region:pseudogene tier3 347 1 0.29 191 153 44.48 0 0 NA 113971 TCGA-AB-2966 AML18 21 21657433 21657433 T C SNP NCAM2 NM_004540.2 human genbank 54_36p 1 reviewed intronic c.1045-10621 e9-10621 0 - - - no_errors tier3 365 1 0.27 509 365 41.76 0 0 NA 113971 TCGA-AB-2966 AML18 21 25053827 25053827 T C SNP - - - - - - - - - - - - - - - tier3 553 0 0 337 221 39.53 0 0 NA 113971 TCGA-AB-2966 AML18 21 43499982 43499982 T C SNP CRYAA NM_000394.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*34523 NULL 0.001 - - - no_errors tier3 318 4 1.24 38 15 28.3 0 0 0 113971 TCGA-AB-2966 AML18 21 43582314 43582314 G A SNP C21orf136 XM_001722584.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-8400 NULL 0.008 - - - no_errors tier3 81 0 0 35 38 52.05 0 0 0 113971 TCGA-AB-2966 AML18 22 20658852 20658852 A G SNP TOP3B NM_003935.3 human genbank 54_36p -1 reviewed missense c.79 p.S27P 1 "superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00493,HMMPfam_Toprim" "PatternScan_TOPOISOMERASE_I_PROK,superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00436,HMMSmart_SM00437,HMMSmart_SM00493,HMMPfam_Toprim,HMMPfam_Topoisom_bac" - no_errors tier1 123 4 3.15 100 75 42.86 7 18 72 113971 TCGA-AB-2966 AML18 22 21399606 21399606 C T SNP ENSG00000207835 ENST00000385100 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-31579 NULL 0 - - - no_errors tier3 263 0 0 143 108 41.7 0 0 0 113971 TCGA-AB-2966 AML18 22 21822294 21822294 C T SNP RAB36 NM_004914.2 human genbank 54_36p 1 validated silent c.312 p.H104 0.967 NULL "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMSmart_SM00177,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 170 2 1.16 139 115 44.75 NA 113971 TCGA-AB-2966 AML18 22 25851613 25851613 C T SNP - - - - - - - - - - - - - - - tier3 827 6 0.72 362 283 43.88 0 0 NA 113971 TCGA-AB-2966 AML18 22 29904757 29904757 G A SNP RNF185 NM_152267.1 human genbank 54_36p 1 validated intronic c.1-8276 e1-8276 0.02 - - - no_errors tier3 570 3 0.52 170 114 40.14 11 4 26.67 113971 TCGA-AB-2966 AML18 22 31099638 31099638 C A SNP RFPL3S NR_001450.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-2666 NULL 0.023 - - - no_errors tier3 362 0 0 243 186 43.36 3 0 0 113971 TCGA-AB-2966 AML18 22 38902616 38902616 T C SNP TNRC6B NM_001024843.1 human genbank 54_36p 1 validated intronic c.113+20484 e2+20484 0.007 - - - no_errors tier3 463 3 0.64 181 169 48.15 12 7 36.84 113971 TCGA-AB-2966 AML18 22 41353367 41353367 C T SNP CYB5R3 NM_000398.5 human genbank 54_36p -1 reviewed intronic c.548-28 e7-28 0 - - - no_errors tier3 40 0 0 67 39 36.79 4 0 0 113971 TCGA-AB-2966 AML18 22 45686539 45686539 A G SNP TBC1D22A NM_014346.1 human genbank 54_36p 1 provisional intronic c.901-95 e8-95 0 - - - no_errors tier3 802 13 1.6 238 202 45.91 2 0 0 456892 TCGA-AB-2967 AML32 Y 4953459 4953459 T C SNP PCDH11Y NM_032971.1 human genbank 54_36p 1 reviewed intronic c.1-6488 e1-6488 0 - - - no_errors tier3 417 76 15.42 16 251 94.01 0 0 NA 456892 TCGA-AB-2967 AML32 X 5178042 5178042 T C SNP - - - - - - - - - - - - - - - tier3 152 20 11.63 2 45 95.74 0 0 NA 456892 TCGA-AB-2967 AML32 X 5461679 5461679 A G SNP - - - - - - - - - - - - - - - tier3 931 192 17.04 20 632 96.78 0 0 NA 456892 TCGA-AB-2967 AML32 X 7807970 7807970 G T SNP VCX NM_013452.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*35913 NULL 0 - - - no_errors tier3 1248 233 15.71 43 875 95.21 0 0 NA 456892 TCGA-AB-2967 AML32 Y 8747646 8747646 C G SNP TTTY11 NR_001548.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-2223 NULL 0.005 - - - no_errors tier3 789 122 13.36 35 514 93.62 0 0 NA 456892 TCGA-AB-2967 AML32 X 36410932 36410932 G T SNP - - - - - - - - - - - - - - - tier3 443 80 15.27 11 216 95.15 0 0 NA 456892 TCGA-AB-2967 AML32 X 52024334 52024334 G A SNP - - - - - - - - - - - - - - - tier3 400 60 13.04 3 150 98.04 0 0 NA 456892 TCGA-AB-2967 AML32 X 111552825 111552825 G C SNP ZCCHC16 NM_001004308.2 human genbank 54_36p 1 validated intronic c.1-31559 e1-31559 0.001 - - - no_errors tier3 790 144 15.42 21 490 95.7 0 0 NA 456892 TCGA-AB-2967 AML32 1 24517512 24517512 C T SNP GRHL3 ENST00000374413 human ensembl 54_36p 1 known intronic c.9+4253 e1+4253 0 - - - no_start_codon tier3 1500 84 5.3 266 230 46.28 0 0 NA 456892 TCGA-AB-2967 AML32 1 33980022 33980022 C A SNP CSMD2 NM_052896.3 human genbank 54_36p -1 validated intronic c.2053+1446 e14+1446 0 - - - no_errors tier3 1508 116 7.13 609 515 45.74 0 0 NA 456892 TCGA-AB-2967 AML32 1 38691383 38691383 C T SNP - - - - - - - - - - - - - - - tier3 1286 112 8 394 362 47.76 1 0 0 456892 TCGA-AB-2967 AML32 1 39482293 39482293 T C SNP MACF1 NM_012090.3 human genbank 54_36p 1 reviewed intronic c.283-5980 e3-5980 0.005 - - - no_errors tier3 936 73 7.21 136 89 39.38 3 1 25 456892 TCGA-AB-2967 AML32 1 42141518 42141518 T G SNP HIVEP3 NM_024503.1 human genbank 54_36p -1 validated intronic c.1+15153 e0+15153 0 - - - no_errors tier3 1925 159 7.62 392 327 45.29 2 1 33.33 456892 TCGA-AB-2967 AML32 1 55656118 55656118 G A SNP ENSG00000199831 ENST00000362961 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41005 NULL 0.016 - - - no_errors tier3 2998 232 7.17 919 815 46.97 0 0 NA 456892 TCGA-AB-2967 AML32 1 80019996 80019996 C T SNP - - - - - - - - - - - - - - - tier3 615 73 10.52 238 200 45.56 0 0 NA 456892 TCGA-AB-2967 AML32 1 83003582 83003582 C T SNP - - - - - - - - - - - - - - - tier3 1475 113 7.11 316 254 44.56 0 0 NA 456892 TCGA-AB-2967 AML32 1 88776486 88776486 T C SNP ENSG00000218691 ENST00000403718 human ensembl 54_36p 1 known 5_prime_flanking_region c.-39665 NULL 0.478 - - - no_coding_region:pseudogene tier2 1133 83 6.83 340 245 41.88 0 0 NA 456892 TCGA-AB-2967 AML32 1 93576355 93576355 T C SNP LOC100131564 XM_001719527.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*1312 NULL 0.005 - - - no_errors tier3 1503 114 7.02 335 253 43.03 8 15 65.22 456892 TCGA-AB-2967 AML32 1 94800397 94800397 G A SNP F3 NM_001993.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20617 NULL 0.01 - - - no_errors tier3 1231 126 9.26 366 316 46.2 0 0 NA 456892 TCGA-AB-2967 AML32 1 103219300 103219300 T C SNP COL11A1 NM_080629.3 human genbank 54_36p -1 reviewed intronic c.2593-1721 e32-1721 0 - - - no_errors tier3 990 77 7.21 349 282 44.55 0 0 NA 456892 TCGA-AB-2967 AML32 1 106550856 106550856 A T SNP - - - - - - - - - - - - - - - tier3 1149 113 8.93 276 290 51.24 0 0 NA 456892 TCGA-AB-2967 AML32 1 112597131 112597131 G A SNP - - - - - - - - - - - - - - - tier3 1533 123 7.39 353 299 45.79 0 0 NA 456892 TCGA-AB-2967 AML32 1 115060267 115060267 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.38 p.G13D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1990 185 8.49 643 549 45.98 22 3 12 456892 TCGA-AB-2967 AML32 1 116054797 116054797 G A SNP CASQ2 NM_001232.3 human genbank 54_36p -1 reviewed intronic c.839-5361 e9-5361 0 - - - no_errors tier3 643 58 8.22 246 229 47.61 0 0 NA 456892 TCGA-AB-2967 AML32 1 117230468 117230468 A T SNP PTGFRN NM_020440.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-23881 NULL 0.764 - - - no_errors tier3 1302 115 8.08 274 242 46.81 0 0 NA 456892 TCGA-AB-2967 AML32 1 143731189 143731189 G A SNP PDE4DIP NM_022359.2 human genbank 54_36p -1 validated intronic c.289+1280 e2+1280 0.013 - - - no_errors tier3 2920 62 2.08 560 91 13.96 0 2 100 456892 TCGA-AB-2967 AML32 1 150653447 150653447 G A SNP CRNN NM_016190.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2114 NULL 0.733 - - - no_errors tier3 1322 91 6.41 386 282 42.22 0 0 NA 456892 TCGA-AB-2967 AML32 1 150662057 150662057 C T SNP CRNN NM_016190.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-10724 NULL 0.088 - - - no_errors tier3 900 72 7.4 365 274 42.88 0 0 NA 456892 TCGA-AB-2967 AML32 1 154392827 154392828 AG - DEL SEMA4A NM_022367.2 human genbank 54_36p 1 provisional splice_site_del c.140-2_140-1 e2-1 0.852:0.849 - - - no_errors tier1 NA NA NA NA NA NA NA 456892 TCGA-AB-2967 AML32 1 158049865 158049865 A T SNP FCRL6 NM_001004310.2 human genbank 54_36p 1 validated intronic c.1010-38 e7-38 0 - - - no_errors tier3 1895 151 7.33 677 580 45.78 0 0 NA 456892 TCGA-AB-2967 AML32 1 159605971 159605971 A G SNP C1orf192 NM_001013625.2 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-1689 NULL 0.354 - - - no_errors tier3 2105 169 7.43 550 516 48.41 2 0 0 456892 TCGA-AB-2967 AML32 1 166929064 166929064 T C SNP DPT NM_001937.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*3347 NULL 0 - - - no_errors tier3 2155 215 9.04 782 717 47.74 0 0 NA 456892 TCGA-AB-2967 AML32 1 176763336 176763336 A T SNP C1orf49 ENST00000258298 human ensembl 54_36p 1 known intronic c.456+2110 e5+2110 0 - - - no_errors tier3 1942 143 6.81 315 306 49.12 0 0 NA 456892 TCGA-AB-2967 AML32 1 184408197 184408197 A T SNP HMCN1 NM_031935.2 human genbank 54_36p 1 reviewed intronic c.15814+311 e102+311 0.001 - - - no_errors tier3 547 56 9.27 58 65 52.85 0 0 NA 456892 TCGA-AB-2967 AML32 1 190126824 190126824 C G SNP - - - - - - - - - - - - - - - tier3 494 62 11.13 86 89 50.86 0 0 NA 456892 TCGA-AB-2967 AML32 1 197695296 197695296 A G SNP - - - - - - - - - - - - - - - tier3 1288 97 7 360 416 53.61 0 0 NA 456892 TCGA-AB-2967 AML32 1 201671709 201671709 G A SNP PRELP NM_002725.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47227 NULL 0.008 - - - no_errors tier3 273 17 5.86 122 122 50 0 0 NA 456892 TCGA-AB-2967 AML32 1 209943114 209943114 G A SNP NEK2 NM_002497.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-27670 NULL 0.018 - - - no_errors tier3 2636 236 8.19 667 593 46.95 0 0 NA 456892 TCGA-AB-2967 AML32 1 213555317 213555317 G C SNP - - - - - - - - - - - - - - - tier3 1351 91 6.28 542 409 42.69 0 0 NA 456892 TCGA-AB-2967 AML32 1 214664339 214664339 A G SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2038 NULL 0 - - - no_errors tier3 811 80 8.97 220 216 49.54 0 0 NA 456892 TCGA-AB-2967 AML32 1 217906150 217906150 A G SNP LOC728518 XM_001127626.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-41437 NULL 0.045 - - - no_errors tier3 1393 95 6.07 436 381 45.47 0 0 NA 456892 TCGA-AB-2967 AML32 1 229963820 229963820 C T SNP DISC1 NM_018662.1 human genbank 54_36p 1 reviewed intronic c.1269-5689 e5-5689 0.162 - - - no_errors tier3 1156 134 10.37 304 240 44.12 1 4 80 456892 TCGA-AB-2967 AML32 2 15791817 15791817 C T SNP - - - - - - - - - - - - - - - tier3 1113 73 6.11 342 300 46.58 0 0 NA 456892 TCGA-AB-2967 AML32 2 25321667 25321667 C A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed nonsense c.1513 p.E505* 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 664 47 6.57 113 135 54.22 8 7 46.67 456892 TCGA-AB-2967 AML32 2 32921849 32921849 G A SNP TTC27 NM_017735.3 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*22340 NULL 0.002 - - - no_errors tier3 675 57 7.77 99 67 40.36 0 0 NA 456892 TCGA-AB-2967 AML32 2 33634674 33634674 A G SNP RASGRP3 NM_170672.1 human genbank 54_36p 1 validated intronic c.1579+536 e13+536 0.009 - - - no_errors tier3 999 82 7.57 250 210 45.65 3 5 62.5 456892 TCGA-AB-2967 AML32 2 35684463 35684463 C T SNP - - - - - - - - - - - - - - - tier3 1014 93 8.36 284 326 52.41 0 0 NA 456892 TCGA-AB-2967 AML32 2 42471201 42471201 G A SNP COX7A2L NM_004718.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29396 NULL 0 - - - no_errors tier3 1472 135 8.39 449 352 43.78 0 0 NA 456892 TCGA-AB-2967 AML32 2 46973242 46973242 C T SNP TTC7A NM_020458.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-48943 NULL 0 - - - no_errors tier3 2637 212 7.42 650 662 50.19 0 1 100 456892 TCGA-AB-2967 AML32 2 50911344 50911344 A G SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.832+91167 e4+91167 0 - - - no_errors tier3 1229 94 7.08 171 183 51.69 0 0 NA 456892 TCGA-AB-2967 AML32 2 52792767 52792767 G T SNP - - - - - - - - - - - - - - - tier3 1310 95 6.74 272 188 40.87 0 0 NA 456892 TCGA-AB-2967 AML32 2 56651126 56651126 C G SNP - - - - - - - - - - - - - - - tier3 2283 178 7.2 456 364 44.39 0 0 NA 456892 TCGA-AB-2967 AML32 2 68742713 68742713 C T SNP PROKR1 NM_138964.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*6501 NULL 0.017 - - - no_errors tier3 2669 194 6.75 605 520 46.18 0 0 NA 456892 TCGA-AB-2967 AML32 2 79340903 79340903 A G SNP CTNNA2 ENST00000409536 human ensembl 54_36p 1 known intronic c.1-52440 e1-52440 0 - - - no_errors tier3 2196 142 6.05 796 740 48.15 0 0 NA 456892 TCGA-AB-2967 AML32 2 102903269 102903269 T C SNP - - - - - - - - - - - - - - - tier3 1496 114 7.07 401 350 46.54 0 0 NA 456892 TCGA-AB-2967 AML32 2 116812951 116812951 T A SNP - - - - - - - - - - - - - - - tier3 1821 141 7.18 902 762 45.77 0 0 NA 456892 TCGA-AB-2967 AML32 2 117290506 117290506 G T SNP - - - - - - - - - - - - - - - tier3 1556 105 6.31 521 406 43.8 0 0 NA 456892 TCGA-AB-2967 AML32 2 121625026 121625026 G A SNP ENSG00000208508 ENST00000385773 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-39537 NULL 0.003 - - - pseudogene tier3 2147 206 8.71 871 753 46.22 0 0 NA 456892 TCGA-AB-2967 AML32 2 125535700 125535700 T A SNP - - - - - - - - - - - - - - - tier3 1030 98 8.68 230 146 38.83 0 0 NA 456892 TCGA-AB-2967 AML32 2 126426924 126426924 C A SNP - - - - - - - - - - - - - - - tier3 1306 116 8.15 418 438 51.17 0 0 NA 456892 TCGA-AB-2967 AML32 2 126427883 126427883 G A SNP - - - - - - - - - - - - - - - tier3 1006 76 6.92 382 303 43.72 0 0 NA 456892 TCGA-AB-2967 AML32 2 127389295 127389295 G A SNP LOC100128699 XM_001723387.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-32868 NULL 0.004 - - - no_errors tier3 994 115 10.3 288 245 45.88 0 0 NA 456892 TCGA-AB-2967 AML32 2 129206626 129206626 G A SNP - - - - - - - - - - - - - - - tier3 1310 129 8.96 347 319 47.75 0 0 NA 456892 TCGA-AB-2967 AML32 2 148239278 148239278 A T SNP LOC100133235 XM_001724976.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-36608 NULL 0.16 - - - pseudogene tier3 1304 100 7.11 340 319 48.41 0 0 NA 456892 TCGA-AB-2967 AML32 2 154818987 154818987 C T SNP GALNT13 NM_052917.2 human genbank 54_36p 1 validated intronic c.858-4793 e6-4793 0 - - - no_errors tier3 802 66 7.59 208 143 40.74 0 0 NA 456892 TCGA-AB-2967 AML32 2 158138707 158138707 T C SNP ACVR1C NM_145259.1 human genbank 54_36p -1 validated intronic c.304+13238 e2+13238 0 - - - no_errors tier3 1366 145 9.59 376 371 49.47 0 0 NA 456892 TCGA-AB-2967 AML32 2 164525060 164525060 G A SNP - - - - - - - - - - - - - - - tier3 1562 158 9.17 438 370 45.74 0 0 NA 456892 TCGA-AB-2967 AML32 2 173445893 173445893 C T SNP RAPGEF4 NM_007023.1 human genbank 54_36p 1 validated intronic c.445-44883 e5-44883 0.001 - - - no_errors tier3 2030 185 8.33 727 649 47.13 0 0 NA 456892 TCGA-AB-2967 AML32 2 175882397 175882397 T C SNP ENSG00000221347 ENST00000408420 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20950 NULL 0 - - - no_errors tier3 1176 108 8.39 339 230 40.42 0 0 NA 456892 TCGA-AB-2967 AML32 2 180587893 180587893 A T SNP CWC22 NM_020943.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-21580 NULL 0 - - - no_errors tier3 594 51 7.89 97 104 51.74 0 0 NA 456892 TCGA-AB-2967 AML32 2 183463113 183463113 C T SNP FRZB NM_001463.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23588 NULL 0.014 - - - no_errors tier3 1051 94 8.18 177 139 43.99 0 0 NA 456892 TCGA-AB-2967 AML32 2 185073664 185073664 A G SNP - - - - - - - - - - - - - - - tier3 470 44 8.56 53 69 56.56 0 0 NA 456892 TCGA-AB-2967 AML32 2 214578588 214578588 G C SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1401-8332 e13-8332 0.054 - - - no_errors tier3 1911 137 6.68 488 468 48.75 0 0 NA 456892 TCGA-AB-2967 AML32 3 12252728 12252728 C A SNP SYN2 ENST00000341648 human ensembl 54_36p 1 known 3_prime_flanking_region c.*45603 NULL 0 - - - no_errors tier3 712 57 7.4 164 142 46.25 0 0 NA 456892 TCGA-AB-2967 AML32 3 13154962 13154962 G A SNP - - - - - - - - - - - - - - - tier3 595 48 7.4 176 139 43.3 0 0 NA 456892 TCGA-AB-2967 AML32 3 15479581 15479581 C A SNP LOC100128342 XM_001721613.1 human genbank 54_36p -1 model silent c.75 p.V25 0 NULL NULL - no_errors tier1 1812 171 8.59 514 436 45.8 2 0 456892 TCGA-AB-2967 AML32 3 25172429 25172429 A G SNP RARB ENST00000404969 human ensembl 54_36p 1 known 5_prime_flanking_region c.-18464 NULL 0.973 - - - no_errors tier3 1447 144 9.01 369 356 49.04 0 0 NA 456892 TCGA-AB-2967 AML32 3 27110357 27110357 T A SNP NEK10 ENST00000396636 human ensembl 54_36p -1 known 3_prime_flanking_region c.*17410 NULL 0.001 - - - no_errors tier3 1243 90 6.75 427 225 34.51 0 0 NA 456892 TCGA-AB-2967 AML32 3 46549403 46549403 C T SNP LRRC2 NM_024512.3 human genbank 54_36p -1 validated missense c.491 p.G164D 0.998 superfamily_SSF52058 "HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058" - no_errors tier1 1882 143 7.05 327 301 47.93 NA 456892 TCGA-AB-2967 AML32 3 54239850 54239850 G A SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.205-89659 e3-89659 0.037 - - - no_errors tier3 564 47 7.67 101 37 26.81 0 0 NA 456892 TCGA-AB-2967 AML32 3 68356312 68356312 T C SNP FAM19A1 NM_213609.2 human genbank 54_36p 1 reviewed intronic c.119-192808 e2-192808 0.008 - - - no_errors tier3 1136 85 6.94 126 152 54.48 0 0 NA 456892 TCGA-AB-2967 AML32 3 69039161 69039161 A G SNP FAM19A4 NM_001005527.1 human genbank 54_36p -1 reviewed intronic c.1-22010 e1-22010 0.003 - - - no_errors tier3 1639 123 6.96 393 355 47.46 0 0 NA 456892 TCGA-AB-2967 AML32 3 73549287 73549287 G A SNP PDZRN3 NM_015009.1 human genbank 54_36p -1 provisional intronic c.919-13051 e4-13051 0.004 - - - no_errors tier3 1313 116 8.11 485 459 48.57 0 0 NA 456892 TCGA-AB-2967 AML32 3 75473496 75473496 G A SNP LOC728135 XM_001714317.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*37977 NULL 0 - - - no_errors tier3 1234 98 7.34 313 322 50.71 0 0 NA 456892 TCGA-AB-2967 AML32 3 76705944 76705944 G A SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-523911 e2-523911 0 - - - no_stop_codon:overly_large_intron tier3 1378 107 7.2 574 496 46.36 0 0 NA 456892 TCGA-AB-2967 AML32 3 76838713 76838714 - T INS ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-391142_110-391141 e2-391141 0.001:0.000 - - - no_stop_codon:overly_large_intron tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 3 86411898 86411898 C T SNP ENSG00000211149 ENST00000388414 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44634 NULL 0 - - - pseudogene tier3 1553 141 8.31 369 314 45.91 0 0 NA 456892 TCGA-AB-2967 AML32 3 99331139 99331139 A G SNP OR5H1 NM_001005338.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-3093 NULL 0.019 - - - no_errors tier3 919 31 3.26 245 63 20.45 0 0 NA 456892 TCGA-AB-2967 AML32 3 110861736 110861736 G T SNP - - - - - - - - - - - - - - - tier3 2186 158 6.71 969 844 46.5 0 0 NA 456892 TCGA-AB-2967 AML32 3 111749650 111749650 A C SNP ENSG00000221206 ENST00000408279 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*3732 NULL 0.02 - - - no_errors tier3 1246 145 10.41 301 330 52.22 0 0 NA 456892 TCGA-AB-2967 AML32 3 112713840 112713840 A G SNP CD96 NM_198196.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29946 NULL 0.011 - - - no_errors tier3 788 51 6.07 75 70 48.28 0 0 NA 456892 TCGA-AB-2967 AML32 3 124632338 124632338 C A SNP ADCY5 NM_183357.1 human genbank 54_36p -1 validated intronic c.1134+16611 e1+16611 0.001 - - - no_errors tier3 1049 92 8.05 168 144 45.86 0 0 NA 456892 TCGA-AB-2967 AML32 3 128674532 128674532 C T SNP - - - - - - - - - - - - - - - tier3 1255 163 11.43 394 346 46.69 0 0 NA 456892 TCGA-AB-2967 AML32 3 135092202 135092202 C T SNP RAB6B NM_016577.3 human genbank 54_36p -1 validated intronic c.70+4729 e1+4729 0.008 - - - no_errors tier3 1361 116 7.84 221 213 48.85 0 0 0 456892 TCGA-AB-2967 AML32 3 143024068 143024068 G T SNP GRK7 NM_139209.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*5486 NULL 0.002 - - - no_errors tier3 1273 109 7.86 356 302 45.9 0 0 NA 456892 TCGA-AB-2967 AML32 3 155441607 155441607 G A SNP uc003ezv.1 ENST00000356448 human ensembl 54_36p 1 known intronic c.2300+545 e12+545 0 - - - no_errors tier3 1626 170 9.44 589 598 50.38 0 0 NA 456892 TCGA-AB-2967 AML32 3 183025535 183025535 C T SNP ENSG00000199839 ENST00000362969 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2063 NULL 0.006 - - - no_errors tier3 2464 231 8.55 588 578 49.44 0 0 NA 456892 TCGA-AB-2967 AML32 3 183577854 183577854 T A SNP - - - - - - - - - - - - - - - tier3 822 72 8.05 151 122 44.69 0 0 NA 456892 TCGA-AB-2967 AML32 3 194030863 194030863 G A SNP C3orf59 NM_178496.3 human genbank 54_36p -1 validated intronic c.206-30730 e2-30730 0 - - - no_errors tier3 2709 231 7.85 809 628 43.58 0 0 NA 456892 TCGA-AB-2967 AML32 4 7192521 7192521 G A SNP ENSG00000200867 ENST00000363997 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27494 NULL 0.002 - - - no_errors tier3 557 41 6.82 220 282 55.84 0 0 NA 456892 TCGA-AB-2967 AML32 4 17157183 17157183 C T SNP QDPR NM_000320.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-34408 NULL 0 - - - no_errors tier3 1127 118 9.41 304 357 53.6 0 0 NA 456892 TCGA-AB-2967 AML32 4 17851919 17851919 T A SNP - - - - - - - - - - - - - - - tier3 967 77 7.35 182 120 39.47 0 0 NA 456892 TCGA-AB-2967 AML32 4 18091826 18091826 C T SNP - - - - - - - - - - - - - - - tier3 3017 206 6.37 680 484 41.51 0 0 NA 456892 TCGA-AB-2967 AML32 4 23948674 23948674 T C SNP - - - - - - - - - - - - - - - tier3 1586 120 7 387 380 49.48 0 0 NA 456892 TCGA-AB-2967 AML32 4 25182723 25182723 T G SNP - - - - - - - - - - - - - - - tier3 2139 175 7.55 507 449 46.92 0 0 NA 456892 TCGA-AB-2967 AML32 4 25651049 25651049 C A SNP LOC389230 XM_943516.3 human genbank 54_36p 1 model 5_prime_flanking_region c.-38709 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 2982 262 8.06 679 547 44.58 0 0 NA 456892 TCGA-AB-2967 AML32 4 26292881 26292881 T C SNP TBC1D19 NM_018317.2 human genbank 54_36p 1 validated intronic c.817-1514 e12-1514 0.009 - - - no_errors tier3 1159 96 7.65 261 253 49.03 0 0 0 456892 TCGA-AB-2967 AML32 4 27836330 27836330 C T SNP - - - - - - - - - - - - - - - tier3 1396 107 7.1 395 355 47.27 0 0 NA 456892 TCGA-AB-2967 AML32 4 27847773 27847773 A T SNP - - - - - - - - - - - - - - - tier3 1354 129 8.67 111 220 66.07 0 0 NA 456892 TCGA-AB-2967 AML32 4 29213694 29213694 C T SNP - - - - - - - - - - - - - - - tier3 565 40 6.55 73 57 43.85 0 0 NA 456892 TCGA-AB-2967 AML32 4 30088340 30088340 C T SNP - - - - - - - - - - - - - - - tier3 1244 114 8.35 476 355 42.51 0 0 NA 456892 TCGA-AB-2967 AML32 4 30944397 30944397 G A SNP - - - - - - - - - - - - - - - tier3 873 61 6.52 230 138 37.5 0 0 NA 456892 TCGA-AB-2967 AML32 4 32533297 32533297 G T SNP - - - - - - - - - - - - - - - tier3 258 21 7.53 18 19 51.35 0 0 NA 456892 TCGA-AB-2967 AML32 4 43337491 43337491 G T SNP ENSG00000222933 ENST00000411001 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41880 NULL 0 - - - no_errors tier3 1899 169 8.16 657 666 50.3 0 0 NA 456892 TCGA-AB-2967 AML32 4 43995199 43995199 T C SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated intronic c.962-123175 e2-123175 0.02 - - - no_errors tier3 394 32 7.49 59 97 62.18 0 0 NA 456892 TCGA-AB-2967 AML32 4 61515342 61515342 G T SNP - - - - - - - - - - - - - - - tier3 396 28 6.59 28 35 55.56 0 0 NA 456892 TCGA-AB-2967 AML32 4 73944915 73944915 G T SNP - - - - - - - - - - - - - - - tier3 892 68 7.08 368 241 39.57 0 0 NA 456892 TCGA-AB-2967 AML32 4 93932936 93932936 G T SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.244+202476 e2+202476 0 - - - no_errors tier3 900 66 6.83 128 40 23.53 0 0 NA 456892 TCGA-AB-2967 AML32 4 96011173 96011173 C T SNP BMPR1B NM_001203.2 human genbank 54_36p 1 reviewed intronic c.1-4832 e1-4832 0.004 - - - no_errors tier3 958 104 9.58 253 245 46.93 0 0 NA 456892 TCGA-AB-2967 AML32 4 102433320 102433320 A G SNP PPP3CA NM_000944.4 human genbank 54_36p -1 validated intronic c.58+53599 e1+53599 0 - - - no_errors tier3 2022 173 7.87 722 654 47.53 6 6 50 456892 TCGA-AB-2967 AML32 4 113239575 113239575 G A SNP C4orf32 NM_152400.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46611 NULL 0 - - - no_errors tier3 1313 130 9 460 342 42.43 0 0 NA 456892 TCGA-AB-2967 AML32 4 114985129 114985129 G A SNP - - - - - - - - - - - - - - - tier3 2114 157 6.9 815 789 49.13 0 0 NA 456892 TCGA-AB-2967 AML32 4 117160741 117160741 G A SNP - - - - - - - - - - - - - - - tier3 643 49 7.08 224 155 40.79 0 0 NA 456892 TCGA-AB-2967 AML32 4 122338735 122338735 G A SNP TNIP3 NM_024873.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-34005 NULL 0.005 - - - no_errors tier3 538 45 7.72 89 94 51.37 0 0 NA 456892 TCGA-AB-2967 AML32 4 127049089 127049090 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 4 134347745 134347745 C T SNP ENSG00000209007 ENST00000386272 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45274 NULL 0.037 - - - pseudogene tier3 390 32 7.57 80 52 39.1 0 0 NA 456892 TCGA-AB-2967 AML32 4 136873530 136873530 T C SNP - - - - - - - - - - - - - - - tier3 935 69 6.87 229 173 43.03 0 0 NA 456892 TCGA-AB-2967 AML32 4 150218224 150218224 C T SNP - - - - - - - - - - - - - - - tier3 374 34 8.29 150 88 36.82 0 0 NA 456892 TCGA-AB-2967 AML32 4 153019761 153019761 C A SNP - - - - - - - - - - - - - - - tier3 1723 137 7.34 740 711 48.93 0 0 NA 456892 TCGA-AB-2967 AML32 4 162101431 162101432 - A INS ENSG00000221362 ENST00000408435 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*43048 NULL 0.043:0.033 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 4 162413796 162413796 G T SNP - - - - - - - - - - - - - - - tier3 1122 94 7.72 147 124 45.76 0 0 NA 456892 TCGA-AB-2967 AML32 4 166906543 166906543 C T SNP - - - - - - - - - - - - - - - tier3 807 66 7.54 203 178 46.72 0 0 NA 456892 TCGA-AB-2967 AML32 4 172430849 172430849 C T SNP - - - - - - - - - - - - - - - tier3 2386 219 8.4 559 451 44.52 0 0 NA 456892 TCGA-AB-2967 AML32 4 178906616 178906616 T C SNP LOC285501 NM_001085490.1 human genbank 54_36p 1 predicted intronic c.1+15989 e0+15989 0.015 - - - no_errors tier3 717 56 7.23 156 133 46.02 0 0 NA 456892 TCGA-AB-2967 AML32 4 182699750 182699750 C T SNP - - - - - - - - - - - - - - - tier3 2367 220 8.48 786 730 48.12 0 0 NA 456892 TCGA-AB-2967 AML32 4 183348460 183348460 C T SNP ENSG00000177822 ENST00000315302 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47391 NULL 0 - - - no_errors tier3 1858 155 7.68 442 352 44.22 0 0 NA 456892 TCGA-AB-2967 AML32 4 183460608 183460608 G A SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-21560 NULL 0.064 - - - no_errors tier3 1532 149 8.85 348 382 52.26 0 0 NA 456892 TCGA-AB-2967 AML32 4 187462193 187462193 C T SNP KLKB1 NM_000892.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45833 NULL 0 - - - no_errors tier3 1358 150 9.91 265 268 50 0 0 NA 456892 TCGA-AB-2967 AML32 4 190559372 190559372 T C SNP - - - - - - - - - - - - - - - tier3 784 76 8.82 55 118 68.21 0 0 NA 456892 TCGA-AB-2967 AML32 5 2465176 2465176 G A SNP - - - - - - - - - - - - - - - tier3 885 75 7.76 266 197 42.37 0 0 NA 456892 TCGA-AB-2967 AML32 5 5274107 5274107 C T SNP ADAMTS16 NM_139056.2 human genbank 54_36p 1 reviewed intronic c.1606-1795 e11-1795 0.001 - - - no_errors tier3 1035 114 9.9 299 288 48.9 0 0 NA 456892 TCGA-AB-2967 AML32 5 16036245 16036245 G C SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45950 NULL 0 - - - no_errors tier3 2488 193 7.19 906 933 50.65 0 0 NA 456892 TCGA-AB-2967 AML32 5 18135472 18135472 T C SNP - - - - - - - - - - - - - - - tier3 1509 162 9.69 428 478 52.76 0 0 NA 456892 TCGA-AB-2967 AML32 5 26013325 26013325 T C SNP ENSG00000222560 ENST00000410628 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-35430 NULL 0.001 - - - no_errors tier3 706 52 6.84 98 130 57.02 0 0 NA 456892 TCGA-AB-2967 AML32 5 26538155 26538155 C T SNP - - - - - - - - - - - - - - - tier3 946 63 6.24 215 192 47.17 0 0 NA 456892 TCGA-AB-2967 AML32 5 27582492 27582492 C T SNP - - - - - - - - - - - - - - - tier3 1892 189 9.07 510 412 44.49 0 0 NA 456892 TCGA-AB-2967 AML32 5 38203236 38203236 T A SNP - - - - - - - - - - - - - - - tier3 1642 138 7.74 817 704 46.19 0 0 NA 456892 TCGA-AB-2967 AML32 5 38658583 38658583 G A SNP LIFR NM_002310.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-92077 NULL 0.982 - - - no_errors tier3 1083 100 8.44 347 302 46.53 0 0 NA 456892 TCGA-AB-2967 AML32 5 62211019 62211019 G A SNP - - - - - - - - - - - - - - - tier3 1015 69 6.37 327 321 49.38 0 0 NA 456892 TCGA-AB-2967 AML32 5 92673022 92673022 T A SNP LOC391811 XR_016127.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*42876 NULL 0.11 - - - pseudogene tier3 2036 182 8.2 648 740 53.28 0 0 NA 456892 TCGA-AB-2967 AML32 5 113096360 113096360 A G SNP - - - - - - - - - - - - - - - tier3 1378 77 5.29 498 401 44.56 0 0 NA 456892 TCGA-AB-2967 AML32 5 113483343 113483343 G A SNP - - - - - - - - - - - - - - - tier3 1775 155 8.02 654 567 46.4 0 0 NA 456892 TCGA-AB-2967 AML32 5 113954637 113954637 C T SNP - - - - - - - - - - - - - - - tier3 1438 107 6.92 255 225 46.68 0 0 NA 456892 TCGA-AB-2967 AML32 5 122410169 122410169 T A SNP LOC100130882 XM_001715346.1 human genbank 54_36p 1 model intronic c.1285-7888 e8-7888 0 - - - no_errors tier3 953 88 8.37 241 207 46 0 0 NA 456892 TCGA-AB-2967 AML32 5 129639553 129639553 C T SNP - - - - - - - - - - - - - - - tier3 773 48 5.84 265 249 48.26 0 0 NA 456892 TCGA-AB-2967 AML32 5 131362889 131362889 G A SNP ACSL6 NM_001009185.1 human genbank 54_36p -1 validated intronic c.50-5046 e2-5046 0.028 - - - no_errors tier3 1078 80 6.89 229 227 49.78 0 0 NA 456892 TCGA-AB-2967 AML32 5 147683155 147683155 T C SNP SPINK9 NM_001040433.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-12215 NULL 0.047 - - - no_errors tier3 1520 127 7.7 301 363 54.5 0 2 100 456892 TCGA-AB-2967 AML32 5 151219955 151219955 T A SNP GLRA1 NM_000171.3 human genbank 54_36p -1 reviewed intronic c.253-193 e4-193 0.001 - - - no_errors tier3 1390 116 7.68 218 198 47.48 0 0 NA 456892 TCGA-AB-2967 AML32 5 155741020 155741020 C T SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.192+36755 e2+36755 0 - - - no_errors tier3 1233 103 7.7 424 371 46.43 0 0 NA 456892 TCGA-AB-2967 AML32 5 160585847 160585847 A T SNP ENSG00000221002 ENST00000408075 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*3788 NULL 0.07 - - - no_errors tier3 313 26 7.67 29 21 42 0 0 NA 456892 TCGA-AB-2967 AML32 5 163920825 163920825 G A SNP - - - - - - - - - - - - - - - tier3 988 113 10.24 269 368 57.68 0 0 NA 456892 TCGA-AB-2967 AML32 5 164345239 164345239 T A SNP - - - - - - - - - - - - - - - tier3 1265 120 8.62 402 399 49.75 0 0 NA 456892 TCGA-AB-2967 AML32 5 166282411 166282411 C A SNP - - - - - - - - - - - - - - - tier3 638 51 7.36 108 96 47.06 0 0 NA 456892 TCGA-AB-2967 AML32 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 456892 TCGA-AB-2967 AML32 5 173599924 173599924 G A SNP - - - - - - - - - - - - - - - tier3 2173 225 9.35 657 648 49.62 0 0 NA 456892 TCGA-AB-2967 AML32 6 16182161 16182161 G A SNP ENSG00000217585 ENST00000408034 human ensembl 54_36p 1 known 5_prime_flanking_region c.-33671 NULL 0.008 - - - no_coding_region:pseudogene tier3 1433 158 9.92 304 265 46.49 0 0 NA 456892 TCGA-AB-2967 AML32 6 19916719 19916719 G A SNP ID4 NM_001546.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-29246 NULL 0.002 - - - no_errors tier3 1369 107 7.24 208 204 49.28 0 0 NA 456892 TCGA-AB-2967 AML32 6 39565663 39565663 C T SNP KIF6 NM_145027.4 human genbank 54_36p -1 validated intronic c.1645+50094 e13+50094 0.002 - - - no_errors tier3 1129 92 7.51 254 188 42.25 0 0 NA 456892 TCGA-AB-2967 AML32 6 46106474 46106474 T A SNP CLIC5 ENST00000185206 human ensembl 54_36p -1 known intronic c.540+48925 e1+48925 0.009 - - - no_errors tier3 1781 144 7.47 357 364 50.35 0 0 NA 456892 TCGA-AB-2967 AML32 6 46902476 46902476 C A SNP MEP1A NM_005588.2 human genbank 54_36p 1 validated intronic c.928+277 e9+277 0.029 - - - no_errors tier3 1501 170 10.16 421 311 42.43 0 0 NA 456892 TCGA-AB-2967 AML32 6 51575208 51575208 C T SNP PKHD1 NM_138694.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*16630 NULL 0.058 - - - no_errors tier3 1308 111 7.81 257 209 44.85 0 0 NA 456892 TCGA-AB-2967 AML32 6 65276215 65276215 G T SNP - - - - - - - - - - - - - - - tier3 661 65 8.95 208 154 42.42 0 0 NA 456892 TCGA-AB-2967 AML32 6 68276638 68276638 G A SNP ENSG00000201015 ENST00000364145 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36627 NULL 0 - - - no_errors tier3 1483 112 7 467 351 42.86 0 0 NA 456892 TCGA-AB-2967 AML32 6 74646426 74646426 T C SNP ENSG00000221434 ENST00000408507 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*17067 NULL 0.031 - - - no_errors tier3 1758 158 8.24 483 478 49.38 0 0 NA 456892 TCGA-AB-2967 AML32 6 78987056 78987056 G A SNP - - - - - - - - - - - - - - - tier3 1821 146 7.41 614 510 45.37 0 0 NA 456892 TCGA-AB-2967 AML32 6 79721355 79721356 - T INS PHIP NM_017934.5 human genbank 54_36p -1 validated frame_shift_ins c.3948_3947 p.Y1316fs 0.845:0.914 superfamily_Bromodomain "HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain,HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,PatternScan_BROMODOMAIN_1,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 NA NA NA NA NA NA NA 456892 TCGA-AB-2967 AML32 6 81991076 81991076 G A SNP - - - - - - - - - - - - - - - tier3 1769 162 8.39 461 437 48.61 0 0 NA 456892 TCGA-AB-2967 AML32 6 93699089 93699089 C T SNP ENSG00000219387 ENST00000406040 human ensembl 54_36p -1 known 5_prime_flanking_region c.-44069 NULL 0 - - - no_coding_region:pseudogene tier3 1557 149 8.71 491 362 42.39 0 0 NA 456892 TCGA-AB-2967 AML32 6 94383470 94383470 A G SNP - - - - - - - - - - - - - - - tier3 267 36 11.88 16 16 50 0 0 NA 456892 TCGA-AB-2967 AML32 6 99337304 99337304 G T SNP ENSG00000187472 ENST00000340697 human ensembl 54_36p -1 known intronic c.NULL NULL 0.002 - - - no_coding_region:pseudogene tier3 1631 144 8.11 485 404 45.44 0 0 NA 456892 TCGA-AB-2967 AML32 6 99751336 99751336 A G SNP ENSG00000168768 ENST00000305402 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21226 NULL 0.007 - - - no_coding_region:pseudogene tier3 1454 117 7.43 324 313 49.14 0 0 NA 456892 TCGA-AB-2967 AML32 6 100800170 100800170 G A SNP - - - - - - - - - - - - - - - tier3 1293 128 9 342 300 46.73 0 0 NA 456892 TCGA-AB-2967 AML32 6 102108920 102108920 T C SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.116-67597 e2-67597 0 - - - no_errors tier3 1678 139 7.62 497 427 46.11 0 0 NA 456892 TCGA-AB-2967 AML32 6 103910510 103910510 C T SNP - - - - - - - - - - - - - - - tier3 1376 118 7.87 303 285 48.22 0 0 NA 456892 TCGA-AB-2967 AML32 6 110706080 110706080 T C SNP C6orf186 ENST00000338882 human ensembl 54_36p -1 known intronic c.786+20738 e4+20738 0.013 - - - no_errors tier3 2087 168 7.45 613 540 46.67 0 0 NA 456892 TCGA-AB-2967 AML32 6 118223738 118223738 C A SNP - - - - - - - - - - - - - - - tier3 1531 121 7.32 512 527 50.67 0 0 NA 456892 TCGA-AB-2967 AML32 6 121040728 121040728 G A SNP ENSG00000200310 ENST00000363440 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8738 NULL 0.01 - - - no_errors tier3 1178 77 6.13 348 265 43.16 0 0 NA 456892 TCGA-AB-2967 AML32 6 128603594 128603594 A G SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.578-606 e5-606 0.003 - - - no_errors tier3 825 48 5.49 115 108 48.43 0 0 NA 456892 TCGA-AB-2967 AML32 6 134133397 134133397 T A SNP - - - - - - - - - - - - - - - tier3 1229 119 8.81 253 217 46.07 0 0 NA 456892 TCGA-AB-2967 AML32 6 134770592 134770592 G A SNP ENSG00000213118 ENST00000392372 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13861 NULL 0 - - - no_coding_region:pseudogene tier3 899 67 6.92 232 174 42.86 0 0 NA 456892 TCGA-AB-2967 AML32 6 139734576 139734576 T C SNP CITED2 NM_006079.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*1386 NULL 0.974 - - - no_errors tier3 1456 133 8.35 173 159 47.6 0 0 NA 456892 TCGA-AB-2967 AML32 6 140647524 140647524 G A SNP - - - - - - - - - - - - - - - tier3 1416 123 7.98 514 364 41.46 0 0 NA 456892 TCGA-AB-2967 AML32 6 153728662 153728662 A G SNP - - - - - - - - - - - - - - - tier3 723 56 7.18 129 153 54.26 0 0 NA 456892 TCGA-AB-2967 AML32 6 154132076 154132076 T A SNP - - - - - - - - - - - - - - - tier3 520 33 5.96 88 39 30.71 0 0 NA 456892 TCGA-AB-2967 AML32 6 159758969 159758969 C G SNP - - - - - - - - - - - - - - - tier3 2314 157 6.34 322 339 51.21 0 0 NA 456892 TCGA-AB-2967 AML32 6 164639553 164639553 C T SNP LOC728275 XM_001127046.2 human genbank 54_36p 1 model intronic c.545-38438 e3-38438 0 - - - no_errors tier3 1680 125 6.92 598 537 47.23 0 0 NA 456892 TCGA-AB-2967 AML32 7 4147390 4147390 C T SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.4229-4490 e29-4490 0 - - - no_errors tier3 1057 56 5.01 254 207 44.52 0 0 NA 456892 TCGA-AB-2967 AML32 7 9088996 9088996 C G SNP - - - - - - - - - - - - - - - tier3 499 32 6.02 106 67 38.73 0 0 NA 456892 TCGA-AB-2967 AML32 7 14721660 14721660 C A SNP DGKB NM_004080.2 human genbank 54_36p -1 reviewed intronic c.466+3032 e5+3032 0 - - - no_errors tier3 2499 205 7.57 1034 917 46.98 0 0 NA 456892 TCGA-AB-2967 AML32 7 15799623 15799623 C A SNP - - - - - - - - - - - - - - - tier3 967 88 8.33 398 373 48.32 0 0 NA 456892 TCGA-AB-2967 AML32 7 29809179 29809179 C T SNP WIPF3 NM_001080529.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-31687 NULL 0.007 - - - no_errors tier3 1851 178 8.76 232 229 49.67 0 0 NA 456892 TCGA-AB-2967 AML32 7 30615576 30615576 T C SNP GARS NM_002047.2 human genbank 54_36p 1 reviewed intronic c.736-150 e7-150 0.702 - - - no_errors tier3 642 45 6.54 125 136 52.11 2 0 0 456892 TCGA-AB-2967 AML32 7 32283556 32283556 T C SNP PDE1C ENST00000284920 human ensembl 54_36p -1 known intronic c.85+21232 e1+21232 0.069 - - - no_errors tier3 689 95 12.09 133 122 47.47 0 0 NA 456892 TCGA-AB-2967 AML32 7 35063387 35063387 G C SNP DPY19L1 NM_015283.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19354 NULL 0.001 - - - no_errors tier3 1202 198 14.11 286 196 40.58 0 0 0 456892 TCGA-AB-2967 AML32 7 41924601 41924601 G A SNP GLI3 NM_000168.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*45852 NULL 0.002 - - - no_errors tier3 1729 152 8.08 538 457 45.88 0 0 NA 456892 TCGA-AB-2967 AML32 7 42406473 42406473 T C SNP - - - - - - - - - - - - - - - tier3 1001 106 9.56 311 299 48.94 0 0 NA 456892 TCGA-AB-2967 AML32 7 51168252 51168252 C T SNP COBL NM_015198.3 human genbank 54_36p -1 validated intronic c.957+3097 e6+3097 0.003 - - - no_errors tier3 1666 120 6.7 440 419 48.61 0 0 NA 456892 TCGA-AB-2967 AML32 7 51904841 51904841 G C SNP - - - - - - - - - - - - - - - tier3 3734 317 7.82 1497 1323 46.8 0 0 NA 456892 TCGA-AB-2967 AML32 7 72524368 72524368 A G SNP BAZ1B NM_032408.2 human genbank 54_36p -1 reviewed intronic c.2594-1619 e8-1619 0.124 - - - no_errors tier3 1050 98 8.51 229 208 47.49 2 6 75 456892 TCGA-AB-2967 AML32 7 75700596 75700596 G A SNP uc003uer.2 ENST00000388802 human ensembl 54_36p 1 known intronic c.1-1686 e1-1686 0.002 - - - no_stop_codon tier3 2094 181 7.93 355 295 45.25 0 0 NA 456892 TCGA-AB-2967 AML32 7 78251095 78251095 A G SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.419-156604 e3-156604 0.248 - - - no_errors tier3 1649 154 8.53 482 499 50.81 0 0 NA 456892 TCGA-AB-2967 AML32 7 78806251 78806251 C T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.301+114021 e1+114021 0.003 - - - no_errors tier3 1006 69 6.39 144 97 39.92 0 0 NA 456892 TCGA-AB-2967 AML32 7 81072046 81072046 G A SNP LOC100128317 XM_001717593.1 human genbank 54_36p -1 model intronic c.116-6968 e2-6968 0.035 - - - no_errors tier3 2652 234 8.1 758 648 45.99 0 0 NA 456892 TCGA-AB-2967 AML32 7 83023196 83023196 T G SNP SEMA3E NM_012431.1 human genbank 54_36p -1 provisional intronic c.116-65670 e2-65670 0 - - - no_errors tier3 1036 78 6.98 266 239 47.23 0 0 NA 456892 TCGA-AB-2967 AML32 7 90446105 90446105 C A SNP PFTK1 NM_012395.2 human genbank 54_36p 1 validated intronic c.894-5294 e9-5294 0.002 - - - no_errors tier3 749 40 5.07 26 18 40.91 2 0 0 456892 TCGA-AB-2967 AML32 7 91817714 91817714 A G SNP ANKIB1 NM_019004.1 human genbank 54_36p 1 validated intronic c.1086-486 e7-486 0.005 - - - no_errors tier3 1418 143 9.15 361 401 52.62 8 13 61.9 456892 TCGA-AB-2967 AML32 7 94987543 94987543 C T SNP ASB4 NM_016116.1 human genbank 54_36p 1 reviewed intronic c.488-7518 e3-7518 0.039 - - - no_errors tier3 1846 217 10.5 583 462 44.13 0 0 NA 456892 TCGA-AB-2967 AML32 7 96748278 96748278 C T SNP ENSG00000221192 ENST00000408265 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*10484 NULL 0.002 - - - no_errors tier3 2047 193 8.6 843 841 49.85 0 0 NA 456892 TCGA-AB-2967 AML32 7 103854773 103854773 C T SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed intronic c.445+97865 e1+97865 0.001 - - - no_errors tier3 1456 125 7.89 742 718 49.08 0 0 NA 456892 TCGA-AB-2967 AML32 7 112881033 112881033 C A SNP - - - - - - - - - - - - - - - tier3 819 82 9.09 173 117 40.34 0 0 NA 456892 TCGA-AB-2967 AML32 7 116976127 116976127 T C SNP CFTR NM_000492.3 human genbank 54_36p 1 reviewed intronic c.1392+14 e10+14 0.001 - - - no_errors tier3 540 48 8.15 143 121 45.83 0 0 NA 456892 TCGA-AB-2967 AML32 7 153269697 153269697 C T SNP DPP6 ENST00000404039 human ensembl 54_36p 1 known intronic c.51+53945 e1+53945 0 - - - no_errors tier3 1411 133 8.56 270 233 46.14 0 0 NA 456892 TCGA-AB-2967 AML32 7 155436671 155436671 A T SNP LOC389602 XM_001721557.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-11614 NULL 0 - - - no_errors tier3 429 39 8.26 157 109 40.82 0 0 NA 456892 TCGA-AB-2967 AML32 7 156925782 156925782 C A SNP DNAJB6 NM_058246.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*24229 NULL 0.003 - - - no_errors tier3 202 17 7.76 43 46 51.69 0 0 NA 456892 TCGA-AB-2967 AML32 7 157742329 157742329 C A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.278-51603 e4-51603 0.095 - - - no_errors tier3 724 56 7.18 113 85 42.71 0 0 0 456892 TCGA-AB-2967 AML32 8 4715196 4715196 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+124066 e1+124066 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 648 21 3.12 160 21 11.6 0 0 NA 456892 TCGA-AB-2967 AML32 8 4811421 4811421 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+27841 e1+27841 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1788 119 6.21 500 469 48.25 0 0 NA 456892 TCGA-AB-2967 AML32 8 24581526 24581526 A G SNP - - - - - - - - - - - - - - - tier3 1249 116 8.5 374 333 47.03 0 0 NA 456892 TCGA-AB-2967 AML32 8 25480529 25480529 C T SNP - - - - - - - - - - - - - - - tier3 939 76 7.47 285 245 46.05 0 0 NA 456892 TCGA-AB-2967 AML32 8 31292624 31292624 G C SNP - - - - - - - - - - - - - - - tier3 2745 215 7.25 1023 950 47.98 0 0 NA 456892 TCGA-AB-2967 AML32 8 39635946 39635946 A G SNP ADAM18 NM_014237.1 human genbank 54_36p 1 reviewed intronic c.1231-4525 e13-4525 0 - - - no_errors tier3 760 76 9.08 170 131 43.52 0 0 NA 456892 TCGA-AB-2967 AML32 8 49880174 49880174 C T SNP - - - - - - - - - - - - - - - tier3 2818 205 6.76 547 461 45.6 0 0 NA 456892 TCGA-AB-2967 AML32 8 55967334 55967334 T C SNP - - - - - - - - - - - - - - - tier3 1309 101 7.14 211 234 52.58 0 0 NA 456892 TCGA-AB-2967 AML32 8 59297061 59297061 T C SNP - - - - - - - - - - - - - - - tier3 1078 92 7.85 392 337 46.1 0 0 NA 456892 TCGA-AB-2967 AML32 8 59951138 59951138 A T SNP TOX NM_014729.2 human genbank 54_36p -1 validated intronic c.412-24220 e4-24220 0.073 - - - no_errors tier3 934 91 8.87 120 165 57.69 2 0 0 456892 TCGA-AB-2967 AML32 8 69267822 69267822 A G SNP PREX2 NM_024870.2 human genbank 54_36p 1 validated intronic c.4604+508 e37+508 0.001 - - - no_errors tier3 985 75 7.06 303 278 47.85 0 0 NA 456892 TCGA-AB-2967 AML32 8 73640018 73640018 G A SNP KCNB2 NM_004770.2 human genbank 54_36p 1 reviewed intronic c.1-2413 e1-2413 0.07 - - - no_errors tier3 943 60 5.98 175 140 44.44 0 0 NA 456892 TCGA-AB-2967 AML32 8 79008003 79008003 A G SNP - - - - - - - - - - - - - - - tier3 516 35 6.34 41 57 58.16 0 0 NA 456892 TCGA-AB-2967 AML32 8 94591009 94591009 C T SNP LOC100129242 XM_001717187.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13877 NULL 0.002 - - - no_errors tier3 2238 147 6.16 269 316 54.02 0 0 NA 456892 TCGA-AB-2967 AML32 8 98789040 98789040 A T SNP MTDH NM_178812.3 human genbank 54_36p 1 validated intronic c.1272+886 e8+886 0 - - - no_errors tier3 1617 141 8 443 376 45.91 4 5 55.56 456892 TCGA-AB-2967 AML32 8 102501178 102501178 G T SNP ENSG00000222841 ENST00000410909 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-21841 NULL 0.004 - - - no_errors tier3 1601 136 7.81 522 424 44.77 0 0 NA 456892 TCGA-AB-2967 AML32 8 112691213 112691213 C T SNP - - - - - - - - - - - - - - - tier3 1556 117 6.96 595 500 45.45 0 0 NA 456892 TCGA-AB-2967 AML32 8 115464393 115464393 C T SNP - - - - - - - - - - - - - - - tier3 858 88 9.28 200 166 45.23 0 0 NA 456892 TCGA-AB-2967 AML32 8 117937673 117937674 - G INS RAD21 NM_006265.2 human genbank 54_36p -1 reviewed frame_shift_ins c.850_849 p.V283fs 1.000:0.980 NULL "HMMPfam_Rad21_Rec8,HMMPfam_Rad21_Rec8_N" - no_errors tier1 NA NA NA NA NA NA NA 456892 TCGA-AB-2967 AML32 8 131004369 131004369 A C SNP FAM49B NM_016623.3 human genbank 54_36p -1 predicted intronic c.1+16667 e0+16667 0.058 - - - no_errors tier3 345 50 12.63 66 66 50 0 6 100 456892 TCGA-AB-2967 AML32 8 132482856 132482856 T C SNP - - - - - - - - - - - - - - - tier3 2138 184 7.9 485 508 51.06 0 0 NA 456892 TCGA-AB-2967 AML32 8 132506477 132506477 G A SNP - - - - - - - - - - - - - - - tier3 1643 110 6.26 467 380 44.71 0 0 NA 456892 TCGA-AB-2967 AML32 8 135542118 135542118 G A SNP ZFAT NM_020863.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*17789 NULL 0 - - - no_errors tier3 4142 348 7.73 870 646 42.53 0 1 100 456892 TCGA-AB-2967 AML32 8 136673116 136673116 T C SNP KHDRBS3 NM_006558.1 human genbank 54_36p 1 provisional intronic c.807+9618 e6+9618 0.001 - - - no_errors tier3 635 66 9.39 198 181 47.63 0 0 NA 456892 TCGA-AB-2967 AML32 8 141744290 141744290 G A SNP PTK2 NM_005607.3 human genbank 54_36p -1 reviewed intronic c.2932-12 e30-12 0.882 - - - no_errors tier3 1705 135 7.32 508 341 40.07 0 0 0 456892 TCGA-AB-2967 AML32 9 2412384 2412384 G A SNP - - - - - - - - - - - - - - - tier3 2012 208 9.35 487 474 49.32 0 0 NA 456892 TCGA-AB-2967 AML32 9 8339765 8339765 C T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.4662-7787 e29-7787 0.093 - - - no_errors tier3 1034 86 7.64 326 290 47 0 0 NA 456892 TCGA-AB-2967 AML32 9 13182093 13182093 T A SNP MPDZ NM_003829.3 human genbank 54_36p -1 validated intronic c.1968+37 e14+37 0.001 - - - no_errors tier3 1276 116 8.3 403 339 45.69 0 0 NA 456892 TCGA-AB-2967 AML32 9 23753432 23753432 T A SNP ELAVL2 NM_004432.2 human genbank 54_36p -1 validated intronic c.1-1185 e1-1185 0.001 - - - no_errors tier3 1701 139 7.54 560 520 48.15 0 0 NA 456892 TCGA-AB-2967 AML32 9 26133784 26133784 G T SNP ENSG00000196478 ENST00000359978 human ensembl 54_36p 1 known 3_prime_flanking_region c.*26931 NULL 0.015 - - - no_errors tier3 867 80 8.44 220 202 47.87 0 0 NA 456892 TCGA-AB-2967 AML32 9 26284948 26284948 C G SNP - - - - - - - - - - - - - - - tier3 2651 194 6.81 881 738 45.56 0 0 NA 456892 TCGA-AB-2967 AML32 9 26614832 26614832 C T SNP - - - - - - - - - - - - - - - tier3 1463 133 8.31 507 503 49.75 0 0 NA 456892 TCGA-AB-2967 AML32 9 36869765 36869765 T C SNP PAX5 NM_016734.1 human genbank 54_36p -1 reviewed intronic c.1012+2236 e8+2236 0 - - - no_errors tier3 1691 116 6.39 434 390 47.27 0 0 0 456892 TCGA-AB-2967 AML32 9 72577690 72577690 T - DEL TRPM3 NM_001007471.1 human genbank 54_36p -1 reviewed intronic c.1148+11151 e7+11151 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 9 99571882 99571882 C T SNP - - - - - - - - - - - - - - - tier3 1931 146 7.02 409 364 47.09 0 0 NA 456892 TCGA-AB-2967 AML32 9 120206988 120206988 C T SNP - - - - - - - - - - - - - - - tier3 465 40 7.89 60 49 44.95 0 0 NA 456892 TCGA-AB-2967 AML32 9 120765603 120765603 C T SNP - - - - - - - - - - - - - - - tier3 2289 513 18.28 367 370 50.14 0 0 NA 456892 TCGA-AB-2967 AML32 9 120958466 120958466 C A SNP DBC1 NM_014618.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*10717 NULL 0 - - - no_errors tier3 2811 296 9.52 810 720 47 0 0 NA 456892 TCGA-AB-2967 AML32 9 126097524 126097524 G T SNP NEK6 NM_014397.1 human genbank 54_36p 1 validated intronic c.1-6512 e1-6512 0.001 - - - no_errors tier3 524 66 11.13 99 103 50.99 1 0 0 456892 TCGA-AB-2967 AML32 9 132252039 132252039 T G SNP HMCN2 ENST00000277491 human ensembl 54_36p 1 known intronic c.103+307 e2+307 0.001 - - - no_errors tier3 460 50 9.77 78 80 50.63 0 0 NA 456892 TCGA-AB-2967 AML32 9 134673001 134673001 C T SNP C9orf98 NM_152572.2 human genbank 54_36p -1 validated intronic c.979+6845 e10+6845 0 - - - no_errors tier3 675 45 6.21 148 83 35.93 0 0 NA 456892 TCGA-AB-2967 AML32 9 137287970 137287970 G A SNP - - - - - - - - - - - - - - - tier3 651 65 9.04 110 114 50.44 0 0 NA 456892 TCGA-AB-2967 AML32 9 138890887 138890887 C T SNP TRAF2 NM_021138.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-22127 NULL 0 - - - no_errors tier3 536 58 9.75 29 22 43.14 0 0 NA 456892 TCGA-AB-2967 AML32 10 11621719 11621719 A G SNP USP6NL ENST00000277575 human ensembl 54_36p -1 known intronic c.5-12147 e2-12147 0.058 - - - no_errors tier3 1180 103 8.01 337 351 51.02 0 8 100 456892 TCGA-AB-2967 AML32 10 14316928 14316928 A G SNP FRMD4A NM_018027.3 human genbank 54_36p -1 validated intronic c.45+95135 e1+95135 0 - - - no_errors tier3 1771 138 7.21 453 477 51.18 0 0 NA 456892 TCGA-AB-2967 AML32 10 20831795 20831795 G A SNP - - - - - - - - - - - - - - - tier3 1190 84 6.57 325 220 40.22 0 0 NA 456892 TCGA-AB-2967 AML32 10 35480843 35480843 G A SNP CREM NM_181571.2 human genbank 54_36p 1 reviewed intronic c.168+3418 e2+3418 0 - - - no_errors tier3 1575 133 7.78 379 319 45.64 8 0 0 456892 TCGA-AB-2967 AML32 10 38154289 38154289 T A SNP ZNF248 ENST00000395874 human ensembl 54_36p -1 known intronic c.330+7670 e4+7670 0.011 - - - no_errors tier3 501 37 6.85 26 28 51.85 3 0 0 456892 TCGA-AB-2967 AML32 10 44571740 44571740 G T SNP - - - - - - - - - - - - - - - tier3 462 36 7.2 183 144 44.04 0 0 NA 456892 TCGA-AB-2967 AML32 10 44661501 44661501 C A SNP LOC100133769 XM_001719363.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13391 NULL 0.002 - - - no_start_codon:pseudogene tier3 1147 108 8.6 341 349 50.51 0 1 100 456892 TCGA-AB-2967 AML32 10 52398521 52398521 C T SNP PRKG1 NM_001098512.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22624 NULL 0.001 - - - no_errors tier3 912 62 6.35 193 158 44.89 0 0 NA 456892 TCGA-AB-2967 AML32 10 53684119 53684119 T G SNP PRKG1 NM_006258.1 human genbank 54_36p 1 validated intronic c.1173+2687 e10+2687 0.002 - - - no_errors tier3 1089 113 9.4 252 272 51.91 0 0 NA 456892 TCGA-AB-2967 AML32 10 59819459 59819459 T A SNP TFAM NM_003201.1 human genbank 54_36p 1 provisional intronic c.441+874 e4+874 0.001 - - - no_errors tier3 1639 126 7.13 428 448 51.08 1 0 0 456892 TCGA-AB-2967 AML32 10 60216627 60216627 C T SNP BICC1 NM_001080512.1 human genbank 54_36p 1 provisional intronic c.388-62 e5-62 0 - - - no_errors tier3 1000 73 6.8 378 384 50.33 0 0 NA 456892 TCGA-AB-2967 AML32 10 61687573 61687573 A G SNP ANK3 NM_020987.2 human genbank 54_36p -1 reviewed intronic c.798+4050 e7+4050 0.006 - - - no_errors tier3 1489 120 7.45 404 356 46.84 0 0 NA 456892 TCGA-AB-2967 AML32 10 63885120 63885120 C A SNP ZNF365 NM_199451.2 human genbank 54_36p 1 validated intronic c.925-4386 e3-4386 0.662 - - - no_errors tier3 1519 128 7.76 320 304 48.72 0 0 NA 456892 TCGA-AB-2967 AML32 10 93712604 93712604 A G SNP BTAF1 NM_003972.2 human genbank 54_36p 1 validated intronic c.1404+189 e12+189 0 - - - no_errors tier3 1497 139 8.49 545 458 45.48 1 0 0 456892 TCGA-AB-2967 AML32 10 95230605 95230605 C T SNP MYOF NM_013451.3 human genbank 54_36p -1 reviewed intronic c.88+1249 e1+1249 0.04 - - - no_errors tier3 1636 154 8.55 329 314 47.94 0 0 0 456892 TCGA-AB-2967 AML32 10 96146690 96146690 C A SNP TBC1D12 NM_015188.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-5671 NULL 0 - - - no_errors tier3 1123 80 6.64 393 296 42.9 0 0 NA 456892 TCGA-AB-2967 AML32 10 124249364 124249364 A C SNP HTRA1 NM_002775.4 human genbank 54_36p 1 reviewed intronic c.778-6833 e4-6833 0.984 - - - no_errors tier3 1361 134 8.93 362 278 43.23 0 0 NA 456892 TCGA-AB-2967 AML32 10 128830860 128830860 G T SNP C10orf141 NM_001039762.2 human genbank 54_36p -1 validated intronic c.1257-4586 e3-4586 0.001 - - - no_errors tier3 1140 102 8.2 506 380 42.84 0 1 100 456892 TCGA-AB-2967 AML32 10 130572896 130572896 G A SNP LOC728327 XR_041016.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-28197 NULL 0 - - - no_errors tier3 2963 308 9.33 760 722 47.94 0 0 NA 456892 TCGA-AB-2967 AML32 10 133092183 133092183 C T SNP - - - - - - - - - - - - - - - tier3 462 30 6.09 168 199 54.08 0 0 NA 456892 TCGA-AB-2967 AML32 11 3546471 3546471 G C SNP LOC730993 XR_038262.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-17870 NULL 0.551 - - - pseudogene tier3 1444 80 5.23 166 117 41.34 0 0 NA 456892 TCGA-AB-2967 AML32 11 15263688 15263688 G T SNP INSC NM_001031853.3 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*39526 NULL 0.001 - - - no_errors tier3 2577 219 7.81 517 460 47.03 0 0 NA 456892 TCGA-AB-2967 AML32 11 25168408 25168408 G T SNP - - - - - - - - - - - - - - - tier3 1483 133 8.21 412 345 45.57 0 0 NA 456892 TCGA-AB-2967 AML32 11 25840601 25840601 C T SNP - - - - - - - - - - - - - - - tier3 1445 121 7.71 657 606 47.87 0 0 NA 456892 TCGA-AB-2967 AML32 11 26375506 26375506 T C SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated intronic c.47-44535 e2-44535 0.002 - - - no_errors tier3 928 73 7.29 152 146 48.83 0 0 NA 456892 TCGA-AB-2967 AML32 11 30782003 30782003 C T SNP LOC100134181 XM_001717375.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-9478 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 909 62 6.38 242 192 44.24 0 0 NA 456892 TCGA-AB-2967 AML32 11 32884068 32884069 - T INS QSER1 NM_001076786.1 human genbank 54_36p 1 provisional intronic c.1+12612_12613 e0+12612 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 11 33531564 33531564 A G SNP C11orf41 NM_012194.1 human genbank 54_36p 1 validated intronic c.2982+1201 e5+1201 0.022 - - - no_errors tier3 1473 128 7.99 276 257 48.22 0 0 NA 456892 TCGA-AB-2967 AML32 11 33584962 33584962 C A SNP C11orf41 NM_012194.1 human genbank 54_36p 1 validated intronic c.4188+18 e13+18 0.006 - - - no_errors tier3 1793 164 8.34 645 605 48.32 0 0 NA 456892 TCGA-AB-2967 AML32 11 35386212 35386212 G A SNP SLC1A2 NM_004171.3 human genbank 54_36p -1 reviewed intronic c.17+10861 e1+10861 0 - - - no_errors tier3 2466 233 8.6 441 394 47.13 0 0 NA 456892 TCGA-AB-2967 AML32 11 39415792 39415792 A T SNP - - - - - - - - - - - - - - - tier3 1600 56 3.37 669 137 16.98 0 0 NA 456892 TCGA-AB-2967 AML32 11 63666585 63666585 C T SNP MACROD1 NM_014067.3 human genbank 54_36p -1 validated intronic c.517+8702 e3+8702 0.003 - - - no_errors tier3 1167 78 6.26 212 134 38.51 0 3 100 456892 TCGA-AB-2967 AML32 11 91783411 91783411 A G SNP FAT3 NM_001008781.2 human genbank 54_36p 1 validated intronic c.3292+55193 e1+55193 0.004 - - - no_errors tier3 1947 148 7.04 285 297 50.77 0 0 NA 456892 TCGA-AB-2967 AML32 11 96790191 96790191 G A SNP - - - - - - - - - - - - - - - tier3 752 52 6.46 84 32 27.59 0 0 NA 456892 TCGA-AB-2967 AML32 11 101591943 101591943 G A SNP YAP1 NM_006106.1 human genbank 54_36p 1 reviewed intronic c.883-7620 e5-7620 0 - - - no_errors tier3 1206 111 8.4 343 259 43.02 0 0 NA 456892 TCGA-AB-2967 AML32 11 111065457 111065457 G A SNP SIK2 NM_015191.1 human genbank 54_36p 1 validated intronic c.478+1361 e4+1361 0.001 - - - no_errors tier3 2717 183 6.3 750 722 48.95 0 2 100 456892 TCGA-AB-2967 AML32 11 114688192 114688192 G A SNP CADM1 NM_014333.1 human genbank 54_36p -1 validated intronic c.125-71842 e2-71842 0.029 - - - no_errors tier3 1392 92 6.19 328 264 44.52 0 0 NA 456892 TCGA-AB-2967 AML32 11 123945508 123945508 G A SNP OR8A1 NM_001005194.1 human genbank 54_36p 1 provisional missense c.334 p.A112T 0.008 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 2444 217 8.14 844 893 51.38 NA 456892 TCGA-AB-2967 AML32 11 128963468 128963468 G A SNP - - - - - - - - - - - - - - - tier3 2084 180 7.94 421 386 47.83 0 0 NA 456892 TCGA-AB-2967 AML32 11 130326436 130326436 G A SNP SNX19 NM_014758.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35392 NULL 0.001 - - - no_errors tier3 1420 137 8.78 394 368 48.23 0 0 NA 456892 TCGA-AB-2967 AML32 11 130616390 130616390 C T SNP - - - - - - - - - - - - - - - tier3 1778 135 7.03 584 460 43.98 0 0 NA 456892 TCGA-AB-2967 AML32 11 131073001 131073001 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.83-213667 e2-213667 0 - - - no_errors tier3 2030 185 8.33 362 356 49.51 0 0 NA 456892 TCGA-AB-2967 AML32 11 132846809 132846809 C G SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+60560 e1+60560 0.004 - - - no_errors tier3 2123 186 8.04 619 529 46.08 0 0 NA 456892 TCGA-AB-2967 AML32 11 133796689 133796689 C T SNP B3GAT1 NM_018644.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33926 NULL 0 - - - no_errors tier3 1262 94 6.91 153 146 48.67 0 0 NA 456892 TCGA-AB-2967 AML32 12 2770943 2770943 T C SNP FKBP4 NM_002014.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3624 NULL 0.001 - - - no_errors tier3 756 69 8.32 83 80 49.08 0 1 100 456892 TCGA-AB-2967 AML32 12 11936128 11936128 A T SNP ETV6 NM_001987.4 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*881 NULL 0 - - - no_errors tier3 1762 163 8.4 581 569 49.35 23 13 36.11 456892 TCGA-AB-2967 AML32 12 13995122 13995122 A G SNP GRIN2B NM_000834.3 human genbank 54_36p -1 reviewed intronic c.1+29007 e0+29007 0 - - - no_errors tier3 1904 205 9.71 398 406 50.5 0 0 NA 456892 TCGA-AB-2967 AML32 12 16578652 16578652 T A SNP LMO3 NM_001001395.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*16771 NULL 0.584 - - - no_errors tier3 1984 139 6.54 624 421 40.29 0 0 NA 456892 TCGA-AB-2967 AML32 12 23675457 23675457 G A SNP SOX5 NM_006940.4 human genbank 54_36p -1 reviewed intronic c.1017+9556 e8+9556 0.001 - - - no_errors tier3 511 34 6.22 69 79 53.38 0 0 NA 456892 TCGA-AB-2967 AML32 12 23844573 23844573 A G SNP SOX5 NM_006940.4 human genbank 54_36p -1 reviewed intronic c.482-44648 e4-44648 0 - - - no_errors tier3 2351 173 6.84 799 778 49.21 0 0 NA 456892 TCGA-AB-2967 AML32 12 31052011 31052011 G T SNP TSPAN11 NM_001080509.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*15894 NULL 0.043 - - - no_errors tier3 1149 104 8.29 237 251 51.33 0 0 NA 456892 TCGA-AB-2967 AML32 12 31823697 31823697 C A SNP LOC440093 NM_001013699.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*12263 NULL 0.052 - - - no_errors tier3 568 37 6.1 162 183 52.89 0 0 NA 456892 TCGA-AB-2967 AML32 12 57324163 57324163 A T SNP - - - - - - - - - - - - - - - tier3 1281 116 8.27 246 411 62.56 0 0 NA 456892 TCGA-AB-2967 AML32 12 57515670 57515670 C T SNP LRIG3 NM_153377.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*36951 NULL 0 - - - no_errors tier3 1372 108 7.28 449 389 46.31 0 0 NA 456892 TCGA-AB-2967 AML32 12 65124752 65124752 G A SNP GRIP1 NM_021150.2 human genbank 54_36p -1 validated silent c.1410 p.D470 1 "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like" "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like" - no_errors tier1 1289 155 10.72 554 587 51.4 NA 456892 TCGA-AB-2967 AML32 12 76659812 76659812 A T SNP LOC100130271 XM_001719244.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-48903 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 1162 90 7.17 203 183 47.41 0 0 NA 456892 TCGA-AB-2967 AML32 12 84321520 84321520 C T SNP - - - - - - - - - - - - - - - tier3 1717 131 7.07 213 196 47.46 0 0 NA 456892 TCGA-AB-2967 AML32 12 122508549 122508549 T C SNP SNRNP35 NM_180699.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1840 NULL 0 - - - no_errors tier3 374 26 6.45 73 35 32.41 1 0 0 456892 TCGA-AB-2967 AML32 13 33731112 33731112 C T SNP - - - - - - - - - - - - - - - tier3 1676 172 9.28 450 478 51.34 0 0 NA 456892 TCGA-AB-2967 AML32 13 34592977 34592977 A G SNP NBEA NM_015678.3 human genbank 54_36p 1 reviewed intronic c.2243+2366 e16+2366 0.006 - - - no_errors tier3 1077 110 9.27 131 184 58.23 0 0 NA 456892 TCGA-AB-2967 AML32 13 55404058 55404058 C T SNP - - - - - - - - - - - - - - - tier3 1459 107 6.82 498 422 45.82 0 0 NA 456892 TCGA-AB-2967 AML32 13 56383643 56383643 T G SNP ENSG00000201665 ENST00000364795 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-25906 NULL 0 - - - no_errors tier3 437 38 8 96 69 41.57 0 0 NA 456892 TCGA-AB-2967 AML32 13 65249488 65249488 G C SNP ENSG00000181836 ENST00000321014 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*10577 NULL 0 - - - no_coding_region:pseudogene tier3 492 43 8.02 47 43 47.78 0 0 NA 456892 TCGA-AB-2967 AML32 13 72585206 72585206 G A SNP ENSG00000200267 ENST00000363397 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-50 NULL 0.026 - - - no_errors tier3 696 47 6.33 197 180 47.49 0 0 NA 456892 TCGA-AB-2967 AML32 13 72639937 72639937 G A SNP ENSG00000201253 ENST00000364383 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23729 NULL 0 - - - no_errors tier3 785 58 6.87 194 171 46.85 0 0 NA 456892 TCGA-AB-2967 AML32 13 72800072 72800072 G T SNP - - - - - - - - - - - - - - - tier3 1130 98 7.94 303 325 51.75 0 0 NA 456892 TCGA-AB-2967 AML32 13 82313844 82313844 G T SNP ENSG00000216454 ENST00000404510 human ensembl 54_36p 1 known 3_prime_flanking_region c.*17572 NULL 0 - - - no_coding_region:pseudogene tier3 616 47 7.09 91 69 43.12 0 0 NA 456892 TCGA-AB-2967 AML32 13 83133382 83133382 C T SNP - - - - - - - - - - - - - - - tier3 1030 77 6.96 258 216 45.38 0 0 NA 456892 TCGA-AB-2967 AML32 13 89597633 89597633 T G SNP ENSG00000220026 ENST00000403945 human ensembl 54_36p 1 known 5_prime_flanking_region c.-23488 NULL 0 - - - no_coding_region:pseudogene tier3 768 78 9.2 178 173 49.15 0 0 NA 456892 TCGA-AB-2967 AML32 13 94750813 94750813 A T SNP ABCC4 NM_005845.1 human genbank 54_36p -1 reviewed intronic c.74+683 e1+683 0 - - - no_errors tier3 966 74 7.04 142 149 51.2 1 5 83.33 456892 TCGA-AB-2967 AML32 13 105298930 105298930 G A SNP - - - - - - - - - - - - - - - tier3 1006 97 8.79 428 354 45.27 0 0 NA 456892 TCGA-AB-2967 AML32 13 108643416 108643416 T G SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.5349+13434 e33+13434 0.101 - - - no_errors tier3 2268 192 7.79 788 771 49.42 0 0 NA 456892 TCGA-AB-2967 AML32 13 111892062 111892062 G A SNP - - - - - - - - - - - - - - - tier3 1148 31 2.63 484 54 10.02 0 0 NA 456892 TCGA-AB-2967 AML32 14 29969264 29969264 G A SNP - - - - - - - - - - - - - - - tier3 2270 176 7.17 544 575 51.29 0 0 NA 456892 TCGA-AB-2967 AML32 14 40287009 40287009 G A SNP - - - - - - - - - - - - - - - tier3 710 50 6.58 288 247 46.17 0 0 NA 456892 TCGA-AB-2967 AML32 14 42634859 42634859 C T SNP - - - - - - - - - - - - - - - tier3 1626 136 7.71 256 192 42.86 0 0 NA 456892 TCGA-AB-2967 AML32 14 47666718 47666718 T A SNP - - - - - - - - - - - - - - - tier3 418 33 7.3 78 82 51.25 0 0 NA 456892 TCGA-AB-2967 AML32 14 50855682 50855682 T A SNP LOC283553 XR_017924.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-14185 NULL 0.964 - - - no_errors tier3 1535 150 8.88 489 411 45.67 0 0 NA 456892 TCGA-AB-2967 AML32 14 52997653 52997653 G A SNP FAM30A XM_001725525.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-74631 NULL 0.368 - - - no_start_codon:pseudogene:no_stop_codon tier3 2444 168 6.41 872 797 47.67 0 0 NA 456892 TCGA-AB-2967 AML32 14 53239980 53239980 A G SNP - - - - - - - - - - - - - - - tier3 678 58 7.87 122 114 48.31 0 0 NA 456892 TCGA-AB-2967 AML32 14 79636442 79636442 C T SNP - - - - - - - - - - - - - - - tier3 718 55 7.07 277 245 46.93 0 0 NA 456892 TCGA-AB-2967 AML32 14 79797449 79797449 A T SNP DIO2 ENST00000388841 human ensembl 54_36p -1 known 5_prime_flanking_region c.-49881 NULL 0.003 - - - no_errors tier3 1145 104 8.31 224 218 49.32 0 0 NA 456892 TCGA-AB-2967 AML32 14 80639550 80639550 C T SNP TSHR NM_000369.2 human genbank 54_36p 1 reviewed intronic c.615-4922 e8-4922 0.008 - - - no_errors tier3 2595 195 6.97 809 686 45.79 0 0 NA 456892 TCGA-AB-2967 AML32 14 83531897 83531897 G A SNP - - - - - - - - - - - - - - - tier3 1282 101 7.28 411 321 43.67 0 0 NA 456892 TCGA-AB-2967 AML32 14 87240765 87240765 C T SNP LOC730121 XM_001132513.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-49399 NULL 0 - - - no_errors tier3 1266 135 9.59 335 343 50.52 0 0 NA 456892 TCGA-AB-2967 AML32 14 89734332 89734332 G A SNP KCNK13 NM_022054.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*13232 NULL 0.002 - - - no_errors tier3 1730 153 8.1 570 587 50.43 0 0 NA 456892 TCGA-AB-2967 AML32 14 98388611 98388611 G A SNP - - - - - - - - - - - - - - - tier3 1700 143 7.75 368 334 47.58 0 0 NA 456892 TCGA-AB-2967 AML32 14 100827109 100827109 G A SNP - - - - - - - - - - - - - - - tier3 1454 126 7.96 328 309 48.43 0 0 NA 456892 TCGA-AB-2967 AML32 15 24379297 24379297 G A SNP GABRB3 NM_000814.4 human genbank 54_36p -1 reviewed intronic c.544+275 e5+275 0.01 - - - no_errors tier3 1270 124 8.88 393 352 47.18 0 0 NA 456892 TCGA-AB-2967 AML32 15 25294192 25294192 G A SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.575-105199 e6-105199 0 - - - no_errors tier3 2232 205 8.4 859 635 42.5 0 0 NA 456892 TCGA-AB-2967 AML32 15 29843840 29843840 G A SNP - - - - - - - - - - - - - - - tier3 683 81 10.53 96 58 37.66 0 0 NA 456892 TCGA-AB-2967 AML32 15 42018055 42018055 G T SNP FRMD5 NM_032892.3 human genbank 54_36p -1 validated intronic c.103-14256 e2-14256 0 - - - no_errors tier3 1389 110 7.33 288 143 33.1 0 0 NA 456892 TCGA-AB-2967 AML32 15 45636375 45636375 C T SNP ENSG00000221202 ENST00000408275 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4315 NULL 0.323 - - - no_errors tier3 1803 164 8.32 779 652 45.4 0 0 NA 456892 TCGA-AB-2967 AML32 15 46877754 46877754 T C SNP CEP152 NM_014985.2 human genbank 54_36p -1 provisional intronic c.88-214 e2-214 0.001 - - - no_errors tier3 588 81 12.09 63 95 60.13 0 0 0 456892 TCGA-AB-2967 AML32 15 47588046 47588046 A C SNP C15orf33 NM_152647.2 human genbank 54_36p -1 validated intronic c.875-209 e10-209 0.154 - - - no_errors tier3 545 55 9.15 164 237 58.66 0 0 NA 456892 TCGA-AB-2967 AML32 15 48156468 48156469 - CG INS ATP8B4 NM_024837.2 human genbank 54_36p -1 validated intronic c.29-2795_29-2794 e2-2794 0.008:0.010 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 15 76261670 76261670 C A SNP ACSBG1 NM_015162.3 human genbank 54_36p -1 reviewed intronic c.895-128 e8-128 0 - - - no_errors tier3 313 19 5.69 81 58 41.73 0 0 NA 456892 TCGA-AB-2967 AML32 15 78479076 78479076 T A SNP LOC730126 XM_001132539.2 human genbank 54_36p -1 model intronic c.56-1673 e2-1673 0.001 - - - no_errors tier3 1739 149 7.87 253 262 50.87 0 0 NA 456892 TCGA-AB-2967 AML32 15 86058531 86058531 G T SNP - - - - - - - - - - - - - - - tier3 1771 140 7.32 312 316 50.32 0 0 NA 456892 TCGA-AB-2967 AML32 15 96636641 96636641 T C SNP - - - - - - - - - - - - - - - tier3 1526 125 7.56 476 469 49.52 0 0 NA 456892 TCGA-AB-2967 AML32 15 98839019 98839019 C T SNP LASS3 NM_178842.3 human genbank 54_36p -1 validated intronic c.408-1245 e4-1245 0.001 - - - no_errors tier3 1183 101 7.85 418 357 45.95 0 0 NA 456892 TCGA-AB-2967 AML32 15 100187642 100187642 C T SNP OR4F13P ENST00000369688 human ensembl 54_36p 1 known 5_prime_flanking_region c.-18847 NULL 0 - - - no_errors tier3 1091 84 7.11 347 256 42.24 0 0 NA 456892 TCGA-AB-2967 AML32 16 7289262 7289262 A T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.28-218888 e2-218888 0.008 - - - no_errors tier3 1457 104 6.64 291 299 50.68 0 0 NA 456892 TCGA-AB-2967 AML32 16 18649707 18649707 C T SNP - - - - - - - - - - - - - - - tier3 1568 131 7.67 194 141 41.96 0 0 NA 456892 TCGA-AB-2967 AML32 16 21130026 21130026 A C SNP ZP2 NM_003460.1 human genbank 54_36p -1 reviewed intronic c.151+103 e2+103 0 - - - no_errors tier3 1083 97 8.19 358 291 44.77 0 0 NA 456892 TCGA-AB-2967 AML32 16 29944637 29944637 G A SNP FAM57B NM_031478.4 human genbank 54_36p -1 validated nonsense c.451 p.R151* 1 "HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724" "HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724" - no_errors tier1 467 51 9.81 89 77 45.83 1 100 456892 TCGA-AB-2967 AML32 16 34884172 34884172 G A SNP FLJ26245 XM_001718343.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*36882 NULL 0 - - - no_errors tier3 936 87 8.46 225 198 46.81 0 0 NA 456892 TCGA-AB-2967 AML32 16 35003939 35003939 G A SNP ENSG00000221580 ENST00000408653 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*9985 NULL 0.002 - - - no_errors tier3 1721 184 9.64 917 872 48.69 0 0 NA 456892 TCGA-AB-2967 AML32 16 48665510 48665510 G A SNP HEATR3 NM_182922.2 human genbank 54_36p 1 provisional intronic c.622+1384 e5+1384 0.015 - - - no_errors tier3 1480 101 6.37 204 145 41.55 0 0 0 456892 TCGA-AB-2967 AML32 16 50058001 50058001 G A SNP - - - - - - - - - - - - - - - tier3 845 68 7.42 207 185 46.95 0 0 NA 456892 TCGA-AB-2967 AML32 16 50217696 50217696 A G SNP ENSG00000212961 ENST00000406883 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19507 NULL 0.003 - - - no_coding_region:pseudogene tier3 704 60 7.83 86 58 40 0 0 NA 456892 TCGA-AB-2967 AML32 16 59434131 59434131 G A SNP - - - - - - - - - - - - - - - tier3 1927 189 8.92 530 491 48.09 0 0 NA 456892 TCGA-AB-2967 AML32 16 61698620 61698620 C G SNP - - - - - - - - - - - - - - - tier3 1708 108 5.94 382 356 48.11 0 0 NA 456892 TCGA-AB-2967 AML32 16 62108257 62108257 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 16 68963551 68963551 T G SNP DDX19A NM_018332.3 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*161 NULL 0.663 - - - no_errors tier3 651 63 8.71 98 78 44.07 18 19 51.35 456892 TCGA-AB-2967 AML32 16 69431528 69431528 G A SNP HYDIN NM_032821.2 human genbank 54_36p -1 validated missense c.12980 p.A4327V 1 superfamily_PapD-like "superfamily_PapD-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 2183 85 3.74 1603 408 20.28 NA 456892 TCGA-AB-2967 AML32 16 72140010 72140010 T C SNP - - - - - - - - - - - - - - - tier3 830 76 8.39 125 154 54.42 0 0 NA 456892 TCGA-AB-2967 AML32 16 73492111 73492111 G C SNP WDR59 NM_030581.3 human genbank 54_36p -1 validated intronic c.1866+3235 e18+3235 0.176 - - - no_errors tier3 2006 154 7.11 452 394 46.35 0 2 100 456892 TCGA-AB-2967 AML32 16 76129874 76129874 A C SNP - - - - - - - - - - - - - - - tier3 2056 220 9.64 643 511 44.17 0 0 NA 456892 TCGA-AB-2967 AML32 16 78384122 78384122 G C SNP LOC440389 XM_498648.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23543 NULL 0.103 - - - no_errors tier3 561 57 9.16 70 59 45.74 0 0 NA 456892 TCGA-AB-2967 AML32 16 82762142 82762142 G A SNP LRRC50 NM_178452.4 human genbank 54_36p 1 validated intronic c.1528+679 e8+679 0.006 - - - no_errors tier3 879 36 3.93 125 44 26.04 0 0 NA 456892 TCGA-AB-2967 AML32 17 6195595 6195595 C T SNP - - - - - - - - - - - - - - - tier3 1788 157 8.03 437 410 48.18 0 0 NA 456892 TCGA-AB-2967 AML32 17 10395206 10395206 A C SNP MYH1 NM_005963.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-34522 NULL 0.001 - - - no_errors tier3 1972 160 7.49 722 656 47.57 0 0 NA 456892 TCGA-AB-2967 AML32 17 11429448 11429448 C A SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13093 NULL 0 - - - no_errors tier3 1070 99 8.46 228 220 49.11 0 0 NA 456892 TCGA-AB-2967 AML32 17 27905711 27905711 G A SNP MYO1D NM_015194.1 human genbank 54_36p -1 provisional intronic c.2864+50507 e21+50507 0.095 - - - no_errors tier3 985 73 6.89 251 187 42.69 0 0 0 456892 TCGA-AB-2967 AML32 17 28282377 28282377 T G SNP TMEM98 NM_001033504.1 human genbank 54_36p 1 validated intronic c.1-229 e1-229 0.001 - - - no_errors tier3 815 62 7.04 118 95 44.6 0 0 NA 456892 TCGA-AB-2967 AML32 17 37999760 37999760 T C SNP FAM134C NM_178126.3 human genbank 54_36p -1 validated intronic c.240-2054 e2-2054 0 - - - no_errors tier3 1585 101 5.98 355 305 46.07 8 8 50 456892 TCGA-AB-2967 AML32 17 45609700 45609700 G A SNP SAMD14 NM_174920.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-52378 NULL 0 - - - no_errors tier3 1057 68 5.99 147 136 48.06 0 0 NA 456892 TCGA-AB-2967 AML32 17 47085672 47085672 C A SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.561+329 e5+329 0 - - - no_errors tier3 1897 242 11.29 479 437 47.6 0 0 NA 456892 TCGA-AB-2967 AML32 17 48765543 48765543 T C SNP - - - - - - - - - - - - - - - tier3 1997 157 7.28 420 348 45.31 0 0 NA 456892 TCGA-AB-2967 AML32 17 51071603 51071603 T C SNP - - - - - - - - - - - - - - - tier3 1686 163 8.79 406 309 43.16 0 0 NA 456892 TCGA-AB-2967 AML32 17 64003144 64003144 T C SNP PRKAR1A NM_002734.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19992 NULL 0 - - - no_errors tier3 318 17 5.06 105 58 35.58 0 0 NA 456892 TCGA-AB-2967 AML32 17 67420475 67420475 C T SNP - - - - - - - - - - - - - - - tier3 1304 105 7.44 371 291 43.96 0 0 NA 456892 TCGA-AB-2967 AML32 17 67632824 67632824 T C SNP SOX9 NM_000346.3 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*701 NULL 0.818 - - - no_errors tier3 868 71 7.55 72 44 37.93 0 0 NA 456892 TCGA-AB-2967 AML32 17 70899627 70899627 A C SNP GRB2 NM_002086.4 human genbank 54_36p -1 reviewed intronic c.78+1600 e1+1600 0.003 - - - no_errors tier3 873 74 7.79 122 131 51.78 9 12 57.14 456892 TCGA-AB-2967 AML32 17 73311245 73311245 C T SNP LOC100128106 XM_001714985.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*45994 NULL 0.017 - - - no_start_codon tier3 1587 143 8.25 316 301 48.78 0 0 NA 456892 TCGA-AB-2967 AML32 17 76643444 76643444 A T SNP BAIAP2 NM_017451.1 human genbank 54_36p 1 reviewed intronic c.130+1306 e2+1306 0 - - - no_errors tier3 379 30 7.26 113 74 39.36 0 0 0 456892 TCGA-AB-2967 AML32 18 3750573 3750573 G T SNP DLGAP1 NM_004746.1 human genbank 54_36p -1 provisional intronic c.1173-18061 e3-18061 0.131 - - - no_errors tier3 2202 66 2.91 610 205 25.12 0 0 NA 456892 TCGA-AB-2967 AML32 18 4740884 4740884 A T SNP - - - - - - - - - - - - - - - tier3 958 84 8.05 167 252 60 0 0 NA 456892 TCGA-AB-2967 AML32 18 5669852 5669852 C T SNP EPB41L3 ENST00000400111 human ensembl 54_36p -1 known 5_prime_flanking_region c.-49212 NULL 0.007 - - - no_start_codon:no_stop_codon tier3 2305 210 8.34 635 638 50 0 0 NA 456892 TCGA-AB-2967 AML32 18 19898922 19898922 A G SNP TTC39C NM_153211.1 human genbank 54_36p 1 validated intronic c.33+772 e1+772 0.001 - - - no_errors tier3 1328 99 6.91 401 362 47.38 0 0 0 456892 TCGA-AB-2967 AML32 18 22230697 22230697 A T SNP ENSG00000207160 ENST00000384431 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30329 NULL 0.01 - - - no_errors tier3 921 79 7.88 266 244 47.84 0 0 NA 456892 TCGA-AB-2967 AML32 18 23025790 23025790 G A SNP CHST9 NM_031422.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49019 NULL 0 - - - no_errors tier3 1172 104 8.12 141 141 49.82 0 0 NA 456892 TCGA-AB-2967 AML32 18 26694828 26694828 C T SNP - - - - - - - - - - - - - - - tier3 1732 158 8.34 628 511 44.82 0 0 NA 456892 TCGA-AB-2967 AML32 18 39986725 39986725 T C SNP - - - - - - - - - - - - - - - tier3 2791 232 7.66 889 742 45.41 0 0 NA 456892 TCGA-AB-2967 AML32 18 41787346 41787346 G A SNP KIAA1632 NM_020964.2 human genbank 54_36p -1 validated intronic c.1009-739 e3-739 0.021 - - - no_errors tier3 2019 159 7.29 656 531 44.66 4 0 0 456892 TCGA-AB-2967 AML32 18 43231765 43231765 T G SNP - - - - - - - - - - - - - - - tier3 1494 161 9.72 499 471 48.51 0 0 NA 456892 TCGA-AB-2967 AML32 18 44966784 44966784 T C SNP DYM NM_017653.3 human genbank 54_36p -1 reviewed intronic c.1461-22629 e13-22629 0.156 - - - no_errors tier3 1910 148 7.17 297 295 49.66 0 0 0 456892 TCGA-AB-2967 AML32 18 49238954 49238954 T C SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.3393-646 e24-646 0.001 - - - no_errors tier3 1702 158 8.49 558 461 45.11 0 0 NA 456892 TCGA-AB-2967 AML32 18 51068091 51068091 G C SNP TCF4 NM_001083962.1 human genbank 54_36p -1 reviewed intronic c.1350+4635 e14+4635 0.026 - - - no_errors tier3 1392 111 7.37 425 341 44.52 2 1 33.33 456892 TCGA-AB-2967 AML32 18 63188145 63188145 A T SNP - - - - - - - - - - - - - - - tier3 925 79 7.85 171 138 44.52 0 0 NA 456892 TCGA-AB-2967 AML32 18 68160995 68160995 G T SNP - - - - - - - - - - - - - - - tier3 757 54 6.65 141 107 43.15 0 0 NA 456892 TCGA-AB-2967 AML32 18 74728629 74728629 G A SNP - - - - - - - - - - - - - - - tier3 1097 79 6.69 279 234 45.44 0 0 NA 456892 TCGA-AB-2967 AML32 19 48276326 48276326 G A SNP PSG2 NM_031246.2 human genbank 54_36p -1 validated intronic c.430+547 e2+547 0.099 - - - no_errors tier3 1697 160 8.6 545 558 50.45 0 0 NA 456892 TCGA-AB-2967 AML32 19 57441231 57441231 A G SNP ZNF766 NM_001010851.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-23448 NULL 0.004 - - - no_errors tier3 998 98 8.92 81 82 50 0 0 NA 456892 TCGA-AB-2967 AML32 20 1248213 1248213 C T SNP SDCBP2 NM_080489.4 human genbank 54_36p -1 validated intronic c.124+21 e2+21 0 - - - no_errors tier3 1518 135 8.13 413 404 49.15 0 0 NA 456892 TCGA-AB-2967 AML32 20 14971618 14971618 C T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.419-186968 e6-186968 0.004 - - - no_errors tier3 1972 196 9.01 540 525 49.2 0 0 NA 456892 TCGA-AB-2967 AML32 20 17854283 17854283 G A SNP C20orf72 NM_052865.2 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-44220 NULL 0.001 - - - no_errors tier3 1738 154 8.12 631 528 45.36 0 0 NA 456892 TCGA-AB-2967 AML32 20 20565792 20565792 C A SNP C20orf74 NM_020343.2 human genbank 54_36p -1 validated intronic c.805+215 e8+215 0 - - - no_errors tier3 709 62 8.02 130 85 39.53 0 4 100 456892 TCGA-AB-2967 AML32 20 26170706 26170706 G A SNP LOC284801 XM_378973.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-33261 NULL 0 - - - no_errors tier3 845 68 7.44 260 189 42.09 0 0 NA 456892 TCGA-AB-2967 AML32 20 29357123 29357123 G A SNP DEFB116 NM_001037731.1 human genbank 54_36p -1 provisional intronic c.68-2206 e2-2206 0.022 - - - no_errors tier3 1714 160 8.51 547 430 43.88 0 0 NA 456892 TCGA-AB-2967 AML32 20 43250759 43250760 - C INS SEMG2 NM_003008.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32686 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 20 53283185 53283185 G A SNP - - - - - - - - - - - - - - - tier3 493 43 8.02 148 112 42.75 0 0 NA 456892 TCGA-AB-2967 AML32 20 54037824 54037824 A G SNP CBLN4 NM_080617.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25190 NULL 0 - - - no_errors tier3 1204 87 6.73 230 190 45.24 0 0 NA 456892 TCGA-AB-2967 AML32 21 15607462 15607462 A G SNP - - - - - - - - - - - - - - - tier3 971 87 8.22 356 357 50 0 0 NA 456892 TCGA-AB-2967 AML32 21 22273646 22273646 G A SNP - - - - - - - - - - - - - - - tier3 1619 116 6.68 342 309 47.47 0 0 NA 456892 TCGA-AB-2967 AML32 21 24415358 24415358 T C SNP - - - - - - - - - - - - - - - tier3 360 29 7.46 29 43 59.72 0 0 NA 456892 TCGA-AB-2967 AML32 21 24488408 24488408 C T SNP - - - - - - - - - - - - - - - tier3 691 54 7.25 68 58 46.03 0 0 NA 456892 TCGA-AB-2967 AML32 21 27520209 27520209 G A SNP - - - - - - - - - - - - - - - tier3 1117 55 4.68 149 39 20.74 0 0 NA 456892 TCGA-AB-2967 AML32 21 30959250 30959250 G A SNP KRTAP6-1 ENST00000399871 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47483 NULL 0.002 - - - no_stop_codon tier3 1008 99 8.89 331 288 46.45 0 0 NA 456892 TCGA-AB-2967 AML32 21 46223024 46223024 C T SNP COL6A1 NM_001848.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3169 NULL 0 - - - no_errors tier3 925 119 11.37 153 151 49.67 0 0 NA 456892 TCGA-AB-2967 AML32 22 22441861 22441861 G T SNP MMP11 NM_005940.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3197 NULL 0.001 - - - no_errors tier3 680 55 7.45 72 73 50 0 0 NA 456892 TCGA-AB-2967 AML32 22 35425416 35425416 C T SNP CACNG2 NM_006078.2 human genbank 54_36p -1 reviewed intronic c.211+2941 e1+2941 0.011 - - - no_errors tier3 1610 135 7.71 126 104 45.02 0 0 NA 456892 TCGA-AB-2967 AML32 22 47147181 47147181 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 456892 TCGA-AB-2967 AML32 22 47631193 47631193 C T SNP LOC100128946 XM_001725064.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-45412 NULL 0.019 - - - no_errors tier3 433 48 9.94 127 133 50.38 0 0 NA 246634 TCGA-AB-2968 AML23 Y 6652750 6652750 C T SNP ENSG00000216530 ENST00000404954 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5529 NULL 0.001 - - - no_coding_region:pseudogene tier3 189 8 4.06 30 205 87.23 NA NA NA 246634 TCGA-AB-2968 AML23 Y 8838144 8838144 A - DEL ENSG00000173357 ENST00000311828 human ensembl 54_36p 1 novel intronic c.NULL NULL 0.795 - - - no_coding_region:pseudogene tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 Y 12401403 12401403 A C SNP ENSG00000220799 ENST00000403040 human ensembl 54_36p -1 known 3_prime_flanking_region c.*10355 NULL 0 - - - no_coding_region:pseudogene tier3 175 2 1.13 34 42 55.26 NA NA NA 246634 TCGA-AB-2968 AML23 X 19985745 19985745 A G SNP MAP7D2 NM_152780.2 human genbank 54_36p -1 provisional intronic c.373-915 e4-915 0.002 - - - no_errors tier3 158 4 2.47 28 200 87.72 NA NA NA 246634 TCGA-AB-2968 AML23 X 21000932 21000932 C G SNP - - - - - - - - - - - - - - - tier3 375 13 3.35 42 320 88.4 NA NA NA 246634 TCGA-AB-2968 AML23 X 29826184 29826184 G A SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.779-19318 e6-19318 0 - - - no_errors tier3 387 16 3.97 39 196 83.4 NA NA NA 246634 TCGA-AB-2968 AML23 X 36578684 36578684 C T SNP - - - - - - - - - - - - - - - tier3 500 1 0.2 221 49 18.15 NA NA NA 246634 TCGA-AB-2968 AML23 X 39817028 39817029 - G INS BCOR NM_017745.1 human genbank 54_36p -1 reviewed frame_shift_ins c.2515_2514 p.K838fs 0.579:0.203 NULL "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" - no_errors tier1 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 X 52595152 52595152 G C SNP LOC644518 XM_001128777.1 human genbank 54_36p 1 model intronic c.358+1720 e4+1720 0.015 - - - no_errors tier3 211 3 1.4 96 14 12.73 NA NA NA 246634 TCGA-AB-2968 AML23 X 53302205 53302205 G A SNP IQSEC2 NM_015075.1 human genbank 54_36p -1 validated intronic c.123-237 e3-237 0.036 - - - no_errors tier3 176 5 2.76 18 128 87.67 NA NA NA 246634 TCGA-AB-2968 AML23 X 63334024 63334024 A T SNP FAM123B NM_152424.3 human genbank 54_36p -1 validated intronic c.1-4035 e1-4035 0.064 - - - no_errors tier3 326 6 1.81 32 236 88.06 NA NA NA 246634 TCGA-AB-2968 AML23 X 68516259 68516259 G A SNP - - - - - - - - - - - - - - - tier3 331 17 4.89 44 302 87.28 NA NA NA 246634 TCGA-AB-2968 AML23 X 74564024 74564024 G A SNP ZDHHC15 NM_144969.1 human genbank 54_36p -1 provisional intronic c.603+1614 e7+1614 0.001 - - - no_errors tier3 383 9 2.3 108 98 47.57 NA NA NA 246634 TCGA-AB-2968 AML23 X 86763845 86763845 G A SNP KLHL4 NM_057162.4 human genbank 54_36p 1 reviewed intronic c.925-22 e5-22 0.001 - - - no_errors tier3 160 1 0.62 95 98 50.78 NA NA NA 246634 TCGA-AB-2968 AML23 X 102252990 102252990 G A SNP NXF3 NM_022052.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-18383 NULL 0.003 - - - no_errors tier3 206 15 6.79 21 133 86.36 NA NA NA 246634 TCGA-AB-2968 AML23 X 120879022 120879022 T C SNP ENSG00000221217 ENST00000408290 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48531 NULL 0 - - - no_errors tier3 261 4 1.51 26 220 89.43 NA NA NA 246634 TCGA-AB-2968 AML23 X 142721649 142721649 A G SNP ENSG00000216543 ENST00000405023 human ensembl 54_36p 1 known 3_prime_flanking_region c.*4155 NULL 0.268 - - - no_coding_region:pseudogene tier3 270 8 2.88 17 133 88.67 NA NA NA 246634 TCGA-AB-2968 AML23 X 145499492 145499492 G T SNP LOC100128265 XM_001720760.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-8938 NULL 0.005 - - - no_errors tier3 355 9 2.47 25 161 86.56 NA NA NA 246634 TCGA-AB-2968 AML23 X 151085930 151085930 G A SNP MAGEA10 NM_001011543.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31182 NULL 0.003 - - - no_errors tier3 268 4 1.47 29 164 84.97 NA NA NA 246634 TCGA-AB-2968 AML23 1 13805509 13805509 C T SNP PDPN NM_006474.1 human genbank 54_36p 1 reviewed intronic c.296-746 e2-746 0.003 - - - no_errors tier3 632 12 1.86 264 219 45.34 NA NA NA 246634 TCGA-AB-2968 AML23 1 14274673 14274673 A - DEL C1orf196 ENST00000401953 human ensembl 54_36p 1 known intronic c.122-104844 e2-104844 0.001 - - - no_stop_codon tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 1 16916846 16916846 C G SNP ESPNP ENST00000270691 human ensembl 54_36p -1 known intronic c.194+2200 e1+2200 0.011 - - - no_start_codon tier3 169 1 0.59 151 65 30.09 NA NA NA 246634 TCGA-AB-2968 AML23 1 23489861 23489861 A G SNP HNRNPR NM_001102398.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*19673 NULL 0 - - - no_errors tier3 348 7 1.97 114 92 44.66 NA NA NA 246634 TCGA-AB-2968 AML23 1 25282638 25282638 C T SNP ENSG00000172823 ENST00000310210 human ensembl 54_36p -1 known 3_prime_flanking_region c.*41493 NULL 0 - - - no_coding_region:pseudogene tier3 279 2 0.71 176 135 43.41 NA NA NA 246634 TCGA-AB-2968 AML23 1 25982957 25982957 G A SNP MAN1C1 NM_020379.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*90 NULL 0.005 - - - no_errors tier3 191 5 2.54 91 63 40.91 NA NA NA 246634 TCGA-AB-2968 AML23 1 28625808 28625808 T A SNP PHACTR4 NM_001048183.1 human genbank 54_36p 1 reviewed intronic c.16+19247 e1+19247 0 - - - no_errors tier3 179 3 1.65 103 73 41.48 NA NA NA 246634 TCGA-AB-2968 AML23 1 30435919 30435919 G A SNP ENSG00000217351 ENST00000404941 human ensembl 54_36p 1 known 5_prime_flanking_region c.-36038 NULL 0.005 - - - no_coding_region:pseudogene tier3 207 3 1.43 181 132 42.17 NA NA NA 246634 TCGA-AB-2968 AML23 1 43842537 43842537 G T SNP PTPRF NM_002840.3 human genbank 54_36p 1 reviewed intronic c.3037+90 e14+90 0.186 - - - no_errors tier3 347 5 1.42 251 173 40.71 NA NA NA 246634 TCGA-AB-2968 AML23 1 60631987 60631987 G A SNP - - - - - - - - - - - - - - - tier3 315 3 0.94 220 173 44.02 NA NA NA 246634 TCGA-AB-2968 AML23 1 63168834 63168834 G A SNP ENSG00000216534 ENST00000403241 human ensembl 54_36p 1 known 3_prime_flanking_region c.*25093 NULL 0 - - - no_coding_region:pseudogene tier3 409 8 1.91 274 176 39.11 NA NA NA 246634 TCGA-AB-2968 AML23 1 72344728 72344728 G A SNP NEGR1 NM_173808.2 human genbank 54_36p -1 validated intronic c.177-171146 e2-171146 0.002 - - - no_errors tier3 512 7 1.35 179 136 43.17 NA NA NA 246634 TCGA-AB-2968 AML23 1 72788910 72788910 G A SNP - - - - - - - - - - - - - - - tier3 387 11 2.76 146 90 38.14 NA NA NA 246634 TCGA-AB-2968 AML23 1 75577462 75577462 G A SNP SLC44A5 NM_152697.1 human genbank 54_36p -1 validated intronic c.101+393 e3+393 0.385 - - - no_errors tier3 385 6 1.53 220 150 40.54 NA NA NA 246634 TCGA-AB-2968 AML23 1 77299614 77299614 A T SNP ST6GALNAC5 NM_030965.1 human genbank 54_36p 1 provisional intronic c.780-1634 e5-1634 0.677 - - - no_errors tier3 275 4 1.43 267 28 9.49 NA NA NA 246634 TCGA-AB-2968 AML23 1 80528284 80528284 C T SNP ENSG00000218484 ENST00000402916 human ensembl 54_36p 1 known 3_prime_flanking_region c.*6041 NULL 0 - - - no_coding_region:pseudogene tier3 337 8 2.32 226 171 43.07 NA NA NA 246634 TCGA-AB-2968 AML23 1 81726156 81726156 T C SNP LPHN2 ENST00000370725 human ensembl 54_36p 1 known intronic c.1+42794 e0+42794 0 - - - no_errors tier3 328 0 0 125 105 45.65 NA NA NA 246634 TCGA-AB-2968 AML23 1 90867453 90867453 A T SNP ENSG00000199666 ENST00000362796 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-28442 NULL 0.001 - - - no_errors tier3 568 2 0.35 173 89 33.97 NA NA NA 246634 TCGA-AB-2968 AML23 1 96128037 96128037 C T SNP ENSG00000221798 ENST00000408871 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*3267 NULL 1 - - - no_errors tier3 384 7 1.79 242 205 45.86 NA NA NA 246634 TCGA-AB-2968 AML23 1 98078553 98078553 C T SNP DPYD NM_000110.3 human genbank 54_36p -1 reviewed intronic c.151-12213 e3-12213 0 - - - no_errors tier3 262 5 1.87 113 96 45.93 NA NA NA 246634 TCGA-AB-2968 AML23 1 104592298 104592298 G A SNP - - - - - - - - - - - - - - - tier3 349 4 1.13 242 152 38.58 NA NA NA 246634 TCGA-AB-2968 AML23 1 104740294 104740295 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 1 115058051 115058051 T A SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.183 p.Q61H 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 474 3 0.63 336 99 22.6 NA NA NA 246634 TCGA-AB-2968 AML23 1 116036000 116036000 G A SNP VANGL1 NM_138959.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*477 NULL 0 - - - no_errors tier3 341 10 2.85 209 170 44.85 NA NA NA 246634 TCGA-AB-2968 AML23 1 118424534 118424534 A C SNP SPAG17 NM_206996.2 human genbank 54_36p -1 validated intronic c.2209+713 e15+713 0 - - - no_errors tier3 483 11 2.23 262 216 45.19 NA NA NA 246634 TCGA-AB-2968 AML23 1 148323241 148323241 T C SNP VPS45 NM_007259.3 human genbank 54_36p 1 reviewed intronic c.1104+1650 e10+1650 0.001 - - - no_errors tier3 676 11 1.6 214 209 49.41 NA NA NA 246634 TCGA-AB-2968 AML23 1 162938513 162938513 A G SNP PBX1 NM_002585.2 human genbank 54_36p 1 validated intronic c.266-89842 e3-89842 0.333 - - - no_errors tier3 413 6 1.43 178 158 47.02 NA NA NA 246634 TCGA-AB-2968 AML23 1 180392353 180392353 T G SNP LOC100130996 XM_001726581.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*26086 NULL 0 - - - no_errors tier3 386 28 6.76 438 114 20.61 NA NA NA 246634 TCGA-AB-2968 AML23 1 187746138 187746138 C G SNP - - - - - - - - - - - - - - - tier3 569 10 1.73 196 149 43.19 NA NA NA 246634 TCGA-AB-2968 AML23 1 189403423 189403423 T G SNP ENSG00000217637 ENST00000405368 human ensembl 54_36p -1 known 5_prime_flanking_region c.-20709 NULL 0.008 - - - no_coding_region:pseudogene tier3 594 8 1.33 286 212 42.57 NA NA NA 246634 TCGA-AB-2968 AML23 1 189442478 189442478 G A SNP - - - - - - - - - - - - - - - tier3 512 12 2.29 249 155 38.37 NA NA NA 246634 TCGA-AB-2968 AML23 1 192582162 192582162 C T SNP - - - - - - - - - - - - - - - tier3 291 4 1.36 160 112 41.18 NA NA NA 246634 TCGA-AB-2968 AML23 1 193552100 193552100 G T SNP - - - - - - - - - - - - - - - tier3 460 7 1.5 282 231 45.03 NA NA NA 246634 TCGA-AB-2968 AML23 1 206792141 206792141 C A SNP - - - - - - - - - - - - - - - tier3 445 6 1.33 267 186 41.06 NA NA NA 246634 TCGA-AB-2968 AML23 1 206909182 206909182 C T SNP ENSG00000217293 ENST00000401691 human ensembl 54_36p -1 known 3_prime_flanking_region c.*28155 NULL 0.001 - - - no_coding_region:pseudogene tier3 405 4 0.98 206 165 44.47 NA NA NA 246634 TCGA-AB-2968 AML23 1 207390102 207390102 T A SNP ENSG00000219339 ENST00000402858 human ensembl 54_36p 1 known 5_prime_flanking_region c.-22880 NULL 0.189 - - - no_coding_region:pseudogene tier3 415 1 0.24 264 92 25.84 NA NA NA 246634 TCGA-AB-2968 AML23 1 210269112 210269112 T A SNP INTS7 NM_015434.2 human genbank 54_36p -1 provisional intronic c.94+6197 e1+6197 0.003 - - - no_errors tier3 650 15 2.25 259 173 39.95 NA NA NA 246634 TCGA-AB-2968 AML23 1 229609203 229609203 C T SNP EGLN1 NM_022051.1 human genbank 54_36p -1 provisional intronic c.891+14164 e1+14164 0.001 - - - no_errors tier3 313 4 1.26 106 79 42.7 NA NA NA 246634 TCGA-AB-2968 AML23 1 235428225 235428225 G A SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.49-72195 e2-72195 0.001 - - - no_errors tier3 563 16 2.76 266 243 47.74 NA NA NA 246634 TCGA-AB-2968 AML23 1 235848150 235848150 G A SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.5916+741 e38+741 0.005 - - - no_errors tier3 393 4 1.01 268 75 21.87 NA NA NA 246634 TCGA-AB-2968 AML23 1 237058579 237058579 A C SNP ENSG00000218598 ENST00000402695 human ensembl 54_36p -1 known 5_prime_flanking_region c.-49456 NULL 0 - - - no_coding_region:pseudogene tier3 521 19 3.52 281 226 44.58 NA NA NA 246634 TCGA-AB-2968 AML23 1 238342974 238342974 C T SNP FMN2 NM_020066.4 human genbank 54_36p 1 validated intronic c.2045-10128 e2-10128 0.022 - - - no_errors tier3 284 2 0.7 133 107 44.58 NA NA NA 246634 TCGA-AB-2968 AML23 1 239555406 239555406 T C SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.78+30216 e1+30216 0 - - - no_errors tier3 339 5 1.45 172 115 40.07 NA NA NA 246634 TCGA-AB-2968 AML23 1 241110842 241110842 T A SNP - - - - - - - - - - - - - - - tier3 419 1 0.24 183 93 33.7 NA NA NA 246634 TCGA-AB-2968 AML23 1 242464186 242464186 G A SNP - - - - - - - - - - - - - - - tier3 392 15 3.69 223 185 45.34 NA NA NA 246634 TCGA-AB-2968 AML23 1 242608830 242608830 C T SNP C1orf100 NM_001012970.1 human genbank 54_36p 1 predicted intronic c.325+266 e3+266 0.004 - - - no_errors tier3 296 4 1.33 159 39 19.6 NA NA NA 246634 TCGA-AB-2968 AML23 2 2125055 2125055 C T SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.1+30596 e0+30596 0.005 - - - no_errors tier3 366 5 1.34 211 139 39.71 NA NA NA 246634 TCGA-AB-2968 AML23 2 3088864 3088864 G A SNP LOC100132738 XM_001714359.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-42640 NULL 0.001 - - - no_errors tier3 490 2 0.41 325 142 30.41 NA NA NA 246634 TCGA-AB-2968 AML23 2 3288441 3288441 C T SNP TSSC1 NM_003310.2 human genbank 54_36p -1 validated intronic c.259+32354 e3+32354 0.019 - - - no_errors tier3 71 0 0 34 19 35.19 NA NA NA 246634 TCGA-AB-2968 AML23 2 5743273 5743273 T A SNP SOX11 NM_003108.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-7032 NULL 0.002 - - - no_errors tier3 356 6 1.66 62 43 40.95 NA NA NA 246634 TCGA-AB-2968 AML23 2 6346127 6346127 C T SNP LOC100131385 XM_001714229.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*19981 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 536 8 1.47 224 147 39.62 NA NA NA 246634 TCGA-AB-2968 AML23 2 8010217 8010217 C A SNP - - - - - - - - - - - - - - - tier3 356 5 1.39 271 185 40.57 NA NA NA 246634 TCGA-AB-2968 AML23 2 11258279 11258279 T A SNP ROCK2 NM_004850.3 human genbank 54_36p -1 reviewed intronic c.2910+255 e23+255 0.014 - - - no_errors tier3 478 10 2.05 200 166 45.36 NA NA NA 246634 TCGA-AB-2968 AML23 2 11998789 11998789 C T SNP - - - - - - - - - - - - - - - tier3 827 25 2.93 439 335 43.23 NA NA NA 246634 TCGA-AB-2968 AML23 2 14135702 14135702 T A SNP - - - - - - - - - - - - - - - tier3 535 9 1.65 273 192 41.2 NA NA NA 246634 TCGA-AB-2968 AML23 2 14211950 14211950 C A SNP - - - - - - - - - - - - - - - tier3 405 5 1.22 209 114 35.29 NA NA NA 246634 TCGA-AB-2968 AML23 2 17850792 17850792 C A SNP LOC284952 XM_001126137.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-51412 NULL 0.001 - - - no_errors tier3 395 12 2.95 193 137 41.52 NA NA NA 246634 TCGA-AB-2968 AML23 2 21817309 21817309 C T SNP LOC645949 XR_040569.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-19144 NULL 0 - - - no_errors tier3 591 12 1.99 306 235 43.44 NA NA NA 246634 TCGA-AB-2968 AML23 2 22630386 22630386 C A SNP - - - - - - - - - - - - - - - tier3 559 9 1.58 203 133 39.47 NA NA NA 246634 TCGA-AB-2968 AML23 2 25316775 25316775 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2222 p.A741V 1 "HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 212 1 0.47 143 132 47.83 NA NA NA 246634 TCGA-AB-2968 AML23 2 25322533 25322533 C A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed nonsense c.1429 p.E477* 1 NULL "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 179 1 0.56 156 104 40 NA NA NA 246634 TCGA-AB-2968 AML23 2 27574151 27574151 A - DEL GCKR NM_001486.3 human genbank 54_36p 1 reviewed intronic c.285+150 e3+150 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 2 30426198 30426198 G C SNP LBH ENST00000404397 human ensembl 54_36p 1 known 3_prime_flanking_region c.*26292 NULL 0.001 - - - no_errors tier3 250 6 2.34 182 140 43.48 NA NA NA 246634 TCGA-AB-2968 AML23 2 34841718 34841718 C T SNP - - - - - - - - - - - - - - - tier3 488 10 2 268 214 44.4 NA NA NA 246634 TCGA-AB-2968 AML23 2 34851503 34851503 T C SNP - - - - - - - - - - - - - - - tier3 485 14 2.79 227 158 41.04 NA NA NA 246634 TCGA-AB-2968 AML23 2 42796927 42796927 G T SNP MTA3 ENST00000405094 human ensembl 54_36p 1 known intronic c.1526-2705 e15-2705 0.001 - - - no_errors tier3 625 7 1.11 295 193 39.55 NA NA NA 246634 TCGA-AB-2968 AML23 2 47274851 47274851 C T SNP CALM2 NM_001743.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-17765 NULL 0.001 - - - no_errors tier3 262 4 1.5 203 61 23.11 NA NA NA 246634 TCGA-AB-2968 AML23 2 47561612 47561612 G A SNP MSH2 NM_000251.1 human genbank 54_36p 1 reviewed intronic c.2634+98 e15+98 0.001 - - - no_errors tier3 207 2 0.96 96 86 47.25 NA NA NA 246634 TCGA-AB-2968 AML23 2 49520782 49520782 G A SNP - - - - - - - - - - - - - - - tier3 451 10 2.17 217 141 39.39 NA NA NA 246634 TCGA-AB-2968 AML23 2 52754842 52754842 G C SNP ENSG00000218862 ENST00000406417 human ensembl 54_36p 1 known 3_prime_flanking_region c.*44122 NULL 0.002 - - - no_coding_region:pseudogene tier3 653 13 1.95 290 254 46.69 NA NA NA 246634 TCGA-AB-2968 AML23 2 59008826 59008826 C A SNP - - - - - - - - - - - - - - - tier3 362 13 3.47 187 154 45.16 NA NA NA 246634 TCGA-AB-2968 AML23 2 61150404 61150404 T - DEL KIAA1841 NM_032506.1 human genbank 54_36p 1 validated intronic c.1-577 e1-577 0.03 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 2 64681730 64681730 G T SNP LOC730184 XM_001132826.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40673 NULL 0 - - - no_errors tier3 190 1 0.52 99 68 40.72 NA NA NA 246634 TCGA-AB-2968 AML23 2 71643297 71643297 G A SNP DYSF NM_003494.1 human genbank 54_36p 1 reviewed intronic c.2355+715 e23+715 0 - - - no_errors tier3 270 2 0.74 219 177 44.7 NA NA NA 246634 TCGA-AB-2968 AML23 2 77399102 77399103 - A INS LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+199849_1554+199848 e2+199849 0.001:0.000 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 2 79468616 79468616 G A SNP CTNNA2 ENST00000409536 human ensembl 54_36p 1 known intronic c.1+13969 e0+13969 0.006 - - - no_errors tier3 603 9 1.47 321 256 44.37 NA NA NA 246634 TCGA-AB-2968 AML23 2 81252257 81252257 A G SNP - - - - - - - - - - - - - - - tier3 626 9 1.42 260 170 39.53 NA NA NA 246634 TCGA-AB-2968 AML23 2 82164870 82164870 G T SNP - - - - - - - - - - - - - - - tier3 642 10 1.53 296 220 42.64 NA NA NA 246634 TCGA-AB-2968 AML23 2 107300650 107300650 T C SNP - - - - - - - - - - - - - - - tier3 591 13 2.15 227 200 46.84 NA NA NA 246634 TCGA-AB-2968 AML23 2 108604070 108604070 T A SNP LIMS1 NM_004987.3 human genbank 54_36p 1 reviewed intronic c.1+32757 e0+32757 1 - - - no_errors tier3 383 5 1.29 290 225 43.69 NA NA NA 246634 TCGA-AB-2968 AML23 2 109336476 109336476 C T SNP SH3RF3 NM_001099289.1 human genbank 54_36p 1 provisional intronic c.849+5639 e2+5639 0.001 - - - no_stop_codon tier3 164 5 2.94 269 192 41.65 NA NA NA 246634 TCGA-AB-2968 AML23 2 115177273 115177273 T - DEL DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+260388 e1+260388 0.002 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 2 121617897 121617897 C G SNP ENSG00000208508 ENST00000385773 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46666 NULL 0 - - - pseudogene tier3 769 19 2.41 417 289 40.93 NA NA NA 246634 TCGA-AB-2968 AML23 2 122504648 122504648 C T SNP - - - - - - - - - - - - - - - tier3 409 3 0.73 293 242 45.23 NA NA NA 246634 TCGA-AB-2968 AML23 2 124758713 124758713 T C SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.381+42273 e3+42273 0.011 - - - no_errors tier3 486 12 2.41 243 204 45.43 NA NA NA 246634 TCGA-AB-2968 AML23 2 133064355 133064355 G A SNP GPR39 NM_001508.2 human genbank 54_36p 1 validated intronic c.857-54789 e2-54789 0.516 - - - no_errors tier3 550 7 1.26 210 179 45.9 NA NA NA 246634 TCGA-AB-2968 AML23 2 136304332 136304332 T G SNP LCT NM_002299.2 human genbank 54_36p -1 reviewed intronic c.721-616 e3-616 0 - - - no_errors tier3 454 13 2.78 269 210 43.84 NA NA NA 246634 TCGA-AB-2968 AML23 2 136880593 136880593 C A SNP - - - - - - - - - - - - - - - tier3 315 4 1.25 293 221 42.91 NA NA NA 246634 TCGA-AB-2968 AML23 2 139353508 139353508 T A SNP LOC647012 XR_017217.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-17856 NULL 0.103 - - - no_errors tier3 594 10 1.66 184 184 50 NA NA NA 246634 TCGA-AB-2968 AML23 2 140112682 140112682 G T SNP - - - - - - - - - - - - - - - tier3 415 13 3.04 358 246 40.73 NA NA NA 246634 TCGA-AB-2968 AML23 2 146023145 146023145 G A SNP - - - - - - - - - - - - - - - tier3 485 9 1.82 423 309 42.21 NA NA NA 246634 TCGA-AB-2968 AML23 2 149566841 149566841 C T SNP KIF5C ENST00000397413 human ensembl 54_36p 1 known intronic c.1677+1299 e14+1299 0 - - - no_errors tier3 624 2 0.32 289 94 24.54 NA NA NA 246634 TCGA-AB-2968 AML23 2 149681257 149681257 C T SNP LYPD6B NM_177964.3 human genbank 54_36p 1 provisional intronic c.1-14386 e1-14386 0 - - - no_errors tier3 636 8 1.24 331 304 47.87 NA NA NA 246634 TCGA-AB-2968 AML23 2 155956753 155956753 G A SNP - - - - - - - - - - - - - - - tier3 508 2 0.39 358 95 20.97 NA NA NA 246634 TCGA-AB-2968 AML23 2 159054315 159054315 T G SNP PKP4 NM_003628.1 human genbank 54_36p 1 reviewed intronic c.1+32339 e0+32339 0 - - - no_errors tier3 1180 17 1.42 429 381 46.98 NA NA NA 246634 TCGA-AB-2968 AML23 2 160301574 160301574 A G SNP MARCH7 NM_022826.2 human genbank 54_36p 1 validated intronic c.154-6244 e2-6244 0.001 - - - no_errors tier3 363 3 0.82 142 94 39.83 NA NA NA 246634 TCGA-AB-2968 AML23 2 162336709 162336709 C T SNP SLC4A10 NM_022058.3 human genbank 54_36p 1 validated intronic c.130+899 e2+899 0.003 - - - no_errors tier3 559 9 1.58 284 226 44.31 NA NA NA 246634 TCGA-AB-2968 AML23 2 164680314 164680314 C T SNP - - - - - - - - - - - - - - - tier3 711 13 1.8 271 209 43.54 NA NA NA 246634 TCGA-AB-2968 AML23 2 165208977 165208977 A G SNP GRB14 NM_004490.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22912 NULL 0.721 - - - no_errors tier3 461 13 2.74 223 155 41.01 NA NA NA 246634 TCGA-AB-2968 AML23 2 170028952 170028952 T A SNP BBS5 NM_152384.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15358 NULL 0 - - - no_errors tier3 149 3 1.97 85 71 45.51 NA NA NA 246634 TCGA-AB-2968 AML23 2 185822118 185822118 A G SNP - - - - - - - - - - - - - - - tier3 482 8 1.63 381 231 37.68 NA NA NA 246634 TCGA-AB-2968 AML23 2 194002116 194002116 G A SNP - - - - - - - - - - - - - - - tier3 379 7 1.81 181 120 39.87 NA NA NA 246634 TCGA-AB-2968 AML23 2 194809372 194809372 C A SNP - - - - - - - - - - - - - - - tier3 734 10 1.34 304 206 40.39 NA NA NA 246634 TCGA-AB-2968 AML23 2 201344239 201344239 G A SNP AOX2P NR_001557.2 human genbank 54_36p 1 provisional intronic c.NULL NULL 0.001 - - - pseudogene tier3 367 8 2.13 266 208 43.88 NA NA NA 246634 TCGA-AB-2968 AML23 2 201387971 201387972 - A INS BZW1 NM_014670.2 human genbank 54_36p 1 validated intronic c.65-338_65-337 e2-337 0.001:0.000 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 2 206891611 206891611 A T SNP ENSG00000212689 ENST00000391383 human ensembl 54_36p 1 known 5_prime_flanking_region c.-37097 NULL 0.044 - - - no_errors tier3 560 8 1.41 225 183 44.85 NA NA NA 246634 TCGA-AB-2968 AML23 2 207171089 207171089 C T SNP ADAM23 NM_003812.2 human genbank 54_36p 1 reviewed intronic c.2359+1958 e24+1958 0.902 - - - no_errors tier3 382 11 2.8 190 134 41.36 NA NA NA 246634 TCGA-AB-2968 AML23 2 227392411 227392411 T A SNP IRS1 NM_005544.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20713 NULL 0 - - - no_errors tier3 370 6 1.6 147 117 44.32 NA NA NA 246634 TCGA-AB-2968 AML23 2 232261282 232261282 G T SNP PTMA NM_001099285.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20379 NULL 0.002 - - - no_errors tier3 262 13 4.73 107 85 44.27 NA NA NA 246634 TCGA-AB-2968 AML23 3 2113628 2113628 C T SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-474560 NULL 0 - - - no_errors tier3 382 9 2.3 153 105 40.54 NA NA NA 246634 TCGA-AB-2968 AML23 3 13021619 13021619 T A SNP IQSEC1 NM_014869.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-37668 NULL 0.002 - - - no_errors tier3 340 11 3.13 179 131 42.26 NA NA NA 246634 TCGA-AB-2968 AML23 3 15268644 15268644 T G SNP CAPN7 NM_014296.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*873 NULL 0.001 - - - no_errors tier3 568 9 1.56 309 208 40.23 NA NA NA 246634 TCGA-AB-2968 AML23 3 16419660 16419660 G A SNP RFTN1 NM_015150.1 human genbank 54_36p -1 validated intronic c.441+6226 e3+6226 0 - - - no_errors tier3 392 9 2.23 273 144 34.53 NA NA NA 246634 TCGA-AB-2968 AML23 3 17262007 17262007 C T SNP TBC1D5 NM_014744.1 human genbank 54_36p -1 validated intronic c.1332-7092 e15-7092 0 - - - no_errors tier3 497 8 1.58 196 146 42.69 NA NA NA 246634 TCGA-AB-2968 AML23 3 22417047 22417047 T A SNP ENSG00000132967 ENST00000255320 human ensembl 54_36p 1 known intronic c.474+18100 e1+18100 0.003 - - - no_stop_codon tier3 575 7 1.2 229 223 49.34 NA NA NA 246634 TCGA-AB-2968 AML23 3 25533606 25533606 A T SNP RARB NM_000965.3 human genbank 54_36p 1 reviewed intronic c.448+15788 e3+15788 0 - - - no_errors tier3 610 14 2.24 241 181 42.89 NA NA NA 246634 TCGA-AB-2968 AML23 3 26809163 26809163 T G SNP ENSG00000221438 ENST00000408511 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-38592 NULL 0.1 - - - no_errors tier3 449 9 1.97 244 160 39.6 NA NA NA 246634 TCGA-AB-2968 AML23 3 29039835 29039835 C T SNP - - - - - - - - - - - - - - - tier3 326 14 4.12 177 133 42.9 NA NA NA 246634 TCGA-AB-2968 AML23 3 33850473 33850473 C A SNP PDCD6IP NM_013374.3 human genbank 54_36p 1 reviewed intronic c.835-2067 e8-2067 0.121 - - - no_errors tier3 273 15 5.21 399 69 14.74 NA NA NA 246634 TCGA-AB-2968 AML23 3 54679163 54679163 G A SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.1167+27855 e11+27855 0.001 - - - no_errors tier3 287 2 0.69 277 131 32.11 NA NA NA 246634 TCGA-AB-2968 AML23 3 55410285 55410285 C T SNP - - - - - - - - - - - - - - - tier3 544 5 0.91 489 418 46.09 NA NA NA 246634 TCGA-AB-2968 AML23 3 57625125 57625125 A C SNP FAM116A NM_152678.2 human genbank 54_36p -1 validated intronic c.433-642 e5-642 0 - - - no_errors tier3 322 2 0.62 157 99 38.67 NA NA NA 246634 TCGA-AB-2968 AML23 3 64244848 64244848 G T SNP - - - - - - - - - - - - - - - tier3 415 10 2.35 182 139 43.3 NA NA NA 246634 TCGA-AB-2968 AML23 3 68985733 68985733 C T SNP FAM19A4 NM_001005527.1 human genbank 54_36p -1 reviewed intronic c.130+26838 e2+26838 0 - - - no_errors tier3 778 8 1.02 348 289 45.37 NA NA NA 246634 TCGA-AB-2968 AML23 3 70599051 70599051 G A SNP - - - - - - - - - - - - - - - tier3 569 8 1.39 278 224 44.62 NA NA NA 246634 TCGA-AB-2968 AML23 3 71282541 71282541 G A SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.181-38063 e2-38063 0.578 - - - no_errors tier3 509 10 1.93 213 147 40.83 NA NA NA 246634 TCGA-AB-2968 AML23 3 78060579 78060579 C T SNP - - - - - - - - - - - - - - - tier3 364 3 0.82 297 87 22.66 NA NA NA 246634 TCGA-AB-2968 AML23 3 79259692 79259692 C T SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-2313 e2-2313 0.014 - - - no_errors tier3 869 14 1.59 342 265 43.66 NA NA NA 246634 TCGA-AB-2968 AML23 3 81103255 81103255 G A SNP LOC728290 XM_001127097.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21653 NULL 0.014 - - - no_errors tier3 385 10 2.53 134 102 43.22 NA NA NA 246634 TCGA-AB-2968 AML23 3 81435434 81435434 C T SNP - - - - - - - - - - - - - - - tier3 461 13 2.74 198 150 43.1 NA NA NA 246634 TCGA-AB-2968 AML23 3 83271425 83271425 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 3 84986510 84986510 T G SNP - - - - - - - - - - - - - - - tier3 213 7 3.17 156 134 46.21 NA NA NA 246634 TCGA-AB-2968 AML23 3 85430998 85430998 A T SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+339489 e1+339489 0 - - - no_errors tier3 367 0 0 160 106 39.85 NA NA NA 246634 TCGA-AB-2968 AML23 3 89477153 89477153 G A SNP EPHA3 NM_005233.5 human genbank 54_36p 1 reviewed intronic c.1306+3223 e5+3223 0.001 - - - no_errors tier3 435 9 2.03 206 149 41.97 NA NA NA 246634 TCGA-AB-2968 AML23 3 89851750 89851750 T C SNP - - - - - - - - - - - - - - - tier3 406 4 0.98 169 144 46.01 NA NA NA 246634 TCGA-AB-2968 AML23 3 103041306 103041307 - T INS NFKBIZ NM_001005474.1 human genbank 54_36p 1 reviewed intronic c.1+10084_10085 e0+10084 0.168:0.147 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 3 105390547 105390547 C T SNP ENSG00000211378 ENST00000388643 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-28262 NULL 0 - - - pseudogene tier3 276 16 5.48 176 134 43.23 NA NA NA 246634 TCGA-AB-2968 AML23 3 110926719 110926719 A T SNP - - - - - - - - - - - - - - - tier3 892 10 1.11 318 269 45.83 NA NA NA 246634 TCGA-AB-2968 AML23 3 117255322 117255322 G A SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.388+32539 e2+32539 0 - - - no_errors tier3 934 16 1.68 335 306 47.66 NA NA NA 246634 TCGA-AB-2968 AML23 3 117967676 117967676 A G SNP - - - - - - - - - - - - - - - tier3 618 10 1.59 368 269 42.23 NA NA NA 246634 TCGA-AB-2968 AML23 3 140725491 140725491 G A SNP RBP1 NM_002899.1 human genbank 54_36p -1 reviewed intronic c.253-5437 e3-5437 0.001 - - - no_errors tier3 359 2 0.55 171 141 45.19 NA NA NA 246634 TCGA-AB-2968 AML23 3 141209001 141209001 C A SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.109+71986 e1+71986 0 - - - no_errors tier3 278 8 2.8 134 96 41.56 NA NA NA 246634 TCGA-AB-2968 AML23 3 141758915 141758915 G A SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.1823+722 e11+722 0 - - - no_errors tier3 339 9 2.58 286 208 42.02 NA NA NA 246634 TCGA-AB-2968 AML23 3 142538718 142538718 G A SNP ZBTB38 NM_001080412.2 human genbank 54_36p 1 validated intronic c.1+12730 e0+12730 0 - - - no_errors tier3 389 9 2.26 186 120 39.22 NA NA NA 246634 TCGA-AB-2968 AML23 3 146956195 146956195 G A SNP - - - - - - - - - - - - - - - tier3 361 13 3.48 228 144 38.71 NA NA NA 246634 TCGA-AB-2968 AML23 3 153350912 153350912 T A SNP - - - - - - - - - - - - - - - tier3 348 6 1.69 177 112 38.75 NA NA NA 246634 TCGA-AB-2968 AML23 3 154198853 154198853 G A SNP - - - - - - - - - - - - - - - tier3 490 7 1.41 236 161 40.55 NA NA NA 246634 TCGA-AB-2968 AML23 3 155097178 155097178 G A SNP - - - - - - - - - - - - - - - tier3 390 5 1.27 190 135 41.54 NA NA NA 246634 TCGA-AB-2968 AML23 3 158456186 158456186 G T SNP VEPH1 NM_024621.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*5431 NULL 0.001 - - - no_errors tier3 823 22 2.6 404 278 40.7 NA NA NA 246634 TCGA-AB-2968 AML23 3 164935797 164935797 T A SNP - - - - - - - - - - - - - - - tier3 323 2 0.62 128 111 46.44 NA NA NA 246634 TCGA-AB-2968 AML23 3 165734868 165734868 T G SNP - - - - - - - - - - - - - - - tier3 544 1 0.18 252 177 41.16 NA NA NA 246634 TCGA-AB-2968 AML23 3 165947630 165947630 G A SNP - - - - - - - - - - - - - - - tier3 483 9 1.83 185 155 45.59 NA NA NA 246634 TCGA-AB-2968 AML23 3 166162554 166162554 A - DEL SI NM_001041.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*17290 NULL 0.036 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 3 182496351 182496351 G A SNP - - - - - - - - - - - - - - - tier3 613 2 0.33 301 114 27.4 NA NA NA 246634 TCGA-AB-2968 AML23 3 183093560 183093560 C T SNP ENSG00000213155 ENST00000392635 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-25924 NULL 0 - - - no_coding_region:pseudogene tier3 310 5 1.59 227 81 26.3 NA NA NA 246634 TCGA-AB-2968 AML23 3 183682792 183682792 A - DEL LOC100132918 XR_042313.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-21238 NULL 0 - - - pseudogene tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 3 192327326 192327326 A T SNP - - - - - - - - - - - - - - - tier3 304 4 1.3 95 77 44.77 NA NA NA 246634 TCGA-AB-2968 AML23 3 194184100 194184100 A C SNP - - - - - - - - - - - - - - - tier3 414 5 1.19 370 310 45.45 NA NA NA 246634 TCGA-AB-2968 AML23 4 15451866 15451866 G A SNP CD38 NM_001775.2 human genbank 54_36p 1 validated intronic c.839+607 e7+607 0.001 - - - no_errors tier3 554 6 1.07 168 108 39.13 NA NA NA 246634 TCGA-AB-2968 AML23 4 16361219 16361219 G A SNP LDB2 NM_001290.1 human genbank 54_36p -1 validated intronic c.235+8660 e2+8660 0.001 - - - no_errors tier3 493 8 1.59 342 285 45.31 NA NA NA 246634 TCGA-AB-2968 AML23 4 28738400 28738400 G A SNP - - - - - - - - - - - - - - - tier3 504 4 0.79 193 103 34.8 NA NA NA 246634 TCGA-AB-2968 AML23 4 29931258 29931258 A G SNP - - - - - - - - - - - - - - - tier3 418 0 0 158 54 25.47 NA NA NA 246634 TCGA-AB-2968 AML23 4 30044310 30044310 C T SNP - - - - - - - - - - - - - - - tier3 650 16 2.4 239 179 42.82 NA NA NA 246634 TCGA-AB-2968 AML23 4 31566698 31566698 A T SNP LOC100133713 XM_001715885.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*32964 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 508 11 2.12 332 158 32.18 NA NA NA 246634 TCGA-AB-2968 AML23 4 33912687 33912687 A T SNP - - - - - - - - - - - - - - - tier3 436 6 1.36 241 199 45.23 NA NA NA 246634 TCGA-AB-2968 AML23 4 37013069 37013069 C T SNP ENSG00000215243 ENST00000389006 human ensembl 54_36p 1 known intronic c.1+9028 e0+9028 0.002 - - - no_start_codon:no_stop_codon tier3 458 12 2.55 336 199 36.99 NA NA NA 246634 TCGA-AB-2968 AML23 4 41897687 41897687 C T SNP BEND4 NM_207406.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-48770 NULL 0.001 - - - no_errors tier3 483 10 2.03 163 143 46.73 NA NA NA 246634 TCGA-AB-2968 AML23 4 57681471 57681471 T A SNP IGFBP7 NM_001553.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-10197 NULL 0 - - - no_errors tier3 349 9 2.51 126 98 43.75 NA NA NA 246634 TCGA-AB-2968 AML23 4 65675282 65675282 C G SNP - - - - - - - - - - - - - - - tier3 468 8 1.68 377 253 40.1 NA NA NA 246634 TCGA-AB-2968 AML23 4 65775916 65775917 - A INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 4 77277751 77277751 A G SNP NUP54 NM_017426.2 human genbank 54_36p -1 reviewed intronic c.296-1162 e4-1162 0.024 - - - no_errors tier3 356 3 0.84 69 89 56.33 NA NA NA 246634 TCGA-AB-2968 AML23 4 78306068 78306068 C - DEL CCNG2 NM_004354.2 human genbank 54_36p 1 reviewed frame_shift_del c.1002 p.F334fs 0.971 NULL "HMMSmart_SM00385,HMMPfam_Cyclin_N,superfamily_Cyclin-like" - no_errors tier1 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 4 79471389 79471389 C T SNP FRAS1 ENST00000380674 human ensembl 54_36p 1 known intronic c.2138-2061 e19-2061 0.008 - - - no_errors tier3 476 6 1.24 221 149 40.27 NA NA NA 246634 TCGA-AB-2968 AML23 4 92399331 92399331 T A SNP - - - - - - - - - - - - - - - tier3 488 4 0.81 335 89 20.99 NA NA NA 246634 TCGA-AB-2968 AML23 4 93796907 93796907 C T SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.244+66447 e2+66447 0.001 - - - no_errors tier3 439 8 1.79 241 176 42.21 NA NA NA 246634 TCGA-AB-2968 AML23 4 97965454 97965454 T C SNP - - - - - - - - - - - - - - - tier3 435 4 0.91 240 168 41.18 NA NA NA 246634 TCGA-AB-2968 AML23 4 104443171 104443171 G A SNP - - - - - - - - - - - - - - - tier3 518 6 1.15 214 168 43.86 NA NA NA 246634 TCGA-AB-2968 AML23 4 105136969 105136969 G A SNP - - - - - - - - - - - - - - - tier3 768 23 2.91 261 238 47.5 NA NA NA 246634 TCGA-AB-2968 AML23 4 109685571 109685571 G A SNP - - - - - - - - - - - - - - - tier3 816 18 2.16 313 223 41.6 NA NA NA 246634 TCGA-AB-2968 AML23 4 112874857 112874857 A G SNP - - - - - - - - - - - - - - - tier3 519 12 2.26 250 178 41.59 NA NA NA 246634 TCGA-AB-2968 AML23 4 114673161 114673161 T C SNP CAMK2D NM_001221.3 human genbank 54_36p -1 reviewed intronic c.518-1257 e8-1257 0 - - - no_errors tier3 365 13 3.44 339 243 41.75 NA NA NA 246634 TCGA-AB-2968 AML23 4 115878136 115878136 A G SNP - - - - - - - - - - - - - - - tier3 306 7 2.24 144 93 39.24 NA NA NA 246634 TCGA-AB-2968 AML23 4 117152135 117152135 T A SNP - - - - - - - - - - - - - - - tier3 522 9 1.69 298 240 44.61 NA NA NA 246634 TCGA-AB-2968 AML23 4 118025493 118025493 C T SNP ENSG00000201752 ENST00000364882 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*45504 NULL 0.001 - - - no_errors tier3 428 8 1.83 185 135 42.19 NA NA NA 246634 TCGA-AB-2968 AML23 4 121931181 121931181 G A SNP PRDM5 NM_018699.2 human genbank 54_36p -1 reviewed intronic c.1189-5485 e11-5485 0.004 - - - no_errors tier3 430 10 2.27 186 115 38.21 NA NA NA 246634 TCGA-AB-2968 AML23 4 132306421 132306421 A T SNP - - - - - - - - - - - - - - - tier3 566 12 2.07 321 245 43.29 NA NA NA 246634 TCGA-AB-2968 AML23 4 133239816 133239816 A T SNP - - - - - - - - - - - - - - - tier3 230 1 0.43 83 53 38.97 NA NA NA 246634 TCGA-AB-2968 AML23 4 134275578 134275578 C G SNP PCDH10 NM_032961.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15168 NULL 0.025 - - - no_errors tier3 347 6 1.69 184 133 41.96 NA NA NA 246634 TCGA-AB-2968 AML23 4 139188338 139188338 C T SNP - - - - - - - - - - - - - - - tier3 291 1 0.34 160 102 38.93 NA NA NA 246634 TCGA-AB-2968 AML23 4 145030703 145030703 G C SNP GYPE NM_002102.3 human genbank 54_36p -1 reviewed intronic c.38-9591 e2-9591 0.014 - - - no_errors tier3 734 15 2 266 220 45.27 NA NA NA 246634 TCGA-AB-2968 AML23 4 160974176 160974176 G A SNP - - - - - - - - - - - - - - - tier3 846 16 1.85 382 293 43.34 NA NA NA 246634 TCGA-AB-2968 AML23 4 163826850 163826850 C T SNP - - - - - - - - - - - - - - - tier3 273 10 3.53 206 149 41.97 NA NA NA 246634 TCGA-AB-2968 AML23 4 163887512 163887512 G A SNP - - - - - - - - - - - - - - - tier3 340 7 2.02 144 107 42.63 NA NA NA 246634 TCGA-AB-2968 AML23 4 164549155 164549155 G A SNP - - - - - - - - - - - - - - - tier3 521 5 0.95 276 134 32.68 NA NA NA 246634 TCGA-AB-2968 AML23 4 169378394 169378394 T C SNP DDX60 NM_017631.5 human genbank 54_36p -1 validated missense c.5026 p.I1676V 0.362 NULL "HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_DEAD,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 466 8 1.68 113 85 42.93 NA NA NA 246634 TCGA-AB-2968 AML23 4 169852995 169852995 A T SNP PALLD NM_016081.3 human genbank 54_36p 1 validated intronic c.1501+3977 e7+3977 0 - - - no_errors tier3 330 8 2.37 151 95 38.62 NA NA NA 246634 TCGA-AB-2968 AML23 4 173879852 173879852 C T SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.554-87235 e5-87235 0.002 - - - no_errors tier3 612 8 1.29 392 219 35.84 NA NA NA 246634 TCGA-AB-2968 AML23 4 175041540 175041540 G A SNP - - - - - - - - - - - - - - - tier3 809 14 1.7 497 390 43.97 NA NA NA 246634 TCGA-AB-2968 AML23 4 178236528 178236529 - AG INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 4 181953869 181953869 G A SNP - - - - - - - - - - - - - - - tier3 511 15 2.85 243 173 41.59 NA NA NA 246634 TCGA-AB-2968 AML23 4 182707404 182707404 C T SNP - - - - - - - - - - - - - - - tier3 419 13 3.01 315 221 41.23 NA NA NA 246634 TCGA-AB-2968 AML23 4 182733429 182733429 G A SNP - - - - - - - - - - - - - - - tier3 700 13 1.82 165 113 40.65 NA NA NA 246634 TCGA-AB-2968 AML23 4 183367683 183367683 G A SNP MIRN1305 ENST00000408300 human ensembl 54_36p 1 known 3_prime_flanking_region c.*40158 NULL 0 - - - no_errors tier3 494 1 0.2 440 176 28.53 NA NA NA 246634 TCGA-AB-2968 AML23 4 188020408 188020408 G A SNP - - - - - - - - - - - - - - - tier3 606 8 1.3 445 397 47.15 NA NA NA 246634 TCGA-AB-2968 AML23 4 190024113 190024113 C T SNP - - - - - - - - - - - - - - - tier3 812 14 1.69 289 202 41.14 NA NA NA 246634 TCGA-AB-2968 AML23 5 715032 715032 G A SNP TPPP NM_007030.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*3185 NULL 0.001 - - - no_errors tier3 66 0 0 45 31 40.79 NA NA NA 246634 TCGA-AB-2968 AML23 5 2964883 2964883 C T SNP - - - - - - - - - - - - - - - tier3 500 5 0.99 164 135 45.15 NA NA NA 246634 TCGA-AB-2968 AML23 5 4431577 4431577 G A SNP - - - - - - - - - - - - - - - tier3 507 5 0.97 293 219 42.77 NA NA NA 246634 TCGA-AB-2968 AML23 5 5781102 5781102 G A SNP - - - - - - - - - - - - - - - tier3 906 15 1.63 462 383 45.33 NA NA NA 246634 TCGA-AB-2968 AML23 5 5853332 5853332 G A SNP - - - - - - - - - - - - - - - tier3 446 7 1.54 362 313 46.3 NA NA NA 246634 TCGA-AB-2968 AML23 5 6870291 6870291 C T SNP ENSG00000200243 ENST00000363373 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*31000 NULL 0.002 - - - no_errors tier3 388 1 0.26 212 188 47 NA NA NA 246634 TCGA-AB-2968 AML23 5 6980639 6980639 C T SNP - - - - - - - - - - - - - - - tier3 695 16 2.25 397 352 46.93 NA NA NA 246634 TCGA-AB-2968 AML23 5 8612082 8612082 C A SNP - - - - - - - - - - - - - - - tier3 537 9 1.65 413 311 42.96 NA NA NA 246634 TCGA-AB-2968 AML23 5 14552858 14552858 C T SNP TRIO NM_007118.2 human genbank 54_36p 1 validated intronic c.8332+1109 e53+1109 0.001 - - - no_errors tier3 166 2 1.19 93 53 36.3 NA NA NA 246634 TCGA-AB-2968 AML23 5 15993835 15993835 C T SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*3540 NULL 0.001 - - - no_errors tier3 299 4 1.32 126 84 40 NA NA NA 246634 TCGA-AB-2968 AML23 5 17080037 17080037 T C SNP - - - - - - - - - - - - - - - tier3 368 5 1.34 131 100 43.29 NA NA NA 246634 TCGA-AB-2968 AML23 5 18597840 18597840 C G SNP ENSG00000210087 ENST00000387352 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*14369 NULL 0 - - - pseudogene tier3 488 12 2.4 165 106 39.11 NA NA NA 246634 TCGA-AB-2968 AML23 5 19092781 19092781 T A SNP - - - - - - - - - - - - - - - tier3 482 7 1.43 247 167 40.24 NA NA NA 246634 TCGA-AB-2968 AML23 5 22295365 22295365 G A SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-46856 e1-46856 0 - - - no_errors tier3 365 3 0.81 189 150 44.25 NA NA NA 246634 TCGA-AB-2968 AML23 5 23184526 23184526 G A SNP - - - - - - - - - - - - - - - tier3 333 10 2.92 235 169 41.73 NA NA NA 246634 TCGA-AB-2968 AML23 5 31408033 31408033 G - DEL CDH6 NM_004932.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*48861 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 5 36610512 36610512 C A SNP SLC1A3 NM_004172.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-33771 NULL 0 - - - no_errors tier3 317 9 2.74 306 164 34.67 NA NA NA 246634 TCGA-AB-2968 AML23 5 37099862 37099862 A G SNP NIPBL NM_015384.4 human genbank 54_36p 1 reviewed missense c.8074 p.I2692V 1 NULL superfamily_ARM-type_fold - no_errors tier1 312 7 2.19 197 149 43.06 NA NA NA 246634 TCGA-AB-2968 AML23 5 37852769 37852769 C T SNP GDNF NM_000514.2 human genbank 54_36p -1 reviewed intronic c.152-775 e2-775 0.003 - - - no_errors tier3 447 8 1.75 216 163 43.01 NA NA NA 246634 TCGA-AB-2968 AML23 5 45464045 45464045 C T SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.1012-31476 e4-31476 0 - - - no_errors tier3 519 10 1.89 185 157 45.91 NA NA NA 246634 TCGA-AB-2968 AML23 5 53303250 53303250 C A SNP ARL15 NM_019087.2 human genbank 54_36p -1 validated intronic c.463-84950 e5-84950 0 - - - no_errors tier3 597 4 0.66 562 68 10.78 NA NA NA 246634 TCGA-AB-2968 AML23 5 74049835 74049835 A G SNP HEXB NM_000521.3 human genbank 54_36p 1 reviewed intronic c.1170-37 e10-37 0.001 - - - no_errors tier3 443 7 1.56 229 207 47.48 NA NA NA 246634 TCGA-AB-2968 AML23 5 77776209 77776209 A G SNP SCAMP1 ENST00000339292 human ensembl 54_36p 1 known intronic c.471-5304 e6-5304 0.007 - - - no_stop_codon tier3 569 13 2.23 277 196 41.44 NA NA NA 246634 TCGA-AB-2968 AML23 5 79261022 79261022 G A SNP MTX3 NM_001010891.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*54241 NULL 0 - - - no_errors tier3 500 11 2.15 396 279 41.27 NA NA NA 246634 TCGA-AB-2968 AML23 5 82033120 82033120 C G SNP - - - - - - - - - - - - - - - tier3 488 7 1.41 217 170 43.81 NA NA NA 246634 TCGA-AB-2968 AML23 5 91412204 91412204 C T SNP - - - - - - - - - - - - - - - tier3 190 1 0.52 27 37 57.81 NA NA NA 246634 TCGA-AB-2968 AML23 5 95759726 95759726 T A SNP PCSK1 NM_000439.3 human genbank 54_36p -1 reviewed intronic c.1588+613 e11+613 0.076 - - - no_errors tier3 566 15 2.58 320 232 42.03 NA NA NA 246634 TCGA-AB-2968 AML23 5 97772613 97772613 G A SNP ENSG00000211351 ENST00000388616 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1164 NULL 0 - - - pseudogene tier3 539 5 0.92 208 176 45.83 NA NA NA 246634 TCGA-AB-2968 AML23 5 101043813 101043813 G A SNP - - - - - - - - - - - - - - - tier3 559 15 2.61 261 229 46.73 NA NA NA 246634 TCGA-AB-2968 AML23 5 105397781 105397781 T G SNP - - - - - - - - - - - - - - - tier3 326 9 2.69 233 215 47.99 NA NA NA 246634 TCGA-AB-2968 AML23 5 107193395 107193395 T C SNP FBXL17 NM_022824.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*31925 NULL 0 - - - no_errors tier3 338 5 1.46 149 116 43.77 NA NA NA 246634 TCGA-AB-2968 AML23 5 108604359 108604359 G A SNP - - - - - - - - - - - - - - - tier3 461 7 1.5 401 139 25.74 NA NA NA 246634 TCGA-AB-2968 AML23 5 109870359 109870359 T A SNP FLJ43080 XM_001719018.2 human genbank 54_36p -1 model intronic c.1449+61688 e10+61688 0.002 - - - no_errors tier3 653 11 1.66 313 283 47.32 NA NA NA 246634 TCGA-AB-2968 AML23 5 113325349 113325349 C A SNP - - - - - - - - - - - - - - - tier3 871 6 0.68 716 315 30.52 NA NA NA 246634 TCGA-AB-2968 AML23 5 114756474 114756474 C T SNP ENSG00000177962 ENST00000317782 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1026 NULL 0.004 - - - no_coding_region:pseudogene tier3 270 5 1.82 242 198 45 NA NA NA 246634 TCGA-AB-2968 AML23 5 115718701 115718701 C T SNP - - - - - - - - - - - - - - - tier3 395 8 1.98 121 88 41.9 NA NA NA 246634 TCGA-AB-2968 AML23 5 116635650 116635650 C T SNP - - - - - - - - - - - - - - - tier3 448 12 2.61 296 232 43.94 NA NA NA 246634 TCGA-AB-2968 AML23 5 118589695 118589695 G A SNP DMXL1 NM_005509.4 human genbank 54_36p 1 validated intronic c.8275+1332 e37+1332 0 - - - no_errors tier3 477 10 2.05 186 147 44.14 NA NA NA 246634 TCGA-AB-2968 AML23 5 122646949 122646949 G A SNP ENSG00000213655 ENST00000395448 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46983 NULL 0 - - - no_coding_region:pseudogene tier3 462 4 0.86 282 104 26.87 NA NA NA 246634 TCGA-AB-2968 AML23 5 129740726 129740726 T G SNP - - - - - - - - - - - - - - - tier3 296 2 0.67 278 80 22.35 NA NA NA 246634 TCGA-AB-2968 AML23 5 130017284 130017284 C T SNP - - - - - - - - - - - - - - - tier3 370 0 0 169 113 40.07 NA NA NA 246634 TCGA-AB-2968 AML23 5 132243445 132243445 C T SNP AFF4 NM_014423.3 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1205 NULL 1 - - - no_errors tier3 246 10 3.91 120 89 42.58 NA NA NA 246634 TCGA-AB-2968 AML23 5 133120267 133120267 C T SNP - - - - - - - - - - - - - - - tier3 290 9 3 210 186 46.85 NA NA NA 246634 TCGA-AB-2968 AML23 5 137274005 137274005 C T SNP PKD2L2 NM_014386.2 human genbank 54_36p 1 validated intronic c.1328+1471 e8+1471 0.007 - - - no_errors tier3 398 8 1.97 196 158 44.63 NA NA NA 246634 TCGA-AB-2968 AML23 5 140518514 140518514 A T SNP PCDHB8 NM_019120.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19286 NULL 0 - - - no_errors tier3 300 7 2.28 93 83 46.89 NA NA NA 246634 TCGA-AB-2968 AML23 5 143696961 143696961 G A SNP KCTD16 NM_020768.3 human genbank 54_36p 1 validated intronic c.832+129659 e1+129659 0 - - - no_errors tier3 479 1 0.21 261 95 26.69 NA NA NA 246634 TCGA-AB-2968 AML23 5 146522195 146522195 G A SNP - - - - - - - - - - - - - - - tier3 471 8 1.67 345 300 46.51 NA NA NA 246634 TCGA-AB-2968 AML23 5 155979312 155979312 A T SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.502+24673 e5+24673 0.644 - - - no_errors tier3 359 7 1.91 137 110 44.53 NA NA NA 246634 TCGA-AB-2968 AML23 5 155997418 155997418 G A SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.503-9634 e6-9634 0.005 - - - no_errors tier3 645 11 1.68 372 260 41.14 NA NA NA 246634 TCGA-AB-2968 AML23 5 166238476 166238476 C T SNP - - - - - - - - - - - - - - - tier3 1519 47 3 484 332 40.69 NA NA NA 246634 TCGA-AB-2968 AML23 5 175012763 175012763 G T SNP HRH2 NM_022304.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30080 NULL 0 - - - no_errors tier3 249 7 2.73 119 103 46.19 NA NA NA 246634 TCGA-AB-2968 AML23 5 175535429 175535429 G A SNP LOC643201 XM_932161.1 human genbank 54_36p -1 model intronic c.411+14 e7+14 0.001 - - - no_errors tier3 362 7 1.9 138 105 43.03 NA NA NA 246634 TCGA-AB-2968 AML23 5 179531456 179531456 G A SNP RASGEF1C NM_175062.3 human genbank 54_36p -1 validated intronic c.1-33792 e1-33792 0 - - - no_errors tier3 212 0 0 104 64 38.1 NA NA NA 246634 TCGA-AB-2968 AML23 6 537581 537581 C G SNP EXOC2 NM_018303.4 human genbank 54_36p -1 reviewed silent c.1080 p.L360 1 NULL "HMMPfam_TIG,superfamily_Ig_E-set" - no_errors tier1 348 2 0.57 180 127 41.37 NA NA NA 246634 TCGA-AB-2968 AML23 6 648469 648469 G A SNP LOC100134355 XR_037800.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.001 - - - pseudogene tier3 435 14 3.12 168 144 46.15 NA NA NA 246634 TCGA-AB-2968 AML23 6 3289237 3289237 G A SNP SLC22A23 NM_021945.1 human genbank 54_36p -1 validated intronic c.71-20002 e2-20002 0 - - - no_errors tier3 467 12 2.51 99 74 42.77 NA NA NA 246634 TCGA-AB-2968 AML23 6 5907073 5907073 A G SNP ENSG00000222735 ENST00000410803 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42997 NULL 0.033 - - - no_errors tier3 565 10 1.74 265 204 43.5 NA NA NA 246634 TCGA-AB-2968 AML23 6 7752351 7752351 G A SNP BMP6 NM_001718.4 human genbank 54_36p 1 reviewed intronic c.665-38021 e2-38021 0.001 - - - no_errors tier3 501 5 0.99 363 32 8.1 NA NA NA 246634 TCGA-AB-2968 AML23 6 14694149 14694149 T G SNP - - - - - - - - - - - - - - - tier3 568 7 1.22 343 328 48.88 NA NA NA 246634 TCGA-AB-2968 AML23 6 15715994 15715994 T C SNP DTNBP1 NM_032122.3 human genbank 54_36p -1 reviewed intronic c.488+7483 e6+7483 0 - - - no_errors tier3 573 18 3.05 266 207 43.67 NA NA NA 246634 TCGA-AB-2968 AML23 6 20431869 20431869 A G SNP ENSG00000210228 ENST00000387493 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41559 NULL 0.003 - - - pseudogene tier3 422 5 1.17 128 64 33.33 NA NA NA 246634 TCGA-AB-2968 AML23 6 22698663 22698663 A G SNP HDGFL1 NM_138574.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*20124 NULL 0.007 - - - no_errors tier3 482 13 2.63 302 226 42.8 NA NA NA 246634 TCGA-AB-2968 AML23 6 26081193 26081193 C T SNP TRIM38 NM_006355.2 human genbank 54_36p 1 reviewed intronic c.739-68 e4-68 0 - - - no_errors tier3 386 7 1.78 226 176 43.78 NA NA NA 246634 TCGA-AB-2968 AML23 6 27915401 27915402 - A INS HIST1H3H ENST00000369387 human ensembl 54_36p 1 known intronic c.411+29150_29151 e1+29150 0.002:0.003 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 6 47074870 47074870 G - DEL GPR116 NM_015234.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-92412 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 6 49488910 49488910 A T SNP MUT NM_000255.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*18490 NULL 0.003 - - - no_errors tier3 384 11 2.78 245 155 38.75 NA NA NA 246634 TCGA-AB-2968 AML23 6 49901789 49901789 C T SNP PGK2 NM_138733.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-38930 NULL 0.008 - - - no_errors tier3 172 3 1.71 20 18 47.37 NA NA NA 246634 TCGA-AB-2968 AML23 6 55140800 55140800 A G SNP HCRTR2 NM_001526.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6545 NULL 0.015 - - - no_errors tier3 392 17 4.16 226 182 44.61 NA NA NA 246634 TCGA-AB-2968 AML23 6 56285437 56285437 A T SNP COL21A1 ENST00000370819 human ensembl 54_36p -1 known intronic c.1+81291 e0+81291 0.238 - - - no_errors tier3 871 2 0.23 721 253 25.95 NA NA NA 246634 TCGA-AB-2968 AML23 6 62509107 62509108 - A INS KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.811-8480_811-8479 e7-8479 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 6 66725116 66725116 A G SNP - - - - - - - - - - - - - - - tier3 440 5 1.12 230 140 37.84 NA NA NA 246634 TCGA-AB-2968 AML23 6 70410405 70410405 G A SNP LMBRD1 NM_018368.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*32366 NULL 0 - - - no_errors tier3 940 5 0.53 418 158 27.43 NA NA NA 246634 TCGA-AB-2968 AML23 6 73404460 73404460 C T SNP KCNQ5 NM_019842.2 human genbank 54_36p 1 reviewed intronic c.398+15424 e1+15424 0 - - - no_errors tier3 266 4 1.48 141 145 50.7 NA NA NA 246634 TCGA-AB-2968 AML23 6 77235203 77235203 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 6 80071829 80071829 T C SNP ENSG00000201464 ENST00000364594 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3327 NULL 0.002 - - - no_errors tier3 412 6 1.44 345 229 39.9 NA NA NA 246634 TCGA-AB-2968 AML23 6 83647160 83647160 G A SNP UBE2CBP NM_198920.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*12300 NULL 0.002 - - - no_errors tier3 459 7 1.5 318 233 42.29 NA NA NA 246634 TCGA-AB-2968 AML23 6 85807071 85807071 T C SNP - - - - - - - - - - - - - - - tier3 1067 18 1.66 352 260 42.48 NA NA NA 246634 TCGA-AB-2968 AML23 6 87779699 87779699 T C SNP HTR1E NM_000865.2 human genbank 54_36p 1 validated intronic c.1-1888 e1-1888 0.078 - - - no_errors tier3 536 7 1.29 268 167 38.3 NA NA NA 246634 TCGA-AB-2968 AML23 6 92923643 92923643 G A SNP ENSG00000200492 ENST00000363622 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*37570 NULL 0 - - - no_errors tier3 235 2 0.84 111 55 33.13 NA NA NA 246634 TCGA-AB-2968 AML23 6 93117136 93117137 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 6 93195376 93195377 TT - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 6 96217332 96217333 - T INS ENSG00000219549 ENST00000401718 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29806 NULL 0.000:0.000 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 6 99086635 99086635 G A SNP - - - - - - - - - - - - - - - tier3 339 9 2.59 351 272 43.66 NA NA NA 246634 TCGA-AB-2968 AML23 6 99172813 99172813 C T SNP - - - - - - - - - - - - - - - tier3 443 0 0 227 141 38.21 NA NA NA 246634 TCGA-AB-2968 AML23 6 100496635 100496635 A G SNP MCHR2 NM_001040179.1 human genbank 54_36p -1 validated intronic c.587+911 e3+911 0.005 - - - no_errors tier3 604 7 1.15 278 183 39.7 NA NA NA 246634 TCGA-AB-2968 AML23 6 103297016 103297016 C T SNP - - - - - - - - - - - - - - - tier3 461 7 1.5 223 172 43.54 NA NA NA 246634 TCGA-AB-2968 AML23 6 103609381 103609381 C T SNP - - - - - - - - - - - - - - - tier3 475 7 1.45 299 239 44.26 NA NA NA 246634 TCGA-AB-2968 AML23 6 104446372 104446372 G T SNP - - - - - - - - - - - - - - - tier3 489 6 1.21 408 68 14.26 NA NA NA 246634 TCGA-AB-2968 AML23 6 104661817 104661817 C A SNP - - - - - - - - - - - - - - - tier3 446 9 1.98 306 252 45.16 NA NA NA 246634 TCGA-AB-2968 AML23 6 108752039 108752039 T G SNP LACE1 NM_145315.3 human genbank 54_36p 1 reviewed intronic c.363+94 e2+94 0.01 - - - no_errors tier3 627 8 1.26 227 165 42.09 NA NA NA 246634 TCGA-AB-2968 AML23 6 110395768 110395768 C T SNP GPR6 NM_005284.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-11241 NULL 0.503 - - - no_errors tier3 941 13 1.36 410 316 43.53 NA NA NA 246634 TCGA-AB-2968 AML23 6 112418023 112418023 C T SNP - - - - - - - - - - - - - - - tier3 557 10 1.76 247 172 41.05 NA NA NA 246634 TCGA-AB-2968 AML23 6 113482405 113482405 A T SNP ENSG00000218490 ENST00000407590 human ensembl 54_36p 1 known 3_prime_flanking_region c.*43095 NULL 0.009 - - - no_coding_region:pseudogene tier3 622 2 0.32 379 256 40.31 NA NA NA 246634 TCGA-AB-2968 AML23 6 123875464 123875464 C T SNP TRDN NM_006073.2 human genbank 54_36p -1 validated intronic c.551-258 e7-258 0 - - - no_errors tier3 367 6 1.61 132 101 43.35 NA NA NA 246634 TCGA-AB-2968 AML23 6 125916117 125916117 A G SNP - - - - - - - - - - - - - - - tier3 161 7 4.17 78 60 43.48 NA NA NA 246634 TCGA-AB-2968 AML23 6 133816597 133816597 G A SNP EYA4 NM_004100.4 human genbank 54_36p 1 reviewed intronic c.278-2790 e5-2790 0 - - - no_errors tier3 462 9 1.91 230 204 47 NA NA NA 246634 TCGA-AB-2968 AML23 6 138288531 138288531 A G SNP TNFAIP3 NM_006290.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*44382 NULL 0.001 - - - no_errors tier3 891 19 2.09 465 366 44.04 NA NA NA 246634 TCGA-AB-2968 AML23 6 138797225 138797225 C G SNP NHSL1 ENST00000342260 human ensembl 54_36p -1 known intronic c.677-715 e5-715 0.132 - - - no_errors tier3 418 8 1.87 149 130 46.43 NA NA NA 246634 TCGA-AB-2968 AML23 6 140741777 140741777 C T SNP - - - - - - - - - - - - - - - tier3 312 10 3.11 133 94 41.41 NA NA NA 246634 TCGA-AB-2968 AML23 6 142299930 142299930 C T SNP - - - - - - - - - - - - - - - tier3 323 7 2.12 210 140 40 NA NA NA 246634 TCGA-AB-2968 AML23 6 148504785 148504785 C T SNP - - - - - - - - - - - - - - - tier3 417 5 1.18 268 102 27.35 NA NA NA 246634 TCGA-AB-2968 AML23 6 149519245 149519245 A G SNP LOC729200 XR_015835.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-43728 NULL 0 - - - pseudogene tier3 615 4 0.65 439 132 23.08 NA NA NA 246634 TCGA-AB-2968 AML23 6 154862950 154862950 T G SNP CNKSR3 NM_173515.2 human genbank 54_36p -1 validated intronic c.52+9939 e1+9939 0 - - - no_errors tier3 690 10 1.43 158 114 41.91 NA NA NA 246634 TCGA-AB-2968 AML23 6 159273476 159273476 T C SNP ENSG00000223191 ENST00000411259 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5885 NULL 0.002 - - - no_errors tier3 399 2 0.5 99 88 47.06 NA NA NA 246634 TCGA-AB-2968 AML23 6 161044908 161044908 G A SNP PLG NM_000301.2 human genbank 54_36p 1 validated intronic c.49+1533 e1+1533 0.012 - - - no_errors tier3 417 5 1.18 208 172 45.26 NA NA NA 246634 TCGA-AB-2968 AML23 7 5506935 5506935 G A SNP FBXL18 ENST00000297035 human ensembl 54_36p -1 known missense c.166 p.R56C 0.174 NULL NULL - no_errors tier1 130 2 1.52 100 73 42.2 NA NA NA 246634 TCGA-AB-2968 AML23 7 6189857 6189857 A G SNP CYTH3 NM_004227.3 human genbank 54_36p -1 reviewed intronic c.249+3349 e4+3349 0.007 - - - no_errors tier3 307 10 3.15 99 65 39.63 NA NA NA 246634 TCGA-AB-2968 AML23 7 10030742 10030742 G A SNP LOC340268 XR_041608.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.004 - - - no_errors tier3 279 2 0.71 131 80 37.91 NA NA NA 246634 TCGA-AB-2968 AML23 7 13579817 13579817 G A SNP - - - - - - - - - - - - - - - tier3 842 8 0.94 495 212 29.99 NA NA NA 246634 TCGA-AB-2968 AML23 7 15849272 15849272 G T SNP - - - - - - - - - - - - - - - tier3 511 8 1.54 163 141 46.38 NA NA NA 246634 TCGA-AB-2968 AML23 7 23657084 23657084 A G SNP C7orf46 NM_199136.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29279 NULL 0.008 - - - no_errors tier3 487 9 1.81 219 150 40.65 NA NA NA 246634 TCGA-AB-2968 AML23 7 26922166 26922166 C A SNP ENSG00000213787 ENST00000396363 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6079 NULL 0.015 - - - no_coding_region:pseudogene tier3 463 11 2.32 257 183 41.59 NA NA NA 246634 TCGA-AB-2968 AML23 7 31290657 31290657 C T SNP ENSG00000221751 ENST00000408824 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32480 NULL 0.008 - - - no_errors tier3 466 8 1.69 232 178 43.41 NA NA NA 246634 TCGA-AB-2968 AML23 7 36182120 36182120 A G SNP EEPD1 NM_030636.2 human genbank 54_36p 1 validated intronic c.878+20784 e1+20784 0 - - - no_errors tier3 318 7 2.15 275 165 37.41 NA NA NA 246634 TCGA-AB-2968 AML23 7 42439377 42439377 G A SNP - - - - - - - - - - - - - - - tier3 395 7 1.74 205 151 42.42 NA NA NA 246634 TCGA-AB-2968 AML23 7 44527405 44527405 T C SNP NPC1L1 NM_013389.1 human genbank 54_36p -1 validated intronic c.2954-163 e13-163 0 - - - no_errors tier3 293 6 2.01 153 141 47.96 NA NA NA 246634 TCGA-AB-2968 AML23 7 46453195 46453195 G A SNP - - - - - - - - - - - - - - - tier3 488 12 2.4 302 220 41.98 NA NA NA 246634 TCGA-AB-2968 AML23 7 47154438 47154438 G A SNP - - - - - - - - - - - - - - - tier3 660 10 1.49 281 196 41.09 NA NA NA 246634 TCGA-AB-2968 AML23 7 52239884 52239884 G C SNP - - - - - - - - - - - - - - - tier3 221 6 2.64 30 39 56.52 NA NA NA 246634 TCGA-AB-2968 AML23 7 53196814 53196814 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 7 53833522 53833522 C T SNP FLJ45974 XR_040790.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 315 11 3.37 235 139 37.17 NA NA NA 246634 TCGA-AB-2968 AML23 7 53918303 53918303 G A SNP - - - - - - - - - - - - - - - tier3 291 5 1.69 185 121 39.54 NA NA NA 246634 TCGA-AB-2968 AML23 7 54071054 54071054 C T SNP - - - - - - - - - - - - - - - tier3 687 8 1.15 416 307 42.46 NA NA NA 246634 TCGA-AB-2968 AML23 7 54609127 54609127 G A SNP ENSG00000200471 ENST00000363601 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-47085 NULL 0 - - - no_errors tier3 514 16 3.02 228 151 39.84 NA NA NA 246634 TCGA-AB-2968 AML23 7 67415341 67415341 G A SNP - - - - - - - - - - - - - - - tier3 497 12 2.36 232 203 46.67 NA NA NA 246634 TCGA-AB-2968 AML23 7 76694073 76694073 T C SNP CCDC146 NM_020879.2 human genbank 54_36p 1 validated intronic c.157-10127 e2-10127 0.131 - - - no_errors tier3 1056 16 1.49 391 342 46.47 NA NA NA 246634 TCGA-AB-2968 AML23 7 78044346 78044346 T C SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.538+50026 e3+50026 0.001 - - - no_errors tier3 411 9 2.14 147 108 42.35 NA NA NA 246634 TCGA-AB-2968 AML23 7 80584862 80584862 C T SNP - - - - - - - - - - - - - - - tier3 539 7 1.28 235 214 47.66 NA NA NA 246634 TCGA-AB-2968 AML23 7 82390321 82390321 T C SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.11113-6196 e7-6196 0 - - - no_errors tier3 507 6 1.17 203 192 48.61 NA NA NA 246634 TCGA-AB-2968 AML23 7 82484708 82484708 A G SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.3301-50969 e4-50969 0.007 - - - no_errors tier3 450 1 0.22 345 111 24.34 NA NA NA 246634 TCGA-AB-2968 AML23 7 82541833 82541833 A G SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.3300+59669 e3+59669 0.001 - - - no_errors tier3 360 1 0.28 148 107 41.96 NA NA NA 246634 TCGA-AB-2968 AML23 7 88131685 88131685 T C SNP ENSG00000211518 ENST00000390184 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23808 NULL 0.002 - - - no_errors tier3 321 9 2.73 170 105 38.18 NA NA NA 246634 TCGA-AB-2968 AML23 7 88845361 88845361 C T SNP ZNF804B NM_181646.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*41079 NULL 0.001 - - - no_errors tier3 435 15 3.33 122 81 39.9 NA NA NA 246634 TCGA-AB-2968 AML23 7 89948600 89948600 G A SNP LOC100129289 XM_001717785.1 human genbank 54_36p 1 model intronic c.192+2076 e2+2076 0.002 - - - no_errors tier3 1027 11 1.06 701 215 23.45 NA NA NA 246634 TCGA-AB-2968 AML23 7 90323664 90323664 A G SNP PFTK1 NM_012395.2 human genbank 54_36p 1 validated intronic c.491-6762 e5-6762 0 - - - no_errors tier3 628 8 1.26 356 154 30.2 NA NA NA 246634 TCGA-AB-2968 AML23 7 93631922 93631922 A C SNP - - - - - - - - - - - - - - - tier3 503 3 0.59 304 218 41.68 NA NA NA 246634 TCGA-AB-2968 AML23 7 94302532 94302532 G A SNP ENSG00000222220 ENST00000410288 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33462 NULL 0.02 - - - no_errors tier3 355 9 2.47 331 223 40.18 NA NA NA 246634 TCGA-AB-2968 AML23 7 104269622 104269622 C T SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed intronic c.683-64248 e3-64248 0.001 - - - no_errors tier3 547 12 2.14 301 229 43.21 NA NA NA 246634 TCGA-AB-2968 AML23 7 110951610 110951610 T C SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional intronic c.1-2869 e1-2869 0.006 - - - no_errors tier3 367 12 3.17 134 88 39.64 NA NA NA 246634 TCGA-AB-2968 AML23 7 114461750 114461750 A G SNP MDFIC ENST00000393486 human ensembl 54_36p 1 known 3_prime_flanking_region c.*18525 NULL 0.001 - - - no_errors tier3 781 12 1.51 273 206 43.01 NA NA NA 246634 TCGA-AB-2968 AML23 7 115094043 115094043 C T SNP - - - - - - - - - - - - - - - tier3 496 9 1.78 253 172 40.47 NA NA NA 246634 TCGA-AB-2968 AML23 7 120451257 120451257 C T SNP C7orf58 NM_024913.1 human genbank 54_36p 1 validated intronic c.433+8119 e2+8119 0 - - - no_errors tier3 546 6 1.09 341 118 25.65 NA NA NA 246634 TCGA-AB-2968 AML23 7 120516417 120516417 A G SNP C7orf58 NM_024913.1 human genbank 54_36p 1 validated intronic c.617-8572 e5-8572 0.051 - - - no_errors tier3 265 3 1.12 212 156 42.39 NA NA NA 246634 TCGA-AB-2968 AML23 7 123921467 123921467 A C SNP LOC136157 NM_001085395.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*17222 NULL 0.062 - - - no_errors tier3 408 6 1.45 93 50 34.97 NA NA NA 246634 TCGA-AB-2968 AML23 7 129472447 129472447 C T SNP ZC3HC1 NM_016478.3 human genbank 54_36p -1 validated intronic c.258+3662 e2+3662 0.001 - - - no_errors tier3 704 14 1.95 291 205 41.33 NA NA NA 246634 TCGA-AB-2968 AML23 7 131179561 131179561 G A SNP - - - - - - - - - - - - - - - tier3 510 4 0.78 385 122 24.06 NA NA NA 246634 TCGA-AB-2968 AML23 7 138507661 138507661 G A SNP TTC26 NM_024926.1 human genbank 54_36p 1 validated intronic c.1069+3023 e12+3023 0.282 - - - no_errors tier3 352 3 0.85 155 126 44.84 NA NA NA 246634 TCGA-AB-2968 AML23 7 142436082 142436082 C T SNP OR6V1 NM_001001667.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-23478 NULL 0.004 - - - no_errors tier3 541 13 2.34 266 228 46.15 NA NA NA 246634 TCGA-AB-2968 AML23 7 145331828 145331828 G T SNP ENSG00000208307 ENST00000385572 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*6412 NULL 0.008 - - - pseudogene tier3 550 14 2.48 284 179 38.66 NA NA NA 246634 TCGA-AB-2968 AML23 7 145441579 145441579 C G SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3323 NULL 0 - - - no_errors tier3 51 3 5.56 38 22 36.67 NA NA NA 246634 TCGA-AB-2968 AML23 7 147469486 147469486 G A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2555-6030 e17-6030 0.001 - - - no_errors tier3 544 2 0.37 334 80 19.32 NA NA NA 246634 TCGA-AB-2968 AML23 7 147736727 147736727 G A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.3716-689 e23-689 0.001 - - - no_errors tier3 445 10 2.2 169 127 42.91 NA NA NA 246634 TCGA-AB-2968 AML23 7 153328491 153328491 C T SNP DPP6 ENST00000404039 human ensembl 54_36p 1 known intronic c.51+112739 e1+112739 0 - - - no_errors tier3 195 5 2.5 159 112 41.33 NA NA NA 246634 TCGA-AB-2968 AML23 7 157200159 157200159 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1789-31769 e13-31769 0.001 - - - no_errors tier3 105 3 2.78 67 57 45.97 NA NA NA 246634 TCGA-AB-2968 AML23 8 1591559 1591559 C G SNP LOC100133915 XM_001715423.1 human genbank 54_36p -1 model missense c.1367 p.C456S 0 NULL NULL - no_start_codon:pseudogene:no_stop_codon tier1 309 4 1.28 196 173 46.51 NA NA NA 246634 TCGA-AB-2968 AML23 8 2113974 2113974 A G SNP MYOM2 NM_003970.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*33662 NULL 0.043 - - - no_errors tier3 407 8 1.93 103 83 44.39 NA NA NA 246634 TCGA-AB-2968 AML23 8 4671991 4671991 A T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+167271 e1+167271 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 607 16 2.57 309 244 44.04 NA NA NA 246634 TCGA-AB-2968 AML23 8 5296412 5296412 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 8 5338678 5338678 G A SNP - - - - - - - - - - - - - - - tier3 304 2 0.65 227 174 43.39 NA NA NA 246634 TCGA-AB-2968 AML23 8 16600380 16600380 T C SNP - - - - - - - - - - - - - - - tier3 481 4 0.82 339 288 45.86 NA NA NA 246634 TCGA-AB-2968 AML23 8 17279046 17279046 G C SNP MTMR7 NM_004686.4 human genbank 54_36p -1 reviewed intronic c.25-3926 e2-3926 0.003 - - - no_errors tier3 441 1 0.23 232 72 23.68 NA NA NA 246634 TCGA-AB-2968 AML23 8 27357729 27357729 G C SNP PTK2B NM_004103.3 human genbank 54_36p 1 reviewed intronic c.2214+24 e22+24 0.001 - - - no_errors tier3 343 1 0.29 262 25 8.71 NA NA NA 246634 TCGA-AB-2968 AML23 8 29576580 29576580 C T SNP LOC646909 XR_017343.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*30476 NULL 0.114 - - - pseudogene tier3 566 9 1.57 178 177 49.86 NA NA NA 246634 TCGA-AB-2968 AML23 8 35433757 35433757 A T SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.104-92595 e2-92595 0.003 - - - no_errors tier3 449 9 1.97 222 160 41.78 NA NA NA 246634 TCGA-AB-2968 AML23 8 36653350 36653350 G T SNP - - - - - - - - - - - - - - - tier3 703 18 2.5 294 218 42.58 NA NA NA 246634 TCGA-AB-2968 AML23 8 38628066 38628066 G A SNP - - - - - - - - - - - - - - - tier3 697 12 1.69 483 392 44.7 NA NA NA 246634 TCGA-AB-2968 AML23 8 40822104 40822104 G A SNP ZMAT4 NM_024645.1 human genbank 54_36p -1 validated intronic c.1-19748 e1-19748 0 - - - no_errors tier3 592 4 0.67 376 166 30.63 NA NA NA 246634 TCGA-AB-2968 AML23 8 41475702 41475702 C A SNP GOLGA7 NM_001002296.1 human genbank 54_36p 1 validated intronic c.264+1365 e2+1365 0.002 - - - no_errors tier3 350 6 1.69 137 112 44.98 NA NA NA 246634 TCGA-AB-2968 AML23 8 54081001 54081001 G A SNP - - - - - - - - - - - - - - - tier3 533 13 2.38 293 253 46.34 NA NA NA 246634 TCGA-AB-2968 AML23 8 54627582 54627582 C T SNP ENSG00000205311 ENST00000379571 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*12073 NULL 0.001 - - - no_coding_region:pseudogene tier3 366 8 2.13 251 176 41.22 NA NA NA 246634 TCGA-AB-2968 AML23 8 55355687 55355687 A T SNP - - - - - - - - - - - - - - - tier3 381 6 1.55 131 103 44.02 NA NA NA 246634 TCGA-AB-2968 AML23 8 56080672 56080672 C T SNP - - - - - - - - - - - - - - - tier3 339 3 0.88 231 186 44.6 NA NA NA 246634 TCGA-AB-2968 AML23 8 57050135 57050135 C T SNP LYN NM_002350.1 human genbank 54_36p 1 validated intronic c.1050+5229 e9+5229 0 - - - no_errors tier3 381 7 1.8 283 250 46.9 NA NA NA 246634 TCGA-AB-2968 AML23 8 57480467 57480467 C T SNP PENK NM_006211.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*35918 NULL 0.01 - - - no_errors tier3 611 6 0.97 321 223 40.99 NA NA NA 246634 TCGA-AB-2968 AML23 8 58704829 58704829 C T SNP LOC100130588 XM_001719422.1 human genbank 54_36p -1 model intronic c.127-35254 e3-35254 0.003 - - - no_errors tier3 357 5 1.38 201 151 42.78 NA NA NA 246634 TCGA-AB-2968 AML23 8 63666797 63666797 A C SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.273+1890 e3+1890 0.033 - - - no_errors tier3 415 10 2.35 206 135 39.59 NA NA NA 246634 TCGA-AB-2968 AML23 8 67852538 67852538 A T SNP SGK3 NM_001033578.1 human genbank 54_36p 1 reviewed intronic c.1-15867 e1-15867 0 - - - no_errors tier3 442 14 3.07 172 136 44.16 NA NA NA 246634 TCGA-AB-2968 AML23 8 72066018 72066018 G T SNP - - - - - - - - - - - - - - - tier3 707 18 2.48 550 400 42.11 NA NA NA 246634 TCGA-AB-2968 AML23 8 72676191 72676191 G A SNP LOC100132809 XM_001715796.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-44381 NULL 0 - - - no_errors tier3 406 8 1.93 224 207 48.03 NA NA NA 246634 TCGA-AB-2968 AML23 8 73524432 73524432 G A SNP LOC100129527 XM_001715839.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*19717 NULL 0.003 - - - no_errors tier3 492 7 1.4 274 185 40.31 NA NA NA 246634 TCGA-AB-2968 AML23 8 76053849 76053849 A - DEL CRISPLD1 NM_031461.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-6929 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 8 76613942 76613942 G A SNP HNF4G ENST00000354370 human ensembl 54_36p 1 known intronic c.1-4659 e1-4659 0 - - - no_errors tier3 344 3 0.86 184 148 44.58 NA NA NA 246634 TCGA-AB-2968 AML23 8 84289429 84289429 C G SNP - - - - - - - - - - - - - - - tier3 484 7 1.43 245 209 45.83 NA NA NA 246634 TCGA-AB-2968 AML23 8 87104090 87104090 T C SNP PSKH2 NM_033126.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*25717 NULL 0.683 - - - no_errors tier3 543 18 3.2 326 214 39.63 NA NA NA 246634 TCGA-AB-2968 AML23 8 93271124 93271124 C A SNP ENSG00000200820 ENST00000363950 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-22173 NULL 0.009 - - - no_errors tier3 402 6 1.46 280 187 40.04 NA NA NA 246634 TCGA-AB-2968 AML23 8 93550792 93550792 C T SNP - - - - - - - - - - - - - - - tier3 354 9 2.48 132 98 42.61 NA NA NA 246634 TCGA-AB-2968 AML23 8 93883273 93883273 C T SNP FLJ46284 XR_041984.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-15809 NULL 0.001 - - - no_errors tier3 350 4 1.13 179 46 20.44 NA NA NA 246634 TCGA-AB-2968 AML23 8 94591658 94591658 G C SNP LOC100129242 XM_001717187.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-14526 NULL 0.004 - - - no_errors tier3 651 18 2.69 176 109 38.25 NA NA NA 246634 TCGA-AB-2968 AML23 8 99620314 99620314 C T SNP STK3 NM_006281.2 human genbank 54_36p -1 validated intronic c.1141+9059 e9+9059 0 - - - no_errors tier3 466 9 1.89 327 192 36.99 NA NA NA 246634 TCGA-AB-2968 AML23 8 104152756 104152756 G A SNP ATP6V1C1 NM_001695.4 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*2605 NULL 0 - - - no_errors tier3 452 12 2.58 318 246 43.62 NA NA NA 246634 TCGA-AB-2968 AML23 8 106428674 106428674 A G SNP ZFPM2 NM_012082.3 human genbank 54_36p 1 reviewed intronic c.40+28289 e1+28289 0.538 - - - no_errors tier3 321 10 3.02 178 98 35.51 NA NA NA 246634 TCGA-AB-2968 AML23 8 110070863 110070863 A G SNP - - - - - - - - - - - - - - - tier3 953 11 1.14 459 333 42.05 NA NA NA 246634 TCGA-AB-2968 AML23 8 111835312 111835313 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 8 114727713 114727713 A G SNP - - - - - - - - - - - - - - - tier3 496 11 2.17 237 180 43.17 NA NA NA 246634 TCGA-AB-2968 AML23 8 117778268 117778268 T A SNP EIF3H NM_003756.2 human genbank 54_36p -1 validated intronic c.289+29168 e2+29168 0.001 - - - no_errors tier3 761 18 2.31 248 210 45.85 NA NA NA 246634 TCGA-AB-2968 AML23 8 118101131 118101131 A T SNP SLC30A8 ENST00000297345 human ensembl 54_36p 1 known intronic c.1-19508 e1-19508 0.016 - - - no_errors tier3 466 3 0.64 252 184 42.2 NA NA NA 246634 TCGA-AB-2968 AML23 8 123704428 123704428 C T SNP ENSG00000208620 ENST00000385885 human ensembl 54_36p 1 known 5_prime_flanking_region c.-48283 NULL 0 - - - pseudogene tier3 563 8 1.4 251 200 44.35 NA NA NA 246634 TCGA-AB-2968 AML23 8 127766479 127766479 G A SNP ENSG00000212451 ENST00000391149 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13398 NULL 0.005 - - - no_errors tier3 981 14 1.41 413 309 42.8 NA NA NA 246634 TCGA-AB-2968 AML23 8 137260994 137260994 G A SNP - - - - - - - - - - - - - - - tier3 1024 20 1.92 335 234 41.12 NA NA NA 246634 TCGA-AB-2968 AML23 8 138259393 138259393 A G SNP - - - - - - - - - - - - - - - tier3 577 10 1.7 244 199 44.92 NA NA NA 246634 TCGA-AB-2968 AML23 8 138656861 138656861 C T SNP - - - - - - - - - - - - - - - tier3 776 12 1.52 327 246 42.86 NA NA NA 246634 TCGA-AB-2968 AML23 8 139232469 139232469 T A SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.3281+150 e12+150 0.001 - - - no_errors tier3 218 8 3.54 37 44 54.32 NA NA NA 246634 TCGA-AB-2968 AML23 8 146047513 146047513 C G SNP COMMD5 NM_001081003.1 human genbank 54_36p -1 validated silent c.15 p.G5 0.745 NULL HMMPfam_HCaRG - no_errors tier1 169 6 3.43 103 72 41.14 NA NA NA 246634 TCGA-AB-2968 AML23 9 3540828 3540828 G A SNP RFX3 NM_134428.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-155240 NULL 0 - - - no_errors tier3 451 11 2.38 194 146 42.94 NA NA NA 246634 TCGA-AB-2968 AML23 9 5416399 5416399 C T SNP C9orf46 NM_018465.2 human genbank 54_36p -1 predicted intronic c.81+5498 e1+5498 0.37 - - - no_errors tier3 265 2 0.75 125 83 39.9 NA NA NA 246634 TCGA-AB-2968 AML23 9 7581946 7581946 T A SNP LOC392285 XR_017134.2 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - pseudogene tier3 432 9 2.04 270 238 46.85 NA NA NA 246634 TCGA-AB-2968 AML23 9 10117903 10117903 G T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-94113 e1-94113 0.001 - - - no_errors tier3 384 1 0.26 263 97 26.94 NA NA NA 246634 TCGA-AB-2968 AML23 9 13279080 13279080 G A SNP MPDZ NM_003829.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-38766 NULL 0.002 - - - no_errors tier3 356 4 1.11 145 89 38.03 NA NA NA 246634 TCGA-AB-2968 AML23 9 13721015 13721015 G A SNP - - - - - - - - - - - - - - - tier3 671 18 2.61 349 270 43.55 NA NA NA 246634 TCGA-AB-2968 AML23 9 13741858 13741858 G A SNP - - - - - - - - - - - - - - - tier3 915 26 2.76 297 210 41.42 NA NA NA 246634 TCGA-AB-2968 AML23 9 14351856 14351856 G A SNP NFIB ENST00000397575 human ensembl 54_36p -1 known intronic c.108+36667 e1+36667 0 - - - no_errors tier3 374 5 1.32 171 121 41.44 NA NA NA 246634 TCGA-AB-2968 AML23 9 14352233 14352233 C T SNP NFIB ENST00000397575 human ensembl 54_36p -1 known intronic c.108+36290 e1+36290 0.621 - - - no_errors tier3 473 8 1.66 266 180 40.36 NA NA NA 246634 TCGA-AB-2968 AML23 9 14748808 14748808 T C SNP FREM1 NM_144966.4 human genbank 54_36p -1 validated intronic c.5334+962 e27+962 0.005 - - - no_errors tier3 488 5 1.01 241 159 39.75 NA NA NA 246634 TCGA-AB-2968 AML23 9 16494434 16494434 C T SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated intronic c.669+48094 e5+48094 0.001 - - - no_errors tier3 713 9 1.25 381 321 45.66 NA NA NA 246634 TCGA-AB-2968 AML23 9 18851540 18851540 G A SNP ADAMTSL1 NM_001040272.4 human genbank 54_36p 1 validated intronic c.4250-26289 e24-26289 0.001 - - - no_errors tier3 503 13 2.52 373 291 43.83 NA NA NA 246634 TCGA-AB-2968 AML23 9 19110440 19110440 A T SNP ADFP NM_001122.2 human genbank 54_36p -1 reviewed intronic c.595+438 e4+438 0.004 - - - no_errors tier3 281 5 1.75 102 70 40.7 NA NA NA 246634 TCGA-AB-2968 AML23 9 23205641 23205641 T G SNP MGC50722 NM_203348.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-2896 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 271 4 1.45 77 64 45.39 NA NA NA 246634 TCGA-AB-2968 AML23 9 24463271 24463271 C A SNP - - - - - - - - - - - - - - - tier3 464 1 0.22 451 73 13.9 NA NA NA 246634 TCGA-AB-2968 AML23 9 25271436 25271436 C T SNP - - - - - - - - - - - - - - - tier3 421 5 1.17 328 224 40.58 NA NA NA 246634 TCGA-AB-2968 AML23 9 25404963 25404963 A G SNP - - - - - - - - - - - - - - - tier3 457 9 1.93 207 163 44.05 NA NA NA 246634 TCGA-AB-2968 AML23 9 25795645 25795645 C T SNP - - - - - - - - - - - - - - - tier3 374 5 1.32 253 109 30.11 NA NA NA 246634 TCGA-AB-2968 AML23 9 26104029 26104029 C A SNP ENSG00000196478 ENST00000359978 human ensembl 54_36p 1 known intronic c.221-353 e3-353 0.113 - - - no_errors tier3 595 11 1.82 255 221 46.43 NA NA NA 246634 TCGA-AB-2968 AML23 9 33980347 33980347 G A SNP UBAP2 NM_018449.2 human genbank 54_36p -1 reviewed intronic c.289-1223 e4-1223 0 - - - no_errors tier3 472 12 2.48 162 137 45.82 NA NA NA 246634 TCGA-AB-2968 AML23 9 37142124 37142124 C T SNP ZCCHC7 NM_032226.2 human genbank 54_36p 1 validated intronic c.610+25185 e1+25185 0 - - - no_errors tier3 398 5 1.24 177 113 38.97 NA NA NA 246634 TCGA-AB-2968 AML23 9 37715655 37715655 C T SNP FRMPD1 NM_014907.1 human genbank 54_36p 1 provisional intronic c.612+1338 e6+1338 0 - - - no_errors tier3 384 5 1.29 144 121 45.66 NA NA NA 246634 TCGA-AB-2968 AML23 9 73132394 73132394 A G SNP TRPM3 ENST00000357533 human ensembl 54_36p -1 known intronic c.183+118995 e1+118995 0.001 - - - no_errors tier3 237 3 1.25 110 84 43.3 NA NA NA 246634 TCGA-AB-2968 AML23 9 88332906 88332906 C T SNP - - - - - - - - - - - - - - - tier3 478 13 2.65 179 166 48.12 NA NA NA 246634 TCGA-AB-2968 AML23 9 90123399 90123399 C T SNP LOC401537 XR_017028.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-5739 NULL 0 - - - pseudogene tier3 533 12 2.2 126 103 44.98 NA NA NA 246634 TCGA-AB-2968 AML23 9 90123945 90123945 C T SNP LOC401537 XR_017028.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-5193 NULL 0 - - - pseudogene tier3 437 12 2.67 129 87 40.28 NA NA NA 246634 TCGA-AB-2968 AML23 9 97269319 97269319 G A SNP PTCH1 NM_000264.3 human genbank 54_36p -1 reviewed silent c.2460 p.Y820 0.971 HMMPfam_Patched "HMMPfam_Patched,superfamily_SSF82866" - no_errors tier1 445 5 1.11 171 83 32.68 NA NA NA 246634 TCGA-AB-2968 AML23 9 97994510 97994510 C T SNP LOC650656 XM_001717913.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-22738 NULL 0 - - - no_errors tier3 365 1 0.27 157 51 24.4 NA NA NA 246634 TCGA-AB-2968 AML23 9 102791999 102791999 G C SNP PRG-3 NM_207299.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-195599 NULL 0 - - - no_errors tier3 518 7 1.33 203 171 45.72 NA NA NA 246634 TCGA-AB-2968 AML23 9 108022006 108022006 T C SNP - - - - - - - - - - - - - - - tier3 491 7 1.41 284 248 46.62 NA NA NA 246634 TCGA-AB-2968 AML23 9 116468870 116468870 T G SNP LOC100129633 XM_001718491.1 human genbank 54_36p -1 model intronic c.1246+1437 e6+1437 0.003 - - - no_errors tier3 305 3 0.97 261 180 40.82 NA NA NA 246634 TCGA-AB-2968 AML23 9 118576945 118576945 G A SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.2396+30787 e13+30787 0.119 - - - no_errors tier3 358 4 1.1 265 204 43.5 NA NA NA 246634 TCGA-AB-2968 AML23 9 130937029 130937029 C T SNP PPP2R4 NM_178001.3 human genbank 54_36p 1 reviewed intronic c.665+35 e7+35 0 - - - no_errors tier3 103 3 2.83 47 45 48.39 NA NA NA 246634 TCGA-AB-2968 AML23 9 134143625 134143625 A T SNP SETX NM_015046.5 human genbank 54_36p -1 reviewed intronic c.6655-160 e19-160 0 - - - no_errors tier3 421 8 1.83 238 84 25.53 NA NA NA 246634 TCGA-AB-2968 AML23 9 136960944 136960944 G A SNP FCN1 NM_002003.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11406 NULL 0.001 - - - no_errors tier3 364 8 2.15 164 152 48.1 NA NA NA 246634 TCGA-AB-2968 AML23 10 426150 426150 C T SNP DIP2C NM_014974.2 human genbank 54_36p -1 reviewed intronic c.1494+54 e12+54 0 - - - no_errors tier3 450 13 2.8 200 170 45.95 NA NA NA 246634 TCGA-AB-2968 AML23 10 2079774 2079774 C A SNP - - - - - - - - - - - - - - - tier3 305 8 2.56 111 94 45.85 NA NA NA 246634 TCGA-AB-2968 AML23 10 4028256 4028256 G A SNP - - - - - - - - - - - - - - - tier3 424 14 3.19 247 203 45.01 NA NA NA 246634 TCGA-AB-2968 AML23 10 7089055 7089055 G A SNP - - - - - - - - - - - - - - - tier3 999 31 3.01 333 256 43.46 NA NA NA 246634 TCGA-AB-2968 AML23 10 24281379 24281379 C T SNP KIAA1217 NM_001098500.1 human genbank 54_36p 1 validated intronic c.1-54781 e1-54781 0.002 - - - no_errors tier3 495 15 2.94 296 267 47.42 NA NA NA 246634 TCGA-AB-2968 AML23 10 24702509 24702509 C A SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated intronic c.355-7295 e3-7295 0.01 - - - no_errors tier3 364 11 2.93 243 176 41.9 NA NA NA 246634 TCGA-AB-2968 AML23 10 26231161 26231161 G A SNP MYO3A NM_017433.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49885 NULL 0 - - - no_errors tier3 677 5 0.73 349 305 46.64 NA NA NA 246634 TCGA-AB-2968 AML23 10 27211932 27211932 G A SNP ABI1 NM_005470.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22134 NULL 0.006 - - - no_errors tier3 274 6 2.14 115 75 39.47 NA NA NA 246634 TCGA-AB-2968 AML23 10 28091949 28091949 T C SNP MKX NM_173576.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19599 NULL 0.001 - - - no_errors tier3 252 9 3.45 90 94 51.09 NA NA NA 246634 TCGA-AB-2968 AML23 10 33866510 33866510 G A SNP - - - - - - - - - - - - - - - tier3 372 7 1.85 261 187 41.65 NA NA NA 246634 TCGA-AB-2968 AML23 10 35390036 35390036 A T SNP CUL2 NM_003591.2 human genbank 54_36p -1 provisional intronic c.223-134 e3-134 0 - - - no_errors tier3 603 15 2.42 181 146 44.65 NA NA NA 246634 TCGA-AB-2968 AML23 10 42222918 42222918 T C SNP uc001izw.1 ENST00000355576 human ensembl 54_36p -1 known 5_prime_flanking_region c.-39419 NULL 0 - - - no_coding_region:pseudogene tier3 323 10 3 249 192 43.54 NA NA NA 246634 TCGA-AB-2968 AML23 10 44239665 44239665 G A SNP CXCL12 NM_001033886.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-39206 NULL 0 - - - no_errors tier3 455 3 0.66 443 170 27.73 NA NA NA 246634 TCGA-AB-2968 AML23 10 58741506 58741506 C T SNP - - - - - - - - - - - - - - - tier3 458 13 2.76 203 157 43.61 NA NA NA 246634 TCGA-AB-2968 AML23 10 58946957 58946957 A G SNP ENSG00000218583 ENST00000403728 human ensembl 54_36p 1 known 3_prime_flanking_region c.*3766 NULL 0.005 - - - no_coding_region:pseudogene tier3 487 8 1.62 176 142 44.65 NA NA NA 246634 TCGA-AB-2968 AML23 10 64165235 64165235 G A SNP ATQL4 ENST00000403297 human ensembl 54_36p -1 known 3_prime_flanking_region c.*5739 NULL 0.02 - - - no_coding_region:pseudogene tier3 640 15 2.29 282 243 46.29 NA NA NA 246634 TCGA-AB-2968 AML23 10 68353763 68353763 T G SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1048-148475 e7-148475 0.001 - - - no_errors tier3 484 11 2.22 338 244 41.92 NA NA NA 246634 TCGA-AB-2968 AML23 10 68653082 68653082 A G SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.580-3448 e5-3448 0.179 - - - no_errors tier3 452 7 1.53 176 153 46.5 NA NA NA 246634 TCGA-AB-2968 AML23 10 80412105 80412105 C T SNP - - - - - - - - - - - - - - - tier3 265 5 1.85 144 85 37.12 NA NA NA 246634 TCGA-AB-2968 AML23 10 82733853 82733853 C A SNP ENSG00000220859 ENST00000403693 human ensembl 54_36p -1 known 5_prime_flanking_region c.-42916 NULL 0 - - - no_coding_region:pseudogene tier3 407 3 0.73 328 135 29.16 NA NA NA 246634 TCGA-AB-2968 AML23 10 97419189 97419189 A G SNP TCTN3 NM_015631.1 human genbank 54_36p -1 validated intronic c.1057-5142 e11-5142 0.013 - - - no_errors tier3 510 7 1.35 207 138 40 NA NA NA 246634 TCGA-AB-2968 AML23 10 102618169 102618169 G T SNP FAM178A NM_018121.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44689 NULL 0.011 - - - no_errors tier3 67 0 0 35 24 40.68 NA NA NA 246634 TCGA-AB-2968 AML23 10 106449880 106449880 C T SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.627+58178 e1+58178 0 - - - no_errors tier3 358 5 1.37 223 166 42.67 NA NA NA 246634 TCGA-AB-2968 AML23 10 106594207 106594207 C T SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.695+1600 e2+1600 0 - - - no_errors tier3 666 16 2.35 337 237 41.15 NA NA NA 246634 TCGA-AB-2968 AML23 10 108255600 108255600 A G SNP ENSG00000213257 ENST00000393172 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44245 NULL 0.001 - - - no_coding_region:pseudogene tier3 808 7 0.86 352 229 39.41 NA NA NA 246634 TCGA-AB-2968 AML23 10 108496490 108496490 A - DEL SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed intronic c.959+14846 e5+14846 0.028 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 10 109809348 109809348 G A SNP - - - - - - - - - - - - - - - tier3 733 16 2.14 403 238 37.13 NA NA NA 246634 TCGA-AB-2968 AML23 10 113482714 113482714 C T SNP - - - - - - - - - - - - - - - tier3 354 3 0.84 203 116 36.36 NA NA NA 246634 TCGA-AB-2968 AML23 10 114335625 114335625 A G SNP VTI1A NM_145206.2 human genbank 54_36p 1 validated intronic c.427+47546 e5+47546 0 - - - no_errors tier3 657 16 2.38 249 203 44.91 NA NA NA 246634 TCGA-AB-2968 AML23 10 115049021 115049021 G A SNP - - - - - - - - - - - - - - - tier3 452 10 2.16 324 281 46.37 NA NA NA 246634 TCGA-AB-2968 AML23 10 117467974 117467974 G A SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.3796-8774 e27-8774 0.002 - - - no_errors tier3 459 11 2.34 191 164 46.2 NA NA NA 246634 TCGA-AB-2968 AML23 10 118653096 118653096 C T SNP KIAA1598 NM_018330.1 human genbank 54_36p -1 validated intronic c.1359+8195 e14+8195 0.003 - - - no_errors tier2 477 11 2.25 291 219 42.94 NA NA NA 246634 TCGA-AB-2968 AML23 10 123441791 123441791 C T SNP LOC729426 XM_001133560.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-46911 NULL 0.053 - - - no_errors tier3 649 4 0.61 500 219 30.42 NA NA NA 246634 TCGA-AB-2968 AML23 10 124255346 124255346 C T SNP HTRA1 NM_002775.4 human genbank 54_36p 1 reviewed intronic c.778-851 e4-851 0 - - - no_errors tier3 205 9 4.21 177 116 39.32 NA NA NA 246634 TCGA-AB-2968 AML23 10 127208365 127208365 G A SNP - - - - - - - - - - - - - - - tier3 446 18 3.88 190 154 44.77 NA NA NA 246634 TCGA-AB-2968 AML23 10 127901123 127901123 C T SNP ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed intronic c.260+56351 e3+56351 0 - - - no_errors tier3 301 4 1.31 238 159 40.05 NA NA NA 246634 TCGA-AB-2968 AML23 10 132831480 132831480 C T SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated intronic c.1189+3279 e7+3279 0 - - - no_errors tier3 406 2 0.49 176 84 32.18 NA NA NA 246634 TCGA-AB-2968 AML23 11 1797874 1797874 G T SNP - - - - - - - - - - - - - - - tier3 137 2 1.44 42 39 48.15 NA NA NA 246634 TCGA-AB-2968 AML23 11 3782052 3782052 G A SNP - - - - - - - - - - - - - - - tier3 227 8 3.4 78 47 37.6 NA NA NA 246634 TCGA-AB-2968 AML23 11 8894746 8894746 G A SNP - - - - - - - - - - - - - - - tier3 161 2 1.23 107 64 37.43 NA NA NA 246634 TCGA-AB-2968 AML23 11 11634970 11634970 G A SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35254 NULL 0 - - - no_errors tier3 777 16 2.02 488 318 39.45 NA NA NA 246634 TCGA-AB-2968 AML23 11 26925816 26925816 G A SNP - - - - - - - - - - - - - - - tier3 799 17 2.08 413 296 41.69 NA NA NA 246634 TCGA-AB-2968 AML23 11 27837445 27837445 T C SNP - - - - - - - - - - - - - - - tier3 404 13 3.12 219 139 38.83 NA NA NA 246634 TCGA-AB-2968 AML23 11 29907055 29907055 C A SNP - - - - - - - - - - - - - - - tier3 443 6 1.34 268 171 38.95 NA NA NA 246634 TCGA-AB-2968 AML23 11 33609266 33609266 T A SNP - - - - - - - - - - - - - - - tier3 568 11 1.9 427 297 41.02 NA NA NA 246634 TCGA-AB-2968 AML23 11 39102900 39102900 C T SNP - - - - - - - - - - - - - - - tier3 479 8 1.64 194 194 50 NA NA NA 246634 TCGA-AB-2968 AML23 11 41637998 41637998 G A SNP - - - - - - - - - - - - - - - tier3 520 7 1.33 329 296 47.21 NA NA NA 246634 TCGA-AB-2968 AML23 11 44128151 44128151 T G SNP - - - - - - - - - - - - - - - tier3 538 12 2.18 241 220 47.62 NA NA NA 246634 TCGA-AB-2968 AML23 11 46873064 46873064 G C SNP - - - - - - - - - - - - - - - tier3 281 4 1.4 160 145 47.54 NA NA NA 246634 TCGA-AB-2968 AML23 11 49170487 49170487 C A SNP - - - - - - - - - - - - - - - tier3 152 6 3.8 64 45 41.28 NA NA NA 246634 TCGA-AB-2968 AML23 11 56851199 56851199 A G SNP - - - - - - - - - - - - - - - tier3 301 9 2.9 69 62 47.33 NA NA NA 246634 TCGA-AB-2968 AML23 11 59494133 59494133 C T SNP - - - - - - - - - - - - - - - tier3 506 2 0.39 319 164 33.95 NA NA NA 246634 TCGA-AB-2968 AML23 11 64121828 64121828 G A SNP - - - - - - - - - - - - - - - tier3 87 3 3.33 101 70 40.94 NA NA NA 246634 TCGA-AB-2968 AML23 11 68470143 68470143 C G SNP - - - - - - - - - - - - - - - tier3 237 3 1.25 74 48 39.34 NA NA NA 246634 TCGA-AB-2968 AML23 11 79340802 79340802 C A SNP - - - - - - - - - - - - - - - tier3 659 18 2.66 296 245 45.12 NA NA NA 246634 TCGA-AB-2968 AML23 11 81819505 81819505 C T SNP - - - - - - - - - - - - - - - tier3 533 10 1.84 322 257 44.39 NA NA NA 246634 TCGA-AB-2968 AML23 11 94672538 94672538 G A SNP - - - - - - - - - - - - - - - tier3 403 4 0.98 308 275 47.17 NA NA NA 246634 TCGA-AB-2968 AML23 11 100149669 100149669 G A SNP - - - - - - - - - - - - - - - tier3 406 13 3.1 203 180 47 NA NA NA 246634 TCGA-AB-2968 AML23 11 100235074 100235074 C T SNP ENSG00000200047 ENST00000363177 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*19187 NULL 0.229 - - - no_errors tier3 302 4 1.31 166 127 43.34 NA NA NA 246634 TCGA-AB-2968 AML23 11 102987027 102987027 G T SNP - - - - - - - - - - - - - - - tier3 371 6 1.59 306 211 40.81 NA NA NA 246634 TCGA-AB-2968 AML23 11 106403795 106403795 G A SNP GUCY1A2 NM_000855.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9804 NULL 0 - - - no_errors tier3 519 15 2.81 172 145 45.74 NA NA NA 246634 TCGA-AB-2968 AML23 11 125375771 125375771 A G SNP CDON NM_016952.4 human genbank 54_36p -1 validated intronic c.2158+1053 e10+1053 0.003 - - - no_errors tier3 686 11 1.58 457 157 25.53 NA NA NA 246634 TCGA-AB-2968 AML23 11 127316318 127316318 G A SNP LOC387820 XR_017453.2 human genbank 54_36p -1 model rna NULL NULL 0.997 - - - pseudogene tier1 286 4 1.38 140 50 26.32 NA NA NA 246634 TCGA-AB-2968 AML23 11 127575050 127575050 T C SNP - - - - - - - - - - - - - - - tier3 543 14 2.51 215 152 41.42 NA NA NA 246634 TCGA-AB-2968 AML23 11 129326837 129326837 G A SNP PRDM10 NM_020228.2 human genbank 54_36p -1 reviewed intronic c.294+3780 e3+3780 0.008 - - - no_errors tier3 347 0 0 167 54 24.32 NA NA NA 246634 TCGA-AB-2968 AML23 11 130770196 130770196 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.82+24203 e1+24203 0.001 - - - no_errors tier3 554 18 3.15 396 314 44.23 NA NA NA 246634 TCGA-AB-2968 AML23 11 134418713 134418713 C T SNP - - - - - - - - - - - - - - - tier3 227 5 2.16 188 205 52.16 NA NA NA 246634 TCGA-AB-2968 AML23 12 7173417 7173418 - G INS LOC100133229 XM_001721004.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*398 NULL 0.146:0.135 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 12 14089388 14089388 C T SNP - - - - - - - - - - - - - - - tier3 414 1 0.24 198 51 20.4 NA NA NA 246634 TCGA-AB-2968 AML23 12 18116115 18116115 C T SNP RERGL NM_024730.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*9277 NULL 0.032 - - - no_errors tier3 428 6 1.38 323 226 41.17 NA NA NA 246634 TCGA-AB-2968 AML23 12 18757102 18757102 G A SNP PLCZ1 NM_033123.2 human genbank 54_36p -1 provisional missense c.655 p.L219F 0.998 "HMMPfam_PI-PLC-X,HMMSmart_SM00148,superfamily_PLC-like phosphodiesterases" "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand" - no_errors tier1 744 9 1.2 296 256 46.38 NA NA NA 246634 TCGA-AB-2968 AML23 12 20975575 20975575 G A SNP SLCO1B3 NM_019844.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*15127 NULL 0.004 - - - no_errors tier3 574 7 1.2 409 336 45.1 NA NA NA 246634 TCGA-AB-2968 AML23 12 21561149 21561149 G T SNP GOLT1B NM_016072.4 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*1241 NULL 0 - - - no_errors tier3 388 3 0.77 211 147 41.06 NA NA NA 246634 TCGA-AB-2968 AML23 12 37901649 37901649 C T SNP - - - - - - - - - - - - - - - tier3 519 9 1.7 365 301 45.06 NA NA NA 246634 TCGA-AB-2968 AML23 12 38182118 38182118 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 12 40141605 40141605 C A SNP PDZRN4 NM_013377.3 human genbank 54_36p 1 validated intronic c.69+23523 e1+23523 0.001 - - - no_errors tier3 893 16 1.76 425 360 45.86 NA NA NA 246634 TCGA-AB-2968 AML23 12 45057245 45057246 - T INS SLC38A2 ENST00000395444 human ensembl 54_36p -1 known intronic c.14+3418_14+3417 e1+3418 0.000:0.000 - - - no_start_codon tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 12 45684896 45684896 G A SNP - - - - - - - - - - - - - - - tier3 432 6 1.37 352 235 39.97 NA NA NA 246634 TCGA-AB-2968 AML23 12 50727375 50727375 T C SNP NR4A1 ENST00000360284 human ensembl 54_36p 1 known intronic c.160+5395 e2+5395 0.005 - - - no_errors tier3 250 1 0.4 149 45 23.2 NA NA NA 246634 TCGA-AB-2968 AML23 12 51699990 51699990 C G SNP EIF4B NM_001417.4 human genbank 54_36p 1 validated silent c.390 p.P130 1 "HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928" "HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928" - no_errors tier1 337 6 1.75 127 86 40.38 NA NA NA 246634 TCGA-AB-2968 AML23 12 53863702 53863702 T A SNP OR10A7 NM_001005280.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-37374 NULL 0 - - - no_errors tier3 227 3 1.3 70 33 32.04 NA NA NA 246634 TCGA-AB-2968 AML23 12 57401308 57401308 T C SNP - - - - - - - - - - - - - - - tier3 575 9 1.54 232 149 39.11 NA NA NA 246634 TCGA-AB-2968 AML23 12 63623957 63623957 C A SNP FLJ41278 XM_001129851.2 human genbank 54_36p 1 model intronic c.441-30661 e5-30661 0 - - - no_errors tier3 353 9 2.49 403 318 44.11 NA NA NA 246634 TCGA-AB-2968 AML23 12 71558022 71558022 G A SNP - - - - - - - - - - - - - - - tier3 438 6 1.35 260 203 43.84 NA NA NA 246634 TCGA-AB-2968 AML23 12 83144657 83144657 A T SNP ENSG00000221148 ENST00000408221 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43299 NULL 0.003 - - - no_errors tier3 337 5 1.46 136 98 41.88 NA NA NA 246634 TCGA-AB-2968 AML23 12 83968802 83968802 G A SNP LRRIQ1 NM_001079910.1 human genbank 54_36p 1 validated intronic c.679-1284 e6-1284 0 - - - no_errors tier3 481 4 0.82 306 145 32.15 NA NA NA 246634 TCGA-AB-2968 AML23 12 85289057 85289057 G A SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1-37021 e1-37021 0 - - - no_errors tier3 567 12 2.07 266 195 42.3 NA NA NA 246634 TCGA-AB-2968 AML23 12 107058016 107058016 G A SNP WSCD2 NM_014653.2 human genbank 54_36p 1 validated intronic c.1+10183 e0+10183 0 - - - no_errors tier3 450 20 4.26 274 215 43.97 NA NA NA 246634 TCGA-AB-2968 AML23 12 107557006 107557006 G A SNP SELPLG NM_003006.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14794 NULL 0.001 - - - no_errors tier3 286 3 1.04 186 122 39.48 NA NA NA 246634 TCGA-AB-2968 AML23 12 112544657 112544657 C T SNP - - - - - - - - - - - - - - - tier3 690 16 2.26 302 258 45.83 NA NA NA 246634 TCGA-AB-2968 AML23 12 114181238 114181238 C T SNP - - - - - - - - - - - - - - - tier3 478 8 1.65 243 182 42.82 NA NA NA 246634 TCGA-AB-2968 AML23 12 116406649 116406649 G A SNP KSR2 NM_173598.4 human genbank 54_36p -1 validated missense c.2042 p.T681M 1 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMPfam_C1_1,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase,superfamily_Cysteine-rich domain" - no_errors tier1 462 10 2.12 240 190 44.08 NA NA NA 246634 TCGA-AB-2968 AML23 12 125316709 125316709 C T SNP - - - - - - - - - - - - - - - tier3 788 14 1.75 437 354 44.75 NA NA NA 246634 TCGA-AB-2968 AML23 12 127237038 127237038 G A SNP - - - - - - - - - - - - - - - tier3 539 19 3.41 184 171 48.17 NA NA NA 246634 TCGA-AB-2968 AML23 12 127420563 127420563 C T SNP - - - - - - - - - - - - - - - tier3 262 1 0.38 168 128 43.24 NA NA NA 246634 TCGA-AB-2968 AML23 13 21090474 21090474 C T SNP EFHA1 NM_152726.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-14187 NULL 0.002 - - - no_errors tier3 458 7 1.51 200 119 37.3 NA NA NA 246634 TCGA-AB-2968 AML23 13 22254880 22254880 G A SNP ENSG00000199850 ENST00000362980 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20404 NULL 0.011 - - - no_errors tier3 662 3 0.45 245 214 46.62 NA NA NA 246634 TCGA-AB-2968 AML23 13 26446444 26446444 C T SNP ENSG00000218572 ENST00000404126 human ensembl 54_36p 1 known 5_prime_flanking_region c.-3236 NULL 0 - - - no_coding_region:pseudogene tier3 1232 29 2.3 565 414 42.29 NA NA NA 246634 TCGA-AB-2968 AML23 13 28753919 28753919 G A SNP KIAA0774 NM_001033602.2 human genbank 54_36p 1 validated missense c.2753 p.R918Q 0.496 NULL NULL - no_errors tier1 259 2 0.77 247 185 42.82 NA NA NA 246634 TCGA-AB-2968 AML23 13 32328819 32328819 C T SNP - - - - - - - - - - - - - - - tier3 306 10 3.15 148 116 43.94 NA NA NA 246634 TCGA-AB-2968 AML23 13 32424054 32424054 G A SNP LOC122038 XR_040920.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*2141 NULL 0 - - - no_errors tier3 779 17 2.14 403 283 41.25 NA NA NA 246634 TCGA-AB-2968 AML23 13 36641315 36641315 C G SNP ENSG00000202395 ENST00000365525 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2520 NULL 0.002 - - - no_errors tier3 459 10 2.13 430 362 45.71 NA NA NA 246634 TCGA-AB-2968 AML23 13 36686275 36686275 G A SNP ENSG00000202395 ENST00000365525 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-47480 NULL 0 - - - no_errors tier3 595 10 1.65 354 273 43.4 NA NA NA 246634 TCGA-AB-2968 AML23 13 37260372 37260372 C T SNP TRPC4 NM_016179.1 human genbank 54_36p -1 validated intronic c.1-4875 e1-4875 0 - - - no_errors tier3 746 11 1.45 399 306 43.4 NA NA NA 246634 TCGA-AB-2968 AML23 13 53894746 53894746 G A SNP LOC387930 XR_041079.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - pseudogene tier3 678 16 2.3 330 255 43.59 NA NA NA 246634 TCGA-AB-2968 AML23 13 54142351 54142351 G T SNP - - - - - - - - - - - - - - - tier3 411 7 1.67 155 120 43.48 NA NA NA 246634 TCGA-AB-2968 AML23 13 55471130 55471130 A G SNP HNF4GP1 ENST00000403841 human ensembl 54_36p -1 known 3_prime_flanking_region c.*226 NULL 0.107 - - - no_coding_region:pseudogene tier3 509 9 1.74 228 174 43.28 NA NA NA 246634 TCGA-AB-2968 AML23 13 55725372 55725372 C T SNP ENSG00000219006 ENST00000404148 human ensembl 54_36p 1 known 3_prime_flanking_region c.*36295 NULL 0.088 - - - no_coding_region:pseudogene tier3 327 5 1.51 237 145 37.96 NA NA NA 246634 TCGA-AB-2968 AML23 13 56091891 56091891 C T SNP - - - - - - - - - - - - - - - tier3 471 9 1.88 263 205 43.8 NA NA NA 246634 TCGA-AB-2968 AML23 13 56281060 56281060 A C SNP - - - - - - - - - - - - - - - tier3 355 3 0.84 245 88 26.43 NA NA NA 246634 TCGA-AB-2968 AML23 13 57000521 57000521 G A SNP - - - - - - - - - - - - - - - tier3 372 5 1.33 316 230 42.12 NA NA NA 246634 TCGA-AB-2968 AML23 13 58572275 58572275 C T SNP ENSG00000220547 ENST00000404304 human ensembl 54_36p -1 known 5_prime_flanking_region c.-28337 NULL 0.009 - - - no_coding_region:pseudogene tier3 592 16 2.63 334 268 44.52 NA NA NA 246634 TCGA-AB-2968 AML23 13 59203727 59203727 C T SNP DIAPH3 NM_001042517.1 human genbank 54_36p -1 validated intronic c.3319+42597 e27+42597 0.479 - - - no_errors tier3 732 9 1.21 320 254 44.17 NA NA NA 246634 TCGA-AB-2968 AML23 13 64194955 64194955 G A SNP - - - - - - - - - - - - - - - tier3 599 8 1.32 239 191 44.42 NA NA NA 246634 TCGA-AB-2968 AML23 13 67821105 67821105 C T SNP ENSG00000220172 ENST00000406450 human ensembl 54_36p -1 known 5_prime_flanking_region c.-45670 NULL 0 - - - no_coding_region:pseudogene tier3 474 12 2.47 161 119 42.5 NA NA NA 246634 TCGA-AB-2968 AML23 13 76879824 76879824 C T SNP - - - - - - - - - - - - - - - tier3 437 12 2.67 253 211 45.47 NA NA NA 246634 TCGA-AB-2968 AML23 13 80044288 80044288 T C SNP ENSG00000220058 ENST00000404823 human ensembl 54_36p -1 known 3_prime_flanking_region c.*46946 NULL 0.998 - - - no_coding_region:pseudogene tier3 690 15 2.13 380 271 41.63 NA NA NA 246634 TCGA-AB-2968 AML23 13 81283771 81283771 A - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 13 84247514 84247514 G A SNP - - - - - - - - - - - - - - - tier3 302 5 1.63 175 115 39.66 NA NA NA 246634 TCGA-AB-2968 AML23 13 97669214 97669214 T A SNP FARP1 NM_005766.2 human genbank 54_36p 1 reviewed intronic c.171+5546 e1+5546 0 - - - no_errors tier3 509 12 2.29 118 108 47.79 NA NA NA 246634 TCGA-AB-2968 AML23 13 100320756 100320756 C T SNP - - - - - - - - - - - - - - - tier3 794 23 2.82 383 282 42.41 NA NA NA 246634 TCGA-AB-2968 AML23 13 110442113 110442113 G A SNP - - - - - - - - - - - - - - - tier3 252 3 1.18 117 94 44.34 NA NA NA 246634 TCGA-AB-2968 AML23 13 111068635 111068635 G A SNP ENSG00000204398 ENST00000375713 human ensembl 54_36p 1 known intronic c.1-7700 e1-7700 0.002 - - - no_errors tier3 714 10 1.38 128 100 43.86 NA NA NA 246634 TCGA-AB-2968 AML23 13 111657833 111657833 C T SNP - - - - - - - - - - - - - - - tier3 168 4 2.31 102 86 45.74 NA NA NA 246634 TCGA-AB-2968 AML23 14 19406690 19406690 G A SNP ENSG00000176290 ENST00000315936 human ensembl 54_36p -1 novel 5_prime_untranslated_region c.-19406690 NULL 0 - - - no_coding_region:pseudogene tier3 318 7 2.15 186 170 47.75 NA NA NA 246634 TCGA-AB-2968 AML23 14 23201120 23201120 C T SNP DHRS2 NM_182908.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*16769 NULL 0.001 - - - no_errors tier3 570 20 3.39 374 256 40.63 NA NA NA 246634 TCGA-AB-2968 AML23 14 23795825 23795825 C T SNP TGM1 NM_000359.2 human genbank 54_36p -1 reviewed intronic c.1403-702 e9-702 0.012 - - - no_errors tier3 221 4 1.77 78 62 44.29 NA NA NA 246634 TCGA-AB-2968 AML23 14 25137096 25137096 G A SNP - - - - - - - - - - - - - - - tier3 471 7 1.46 258 185 41.76 NA NA NA 246634 TCGA-AB-2968 AML23 14 26225497 26225497 C T SNP - - - - - - - - - - - - - - - tier3 568 9 1.56 231 168 42 NA NA NA 246634 TCGA-AB-2968 AML23 14 27625274 27625274 G A SNP - - - - - - - - - - - - - - - tier3 467 3 0.64 392 122 23.74 NA NA NA 246634 TCGA-AB-2968 AML23 14 30180770 30180770 T G SNP SCFD1 NM_016106.2 human genbank 54_36p 1 validated intronic c.524-1503 e7-1503 0.022 - - - no_errors tier3 430 6 1.38 185 150 44.78 NA NA NA 246634 TCGA-AB-2968 AML23 14 32446390 32446390 C T SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-31884 NULL 0 - - - no_errors tier3 546 13 2.33 314 265 45.77 NA NA NA 246634 TCGA-AB-2968 AML23 14 39201840 39201840 C T SNP - - - - - - - - - - - - - - - tier3 529 3 0.56 441 166 27.35 NA NA NA 246634 TCGA-AB-2968 AML23 14 43260927 43260927 G A SNP - - - - - - - - - - - - - - - tier3 415 2 0.48 416 109 20.72 NA NA NA 246634 TCGA-AB-2968 AML23 14 46031898 46031898 G C SNP - - - - - - - - - - - - - - - tier3 477 11 2.25 321 262 44.94 NA NA NA 246634 TCGA-AB-2968 AML23 14 53287726 53287726 G A SNP - - - - - - - - - - - - - - - tier3 293 5 1.68 215 115 34.85 NA NA NA 246634 TCGA-AB-2968 AML23 14 61502165 61502165 T C SNP SYT16 NM_031914.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30326 NULL 0.001 - - - no_errors tier3 356 5 1.39 151 139 47.77 NA NA NA 246634 TCGA-AB-2968 AML23 14 64245974 64245974 C T SNP PLEKHG3 NM_015549.1 human genbank 54_36p 1 validated intronic c.1+4799 e0+4799 0 - - - no_errors tier3 472 6 1.26 180 130 41.94 NA NA NA 246634 TCGA-AB-2968 AML23 14 76179734 76179734 G A SNP - - - - - - - - - - - - - - - tier3 184 1 0.54 225 201 47.18 NA NA NA 246634 TCGA-AB-2968 AML23 14 78991968 78991968 T A SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2144-11349 e11-11349 0.02 - - - no_errors tier3 287 5 1.71 80 61 43.26 NA NA NA 246634 TCGA-AB-2968 AML23 14 82162620 82162620 C T SNP - - - - - - - - - - - - - - - tier3 621 15 2.35 374 292 43.84 NA NA NA 246634 TCGA-AB-2968 AML23 14 82808030 82808030 T C SNP - - - - - - - - - - - - - - - tier3 529 20 3.64 271 215 44.24 NA NA NA 246634 TCGA-AB-2968 AML23 14 83322836 83322836 G A SNP ENSG00000210408 ENST00000387673 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36240 NULL 0 - - - pseudogene tier3 438 9 2.01 321 203 38.74 NA NA NA 246634 TCGA-AB-2968 AML23 14 85107938 85107938 T G SNP FLRT2 NM_013231.4 human genbank 54_36p 1 reviewed intronic c.1+41307 e0+41307 0 - - - no_errors tier3 974 9 0.92 403 316 43.95 NA NA NA 246634 TCGA-AB-2968 AML23 14 86508173 86508173 C A SNP LOC283585 XR_041537.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*49321 NULL 0.009 - - - no_errors tier3 808 16 1.94 481 322 40.1 NA NA NA 246634 TCGA-AB-2968 AML23 14 87202667 87202667 A G SNP LOC730121 XM_001132513.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-11301 NULL 0 - - - no_errors tier3 551 13 2.3 311 216 40.99 NA NA NA 246634 TCGA-AB-2968 AML23 14 88569384 88569384 G T SNP - - - - - - - - - - - - - - - tier3 319 4 1.24 150 137 47.74 NA NA NA 246634 TCGA-AB-2968 AML23 14 93278910 93278910 C T SNP PRIMA1 NM_178013.3 human genbank 54_36p -1 reviewed intronic c.230-5441 e3-5441 0.001 - - - no_errors tier3 322 6 1.83 183 167 47.58 NA NA NA 246634 TCGA-AB-2968 AML23 14 95706181 95706181 G A SNP BDKRB2 NM_000623.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-67017 NULL 0.199 - - - no_errors tier3 399 10 2.44 253 177 41.16 NA NA NA 246634 TCGA-AB-2968 AML23 14 102734558 102734558 C T SNP LOC100131366 XM_001726597.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10212 NULL 0.028 - - - no_errors tier3 195 4 2.01 86 62 41.89 NA NA NA 246634 TCGA-AB-2968 AML23 14 104518194 104518194 C T SNP AHNAK2 NM_138420.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2575 NULL 0.001 - - - no_errors tier3 142 5 3.4 102 73 41.71 NA NA NA 246634 TCGA-AB-2968 AML23 15 19882945 19882945 C A SNP OR4N4 ENST00000328795 human ensembl 54_36p 1 known intronic c.1-883 e1-883 0.002 - - - no_errors tier3 279 15 5.1 35 155 81.58 NA NA NA 246634 TCGA-AB-2968 AML23 15 20703754 20703754 T C SNP LOC283683 XR_015696.2 human genbank 54_36p -1 model intronic c.NULL NULL 0.04 - - - no_errors tier3 235 7 2.89 135 104 43.51 NA NA NA 246634 TCGA-AB-2968 AML23 15 26739262 26739262 C T SNP LOC100132475 XM_001724230.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-7735 NULL 0 - - - no_errors tier3 224 2 0.88 91 60 39.74 NA NA NA 246634 TCGA-AB-2968 AML23 15 27750090 27750090 C T SNP LOC100130111 XM_001718651.1 human genbank 54_36p 1 model intronic c.932+2241 e7+2241 0.001 - - - no_errors tier3 137 4 2.84 47 34 41.98 NA NA NA 246634 TCGA-AB-2968 AML23 15 46930445 46930445 G A SNP SHC4 NM_203349.3 human genbank 54_36p -1 validated intronic c.1303+232 e9+232 0 - - - no_errors tier3 423 5 1.17 224 183 44.96 NA NA NA 246634 TCGA-AB-2968 AML23 15 51889401 51889401 C T SNP WDR72 ENST00000396328 human ensembl 54_36p -1 known 5_prime_flanking_region c.-76763 NULL 0.004 - - - no_errors tier3 502 3 0.59 431 339 44.03 NA NA NA 246634 TCGA-AB-2968 AML23 15 62845729 62845729 G T SNP RBPMS2 NM_194272.1 human genbank 54_36p -1 provisional intronic c.87+8756 e1+8756 0.014 - - - no_errors tier3 543 12 2.16 219 141 39.17 NA NA NA 246634 TCGA-AB-2968 AML23 15 83185197 83185197 C T SNP ALPK3 NM_020778.4 human genbank 54_36p 1 validated intronic c.2259+30 e5+30 0.003 - - - no_errors tier3 193 4 2.03 173 127 42.33 NA NA NA 246634 TCGA-AB-2968 AML23 15 85925056 85925056 G A SNP TMEM83 ENST00000404772 human ensembl 54_36p 1 known 3_prime_flanking_region c.*2427 NULL 0.078 - - - no_errors tier3 408 4 0.97 261 165 38.73 NA NA NA 246634 TCGA-AB-2968 AML23 15 87639098 87639098 A G SNP FANCI NM_018193.1 human genbank 54_36p 1 reviewed intronic c.2456+866 e22+866 0.003 - - - no_errors tier3 469 9 1.88 214 144 40.22 NA NA NA 246634 TCGA-AB-2968 AML23 15 90847051 90847051 G T SNP ST8SIA2 NM_006011.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*38432 NULL 0.052 - - - no_errors tier3 343 11 3.11 298 208 41.11 NA NA NA 246634 TCGA-AB-2968 AML23 15 97497293 97497293 G A SNP TTC23 NM_001040655.1 human genbank 54_36p -1 validated intronic c.1144-166 e9-166 0.002 - - - no_errors tier3 302 8 2.56 158 120 43.17 NA NA NA 246634 TCGA-AB-2968 AML23 16 112509 112509 A G SNP C16orf35 ENST00000262313 human ensembl 54_36p -1 known intronic c.189-3255 e3-3255 0 - - - no_errors tier3 208 3 1.42 77 47 37.9 NA NA NA 246634 TCGA-AB-2968 AML23 16 20531745 20531745 C A SNP ACSM2B NM_001105069.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-48077 NULL 0.925 - - - no_errors tier3 474 14 2.86 476 345 41.92 NA NA NA 246634 TCGA-AB-2968 AML23 16 25466347 25466347 G A SNP - - - - - - - - - - - - - - - tier3 445 12 2.63 335 292 46.57 NA NA NA 246634 TCGA-AB-2968 AML23 16 26227792 26227792 C T SNP ENSG00000217478 ENST00000402112 human ensembl 54_36p -1 known 3_prime_flanking_region c.*45826 NULL 0.001 - - - no_coding_region:pseudogene tier3 678 12 1.74 366 262 41.72 NA NA NA 246634 TCGA-AB-2968 AML23 16 26463951 26463951 C T SNP - - - - - - - - - - - - - - - tier3 449 13 2.8 183 152 45.24 NA NA NA 246634 TCGA-AB-2968 AML23 16 31958984 31958984 C T SNP LOC100128100 XM_001725785.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-15554 NULL 0.217 - - - no_errors tier3 250 1 0.4 359 92 20.35 NA NA NA 246634 TCGA-AB-2968 AML23 16 59184597 59184597 G A SNP - - - - - - - - - - - - - - - tier3 343 5 1.44 204 143 41.21 NA NA NA 246634 TCGA-AB-2968 AML23 16 59857780 59857780 A C SNP - - - - - - - - - - - - - - - tier3 457 6 1.3 162 129 44.33 NA NA NA 246634 TCGA-AB-2968 AML23 16 60258711 60258712 - A INS CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.1655-11586_1655-11585 e10-11585 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 16 62004728 62004728 G T SNP - - - - - - - - - - - - - - - tier3 454 9 1.94 297 241 44.71 NA NA NA 246634 TCGA-AB-2968 AML23 16 63090152 63090152 T A SNP - - - - - - - - - - - - - - - tier3 661 13 1.93 342 236 40.83 NA NA NA 246634 TCGA-AB-2968 AML23 16 63759293 63759293 C A SNP CDH11 NM_001797.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-163020 NULL 0.182 - - - no_errors tier3 675 11 1.6 318 85 21.09 NA NA NA 246634 TCGA-AB-2968 AML23 16 77751482 77751482 G A SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1057-51524 e9-51524 0.029 - - - no_errors tier3 582 17 2.84 424 310 42.23 NA NA NA 246634 TCGA-AB-2968 AML23 16 85884163 85884163 C A SNP LOC730018 XM_001132101.2 human genbank 54_36p -1 model intronic c.102+9597 e1+9597 0.008 - - - no_errors tier3 368 12 3.16 107 108 50 NA NA NA 246634 TCGA-AB-2968 AML23 17 11248125 11248125 A T SNP uc002gna.2 ENST00000409168 human ensembl 54_36p 1 known intronic c.895+24574 e3+24574 0.004 - - - no_errors tier3 535 9 1.65 295 241 44.88 NA NA NA 246634 TCGA-AB-2968 AML23 17 21877361 21877361 C T SNP LOC100131001 XM_001723720.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-42093 NULL 0 - - - no_errors tier3 425 15 3.41 155 105 40.23 NA NA NA 246634 TCGA-AB-2968 AML23 17 21949503 21949503 G A SNP ENSG00000209244 ENST00000386509 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5198 NULL 1 - - - pseudogene tier3 374 17 4.34 147 100 40.49 NA NA NA 246634 TCGA-AB-2968 AML23 17 22053899 22053899 T G SNP - - - - - - - - - - - - - - - tier3 245 3 1.2 175 120 40.68 NA NA NA 246634 TCGA-AB-2968 AML23 17 27169580 27169580 C T SNP UTP6 NM_018428.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*44911 NULL 0 - - - no_errors tier3 286 5 1.72 198 181 47.63 NA NA NA 246634 TCGA-AB-2968 AML23 17 42576887 42576887 C T SNP CDC27 NM_001256.1 human genbank 54_36p -1 reviewed intronic c.1071-540 e10-540 0 - - - no_errors tier3 465 4 0.85 152 92 37.7 NA NA NA 246634 TCGA-AB-2968 AML23 17 45621465 45621465 C T SNP COL1A1 NM_000088.3 human genbank 54_36p -1 reviewed intronic c.2937+63 e40+63 0 - - - no_errors tier3 196 4 1.99 92 76 45.24 NA NA NA 246634 TCGA-AB-2968 AML23 17 46785083 46785083 C T SNP - - - - - - - - - - - - - - - tier3 464 13 2.73 369 264 41.71 NA NA NA 246634 TCGA-AB-2968 AML23 17 47194125 47194125 G A SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.280-13948 e4-13948 0.056 - - - no_errors tier3 704 16 2.22 408 194 32.12 NA NA NA 246634 TCGA-AB-2968 AML23 17 57799642 57799642 A T SNP EFCAB3 NM_173503.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14431 NULL 0.002 - - - no_errors tier3 432 8 1.82 253 212 45.49 NA NA NA 246634 TCGA-AB-2968 AML23 17 58320611 58320611 C T SNP - - - - - - - - - - - - - - - tier3 468 16 3.31 175 133 43.18 NA NA NA 246634 TCGA-AB-2968 AML23 17 59822021 59822021 A G SNP ENSG00000201849 ENST00000364979 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4893 NULL 0.166 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 17 61553347 61553347 T G SNP CCDC46 NM_145036.2 human genbank 54_36p -1 validated intronic c.642+2979 e5+2979 0.006 - - - no_errors tier3 526 7 1.31 219 113 34.04 NA NA NA 246634 TCGA-AB-2968 AML23 17 63338445 63338445 T G SNP BPTF NM_182641.6 human genbank 54_36p 1 reviewed missense c.3983 p.V1328G 0.02 NULL "HMMPfam_Bromodomain,HMMSmart_BROMO,superfamily_Bromodomain,HMMSmart_PHD,HMMPfam_DDT,superfamily_FYVE_PHD_ZnF,HMMPfam_FYDLN_acid,PatternScan_EGF_2,PatternScan_BROMODOMAIN_1,HMMSmart_DDT,PatternScan_ZF_PHD_1,HMMPfam_PHD" - no_errors tier1 407 5 1.21 236 145 38.06 NA NA NA 246634 TCGA-AB-2968 AML23 17 63897222 63897222 G A SNP ARSG NM_014960.3 human genbank 54_36p 1 validated intronic c.1091+4314 e8+4314 0 - - - no_errors tier2 726 21 2.8 358 285 44.32 NA NA NA 246634 TCGA-AB-2968 AML23 17 66617279 66617279 C T SNP - - - - - - - - - - - - - - - tier3 725 9 1.22 363 285 43.98 NA NA NA 246634 TCGA-AB-2968 AML23 17 67107593 67107593 A T SNP LOC124685 XR_040247.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.058 - - - no_errors tier3 268 6 2.18 104 81 43.78 NA NA NA 246634 TCGA-AB-2968 AML23 17 67741540 67741540 C A SNP LOC727973 XR_039997.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - no_errors tier3 192 5 2.54 89 88 49.72 NA NA NA 246634 TCGA-AB-2968 AML23 17 70362102 70362102 G A SNP GRIN2C NM_000835.3 human genbank 54_36p -1 reviewed intronic c.399+326 e1+326 0.079 - - - no_errors tier3 228 3 1.3 150 58 27.88 NA NA NA 246634 TCGA-AB-2968 AML23 17 74649845 74649845 G T SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1-26420 e1-26420 0.015 - - - no_errors tier3 65 1 1.52 20 19 48.72 NA NA NA 246634 TCGA-AB-2968 AML23 17 74749932 74749932 G A SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1-6450 e1-6450 0.001 - - - no_errors tier3 155 4 2.52 80 77 49.04 NA NA NA 246634 TCGA-AB-2968 AML23 17 76088073 76088073 A G SNP NPTX1 NM_002522.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-23232 NULL 0.007 - - - no_errors tier3 217 6 2.68 53 43 44.79 NA NA NA 246634 TCGA-AB-2968 AML23 18 8155411 8155411 C A SNP PTPRM NM_001105244.1 human genbank 54_36p 1 reviewed intronic c.2300+21634 e14+21634 0 - - - no_errors tier3 462 0 0 282 130 31.48 NA NA NA 246634 TCGA-AB-2968 AML23 18 8482236 8482236 A G SNP ENSG00000222891 ENST00000410959 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*20112 NULL 0.032 - - - no_errors tier3 716 12 1.65 443 301 40.46 NA NA NA 246634 TCGA-AB-2968 AML23 18 9984035 9984035 G T SNP VAPA NM_003574.5 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*39827 NULL 0.001 - - - no_errors tier3 321 9 2.73 206 165 44.47 NA NA NA 246634 TCGA-AB-2968 AML23 18 17877815 17877815 A G SNP - - - - - - - - - - - - - - - tier3 377 10 2.58 185 152 45.1 NA NA NA 246634 TCGA-AB-2968 AML23 18 27684801 27684801 A G SNP KIAA1012 NM_014939.3 human genbank 54_36p -1 validated intronic c.3562-1101 e25-1101 0.017 - - - no_errors tier3 503 15 2.9 181 115 38.85 NA NA NA 246634 TCGA-AB-2968 AML23 18 29663825 29663825 C T SNP NOL4 NM_003787.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*22979 NULL 0.202 - - - no_errors tier3 995 10 0.99 372 276 42.59 NA NA NA 246634 TCGA-AB-2968 AML23 18 29930348 29930348 G A SNP NOL4 NM_003787.3 human genbank 54_36p -1 validated intronic c.640-2789 e5-2789 0.002 - - - no_errors tier3 773 21 2.64 375 242 39.22 NA NA NA 246634 TCGA-AB-2968 AML23 18 33236575 33236575 C T SNP BRUNOL4 NM_020180.1 human genbank 54_36p -1 reviewed intronic c.370-80733 e3-80733 0.015 - - - no_errors tier3 239 4 1.65 98 56 36.36 NA NA NA 246634 TCGA-AB-2968 AML23 18 33332937 33332937 A T SNP BRUNOL4 NM_020180.1 human genbank 54_36p -1 reviewed intronic c.287-13369 e2-13369 0 - - - no_errors tier3 327 4 1.21 168 128 42.95 NA NA NA 246634 TCGA-AB-2968 AML23 18 35652786 35652786 G A SNP - - - - - - - - - - - - - - - tier3 796 22 2.69 337 208 38.17 NA NA NA 246634 TCGA-AB-2968 AML23 18 36393752 36393752 G A SNP - - - - - - - - - - - - - - - tier3 285 4 1.38 232 158 40.51 NA NA NA 246634 TCGA-AB-2968 AML23 18 37695586 37695586 C T SNP ENSG00000218954 ENST00000404042 human ensembl 54_36p 1 known 3_prime_flanking_region c.*42202 NULL 0.04 - - - no_coding_region:pseudogene tier3 384 3 0.77 158 111 41.26 NA NA NA 246634 TCGA-AB-2968 AML23 18 41186414 41186414 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 18 50401823 50401823 C T SNP C18orf26 NM_173629.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-7611 NULL 0.001 - - - no_errors tier3 573 10 1.71 313 203 39.34 NA NA NA 246634 TCGA-AB-2968 AML23 18 55287905 55287905 G A SNP CCBE1 NM_133459.1 human genbank 54_36p -1 provisional intronic c.266-86 e4-86 0 - - - no_errors tier3 133 3 2.21 131 92 41.26 NA NA NA 246634 TCGA-AB-2968 AML23 18 58455477 58455477 C T SNP ENSG00000222223 ENST00000410291 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13046 NULL 0.001 - - - no_errors tier3 516 9 1.71 223 147 39.73 NA NA NA 246634 TCGA-AB-2968 AML23 18 60233457 60233457 G A SNP ENSG00000210488 ENST00000387753 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45544 NULL 0.004 - - - pseudogene tier3 643 26 3.89 289 214 42.54 NA NA NA 246634 TCGA-AB-2968 AML23 18 62256058 62256058 C G SNP - - - - - - - - - - - - - - - tier3 354 5 1.39 188 135 41.8 NA NA NA 246634 TCGA-AB-2968 AML23 18 65290727 65290727 C A SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.66+71201 e1+71201 0 - - - no_errors tier3 776 15 1.9 334 266 44.33 NA NA NA 246634 TCGA-AB-2968 AML23 18 66809652 66809652 A G SNP - - - - - - - - - - - - - - - tier3 404 6 1.46 187 137 42.28 NA NA NA 246634 TCGA-AB-2968 AML23 18 67073212 67073212 C A SNP - - - - - - - - - - - - - - - tier3 496 1 0.2 342 94 21.56 NA NA NA 246634 TCGA-AB-2968 AML23 18 67687092 67687092 A G SNP - - - - - - - - - - - - - - - tier3 563 13 2.26 371 259 41.11 NA NA NA 246634 TCGA-AB-2968 AML23 18 68167680 68167680 C T SNP - - - - - - - - - - - - - - - tier3 632 11 1.71 474 288 37.8 NA NA NA 246634 TCGA-AB-2968 AML23 18 69378173 69378173 G A SNP - - - - - - - - - - - - - - - tier3 303 7 2.26 262 221 45.66 NA NA NA 246634 TCGA-AB-2968 AML23 18 71026153 71026153 C T SNP TSHZ1 NM_005786.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-100333 NULL 0 - - - no_errors tier3 192 0 0 172 65 27.31 NA NA NA 246634 TCGA-AB-2968 AML23 18 71883212 71883212 G A SNP - - - - - - - - - - - - - - - tier3 544 7 1.27 291 130 30.88 NA NA NA 246634 TCGA-AB-2968 AML23 18 74193111 74193111 G A SNP - - - - - - - - - - - - - - - tier3 305 9 2.87 210 147 41.18 NA NA NA 246634 TCGA-AB-2968 AML23 19 316016 316016 G A SNP THEG NM_016585.3 human genbank 54_36p -1 reviewed intronic c.913+2049 e7+2049 0.007 - - - no_errors tier3 346 7 1.98 134 84 38.36 NA NA NA 246634 TCGA-AB-2968 AML23 19 13198505 13198505 C T SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known intronic c.5629-1919 e38-1919 0.088 - - - no_errors tier3 130 2 1.5 102 49 32.45 NA NA NA 246634 TCGA-AB-2968 AML23 19 15747765 15747765 G A SNP LOC388514 XR_017598.2 human genbank 54_36p -1 model intronic c.NULL NULL 0.005 - - - no_errors tier3 92 2 2.13 89 52 36.88 NA NA NA 246634 TCGA-AB-2968 AML23 19 16120758 16120758 T G SNP HSH2D ENST00000397369 human ensembl 54_36p 1 known intronic c.125+73 e1+73 0.011 - - - no_errors tier3 361 3 0.82 124 97 43.89 NA NA NA 246634 TCGA-AB-2968 AML23 19 35017037 35017038 - C INS CCNE1 NM_001238.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*10513 NULL 0.000:0.003 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 19 39551462 39551462 G A SNP GPI ENST00000392234 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*1548 NULL 0.001 - - - no_start_codon tier3 246 1 0.4 73 63 45.99 NA NA NA 246634 TCGA-AB-2968 AML23 19 40383693 40383693 G A SNP LSR NM_205834.5 human genbank 54_36p 1 validated 5_prime_flanking_region c.-47929 NULL 0.002 - - - no_errors tier3 397 6 1.49 215 135 38.57 NA NA NA 246634 TCGA-AB-2968 AML23 19 40995491 40995491 C T SNP PRODH2 NM_021232.1 human genbank 54_36p -1 reviewed nonsense c.285 p.W95* 0.998 NULL "HMMPfam_Pro_dh,superfamily_SSF51730" - no_errors tier1 537 8 1.47 181 148 44.98 NA NA NA 246634 TCGA-AB-2968 AML23 19 57668273 57668274 AA - DEL ZNF578 NM_001099694.1 human genbank 54_36p 1 validated intronic c.1+16250_16251 e0+16250 0.577:0.597 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 246634 TCGA-AB-2968 AML23 19 59801852 59801852 C T SNP LILRA1 NM_006863.1 human genbank 54_36p 1 provisional intronic c.1262-661 e7-661 0.001 - - - no_errors tier3 263 4 1.49 102 84 45.16 NA NA NA 246634 TCGA-AB-2968 AML23 19 61718513 61718513 A G SNP ZNF471 NM_020813.2 human genbank 54_36p 1 validated intronic c.34-943 e2-943 0.187 - - - no_errors tier3 537 10 1.83 190 166 46.63 NA NA NA 246634 TCGA-AB-2968 AML23 20 5711201 5711201 A G SNP C20orf196 NM_152504.2 human genbank 54_36p 1 predicted intronic c.178+9512 e1+9512 0.014 - - - no_errors tier3 299 3 0.99 152 103 40.39 NA NA NA 246634 TCGA-AB-2968 AML23 20 9405450 9405450 G T SNP PLCB4 NM_000933.2 human genbank 54_36p 1 reviewed intronic c.3496+50 e35+50 0 - - - no_errors tier3 684 9 1.3 408 309 43.1 NA NA NA 246634 TCGA-AB-2968 AML23 20 15371459 15371459 G A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.571+11379 e7+11379 0 - - - no_errors tier3 419 6 1.41 302 229 43.13 NA NA NA 246634 TCGA-AB-2968 AML23 20 16902013 16902013 C T SNP ENSG00000212165 ENST00000390863 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9464 NULL 0.014 - - - no_errors tier3 475 10 2.06 181 165 47.69 NA NA NA 246634 TCGA-AB-2968 AML23 20 18834347 18834347 G A SNP - - - - - - - - - - - - - - - tier3 462 11 2.32 343 293 46.07 NA NA NA 246634 TCGA-AB-2968 AML23 20 19264151 19264151 G A SNP SLC24A3 NM_020689.3 human genbank 54_36p 1 validated intronic c.271+54420 e2+54420 0 - - - no_errors tier3 429 2 0.46 239 198 45.31 NA NA NA 246634 TCGA-AB-2968 AML23 20 42239333 42239333 A C SNP JPH2 NM_175913.4 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*683 NULL 0.836 - - - no_errors tier3 118 1 0.84 81 39 32.5 NA NA NA 246634 TCGA-AB-2968 AML23 20 47926882 47926882 G A SNP SLC9A8 NM_015266.1 human genbank 54_36p 1 validated intronic c.1076-1043 e12-1043 0.01 - - - no_errors tier3 255 6 2.3 147 73 33.18 NA NA NA 246634 TCGA-AB-2968 AML23 20 53709435 53709435 A G SNP - - - - - - - - - - - - - - - tier3 351 8 2.23 189 186 49.47 NA NA NA 246634 TCGA-AB-2968 AML23 20 54183271 54183271 A G SNP ENSG00000222118 ENST00000410186 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*30246 NULL 0.001 - - - no_errors tier3 579 5 0.85 350 87 19.91 NA NA NA 246634 TCGA-AB-2968 AML23 20 54262032 54262032 C T SNP ENSG00000222118 ENST00000410186 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48396 NULL 0 - - - no_errors tier3 415 13 3.04 214 135 38.68 NA NA NA 246634 TCGA-AB-2968 AML23 20 56605446 56605446 G A SNP MGC4294 XR_041176.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-38093 NULL 0 - - - no_errors tier3 474 8 1.65 305 221 41.54 NA NA NA 246634 TCGA-AB-2968 AML23 20 59122380 59122380 G A SNP - - - - - - - - - - - - - - - tier3 214 3 1.38 213 162 43.2 NA NA NA 246634 TCGA-AB-2968 AML23 21 10004985 10004985 A G SNP TPTE NM_199261.2 human genbank 54_36p -1 validated intronic c.1+1931 e0+1931 0.014 - - - no_errors tier3 850 11 1.28 457 121 20.93 NA NA NA 246634 TCGA-AB-2968 AML23 21 19239964 19239964 C T SNP LOC100134323 XM_001724941.1 human genbank 54_36p -1 model intronic c.267+43406 e1+43406 0 - - - pseudogene:no_stop_codon tier3 481 5 1.03 391 125 24.22 NA NA NA 246634 TCGA-AB-2968 AML23 21 19694652 19694652 G A SNP - - - - - - - - - - - - - - - tier3 381 12 3.05 234 149 38.9 NA NA NA 246634 TCGA-AB-2968 AML23 21 20538763 20538763 T C SNP - - - - - - - - - - - - - - - tier3 280 4 1.41 116 117 50.21 NA NA NA 246634 TCGA-AB-2968 AML23 21 24006428 24006428 C T SNP - - - - - - - - - - - - - - - tier3 461 8 1.71 278 215 43.61 NA NA NA 246634 TCGA-AB-2968 AML23 21 29032991 29032991 C T SNP - - - - - - - - - - - - - - - tier3 601 8 1.31 278 200 41.84 NA NA NA 246634 TCGA-AB-2968 AML23 21 29902891 29902891 T G SNP GRIK1 NM_000830.3 human genbank 54_36p -1 reviewed intronic c.1099-9763 e8-9763 0.007 - - - no_errors tier3 619 7 1.12 295 221 42.83 NA NA NA 246634 TCGA-AB-2968 AML23 21 30915782 30915782 C G SNP KRTAP6-1 NM_181602.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-7688 NULL 0.061 - - - no_errors tier3 347 4 1.14 214 172 44.44 NA NA NA 246634 TCGA-AB-2968 AML23 21 32205931 32205931 G A SNP HUNK NM_014586.1 human genbank 54_36p 1 validated intronic c.262-12720 e2-12720 0.001 - - - no_errors tier3 350 4 1.13 204 164 44.57 NA NA NA 246634 TCGA-AB-2968 AML23 21 38426506 38426506 A G SNP DSCR8 ENST00000357704 human ensembl 54_36p 1 known intronic c.80+10131 e1+10131 0 - - - no_errors tier3 602 17 2.75 281 256 47.67 NA NA NA 246634 TCGA-AB-2968 AML23 21 40195625 40195625 G A SNP PCP4 NM_006198.2 human genbank 54_36p 1 validated intronic c.61+3303 e2+3303 0 - - - no_errors tier3 364 1 0.27 177 65 26.86 NA NA NA 246634 TCGA-AB-2968 AML23 21 42190006 42190006 T C SNP C2CD2 NM_015500.1 human genbank 54_36p -1 validated intronic c.1870+2225 e13+2225 0 - - - no_errors tier3 448 13 2.82 180 152 45.65 NA NA NA 246634 TCGA-AB-2968 AML23 21 43397525 43397525 G A SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.101 p.S34F 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 252 10 3.82 77 62 44.6 NA NA NA 246634 TCGA-AB-2968 AML23 21 46545887 46545887 A G SNP C21orf58 NM_058180.3 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*454 NULL 0 - - - no_errors tier3 172 3 1.7 62 55 47.01 NA NA NA 246634 TCGA-AB-2968 AML23 22 21530915 21530915 T C SNP uc002zwr.1 ENST00000410090 human ensembl 54_36p 1 known 5_prime_flanking_region c.-29319 NULL 0 - - - no_errors tier3 406 9 2.17 225 192 46.04 NA NA NA 246634 TCGA-AB-2968 AML23 22 33801443 33801443 T G SNP ISX NM_001008494.1 human genbank 54_36p 1 validated intronic c.230-7068 e2-7068 0.002 - - - no_errors tier3 499 7 1.38 186 162 46.55 NA NA NA 246634 TCGA-AB-2968 AML23 22 42427561 42427561 G A SNP EFCAB6 NM_022785.2 human genbank 54_36p -1 validated intronic c.1031+11127 e8+11127 0.001 - - - no_errors tier3 484 9 1.83 162 142 46.71 NA NA NA 246634 TCGA-AB-2968 AML23 22 43969913 43969913 C G SNP C22orf9 NM_015264.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1808 NULL 0.012 - - - no_errors tier3 172 0 0 162 118 42.14 NA NA NA 246634 TCGA-AB-2968 AML23 22 46165086 46165086 C T SNP - - - - - - - - - - - - - - - tier3 379 10 2.57 280 262 48.25 NA NA NA 452198 TCGA-AB-2969 AML31 X 25476033 25476033 C T SNP ENSG00000217775 ENST00000403311 human ensembl 54_36p -1 known 3_prime_flanking_region c.*43358 NULL 0.007 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 X 86570002 86570002 G A SNP ENSG00000219690 ENST00000405840 human ensembl 54_36p -1 known 5_prime_flanking_region c.-2653 NULL 0.107 - - - no_coding_region:pseudogene tier2 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 X 92941267 92941267 A C SNP - - - - - - - - - - - - - - - tier3 509 49 8.78 633 221 25.85 0 0 NA 452198 TCGA-AB-2969 AML31 X 105826475 105826475 T C SNP RNF128 NM_024539.3 human genbank 54_36p 1 reviewed intronic c.406+2181 e1+2181 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 1 93246772 93246772 G A SNP FAM69A NM_001006605.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-47198 NULL 0 - - - no_errors tier2 869 130 12.94 633 313 33.09 0 0 NA 452198 TCGA-AB-2969 AML31 1 107357719 107357719 C T SNP PRMT6 NM_018137.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-43319 NULL 0.108 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 1 108346944 108346944 A G SNP VAV3 NM_006113.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37930 NULL 0.002 - - - no_errors tier3 415 96 18.79 681 625 47.86 0 0 NA 452198 TCGA-AB-2969 AML31 1 147392656 147392656 C A SNP ENSG00000219033 ENST00000407608 human ensembl 54_36p -1 known intronic c.NULL NULL 0.071 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 0 452198 TCGA-AB-2969 AML31 1 168399126 168399126 C T SNP METTL11B ENST00000367764 human ensembl 54_36p 1 known intronic c.324+2674 e2+2674 0.994 - - - no_stop_codon tier2 812 32 3.78 1227 194 13.62 0 0 NA 452198 TCGA-AB-2969 AML31 1 179307551 179307551 A G SNP IER5 NM_016545.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17111 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 1 218018901 218018901 G A SNP ENSG00000208186 ENST00000385451 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*17061 NULL 0.013 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 1 224145610 224145610 T C SNP LEFTY1 NM_020997.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2221 NULL 0 - - - no_errors tier3 NA NA NA 2 0 0 0 0 NA 452198 TCGA-AB-2969 AML31 1 230352346 230352346 G A SNP - - - - - - - - - - - - - - - tier3 1013 197 16.27 900 826 47.86 0 0 NA 452198 TCGA-AB-2969 AML31 2 23527066 23527066 T C SNP KLHL29 XM_001717454.1 human genbank 54_36p 1 model intronic c.658-24869 e4-24869 0.006 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 386 40 9.37 475 250 34.44 0 0 NA 452198 TCGA-AB-2969 AML31 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 1018 175 14.67 459 387 45.64 6 16 72.73 452198 TCGA-AB-2969 AML31 2 77165972 77165972 G A SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1555-336422 e3-336422 0.035 - - - no_errors tier3 188 47 20 371 297 44.39 0 0 NA 452198 TCGA-AB-2969 AML31 2 140418446 140418446 C G SNP ENSG00000208291 ENST00000385556 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38277 NULL 0 - - - pseudogene tier3 1018 221 17.78 777 693 47.08 0 0 NA 452198 TCGA-AB-2969 AML31 2 184186967 184186967 G T SNP LOC644877 XR_017355.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-5725 NULL 0.002 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 2 208821357 208821357 C T SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.395 p.R132H 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 811 129 13.71 865 412 32.24 142 90 38.63 452198 TCGA-AB-2969 AML31 2 213886052 213886052 G T SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.398+2906 e4+2906 0.002 - - - no_errors tier3 NA NA NA NA NA NA 6 0 0 452198 TCGA-AB-2969 AML31 3 21310708 21310708 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 3 43135962 43135962 G A SNP C3orf39 NM_032806.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-38035 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 3 71109483 71109483 C G SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed splice_site c.1428+1 e11+1 1 - - - no_errors tier1 671 30 4.27 973 157 13.88 20 0 452198 TCGA-AB-2969 AML31 3 85564094 85564094 C T SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.62-369793 e2-369793 0 - - - no_errors tier3 1462 172 10.51 1386 719 34.16 0 0 NA 452198 TCGA-AB-2969 AML31 3 135449546 135449546 G A SNP RYK NM_001005861.2 human genbank 54_36p -1 reviewed intronic c.230+2411 e1+2411 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 NA NA NA NA NA NA 3 0 0 452198 TCGA-AB-2969 AML31 3 182087434 182087434 G C SNP FXR1 NM_005087.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25734 NULL 0.002 - - - no_errors tier3 1265 239 15.86 500 417 45.42 0 0 NA 452198 TCGA-AB-2969 AML31 3 191103363 191103363 T C SNP TP63 ENST00000392463 human ensembl 54_36p 1 known intronic c.1653-4560 e13-4560 0 - - - no_stop_codon tier3 442 269 37.62 570 497 46.32 0 0 NA 452198 TCGA-AB-2969 AML31 3 192532267 192532267 C T SNP CCDC50 NM_178335.3 human genbank 54_36p 1 reviewed intronic c.49+2061 e1+2061 0.005 - - - no_errors tier3 1030 179 14.77 728 620 45.93 0 0 0 452198 TCGA-AB-2969 AML31 4 7394775 7394775 C T SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.31-54141 e2-54141 0.001 - - - no_errors tier3 587 74 11.16 692 576 45.35 0 0 NA 452198 TCGA-AB-2969 AML31 4 26362673 26362673 T G SNP TBC1D19 NM_018317.2 human genbank 54_36p 1 validated intronic c.1436-1867 e20-1867 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 452198 TCGA-AB-2969 AML31 4 63345784 63345784 G A SNP LOC644556 XM_001719457.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-20283 NULL 0.002 - - - no_errors tier2 643 88 12.04 945 420 30.7 0 0 NA 452198 TCGA-AB-2969 AML31 4 72616906 72616906 T C SNP SLC4A4 NM_001098484.2 human genbank 54_36p 1 reviewed intronic c.2280+150 e16+150 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 4 119477364 119477364 C T SNP PRSS12 NM_003619.2 human genbank 54_36p -1 reviewed intronic c.642-1110 e3-1110 0.021 - - - no_errors tier3 803 144 15.19 668 604 47.34 0 0 NA 452198 TCGA-AB-2969 AML31 4 186999154 186999154 T G SNP SORBS2 NM_021069.1 human genbank 54_36p -1 reviewed intronic c.1-65640 e1-65640 0 - - - no_errors tier3 484 94 16.26 306 297 49.25 0 0 NA 452198 TCGA-AB-2969 AML31 5 22595465 22595465 T G SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-54235 e1-54235 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 5 45880881 45880881 C T SNP - - - - - - - - - - - - - - - tier3 252 30 10.64 261 234 47.27 0 0 NA 452198 TCGA-AB-2969 AML31 5 67369605 67369605 C T SNP - - - - - - - - - - - - - - - tier3 761 153 16.72 488 438 47.3 0 0 NA 452198 TCGA-AB-2969 AML31 5 80124072 80124072 G A SNP MSH3 NM_002439.2 human genbank 54_36p 1 validated intronic c.2544-236 e19-236 0 - - - no_errors tier3 236 58 19.66 586 487 45.34 2 3 60 452198 TCGA-AB-2969 AML31 5 93857376 93857376 C G SNP uc003kko.1 ENST00000312498 human ensembl 54_36p -1 known 5_prime_flanking_region c.-18733 NULL 0.003 - - - no_start_codon tier3 NA NA NA NA NA NA 0 0 0 452198 TCGA-AB-2969 AML31 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 452198 TCGA-AB-2969 AML31 6 40467367 40467367 C A SNP LRFN2 NM_020737.1 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*293 NULL 0.999 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 6 77123405 77123405 C T SNP - - - - - - - - - - - - - - - tier3 660 155 18.97 1075 907 45.65 0 0 NA 452198 TCGA-AB-2969 AML31 6 95631430 95631430 T A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 6 135462445 135462445 T C SNP HBS1L NM_006620.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44923 NULL 0.002 - - - no_errors tier3 891 221 19.84 899 807 47.19 0 0 NA 452198 TCGA-AB-2969 AML31 7 48632191 48632191 C T SNP ABCA13 NM_152701.2 human genbank 54_36p 1 reviewed intronic c.14674+6672 e57+6672 0.001 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 787 194 19.78 916 736 44.55 0 0 NA 452198 TCGA-AB-2969 AML31 7 57515887 57515887 C T SNP ZNF716 XM_001714654.1 human genbank 54_36p 1 model intronic c.39+1912 e1+1912 0 - - - no_errors tier3 366 85 18.81 190 170 47.09 0 0 NA 452198 TCGA-AB-2969 AML31 7 85476859 85476859 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 7 120917535 120917535 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 7 140451920 140451920 G A SNP LOC100129514 XM_001716072.1 human genbank 54_36p 1 model intronic c.382+30959 e1+30959 0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 7 157185399 157185399 A T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1789-17009 e13-17009 0 - - - no_errors tier2 210 53 20.15 233 227 49.13 0 0 NA 452198 TCGA-AB-2969 AML31 8 25022615 25022615 A G SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 8 34151385 34151385 G A SNP - - - - - - - - - - - - - - - tier3 303 38 11.01 560 305 34.62 0 0 NA 452198 TCGA-AB-2969 AML31 8 34167561 34167561 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 8 35476742 35476742 G C SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.104-49610 e2-49610 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 8 51256369 51256369 A G SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1+8621 e0+8621 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 8 66049865 66049865 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 8 71467490 71467490 T G SNP NCOA2 NM_006540.2 human genbank 54_36p -1 validated intronic c.1+10999 e0+10999 0.747 - - - no_errors tier3 483 121 19.97 521 450 46.3 5 0 0 452198 TCGA-AB-2969 AML31 8 100665275 100665275 T A SNP VPS13B NM_017890.2 human genbank 54_36p 1 reviewed intronic c.5295+6238 e32+6238 0.043 - - - no_errors tier3 975 246 20.13 805 649 44.6 3 0 0 452198 TCGA-AB-2969 AML31 8 115809334 115809334 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 9 25080204 25080204 T C SNP ENSG00000222693 ENST00000410761 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1055 NULL 0 - - - no_errors tier3 328 61 15.68 358 293 44.87 0 0 NA 452198 TCGA-AB-2969 AML31 9 36887024 36887024 C A SNP PAX5 NM_016734.1 human genbank 54_36p -1 reviewed intronic c.911-14922 e8-14922 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 9 100568848 100568848 A T SNP ANKS6 NM_173551.3 human genbank 54_36p -1 provisional intronic c.2142+1336 e11+1336 0 - - - no_errors tier3 579 186 24.31 419 374 47.16 0 0 NA 452198 TCGA-AB-2969 AML31 9 100720074 100720074 A G SNP COL15A1 NM_001855.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26091 NULL 0 - - - no_errors tier3 804 205 20.28 689 522 42.89 0 0 NA 452198 TCGA-AB-2969 AML31 9 108714159 108714159 C T SNP ZNF462 NM_021224.4 human genbank 54_36p 1 validated intronic c.1-11297 e1-11297 0 - - - no_errors tier3 468 61 11.44 640 277 30.04 0 0 NA 452198 TCGA-AB-2969 AML31 9 121538471 121538471 C T SNP - - - - - - - - - - - - - - - tier3 1891 457 19.4 1647 1440 46.57 0 0 NA 452198 TCGA-AB-2969 AML31 9 137726092 137726092 G A SNP SOHLH1 NM_001101677.2 human genbank 54_36p -1 validated missense c.908 p.T303M 0 NULL "HMMPfam_HLH,HMMSmart_SM00353,superfamily_HLH helix-loop-helix DNA-binding domain" - no_errors tier1 NA NA NA NA NA NA NA 452198 TCGA-AB-2969 AML31 9 137816463 137816463 G A SNP KCNT1 NM_020822.1 human genbank 54_36p 1 provisional silent c.3063 p.T1021 0.991 NULL "HMMPfam_BK_channel_a,HMMPfam_Ion_trans_2,superfamily_NAD(P)-bd,superfamily_SSF81324" - no_errors tier1 NA NA NA NA NA NA NA 452198 TCGA-AB-2969 AML31 10 19424827 19424827 C T SNP LOC100130846 XM_001715968.1 human genbank 54_36p 1 model intronic c.585+7707 e5+7707 0 - - - no_errors tier3 473 23 4.61 1053 163 13.39 0 0 NA 452198 TCGA-AB-2969 AML31 10 67480185 67480185 T C SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.2159+18887 e14+18887 0.002 - - - no_errors tier2 708 154 17.82 940 758 44.51 0 0 NA 452198 TCGA-AB-2969 AML31 10 73025816 73025816 T A SNP CDH23 NM_022124.4 human genbank 54_36p 1 reviewed intronic c.832+18061 e8+18061 0.003 - - - no_errors tier3 552 91 14.11 330 285 46.34 0 0 NA 452198 TCGA-AB-2969 AML31 11 20709294 20709294 G T SNP - - - - - - - - - - - - - - - tier3 970 232 19.3 687 585 45.92 0 0 NA 452198 TCGA-AB-2969 AML31 11 23583427 23583427 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 11 40183906 40183906 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 11 64821076 64821076 G A SNP - - - - - - - - - - - - - - - tier3 480 116 19.46 497 462 48.07 3 2 40 452198 TCGA-AB-2969 AML31 11 81529767 81529767 G A SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 11 87110939 87110939 G T SNP - - - - - - - - - - - - - - - tier3 668 14 2.05 788 101 11.35 0 0 NA 452198 TCGA-AB-2969 AML31 11 134164355 134164355 C T SNP - - - - - - - - - - - - - - - tier3 890 238 21.04 719 693 49.04 0 0 NA 452198 TCGA-AB-2969 AML31 12 9702101 9702101 A G SNP LOC374443 NR_002814.1 human genbank 54_36p 1 provisional rna NULL NULL 0 - - - pseudogene tier1 NA NA NA NA NA NA 20 0 452198 TCGA-AB-2969 AML31 12 22283439 22283439 A C SNP ST8SIA1 NM_003034.3 human genbank 54_36p -1 reviewed intronic c.584+9768 e4+9768 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 12 32680434 32680434 G T SNP FGD4 NM_139241.2 human genbank 54_36p 1 reviewed intronic c.1903-2422 e14-2422 0.026 - - - no_errors tier2 532 124 18.84 564 527 48.3 1 0 0 452198 TCGA-AB-2969 AML31 12 38373226 38373226 A T SNP C12orf40 NM_001031748.2 human genbank 54_36p 1 validated intronic c.1411+1045 e11+1045 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 12 56144791 56144791 C A SNP GLI1 NM_005269.2 human genbank 54_36p 1 reviewed missense c.262 p.L88M 1 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 1538 337 17.95 656 591 47.39 1 0 452198 TCGA-AB-2969 AML31 12 57438067 57438067 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 12 126748215 126748215 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 13 21865814 21865814 C A SNP - - - - - - - - - - - - - - - tier3 410 139 25.32 419 642 60.45 0 0 NA 452198 TCGA-AB-2969 AML31 13 27490642 27490642 C G SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835H 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 1256 159 11.22 866 429 33.08 222 95 29.78 452198 TCGA-AB-2969 AML31 13 60889651 60889651 C G SNP PCDH20 ENST00000409186 human ensembl 54_36p -1 known intronic c.1-1633 e1-1633 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 13 74029037 74029037 G T SNP - - - - - - - - - - - - - - - tier3 815 134 14.12 1481 715 32.56 0 0 NA 452198 TCGA-AB-2969 AML31 13 92398000 92398000 T C SNP - - - - - - - - - - - - - - - tier3 322 55 14.59 464 246 34.65 0 0 NA 452198 TCGA-AB-2969 AML31 13 92466026 92466026 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 13 104876739 104876739 A G SNP DAOA NM_172370.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-39900 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 13 109935418 109935418 G A SNP COL4A2 NM_001846.2 human genbank 54_36p 1 reviewed intronic c.3025+43 e32+43 0 - - - no_errors tier3 260 74 22.16 166 160 48.78 0 0 NA 452198 TCGA-AB-2969 AML31 14 47961450 47961450 T C SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 14 76301667 76301667 G A SNP VASH1 NM_014909.4 human genbank 54_36p 1 validated intronic c.309+2441 e1+2441 0 - - - no_errors tier3 120 29 18.59 64 44 39.64 0 0 0 452198 TCGA-AB-2969 AML31 14 82608644 82608644 G A SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 15 23386323 23386323 G A SNP ENSG00000220571 ENST00000403285 human ensembl 54_36p 1 known 3_prime_flanking_region c.*8960 NULL 0.002 - - - no_coding_region:pseudogene tier3 1404 189 11.85 955 433 31.15 0 0 NA 452198 TCGA-AB-2969 AML31 15 25337871 25337871 G T SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.575-61520 e6-61520 0.001 - - - no_errors tier3 1484 69 4.44 1167 154 11.66 0 0 NA 452198 TCGA-AB-2969 AML31 15 29317077 29317077 G A SNP LOC283710 XM_211174.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-6849 NULL 0.068 - - - no_errors tier3 926 191 17.1 641 507 44.16 0 0 NA 452198 TCGA-AB-2969 AML31 15 86528277 86528277 G A SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed intronic c.323+183 e2+183 0.001 - - - no_errors tier3 802 196 19.6 737 663 47.32 0 0 NA 452198 TCGA-AB-2969 AML31 15 88782837 88782837 G A SNP IQGAP1 NM_003870.3 human genbank 54_36p 1 reviewed intronic c.468-731 e6-731 0 - - - no_errors tier2 312 62 16.58 411 301 42.28 8 1 11.11 452198 TCGA-AB-2969 AML31 15 97047801 97047801 G C SNP IGF1R NM_000875.3 human genbank 54_36p 1 reviewed intronic c.95-20513 e2-20513 0.001 - - - no_errors tier3 2182 400 15.47 1129 1081 48.8 0 0 NA 452198 TCGA-AB-2969 AML31 16 7868630 7868630 C T SNP ENSG00000222109 ENST00000410177 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*20711 NULL 0.102 - - - no_errors tier3 1333 36 2.62 1129 160 12.41 0 0 NA 452198 TCGA-AB-2969 AML31 16 7941529 7941529 T A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 16 10944428 10944428 A G SNP CLEC16A NM_015226.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-1648 NULL 0.001 - - - no_errors tier2 248 44 15.07 270 153 36.17 0 0 NA 452198 TCGA-AB-2969 AML31 16 22599053 22599053 G A SNP - - - - - - - - - - - - - - - tier2 1201 190 13.62 953 409 29.99 0 0 NA 452198 TCGA-AB-2969 AML31 16 34545748 34545748 G C SNP ENSG00000214581 ENST00000398617 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5991 NULL 0 - - - no_stop_codon tier3 589 51 7.97 500 211 29.68 0 0 NA 452198 TCGA-AB-2969 AML31 16 58050635 58050635 G T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 16 60042403 60042403 T A SNP - - - - - - - - - - - - - - - tier3 741 126 14.53 856 661 43.54 0 0 NA 452198 TCGA-AB-2969 AML31 16 77431224 77431224 C T SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1057-371782 e9-371782 0 - - - no_errors tier3 1 0 0 NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 16 88321243 88321243 C T SNP ZNF276 NM_152287.1 human genbank 54_36p 1 validated silent c.837 p.D279 1 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMPfam_zf-AD,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA 26 0 452198 TCGA-AB-2969 AML31 17 49416138 49416138 C T SNP - - - - - - - - - - - - - - - tier3 847 158 15.72 880 841 48.87 0 0 NA 452198 TCGA-AB-2969 AML31 17 67861248 67861248 A G SNP ENSG00000211264 ENST00000388529 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24394 NULL 0.008 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 18 13606633 13606633 C T SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.182-4483 e3-4483 0.004 - - - no_errors tier3 171 40 18.87 138 129 48.31 0 0 NA 452198 TCGA-AB-2969 AML31 19 806779 806779 G T SNP ELA2 NM_001972.2 human genbank 54_36p 1 reviewed missense c.582 p.Q194H 0.937 "HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys" "HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER" - no_errors tier1 181 33 15.42 57 34 37.36 88 54 37.76 452198 TCGA-AB-2969 AML31 19 13231692 13231692 G A SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known intronic c.4254-177 e27-177 0.004 - - - no_errors tier3 1485 197 11.68 1033 558 35.05 0 0 0 452198 TCGA-AB-2969 AML31 20 17261178 17261178 A G SNP PCSK2 NM_002594.2 human genbank 54_36p 1 reviewed intronic c.283-25794 e3-25794 0.013 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 20 58861532 58861532 G C SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 21 23370033 23370033 T C SNP ENSG00000216619 ENST00000406433 human ensembl 54_36p 1 known 5_prime_flanking_region c.-25383 NULL 0 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 452198 TCGA-AB-2969 AML31 21 30506365 30506365 T C SNP CLDN17 NM_012131.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-45559 NULL 0.015 - - - no_errors tier3 657 124 15.86 588 496 45.76 0 0 NA 452198 TCGA-AB-2969 AML31 22 26004684 26004684 T G SNP - - - - - - - - - - - - - - - tier3 2650 550 17.18 1403 1004 41.69 0 0 NA 400220 TCGA-AB-2970 AML27 X 7138841 7138841 G A SNP STS NM_000351.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8876 NULL 0 - - - no_errors tier3 3 1 25 1 6 85.71 0 0 NA 400220 TCGA-AB-2970 AML27 X 7449501 7449501 C A SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 X 14703698 14703698 C A SNP ENSG00000221278 ENST00000408351 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-10538 NULL 0.006 - - - no_errors tier3 757 92 10.84 394 276 41.13 0 0 NA 400220 TCGA-AB-2970 AML27 X 20146561 20146561 A G SNP RPS6KA3 NM_004586.2 human genbank 54_36p -1 reviewed intronic c.127-9118 e3-9118 0.042 - - - no_errors tier3 308 41 11.71 174 143 44.97 7 0 0 400220 TCGA-AB-2970 AML27 X 21650360 21650360 C T SNP SMPX NM_014332.1 human genbank 54_36p -1 provisional intronic c.267+15228 e3+15228 0.346 - - - no_errors tier3 506 62 10.92 189 124 39.62 0 0 NA 400220 TCGA-AB-2970 AML27 X 26806418 26806418 G A SNP - - - - - - - - - - - - - - - tier3 600 59 8.95 185 144 43.77 0 0 NA 400220 TCGA-AB-2970 AML27 X 27321309 27321323 AAAACATATTCCAAA - DEL ENSG00000219351 ENST00000406095 human ensembl 54_36p -1 known 3_prime_flanking_region c.*34506 NULL 0.007:0.008:0.007:0.008:0.002:0.001:0.002:0.001:0.000:0.001:0.001:0.001:0.001:0.004:0.007 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 X 27677257 27677257 C T SNP ENSG00000218243 ENST00000404403 human ensembl 54_36p -1 known 5_prime_flanking_region c.-433 NULL 0 - - - no_coding_region:pseudogene tier3 934 54 5.47 261 65 19.88 0 0 NA 400220 TCGA-AB-2970 AML27 X 37616787 37616787 T C SNP DYNLT3 NM_006520.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-25080 NULL 0.705 - - - no_errors tier3 551 67 10.81 150 132 46.64 0 0 NA 400220 TCGA-AB-2970 AML27 X 39818802 39818802 C - DEL BCOR NM_017745.1 human genbank 54_36p -1 reviewed frame_shift_del c.741 p.P248fs 1 NULL "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" - no_errors tier1 NA NA NA NA NA NA NA 400220 TCGA-AB-2970 AML27 X 41959339 41959339 C T SNP ENSG00000206896 ENST00000384169 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40757 NULL 0.043 - - - no_errors tier2 1268 131 9.33 677 571 45.64 0 0 NA 400220 TCGA-AB-2970 AML27 X 89105562 89105562 G T SNP TGIF2LX NM_138960.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*41096 NULL 0.002 - - - no_errors tier3 343 28 7.53 88 71 44.65 0 0 NA 400220 TCGA-AB-2970 AML27 X 89181903 89181903 C T SNP LOC100130134 XR_037810.1 human genbank 54_36p -1 model rna NULL NULL 0.994 - - - pseudogene tier1 NA NA NA NA NA NA NA 400220 TCGA-AB-2970 AML27 X 110529928 110529928 G T SNP DCX NM_000555.2 human genbank 54_36p -1 reviewed intronic c.948+946 e3+946 0.118 - - - no_errors tier3 798 105 11.63 347 269 43.67 0 0 NA 400220 TCGA-AB-2970 AML27 X 125965730 125965730 C T SNP - - - - - - - - - - - - - - - tier3 1059 150 12.37 513 471 47.82 0 0 NA 400220 TCGA-AB-2970 AML27 X 132149351 132149351 G A SNP ENSG00000220625 ENST00000402273 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43717 NULL 0 - - - no_coding_region:pseudogene tier3 2067 319 13.35 579 497 46.15 0 0 NA 400220 TCGA-AB-2970 AML27 X 138598168 138598168 C A SNP MCF2 NM_001099855.1 human genbank 54_36p -1 validated intronic c.1+19763 e0+19763 0 - - - no_errors tier2 1109 115 9.37 222 191 46.14 0 0 NA 400220 TCGA-AB-2970 AML27 X 139300091 139300091 C G SNP ENSG00000218684 ENST00000403202 human ensembl 54_36p 1 known 5_prime_flanking_region c.-6802 NULL 0 - - - no_coding_region:pseudogene tier3 687 91 11.65 370 290 43.81 0 0 NA 400220 TCGA-AB-2970 AML27 X 149619579 149619579 T C SNP MTMR1 NM_003828.2 human genbank 54_36p 1 reviewed intronic c.252+1148 e2+1148 0 - - - no_errors tier3 930 115 10.97 441 366 45.35 5 0 0 400220 TCGA-AB-2970 AML27 1 5687865 5687865 G A SNP - - - - - - - - - - - - - - - tier2 322 28 8 135 121 47.27 0 0 NA 400220 TCGA-AB-2970 AML27 1 8042643 8042643 G A SNP ERRFI1 NM_018948.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44377 NULL 0 - - - no_errors tier3 606 63 9.38 189 178 48.5 0 0 NA 400220 TCGA-AB-2970 AML27 1 22173237 22173237 G A SNP ELA3A NM_005747.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27518 NULL 0.001 - - - no_errors tier2 1409 113 7.41 653 171 20.63 0 0 NA 400220 TCGA-AB-2970 AML27 1 30665401 30665401 C T SNP - - - - - - - - - - - - - - - tier3 740 96 11.47 270 177 39.6 0 0 NA 400220 TCGA-AB-2970 AML27 1 41737443 41737443 G A SNP EDN2 NM_001956.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14584 NULL 0 - - - no_errors tier3 409 84 17.04 203 159 43.92 0 0 NA 400220 TCGA-AB-2970 AML27 1 49957752 49957752 G A SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.158-22056 e3-22056 0 - - - no_errors tier3 1264 180 12.45 509 428 45.68 0 0 NA 400220 TCGA-AB-2970 AML27 1 70152592 70152592 G A SNP LRRC7 NM_020794.2 human genbank 54_36p 1 validated intronic c.534-17186 e6-17186 0.992 - - - no_errors tier2 324 33 9.24 151 116 43.45 0 0 NA 400220 TCGA-AB-2970 AML27 1 80774045 80774045 T C SNP ENSG00000217175 ENST00000402172 human ensembl 54_36p 1 known 3_prime_flanking_region c.*39539 NULL 0.001 - - - no_coding_region:pseudogene tier3 784 132 14.39 275 277 50.18 0 0 NA 400220 TCGA-AB-2970 AML27 1 97674645 97674645 G C SNP DPYD NM_000110.3 human genbank 54_36p -1 reviewed intronic c.1905+13558 e14+13558 0 - - - no_errors tier3 1335 127 8.69 466 350 42.84 2 3 60 400220 TCGA-AB-2970 AML27 1 105196784 105196784 A C SNP - - - - - - - - - - - - - - - tier3 476 56 10.49 158 126 44.37 0 0 NA 400220 TCGA-AB-2970 AML27 1 105905196 105905196 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 1 107653116 107653116 C A SNP NTNG1 NM_014917.1 human genbank 54_36p 1 provisional intronic c.247-15311 e2-15311 0 - - - no_errors tier3 2270 264 10.4 910 566 38.35 0 0 NA 400220 TCGA-AB-2970 AML27 1 114603068 114603068 C T SNP - - - - - - - - - - - - - - - tier3 1433 179 11.1 526 434 45.02 0 0 NA 400220 TCGA-AB-2970 AML27 1 117954113 117954114 - CTT INS FAM46C NM_017709.3 human genbank 54_36p 1 validated intronic c.1+3815_3816 e0+3815 0.919:0.940 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 1 158409868 158409868 T C SNP ATP1A4 NM_144699.1 human genbank 54_36p 1 reviewed intronic c.1855-127 e13-127 0 - - - no_errors tier3 1381 187 11.91 402 390 49.18 0 0 NA 400220 TCGA-AB-2970 AML27 1 164924681 164924681 T C SNP FMO10P ENST00000401521 human ensembl 54_36p 1 known 3_prime_flanking_region c.*6624 NULL 0.066 - - - no_coding_region:pseudogene tier3 839 121 12.6 341 326 48.8 0 0 NA 400220 TCGA-AB-2970 AML27 1 167212445 167212445 G T SNP LOC391132 XR_017287.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*37589 NULL 0.013 - - - pseudogene tier3 1664 199 10.66 558 467 45.52 0 0 NA 400220 TCGA-AB-2970 AML27 1 174612237 174612237 T G SNP ENSG00000218601 ENST00000404471 human ensembl 54_36p -1 known 5_prime_flanking_region c.-8077 NULL 0.182 - - - no_coding_region:pseudogene tier3 NA NA NA 1 0 0 0 0 NA 400220 TCGA-AB-2970 AML27 1 175056645 175056645 A G SNP PAPPA2 NM_020318.2 human genbank 54_36p 1 validated intronic c.5203-19287 e21-19287 0.852 - - - no_errors tier2 1870 234 11.11 529 374 41.42 0 0 NA 400220 TCGA-AB-2970 AML27 1 175979341 175979341 A G SNP - - - - - - - - - - - - - - - tier3 654 81 10.96 264 239 47.42 0 0 NA 400220 TCGA-AB-2970 AML27 1 189339598 189339598 A G SNP ENSG00000217637 ENST00000405368 human ensembl 54_36p -1 known 3_prime_flanking_region c.*42158 NULL 0.001 - - - no_coding_region:pseudogene tier3 330 39 10.57 130 69 34.67 0 0 NA 400220 TCGA-AB-2970 AML27 1 195382470 195382470 C T SNP ASPM NM_018136.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-280 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 1 199100456 199100456 C T SNP C1orf106 NM_018265.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26836 NULL 0.004 - - - no_errors tier3 748 88 10.5 264 185 41.2 0 0 NA 400220 TCGA-AB-2970 AML27 1 202854975 202854975 G A SNP LRRN2 NM_006338.2 human genbank 54_36p -1 reviewed silent c.769 p.L257 0.995 "HMMSmart_SM00369,HMMSmart_SM00365,superfamily_L domain-like" "HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMSmart_SM00365,superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 266 45 14.47 176 169 48.99 8 100 400220 TCGA-AB-2970 AML27 1 207486021 207486021 G A SNP LOC391158 XR_016375.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*12634 NULL 0.001 - - - pseudogene tier3 1645 211 11.37 687 624 47.6 0 0 NA 400220 TCGA-AB-2970 AML27 1 213073767 213073767 G A SNP ENSG00000185221 ENST00000328713 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-37456 NULL 0.001 - - - no_coding_region:pseudogene tier3 341 53 13.42 123 132 51.76 0 0 NA 400220 TCGA-AB-2970 AML27 1 244551235 244551235 C T SNP SMYD3 NM_022743.1 human genbank 54_36p -1 provisional intronic c.354+5891 e4+5891 0 - - - no_errors tier3 199 19 8.6 26 30 53.57 3 4 57.14 400220 TCGA-AB-2970 AML27 2 4688780 4688780 A - DEL LOC727982 XR_039999.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-7112 NULL 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 2 20689966 20689966 C T SNP HS1BP3 NM_022460.3 human genbank 54_36p -1 reviewed intronic c.624-1833 e5-1833 0 - - - no_errors tier3 536 74 12.11 237 176 42.51 0 0 0 400220 TCGA-AB-2970 AML27 2 26593335 26593335 G A SNP OTOF NM_194248.3 human genbank 54_36p -1 reviewed intronic c.328-364 e5-364 0.004 - - - no_errors tier2 458 79 14.68 185 198 51.43 0 0 NA 400220 TCGA-AB-2970 AML27 2 29044813 29044813 G A SNP FAM179A ENST00000401723 human ensembl 54_36p 1 known intronic c.1+11746 e0+11746 0.001 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 714 104 12.48 347 259 42.74 0 0 NA 400220 TCGA-AB-2970 AML27 2 30465534 30465534 G A SNP ENSG00000221377 ENST00000408450 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*43189 NULL 0.001 - - - no_errors tier3 1045 150 12.54 457 382 45.42 0 0 NA 400220 TCGA-AB-2970 AML27 2 31191770 31191770 G C SNP GALNT14 NM_024572.2 human genbank 54_36p -1 validated intronic c.129+22558 e1+22558 0 - - - no_errors tier3 605 78 11.39 187 156 45.35 1 0 0 400220 TCGA-AB-2970 AML27 2 41102181 41102181 C T SNP LOC285176 XM_001725319.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-22428 NULL 0.072 - - - no_start_codon:pseudogene:no_stop_codon tier2 1956 301 13.32 834 770 47.95 0 0 NA 400220 TCGA-AB-2970 AML27 2 48298360 48298360 A G SNP ENSG00000201010 ENST00000364140 human ensembl 54_36p 1 novel rna NULL NULL 1 - - - no_errors tier1 1276 202 13.66 560 462 45.21 NA 400220 TCGA-AB-2970 AML27 2 65852014 65852014 C A SNP KRT18P33 XR_017456.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*35026 NULL 0.001 - - - pseudogene tier3 983 103 9.47 398 265 39.97 0 0 NA 400220 TCGA-AB-2970 AML27 2 71775215 71775215 T A SNP DYSF NM_003494.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*8085 NULL 0 - - - no_errors tier3 752 106 12.23 273 245 47.3 0 0 NA 400220 TCGA-AB-2970 AML27 2 77025856 77025856 C T SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1555-196306 e3-196306 0.006 - - - no_errors tier3 719 63 8.05 179 127 41.5 0 0 NA 400220 TCGA-AB-2970 AML27 2 79485391 79485391 G T SNP CTNNA2 ENST00000409536 human ensembl 54_36p 1 known intronic c.1+30744 e0+30744 0.498 - - - no_errors tier2 1275 168 11.63 522 393 42.95 0 0 NA 400220 TCGA-AB-2970 AML27 2 81686313 81686313 A T SNP ENSG00000198702 ENST00000361614 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21959 NULL 0.005 - - - no_coding_region:pseudogene tier3 1048 142 11.91 301 219 42.12 0 0 NA 400220 TCGA-AB-2970 AML27 2 86918974 86918974 C T SNP CD8B NM_172213.3 human genbank 54_36p -1 reviewed intronic c.620+6582 e5+6582 0 - - - no_errors tier3 259 28 9.72 27 37 57.81 0 0 0 400220 TCGA-AB-2970 AML27 2 103478832 103478832 C A SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 2 114539392 114539392 G A SNP - - - - - - - - - - - - - - - tier2 843 89 9.53 209 144 40.79 0 0 NA 400220 TCGA-AB-2970 AML27 2 121434942 121434942 G - DEL GLI2 NM_005270.4 human genbank 54_36p 1 reviewed intronic c.643+5466 e4+5466 0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 2 126663892 126663892 G T SNP - - - - - - - - - - - - - - - tier2 830 93 10.08 247 163 39.76 0 0 NA 400220 TCGA-AB-2970 AML27 2 132963412 132963412 C T SNP GPR39 NM_001508.2 human genbank 54_36p 1 validated intronic c.856+71471 e1+71471 0.15 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 2 133246731 133246731 A G SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.5128+1128 e14+1128 0.998 - - - no_errors tier3 614 79 11.33 187 144 43.37 0 0 NA 400220 TCGA-AB-2970 AML27 2 135287366 135287366 C T SNP ACMSD NM_138326.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25357 NULL 0 - - - no_errors tier2 662 86 11.5 253 194 43.4 0 0 NA 400220 TCGA-AB-2970 AML27 2 167372682 167372682 G A SNP - - - - - - - - - - - - - - - tier3 238 24 9.16 76 75 49.67 0 0 NA 400220 TCGA-AB-2970 AML27 2 205704415 205704415 G T SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated intronic c.1434+5709 e10+5709 0.001 - - - no_errors tier3 837 93 10 297 230 43.64 0 0 NA 400220 TCGA-AB-2970 AML27 2 212759483 212759483 G A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.83-61610 e2-61610 0 - - - no_errors tier3 749 100 11.72 374 335 47.25 0 0 NA 400220 TCGA-AB-2970 AML27 2 223664729 223664729 G A SNP KCNE4 NM_080671.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*38424 NULL 0 - - - no_errors tier3 1509 218 12.59 596 500 45.58 0 0 NA 400220 TCGA-AB-2970 AML27 2 236277472 236277472 G A SNP AGAP1 NM_001037131.1 human genbank 54_36p 1 validated intronic c.164-5090 e2-5090 0.019 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 2 236651869 236651870 - CT INS AGAP1 NM_001037131.1 human genbank 54_36p 1 validated intronic c.2114+29205_2114+29204 e16+29205 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 3 8577158 8577158 C A SNP LMCD1 NM_014583.2 human genbank 54_36p 1 reviewed intronic c.724-4960 e5-4960 0 - - - no_errors tier3 590 55 8.51 312 224 41.79 0 0 NA 400220 TCGA-AB-2970 AML27 3 16741744 16741744 T C SNP - - - - - - - - - - - - - - - tier3 1165 142 10.86 371 358 49.04 0 0 NA 400220 TCGA-AB-2970 AML27 3 21285104 21285104 G A SNP - - - - - - - - - - - - - - - tier3 729 65 8.16 245 204 45.43 0 0 NA 400220 TCGA-AB-2970 AML27 3 47267043 47267043 G A SNP SNORD13 ENST00000387814 human ensembl 54_36p -1 known rna NULL NULL 0.21 - - - pseudogene tier1 1 0 NA NA NA 5 0 400220 TCGA-AB-2970 AML27 3 55812597 55812598 - T INS ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2565-68612_2565-68611 e14-68611 0.247:0.249 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 3 62186142 62186142 C A SNP PTPRG NM_002841.3 human genbank 54_36p 1 reviewed intronic c.2289-5797 e14-5797 0.001 - - - no_errors tier3 633 91 12.55 236 182 43.54 0 0 0 400220 TCGA-AB-2970 AML27 3 62667097 62667097 C T SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.889-43988 e4-43988 0.001 - - - no_errors tier2 1021 202 16.5 528 440 45.41 0 0 NA 400220 TCGA-AB-2970 AML27 3 78453063 78453063 C A SNP - - - - - - - - - - - - - - - tier3 1372 190 12.16 762 532 41.11 0 0 NA 400220 TCGA-AB-2970 AML27 3 80944362 80944362 G A SNP ENSG00000211106 ENST00000388371 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19626 NULL 0.004 - - - pseudogene tier3 84 8 8.7 56 45 44.55 0 0 NA 400220 TCGA-AB-2970 AML27 3 83012162 83012162 G A SNP - - - - - - - - - - - - - - - tier3 598 83 12.15 288 230 44.23 0 0 NA 400220 TCGA-AB-2970 AML27 3 84524853 84524853 C T SNP - - - - - - - - - - - - - - - tier3 171 21 10.94 61 38 38 0 0 NA 400220 TCGA-AB-2970 AML27 3 84703230 84703230 A T SNP - - - - - - - - - - - - - - - tier3 727 92 11.22 207 172 45.38 0 0 NA 400220 TCGA-AB-2970 AML27 3 117821246 117821246 C T SNP ENSG00000209192 ENST00000386457 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36879 NULL 0.002 - - - pseudogene tier3 1047 145 12.15 352 266 43.04 0 0 NA 400220 TCGA-AB-2970 AML27 3 137858004 137858004 C T SNP STAG1 NM_005862.2 human genbank 54_36p -1 reviewed intronic c.1-25491 e1-25491 0.004 - - - no_errors tier2 NA NA NA NA NA NA 9 6 40 400220 TCGA-AB-2970 AML27 3 140894661 140894661 T G SNP NMNAT3 NM_178177.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-114076 NULL 0.005 - - - no_errors tier3 1281 179 12.26 453 361 44.35 0 0 NA 400220 TCGA-AB-2970 AML27 3 144167201 144167201 C G SNP PAQR9 NM_198504.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2333 NULL 0 - - - no_errors tier3 262 34 11.41 71 60 44.78 0 0 0 400220 TCGA-AB-2970 AML27 3 157519440 157519440 T A SNP KCNAB1 NM_172160.3 human genbank 54_36p 1 reviewed intronic c.276-102659 e2-102659 0 - - - no_errors tier3 761 123 13.88 437 337 43.48 0 0 NA 400220 TCGA-AB-2970 AML27 3 160816053 160816053 A G SNP SCHIP1 NM_014575.2 human genbank 54_36p 1 provisional intronic c.64-148873 e2-148873 0 - - - no_errors tier2 1946 285 12.73 1081 832 43.49 0 0 NA 400220 TCGA-AB-2970 AML27 3 166118808 166118808 G A SNP - - - - - - - - - - - - - - - tier3 328 34 9.37 136 108 44.26 0 0 NA 400220 TCGA-AB-2970 AML27 4 9996433 9996433 C T SNP - - - - - - - - - - - - - - - tier3 544 68 11.11 296 281 48.7 0 0 NA 400220 TCGA-AB-2970 AML27 4 42878328 42878328 G A SNP - - - - - - - - - - - - - - - tier3 311 32 9.3 204 134 39.41 0 0 NA 400220 TCGA-AB-2970 AML27 4 57086890 57086890 T A SNP SRP72 NM_006947.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*24106 NULL 0 - - - no_errors tier3 1244 143 10.3 501 432 46.3 0 0 NA 400220 TCGA-AB-2970 AML27 4 57892553 57892553 G A SNP - - - - - - - - - - - - - - - tier3 839 52 5.82 580 172 22.87 0 0 NA 400220 TCGA-AB-2970 AML27 4 59692624 59692624 G T SNP - - - - - - - - - - - - - - - tier3 736 85 10.34 402 336 45.53 0 0 NA 400220 TCGA-AB-2970 AML27 4 95813425 95813425 G A SNP PDLIM5 NM_006457.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*9184 NULL 1 - - - no_errors tier2 1283 172 11.78 667 552 45.25 0 0 NA 400220 TCGA-AB-2970 AML27 4 103771667 103771667 C T SNP NFKB1 NM_003998.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*14870 NULL 0 - - - no_errors tier3 325 32 8.96 102 78 43.33 0 0 NA 400220 TCGA-AB-2970 AML27 4 128375877 128375877 C T SNP - - - - - - - - - - - - - - - tier3 594 58 8.9 314 232 42.49 0 0 NA 400220 TCGA-AB-2970 AML27 4 138437576 138437576 A C SNP - - - - - - - - - - - - - - - tier2 2046 260 11.26 1255 1053 45.62 0 0 NA 400220 TCGA-AB-2970 AML27 4 149854954 149854954 C T SNP - - - - - - - - - - - - - - - tier3 1010 130 11.38 397 320 44.63 0 0 NA 400220 TCGA-AB-2970 AML27 4 159757814 159757814 G A SNP RXFP1 NM_021634.2 human genbank 54_36p 1 provisional splice_region c.755+7 e9+7 0.012 - - - no_errors tier2 839 114 11.96 224 204 47.66 5 1 16.67 400220 TCGA-AB-2970 AML27 4 163972670 163972670 G A SNP - - - - - - - - - - - - - - - tier3 197 19 8.76 135 74 35.24 0 0 NA 400220 TCGA-AB-2970 AML27 4 182241806 182241806 G A SNP LOC728081 XM_001127776.1 human genbank 54_36p -1 model intronic c.133-19179 e3-19179 0.001 - - - no_errors tier3 362 31 7.85 115 119 50.64 0 0 NA 400220 TCGA-AB-2970 AML27 5 7054382 7054382 G A SNP ENSG00000212258 ENST00000390956 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-45958 NULL 0.003 - - - no_errors tier3 1476 179 10.81 513 457 47.06 0 0 NA 400220 TCGA-AB-2970 AML27 5 10128058 10128058 G A SNP - - - - - - - - - - - - - - - tier3 492 63 11.33 150 117 43.82 0 0 NA 400220 TCGA-AB-2970 AML27 5 15604235 15604235 C T SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.37+50413 e1+50413 0.002 - - - no_errors tier3 1555 227 12.71 698 657 48.49 0 0 NA 400220 TCGA-AB-2970 AML27 5 18609048 18609048 C T SNP ENSG00000210087 ENST00000387352 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*25577 NULL 0 - - - pseudogene tier3 1207 171 12.4 237 193 44.88 0 0 NA 400220 TCGA-AB-2970 AML27 5 21019091 21019091 G A SNP - - - - - - - - - - - - - - - tier3 589 71 10.57 266 271 50 0 0 NA 400220 TCGA-AB-2970 AML27 5 26999460 26999460 G A SNP CDH9 NM_016279.3 human genbank 54_36p -1 reviewed intronic c.228+24510 e1+24510 0.001 - - - no_errors tier2 397 51 11.38 127 110 46.41 0 0 NA 400220 TCGA-AB-2970 AML27 5 33822985 33822985 G T SNP ADAMTS12 NM_030955.2 human genbank 54_36p -1 reviewed intronic c.490-35575 e3-35575 0.003 - - - no_errors tier3 1061 96 8.29 565 371 39.64 0 0 NA 400220 TCGA-AB-2970 AML27 5 51307451 51307451 G A SNP - - - - - - - - - - - - - - - tier3 274 23 7.74 87 57 39.58 0 0 NA 400220 TCGA-AB-2970 AML27 5 58678318 58678318 G A SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.456-130767 e2-130767 0 - - - no_errors tier3 1460 202 12.15 554 537 49.18 0 0 NA 400220 TCGA-AB-2970 AML27 5 117968777 117968777 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 5 120072505 120072505 C A SNP PRR16 NM_016644.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*22202 NULL 0 - - - no_errors tier3 402 52 11.43 179 152 45.78 0 0 NA 400220 TCGA-AB-2970 AML27 5 133094851 133094851 G A SNP - - - - - - - - - - - - - - - tier3 1920 265 12.11 739 547 42.53 0 0 NA 400220 TCGA-AB-2970 AML27 5 144608757 144608757 A G SNP ENSG00000213487 ENST00000394451 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*19386 NULL 0.007 - - - no_coding_region:pseudogene tier3 617 103 14.31 204 191 48.35 0 0 NA 400220 TCGA-AB-2970 AML27 5 151603256 151603256 G A SNP - - - - - - - - - - - - - - - tier3 1783 240 11.86 820 619 43.02 0 0 NA 400220 TCGA-AB-2970 AML27 5 152414334 152414334 G A SNP - - - - - - - - - - - - - - - tier3 1009 126 11.1 250 163 39.47 0 0 NA 400220 TCGA-AB-2970 AML27 5 163388728 163388728 C T SNP - - - - - - - - - - - - - - - tier2 930 100 9.69 385 285 42.54 0 0 NA 400220 TCGA-AB-2970 AML27 5 180444238 180444238 G A SNP ENSG00000214293 ENST00000398043 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29445 NULL 0.005 - - - no_coding_region:pseudogene tier3 540 63 10.45 142 103 42.04 0 0 NA 400220 TCGA-AB-2970 AML27 6 25534026 25534026 C T SNP LRRC16A NM_017640.4 human genbank 54_36p 1 validated intronic c.190-682 e4-682 0 - - - no_errors tier3 998 122 10.85 364 281 43.57 5 11 68.75 400220 TCGA-AB-2970 AML27 6 35320457 35320457 C T SNP SCUBE3 NM_152753.2 human genbank 54_36p 1 provisional silent c.2292 p.R764 1 "HMMSmart_SM00181,superfamily_Growth factor receptor domain,HMMPfam_GCC2_GCC3" "PatternScan_ASX_HYDROXYL,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Growth factor receptor domain,HMMPfam_GCC2_GCC3,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 878 122 12.18 381 326 46.11 2 0 400220 TCGA-AB-2970 AML27 6 39215608 39215608 C T SNP C6orf64 NM_018322.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-24765 NULL 0 - - - no_errors tier3 1343 212 13.63 398 304 43.3 0 0 NA 400220 TCGA-AB-2970 AML27 6 42172380 42172380 G T SNP CCND3 ENST00000372988 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47978 NULL 0 - - - no_start_codon tier3 1066 105 8.95 272 215 43.97 0 1 100 400220 TCGA-AB-2970 AML27 6 43917751 43917751 T C SNP - - - - - - - - - - - - - - - tier2 703 98 12.2 215 168 43.86 0 0 NA 400220 TCGA-AB-2970 AML27 6 48934792 48934792 C T SNP ENSG00000221175 ENST00000408248 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*9194 NULL 0 - - - no_errors tier3 1046 151 12.57 303 277 47.76 0 0 NA 400220 TCGA-AB-2970 AML27 6 50327431 50327431 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 6 54584891 54584891 A T SNP ENSG00000216347 ENST00000403509 human ensembl 54_36p -1 known 5_prime_flanking_region c.-8984 NULL 0.98 - - - no_coding_region:pseudogene tier3 131 26 16.56 61 46 42.99 0 0 NA 400220 TCGA-AB-2970 AML27 6 62769565 62769565 C T SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.337-23489 e4-23489 0.004 - - - no_errors tier3 823 90 9.85 283 233 45.16 2 0 0 400220 TCGA-AB-2970 AML27 6 69657302 69657302 A C SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.758-39870 e2-39870 0.019 - - - no_errors tier2 526 74 12.31 135 115 46 0 0 NA 400220 TCGA-AB-2970 AML27 6 72286158 72286158 G T SNP ENSG00000212099 ENST00000390810 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19150 NULL 0 - - - no_errors tier3 613 70 10.25 231 162 41.22 0 0 NA 400220 TCGA-AB-2970 AML27 6 74131215 74131215 C T SNP DDX43 NM_018665.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30135 NULL 0.001 - - - no_errors tier3 794 89 10.07 189 150 44.25 0 0 0 400220 TCGA-AB-2970 AML27 6 87528255 87528255 C A SNP ENSG00000218561 ENST00000407695 human ensembl 54_36p -1 known 5_prime_flanking_region c.-31710 NULL 0 - - - no_coding_region:pseudogene tier3 997 126 11.22 291 238 44.91 0 0 NA 400220 TCGA-AB-2970 AML27 6 91777441 91777441 G A SNP - - - - - - - - - - - - - - - tier3 897 114 11.25 252 194 43.4 0 0 NA 400220 TCGA-AB-2970 AML27 6 102435823 102435823 A G SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.1525-8385 e11-8385 0 - - - no_errors tier3 13 4 23.53 29 19 39.58 0 0 NA 400220 TCGA-AB-2970 AML27 6 102637676 102637676 G T SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*14597 NULL 0.001 - - - no_errors tier3 718 73 9.23 225 157 41.1 0 0 NA 400220 TCGA-AB-2970 AML27 6 108659871 108659871 T C SNP SNX3 NM_003795.4 human genbank 54_36p -1 reviewed intronic c.163-8929 e2-8929 0.042 - - - no_errors tier3 500 55 9.87 126 85 40.28 5 1 16.67 400220 TCGA-AB-2970 AML27 6 112111782 112111782 A G SNP FYN NM_002037.3 human genbank 54_36p -1 reviewed intronic c.1274-9256 e10-9256 0.978 - - - no_errors tier3 622 72 10.34 199 196 49.62 2 3 60 400220 TCGA-AB-2970 AML27 6 117330941 117330941 C T SNP RFX6 NM_173560.1 human genbank 54_36p 1 provisional intronic c.673-7850 e7-7850 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 6 129651674 129651674 C G SNP LAMA2 NM_000426.3 human genbank 54_36p 1 reviewed intronic c.2749+778 e19+778 0 - - - no_errors tier3 1083 142 11.55 408 307 42.94 0 0 NA 400220 TCGA-AB-2970 AML27 6 133869595 133869595 C A SNP EYA4 NM_004100.4 human genbank 54_36p 1 reviewed intronic c.1281+569 e13+569 0.002 - - - no_errors tier3 448 39 8.01 232 177 43.28 0 0 NA 400220 TCGA-AB-2970 AML27 6 136639071 136639071 G A SNP BCLAF1 NM_014739.1 human genbank 54_36p -1 reviewed missense c.1285 p.R429W 1 NULL NULL - no_errors tier1 1318 90 6.37 623 155 19.87 53 56 51.38 400220 TCGA-AB-2970 AML27 6 138073427 138073428 - TTAAGGAGGGCGGAC INS ENSG00000220412 ENST00000404534 human ensembl 54_36p -1 known 5_prime_flanking_region c.-3396 NULL 0.001:0.000 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 6 140834440 140834440 C T SNP - - - - - - - - - - - - - - - tier3 588 73 10.99 261 185 41.39 0 0 NA 400220 TCGA-AB-2970 AML27 6 144959652 144959652 G T SNP UTRN NM_007124.2 human genbank 54_36p 1 reviewed intronic c.7479+19535 e50+19535 0 - - - no_errors tier3 467 68 12.66 258 196 43.17 6 12 66.67 400220 TCGA-AB-2970 AML27 6 148467197 148467197 G C SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 6 155039699 155039699 C G SNP ENSG00000205625 ENST00000307155 human ensembl 54_36p 1 known 5_prime_flanking_region c.-29770 NULL 0.002 - - - no_coding_region:pseudogene tier3 955 138 12.55 226 192 45.71 0 0 NA 400220 TCGA-AB-2970 AML27 6 170584453 170584453 C A SNP LOC732174 XM_001720536.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-31327 NULL 0.378 - - - no_errors tier3 273 49 15.22 179 126 41.31 0 0 NA 400220 TCGA-AB-2970 AML27 7 11736619 11736619 G A SNP THSD7A NM_015204.1 human genbank 54_36p -1 validated intronic c.191-93506 e2-93506 0 - - - no_errors tier3 62 8 11.43 35 17 32.69 0 0 NA 400220 TCGA-AB-2970 AML27 7 34575612 34575612 C A SNP ENSG00000197085 ENST00000357959 human ensembl 54_36p -1 known intronic c.189+237 e3+237 0 - - - no_errors tier3 1534 254 14.21 953 774 44.82 0 0 NA 400220 TCGA-AB-2970 AML27 7 36164668 36164668 T C SNP EEPD1 NM_030636.2 human genbank 54_36p 1 validated intronic c.878+3332 e1+3332 0 - - - no_errors tier3 572 89 13.46 195 166 45.98 0 1 100 400220 TCGA-AB-2970 AML27 7 53419185 53419185 A G SNP LOC100129159 XM_001716383.1 human genbank 54_36p -1 model intronic c.70-3257 e2-3257 0.02 - - - no_errors tier3 136 26 16.05 73 48 39.67 0 0 NA 400220 TCGA-AB-2970 AML27 7 55021646 55021646 C T SNP EGFR NM_005228.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32819 NULL 0 - - - no_errors tier3 305 41 11.78 134 84 38.53 0 0 NA 400220 TCGA-AB-2970 AML27 7 57590107 57590107 G A SNP - - - - - - - - - - - - - - - tier3 786 66 7.75 396 265 40.09 0 0 NA 400220 TCGA-AB-2970 AML27 7 57788624 57788624 A C SNP - - - - - - - - - - - - - - - tier3 604 81 11.81 134 169 55.78 0 0 NA 400220 TCGA-AB-2970 AML27 7 61075177 61075177 T A SNP - - - - - - - - - - - - - - - tier3 414 41 8.99 138 89 39.04 0 0 NA 400220 TCGA-AB-2970 AML27 7 63378125 63378125 C T SNP LOC728927 XM_001128828.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-33839 NULL 0 - - - no_errors tier2 581 73 11.13 234 193 45.09 0 0 0 400220 TCGA-AB-2970 AML27 7 77408266 77408266 G A SNP PHTF2 NM_020432.1 human genbank 54_36p 1 validated intronic c.1872+354 e14+354 0.001 - - - no_errors tier3 788 107 11.94 185 183 49.46 10 5 33.33 400220 TCGA-AB-2970 AML27 7 79502966 79502966 A G SNP - - - - - - - - - - - - - - - tier2 1072 164 13.23 674 538 44.35 0 0 NA 400220 TCGA-AB-2970 AML27 7 120243306 120243306 G A SNP TSPAN12 NM_012338.3 human genbank 54_36p -1 reviewed intronic c.286-213 e4-213 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 7 125947995 125947995 G A SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.2430+12247 e8+12247 0 - - - no_errors tier3 351 54 13.3 205 195 48.75 0 0 NA 400220 TCGA-AB-2970 AML27 7 134071389 134071389 C T SNP CALD1 NM_033138.5 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-131636 NULL 0 - - - no_errors tier3 1541 161 9.42 487 344 41.4 0 0 NA 400220 TCGA-AB-2970 AML27 7 134484051 134484051 T C SNP TMEM140 NM_018295.2 human genbank 54_36p 1 validated intronic c.1+489 e0+489 0.009 - - - no_errors tier3 1674 248 12.88 494 464 48.28 2 0 0 400220 TCGA-AB-2970 AML27 7 141400429 141400429 C A SNP MGAM NM_004668.2 human genbank 54_36p 1 reviewed intronic c.3160-594 e26-594 0 - - - no_errors tier3 NA NA NA 1 0 0 0 0 NA 400220 TCGA-AB-2970 AML27 7 153522252 153522252 G T SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.243+141171 e1+141171 0.022 - - - no_errors tier2 1112 97 8.02 473 360 43.22 0 0 NA 400220 TCGA-AB-2970 AML27 8 6610082 6610082 T C SNP AGPAT5 NM_018361.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*7765 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 8 16022443 16022443 G A SNP MSR1 NM_138715.3 human genbank 54_36p -1 reviewed silent c.1077 p.H359 0.042 "HMMPfam_SRCR,PatternScan_SRCR_1,HMMSmart_SM00202,superfamily_SRCR-like" "HMMPfam_SRCR,PatternScan_SRCR_1,HMMPfam_Macscav_rec,HMMPfam_Collagen,HMMSmart_SM00202,superfamily_SRCR-like" - no_errors tier1 338 44 11.52 200 173 46.38 NA 400220 TCGA-AB-2970 AML27 8 23156984 23156984 T C SNP LOC100133627 XR_037285.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - pseudogene tier2 394 54 12.03 225 154 40.63 1 0 0 400220 TCGA-AB-2970 AML27 8 35701905 35701905 G A SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.1289-1307 e10-1307 0.032 - - - no_errors tier3 881 127 12.59 522 422 44.7 0 0 NA 400220 TCGA-AB-2970 AML27 8 41907838 41907838 G C SNP MYST3 NM_001099412.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1042 NULL 1 - - - no_errors tier2 553 81 12.76 215 188 46.65 57 41 41.84 400220 TCGA-AB-2970 AML27 8 65301702 65301702 C A SNP - - - - - - - - - - - - - - - tier2 370 59 13.75 182 127 40.97 0 0 NA 400220 TCGA-AB-2970 AML27 8 70296360 70296360 T A SNP - - - - - - - - - - - - - - - tier3 1101 122 9.98 338 305 47.43 0 0 NA 400220 TCGA-AB-2970 AML27 8 107021016 107021016 G A SNP ENSG00000201627 ENST00000364757 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-10374 NULL 0.001 - - - no_errors tier3 313 45 12.53 142 64 31.07 0 0 NA 400220 TCGA-AB-2970 AML27 8 136135323 136135323 C T SNP - - - - - - - - - - - - - - - tier2 836 122 12.72 367 301 44.99 0 0 NA 400220 TCGA-AB-2970 AML27 8 137761297 137761297 G A SNP - - - - - - - - - - - - - - - tier3 1303 152 10.44 503 367 42.09 0 0 NA 400220 TCGA-AB-2970 AML27 8 139534894 139534894 A G SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.1+43202 e0+43202 0 - - - no_errors tier2 679 100 12.8 261 222 45.96 0 0 NA 400220 TCGA-AB-2970 AML27 9 25406366 25406366 G T SNP - - - - - - - - - - - - - - - tier3 240 14 5.51 112 75 40.11 0 0 NA 400220 TCGA-AB-2970 AML27 9 44704024 44704024 C T SNP LOC100131427 XM_001719149.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13522 NULL 0.014 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 9 72996586 72996586 C T SNP TRPM3 ENST00000357533 human ensembl 54_36p -1 known intronic c.183+254803 e1+254803 0 - - - no_errors tier3 401 34 7.8 248 205 45.25 0 0 NA 400220 TCGA-AB-2970 AML27 9 82162464 82162464 C T SNP ENSG00000218777 ENST00000404193 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-82162464 NULL 0 - - - no_coding_region:pseudogene tier3 535 87 13.99 290 231 44.34 0 0 NA 400220 TCGA-AB-2970 AML27 9 98933679 98933679 C T SNP LOC340508 NR_002942.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-49631 NULL 0.009 - - - pseudogene tier3 350 50 12.5 271 168 38.18 0 5 100 400220 TCGA-AB-2970 AML27 9 103397767 103397767 C T SNP GRIN3A NM_133445.2 human genbank 54_36p -1 reviewed intronic c.2767-16304 e7-16304 0 - - - no_errors tier3 791 147 15.67 269 231 46.2 0 0 NA 400220 TCGA-AB-2970 AML27 9 120838579 120838579 G A SNP - - - - - - - - - - - - - - - tier2 1109 133 10.71 298 258 46.15 0 0 NA 400220 TCGA-AB-2970 AML27 9 136294980 136294981 - GTCTGT INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 10 445252 445252 C T SNP DIP2C NM_014974.2 human genbank 54_36p -1 reviewed intronic c.1058-295 e9-295 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 10 2310893 2310893 C T SNP - - - - - - - - - - - - - - - tier3 569 81 12.39 310 195 38.61 0 0 NA 400220 TCGA-AB-2970 AML27 10 14343374 14343374 C T SNP FRMD4A NM_018027.3 human genbank 54_36p -1 validated intronic c.45+68689 e1+68689 0.004 - - - no_errors tier3 1535 196 11.28 482 437 47.45 0 0 NA 400220 TCGA-AB-2970 AML27 10 15469409 15469409 C T SNP FAM171A1 NM_001010924.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16352 NULL 0 - - - no_errors tier3 799 79 8.96 208 149 41.74 0 0 NA 400220 TCGA-AB-2970 AML27 10 21723192 21723192 G A SNP ENSG00000216589 ENST00000404552 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*21723192 NULL 0.045 - - - no_coding_region:pseudogene tier2 1099 155 12.35 275 249 47.43 0 0 NA 400220 TCGA-AB-2970 AML27 10 24317005 24317005 C T SNP KIAA1217 NM_001098500.1 human genbank 54_36p 1 validated intronic c.1-19155 e1-19155 0.01 - - - no_errors tier3 277 31 10.06 104 71 40.57 0 0 NA 400220 TCGA-AB-2970 AML27 10 36300363 36300363 C T SNP - - - - - - - - - - - - - - - tier3 0 1 100 1 0 0 0 0 NA 400220 TCGA-AB-2970 AML27 10 53994688 53994688 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 10 69053381 69053381 C A SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.100-16568 e2-16568 0 - - - no_errors tier3 1144 126 9.91 544 442 44.83 0 0 NA 400220 TCGA-AB-2970 AML27 10 73351816 73351816 C T SNP CHST3 NM_004273.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-83791 NULL 0.001 - - - no_errors tier3 1265 152 10.73 451 373 45.27 0 0 NA 400220 TCGA-AB-2970 AML27 10 83385703 83385703 A T SNP - - - - - - - - - - - - - - - tier3 971 139 12.51 424 324 43.26 0 0 NA 400220 TCGA-AB-2970 AML27 10 109432943 109432943 A T SNP - - - - - - - - - - - - - - - tier3 988 108 9.84 363 275 43.1 0 0 NA 400220 TCGA-AB-2970 AML27 10 112925930 112925930 T G SNP - - - - - - - - - - - - - - - tier3 1354 162 10.64 408 330 44.59 2 0 0 400220 TCGA-AB-2970 AML27 10 119239116 119239116 T C SNP EMX2OS NR_002791.2 human genbank 54_36p -1 provisional rna NULL NULL 0.001 - - - no_errors tier1 NA NA NA NA NA NA NA 400220 TCGA-AB-2970 AML27 11 9088726 9088726 G A SNP SCUBE2 NM_020974.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-19075 NULL 0.029 - - - no_errors tier3 1065 136 11.3 353 272 43.45 0 0 NA 400220 TCGA-AB-2970 AML27 11 12871691 12871691 G A SNP TEAD1 NM_021961.4 human genbank 54_36p 1 validated intronic c.655-8372 e8-8372 0.001 - - - no_errors tier3 751 93 10.94 350 276 43.95 0 0 NA 400220 TCGA-AB-2970 AML27 11 13467397 13467397 G A SNP BTBD10 NM_032320.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44150 NULL 0.963 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 11 28296404 28296404 G A SNP METT5D1 NM_152636.1 human genbank 54_36p 1 validated intronic c.779-9814 e5-9814 0.005 - - - no_errors tier3 557 51 8.39 208 163 43.94 0 1 100 400220 TCGA-AB-2970 AML27 11 32370187 32370187 C T SNP WT1 NM_024426.3 human genbank 54_36p -1 reviewed splice_site c.1340-1 e9-1 1 - - - no_errors tier1 1126 137 10.8 311 239 43.38 5 3 37.5 400220 TCGA-AB-2970 AML27 11 34548817 34548817 C A SNP - - - - - - - - - - - - - - - tier3 1382 211 13.22 538 460 46.05 0 0 NA 400220 TCGA-AB-2970 AML27 11 35949062 35949062 G - DEL LDLRAD3 NM_174902.2 human genbank 54_36p 1 provisional intronic c.46+26792 e1+26792 0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 11 69669846 69669846 C T SNP ANO1 NM_018043.5 human genbank 54_36p 1 validated intronic c.1259-3618 e12-3618 0.003 - - - no_errors tier3 537 79 12.8 117 98 45.58 0 0 NA 400220 TCGA-AB-2970 AML27 11 75568902 75568902 T A SNP UVRAG NM_003369.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*38797 NULL 0 - - - no_errors tier3 646 126 15.97 329 309 48.21 0 0 NA 400220 TCGA-AB-2970 AML27 11 83201983 83201983 C T SNP DLG2 NM_001364.1 human genbank 54_36p -1 reviewed intronic c.1407+20322 e12+20322 0 - - - no_errors tier3 1537 180 10.47 483 378 43.85 0 0 NA 400220 TCGA-AB-2970 AML27 11 90731004 90731004 C T SNP - - - - - - - - - - - - - - - tier2 594 50 7.73 176 131 42.67 0 0 NA 400220 TCGA-AB-2970 AML27 11 92651150 92651150 C A SNP - - - - - - - - - - - - - - - tier3 354 56 13.56 157 119 43.12 0 0 NA 400220 TCGA-AB-2970 AML27 11 124756282 124756283 - TGACCA INS PKNOX2 NM_022062.2 human genbank 54_36p 1 validated intronic c.228-4375_228-4374 e3-4374 0.008:0.000 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 11 127853905 127853905 A G SNP ETS1 NM_005238.1 human genbank 54_36p -1 validated intronic c.991+1391 e6+1391 0 - - - no_errors tier3 1619 191 10.55 481 380 44.08 0 0 0 400220 TCGA-AB-2970 AML27 11 130217645 130217645 T G SNP SNX19 NM_014758.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*35882 NULL 0 - - - no_errors tier3 1907 259 11.94 531 454 46.09 0 0 NA 400220 TCGA-AB-2970 AML27 12 5273188 5273188 G T SNP LOC100133418 XM_001714459.1 human genbank 54_36p -1 model intronic c.445-47490 e3-47490 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1199 132 9.9 468 389 45.39 0 0 NA 400220 TCGA-AB-2970 AML27 12 10043169 10043169 T C SNP CLEC12A ENST00000396507 human ensembl 54_36p 1 known intronic c.254-15909 e4-15909 0.096 - - - no_stop_codon tier3 1044 118 10.14 378 328 46.46 3 15 83.33 400220 TCGA-AB-2970 AML27 12 16142063 16142063 C G SNP - - - - - - - - - - - - - - - tier3 907 109 10.69 429 396 47.94 0 0 NA 400220 TCGA-AB-2970 AML27 12 18881529 18881529 T G SNP LOC100134190 XR_037669.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*38790 NULL 0.999 - - - pseudogene tier2 1286 151 10.51 548 419 43.29 0 0 NA 400220 TCGA-AB-2970 AML27 12 23767511 23767511 G A SNP SOX5 NM_006940.4 human genbank 54_36p -1 reviewed intronic c.810+11374 e6+11374 0 - - - no_errors tier3 763 73 8.69 246 148 37.47 0 0 NA 400220 TCGA-AB-2970 AML27 12 36181843 36181843 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 12 41180619 41180619 G A SNP PRICKLE1 NM_153026.1 human genbank 54_36p -1 validated intronic c.1-27986 e1-27986 0.002 - - - no_errors tier3 837 114 11.99 246 177 41.84 0 3 100 400220 TCGA-AB-2970 AML27 12 48009870 48009870 G T SNP TROAP NM_005480.1 human genbank 54_36p 1 validated intronic c.1165-37 e11-37 0 - - - no_errors tier2 1006 192 16.01 339 327 49.1 11 16 59.26 400220 TCGA-AB-2970 AML27 12 67316409 67316409 A G SNP RAP1B NM_001010942.1 human genbank 54_36p 1 validated intronic c.1-12337 e1-12337 0.001 - - - no_errors tier2 NA NA NA NA NA NA 54 1 1.82 400220 TCGA-AB-2970 AML27 12 70956260 70956260 C G SNP TRHDE NM_013381.2 human genbank 54_36p 1 reviewed intronic c.779+2656 e1+2656 0.009 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 12 72731206 72731207 - GATGAAGT INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 12 80233010 80233010 C G SNP PPFIA2 NM_003625.2 human genbank 54_36p -1 reviewed intronic c.2642+10677 e20+10677 0.001 - - - no_errors tier3 843 65 7.16 267 234 46.61 0 0 NA 400220 TCGA-AB-2970 AML27 12 95491709 95491709 C T SNP C12orf55 XM_001715090.2 human genbank 54_36p 1 model intronic c.2287-2785 e17-2785 0.008 - - - no_errors tier3 1284 184 12.43 659 513 43.7 0 0 NA 400220 TCGA-AB-2970 AML27 12 104412753 104412753 G T SNP - - - - - - - - - - - - - - - tier3 1172 114 8.84 489 326 40 0 0 NA 400220 TCGA-AB-2970 AML27 12 104628978 104628978 G T SNP - - - - - - - - - - - - - - - tier3 1329 208 13.53 492 430 46.64 0 0 NA 400220 TCGA-AB-2970 AML27 13 18521192 18521192 C T SNP DKFZp686A1627 NR_002801.1 human genbank 54_36p -1 provisional intronic c.NULL NULL 0.002 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 13 27294628 27294628 C T SNP ENSG00000207330 ENST00000384600 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6272 NULL 1 - - - no_errors tier2 516 32 5.82 202 94 31.76 0 0 NA 400220 TCGA-AB-2970 AML27 13 27506258 27506259 - GGCGATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1798_1797 p.599in_frame_insPAPQIMSTSTLISENMNIA 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 400220 TCGA-AB-2970 AML27 13 30620781 30620781 T C SNP HSPH1 NM_006644.2 human genbank 54_36p -1 validated intronic c.1138-164 e9-164 0.002 - - - no_errors tier3 372 61 14.09 104 70 40.23 1 0 0 400220 TCGA-AB-2970 AML27 13 52627792 52627792 G A SNP ENSG00000218221 ENST00000401786 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44325 NULL 0.002 - - - no_coding_region:pseudogene tier3 1433 198 12.11 443 362 44.86 0 0 NA 400220 TCGA-AB-2970 AML27 13 57520872 57520872 G T SNP - - - - - - - - - - - - - - - tier3 591 48 7.5 240 153 38.83 0 0 NA 400220 TCGA-AB-2970 AML27 13 63492022 63492022 G A SNP ENSG00000219998 ENST00000402976 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43466 NULL 0.002 - - - no_coding_region:pseudogene tier3 778 100 11.38 188 178 48.63 0 0 NA 400220 TCGA-AB-2970 AML27 13 77038729 77038729 T G SNP SCEL NM_144777.2 human genbank 54_36p 1 reviewed intronic c.291-1087 e5-1087 0.013 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 13 81847267 81847267 G A SNP - - - - - - - - - - - - - - - tier3 477 56 10.51 164 115 41.07 0 0 NA 400220 TCGA-AB-2970 AML27 13 89301744 89301744 A C SNP ENSG00000184837 ENST00000330770 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-17982 NULL 0 - - - no_coding_region:pseudogene tier3 128 14 9.86 47 62 56.88 0 0 NA 400220 TCGA-AB-2970 AML27 13 89576015 89576015 G T SNP ENSG00000220026 ENST00000403945 human ensembl 54_36p 1 known 5_prime_flanking_region c.-45106 NULL 0.001 - - - no_coding_region:pseudogene tier3 552 70 11.24 312 184 37.1 0 0 NA 400220 TCGA-AB-2970 AML27 13 89768066 89768066 A G SNP - - - - - - - - - - - - - - - tier3 148 25 14.45 34 56 62.22 0 0 NA 400220 TCGA-AB-2970 AML27 13 91491784 91491784 A G SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1402-103300 e7-103300 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 13 112600111 112600111 G A SNP MCF2L ENST00000375608 human ensembl 54_36p 1 known intronic c.1+3365 e0+3365 0.006 - - - no_errors tier3 189 16 7.8 112 74 39.78 0 0 0 400220 TCGA-AB-2970 AML27 14 24812988 24812988 G A SNP ENSG00000179020 ENST00000323440 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-6606 NULL 0.002 - - - no_coding_region:pseudogene tier3 1002 125 11.09 365 252 40.78 0 0 NA 400220 TCGA-AB-2970 AML27 14 25372740 25372740 C T SNP ENSG00000212270 ENST00000390968 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26982 NULL 0.997 - - - no_errors tier3 1051 161 13.25 392 345 46.75 0 0 NA 400220 TCGA-AB-2970 AML27 14 36242523 36242523 G C SNP SLC25A21 NM_030631.2 human genbank 54_36p -1 provisional intronic c.603+7751 e7+7751 0.958 - - - no_errors tier2 718 110 13.29 201 148 42.29 0 0 NA 400220 TCGA-AB-2970 AML27 14 41568235 41568235 G A SNP - - - - - - - - - - - - - - - tier3 512 48 8.57 192 143 42.69 0 0 NA 400220 TCGA-AB-2970 AML27 14 50644101 50644101 T C SNP TRIM9 NM_015163.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12694 NULL 0.02 - - - no_errors tier3 449 63 12.28 123 98 44.34 0 0 NA 400220 TCGA-AB-2970 AML27 14 65694596 65694596 C A SNP ENSG00000200860 ENST00000363990 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19402 NULL 0 - - - no_errors tier3 700 74 9.54 362 287 44.22 0 0 NA 400220 TCGA-AB-2970 AML27 14 67106471 67106471 G A SNP PLEKHH1 NM_020715.2 human genbank 54_36p 1 validated missense c.1423 p.A475T 0.998 NULL "HMMPfam_MyTH4,HMMSmart_SM00139,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_FERM_M,superfamily_Second domain of FERM,HMMSmart_SM00295,superfamily_PH domain-like" - no_errors tier1 793 114 12.56 363 313 46.3 NA 400220 TCGA-AB-2970 AML27 14 91744188 91744188 C A SNP CPSF2 NM_017437.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*46347 NULL 0.025 - - - no_errors tier3 1098 128 10.44 442 358 44.64 0 0 NA 400220 TCGA-AB-2970 AML27 14 99476952 99476952 G A SNP EML1 NM_001008707.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*750 NULL 0.001 - - - no_errors tier3 435 52 10.66 93 82 46.59 0 0 NA 400220 TCGA-AB-2970 AML27 15 24251354 24251354 C A SNP - - - - - - - - - - - - - - - tier2 1846 256 12.16 776 657 45.85 0 0 NA 400220 TCGA-AB-2970 AML27 15 25047792 25047792 C T SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.271-106910 e4-106910 0.002 - - - no_errors tier3 614 89 12.64 247 206 45.47 0 0 NA 400220 TCGA-AB-2970 AML27 15 25824399 25824399 C T SNP OCA2 NM_000275.2 human genbank 54_36p -1 reviewed intronic c.2079+20469 e18+20469 0.003 - - - no_errors tier3 536 103 16.04 258 213 45.22 0 0 NA 400220 TCGA-AB-2970 AML27 15 27767329 27767329 C A SNP ENSG00000212769 ENST00000391458 human ensembl 54_36p 1 known 5_prime_flanking_region c.-42779 NULL 0 - - - no_coding_region:pseudogene tier3 304 56 15.51 166 107 39.19 0 0 NA 400220 TCGA-AB-2970 AML27 15 35693981 35693981 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 15 37389389 37389389 C T SNP - - - - - - - - - - - - - - - tier3 1577 181 10.25 826 603 42.2 0 0 NA 400220 TCGA-AB-2970 AML27 15 43014382 43014382 G T SNP C15orf43 NM_152448.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-21827 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 400220 TCGA-AB-2970 AML27 15 47931525 47931525 C - DEL ATP8B4 NM_024837.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*8158 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 15 49479651 49479651 C A SNP GLDN NM_181789.2 human genbank 54_36p 1 validated intronic c.818-30 e7-30 0 - - - no_errors tier3 656 127 16.2 340 291 46.12 0 0 NA 400220 TCGA-AB-2970 AML27 15 56011723 56011723 C T SNP ALDH1A2 NM_003888.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*22964 NULL 0.022 - - - no_errors tier3 674 90 11.73 326 249 43.3 0 0 NA 400220 TCGA-AB-2970 AML27 15 58437648 58437648 C T SNP ANXA2 NM_001002858.1 human genbank 54_36p -1 reviewed intronic c.412-921 e6-921 1 - - - no_errors tier2 444 86 16.17 113 119 51.29 2 2 50 400220 TCGA-AB-2970 AML27 15 62822332 62822332 G A SNP RBPMS2 NM_194272.1 human genbank 54_36p -1 provisional intronic c.568-1838 e7-1838 0.025 - - - no_errors tier3 446 41 8.42 195 139 41.62 0 0 0 400220 TCGA-AB-2970 AML27 15 68511669 68511669 T G SNP - - - - - - - - - - - - - - - tier3 759 90 10.6 240 181 42.89 0 0 NA 400220 TCGA-AB-2970 AML27 15 89955134 89955134 G A SNP - - - - - - - - - - - - - - - tier3 1593 238 13 507 466 47.89 0 0 NA 400220 TCGA-AB-2970 AML27 15 94882853 94882853 C T SNP - - - - - - - - - - - - - - - tier2 617 88 12.46 251 179 41.63 0 0 NA 400220 TCGA-AB-2970 AML27 15 96495601 96495601 C T SNP LOC728459 XM_001129411.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-46215 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 16 9862551 9862551 G A SNP GRIN2A NM_000833.3 human genbank 54_36p -1 reviewed intronic c.1123-11232 e4-11232 0 - - - no_errors tier3 1120 175 13.46 515 458 47.07 0 0 NA 400220 TCGA-AB-2970 AML27 16 30039332 30039332 A - DEL MAPK3 NM_002746.1 human genbank 54_36p -1 reviewed intronic c.353+1314 e2+1314 0.248 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 16 59035934 59035934 A T SNP - - - - - - - - - - - - - - - tier3 1143 107 8.55 317 228 41.83 0 0 NA 400220 TCGA-AB-2970 AML27 16 63669317 63669317 G C SNP CDH11 NM_001797.2 human genbank 54_36p -1 reviewed intronic c.1-23985 e1-23985 0 - - - no_errors tier3 850 124 12.69 272 263 49.16 0 0 NA 400220 TCGA-AB-2970 AML27 17 2582250 2582250 C T SNP LOC100128142 XM_001715360.1 human genbank 54_36p -1 model intronic c.205-573 e3-573 0 - - - no_errors tier3 1021 138 11.87 213 177 45.38 0 0 NA 400220 TCGA-AB-2970 AML27 17 17733750 17733750 C T SNP TOM1L2 NM_001082968.2 human genbank 54_36p -1 validated intronic c.366+3950 e4+3950 0 - - - no_errors tier3 750 122 13.97 269 242 47.36 0 1 100 400220 TCGA-AB-2970 AML27 17 61881559 61881559 C T SNP PRKCA NM_002737.2 human genbank 54_36p 1 reviewed intronic c.206-41222 e3-41222 0 - - - no_errors tier3 939 118 11.12 488 398 44.67 1 1 50 400220 TCGA-AB-2970 AML27 17 73286340 73286340 G A SNP - - - - - - - - - - - - - - - tier3 459 67 12.74 245 193 44.06 0 0 NA 400220 TCGA-AB-2970 AML27 18 3829146 3829146 T C SNP DLGAP1 NM_004746.1 human genbank 54_36p -1 provisional intronic c.958-24873 e2-24873 0 - - - no_errors tier3 1040 158 13.18 242 213 46.81 0 0 NA 400220 TCGA-AB-2970 AML27 18 5127130 5127130 C A SNP ENSG00000215368 ENST00000400144 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3962 NULL 0.02 - - - no_coding_region:pseudogene tier3 1010 118 10.46 508 325 39.02 0 0 NA 400220 TCGA-AB-2970 AML27 18 13420874 13420874 C A SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.41-7369 e2-7369 0.001 - - - no_errors tier3 620 143 18.62 333 346 50.88 0 0 0 400220 TCGA-AB-2970 AML27 18 38616423 38616423 G A SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional intronic c.427-38740 e5-38740 0 - - - no_errors tier2 211 19 8.26 67 49 42.24 0 0 NA 400220 TCGA-AB-2970 AML27 18 47832910 47832910 G T SNP - - - - - - - - - - - - - - - tier3 1162 138 10.62 506 374 42.5 0 0 NA 400220 TCGA-AB-2970 AML27 18 54996149 54996149 G A SNP GRP NM_002091.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-42329 NULL 0 - - - no_errors tier2 741 87 10.49 220 188 46.08 0 0 0 400220 TCGA-AB-2970 AML27 18 60822336 60822336 G A SNP - - - - - - - - - - - - - - - tier3 150 21 12.28 100 63 38.41 0 0 NA 400220 TCGA-AB-2970 AML27 18 67016988 67016988 G C SNP - - - - - - - - - - - - - - - tier3 NA NA NA 1 0 0 0 0 NA 400220 TCGA-AB-2970 AML27 18 67500844 67500844 G A SNP - - - - - - - - - - - - - - - tier3 826 67 7.5 249 197 44.07 0 0 NA 400220 TCGA-AB-2970 AML27 18 74862688 74862688 C T SNP LOC645321 XM_001714545.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-21587 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 19 2461036 2461036 C - DEL LOC100132469 XM_001726134.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-33032 NULL 0.016 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 19 3935873 3935873 G A SNP EEF2 NM_001961.3 human genbank 54_36p -1 reviewed intronic c.3+503 e1+503 0 - - - no_errors tier2 327 24 6.84 84 77 47.83 6 1 14.29 400220 TCGA-AB-2970 AML27 19 11013955 11013955 G A SNP SMARCA4 NM_003072.1 human genbank 54_36p 1 reviewed intronic c.4424+719 e29+719 0.007 - - - no_errors tier3 489 58 10.6 121 79 39.3 11 12 52.17 400220 TCGA-AB-2970 AML27 19 15919303 15919303 C G SNP CYP4F11 NM_021187.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-13085 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 19 55429652 55429652 C T SNP MYH14 NM_001077186.1 human genbank 54_36p 1 reviewed intronic c.1114+2513 e9+2513 0.002 - - - no_errors tier2 693 63 8.3 217 136 38.53 0 0 NA 400220 TCGA-AB-2970 AML27 19 59835082 59835082 A T SNP LILRB1 NM_001081637.1 human genbank 54_36p 1 reviewed intronic c.358+32 e3+32 0 - - - no_errors tier3 279 42 13.04 198 168 45.78 0 0 0 400220 TCGA-AB-2970 AML27 20 11130236 11130236 T C SNP - - - - - - - - - - - - - - - tier3 201 30 12.99 87 76 46.63 0 0 NA 400220 TCGA-AB-2970 AML27 20 15271865 15271865 G A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.541-88185 e7-88185 0 - - - no_errors tier3 1316 186 12.36 509 414 44.85 0 0 NA 400220 TCGA-AB-2970 AML27 20 43334043 43334043 T A SNP RBPJL NM_014276.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34934 NULL 0.001 - - - no_errors tier3 1262 202 13.77 584 533 47.5 0 0 NA 400220 TCGA-AB-2970 AML27 20 46462856 46462856 C T SNP - - - - - - - - - - - - - - - tier3 918 132 12.51 695 616 46.88 0 0 NA 400220 TCGA-AB-2970 AML27 20 51492752 51492752 G A SNP TSHZ2 NM_173485.4 human genbank 54_36p 1 validated intronic c.3105-44338 e3-44338 0.007 - - - no_errors tier3 997 129 11.31 384 285 42.41 0 0 NA 400220 TCGA-AB-2970 AML27 20 58825522 58825522 G A SNP - - - - - - - - - - - - - - - tier3 1252 161 11.39 738 603 44.83 0 0 NA 400220 TCGA-AB-2970 AML27 20 61150611 61150611 C T SNP C20orf51 XR_040056.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 328 55 14.21 344 303 46.4 0 0 NA 400220 TCGA-AB-2970 AML27 21 16218382 16218382 T C SNP USP25 NM_013396.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*45717 NULL 0.003 - - - no_errors tier2 843 254 23.13 74 791 91.34 0 0 NA 400220 TCGA-AB-2970 AML27 21 24493749 24493749 G T SNP - - - - - - - - - - - - - - - tier3 145 3 2.03 41 19 31.67 0 0 NA 400220 TCGA-AB-2970 AML27 21 35181023 35181023 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.338 p.P113L 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 138 43 23.76 15 116 87.88 6 280 97.9 400220 TCGA-AB-2970 AML27 22 40742783 40742783 T C SNP WBP2NL NM_152613.2 human genbank 54_36p 1 validated intronic c.63-2478 e2-2478 0.001 - - - no_errors tier3 969 96 9 269 200 42.64 1 3 75 400220 TCGA-AB-2970 AML27 22 43706552 43706552 G T SNP PHF21B NM_138415.1 human genbank 54_36p -1 validated intronic c.121-11518 e3-11518 0.007 - - - no_errors tier3 465 83 15.15 211 151 41.71 0 0 NA 400220 TCGA-AB-2970 AML27 22 46504211 46504211 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 400220 TCGA-AB-2970 AML27 22 47104940 47104940 C T SNP - - - - - - - - - - - - - - - tier3 936 151 13.88 246 200 44.74 0 0 NA 906708 TCGA-AB-2971 AML44 X 6991633 6991633 A G SNP HDHD1A NM_012080.1 human genbank 54_36p -1 validated intronic c.469-13120 e4-13120 0.006 - - - no_errors tier3 708 53 6.96 667 595 47.15 7 11 61.11 906708 TCGA-AB-2971 AML44 X 15981862 15981862 A G SNP - - - - - - - - - - - - - - - tier3 389 35 8.25 572 518 47.52 0 0 NA 906708 TCGA-AB-2971 AML44 X 26516935 26516935 G A SNP VENTXP1 NR_001559.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*27845 NULL 0.006 - - - pseudogene tier3 646 40 5.83 747 551 42.42 0 0 NA 906708 TCGA-AB-2971 AML44 X 30058942 30058942 G A SNP - - - - - - - - - - - - - - - tier3 1144 56 4.66 1048 861 45.08 0 0 NA 906708 TCGA-AB-2971 AML44 X 31585772 31585772 A G SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.8027+256 e54+256 0.041 - - - no_errors tier3 625 77 10.95 904 883 49.38 0 0 NA 906708 TCGA-AB-2971 AML44 X 31894109 31894109 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6614+2268 e45+2268 0.04 - - - no_errors tier3 550 31 5.34 609 493 44.66 0 0 NA 906708 TCGA-AB-2971 AML44 X 34199207 34199207 G A SNP - - - - - - - - - - - - - - - tier3 1031 59 5.41 811 671 45.28 0 0 NA 906708 TCGA-AB-2971 AML44 X 36740758 36740758 C T SNP - - - - - - - - - - - - - - - tier3 124 14 10.07 134 141 51.09 0 0 NA 906708 TCGA-AB-2971 AML44 X 42757264 42757264 G A SNP - - - - - - - - - - - - - - - tier3 378 14 3.57 386 216 35.88 0 0 NA 906708 TCGA-AB-2971 AML44 X 47775957 47775957 T C SNP ZNF182 NM_006962.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-43018 NULL 0.001 - - - no_errors tier3 949 84 8.1 628 462 42.39 0 2 100 906708 TCGA-AB-2971 AML44 X 63405327 63405327 C T SNP MTMR8 NM_017677.2 human genbank 54_36p -1 provisional missense c.1930 p.E644K 0.003 NULL "HMMSmart_SM00404,HMMPfam_Myotub-related,PatternScan_TYR_PHOSPHATASE_1,superfamily_PH domain-like,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 882 66 6.95 737 632 46.13 1 100 906708 TCGA-AB-2971 AML44 X 66471433 66471433 G C SNP LOC100129144 XM_001721427.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-39226 NULL 0.001 - - - no_errors tier3 962 53 5.22 920 797 46.36 0 0 NA 906708 TCGA-AB-2971 AML44 X 86837792 86837792 G A SNP KLHL4 NM_057162.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*26742 NULL 0.167 - - - no_errors tier3 1197 49 3.93 847 669 44.07 0 0 NA 906708 TCGA-AB-2971 AML44 X 97608343 97608343 G A SNP ENSG00000217861 ENST00000402099 human ensembl 54_36p 1 known 3_prime_flanking_region c.*43882 NULL 0.037 - - - no_coding_region:pseudogene tier3 289 5 1.7 525 126 19.33 0 0 NA 906708 TCGA-AB-2971 AML44 X 98852667 98852667 G C SNP ENSG00000215070 ENST00000399535 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8342 NULL 0 - - - no_coding_region:pseudogene tier3 401 24 5.65 459 355 43.61 0 0 NA 906708 TCGA-AB-2971 AML44 X 109892011 109892011 C T SNP CHRDL1 NM_145234.1 human genbank 54_36p -1 reviewed intronic c.207+568 e2+568 0.002 - - - no_errors tier3 1139 90 7.31 956 679 41.48 0 0 NA 906708 TCGA-AB-2971 AML44 X 117360163 117360163 C T SNP WDR44 NM_019045.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-4332 NULL 0 - - - no_errors tier3 681 67 8.95 598 495 45.21 0 0 NA 906708 TCGA-AB-2971 AML44 X 121272789 121272789 C A SNP - - - - - - - - - - - - - - - tier3 300 14 4.44 454 260 36.41 0 0 NA 906708 TCGA-AB-2971 AML44 X 128061240 128061240 C A SNP - - - - - - - - - - - - - - - tier3 1613 104 6.06 1181 889 42.91 0 0 NA 906708 TCGA-AB-2971 AML44 X 129386657 129386657 C T SNP GPR119 NM_178471.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-39555 NULL 0.015 - - - no_errors tier3 303 10 3.19 361 238 39.67 1 0 0 906708 TCGA-AB-2971 AML44 X 136355180 136355180 A G SNP ENSG00000134598 ENST00000257021 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3519 NULL 0.156 - - - no_coding_region:pseudogene tier3 549 49 8.18 372 279 42.86 0 0 NA 906708 TCGA-AB-2971 AML44 X 140336812 140336812 G T SNP ENSG00000220346 ENST00000407507 human ensembl 54_36p 1 known 3_prime_flanking_region c.*33875 NULL 0 - - - no_coding_region:pseudogene tier3 410 45 9.83 515 581 52.96 0 0 NA 906708 TCGA-AB-2971 AML44 X 144881122 144881122 C T SNP ENSG00000216032 ENST00000401213 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-975 NULL 0 - - - no_errors tier3 1467 74 4.79 1602 1310 44.94 0 0 NA 906708 TCGA-AB-2971 AML44 X 147806638 147806638 A G SNP AFF2 NM_002025.2 human genbank 54_36p 1 validated intronic c.1397+13159 e9+13159 0.002 - - - no_errors tier3 935 94 9.14 883 761 46.23 0 0 0 906708 TCGA-AB-2971 AML44 X 152627539 152627539 C T SNP BCAP31 NM_005745.1 human genbank 54_36p -1 reviewed intronic c.342-4796 e4-4796 0.002 - - - no_errors tier3 446 17 3.66 119 75 38.66 3 0 0 906708 TCGA-AB-2971 AML44 1 1896926 1896926 G A SNP KIAA1751 NM_001080484.1 human genbank 54_36p -1 predicted intronic c.501-1429 e6-1429 0.019 - - - no_errors tier3 230 19 7.63 86 86 50 0 0 NA 906708 TCGA-AB-2971 AML44 1 4971622 4971622 G A SNP - - - - - - - - - - - - - - - tier3 558 44 7.27 623 426 40.61 0 0 NA 906708 TCGA-AB-2971 AML44 1 36909630 36909630 C G SNP ENSG00000220821 ENST00000404010 human ensembl 54_36p 1 known 3_prime_flanking_region c.*40585 NULL 0.016 - - - no_coding_region:pseudogene tier3 1438 111 7.16 1059 888 45.59 0 0 NA 906708 TCGA-AB-2971 AML44 1 39920115 39920115 C T SNP HPCAL4 NM_016257.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*680 NULL 0.001 - - - no_errors tier3 631 56 8.15 211 199 48.42 0 0 NA 906708 TCGA-AB-2971 AML44 1 50549064 50549064 A T SNP LOC343184 XR_016832.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-15327 NULL 0.986 - - - pseudogene tier3 538 47 8.03 393 360 47.75 0 0 NA 906708 TCGA-AB-2971 AML44 1 56186278 56186278 C T SNP ENSG00000217577 ENST00000406132 human ensembl 54_36p -1 known 5_prime_flanking_region c.-8748 NULL 0.001 - - - no_coding_region:pseudogene tier3 1318 84 5.98 865 739 45.96 0 0 NA 906708 TCGA-AB-2971 AML44 1 61740231 61740231 T C SNP NFIA NM_005595.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*46592 NULL 0.981 - - - no_errors tier3 767 43 5.3 892 683 43.31 0 0 NA 906708 TCGA-AB-2971 AML44 1 88153889 88153889 C T SNP - - - - - - - - - - - - - - - tier3 500 21 4.01 449 294 39.52 0 0 NA 906708 TCGA-AB-2971 AML44 1 161347398 161347398 C A SNP RGS4 NM_001102445.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*36424 NULL 0.001 - - - no_errors tier3 348 23 6.2 355 289 44.88 0 0 NA 906708 TCGA-AB-2971 AML44 1 161932513 161932513 G A SNP - - - - - - - - - - - - - - - tier3 438 44 9.11 733 586 44.43 0 0 NA 906708 TCGA-AB-2971 AML44 1 180553497 180553497 A G SNP LOC730144 XM_001132642.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-17619 NULL 0.591 - - - no_errors tier3 874 63 6.71 816 422 34.09 0 0 NA 906708 TCGA-AB-2971 AML44 1 181376048 181376048 A G SNP LAMC1 NM_002293.3 human genbank 54_36p 1 reviewed intronic c.4474-114 e27-114 0.018 - - - no_errors tier3 182 9 4.69 312 143 31.29 0 0 0 906708 TCGA-AB-2971 AML44 1 209080561 209080561 C T SNP KCNH1 NM_172362.3 human genbank 54_36p -1 reviewed intronic c.1463-36430 e8-36430 0.002 - - - no_errors tier3 741 56 7.01 714 577 44.66 0 0 NA 906708 TCGA-AB-2971 AML44 1 217733920 217733920 A T SNP LOC728510 XM_001127601.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-24147 NULL 0.007 - - - no_errors tier3 278 9 3.14 311 254 44.8 0 0 NA 906708 TCGA-AB-2971 AML44 1 220492241 220492241 T C SNP ENSG00000217821 ENST00000405699 human ensembl 54_36p -1 known 3_prime_flanking_region c.*9557 NULL 0.014 - - - no_coding_region:pseudogene tier3 610 39 6.01 790 671 45.93 0 0 NA 906708 TCGA-AB-2971 AML44 1 226107218 226107218 C T SNP MPN2 NM_183062.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*6686 NULL 0 - - - no_errors tier3 520 39 6.95 351 276 43.95 0 0 NA 906708 TCGA-AB-2971 AML44 1 239056663 239056664 - A INS RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.684+357_684+356 e9+357 0.004:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 1 240362646 240362646 G T SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.460-8056 e5-8056 0.006 - - - no_errors tier3 1046 68 6.1 793 655 45.17 0 0 NA 906708 TCGA-AB-2971 AML44 1 242077300 242077300 A T SNP AKT3 ENST00000366539 human ensembl 54_36p -1 known intronic c.1+2665 e0+2665 0.015 - - - no_errors tier3 429 19 4.24 288 211 42.28 1 0 0 906708 TCGA-AB-2971 AML44 2 2787616 2787616 C T SNP - - - - - - - - - - - - - - - tier3 854 20 2.28 733 229 23.76 0 0 NA 906708 TCGA-AB-2971 AML44 2 15971636 15971636 C T SNP MYCN NM_005378.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28002 NULL 0 - - - no_errors tier3 764 63 7.62 542 483 47.12 0 0 NA 906708 TCGA-AB-2971 AML44 2 31008251 31008251 C T SNP GALNT14 NM_024572.2 human genbank 54_36p -1 validated intronic c.1058+187 e10+187 0.001 - - - no_errors tier3 1396 118 7.78 1566 1250 44.33 0 1 100 906708 TCGA-AB-2971 AML44 2 31110271 31110271 C T SNP GALNT14 NM_024572.2 human genbank 54_36p -1 validated intronic c.130-40894 e2-40894 0 - - - no_errors tier3 1332 159 10.62 1221 1071 46.65 0 0 NA 906708 TCGA-AB-2971 AML44 2 31323092 31323092 G C SNP EHD3 NM_014600.1 human genbank 54_36p 1 provisional intronic c.404+2272 e2+2272 0 - - - no_errors tier3 464 31 6.24 306 243 44.02 0 0 0 906708 TCGA-AB-2971 AML44 2 31893924 31893924 C T SNP AK2P2 XR_017211.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*7271 NULL 0.003 - - - pseudogene tier3 326 21 6.05 294 195 39.88 1 0 0 906708 TCGA-AB-2971 AML44 2 33855220 33855220 T G SNP MYADML ENST00000322472 human ensembl 54_36p -1 known 5_prime_flanking_region c.-48874 NULL 0.244 - - - no_errors tier3 530 65 10.91 512 488 48.7 0 0 NA 906708 TCGA-AB-2971 AML44 2 35035557 35035557 C T SNP - - - - - - - - - - - - - - - tier3 379 34 8.21 388 247 38.84 0 0 NA 906708 TCGA-AB-2971 AML44 2 38760215 38760215 T C SNP GALM NM_138801.2 human genbank 54_36p 1 reviewed intronic c.346-1711 e3-1711 0.59 - - - no_errors tier3 807 43 5.05 579 457 44.07 0 0 0 906708 TCGA-AB-2971 AML44 2 40609382 40609382 T C SNP SLC8A1 ENST00000405269 human ensembl 54_36p -1 known intronic c.1+82192 e0+82192 0.085 - - - no_errors tier3 698 41 5.55 651 420 39.18 1 1 50 906708 TCGA-AB-2971 AML44 2 43934831 43934831 T C SNP ABCG8 NM_022437.2 human genbank 54_36p 1 reviewed intronic c.964+1320 e6+1320 0.001 - - - no_errors tier3 474 29 5.77 509 398 43.78 0 0 NA 906708 TCGA-AB-2971 AML44 2 44117253 44117253 A G SNP LRPPRC NM_133259.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-40663 NULL 0.04 - - - no_errors tier3 671 61 8.33 718 588 45.02 0 0 NA 906708 TCGA-AB-2971 AML44 2 46340914 46340914 C A SNP EPAS1 NM_001430.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37641 NULL 0.003 - - - no_errors tier3 168 12 6.67 118 122 50.83 0 0 NA 906708 TCGA-AB-2971 AML44 2 46982280 46982280 C T SNP TTC7A NM_020458.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-39905 NULL 0.002 - - - no_errors tier3 429 40 8.53 231 167 41.96 0 0 NA 906708 TCGA-AB-2971 AML44 2 47680449 47680449 A - DEL KCNK12 NM_022055.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29475 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 2 49927237 49927237 T C SNP LOC130728 XR_017361.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-4085 NULL 0.008 - - - pseudogene tier3 514 40 7.21 478 447 48.27 0 0 NA 906708 TCGA-AB-2971 AML44 2 50115825 50115825 T C SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.4038+18088 e19+18088 0.097 - - - no_errors tier3 284 37 11.49 294 253 46.08 0 0 NA 906708 TCGA-AB-2971 AML44 2 54936711 54936711 C T SNP EML6 XM_001725001.2 human genbank 54_36p 1 model intronic c.1657+2215 e10+2215 0 - - - no_errors tier3 709 28 3.8 669 492 42.38 0 0 NA 906708 TCGA-AB-2971 AML44 2 55841268 55841268 C T SNP - - - - - - - - - - - - - - - tier3 801 53 6.18 450 335 42.57 0 0 NA 906708 TCGA-AB-2971 AML44 2 69148756 69148756 T A SNP ANTXR1 NM_032208.3 human genbank 54_36p 1 reviewed intronic c.297-2527 e4-2527 0 - - - no_errors tier3 673 28 3.97 1094 866 44.18 0 0 0 906708 TCGA-AB-2971 AML44 2 73683017 73683017 G A SNP ALMS1 NM_015120.4 human genbank 54_36p 1 reviewed intronic c.12295+14 e20+14 0 - - - no_errors tier3 474 34 6.69 512 422 44.94 0 0 0 906708 TCGA-AB-2971 AML44 2 77573282 77573282 T C SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+25670 e2+25670 0 - - - no_errors tier3 584 41 6.56 555 491 46.9 0 0 NA 906708 TCGA-AB-2971 AML44 2 78043066 78043066 T C SNP - - - - - - - - - - - - - - - tier3 54 4 6.9 160 160 49.84 0 0 NA 906708 TCGA-AB-2971 AML44 2 78532364 78532364 T G SNP ENSG00000214429 ENST00000398312 human ensembl 54_36p -1 known intronic c.1+34064 e0+34064 0.001 - - - no_errors tier3 110 1 0.9 165 163 49.7 0 0 NA 906708 TCGA-AB-2971 AML44 2 82194640 82194640 C T SNP - - - - - - - - - - - - - - - tier3 516 36 6.5 518 423 44.95 0 0 NA 906708 TCGA-AB-2971 AML44 2 83736093 83736093 A T SNP ENSG00000199295 ENST00000362425 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2277 NULL 0.038 - - - no_errors tier3 266 17 6.01 363 287 44.09 0 0 NA 906708 TCGA-AB-2971 AML44 2 95036506 95036506 C T SNP MAL NM_002371.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-18759 NULL 0 - - - no_errors tier3 698 65 8.47 345 310 47.18 0 0 NA 906708 TCGA-AB-2971 AML44 2 95341414 95341414 G A SNP KCNIP3 NM_013434.1 human genbank 54_36p 1 reviewed intronic c.181+1419 e2+1419 0 - - - no_errors tier3 314 24 7.1 245 213 46.51 0 0 NA 906708 TCGA-AB-2971 AML44 2 114977529 114977529 G C SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+60644 e1+60644 0.001 - - - no_errors tier3 1133 65 5.42 1053 780 42.53 0 0 NA 906708 TCGA-AB-2971 AML44 2 121240330 121240330 C G SNP GLI2 NM_005270.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-31037 NULL 0.001 - - - no_errors tier3 642 59 8.38 321 302 48.4 0 0 NA 906708 TCGA-AB-2971 AML44 2 126143810 126143810 C A SNP - - - - - - - - - - - - - - - tier3 1212 100 7.62 1019 858 45.71 0 0 NA 906708 TCGA-AB-2971 AML44 2 128487156 128487156 G A SNP SAP130 NM_024545.1 human genbank 54_36p -1 validated missense c.740 p.T247I 0.999 NULL NULL - no_errors tier1 364 22 5.7 269 243 47.46 16 11 40.74 906708 TCGA-AB-2971 AML44 2 132309643 132309643 G A SNP MGC50273 NM_214461.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-34663 NULL 0.003 - - - no_errors tier3 111 7 5.93 94 74 43.79 0 0 NA 906708 TCGA-AB-2971 AML44 2 142515513 142515513 G A SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.82+89174 e1+89174 0.017 - - - no_errors tier3 616 44 6.65 557 459 45.18 0 0 NA 906708 TCGA-AB-2971 AML44 2 145882962 145882962 G A SNP - - - - - - - - - - - - - - - tier3 759 55 6.74 672 574 46.07 0 0 NA 906708 TCGA-AB-2971 AML44 2 147729408 147729408 C T SNP - - - - - - - - - - - - - - - tier3 620 23 3.57 695 456 39.62 0 0 NA 906708 TCGA-AB-2971 AML44 2 158403247 158403247 A C SNP ACVR1 ENST00000263640 human ensembl 54_36p -1 known intronic c.1-19930 e1-19930 0 - - - no_errors tier3 268 17 5.94 260 221 45.95 5 0 0 906708 TCGA-AB-2971 AML44 2 162052203 162052203 C A SNP ENSG00000174470 ENST00000312302 human ensembl 54_36p -1 known 3_prime_flanking_region c.*18451 NULL 0.003 - - - no_coding_region:pseudogene tier3 298 14 4.26 262 147 32.96 0 0 NA 906708 TCGA-AB-2971 AML44 2 167507088 167507088 T C SNP XIRP2 NM_152381.2 human genbank 54_36p 1 validated intronic c.408+38442 e1+38442 0.001 - - - no_errors tier3 444 25 5.33 489 411 45.67 0 0 NA 906708 TCGA-AB-2971 AML44 2 182745342 182745342 C T SNP PDE1A NM_005019.1 human genbank 54_36p -1 validated intronic c.1564+13522 e13+13522 0.002 - - - no_errors tier3 464 22 4.53 391 349 46.97 0 0 NA 906708 TCGA-AB-2971 AML44 2 192284385 192284385 G A SNP LOC100132133 XM_001717052.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-7691 NULL 0.35 - - - no_errors tier3 243 18 6.9 318 211 39.74 0 1 100 906708 TCGA-AB-2971 AML44 2 194217794 194217794 C G SNP - - - - - - - - - - - - - - - tier3 516 31 5.67 466 437 48.18 0 0 NA 906708 TCGA-AB-2971 AML44 2 207148563 207148563 A T SNP ADAM23 NM_003812.2 human genbank 54_36p 1 reviewed intronic c.1737+2399 e18+2399 0.005 - - - no_errors tier3 649 55 7.8 733 611 45.43 0 0 0 906708 TCGA-AB-2971 AML44 2 215283848 215283848 C T SNP BARD1 NM_000465.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*17797 NULL 0.001 - - - no_errors tier3 407 31 7.08 441 386 46.62 1 0 0 906708 TCGA-AB-2971 AML44 2 219472484 219472484 G T SNP WNT10A NM_025216.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*6247 NULL 0.048 - - - no_errors tier3 587 30 4.85 131 129 49.62 0 0 NA 906708 TCGA-AB-2971 AML44 2 223678178 223678178 A G SNP KCNE4 NM_080671.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*51873 NULL 0.001 - - - no_errors tier3 845 77 8.35 698 592 45.89 0 0 NA 906708 TCGA-AB-2971 AML44 2 229615855 229615855 T G SNP PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.271-16787 e3-16787 0.512 - - - no_errors tier3 228 12 5 304 234 43.41 0 0 0 906708 TCGA-AB-2971 AML44 2 230545578 230545578 A G SNP FBXO36 NM_174899.4 human genbank 54_36p 1 validated intronic c.97-3623 e2-3623 0.003 - - - no_errors tier3 606 63 9.4 417 363 46.54 0 0 NA 906708 TCGA-AB-2971 AML44 2 238407723 238407723 A G SNP RBM44 NM_001080504.2 human genbank 54_36p 1 validated silent c.3096 p.L1032 0.992 NULL "HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928" - no_errors tier1 344 29 7.77 285 193 40.29 2 0 906708 TCGA-AB-2971 AML44 3 13880888 13880888 G A SNP WNT7A NM_004625.3 human genbank 54_36p -1 reviewed intronic c.299-9587 e3-9587 0 - - - no_errors tier3 456 34 6.94 211 130 38.12 0 0 0 906708 TCGA-AB-2971 AML44 3 24767231 24767231 A G SNP - - - - - - - - - - - - - - - tier3 730 66 8.28 694 626 47.42 0 0 NA 906708 TCGA-AB-2971 AML44 3 31818200 31818200 C T SNP OSBPL10 NM_017784.3 human genbank 54_36p -1 reviewed intronic c.729+28336 e4+28336 0.016 - - - no_errors tier3 679 63 8.46 900 749 45.42 0 0 NA 906708 TCGA-AB-2971 AML44 3 36655842 36655842 C A SNP ENSG00000201315 ENST00000364445 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-45693 NULL 0.012 - - - no_errors tier3 627 25 3.83 336 308 47.75 0 0 NA 906708 TCGA-AB-2971 AML44 3 45791305 45791305 A C SNP SLC6A20 NM_020208.3 human genbank 54_36p -1 reviewed intronic c.582+952 e4+952 0 - - - no_errors tier3 779 66 7.79 762 604 44.18 0 0 NA 906708 TCGA-AB-2971 AML44 3 45939154 45939154 C T SNP FYCO1 NM_024513.2 human genbank 54_36p -1 validated intronic c.4362-818 e17-818 0 - - - no_errors tier3 712 53 6.93 586 509 46.31 3 2 40 906708 TCGA-AB-2971 AML44 3 51577264 51577264 T A SNP RAD54L2 ENST00000409535 human ensembl 54_36p 1 known intronic c.1-22159 e1-22159 0.008 - - - no_errors tier3 901 73 7.49 558 475 45.98 4 2 33.33 906708 TCGA-AB-2971 AML44 3 52239470 52239470 G A SNP TWF2 NM_007284.3 human genbank 54_36p -1 reviewed intronic c.610-344 e7-344 0.001 - - - no_errors tier3 357 28 7.25 173 137 44.19 1 2 66.67 906708 TCGA-AB-2971 AML44 3 62363750 62363750 T C SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.3882+46 e29+46 0.001 - - - no_errors tier3 433 31 6.67 342 305 47.14 0 0 NA 906708 TCGA-AB-2971 AML44 3 63393330 63393330 C A SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-10832 NULL 0.004 - - - no_errors tier3 1072 90 7.75 1105 923 45.49 0 0 NA 906708 TCGA-AB-2971 AML44 3 67640455 67640455 G A SNP SUCLG2 NM_003848.2 human genbank 54_36p -1 validated intronic c.757+1466 e7+1466 0 - - - no_errors tier3 710 43 5.69 885 736 45.38 1 1 50 906708 TCGA-AB-2971 AML44 3 79540097 79540097 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.88+181567 e1+181567 0.006 - - - no_errors tier3 73 3 3.9 90 72 44.44 0 0 NA 906708 TCGA-AB-2971 AML44 3 82609581 82609581 C A SNP - - - - - - - - - - - - - - - tier3 856 73 7.86 1133 865 43.27 0 0 NA 906708 TCGA-AB-2971 AML44 3 82899847 82899847 A G SNP - - - - - - - - - - - - - - - tier3 449 30 6.26 428 345 44.52 0 0 NA 906708 TCGA-AB-2971 AML44 3 84482737 84482737 C T SNP - - - - - - - - - - - - - - - tier3 1287 79 5.78 956 781 44.91 0 0 NA 906708 TCGA-AB-2971 AML44 3 84996635 84996635 T A SNP - - - - - - - - - - - - - - - tier3 661 43 6.11 863 728 45.73 0 0 NA 906708 TCGA-AB-2971 AML44 3 85553409 85553409 A G SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.62-380478 e2-380478 0 - - - no_errors tier3 544 27 4.73 661 520 43.99 0 0 NA 906708 TCGA-AB-2971 AML44 3 89493133 89493133 A T SNP EPHA3 NM_005233.5 human genbank 54_36p 1 reviewed intronic c.1306+19203 e5+19203 0.002 - - - no_errors tier3 756 77 9.24 548 426 43.56 0 0 NA 906708 TCGA-AB-2971 AML44 3 90026345 90026345 C A SNP - - - - - - - - - - - - - - - tier3 245 11 4.3 276 155 35.96 0 0 NA 906708 TCGA-AB-2971 AML44 3 104007546 104007546 C A SNP - - - - - - - - - - - - - - - tier3 227 5 2.16 438 286 39.5 0 0 NA 906708 TCGA-AB-2971 AML44 3 104393798 104393798 G A SNP ENSG00000198957 ENST00000362039 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48725 NULL 0.001 - - - no_coding_region:pseudogene tier3 1182 52 4.21 1166 906 43.68 0 0 NA 906708 TCGA-AB-2971 AML44 3 111081220 111081220 G A SNP ENSG00000214380 ENST00000398237 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*36293 NULL 0 - - - no_coding_region:pseudogene tier3 609 19 3.03 875 678 43.63 0 0 NA 906708 TCGA-AB-2971 AML44 3 111681702 111681702 C T SNP - - - - - - - - - - - - - - - tier3 529 23 4.16 520 392 42.98 0 0 NA 906708 TCGA-AB-2971 AML44 3 133002808 133002808 G A SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.181-77649 e2-77649 1 - - - no_errors tier3 254 13 4.87 180 141 43.79 0 0 NA 906708 TCGA-AB-2971 AML44 3 135960782 135960782 C T SNP EPHB1 NM_004441.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36382 NULL 0.015 - - - no_errors tier3 857 62 6.72 781 612 43.87 0 0 NA 906708 TCGA-AB-2971 AML44 3 138529438 138529438 G A SNP - - - - - - - - - - - - - - - tier3 670 46 6.42 608 500 45.05 0 0 NA 906708 TCGA-AB-2971 AML44 3 146425765 146425765 C T SNP - - - - - - - - - - - - - - - tier3 308 6 1.9 478 265 35.62 0 0 NA 906708 TCGA-AB-2971 AML44 3 173671315 173671315 T C SNP GHSR NM_198407.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22418 NULL 0.017 - - - no_errors tier3 598 30 4.77 465 320 40.71 0 0 NA 906708 TCGA-AB-2971 AML44 3 177131114 177131114 G T SNP - - - - - - - - - - - - - - - tier3 504 39 7.14 364 278 43.3 0 0 NA 906708 TCGA-AB-2971 AML44 3 191036668 191036668 T G SNP TP63 NM_003722.1 human genbank 54_36p 1 reviewed intronic c.579+27659 e4+27659 0.002 - - - no_errors tier3 848 44 4.93 822 587 41.6 1 3 75 906708 TCGA-AB-2971 AML44 4 7615798 7615798 G A SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.198+31542 e3+31542 0.007 - - - no_errors tier3 632 34 5.11 233 203 46.56 0 0 NA 906708 TCGA-AB-2971 AML44 4 20861388 20861388 C T SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.100+53140 e1+53140 0 - - - no_errors tier3 289 25 7.91 441 344 43.27 0 0 NA 906708 TCGA-AB-2971 AML44 4 27200184 27200184 G A SNP ENSG00000221807 ENST00000408880 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*44814 NULL 0 - - - no_errors tier3 635 34 5.07 704 570 44.74 0 0 NA 906708 TCGA-AB-2971 AML44 4 38381656 38381656 A G SNP LOC100132861 XM_001716443.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-39104 NULL 0.011 - - - no_errors tier3 1286 63 4.67 1075 798 42.56 0 0 NA 906708 TCGA-AB-2971 AML44 4 45666810 45666810 A G SNP ENSG00000222257 ENST00000410325 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-25083 NULL 0 - - - no_errors tier3 232 15 6.07 249 275 52.48 0 0 NA 906708 TCGA-AB-2971 AML44 4 61942377 61942377 G C SNP ENSG00000205682 ENST00000381217 human ensembl 54_36p -1 known 3_prime_flanking_region c.*33305 NULL 0.004 - - - no_errors tier3 159 12 7.02 159 134 45.58 0 0 NA 906708 TCGA-AB-2971 AML44 4 67467976 67467976 A T SNP - - - - - - - - - - - - - - - tier3 554 41 6.89 521 369 41.46 0 0 NA 906708 TCGA-AB-2971 AML44 4 71106342 71106342 C T SNP CSN3 NM_005212.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38784 NULL 0.006 - - - no_errors tier3 368 26 6.57 430 396 47.88 0 0 NA 906708 TCGA-AB-2971 AML44 4 78457645 78457645 C A SNP - - - - - - - - - - - - - - - tier3 916 59 6.04 1159 852 42.35 0 1 100 906708 TCGA-AB-2971 AML44 4 81680650 81680650 G A SNP C4orf22 NM_152770.1 human genbank 54_36p 1 predicted intronic c.243-42621 e3-42621 0 - - - no_errors tier3 934 48 4.88 1145 933 44.88 0 0 NA 906708 TCGA-AB-2971 AML44 4 89195305 89195305 T - DEL PKD2 NM_000297.2 human genbank 54_36p 1 reviewed intronic c.1717-957 e8-957 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 4 93240578 93240578 A G SNP - - - - - - - - - - - - - - - tier3 242 13 5.1 218 181 45.14 0 0 NA 906708 TCGA-AB-2971 AML44 4 94131865 94131865 G A SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.245-93304 e3-93304 0 - - - no_errors tier3 259 9 3.36 313 221 41.31 0 0 NA 906708 TCGA-AB-2971 AML44 4 97941402 97941402 C G SNP - - - - - - - - - - - - - - - tier3 1052 93 8.1 941 823 46.63 0 0 NA 906708 TCGA-AB-2971 AML44 4 99892327 99892327 G T SNP ENSG00000174991 ENST00000309260 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*10855 NULL 0.012 - - - no_coding_region:pseudogene tier3 458 21 4.38 495 368 42.64 0 0 NA 906708 TCGA-AB-2971 AML44 4 100611007 100611007 C T SNP ADH7 NM_000673.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-35558 NULL 0.051 - - - no_errors tier3 532 32 5.66 443 404 47.64 0 0 NA 906708 TCGA-AB-2971 AML44 4 106377758 106377758 T - DEL TET2 NM_017628.1 human genbank 54_36p 1 validated frame_shift_del c.3210 p.A1071fs 0.932 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA 906708 TCGA-AB-2971 AML44 4 106416704 106416704 C A SNP TET2 ENST00000265149 human ensembl 54_36p 1 known missense c.1994 p.A665D 0.997 NULL NULL - no_start_codon tier1 424 44 9.36 672 547 44.84 30 35 53.85 906708 TCGA-AB-2971 AML44 4 118026906 118026906 G A SNP ENSG00000201752 ENST00000364882 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46917 NULL 0.001 - - - no_errors tier3 392 25 5.98 436 325 42.6 0 0 NA 906708 TCGA-AB-2971 AML44 4 120331771 120331771 C T SNP USP53 NM_019050.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-48592 NULL 0.002 - - - no_errors tier3 382 30 7.28 451 329 42.13 0 0 NA 906708 TCGA-AB-2971 AML44 4 120510378 120510378 T - DEL LOC729249 XM_001129755.2 human genbank 54_36p 1 model intronic c.376-8340 e5-8340 0.043 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 4 126682916 126682916 G A SNP FAT4 ENST00000394329 human ensembl 54_36p 1 known 3_prime_flanking_region c.*50543 NULL 0 - - - no_errors tier3 602 34 5.33 492 403 44.98 0 0 NA 906708 TCGA-AB-2971 AML44 4 127079555 127079555 C A SNP - - - - - - - - - - - - - - - tier3 697 39 5.29 819 508 38.28 0 0 NA 906708 TCGA-AB-2971 AML44 4 127323988 127323988 T A SNP - - - - - - - - - - - - - - - tier3 200 6 2.9 180 103 36.27 0 0 NA 906708 TCGA-AB-2971 AML44 4 130579958 130579958 C T SNP - - - - - - - - - - - - - - - tier3 683 31 4.31 603 483 44.39 0 0 NA 906708 TCGA-AB-2971 AML44 4 139488589 139488589 A C SNP - - - - - - - - - - - - - - - tier3 806 65 7.45 838 609 42.03 0 0 NA 906708 TCGA-AB-2971 AML44 4 143909170 143909170 T - DEL INPP4B NM_001101669.1 human genbank 54_36p -1 reviewed intronic c.1-42666 e1-42666 0.083 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 4 152478697 152478697 C T SNP ESSPL NM_183375.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*46642 NULL 0 - - - no_errors tier3 1172 68 5.48 546 403 42.42 0 0 NA 906708 TCGA-AB-2971 AML44 4 154174004 154174004 G A SNP - - - - - - - - - - - - - - - tier3 1166 76 6.11 891 726 44.9 0 0 NA 906708 TCGA-AB-2971 AML44 4 155307294 155307294 G T SNP - - - - - - - - - - - - - - - tier3 493 38 7.16 709 546 43.51 0 0 NA 906708 TCGA-AB-2971 AML44 4 179636763 179636763 G T SNP - - - - - - - - - - - - - - - tier3 978 34 3.36 1049 734 41.17 0 0 NA 906708 TCGA-AB-2971 AML44 4 189132274 189132274 G A SNP ZFP42 NM_174900.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28682 NULL 0.011 - - - no_errors tier3 888 42 4.51 505 410 44.81 0 0 NA 906708 TCGA-AB-2971 AML44 5 3244067 3244067 C G SNP - - - - - - - - - - - - - - - tier3 998 61 5.76 503 485 49.09 0 0 NA 906708 TCGA-AB-2971 AML44 5 4863704 4863704 G A SNP LOC730926 XM_001129902.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-41464 NULL 0.007 - - - no_start_codon:pseudogene:no_stop_codon tier3 679 47 6.47 441 372 45.76 0 0 NA 906708 TCGA-AB-2971 AML44 5 17227850 17227850 G A SNP ENSG00000215196 ENST00000399760 human ensembl 54_36p -1 known intronic c.570-4240 e2-4240 0.001 - - - no_errors tier3 838 46 5.2 717 539 42.85 0 0 NA 906708 TCGA-AB-2971 AML44 5 17653781 17653781 G A SNP LOC729698 XM_001131072.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-49784 NULL 0.001 - - - no_errors tier3 290 35 10.77 355 255 41.8 0 0 NA 906708 TCGA-AB-2971 AML44 5 18152867 18152867 C T SNP - - - - - - - - - - - - - - - tier3 1081 81 6.93 1125 830 42.35 0 0 NA 906708 TCGA-AB-2971 AML44 5 30958713 30958713 A T SNP - - - - - - - - - - - - - - - tier3 430 20 4.44 481 386 44.52 0 0 NA 906708 TCGA-AB-2971 AML44 5 44734628 44734628 A G SNP ENSG00000222995 ENST00000411063 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-17421 NULL 0.676 - - - no_errors tier3 1266 93 6.83 1116 824 42.45 0 0 NA 906708 TCGA-AB-2971 AML44 5 53943023 53943023 C T SNP - - - - - - - - - - - - - - - tier3 622 38 5.74 542 376 40.91 0 0 NA 906708 TCGA-AB-2971 AML44 5 59669781 59669781 C T SNP LOC653198 XR_039820.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - no_errors tier3 1030 72 6.51 735 568 43.59 0 0 NA 906708 TCGA-AB-2971 AML44 5 63071274 63071274 G A SNP - - - - - - - - - - - - - - - tier3 823 40 4.62 850 626 42.38 0 0 NA 906708 TCGA-AB-2971 AML44 5 67877382 67877382 G A SNP - - - - - - - - - - - - - - - tier3 939 64 6.38 1282 985 43.45 0 0 NA 906708 TCGA-AB-2971 AML44 5 75288218 75288218 T A SNP - - - - - - - - - - - - - - - tier3 1098 97 8.11 962 876 47.63 0 0 NA 906708 TCGA-AB-2971 AML44 5 91355063 91355063 G A SNP - - - - - - - - - - - - - - - tier3 582 41 6.58 800 557 41.05 0 0 NA 906708 TCGA-AB-2971 AML44 5 104408707 104408707 T C SNP - - - - - - - - - - - - - - - tier3 550 35 5.98 645 430 39.96 0 0 NA 906708 TCGA-AB-2971 AML44 5 105289020 105289020 C T SNP ENSG00000201790 ENST00000364920 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2312 NULL 0.001 - - - no_errors tier3 501 27 5.1 623 468 42.9 0 0 NA 906708 TCGA-AB-2971 AML44 5 108280975 108280975 A C SNP FER NM_005246.2 human genbank 54_36p 1 reviewed intronic c.1236+19527 e8+19527 0.001 - - - no_errors tier3 574 40 6.51 452 314 40.99 0 3 100 906708 TCGA-AB-2971 AML44 5 110676379 110676379 C T SNP CAMK4 NM_001744.3 human genbank 54_36p 1 reviewed intronic c.162-31242 e2-31242 0 - - - no_errors tier3 462 41 8.15 478 406 45.82 1 0 0 906708 TCGA-AB-2971 AML44 5 120832636 120832636 G A SNP - - - - - - - - - - - - - - - tier3 687 51 6.9 665 555 45.49 0 0 NA 906708 TCGA-AB-2971 AML44 5 125438180 125438180 G A SNP - - - - - - - - - - - - - - - tier3 229 7 2.97 346 224 39.3 0 0 NA 906708 TCGA-AB-2971 AML44 5 133145105 133145105 C T SNP - - - - - - - - - - - - - - - tier3 1245 93 6.95 1195 1037 46.46 0 0 NA 906708 TCGA-AB-2971 AML44 5 152242315 152242315 G A SNP - - - - - - - - - - - - - - - tier3 904 45 4.74 1152 789 40.63 0 0 NA 906708 TCGA-AB-2971 AML44 5 154826237 154826237 C G SNP - - - - - - - - - - - - - - - tier3 550 37 6.29 592 534 47.38 0 0 NA 906708 TCGA-AB-2971 AML44 5 156085976 156085976 C T SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.576-31194 e7-31194 0 - - - no_errors tier3 1801 132 6.81 1857 1438 43.56 0 0 NA 906708 TCGA-AB-2971 AML44 5 163205926 163205926 G T SNP - - - - - - - - - - - - - - - tier3 1123 78 6.49 1075 934 46.44 0 0 NA 906708 TCGA-AB-2971 AML44 5 164846676 164846676 A T SNP - - - - - - - - - - - - - - - tier3 532 24 4.32 637 528 45.32 0 0 NA 906708 TCGA-AB-2971 AML44 5 164940147 164940147 A G SNP ENSG00000208461 ENST00000385726 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29412 NULL 0 - - - pseudogene tier3 163 14 7.91 274 290 51.42 0 0 NA 906708 TCGA-AB-2971 AML44 6 8101425 8101425 T C SNP - - - - - - - - - - - - - - - tier3 615 49 7.38 315 266 45.63 0 0 NA 906708 TCGA-AB-2971 AML44 6 11344606 11344606 T G SNP NEDD9 NM_006403.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-3872 NULL 0.155 - - - no_errors tier3 1236 104 7.76 674 607 47.38 0 1 100 906708 TCGA-AB-2971 AML44 6 16825716 16825717 - A INS ATXN1 NM_000332.3 human genbank 54_36p -1 reviewed intronic c.1+35726_35725 e0+35726 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 6 19821229 19821229 A G SNP - - - - - - - - - - - - - - - tier3 592 41 6.48 647 560 46.36 0 0 NA 906708 TCGA-AB-2971 AML44 6 36726134 36726134 G A SNP CDKN1A NM_000389.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33723 NULL 0.001 - - - no_errors tier3 811 67 7.63 492 496 50.1 0 0 NA 906708 TCGA-AB-2971 AML44 6 45052997 45052997 C G SNP SUPT3H NM_181356.2 human genbank 54_36p -1 provisional intronic c.538-15454 e7-15454 0.09 - - - no_errors tier3 665 42 5.93 661 502 43.13 1 0 0 906708 TCGA-AB-2971 AML44 6 47188886 47188886 A T SNP - - - - - - - - - - - - - - - tier3 342 23 6.3 419 295 41.32 0 0 NA 906708 TCGA-AB-2971 AML44 6 48658463 48658463 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 6 55746872 55746872 G A SNP BMP5 NM_021073.2 human genbank 54_36p -1 reviewed nonsense c.961 p.R321* 1 NULL "HMMPfam_TGFb_propeptide,HMMPfam_TGF_beta,HMMSmart_TGFB,PatternScan_TGF_BETA_1,superfamily_SSF57501" - no_errors tier1 515 50 8.85 545 451 45.28 NA 906708 TCGA-AB-2971 AML44 6 74492557 74492557 T C SNP CD109 NM_133493.3 human genbank 54_36p 1 validated intronic c.276+2834 e3+2834 0.027 - - - no_errors tier3 240 17 6.61 224 196 46.56 0 1 100 906708 TCGA-AB-2971 AML44 6 75842832 75842832 T C SNP COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*10151 NULL 0.088 - - - no_errors tier3 56 5 8.2 85 119 58.33 0 0 NA 906708 TCGA-AB-2971 AML44 6 77963295 77963295 G A SNP - - - - - - - - - - - - - - - tier3 518 27 4.95 677 422 38.36 1 0 0 906708 TCGA-AB-2971 AML44 6 96615585 96615585 C A SNP FUT9 NM_006581.3 human genbank 54_36p 1 validated intronic c.1+44776 e0+44776 0.008 - - - no_errors tier3 329 15 4.34 423 268 38.67 0 0 NA 906708 TCGA-AB-2971 AML44 6 97173161 97173161 G A SNP ENSG00000219139 ENST00000407851 human ensembl 54_36p 1 known 5_prime_flanking_region c.-34710 NULL 0.134 - - - no_coding_region:pseudogene tier3 697 60 7.92 851 691 44.81 0 0 NA 906708 TCGA-AB-2971 AML44 6 98302635 98302635 G A SNP - - - - - - - - - - - - - - - tier3 713 60 7.76 691 582 45.61 0 0 NA 906708 TCGA-AB-2971 AML44 6 98889536 98889536 C T SNP - - - - - - - - - - - - - - - tier3 557 26 4.45 748 207 21.68 0 0 NA 906708 TCGA-AB-2971 AML44 6 108275434 108275434 T C SNP SCML4 ENST00000369020 human ensembl 54_36p -1 known 5_prime_flanking_region c.-75210 NULL 0.016 - - - no_errors tier3 198 8 3.86 268 221 45.1 0 0 NA 906708 TCGA-AB-2971 AML44 6 113822705 113822705 G A SNP - - - - - - - - - - - - - - - tier3 375 27 6.7 442 373 45.71 0 0 NA 906708 TCGA-AB-2971 AML44 6 119071708 119071708 C T SNP C6orf204 NM_001042475.1 human genbank 54_36p -1 validated intronic c.73+7345 e1+7345 0.004 - - - no_errors tier3 711 43 5.7 356 288 44.72 0 0 0 906708 TCGA-AB-2971 AML44 6 126980034 126980034 C G SNP LOC728666 XR_015645.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-26281 NULL 0 - - - no_errors tier3 415 34 7.57 324 266 45.08 2 0 0 906708 TCGA-AB-2971 AML44 6 127986634 127986634 G A SNP C6orf58 NM_001010905.1 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*32174 NULL 0.003 - - - no_errors tier3 161 3 1.83 210 166 44.15 0 0 NA 906708 TCGA-AB-2971 AML44 6 140591895 140591895 C T SNP - - - - - - - - - - - - - - - tier3 434 23 5.03 457 357 43.86 0 0 NA 906708 TCGA-AB-2971 AML44 6 144059941 144059941 G A SNP PHACTR2 NM_001100164.1 human genbank 54_36p 1 validated intronic c.47-14905 e2-14905 0.005 - - - no_errors tier3 612 24 3.77 475 330 40.99 1 3 75 906708 TCGA-AB-2971 AML44 6 155258982 155258982 A G SNP LOC729436 XM_001133246.1 human genbank 54_36p 1 model intronic c.139+35158 e1+35158 0.003 - - - no_errors tier3 592 57 8.78 569 508 47.12 7 1 12.5 906708 TCGA-AB-2971 AML44 6 158645291 158645291 A G SNP TULP4 NM_020245.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-9746 NULL 0.006 - - - no_errors tier3 889 63 6.6 452 325 41.83 0 0 NA 906708 TCGA-AB-2971 AML44 6 164541063 164541063 G A SNP LOC728275 XM_001127046.2 human genbank 54_36p 1 model intronic c.545-136928 e3-136928 0.001 - - - no_errors tier3 98 9 8.41 104 139 57.2 0 0 NA 906708 TCGA-AB-2971 AML44 7 32002196 32002196 G A SNP PDE1C NM_005020.1 human genbank 54_36p -1 provisional intronic c.128+55495 e2+55495 0.863 - - - no_errors tier3 1035 64 5.81 857 619 41.94 0 0 NA 906708 TCGA-AB-2971 AML44 7 41550318 41550318 T G SNP - - - - - - - - - - - - - - - tier3 83 9 9.68 102 100 48.78 0 0 NA 906708 TCGA-AB-2971 AML44 7 45976272 45976272 G C SNP IGFBP3 NM_001013398.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49008 NULL 0 - - - no_errors tier3 421 15 3.43 313 186 37.27 0 0 NA 906708 TCGA-AB-2971 AML44 7 54019704 54019704 G A SNP LOC100134708 XM_001726848.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*20248 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 750 47 5.89 756 549 42.07 0 0 NA 906708 TCGA-AB-2971 AML44 7 56329229 56329229 A G SNP LOC441228 XR_016387.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*2055 NULL 0.02 - - - no_errors tier3 1232 93 7.02 1032 802 43.71 0 0 NA 906708 TCGA-AB-2971 AML44 7 62354089 62354089 C - DEL LOC643955 NR_003952.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*35011 NULL 0 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 7 67324801 67324801 A T SNP - - - - - - - - - - - - - - - tier3 366 12 3.17 203 151 42.54 0 0 NA 906708 TCGA-AB-2971 AML44 7 67963973 67963973 G A SNP - - - - - - - - - - - - - - - tier3 663 60 8.3 402 274 40.47 0 0 NA 906708 TCGA-AB-2971 AML44 7 70145803 70145803 C T SNP - - - - - - - - - - - - - - - tier3 765 56 6.81 479 367 43.33 0 0 NA 906708 TCGA-AB-2971 AML44 7 70789706 70789706 C G SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.1500+9479 e9+9479 0.003 - - - no_errors tier3 701 53 7.01 478 403 45.74 0 0 NA 906708 TCGA-AB-2971 AML44 7 90576658 90576658 T - DEL PFTK1 NM_012395.2 human genbank 54_36p 1 validated intronic c.1101-3135 e12-3135 0.738 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 7 96120704 96120704 C T SNP LOC100128444 XM_001724728.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-7551 NULL 0.001 - - - no_errors tier3 761 63 7.64 984 812 45.09 0 0 NA 906708 TCGA-AB-2971 AML44 7 101365724 101365724 G A SNP CUX1 NM_181552.2 human genbank 54_36p 1 reviewed intronic c.141+19499 e2+19499 0.003 - - - no_errors tier3 485 31 6 342 262 43.38 5 3 37.5 906708 TCGA-AB-2971 AML44 7 115410131 115410131 A T SNP TFEC NM_012252.1 human genbank 54_36p -1 validated intronic c.180+1421 e1+1421 0.001 - - - no_errors tier3 185 7 3.65 247 197 44.37 2 1 33.33 906708 TCGA-AB-2971 AML44 7 118897211 118897211 G C SNP - - - - - - - - - - - - - - - tier3 511 36 6.57 624 448 41.75 0 0 NA 906708 TCGA-AB-2971 AML44 7 128960154 128960154 G A SNP FAM40B NM_020704.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*47248 NULL 0.004 - - - no_errors tier3 708 68 8.76 557 458 45.08 0 0 NA 906708 TCGA-AB-2971 AML44 7 133231045 133231045 G C SNP EXOC4 NM_021807.1 human genbank 54_36p 1 reviewed intronic c.1871+17 e12+17 0 - - - no_errors tier3 946 78 7.62 701 601 46.09 1 4 80 906708 TCGA-AB-2971 AML44 7 151057795 151057795 G A SNP PRKAG2 NM_016203.1 human genbank 54_36p -1 reviewed intronic c.466+51376 e3+51376 0.002 - - - no_errors tier3 357 24 6.28 271 242 47.17 2 0 0 906708 TCGA-AB-2971 AML44 7 155764499 155764499 C T SNP LOC393076 XR_016902.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*12777 NULL 0.001 - - - no_errors tier3 959 42 4.19 1240 993 44.41 0 0 NA 906708 TCGA-AB-2971 AML44 7 157089515 157089515 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed silent c.2358 p.R786 1 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 169 7 3.98 90 68 43.04 1 1 50 906708 TCGA-AB-2971 AML44 8 20878527 20878527 G A SNP - - - - - - - - - - - - - - - tier3 599 30 4.76 766 565 42.42 0 0 NA 906708 TCGA-AB-2971 AML44 8 36132595 36132595 C T SNP - - - - - - - - - - - - - - - tier3 804 45 5.28 729 510 41.06 0 0 NA 906708 TCGA-AB-2971 AML44 8 37193844 37193844 G A SNP - - - - - - - - - - - - - - - tier3 792 72 8.33 855 644 42.9 0 0 NA 906708 TCGA-AB-2971 AML44 8 51899301 51899301 C T SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*31359 NULL 0.065 - - - no_errors tier3 436 34 7.22 445 403 47.52 0 0 NA 906708 TCGA-AB-2971 AML44 8 54089418 54089418 C T SNP - - - - - - - - - - - - - - - tier3 958 62 6.07 800 705 46.84 0 0 NA 906708 TCGA-AB-2971 AML44 8 54705979 54705979 T C SNP - - - - - - - - - - - - - - - tier3 678 34 4.76 781 640 45.01 0 0 NA 906708 TCGA-AB-2971 AML44 8 58716731 58716731 C T SNP LOC100130588 XM_001719422.1 human genbank 54_36p -1 model intronic c.127-47156 e3-47156 0.004 - - - no_errors tier3 593 50 7.78 715 636 47.04 0 0 NA 906708 TCGA-AB-2971 AML44 8 63473733 63473733 G T SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.54+149493 e1+149493 0 - - - no_errors tier3 664 43 6.07 515 414 44.56 0 0 NA 906708 TCGA-AB-2971 AML44 8 67476823 67476823 G A SNP ADHFE1 NM_144650.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30483 NULL 0.015 - - - no_errors tier3 801 42 4.97 677 544 44.44 0 0 NA 906708 TCGA-AB-2971 AML44 8 79537941 79537941 C T SNP - - - - - - - - - - - - - - - tier3 605 36 5.61 748 539 41.82 0 0 NA 906708 TCGA-AB-2971 AML44 8 84863882 84863882 G C SNP - - - - - - - - - - - - - - - tier3 1178 52 4.22 1105 819 42.48 0 0 NA 906708 TCGA-AB-2971 AML44 8 90078425 90078426 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 8 101885373 101885373 G A SNP ENSG00000202001 ENST00000365131 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48774 NULL 0.001 - - - no_errors tier3 575 43 6.95 437 376 46.25 0 0 NA 906708 TCGA-AB-2971 AML44 8 105919585 105919585 C T SNP - - - - - - - - - - - - - - - tier3 348 18 4.9 523 336 39.07 0 0 NA 906708 TCGA-AB-2971 AML44 8 127344983 127344983 C T SNP - - - - - - - - - - - - - - - tier3 1141 82 6.7 926 723 43.84 0 0 NA 906708 TCGA-AB-2971 AML44 8 136900264 136900264 C T SNP - - - - - - - - - - - - - - - tier3 1636 127 7.2 1664 1287 43.6 0 0 NA 906708 TCGA-AB-2971 AML44 8 138608680 138608680 C T SNP - - - - - - - - - - - - - - - tier3 377 30 7.35 385 317 45.09 0 0 NA 906708 TCGA-AB-2971 AML44 9 1983943 1983943 T C SNP SMARCA2 NM_003070.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35080 NULL 0 - - - no_errors tier3 576 54 8.57 541 414 43.26 0 0 NA 906708 TCGA-AB-2971 AML44 9 9130024 9130024 A C SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1+43280 e0+43280 0 - - - no_errors tier3 602 40 6.22 819 594 41.98 0 0 NA 906708 TCGA-AB-2971 AML44 9 30392365 30392365 C T SNP - - - - - - - - - - - - - - - tier3 157 11 6.55 211 155 42.35 0 0 NA 906708 TCGA-AB-2971 AML44 9 35971848 35971848 C T SNP OR2S2 NM_019897.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-23783 NULL 0.094 - - - no_errors tier3 520 67 11.39 354 305 46.28 0 0 NA 906708 TCGA-AB-2971 AML44 9 85966509 85966509 G A SNP - - - - - - - - - - - - - - - tier3 534 43 7.44 99 477 82.81 0 0 NA 906708 TCGA-AB-2971 AML44 9 86982660 86982660 A G SNP ENSG00000218863 ENST00000402586 human ensembl 54_36p 1 known 3_prime_flanking_region c.*17975 NULL 0.001 - - - no_coding_region:pseudogene tier3 548 46 7.74 98 457 82.34 0 0 NA 906708 TCGA-AB-2971 AML44 9 92515402 92515402 T C SNP ENSG00000187503 ENST00000339424 human ensembl 54_36p -1 known 3_prime_flanking_region c.*29226 NULL 0 - - - no_coding_region:pseudogene tier3 761 57 6.96 768 587 43.29 0 0 NA 906708 TCGA-AB-2971 AML44 9 102505787 102505787 A G SNP ENSG00000219293 ENST00000404047 human ensembl 54_36p 1 known 5_prime_flanking_region c.-27556 NULL 0.001 - - - no_coding_region:pseudogene tier3 854 51 5.64 865 714 45.19 0 0 NA 906708 TCGA-AB-2971 AML44 9 110952742 110952742 G A SNP C9orf4 NM_014334.2 human genbank 54_36p -1 validated intronic c.392-921 e2-921 0.035 - - - no_errors tier3 1386 69 4.73 841 591 41.27 0 0 NA 906708 TCGA-AB-2971 AML44 9 117618172 117618172 G T SNP - - - - - - - - - - - - - - - tier3 714 63 8.11 809 632 43.86 0 0 NA 906708 TCGA-AB-2971 AML44 9 119101227 119101227 A G SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.443-7614 e2-7614 0.002 - - - no_errors tier3 753 65 7.95 828 663 44.47 0 0 NA 906708 TCGA-AB-2971 AML44 9 120274859 120274859 C A SNP - - - - - - - - - - - - - - - tier3 190 16 7.77 230 190 45.24 0 0 NA 906708 TCGA-AB-2971 AML44 9 131293063 131293063 T G SNP LOC100128077 XM_001726459.1 human genbank 54_36p 1 model missense c.483 p.H161Q 0.001 NULL NULL - no_errors tier1 207 22 9.57 87 76 46.63 1 4 80 906708 TCGA-AB-2971 AML44 10 1945235 1945235 C T SNP - - - - - - - - - - - - - - - tier3 539 22 3.9 628 381 37.61 0 0 NA 906708 TCGA-AB-2971 AML44 10 2281420 2281420 C T SNP LOC728209 XM_001126868.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*27281 NULL 0 - - - no_errors tier3 923 45 4.64 1002 797 44.25 0 0 NA 906708 TCGA-AB-2971 AML44 10 2448487 2448487 C T SNP - - - - - - - - - - - - - - - tier3 640 52 7.51 547 634 53.46 0 0 NA 906708 TCGA-AB-2971 AML44 10 3355378 3355378 C T SNP - - - - - - - - - - - - - - - tier3 282 23 7.54 170 189 52.5 0 0 NA 906708 TCGA-AB-2971 AML44 10 12624654 12624654 C T SNP CAMK1D NM_153498.2 human genbank 54_36p 1 reviewed intronic c.93-10576 e2-10576 0.001 - - - no_errors tier3 585 29 4.7 355 249 41.23 0 3 100 906708 TCGA-AB-2971 AML44 10 14066119 14066119 C T SNP FRMD4A NM_018027.3 human genbank 54_36p -1 validated intronic c.46-125201 e2-125201 0.001 - - - no_errors tier3 518 33 5.99 486 394 44.67 0 0 NA 906708 TCGA-AB-2971 AML44 10 15042402 15042402 G C SNP MEIG1 NM_001080836.2 human genbank 54_36p 1 validated intronic c.1+840 e0+840 0.001 - - - no_errors tier3 180 10 5.26 115 85 42.29 0 0 0 906708 TCGA-AB-2971 AML44 10 35616065 35616065 G C SNP CCNY NM_181698.4 human genbank 54_36p 1 validated intronic c.1+36505 e0+36505 0.101 - - - no_errors tier3 300 16 5.02 275 224 44.62 0 0 NA 906708 TCGA-AB-2971 AML44 10 45406968 45406968 C A SNP MARCH8 NM_001002265.1 human genbank 54_36p -1 validated intronic c.1+2721 e0+2721 0.077 - - - no_errors tier3 657 24 3.52 249 215 46.34 0 0 0 906708 TCGA-AB-2971 AML44 10 54080490 54080490 A G SNP - - - - - - - - - - - - - - - tier3 94 1 1.05 124 104 45.61 5 7 58.33 906708 TCGA-AB-2971 AML44 10 108691491 108691491 G T SNP SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed intronic c.626+14770 e2+14770 0 - - - no_errors tier3 418 27 6.05 267 239 47.23 0 0 NA 906708 TCGA-AB-2971 AML44 10 120897135 120897135 C T SNP SFXN4 NM_213649.1 human genbank 54_36p -1 validated intronic c.818+142 e12+142 0 - - - no_errors tier3 808 46 5.36 404 298 42.45 0 0 0 906708 TCGA-AB-2971 AML44 10 121784779 121784779 A G SNP ENSG00000219822 ENST00000405474 human ensembl 54_36p -1 known 5_prime_flanking_region c.-37568 NULL 0 - - - no_coding_region:pseudogene tier3 1172 94 7.42 1002 864 46.3 0 0 NA 906708 TCGA-AB-2971 AML44 10 127480829 127480829 G A SNP UROS NM_000375.2 human genbank 54_36p -1 reviewed intronic c.395-4125 e6-4125 0.002 - - - no_errors tier3 258 14 5.15 151 146 49.16 0 0 0 906708 TCGA-AB-2971 AML44 10 132902876 132902876 G A SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated intronic c.856+45636 e4+45636 0 - - - no_errors tier3 446 33 6.85 575 419 42.15 0 0 NA 906708 TCGA-AB-2971 AML44 11 9566612 9566612 G A SNP WEE1 NM_003390.1 human genbank 54_36p 1 reviewed missense c.1828 p.E610K 1 NULL "PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 509 14 2.67 231 146 38.73 19 13 40.62 906708 TCGA-AB-2971 AML44 11 13314611 13314611 G A SNP ARNTL NM_001030272.1 human genbank 54_36p 1 reviewed intronic c.1-13457 e1-13457 0.003 - - - no_errors tier3 1036 74 6.67 971 833 46.12 0 0 0 906708 TCGA-AB-2971 AML44 11 15204136 15204136 C A SNP INSC NM_001031853.3 human genbank 54_36p 1 provisional intronic c.1311+186 e9+186 0.021 - - - no_errors tier3 790 16 1.99 1086 219 16.78 0 0 NA 906708 TCGA-AB-2971 AML44 11 16599729 16599729 T C SNP ENSG00000209504 ENST00000386769 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44526 NULL 0.004 - - - pseudogene tier3 384 29 7.02 296 254 46.18 0 0 NA 906708 TCGA-AB-2971 AML44 11 19207681 19207681 C A SNP E2F8 NM_024680.2 human genbank 54_36p -1 validated nonsense c.1789 p.E597* 0.065 NULL "HMMPfam_E2F_TDP,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 650 39 5.66 350 336 48.98 2 1 33.33 906708 TCGA-AB-2971 AML44 11 28110141 28110141 G A SNP METT5D1 NM_152636.1 human genbank 54_36p 1 validated intronic c.270+18414 e1+18414 0.004 - - - no_errors tier3 278 14 4.78 363 250 40.78 0 6 100 906708 TCGA-AB-2971 AML44 11 28912573 28912573 A G SNP - - - - - - - - - - - - - - - tier3 499 19 3.67 616 497 44.65 0 0 NA 906708 TCGA-AB-2971 AML44 11 34696385 34696385 G A SNP - - - - - - - - - - - - - - - tier3 590 43 6.79 567 448 44.14 0 0 NA 906708 TCGA-AB-2971 AML44 11 38414362 38414362 T C SNP - - - - - - - - - - - - - - - tier3 37 3 7.5 45 53 53.54 0 0 NA 906708 TCGA-AB-2971 AML44 11 55356331 55356331 A C SNP OR5D16 NM_001005496.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-6473 NULL 0.009 - - - no_errors tier3 331 21 5.97 368 364 49.73 0 0 NA 906708 TCGA-AB-2971 AML44 11 56792889 56792889 C T SNP APLNR NM_005161.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31835 NULL 0.001 - - - no_errors tier3 286 10 3.37 398 254 38.96 0 0 NA 906708 TCGA-AB-2971 AML44 11 68176338 68176338 G A SNP GAL NM_015973.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-32630 NULL 0.002 - - - no_errors tier3 156 13 7.65 84 74 46.54 0 0 NA 906708 TCGA-AB-2971 AML44 11 71783653 71783653 C T SNP CLPB NM_030813.3 human genbank 54_36p -1 provisional intronic c.542+8005 e3+8005 0.001 - - - no_errors tier3 825 51 5.82 853 653 43.36 0 0 0 906708 TCGA-AB-2971 AML44 11 75904466 75904466 A G SNP C11orf30 NM_020193.3 human genbank 54_36p 1 validated intronic c.1514-368 e10-368 0.002 - - - no_errors tier3 520 25 4.59 482 380 44.03 1 0 0 906708 TCGA-AB-2971 AML44 11 79697595 79697595 G A SNP - - - - - - - - - - - - - - - tier3 1090 64 5.55 1068 928 46.47 0 0 NA 906708 TCGA-AB-2971 AML44 11 80389503 80389503 T C SNP - - - - - - - - - - - - - - - tier3 1173 54 4.39 1090 773 41.4 0 0 NA 906708 TCGA-AB-2971 AML44 11 83824461 83824461 G C SNP DLG2 NM_001364.1 human genbank 54_36p -1 reviewed intronic c.204+98800 e2+98800 0 - - - no_errors tier3 564 42 6.93 654 445 40.49 0 0 NA 906708 TCGA-AB-2971 AML44 11 98693115 98693116 AT - DEL CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-8172_8171 e1-8171 0.002:0.088 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 11 102937761 102937761 C T SNP - - - - - - - - - - - - - - - tier3 1051 41 3.74 862 675 43.77 1 0 0 906708 TCGA-AB-2971 AML44 11 106554583 106554583 C T SNP LOC341230 XR_016383.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*902 NULL 0.034 - - - pseudogene tier3 700 46 6.17 621 657 51.33 0 0 NA 906708 TCGA-AB-2971 AML44 11 119056058 119056058 T - DEL PVRL1 NM_002855.4 human genbank 54_36p -1 validated intronic c.80-1373 e2-1373 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 11 123430613 123430613 A T SNP OR10G7 NM_001004463.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-15695 NULL 0 - - - no_errors tier3 569 35 5.79 755 599 44.17 0 0 NA 906708 TCGA-AB-2971 AML44 11 124751047 124751047 G A SNP PKNOX2 NM_022062.2 human genbank 54_36p 1 validated intronic c.227+7956 e2+7956 0.011 - - - no_errors tier3 858 50 5.49 551 411 42.59 0 0 NA 906708 TCGA-AB-2971 AML44 11 134332441 134332441 G A SNP - - - - - - - - - - - - - - - tier3 543 26 4.56 385 321 45.4 0 0 NA 906708 TCGA-AB-2971 AML44 12 5545241 5545241 T C SNP ANO2 NM_020373.2 human genbank 54_36p -1 validated intronic c.2625-151 e26-151 0 - - - no_errors tier3 953 65 6.39 1081 856 44.1 0 0 NA 906708 TCGA-AB-2971 AML44 12 13497947 13497947 G A SNP ENSG00000201476 ENST00000364606 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12745 NULL 0 - - - no_errors tier3 552 36 6.11 426 364 46.08 0 0 NA 906708 TCGA-AB-2971 AML44 12 25841961 25841961 C T SNP ENSG00000222950 ENST00000411018 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18191 NULL 0.027 - - - no_errors tier3 611 46 6.99 621 459 42.46 0 0 NA 906708 TCGA-AB-2971 AML44 12 36743042 36743042 C T SNP - - - - - - - - - - - - - - - tier3 766 49 6.01 578 443 43.35 0 0 NA 906708 TCGA-AB-2971 AML44 12 39094399 39094399 T C SNP MUC19 XM_497341.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-6967 NULL 0.011 - - - no_errors tier3 353 17 4.58 396 378 48.77 0 0 NA 906708 TCGA-AB-2971 AML44 12 44507237 44507237 T C SNP ARID2 NM_152641.2 human genbank 54_36p 1 validated intronic c.705+5700 e6+5700 0.089 - - - no_errors tier3 724 61 7.77 892 734 45.14 3 3 50 906708 TCGA-AB-2971 AML44 12 80488938 80488938 G T SNP PPFIA2 NM_003625.2 human genbank 54_36p -1 reviewed intronic c.303+105763 e2+105763 0 - - - no_errors tier3 279 10 3.46 320 233 42.06 0 0 NA 906708 TCGA-AB-2971 AML44 12 84555568 84555568 C T SNP - - - - - - - - - - - - - - - tier3 298 15 4.79 301 205 40.35 0 0 NA 906708 TCGA-AB-2971 AML44 12 86403282 86403282 C A SNP LOC100132846 XM_001714729.1 human genbank 54_36p 1 model intronic c.29-264 e2-264 0.001 - - - no_errors tier3 173 4 2.26 246 106 30.03 0 0 NA 906708 TCGA-AB-2971 AML44 12 87711623 87711623 T C SNP - - - - - - - - - - - - - - - tier3 640 37 5.47 821 628 43.34 0 0 NA 906708 TCGA-AB-2971 AML44 12 89170666 89170666 G C SNP - - - - - - - - - - - - - - - tier3 424 27 5.99 594 496 45.38 0 0 NA 906708 TCGA-AB-2971 AML44 12 98546207 98546207 G A SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.1272+26769 e9+26769 0.027 - - - no_errors tier3 513 27 5 677 497 42.33 0 0 NA 906708 TCGA-AB-2971 AML44 12 98796101 98796101 G A SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.135-52803 e2-52803 0.006 - - - no_errors tier3 1178 49 3.99 1024 846 45.22 0 0 NA 906708 TCGA-AB-2971 AML44 12 99724746 99724746 G A SNP ANO4 NM_178826.3 human genbank 54_36p 1 validated intronic c.1+11810 e0+11810 0.012 - - - no_errors tier3 278 13 4.47 302 181 37.47 0 0 NA 906708 TCGA-AB-2971 AML44 12 109272180 109272180 T A SNP ATP2A2 NM_001681.1 human genbank 54_36p 1 reviewed intronic c.2981-300 e21-300 0.001 - - - no_errors tier3 462 34 6.85 389 376 49.09 10 13 56.52 906708 TCGA-AB-2971 AML44 12 112816189 112816189 C A SNP RBM19 NM_016196.2 human genbank 54_36p -1 provisional intronic c.2558+20968 e21+20968 0.008 - - - no_errors tier3 826 50 5.71 546 465 45.99 0 1 100 906708 TCGA-AB-2971 AML44 12 114733756 114733756 T A SNP ENSG00000200112 ENST00000363242 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*41080 NULL 0 - - - no_errors tier3 1384 98 6.6 760 620 44.93 0 0 NA 906708 TCGA-AB-2971 AML44 12 116987733 116987733 G C SNP WSB2 NM_018639.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4497 NULL 0.001 - - - no_errors tier3 618 49 7.31 250 215 46.24 6 1 14.29 906708 TCGA-AB-2971 AML44 12 118416532 118416532 G C SNP CCDC60 NM_178499.3 human genbank 54_36p 1 validated intronic c.557+5478 e5+5478 0.002 - - - no_errors tier3 1004 58 5.44 786 591 42.8 0 0 NA 906708 TCGA-AB-2971 AML44 12 120198790 120198790 T C SNP CAMKK2 NM_006549.3 human genbank 54_36p -1 reviewed intronic c.1-2019 e1-2019 0.006 - - - no_errors tier3 696 49 6.57 265 232 46.68 1 1 50 906708 TCGA-AB-2971 AML44 12 124689743 124689743 T A SNP TMEM132B NM_052907.2 human genbank 54_36p 1 provisional intronic c.1423-4832 e6-4832 0.04 - - - no_errors tier3 770 61 7.34 642 573 47.16 0 0 NA 906708 TCGA-AB-2971 AML44 13 18518150 18518150 C T SNP ENSG00000218236 ENST00000405207 human ensembl 54_36p -1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 346 25 6.72 304 232 43.28 0 0 0 906708 TCGA-AB-2971 AML44 13 28638595 28638595 C T SNP KIAA0774 NM_001033602.2 human genbank 54_36p 1 validated intronic c.2674+65488 e3+65488 0.001 - - - no_errors tier3 788 51 6.08 761 547 41.79 5 6 54.55 906708 TCGA-AB-2971 AML44 13 39780476 39780476 C T SNP ENSG00000215483 ENST00000400432 human ensembl 54_36p -1 known 3_prime_flanking_region c.*41901 NULL 0.001 - - - no_errors tier3 876 67 7.09 923 747 44.68 0 0 NA 906708 TCGA-AB-2971 AML44 13 42644330 42644330 T A SNP ENOX1 NM_017993.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*41796 NULL 0 - - - no_errors tier3 652 62 8.68 603 593 49.58 0 0 NA 906708 TCGA-AB-2971 AML44 13 42737495 42737495 T A SNP ENOX1 NM_017993.1 human genbank 54_36p -1 validated intronic c.1611+39 e11+39 0.249 - - - no_errors tier3 787 43 5.18 1062 799 42.89 0 0 NA 906708 TCGA-AB-2971 AML44 13 49340929 49340929 G T SNP LOC220429 NR_003268.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21721 NULL 0.017 - - - pseudogene tier3 1189 100 7.74 848 690 44.83 0 0 NA 906708 TCGA-AB-2971 AML44 13 59078434 59078434 G A SNP - - - - - - - - - - - - - - - tier3 555 36 6.09 690 553 44.45 0 0 NA 906708 TCGA-AB-2971 AML44 13 65518537 65518537 G A SNP - - - - - - - - - - - - - - - tier3 385 12 3.02 406 293 41.86 0 0 NA 906708 TCGA-AB-2971 AML44 13 69392865 69392865 G A SNP KLHL1 NM_020866.2 human genbank 54_36p -1 validated intronic c.1014+19308 e4+19308 0.001 - - - no_errors tier3 228 17 6.91 257 236 47.77 0 0 NA 906708 TCGA-AB-2971 AML44 13 75632787 75632787 T A SNP ENSG00000222885 ENST00000410953 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*25409 NULL 0.005 - - - no_errors tier3 815 46 5.34 783 487 38.32 0 0 NA 906708 TCGA-AB-2971 AML44 13 87235022 87235022 A G SNP - - - - - - - - - - - - - - - tier3 399 47 10.49 358 383 51.62 1 0 0 906708 TCGA-AB-2971 AML44 13 88222733 88222733 A T SNP - - - - - - - - - - - - - - - tier3 184 7 3.66 213 131 38.08 0 0 NA 906708 TCGA-AB-2971 AML44 13 94415203 94415203 C T SNP - - - - - - - - - - - - - - - tier3 471 23 4.64 196 131 40.06 0 0 NA 906708 TCGA-AB-2971 AML44 13 98709186 98709186 A C SNP UBAC2 NM_177967.1 human genbank 54_36p 1 validated intronic c.284+20377 e2+20377 0 - - - no_errors tier3 348 17 4.66 288 244 45.86 8 7 46.67 906708 TCGA-AB-2971 AML44 13 98796667 98796667 C G SNP UBAC2 NM_177967.1 human genbank 54_36p 1 validated intronic c.702+5847 e5+5847 0.033 - - - no_errors tier3 841 71 7.75 728 634 46.48 9 4 30.77 906708 TCGA-AB-2971 AML44 13 101668837 101668837 C T SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.208+182985 e1+182985 0.006 - - - no_errors tier3 313 10 3.1 442 294 39.95 0 0 NA 906708 TCGA-AB-2971 AML44 13 102238628 102238628 C T SNP KDELC1 NM_024089.2 human genbank 54_36p -1 reviewed intronic c.1294-354 e8-354 0.051 - - - no_errors tier3 586 21 3.45 225 158 41.25 0 0 NA 906708 TCGA-AB-2971 AML44 13 104098224 104098224 C T SNP - - - - - - - - - - - - - - - tier3 329 15 4.36 367 276 42.92 0 0 NA 906708 TCGA-AB-2971 AML44 13 111710066 111710066 C T SNP ENSG00000200072 ENST00000363202 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44327 NULL 0.001 - - - no_errors tier3 874 55 5.91 460 338 42.3 0 0 NA 906708 TCGA-AB-2971 AML44 14 18141929 18141929 G A SNP ENSG00000206906 ENST00000384179 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-47586 NULL 0.009 - - - no_errors tier3 582 18 2.98 580 195 25.13 0 0 NA 906708 TCGA-AB-2971 AML44 14 28397220 28397220 C T SNP ENSG00000207164 ENST00000384435 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*42973 NULL 0.057 - - - no_errors tier3 811 57 6.55 828 700 45.75 0 0 NA 906708 TCGA-AB-2971 AML44 14 31772175 31772175 G T SNP RNU6-1 ENST00000365467 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29949 NULL 0 - - - no_errors tier3 1059 69 6.12 1014 835 45.16 0 0 NA 906708 TCGA-AB-2971 AML44 14 36533725 36533725 C T SNP SLC25A21 NM_030631.2 human genbank 54_36p -1 provisional intronic c.71-119765 e2-119765 0.001 - - - no_errors tier3 1791 112 5.86 1501 1107 42.41 0 0 NA 906708 TCGA-AB-2971 AML44 14 36808216 36808216 A G SNP MIPOL1 NM_138731.5 human genbank 54_36p 1 validated intronic c.387+467 e3+467 0 - - - no_errors tier3 635 56 8.09 719 625 46.5 0 0 NA 906708 TCGA-AB-2971 AML44 14 41395574 41395574 A G SNP LRFN5 NM_152447.3 human genbank 54_36p 1 validated intronic c.1-29985 e1-29985 0 - - - no_errors tier3 391 26 6.24 466 343 42.29 0 0 NA 906708 TCGA-AB-2971 AML44 14 56924529 56924529 T C SNP NAT12 NM_001011713.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-2900 NULL 0 - - - no_errors tier3 516 54 9.47 253 234 47.95 0 0 NA 906708 TCGA-AB-2971 AML44 14 62538819 62538819 G A SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed intronic c.305-889 e4-889 0.001 - - - no_errors tier3 652 49 6.96 702 527 42.88 0 0 NA 906708 TCGA-AB-2971 AML44 14 83582035 83582035 A G SNP - - - - - - - - - - - - - - - tier3 232 25 9.73 293 364 55.4 0 0 NA 906708 TCGA-AB-2971 AML44 14 85106387 85106387 T C SNP FLRT2 NM_013231.4 human genbank 54_36p 1 reviewed intronic c.1+39756 e0+39756 0 - - - no_errors tier3 737 44 5.63 600 495 45.12 0 0 NA 906708 TCGA-AB-2971 AML44 14 98357457 98357457 C T SNP - - - - - - - - - - - - - - - tier3 845 72 7.84 762 626 45.1 0 0 NA 906708 TCGA-AB-2971 AML44 14 101510678 101510678 A G SNP DYNC1H1 NM_001376.4 human genbank 54_36p 1 reviewed intronic c.257-1124 e2-1124 0 - - - no_errors tier3 126 7 5.26 88 107 54.87 5 9 64.29 906708 TCGA-AB-2971 AML44 15 52228904 52228904 G C SNP UNC13C NM_001080534.1 human genbank 54_36p 1 provisional intronic c.3071+5731 e3+5731 0 - - - no_errors tier3 552 70 11.22 660 681 50.75 0 0 NA 906708 TCGA-AB-2971 AML44 15 69906600 69906600 T A SNP MYO9A NM_006901.2 human genbank 54_36p -1 validated intronic c.7184-162 e41-162 0 - - - no_errors tier3 851 34 3.84 542 449 45.26 3 3 50 906708 TCGA-AB-2971 AML44 15 82516236 82516236 T C SNP LOC642677 XR_036878.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.021 - - - pseudogene tier3 828 46 5.25 942 679 41.89 0 0 NA 906708 TCGA-AB-2971 AML44 15 83419211 83419211 G A SNP PDE8A NM_002605.2 human genbank 54_36p 1 validated intronic c.435-886 e4-886 0.001 - - - no_errors tier3 810 48 5.59 748 586 43.83 1 5 83.33 906708 TCGA-AB-2971 AML44 15 89011417 89011417 T C SNP CRTC3 NM_022769.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*25041 NULL 0.002 - - - no_errors tier3 522 31 5.6 222 174 43.83 0 3 100 906708 TCGA-AB-2971 AML44 15 96615144 96615144 C T SNP - - - - - - - - - - - - - - - tier3 1012 65 6.03 869 692 44.3 0 0 NA 906708 TCGA-AB-2971 AML44 15 96924000 96924000 A - DEL FAM169B NM_182562.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-77351 NULL 0.02 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 906708 TCGA-AB-2971 AML44 15 98149348 98149348 C T SNP LOC644800 XM_001715415.1 human genbank 54_36p 1 model silent c.99 p.D33 0.992 NULL NULL - no_errors tier1 313 20 5.95 203 213 51.2 NA 906708 TCGA-AB-2971 AML44 15 98636164 98636164 C T SNP ADAMTS17 NM_139057.2 human genbank 54_36p -1 reviewed intronic c.789+2793 e4+2793 0.001 - - - no_errors tier3 666 46 6.44 439 329 42.78 0 0 NA 906708 TCGA-AB-2971 AML44 16 5965647 5965647 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1076427 NULL 0.001 - - - no_errors tier3 558 24 4.12 563 382 40.42 0 0 NA 906708 TCGA-AB-2971 AML44 16 19168554 19168554 C A SNP SYT17 NM_016524.2 human genbank 54_36p 1 validated intronic c.1229-17149 e8-17149 0.006 - - - no_errors tier3 1383 107 7.17 946 655 40.86 0 0 0 906708 TCGA-AB-2971 AML44 16 26254344 26254344 G A SNP ENSG00000217478 ENST00000402112 human ensembl 54_36p -1 known 3_prime_flanking_region c.*19274 NULL 0.001 - - - no_coding_region:pseudogene tier3 648 32 4.7 740 569 43.47 0 0 NA 906708 TCGA-AB-2971 AML44 16 53295219 53295219 T C SNP - - - - - - - - - - - - - - - tier3 287 29 9.15 328 231 41.32 0 0 NA 906708 TCGA-AB-2971 AML44 16 59004007 59004007 T C SNP - - - - - - - - - - - - - - - tier3 656 62 8.62 718 663 48.01 0 0 NA 906708 TCGA-AB-2971 AML44 16 75018881 75018881 T A SNP CNTNAP4 NM_138994.3 human genbank 54_36p 1 validated missense c.347 p.V116D 0.998 "HMMPfam_F5_F8_type_C,HMMSmart_SM00231,superfamily_Galactose-binding domain-like" "HMMPfam_F5_F8_type_C,HMMSmart_SM00231,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMSmart_SM00282,superfamily_Fibrinogen C-terminal domain-like,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Galactose-binding domain-like,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2" - no_errors tier1 1284 97 7.02 1084 851 43.93 NA 906708 TCGA-AB-2971 AML44 17 11734175 11734175 C T SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed intronic c.11113-1644 e58-1644 0 - - - no_errors tier3 405 11 2.63 458 333 42.05 0 0 NA 906708 TCGA-AB-2971 AML44 17 12888528 12888528 C T SNP ELAC2 NM_018127.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-26539 NULL 0.043 - - - no_errors tier3 1269 63 4.73 820 552 40.23 0 0 NA 906708 TCGA-AB-2971 AML44 17 12979790 12979790 C A SNP - - - - - - - - - - - - - - - tier3 660 54 7.56 572 457 44.41 0 0 NA 906708 TCGA-AB-2971 AML44 17 24404392 24404392 G A SNP PIPOX NM_016518.2 human genbank 54_36p 1 validated intronic c.477+115 e3+115 0.001 - - - no_errors tier3 469 53 10.15 369 237 39.04 1 0 0 906708 TCGA-AB-2971 AML44 17 29482111 29482111 G A SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.555+24999 e1+24999 0 - - - overly_large_intron tier3 658 40 5.71 625 562 47.31 0 0 NA 906708 TCGA-AB-2971 AML44 17 48420906 48420906 G A SNP LOC339209 XM_294854.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*1226 NULL 0 - - - no_errors tier3 493 22 4.27 449 382 45.86 0 0 NA 906708 TCGA-AB-2971 AML44 18 571363 571363 G A SNP CETN1 NM_004066.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*436 NULL 0 - - - no_errors tier3 625 58 8.45 372 313 45.69 0 0 NA 906708 TCGA-AB-2971 AML44 18 2196545 2196545 G A SNP LOC100131655 XM_001732884.1 human genbank 54_36p -1 model intronic c.4006+3881 e18+3881 0 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 984 72 6.81 1202 1005 45.54 0 0 NA 906708 TCGA-AB-2971 AML44 18 5085429 5085429 G C SNP ENSG00000215368 ENST00000400144 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*37318 NULL 0.029 - - - no_coding_region:pseudogene tier3 1126 84 6.93 1053 890 45.76 0 0 NA 906708 TCGA-AB-2971 AML44 18 6928137 6928137 C T SNP FLJ38028 XR_040234.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-7961 NULL 0 - - - no_errors tier3 304 25 7.6 193 147 43.24 0 0 NA 906708 TCGA-AB-2971 AML44 18 15069887 15069887 G A SNP LOC100131500 XM_001723630.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22541 NULL 0.006 - - - no_errors tier3 145 8 5.23 181 153 45.54 0 0 NA 906708 TCGA-AB-2971 AML44 18 23664390 23664390 G T SNP - - - - - - - - - - - - - - - tier3 696 47 6.33 795 690 46.4 0 0 NA 906708 TCGA-AB-2971 AML44 18 24292648 24292648 G T SNP - - - - - - - - - - - - - - - tier3 100 13 11.5 144 122 45.86 0 0 NA 906708 TCGA-AB-2971 AML44 18 28096583 28096583 A G SNP MEP1B NM_005925.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*42377 NULL 0 - - - no_errors tier3 498 34 6.38 550 443 44.61 0 0 NA 906708 TCGA-AB-2971 AML44 18 28529773 28529773 C A SNP KLHL14 NM_020805.1 human genbank 54_36p -1 provisional intronic c.1070-260 e3-260 0.915 - - - no_errors tier3 1253 58 4.41 1236 860 41.01 0 0 0 906708 TCGA-AB-2971 AML44 18 33718128 33718128 C A SNP - - - - - - - - - - - - - - - tier3 1245 79 5.96 1195 873 42.21 0 0 NA 906708 TCGA-AB-2971 AML44 18 34189784 34189784 T G SNP - - - - - - - - - - - - - - - tier3 820 63 7.13 828 686 45.25 0 0 NA 906708 TCGA-AB-2971 AML44 18 37244958 37244958 T C SNP - - - - - - - - - - - - - - - tier3 1302 121 8.47 1202 1080 47.31 0 0 NA 906708 TCGA-AB-2971 AML44 18 39693820 39693820 C T SNP ENSG00000202250 ENST00000365380 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27592 NULL 0.006 - - - no_errors tier3 319 14 4.19 393 287 42.21 0 0 NA 906708 TCGA-AB-2971 AML44 18 41708852 41708852 C T SNP KIAA1632 NM_020964.2 human genbank 54_36p -1 validated intronic c.6049+1347 e35+1347 0.014 - - - no_errors tier3 854 40 4.46 841 578 40.62 1 3 75 906708 TCGA-AB-2971 AML44 18 46370510 46370510 G A SNP MAPK4 NM_002747.3 human genbank 54_36p 1 reviewed intronic c.1+29899 e0+29899 0 - - - no_errors tier3 951 74 7.21 558 484 46.45 0 0 NA 906708 TCGA-AB-2971 AML44 18 48819401 48819401 C T SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.986-24272 e6-24272 0.528 - - - no_errors tier3 671 39 5.49 562 483 46.18 0 0 NA 906708 TCGA-AB-2971 AML44 18 50874337 50874337 C T SNP - - - - - - - - - - - - - - - tier3 758 58 7.11 998 823 45.19 0 0 NA 906708 TCGA-AB-2971 AML44 18 51454971 51454971 G A SNP TCF4 NM_001083962.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49626 NULL 0 - - - no_errors tier3 1495 56 3.6 893 698 43.84 0 0 NA 906708 TCGA-AB-2971 AML44 18 55765900 55765900 T A SNP ENSG00000222539 ENST00000410607 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-25226 NULL 0.03 - - - no_errors tier3 349 21 5.66 359 224 38.42 0 0 NA 906708 TCGA-AB-2971 AML44 18 57559490 57559490 T C SNP - - - - - - - - - - - - - - - tier3 626 29 4.43 664 607 47.68 0 0 NA 906708 TCGA-AB-2971 AML44 18 60034379 60034379 C T SNP - - - - - - - - - - - - - - - tier3 368 21 5.38 514 446 46.31 0 0 NA 906708 TCGA-AB-2971 AML44 18 61159001 61159001 A G SNP - - - - - - - - - - - - - - - tier3 206 16 7.17 245 217 46.97 0 0 NA 906708 TCGA-AB-2971 AML44 18 62750780 62750780 C A SNP - - - - - - - - - - - - - - - tier3 317 26 7.56 377 387 50.65 0 0 NA 906708 TCGA-AB-2971 AML44 18 64089799 64089799 A T SNP - - - - - - - - - - - - - - - tier3 434 35 7.45 478 367 43.43 0 0 NA 906708 TCGA-AB-2971 AML44 18 67519048 67519048 G A SNP - - - - - - - - - - - - - - - tier3 55 3 5.08 72 62 46.27 0 0 NA 906708 TCGA-AB-2971 AML44 18 71788890 71788890 G A SNP - - - - - - - - - - - - - - - tier3 500 25 4.75 398 385 49.11 0 0 NA 906708 TCGA-AB-2971 AML44 19 5511827 5511827 T G SNP LOC100129680 XM_001726384.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*106 NULL 0.016 - - - no_errors tier3 613 28 4.36 160 138 46.31 2 1 33.33 906708 TCGA-AB-2971 AML44 19 10291823 10291823 G A SNP RAVER1 NM_133452.2 human genbank 54_36p -1 validated intronic c.1821+508 e9+508 0.002 - - - no_errors tier3 381 24 5.93 170 130 43.33 6 0 0 906708 TCGA-AB-2971 AML44 19 34269277 34269277 G A SNP - - - - - - - - - - - - - - - tier3 1295 69 5.04 1089 788 41.98 0 0 NA 906708 TCGA-AB-2971 AML44 19 38660609 38660609 A G SNP PEPD NM_000285.2 human genbank 54_36p -1 validated intronic c.548+183 e7+183 0 - - - no_errors tier3 533 39 6.82 328 318 49.23 0 0 0 906708 TCGA-AB-2971 AML44 19 59111527 59111527 T C SNP CACNG7 NM_031896.3 human genbank 54_36p 1 reviewed intronic c.424+956 e3+956 0.012 - - - no_errors tier3 341 20 5.54 110 123 52.79 0 0 NA 906708 TCGA-AB-2971 AML44 19 62154816 62154816 C T SNP ENSG00000210698 ENST00000387963 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29346 NULL 0.001 - - - pseudogene tier3 921 37 3.85 455 238 34.24 0 0 NA 906708 TCGA-AB-2971 AML44 20 12058774 12058774 A T SNP - - - - - - - - - - - - - - - tier3 489 24 4.67 526 446 45.88 0 1 100 906708 TCGA-AB-2971 AML44 20 16952991 16952991 A G SNP ENSG00000212165 ENST00000390863 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41313 NULL 0.003 - - - no_errors tier3 312 15 4.59 469 317 40.33 0 0 NA 906708 TCGA-AB-2971 AML44 20 21803225 21803225 G A SNP - - - - - - - - - - - - - - - tier3 317 19 5.65 454 395 46.47 0 0 NA 906708 TCGA-AB-2971 AML44 20 23919112 23919112 C T SNP ENSG00000167390 ENST00000319850 human ensembl 54_36p 1 known silent c.666 p.Y222 0.044 NULL NULL - no_stop_codon tier1 119 10 7.75 89 69 43.4 NA 906708 TCGA-AB-2971 AML44 20 25543177 25543177 C T SNP NANP NM_152667.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1384 NULL 0.005 - - - no_errors tier3 347 21 5.68 219 147 40.16 4 6 60 906708 TCGA-AB-2971 AML44 20 38655686 38655686 C T SNP - - - - - - - - - - - - - - - tier3 396 26 6.13 389 346 47.07 0 0 NA 906708 TCGA-AB-2971 AML44 20 41411311 41411311 A G SNP ENSG00000223025 ENST00000411093 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44578 NULL 0.029 - - - no_errors tier3 629 60 8.71 472 365 43.61 0 0 NA 906708 TCGA-AB-2971 AML44 20 42855078 42855078 G A SNP RIMS4 NM_182970.2 human genbank 54_36p -1 validated intronic c.97+17152 e1+17152 0.009 - - - no_errors tier3 579 46 7.36 325 288 46.98 0 0 NA 906708 TCGA-AB-2971 AML44 20 50550395 50550395 T A SNP ENSG00000217673 ENST00000406736 human ensembl 54_36p 1 known 5_prime_flanking_region c.-10803 NULL 0.641 - - - no_coding_region:pseudogene tier3 533 39 6.82 678 482 41.44 0 0 NA 906708 TCGA-AB-2971 AML44 21 25336482 25336482 T C SNP - - - - - - - - - - - - - - - tier3 927 11 1.17 867 204 19.03 0 0 NA 906708 TCGA-AB-2971 AML44 21 28059795 28059795 C T SNP - - - - - - - - - - - - - - - tier3 621 29 4.46 481 359 42.64 0 0 NA 906708 TCGA-AB-2971 AML44 21 31196335 31196335 C T SNP KRTAP11-1 NM_175858.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20621 NULL 0.105 - - - no_errors tier3 349 17 4.63 443 368 45.15 0 0 NA 906708 TCGA-AB-2971 AML44 21 31285466 31285466 C T SNP KRTAP19-8 NM_001099219.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*46976 NULL 0.48 - - - no_errors tier3 274 16 5.52 359 286 44.27 0 0 NA 906708 TCGA-AB-2971 AML44 21 35242883 35242883 A C SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed intronic c.59-55753 e2-55753 0.01 - - - no_errors tier3 507 34 6.28 448 376 45.63 31 33 51.56 906708 TCGA-AB-2971 AML44 21 40326639 40326639 A G SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.5686+9529 e32+9529 0.294 - - - no_errors tier3 552 26 4.5 391 366 48.35 0 0 NA 906708 TCGA-AB-2971 AML44 21 41376006 41376006 A T SNP - - - - - - - - - - - - - - - tier3 1049 60 5.41 760 577 43.09 0 0 NA 906708 TCGA-AB-2971 AML44 21 42700141 42700141 G T SNP UBASH3A NM_018961.1 human genbank 54_36p 1 validated intronic c.167+602 e2+602 0 - - - no_errors tier3 1343 82 5.75 963 752 43.85 0 0 0 906708 TCGA-AB-2971 AML44 21 43283745 43283745 G C SNP PKNOX1 NM_004571.3 human genbank 54_36p 1 validated intronic c.1-13760 e1-13760 0 - - - no_errors tier3 445 19 4.09 245 179 42.22 2 0 0 906708 TCGA-AB-2971 AML44 21 45296682 45296682 G A SNP ADARB1 NM_015833.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-119318 NULL 0.013 - - - no_errors tier3 322 19 5.56 234 178 43 0 0 NA 906708 TCGA-AB-2971 AML44 22 20483395 20483395 C T SNP MAPK1 NM_002745.4 human genbank 54_36p -1 reviewed missense c.515 p.R172H 1 "HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_MAPK,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 557 44 7.28 675 546 44.64 41 44 51.76 906708 TCGA-AB-2971 AML44 22 21684977 21684977 G T SNP RTDR1 NM_014433.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*46663 NULL 0 - - - no_errors tier3 503 36 6.67 296 291 49.57 0 0 NA 906708 TCGA-AB-2971 AML44 22 26871387 26871387 C T SNP TTC28 ENST00000397906 human ensembl 54_36p -1 known intronic c.1441+17693 e6+17693 0.001 - - - no_errors tier3 667 30 4.3 689 500 42.02 2 0 0 906708 TCGA-AB-2971 AML44 22 28688206 28688206 C T SNP MTMR3 NM_021090.3 human genbank 54_36p 1 reviewed intronic c.1+5129 e0+5129 0.008 - - - no_errors tier3 317 17 5.06 500 310 38.27 5 8 53.33 906708 TCGA-AB-2971 AML44 22 33530100 33530100 C T SNP - - - - - - - - - - - - - - - tier3 815 89 9.83 890 697 43.89 0 0 NA 906708 TCGA-AB-2971 AML44 22 37200206 37200206 C T SNP KDELR3 NM_016657.2 human genbank 54_36p 1 reviewed intronic c.92-268 e2-268 0 - - - no_errors tier3 354 31 8.03 136 105 43.57 1 0 0 179223 TCGA-AB-2972 AML20 X 533540 533540 G A SNP SHOX NM_006883.3 human genbank 54_36p 1 reviewed intronic c.634-5980 e5-5980 0.004 - - - no_errors tier3 937 0 0 172 122 41.5 0 0 NA 179223 TCGA-AB-2972 AML20 X 3332771 3332771 A T SNP LOC100130844 XR_042509.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-9410 NULL 0.104 - - - pseudogene tier3 847 1 0.12 546 181 24.9 0 0 NA 179223 TCGA-AB-2972 AML20 X 7765970 7765970 C A SNP VCX NM_013452.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-5275 NULL 0 - - - no_errors tier3 911 9 0.98 144 78 35.14 0 0 NA 179223 TCGA-AB-2972 AML20 X 10322611 10322611 C T SNP - - - - - - - - - - - - - - - tier3 1779 6 0.34 1020 716 41.2 0 0 NA 179223 TCGA-AB-2972 AML20 X 11898424 11898424 G A SNP - - - - - - - - - - - - - - - tier3 1179 4 0.34 660 266 28.69 0 0 NA 179223 TCGA-AB-2972 AML20 X 13669221 13669221 C G SNP OFD1 NM_003611.2 human genbank 54_36p 1 reviewed intronic c.412+2149 e5+2149 0.083 - - - no_errors tier3 579 1 0.17 242 179 42.52 13 0 0 179223 TCGA-AB-2972 AML20 X 17440414 17440414 T G SNP NHS NM_198270.2 human genbank 54_36p 1 reviewed intronic c.565+136048 e1+136048 0.001 - - - no_errors tier3 451 0 0 239 232 49.26 0 0 NA 179223 TCGA-AB-2972 AML20 X 18907630 18907630 C T SNP PHKA2 NM_000292.2 human genbank 54_36p -1 validated intronic c.78+4264 e1+4264 0 - - - no_errors tier3 324 0 0 131 108 45.19 0 1 100 179223 TCGA-AB-2972 AML20 X 20014706 20014706 G A SNP MAP7D2 NM_152780.2 human genbank 54_36p -1 provisional intronic c.131-21862 e2-21862 0 - - - no_errors tier3 1112 8 0.71 364 279 43.32 0 0 NA 179223 TCGA-AB-2972 AML20 X 21770124 21770124 T C SNP MBTPS2 NM_015884.2 human genbank 54_36p 1 validated intronic c.76-1085 e2-1085 0.025 - - - no_errors tier3 802 4 0.5 230 216 48.43 0 0 0 179223 TCGA-AB-2972 AML20 X 28556872 28556872 G A SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.1+40787 e0+40787 0 - - - no_errors tier3 964 5 0.52 512 409 44.31 0 0 NA 179223 TCGA-AB-2972 AML20 X 28977775 28977775 C A SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.83-233201 e2-233201 0 - - - no_errors tier3 433 0 0 277 150 35.13 0 0 NA 179223 TCGA-AB-2972 AML20 X 33088846 33088846 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.31+50474 e1+50474 0.012 - - - no_errors tier3 644 2 0.31 247 183 42.56 0 0 NA 179223 TCGA-AB-2972 AML20 X 33585761 33585761 C T SNP ENSG00000221404 ENST00000408477 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47672 NULL 0 - - - no_errors tier3 558 0 0 315 259 45.12 0 0 NA 179223 TCGA-AB-2972 AML20 X 39941579 39941579 T C SNP BCOR ENST00000378455 human ensembl 54_36p -1 known 5_prime_flanking_region c.-119453 NULL 0.006 - - - no_errors tier3 906 5 0.55 207 123 37.16 0 0 NA 179223 TCGA-AB-2972 AML20 X 51677174 51677174 A G SNP LOC644310 XM_927480.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-6214 NULL 0.01 - - - no_errors tier3 1321 9 0.68 519 387 42.72 0 0 NA 179223 TCGA-AB-2972 AML20 X 57025608 57025608 G C SNP SPIN3 NM_001010862.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*11721 NULL 0.121 - - - no_errors tier3 1128 3 0.26 807 265 24.72 0 0 0 179223 TCGA-AB-2972 AML20 X 62695894 62695894 G T SNP - - - - - - - - - - - - - - - tier3 559 5 0.88 265 184 40.98 2 0 0 179223 TCGA-AB-2972 AML20 X 63492967 63492967 G A SNP MTMR8 NM_017677.2 human genbank 54_36p -1 provisional intronic c.148-24 e3-24 0 - - - no_errors tier3 1204 4 0.33 541 401 42.57 0 0 0 179223 TCGA-AB-2972 AML20 X 70354098 70354098 G A SNP GJB1 NM_001097642.5 human genbank 54_36p 1 reviewed intronic c.1+2233 e0+2233 0.03 - - - no_errors tier3 1438 5 0.35 332 286 46.28 0 0 NA 179223 TCGA-AB-2972 AML20 X 79934945 79934945 T A SNP BRWD3 NM_153252.3 human genbank 54_36p -1 validated intronic c.331+832 e5+832 0.007 - - - no_errors tier3 453 0 0 398 117 22.72 0 0 0 179223 TCGA-AB-2972 AML20 X 94156294 94156294 A C SNP MIRN548M ENST00000408260 human ensembl 54_36p -1 known 3_prime_flanking_region c.*48502 NULL 0.004 - - - no_errors tier3 542 0 0 354 274 43.63 0 0 NA 179223 TCGA-AB-2972 AML20 X 94907337 94907337 A T SNP - - - - - - - - - - - - - - - tier3 1126 1 0.09 473 378 44.31 0 0 NA 179223 TCGA-AB-2972 AML20 X 99315375 99315375 C T SNP ENSG00000220672 ENST00000405682 human ensembl 54_36p -1 known 5_prime_flanking_region c.-22344 NULL 0.002 - - - no_coding_region:pseudogene tier3 1353 6 0.44 750 578 43.46 0 0 NA 179223 TCGA-AB-2972 AML20 X 104978714 104978714 C G SNP NRK ENST00000243300 human ensembl 54_36p 1 known intronic c.123+16946 e2+16946 0.003 - - - no_errors tier3 1494 1 0.07 998 179 15.18 0 0 NA 179223 TCGA-AB-2972 AML20 X 112234794 112234794 C G SNP - - - - - - - - - - - - - - - tier3 850 1 0.12 515 104 16.77 0 0 NA 179223 TCGA-AB-2972 AML20 X 114568210 114568210 C A SNP ENSG00000220726 ENST00000404380 human ensembl 54_36p -1 known 5_prime_flanking_region c.-1884 NULL 0.004 - - - no_coding_region:pseudogene tier3 913 2 0.22 453 304 40.05 0 0 NA 179223 TCGA-AB-2972 AML20 X 116448015 116448015 A G SNP ENSG00000220345 ENST00000405447 human ensembl 54_36p 1 known 3_prime_flanking_region c.*31818 NULL 0 - - - no_coding_region:pseudogene tier3 915 7 0.76 377 305 44.72 0 0 NA 179223 TCGA-AB-2972 AML20 X 117259210 117259210 C T SNP ENSG00000208803 ENST00000386068 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40992 NULL 0 - - - pseudogene tier3 501 2 0.4 281 229 44.81 0 0 NA 179223 TCGA-AB-2972 AML20 X 119389085 119389085 T C SNP ATP1B4 NM_012069.1 human genbank 54_36p 1 validated missense c.542 p.F181S 1 HMMPfam_Na_K-ATPase "HMMPfam_Na_K-ATPase,PatternScan_ATPASE_NA_K_BETA_1,PatternScan_ATPASE_NA_K_BETA_2" - no_errors tier1 832 1 0.12 339 258 43 NA 179223 TCGA-AB-2972 AML20 X 120882341 120882341 C T SNP - - - - - - - - - - - - - - - tier3 1175 4 0.34 640 465 41.93 0 0 NA 179223 TCGA-AB-2972 AML20 X 122452888 122452888 C A SNP ENSG00000179101 ENST00000316450 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23117 NULL 0.001 - - - no_coding_region:pseudogene tier3 1456 1 0.07 758 273 26.48 0 0 NA 179223 TCGA-AB-2972 AML20 X 123025397 123025397 C T SNP STAG2 NM_001042749.1 human genbank 54_36p 1 validated nonsense c.1840 p.R614* 1 superfamily_ARM-type_fold "HMMPfam_STAG,superfamily_ARM-type_fold" - no_errors tier1 587 0 313 267 46.03 7 58 89.23 179223 TCGA-AB-2972 AML20 X 123931941 123931941 G A SNP ODZ1 NM_014253.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-6658 NULL 0 - - - no_errors tier3 1028 4 0.39 438 299 40.51 0 0 NA 179223 TCGA-AB-2972 AML20 X 126927497 126927497 G C SNP - - - - - - - - - - - - - - - tier3 944 1 0.11 530 351 39.84 0 0 NA 179223 TCGA-AB-2972 AML20 X 128191016 128191016 T A SNP - - - - - - - - - - - - - - - tier2 1193 0 0 632 479 43 0 0 NA 179223 TCGA-AB-2972 AML20 X 131368998 131368998 C T SNP MBNL3 NM_018388.2 human genbank 54_36p -1 provisional intronic c.178-897 e2-897 0.009 - - - no_errors tier3 1206 8 0.66 498 404 44.69 3 0 0 179223 TCGA-AB-2972 AML20 X 134479734 134479734 A G SNP DDX26B NM_182540.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-2850 NULL 0.042 - - - no_errors tier3 998 3 0.3 475 184 27.84 0 0 NA 179223 TCGA-AB-2972 AML20 X 135978135 135978135 C A SNP GPR101 NM_054021.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-36636 NULL 0.983 - - - no_errors tier3 1135 3 0.26 498 387 43.68 0 0 NA 179223 TCGA-AB-2972 AML20 X 136415231 136415231 A T SNP LOC100129230 XM_001715555.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-45435 NULL 0.004 - - - no_errors tier3 838 1 0.12 418 297 41.48 0 0 NA 179223 TCGA-AB-2972 AML20 X 145061789 145061789 T G SNP - - - - - - - - - - - - - - - tier3 1273 6 0.47 605 401 39.86 0 0 NA 179223 TCGA-AB-2972 AML20 X 146124944 146124944 G A SNP MIRN506 ENST00000384998 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4891 NULL 0 - - - no_errors tier3 2117 12 0.56 607 445 42.3 0 0 NA 179223 TCGA-AB-2972 AML20 X 146746450 146746450 C T SNP ENSG00000202051 ENST00000365181 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29856 NULL 0 - - - no_errors tier3 931 1 0.11 488 412 45.73 0 0 NA 179223 TCGA-AB-2972 AML20 X 148461876 148461876 G T SNP LOC100133153 XR_038485.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-21884 NULL 0.01 - - - pseudogene tier3 865 1 0.12 346 130 27.25 0 0 NA 179223 TCGA-AB-2972 AML20 X 154283031 154283031 T C SNP MIRN1184 ENST00000408263 human ensembl 54_36p -1 known 5_prime_flanking_region c.-16990 NULL 0 - - - no_errors tier3 752 2 0.26 263 224 46 1 1 50 179223 TCGA-AB-2972 AML20 X 154784113 154784113 G A SNP VAMP7 NM_005638.1 human genbank 54_36p 1 validated intronic c.433+668 e4+668 0.187 - - - no_errors tier3 519 2 0.38 243 184 42.99 2 0 0 179223 TCGA-AB-2972 AML20 1 3093967 3093967 G C SNP PRDM16 NM_022114.2 human genbank 54_36p 1 reviewed intronic c.387+1069 e2+1069 0.003 - - - no_errors tier3 76 0 0 24 15 38.46 0 1 100 179223 TCGA-AB-2972 AML20 1 6496144 6496144 C T SNP PLEKHG5 NM_198681.1 human genbank 54_36p -1 reviewed intronic c.67+5948 e1+5948 0.003 - - - no_errors tier3 129 0 0 33 33 50 0 0 NA 179223 TCGA-AB-2972 AML20 1 7651332 7651332 C T SNP CAMTA1 NM_015215.1 human genbank 54_36p 1 validated intronic c.2653-2226 e10-2226 0.429 - - - no_errors tier3 152 1 0.65 46 35 43.21 0 0 NA 179223 TCGA-AB-2972 AML20 1 14111455 14111455 G A SNP C1orf196 ENST00000401953 human ensembl 54_36p 1 known intronic c.121+18617 e1+18617 0.001 - - - no_stop_codon tier3 896 3 0.33 337 130 27.84 0 0 NA 179223 TCGA-AB-2972 AML20 1 19205841 19205841 C T SNP - - - - - - - - - - - - - - - tier3 731 1 0.14 223 183 44.85 0 0 NA 179223 TCGA-AB-2972 AML20 1 22960335 22960335 C T SNP EPHB2 NM_004442.6 human genbank 54_36p 1 reviewed intronic c.62-20166 e2-20166 0.001 - - - no_errors tier3 445 3 0.67 156 147 48.36 0 0 NA 179223 TCGA-AB-2972 AML20 1 33944811 33944811 C T SNP CSMD2 NM_052896.3 human genbank 54_36p -1 validated intronic c.3456+2465 e22+2465 0.001 - - - no_errors tier3 985 3 0.3 291 203 41.09 0 0 NA 179223 TCGA-AB-2972 AML20 1 37408653 37408653 C G SNP ENSG00000207328 ENST00000384598 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33145 NULL 0.983 - - - no_errors tier3 1196 4 0.33 454 348 43.28 0 0 NA 179223 TCGA-AB-2972 AML20 1 40042305 40042305 C G SNP BMP8B NM_001720.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15561 NULL 0.002 - - - no_errors tier3 702 4 0.57 157 116 42.49 1 2 66.67 179223 TCGA-AB-2972 AML20 1 54618095 54618095 G A SNP SSBP3 NM_145716.2 human genbank 54_36p -1 validated intronic c.276+22027 e4+22027 0.001 - - - no_errors tier3 580 3 0.51 183 143 43.87 4 3 42.86 179223 TCGA-AB-2972 AML20 1 61805443 61805443 A G SNP - - - - - - - - - - - - - - - tier3 1371 4 0.29 829 599 41.95 0 0 NA 179223 TCGA-AB-2972 AML20 1 66591905 66591905 G C SNP PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.748-1893 e8-1893 0.014 - - - no_errors tier3 279 2 0.71 136 121 47.08 2 0 0 179223 TCGA-AB-2972 AML20 1 66716241 66716241 A G SNP - - - - - - - - - - - - - - - tier3 1345 11 0.81 586 441 42.9 0 0 NA 179223 TCGA-AB-2972 AML20 1 68159611 68159611 G A SNP LOC100133029 XM_001726661.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24806 NULL 0.001 - - - no_errors tier3 751 2 0.27 315 280 46.98 0 0 NA 179223 TCGA-AB-2972 AML20 1 69791209 69791209 A C SNP LRRC7 ENST00000310961 human ensembl 54_36p 1 known 5_prime_flanking_region c.-163280 NULL 0.134 - - - no_errors tier3 956 13 1.34 300 258 46.15 0 0 NA 179223 TCGA-AB-2972 AML20 1 77720458 77720458 G C SNP AK5 NM_174858.2 human genbank 54_36p 1 reviewed intronic c.1060-1132 e9-1132 0.012 - - - no_errors tier3 600 2 0.33 311 204 39.46 0 0 NA 179223 TCGA-AB-2972 AML20 1 79038873 79038874 - A INS ENSG00000220148 ENST00000404761 human ensembl 54_36p 1 known 3_prime_flanking_region c.*49941 NULL 0.000:0.000 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 1 79714636 79714636 A G SNP ADH5P2 ENST00000402790 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44717 NULL 0.001 - - - no_coding_region:pseudogene tier3 555 2 0.36 349 46 11.65 0 0 NA 179223 TCGA-AB-2972 AML20 1 82257552 82257552 G A SNP LPHN2 NM_012302.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*28135 NULL 0.012 - - - no_errors tier3 931 1 0.11 476 353 42.53 0 0 NA 179223 TCGA-AB-2972 AML20 1 82544538 82544538 C G SNP - - - - - - - - - - - - - - - tier3 627 1 0.16 518 412 44.3 0 0 NA 179223 TCGA-AB-2972 AML20 1 97435523 97435523 T C SNP DPYD NM_000110.3 human genbank 54_36p -1 reviewed intronic c.2443-4131 e20-4131 0.06 - - - no_errors tier3 581 1 0.17 397 277 41.1 6 0 0 179223 TCGA-AB-2972 AML20 1 102142661 102142661 C T SNP OLFM3 NM_058170.2 human genbank 54_36p -1 validated intronic c.70-67492 e2-67492 0.317 - - - no_errors tier3 1130 3 0.26 762 503 39.76 0 0 NA 179223 TCGA-AB-2972 AML20 1 116074240 116074240 A C SNP CASQ2 NM_001232.3 human genbank 54_36p -1 reviewed intronic c.606+2805 e5+2805 0.001 - - - no_errors tier3 1351 3 0.22 487 365 42.59 0 0 NA 179223 TCGA-AB-2972 AML20 1 119767306 119767306 C T SNP ENSG00000187481 ENST00000286193 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44061 NULL 0 - - - no_coding_region:pseudogene tier3 466 2 0.43 237 169 41.52 0 0 NA 179223 TCGA-AB-2972 AML20 1 149813415 149813415 G A SNP TUFT1 NM_020127.1 human genbank 54_36p 1 validated missense c.640 p.A214T 0.973 NULL NULL - no_errors tier1 912 0 308 235 43.28 NA 179223 TCGA-AB-2972 AML20 1 154667845 154667845 C G SNP C1orf61 NM_006365.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-14590 NULL 0.001 - - - no_errors tier3 259 0 0 75 18 19.35 0 0 NA 179223 TCGA-AB-2972 AML20 1 158847860 158847860 A G SNP SLAMF1 NM_003037.2 human genbank 54_36p -1 validated intronic c.958-648 e7-648 0.007 - - - no_errors tier3 992 2 0.2 511 417 44.94 1 0 0 179223 TCGA-AB-2972 AML20 1 159965862 159965862 T C SNP DUSP12 NM_007240.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20354 NULL 0 - - - no_errors tier3 1388 5 0.36 666 251 27.25 0 0 NA 179223 TCGA-AB-2972 AML20 1 167833746 167833746 C T SNP SELP NM_003005.3 human genbank 54_36p -1 reviewed intronic c.1706-708 e11-708 0.004 - - - no_errors tier3 1018 0 0 426 356 45.35 1 0 0 179223 TCGA-AB-2972 AML20 1 184174198 184174198 G T SNP HMCN1 NM_031935.2 human genbank 54_36p 1 reviewed intronic c.1828+4619 e11+4619 0 - - - no_errors tier3 856 2 0.23 333 275 45.23 0 0 NA 179223 TCGA-AB-2972 AML20 1 184225244 184225244 A G SNP HMCN1 NM_031935.2 human genbank 54_36p 1 reviewed missense c.3050 p.K1017R 1 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin" "PatternScan_ASX_HYDROXYL,PatternScan_CECROPIN,HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMSmart_SM00179,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,HMMPfam_G2F,HMMSmart_SM00682,superfamily_GFP-like,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_I-set,HMMPfam_ig,PatternScan_EGF_CA,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_EGF/Laminin" - no_errors tier1 672 1 0.15 361 341 48.58 NA 179223 TCGA-AB-2972 AML20 1 187204259 187204259 T C SNP - - - - - - - - - - - - - - - tier3 940 1 0.11 457 137 23.03 0 0 NA 179223 TCGA-AB-2972 AML20 1 187436594 187436594 A G SNP - - - - - - - - - - - - - - - tier3 833 1 0.12 360 296 45.05 0 0 NA 179223 TCGA-AB-2972 AML20 1 188608057 188608057 G A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional intronic c.236+82351 e1+82351 0.003 - - - no_errors tier3 1003 0 0 674 179 20.98 0 0 NA 179223 TCGA-AB-2972 AML20 1 189458860 189458860 G C SNP - - - - - - - - - - - - - - - tier3 578 0 0 364 81 18.16 0 0 NA 179223 TCGA-AB-2972 AML20 1 190198184 190198184 T A SNP - - - - - - - - - - - - - - - tier3 304 4 1.3 209 202 49.15 0 0 NA 179223 TCGA-AB-2972 AML20 1 199071064 199071064 G A SNP CAMSAP1L1 NM_203459.1 human genbank 54_36p 1 validated intronic c.927+2468 e6+2468 0.479 - - - no_errors tier3 933 3 0.32 321 282 46.77 0 0 0 179223 TCGA-AB-2972 AML20 1 201654450 201654450 C G SNP - - - - - - - - - - - - - - - tier3 906 2 0.22 429 343 44.37 0 0 NA 179223 TCGA-AB-2972 AML20 1 204762265 204762265 G A SNP RASSF5 NM_182663.2 human genbank 54_36p 1 reviewed intronic c.457+14250 e1+14250 0.001 - - - no_errors tier3 617 3 0.48 185 149 44.61 3 1 25 179223 TCGA-AB-2972 AML20 1 207560745 207560745 A C SNP - - - - - - - - - - - - - - - tier3 779 0 0 345 266 43.54 0 0 NA 179223 TCGA-AB-2972 AML20 1 212160427 212160427 G A SNP - - - - - - - - - - - - - - - tier3 1038 4 0.38 644 481 42.76 0 0 NA 179223 TCGA-AB-2972 AML20 1 217767588 217767588 G C SNP - - - - - - - - - - - - - - - tier3 695 0 0 370 112 23.24 0 0 NA 179223 TCGA-AB-2972 AML20 1 219345518 219345518 G A SNP ENSG00000219735 ENST00000405558 human ensembl 54_36p -1 known 3_prime_flanking_region c.*28312 NULL 0.001 - - - no_coding_region:pseudogene tier3 1074 5 0.46 480 393 44.97 0 0 NA 179223 TCGA-AB-2972 AML20 1 224174658 224174658 A G SNP PYCR2 NM_013328.2 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*120 NULL 0.005 - - - no_errors tier3 326 0 0 79 67 45.89 47 43 47.78 179223 TCGA-AB-2972 AML20 1 226608363 226608363 C T SNP OBSCN NM_001098623.1 human genbank 54_36p 1 reviewed intronic c.18661+977 e79+977 0 - - - no_errors tier3 436 2 0.46 98 79 44.63 0 1 100 179223 TCGA-AB-2972 AML20 1 230183141 230183141 A G SNP DISC1 NM_018662.1 human genbank 54_36p 1 reviewed intronic c.2042+21884 e10+21884 0.013 - - - no_errors tier3 254 1 0.39 85 74 46.54 0 0 0 179223 TCGA-AB-2972 AML20 1 230725847 230725847 T C SNP LOC729336 XM_001129978.2 human genbank 54_36p -1 model intronic c.1318-7870 e6-7870 0.852 - - - no_errors tier3 638 4 0.62 339 286 45.76 0 0 NA 179223 TCGA-AB-2972 AML20 1 238676972 238676972 C T SNP FMN2 NM_020066.4 human genbank 54_36p 1 validated intronic c.5489+8839 e16+8839 0 - - - no_errors tier3 1168 4 0.34 502 334 39.9 0 0 NA 179223 TCGA-AB-2972 AML20 1 244541284 244541284 A G SNP SMYD3 NM_022743.1 human genbank 54_36p -1 provisional intronic c.354+15842 e4+15842 0.028 - - - no_errors tier3 730 6 0.82 217 218 50 1 2 66.67 179223 TCGA-AB-2972 AML20 2 741744 741744 C T SNP LOC728086 XM_001719707.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13433 NULL 0.001 - - - no_start_codon:pseudogene tier3 501 1 0.2 152 118 43.54 0 0 NA 179223 TCGA-AB-2972 AML20 2 5904757 5904757 A G SNP - - - - - - - - - - - - - - - tier3 1161 2 0.17 530 411 43.58 0 0 NA 179223 TCGA-AB-2972 AML20 2 10493788 10493788 G A SNP ENSG00000217258 ENST00000404616 human ensembl 54_36p 1 known 5_prime_flanking_region c.-17810 NULL 0.002 - - - no_errors tier3 662 0 0 122 110 47.41 0 0 NA 179223 TCGA-AB-2972 AML20 2 12624767 12624767 C T SNP - - - - - - - - - - - - - - - tier3 1101 0 0 1299 161 11.03 0 0 NA 179223 TCGA-AB-2972 AML20 2 17626723 17626723 G A SNP VSNL1 NM_003385.4 human genbank 54_36p 1 reviewed intronic c.1-10095 e1-10095 0.001 - - - no_errors tier3 394 1 0.25 192 145 43.03 0 0 NA 179223 TCGA-AB-2972 AML20 2 20999268 20999268 C T SNP - - - - - - - - - - - - - - - tier3 1125 1 0.09 389 312 44.44 0 0 NA 179223 TCGA-AB-2972 AML20 2 22589438 22589438 G C SNP - - - - - - - - - - - - - - - tier3 995 6 0.6 777 274 26.05 0 0 NA 179223 TCGA-AB-2972 AML20 2 32889892 32889892 G A SNP TTC27 NM_017735.3 human genbank 54_36p 1 provisional intronic c.2196+100 e17+100 0 - - - no_errors tier3 989 1 0.1 399 252 38.71 1 3 75 179223 TCGA-AB-2972 AML20 2 33871595 33871595 C A SNP ENSG00000219819 ENST00000403342 human ensembl 54_36p -1 known 3_prime_flanking_region c.*46758 NULL 0 - - - no_coding_region:pseudogene tier3 887 5 0.56 316 244 43.42 0 0 NA 179223 TCGA-AB-2972 AML20 2 38342886 38342886 C T SNP ENSG00000213594 ENST00000395092 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23170 NULL 0.257 - - - no_coding_region:pseudogene tier3 913 0 0 382 283 42.56 0 0 NA 179223 TCGA-AB-2972 AML20 2 39968834 39968834 G A SNP LOC100128590 XM_001723678.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-34682 NULL 0 - - - no_errors tier3 1091 0 0 946 270 22.19 0 0 NA 179223 TCGA-AB-2972 AML20 2 42033936 42033936 C G SNP uc002rsf.1 ENST00000403980 human ensembl 54_36p -1 known missense c.118 p.V40L 0 NULL NULL - no_errors tier1 462 0 219 142 39.34 NA 179223 TCGA-AB-2972 AML20 2 48061827 48061827 A C SNP ENSG00000217681 ENST00000405344 human ensembl 54_36p -1 known 5_prime_flanking_region c.-40966 NULL 0.025 - - - no_coding_region:pseudogene tier3 625 6 0.95 369 299 44.69 0 1 100 179223 TCGA-AB-2972 AML20 2 49391186 49391186 G A SNP - - - - - - - - - - - - - - - tier3 1021 2 0.2 460 378 45.11 0 0 NA 179223 TCGA-AB-2972 AML20 2 50407458 50407458 T C SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.3365-89846 e17-89846 0 - - - no_errors tier3 1546 2 0.13 519 403 43.71 0 0 NA 179223 TCGA-AB-2972 AML20 2 50593294 50593294 G T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.2375-6035 e12-6035 0.001 - - - no_errors tier3 956 5 0.52 515 333 39.27 0 0 NA 179223 TCGA-AB-2972 AML20 2 50634064 50634064 G T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.1321-397 e8-397 0.1 - - - no_errors tier3 737 0 0 391 253 39.29 0 0 NA 179223 TCGA-AB-2972 AML20 2 51992203 51992203 C T SNP ENSG00000220786 ENST00000404352 human ensembl 54_36p -1 known 3_prime_flanking_region c.*15321 NULL 0.03 - - - no_coding_region:pseudogene tier3 385 0 0 245 180 42.35 0 0 NA 179223 TCGA-AB-2972 AML20 2 52169839 52169839 T A SNP ZNF863P ENST00000407098 human ensembl 54_36p 1 known 3_prime_flanking_region c.*12000 NULL 0 - - - no_coding_region:pseudogene tier3 436 1 0.23 246 169 40.72 0 0 NA 179223 TCGA-AB-2972 AML20 2 52769301 52769301 A T SNP - - - - - - - - - - - - - - - tier3 694 2 0.29 668 171 20.38 0 0 NA 179223 TCGA-AB-2972 AML20 2 53625988 53625988 G A SNP ASB3 ENST00000406053 human ensembl 54_36p -1 known intronic c.1323-11462 e10-11462 0 - - - no_errors tier3 708 1 0.14 370 287 43.48 0 0 NA 179223 TCGA-AB-2972 AML20 2 54138255 54138255 G A SNP ENSG00000218522 ENST00000402786 human ensembl 54_36p -1 known 5_prime_flanking_region c.-26932 NULL 0.052 - - - no_coding_region:pseudogene tier3 478 1 0.21 386 71 15.54 3 0 0 179223 TCGA-AB-2972 AML20 2 57132787 57132787 A G SNP LOC100133982 XM_001726700.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*30170 NULL 0.003 - - - no_start_codon:pseudogene:no_stop_codon tier3 1010 6 0.59 499 346 40.95 0 0 NA 179223 TCGA-AB-2972 AML20 2 58359076 58359076 C T SNP FANCL NM_018062.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37124 NULL 0 - - - no_errors tier3 1076 3 0.28 517 395 43.31 0 0 NA 179223 TCGA-AB-2972 AML20 2 61686717 61686717 T C SNP LOC100132037 XM_001725387.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16415 NULL 0.003 - - - pseudogene tier3 1034 5 0.48 464 354 43.28 0 0 NA 179223 TCGA-AB-2972 AML20 2 63018512 63018512 T C SNP EHBP1 NM_015252.1 human genbank 54_36p 1 validated intronic c.1291-4845 e11-4845 0 - - - no_errors tier3 529 0 0 401 291 41.99 5 0 0 179223 TCGA-AB-2972 AML20 2 74839498 74839498 C T SNP - - - - - - - - - - - - - - - tier3 854 1 0.12 337 255 42.93 0 0 NA 179223 TCGA-AB-2972 AML20 2 75550630 75550630 T C SNP FAM176A NM_032181.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*23240 NULL 0 - - - no_errors tier3 864 0 0 461 362 43.99 0 0 NA 179223 TCGA-AB-2972 AML20 2 79327458 79327458 A T SNP CTNNA2 ENST00000409536 human ensembl 54_36p 1 known intronic c.1+48748 e0+48748 0 - - - no_errors tier3 1411 2 0.14 962 343 26.28 0 0 NA 179223 TCGA-AB-2972 AML20 2 79898653 79898653 T - DEL CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.299-39994 e3-39994 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 2 81765416 81765416 T C SNP - - - - - - - - - - - - - - - tier3 488 3 0.61 272 178 39.38 0 0 NA 179223 TCGA-AB-2972 AML20 2 82298974 82298974 C A SNP - - - - - - - - - - - - - - - tier3 941 0 0 528 411 43.72 0 0 NA 179223 TCGA-AB-2972 AML20 2 83639983 83639983 A G SNP - - - - - - - - - - - - - - - tier3 898 3 0.33 483 388 44.55 0 0 NA 179223 TCGA-AB-2972 AML20 2 96164876 96164876 G A SNP ASTL NM_001002036.3 human genbank 54_36p -1 validated missense c.184 p.L62F 0.996 NULL "HMMPfam_Astacin,HMMSmart_SM00235,superfamily_Metalloproteases (""zincins"") catalytic domain" - no_errors tier1 664 1 0.15 126 75 36.95 1 4 80 179223 TCGA-AB-2972 AML20 2 100036202 100036202 G A SNP AFF3 NM_001025108.1 human genbank 54_36p -1 reviewed intronic c.54-41737 e2-41737 0.616 - - - no_errors tier3 921 8 0.86 497 346 41.04 1 2 66.67 179223 TCGA-AB-2972 AML20 2 100434424 100434424 C T SNP CHST10 NM_004854.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44855 NULL 0 - - - no_errors tier3 711 3 0.42 310 262 45.8 0 0 NA 179223 TCGA-AB-2972 AML20 2 105640054 105640054 T C SNP - - - - - - - - - - - - - - - tier3 939 1 0.11 423 330 43.82 0 0 NA 179223 TCGA-AB-2972 AML20 2 120404660 120404660 A G SNP PTPN4 NM_002830.2 human genbank 54_36p 1 reviewed intronic c.1071-1810 e13-1810 0.001 - - - no_errors tier3 819 0 0 504 361 41.69 1 2 66.67 179223 TCGA-AB-2972 AML20 2 123543259 123543259 T C SNP - - - - - - - - - - - - - - - tier3 956 3 0.31 551 378 40.69 0 0 NA 179223 TCGA-AB-2972 AML20 2 128184386 128184386 T C SNP WDR33 NM_018383.1 human genbank 54_36p -1 reviewed intronic c.3309-486 e18-486 0.015 - - - no_errors tier3 1001 3 0.3 363 263 41.95 2 1 33.33 179223 TCGA-AB-2972 AML20 2 130085924 130085924 C T SNP - - - - - - - - - - - - - - - tier3 1307 7 0.53 441 301 40.4 0 0 NA 179223 TCGA-AB-2972 AML20 2 130370642 130370642 C T SNP ENSG00000214100 ENST00000397540 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*26331 NULL 0.001 - - - no_errors tier3 447 1 0.22 120 100 45.45 0 0 NA 179223 TCGA-AB-2972 AML20 2 132329662 132329662 C G SNP LOC100129663 XM_001724181.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-33514 NULL 0.001 - - - no_errors tier3 626 0 0 201 199 49.75 0 0 NA 179223 TCGA-AB-2972 AML20 2 136930644 136930644 T A SNP - - - - - - - - - - - - - - - tier3 790 0 0 427 284 39.78 0 0 NA 179223 TCGA-AB-2972 AML20 2 139172391 139172391 A G SNP NXPH2 NM_007226.2 human genbank 54_36p -1 validated intronic c.52-26686 e2-26686 0.047 - - - no_errors tier3 371 0 0 354 123 25.79 0 0 NA 179223 TCGA-AB-2972 AML20 2 139767315 139767315 G A SNP - - - - - - - - - - - - - - - tier3 1048 1 0.1 465 370 44.31 0 0 NA 179223 TCGA-AB-2972 AML20 2 141911074 141911074 T A SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.343+43361 e3+43361 1 - - - no_errors tier3 877 4 0.45 518 386 42.7 0 0 NA 179223 TCGA-AB-2972 AML20 2 144134261 144134261 G C SNP ARHGAP15 NM_018460.3 human genbank 54_36p 1 validated intronic c.1138+35955 e11+35955 0 - - - no_errors tier3 1054 3 0.28 444 323 42.11 11 3 21.43 179223 TCGA-AB-2972 AML20 2 146771512 146771512 A G SNP LOC100129653 XM_001717973.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*30082 NULL 0 - - - no_errors tier3 623 1 0.16 395 261 39.79 0 0 NA 179223 TCGA-AB-2972 AML20 2 148760368 148760368 T C SNP MBD5 ENST00000407073 human ensembl 54_36p 1 known intronic c.1+52934 e0+52934 0.043 - - - no_errors tier3 381 4 1.04 214 180 45.69 3 2 40 179223 TCGA-AB-2972 AML20 2 151291012 151291012 C A SNP - - - - - - - - - - - - - - - tier3 1514 2 0.13 587 422 41.78 0 0 NA 179223 TCGA-AB-2972 AML20 2 151967294 151967294 G T SNP RIF1 NM_018151.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7890 NULL 0.254 - - - no_errors tier3 466 0 0 152 125 45.13 0 0 NA 179223 TCGA-AB-2972 AML20 2 152774356 152774356 G A SNP STAM2 NM_005843.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33954 NULL 0.015 - - - no_errors tier3 1555 3 0.19 775 270 25.84 0 0 NA 179223 TCGA-AB-2972 AML20 2 152811261 152811261 G A SNP ENSG00000199884 ENST00000363014 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*37849 NULL 0.003 - - - no_errors tier3 872 4 0.46 437 296 40.38 0 0 NA 179223 TCGA-AB-2972 AML20 2 155577629 155577629 G T SNP - - - - - - - - - - - - - - - tier3 179 1 0.56 75 58 43.28 0 0 NA 179223 TCGA-AB-2972 AML20 2 157631755 157631755 G A SNP - - - - - - - - - - - - - - - tier3 1613 2 0.12 797 584 42.23 0 0 NA 179223 TCGA-AB-2972 AML20 2 160492518 160492518 G A SNP LY75 NM_002349.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23079 NULL 0.005 - - - no_errors tier3 1545 3 0.19 482 367 43.23 0 0 NA 179223 TCGA-AB-2972 AML20 2 165413092 165413092 G C SNP COBLL1 NM_014900.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-7140 NULL 0 - - - no_errors tier3 572 3 0.52 229 182 44.28 0 0 NA 179223 TCGA-AB-2972 AML20 2 167134394 167134394 T C SNP - - - - - - - - - - - - - - - tier3 828 1 0.12 424 322 43.05 0 0 NA 179223 TCGA-AB-2972 AML20 2 168119535 168119535 A G SNP LOC643496 XR_041928.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.15 - - - no_errors tier3 583 0 0 226 184 44.88 0 0 NA 179223 TCGA-AB-2972 AML20 2 168983992 168983992 G T SNP LASS6 NM_203463.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37213 NULL 0 - - - no_errors tier3 541 3 0.55 371 121 24.54 0 0 NA 179223 TCGA-AB-2972 AML20 2 171238492 171238492 C T SNP ENSG00000213981 ENST00000397142 human ensembl 54_36p -1 known intronic c.372-5248 e4-5248 0.056 - - - no_stop_codon tier3 546 2 0.36 147 98 39.84 0 0 NA 179223 TCGA-AB-2972 AML20 2 172186344 172186344 G C SNP - - - - - - - - - - - - - - - tier3 816 0 0 490 347 41.31 0 0 NA 179223 TCGA-AB-2972 AML20 2 182500398 182500398 G A SNP SSFA2 NM_006751.1 human genbank 54_36p 1 validated intronic c.3676-2135 e17-2135 0.601 - - - no_errors tier3 794 2 0.25 409 283 40.84 0 3 100 179223 TCGA-AB-2972 AML20 2 188020469 188020470 - A INS CALCRL NM_005795.4 human genbank 54_36p -1 validated intronic c.1+541_540 e0+541 0.004:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 2 189058269 189058269 T C SNP GULP1 NM_016315.2 human genbank 54_36p 1 validated intronic c.90+1805 e2+1805 0.001 - - - no_errors tier3 485 3 0.61 416 358 46.25 0 0 NA 179223 TCGA-AB-2972 AML20 2 189239862 189239862 G T SNP - - - - - - - - - - - - - - - tier3 548 3 0.54 263 203 43.56 0 0 NA 179223 TCGA-AB-2972 AML20 2 192098207 192098207 C T SNP - - - - - - - - - - - - - - - tier3 1170 4 0.34 500 325 39.35 0 0 NA 179223 TCGA-AB-2972 AML20 2 193321215 193321215 G T SNP PCGEM1 NR_002769.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1601 NULL 0.004 - - - no_errors tier3 631 0 0 285 253 47.03 0 0 NA 179223 TCGA-AB-2972 AML20 2 194200259 194200259 A G SNP - - - - - - - - - - - - - - - tier3 815 3 0.37 494 392 44.19 0 0 NA 179223 TCGA-AB-2972 AML20 2 198963174 198963174 G T SNP - - - - - - - - - - - - - - - tier3 832 8 0.95 391 257 39.66 0 0 NA 179223 TCGA-AB-2972 AML20 2 202884658 202884658 T C SNP ENSG00000223083 ENST00000411151 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21749 NULL 0.001 - - - no_errors tier3 1057 1 0.09 429 319 42.48 0 6 100 179223 TCGA-AB-2972 AML20 2 215305783 215305783 G T SNP BARD1 NM_000465.2 human genbank 54_36p -1 reviewed intronic c.1904-2306 e10-2306 0.002 - - - no_errors tier3 735 3 0.41 553 391 41.33 0 0 0 179223 TCGA-AB-2972 AML20 2 215747650 215747650 C G SNP ABCA12 NM_173076.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-36474 NULL 0 - - - no_errors tier3 900 0 0 282 254 47.21 0 0 NA 179223 TCGA-AB-2972 AML20 2 219843817 219843817 C T SNP TUBA4B ENST00000295766 human ensembl 54_36p 1 known intronic c.193-315 e4-315 0 - - - no_errors tier3 530 3 0.56 107 101 48.33 0 0 NA 179223 TCGA-AB-2972 AML20 2 223840057 223840057 A G SNP ENSG00000222485 ENST00000410553 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18301 NULL 0 - - - no_errors tier3 881 6 0.68 418 308 42.25 0 0 NA 179223 TCGA-AB-2972 AML20 2 224127556 224127556 T C SNP SCG2 NM_003469.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*42835 NULL 0 - - - no_errors tier3 921 0 0 394 330 45.39 0 0 NA 179223 TCGA-AB-2972 AML20 2 226206009 226206009 G T SNP KIAA1486 NM_020864.1 human genbank 54_36p 1 validated intronic c.1828+5923 e4+5923 0.006 - - - no_errors tier3 678 8 1.17 343 280 44.94 0 0 NA 179223 TCGA-AB-2972 AML20 2 229711355 229711355 G - DEL PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.270+17423 e2+17423 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 2 231365861 231365861 T C SNP CAB39 NM_016289.1 human genbank 54_36p 1 validated intronic c.280-311 e3-311 0 - - - no_errors tier3 854 2 0.23 419 296 41.23 1 4 80 179223 TCGA-AB-2972 AML20 2 234384568 234384568 G T SNP LOC339766 XM_291007.1 human genbank 54_36p 1 model intronic c.2670+267 e23+267 0.005 - - - no_errors tier3 327 1 0.3 122 92 42.99 0 0 NA 179223 TCGA-AB-2972 AML20 2 238746408 238746408 C T SNP ILKAP NM_030768.2 human genbank 54_36p -1 reviewed intronic c.956+506 e10+506 0 - - - no_errors tier3 513 2 0.39 124 88 41.51 3 2 40 179223 TCGA-AB-2972 AML20 2 241045148 241045148 T A SNP GPC1 NM_002081.2 human genbank 54_36p 1 reviewed intronic c.167-1972 e2-1972 0.001 - - - no_errors tier3 78 1 1.22 33 20 34.48 0 0 0 179223 TCGA-AB-2972 AML20 3 14390883 14390883 G A SNP SLC6A6 NM_003043.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-69264 NULL 0 - - - no_errors tier3 235 0 0 56 51 47.66 0 0 NA 179223 TCGA-AB-2972 AML20 3 17858550 17858550 A T SNP ENSG00000213890 ENST00000396744 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*29679 NULL 0.001 - - - no_coding_region:pseudogene tier3 1529 11 0.71 538 401 42.52 0 0 NA 179223 TCGA-AB-2972 AML20 3 19186229 19186229 T C SNP KCNH8 NM_144633.2 human genbank 54_36p 1 reviewed intronic c.76+20938 e1+20938 0.096 - - - no_errors tier3 742 0 0 300 261 46.52 0 0 NA 179223 TCGA-AB-2972 AML20 3 19535023 19535023 G C SNP KCNH8 NM_144633.2 human genbank 54_36p 1 reviewed intronic c.2619+453 e15+453 0 - - - no_errors tier3 792 6 0.75 428 317 42.44 0 0 NA 179223 TCGA-AB-2972 AML20 3 21310539 21310539 C A SNP - - - - - - - - - - - - - - - tier3 950 2 0.21 412 314 43.19 0 0 NA 179223 TCGA-AB-2972 AML20 3 21380169 21380169 G T SNP VENTXP7 NR_002311.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-42053 NULL 0.001 - - - pseudogene tier3 1104 2 0.18 387 302 43.83 0 0 NA 179223 TCGA-AB-2972 AML20 3 22039917 22039917 C T SNP - - - - - - - - - - - - - - - tier3 701 1 0.14 561 106 15.84 0 0 NA 179223 TCGA-AB-2972 AML20 3 24719702 24719702 A G SNP - - - - - - - - - - - - - - - tier3 694 1 0.14 355 292 45.13 0 0 NA 179223 TCGA-AB-2972 AML20 3 24752271 24752271 G T SNP - - - - - - - - - - - - - - - tier3 375 6 1.57 199 154 43.63 0 0 NA 179223 TCGA-AB-2972 AML20 3 27823044 27823044 G A SNP - - - - - - - - - - - - - - - tier3 856 3 0.35 517 404 43.82 0 0 NA 179223 TCGA-AB-2972 AML20 3 28798652 28798652 G T SNP - - - - - - - - - - - - - - - tier3 794 1 0.13 505 179 26.17 0 0 NA 179223 TCGA-AB-2972 AML20 3 29534759 29534759 C T SNP RBMS3 NM_001003793.1 human genbank 54_36p 1 reviewed intronic c.307+29765 e3+29765 0.001 - - - no_errors tier3 1273 3 0.23 564 431 43.23 0 0 NA 179223 TCGA-AB-2972 AML20 3 30811073 30811073 G A SNP GADL1 NM_207359.2 human genbank 54_36p -1 validated intronic c.698+6312 e7+6312 0.017 - - - no_errors tier3 740 0 0 435 301 40.84 0 0 NA 179223 TCGA-AB-2972 AML20 3 35151914 35151914 T C SNP - - - - - - - - - - - - - - - tier3 370 2 0.54 215 193 47.3 0 0 NA 179223 TCGA-AB-2972 AML20 3 37557519 37557519 C T SNP ITGA9 NM_002207.2 human genbank 54_36p 1 reviewed intronic c.1529-1401 e15-1401 0 - - - no_errors tier3 903 1 0.11 330 276 45.39 0 0 NA 179223 TCGA-AB-2972 AML20 3 38704591 38704591 A G SNP SCN5A NM_001099404.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-54789 NULL 0.001 - - - no_errors tier3 1729 12 0.69 757 590 43.77 0 0 NA 179223 TCGA-AB-2972 AML20 3 38772790 38772790 G A SNP SCN10A NM_006514.2 human genbank 54_36p -1 validated intronic c.1291-337 e10-337 0 - - - no_errors tier3 759 3 0.39 277 226 44.84 0 0 NA 179223 TCGA-AB-2972 AML20 3 43270312 43270312 C T SNP SNRK NM_001100594.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49388 NULL 0.019 - - - no_errors tier3 1505 0 0 672 130 16.15 0 0 NA 179223 TCGA-AB-2972 AML20 3 43615497 43615497 G A SNP ANO10 NM_018075.3 human genbank 54_36p -1 validated intronic c.338-335 e3-335 0.007 - - - no_errors tier3 730 0 0 423 290 40.62 0 0 0 179223 TCGA-AB-2972 AML20 3 51103698 51103698 G A SNP DOCK3 NM_004947.3 human genbank 54_36p 1 validated intronic c.746+843 e12+843 0.004 - - - no_errors tier3 1091 3 0.27 593 435 42.32 0 0 NA 179223 TCGA-AB-2972 AML20 3 52154828 52154828 C T SNP WDR51A NM_015426.3 human genbank 54_36p -1 provisional intronic c.679+74 e6+74 0.004 - - - no_errors tier3 368 0 0 95 85 47.22 2 0 0 179223 TCGA-AB-2972 AML20 3 52623935 52623935 C T SNP PBRM1 NM_018165.4 human genbank 54_36p -1 validated intronic c.1828+472 e14+472 0 - - - no_errors tier3 893 3 0.33 465 301 39.19 0 0 0 179223 TCGA-AB-2972 AML20 3 53945554 53945554 G A SNP uc003dhe.1 ENST00000231908 human ensembl 54_36p -1 known 5_prime_flanking_region c.-44699 NULL 0.002 - - - no_errors tier3 694 3 0.43 353 264 42.79 0 0 NA 179223 TCGA-AB-2972 AML20 3 54795210 54795210 G C SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.1380+21792 e13+21792 0 - - - no_errors tier3 1134 4 0.35 589 422 41.66 0 0 NA 179223 TCGA-AB-2972 AML20 3 59656948 59656948 T G SNP LOC339902 XR_041475.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37685 NULL 0 - - - no_errors tier3 1243 2 0.16 709 268 27.4 0 0 NA 179223 TCGA-AB-2972 AML20 3 63448376 63448376 C T SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated intronic c.149+6704 e2+6704 0.003 - - - no_errors tier3 406 1 0.25 367 232 38.67 0 0 NA 179223 TCGA-AB-2972 AML20 3 64630622 64630622 T C SNP ADAMTS9 NM_182920.1 human genbank 54_36p -1 reviewed intronic c.680-11115 e4-11115 0.001 - - - no_errors tier3 542 0 0 218 203 48.22 0 0 NA 179223 TCGA-AB-2972 AML20 3 64932028 64932028 C T SNP - - - - - - - - - - - - - - - tier3 535 1 0.19 361 280 43.61 0 0 NA 179223 TCGA-AB-2972 AML20 3 67981572 67981572 T C SNP ENSG00000210957 ENST00000388222 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13922 NULL 0.002 - - - pseudogene tier3 1007 3 0.3 355 319 47.19 0 0 NA 179223 TCGA-AB-2972 AML20 3 68340392 68340392 G A SNP FAM19A1 NM_213609.2 human genbank 54_36p 1 reviewed intronic c.118+201815 e1+201815 0.032 - - - no_errors tier3 906 0 0 428 354 45.15 0 0 NA 179223 TCGA-AB-2972 AML20 3 69750051 69750051 T G SNP - - - - - - - - - - - - - - - tier3 608 3 0.49 485 145 22.94 0 0 NA 179223 TCGA-AB-2972 AML20 3 70324477 70324477 G A SNP LOC100128160 XM_001714107.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*4290 NULL 0 - - - no_errors tier3 1234 5 0.4 725 506 41.1 0 0 NA 179223 TCGA-AB-2972 AML20 3 72003950 72003950 A G SNP ENSG00000222241 ENST00000410309 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44646 NULL 0 - - - no_errors tier3 359 2 0.55 234 178 43.1 0 0 NA 179223 TCGA-AB-2972 AML20 3 74297211 74297211 C T SNP ENSG00000212585 ENST00000391283 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-682 NULL 0.268 - - - no_errors tier3 842 3 0.36 391 296 42.96 0 0 NA 179223 TCGA-AB-2972 AML20 3 76897825 76897825 C T SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-332030 e2-332030 0 - - - no_stop_codon:overly_large_intron tier3 520 0 0 559 103 15.56 0 0 NA 179223 TCGA-AB-2972 AML20 3 77193538 77193538 G A SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.61+20851 e1+20851 0 - - - no_errors tier3 900 3 0.33 352 250 41.53 0 0 NA 179223 TCGA-AB-2972 AML20 3 78565594 78565594 T C SNP - - - - - - - - - - - - - - - tier3 582 2 0.34 503 122 19.49 0 0 NA 179223 TCGA-AB-2972 AML20 3 79654038 79654038 C T SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.88+67626 e1+67626 0 - - - no_errors tier3 541 2 0.37 255 180 41.38 0 0 NA 179223 TCGA-AB-2972 AML20 3 80583748 80583748 C T SNP - - - - - - - - - - - - - - - tier3 241 0 0 235 138 37 0 0 NA 179223 TCGA-AB-2972 AML20 3 84578632 84578632 G T SNP - - - - - - - - - - - - - - - tier3 545 1 0.18 460 72 13.53 0 0 NA 179223 TCGA-AB-2972 AML20 3 85387144 85387144 C - DEL CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+295635 e1+295635 0.096 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 3 85893124 85893124 G A SNP CADM2 NM_153184.2 human genbank 54_36p 1 validated intronic c.67+34736 e1+34736 0 - - - no_errors tier3 888 2 0.22 540 405 42.81 0 0 NA 179223 TCGA-AB-2972 AML20 3 86206404 86206404 C T SNP CADM2 NM_153184.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*7781 NULL 0 - - - no_errors tier3 450 0 0 269 181 40.22 0 0 NA 179223 TCGA-AB-2972 AML20 3 89640196 89640196 T C SNP EPHA3 NM_005233.5 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*28854 NULL 0 - - - no_errors tier3 206 0 0 143 145 50.35 0 0 NA 179223 TCGA-AB-2972 AML20 3 96621711 96621711 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 3 96993463 96993463 A G SNP - - - - - - - - - - - - - - - tier3 232 2 0.85 130 98 42.98 0 0 NA 179223 TCGA-AB-2972 AML20 3 97013718 97013718 C A SNP - - - - - - - - - - - - - - - tier3 412 0 0 218 118 35.12 0 0 NA 179223 TCGA-AB-2972 AML20 3 98734125 98734125 T - DEL EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.2386+48 e11+48 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 3 102274336 102274336 G A SNP - - - - - - - - - - - - - - - tier3 412 1 0.24 276 208 42.98 0 0 NA 179223 TCGA-AB-2972 AML20 3 107089818 107089818 T C SNP CBLB NM_170662.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20707 NULL 0.068 - - - no_errors tier3 393 1 0.25 220 191 46.36 0 0 NA 179223 TCGA-AB-2972 AML20 3 107222764 107222764 G C SNP - - - - - - - - - - - - - - - tier3 1217 1 0.08 580 451 43.74 0 0 NA 179223 TCGA-AB-2972 AML20 3 110077005 110077005 G A SNP GUCA1C NM_005459.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*32554 NULL 0.059 - - - no_errors tier3 960 2 0.21 354 271 43.36 0 0 NA 179223 TCGA-AB-2972 AML20 3 113412600 113412600 T C SNP SLC9A10 NM_183061.1 human genbank 54_36p -1 validated intronic c.1791-2690 e15-2690 0 - - - no_errors tier3 247 0 0 161 122 43.11 0 0 NA 179223 TCGA-AB-2972 AML20 3 116227538 116227538 T C SNP ZBTB20 NM_015642.3 human genbank 54_36p -1 provisional intronic c.1-51585 e1-51585 0.001 - - - no_errors tier3 753 2 0.26 381 258 40.31 0 0 0 179223 TCGA-AB-2972 AML20 3 118377174 118377174 G A SNP - - - - - - - - - - - - - - - tier3 856 0 0 417 174 29.44 0 0 NA 179223 TCGA-AB-2972 AML20 3 125731756 125731756 A G SNP KALRN NM_001024660.2 human genbank 54_36p 1 reviewed intronic c.4930-32624 e34-32624 0.002 - - - no_errors tier3 1520 1 0.07 653 482 42.47 0 0 NA 179223 TCGA-AB-2972 AML20 3 126068564 126068564 G T SNP ITGB5 NM_002213.3 human genbank 54_36p -1 provisional intronic c.156+6419 e2+6419 0.077 - - - no_errors tier3 1483 6 0.4 390 260 40 0 0 NA 179223 TCGA-AB-2972 AML20 3 132968472 132968472 T A SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.181-43313 e2-43313 0 - - - no_errors tier3 1193 5 0.42 602 463 43.43 0 0 NA 179223 TCGA-AB-2972 AML20 3 133454342 133454342 A G SNP LOC729677 XR_015625.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-8535 NULL 0.004 - - - pseudogene tier3 823 1 0.12 368 253 40.74 0 0 NA 179223 TCGA-AB-2972 AML20 3 135808551 135808551 A G SNP KY ENST00000383222 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*1385 NULL 0.001 - - - no_errors tier3 210 1 0.47 79 74 48.37 0 0 NA 179223 TCGA-AB-2972 AML20 3 141323057 141323057 G A SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.110-54426 e2-54426 0.001 - - - no_errors tier3 431 0 0 163 121 42.61 0 0 NA 179223 TCGA-AB-2972 AML20 3 145342463 145342463 C T SNP ENSG00000222778 ENST00000410846 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*45974 NULL 0.005 - - - no_errors tier3 1672 4 0.24 1129 211 15.72 2 0 0 179223 TCGA-AB-2972 AML20 3 145546923 145546923 G A SNP - - - - - - - - - - - - - - - tier3 666 1 0.15 403 269 39.97 0 0 NA 179223 TCGA-AB-2972 AML20 3 146324347 146324347 T C SNP - - - - - - - - - - - - - - - tier3 417 0 0 318 103 24.41 0 0 NA 179223 TCGA-AB-2972 AML20 3 148081374 148081374 G A SNP - - - - - - - - - - - - - - - tier3 1039 5 0.48 465 419 47.29 0 0 NA 179223 TCGA-AB-2972 AML20 3 154697976 154697976 A C SNP LOC152118 NM_001101337.1 human genbank 54_36p 1 inferred intronic c.224-4906 e3-4906 0.001 - - - no_errors tier3 1018 1 0.1 420 388 48.02 1 0 0 179223 TCGA-AB-2972 AML20 3 160505595 160505595 C T SNP SCHIP1 NM_014575.2 human genbank 54_36p 1 provisional intronic c.63+31229 e1+31229 0 - - - no_errors tier3 1248 2 0.16 495 375 43.05 0 0 NA 179223 TCGA-AB-2972 AML20 3 161266787 161266787 T C SNP BRD7P2 XR_017374.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-34545 NULL 0 - - - pseudogene tier3 244 1 0.41 148 99 39.76 0 0 NA 179223 TCGA-AB-2972 AML20 3 164713872 164713872 A G SNP ENSG00000221205 ENST00000408278 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*3012 NULL 0 - - - no_errors tier3 590 1 0.17 132 103 43.83 0 0 NA 179223 TCGA-AB-2972 AML20 3 164727320 164727320 C A SNP ENSG00000221205 ENST00000408278 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-10351 NULL 0 - - - no_errors tier3 982 6 0.61 261 198 43.14 0 0 NA 179223 TCGA-AB-2972 AML20 3 166411970 166411970 T A SNP SLITRK3 NM_014926.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20658 NULL 0.003 - - - no_errors tier3 708 0 0 338 257 43.19 0 0 NA 179223 TCGA-AB-2972 AML20 3 181691913 181691913 C T SNP - - - - - - - - - - - - - - - tier3 1176 5 0.42 649 452 40.94 0 0 NA 179223 TCGA-AB-2972 AML20 3 190995023 190995023 G A SNP TP63 NM_003722.1 human genbank 54_36p 1 reviewed intronic c.325-13732 e4-13732 0.001 - - - no_errors tier3 991 3 0.3 472 376 44.34 0 0 NA 179223 TCGA-AB-2972 AML20 3 191805225 191805225 G C SNP IL1RAP NM_002182.2 human genbank 54_36p 1 reviewed intronic c.350+329 e2+329 0.005 - - - no_errors tier3 1124 0 0 433 326 42.89 0 0 0 179223 TCGA-AB-2972 AML20 4 6837447 6837447 T A SNP KIAA0232 NM_001100590.1 human genbank 54_36p 1 validated intronic c.1+1978 e0+1978 0.004 - - - no_errors tier3 613 0 0 303 53 14.89 5 0 0 179223 TCGA-AB-2972 AML20 4 8697865 8697865 G A SNP LOC100133683 XM_001715679.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-26017 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 195 1 0.51 110 95 45.89 0 0 NA 179223 TCGA-AB-2972 AML20 4 9996753 9996753 A G SNP - - - - - - - - - - - - - - - tier3 708 0 0 336 275 44.93 0 0 NA 179223 TCGA-AB-2972 AML20 4 15123914 15123914 G A SNP CC2D2A NM_001080522.2 human genbank 54_36p 1 validated intronic c.718-1514 e8-1514 0.003 - - - no_errors tier3 1954 4 0.2 807 586 42.04 0 3 100 179223 TCGA-AB-2972 AML20 4 20418927 20418927 C T SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.225+42337 e2+42337 0 - - - no_errors tier3 1365 2 0.15 541 391 41.91 0 0 NA 179223 TCGA-AB-2972 AML20 4 20778674 20778674 T G SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.100+135854 e1+135854 0.002 - - - no_errors tier3 802 5 0.62 471 349 42.56 0 0 NA 179223 TCGA-AB-2972 AML20 4 20901261 20901261 C G SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.100+13267 e1+13267 0 - - - no_errors tier3 1062 1 0.09 646 223 25.63 0 0 NA 179223 TCGA-AB-2972 AML20 4 21792646 21792646 G A SNP - - - - - - - - - - - - - - - tier3 1001 4 0.4 386 325 45.65 0 0 NA 179223 TCGA-AB-2972 AML20 4 23378573 23378573 T C SNP PPARGC1A NM_013261.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*27970 NULL 0.188 - - - no_errors tier3 839 3 0.36 330 263 44.35 0 0 NA 179223 TCGA-AB-2972 AML20 4 27280822 27280822 G A SNP ENSG00000221807 ENST00000408880 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35732 NULL 0 - - - no_errors tier3 728 2 0.27 285 239 45.61 0 0 NA 179223 TCGA-AB-2972 AML20 4 29138284 29138284 G A SNP ENSG00000209052 ENST00000386317 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*16827 NULL 0.965 - - - pseudogene tier3 270 0 0 214 75 25.95 0 0 NA 179223 TCGA-AB-2972 AML20 4 30549781 30549781 A G SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3226+18716 e3+18716 0 - - - no_errors tier3 539 0 0 289 208 41.85 0 0 NA 179223 TCGA-AB-2972 AML20 4 32155217 32155217 G A SNP - - - - - - - - - - - - - - - tier3 994 7 0.7 459 339 42.43 0 0 NA 179223 TCGA-AB-2972 AML20 4 34806202 34806202 A C SNP - - - - - - - - - - - - - - - tier3 863 1 0.12 393 341 46.46 0 0 NA 179223 TCGA-AB-2972 AML20 4 36633809 36633809 G T SNP - - - - - - - - - - - - - - - tier3 837 4 0.48 497 388 43.84 0 0 NA 179223 TCGA-AB-2972 AML20 4 46915638 46915638 T C SNP GABRB1 NM_000812.3 human genbank 54_36p 1 reviewed intronic c.461+57395 e4+57395 0.011 - - - no_errors tier3 1456 1 0.07 1035 418 28.77 0 0 NA 179223 TCGA-AB-2972 AML20 4 47782016 47782016 G C SNP TXK NM_003328.2 human genbank 54_36p -1 validated intronic c.956+1224 e10+1224 0.063 - - - no_errors tier3 732 1 0.14 271 241 46.98 11 1 8.33 179223 TCGA-AB-2972 AML20 4 59967022 59967022 C A SNP - - - - - - - - - - - - - - - tier3 299 0 0 179 106 37.19 0 0 NA 179223 TCGA-AB-2972 AML20 4 61950180 61950180 T C SNP ENSG00000205682 ENST00000381217 human ensembl 54_36p -1 known 3_prime_flanking_region c.*25502 NULL 0 - - - no_errors tier3 608 0 0 257 227 46.71 0 0 NA 179223 TCGA-AB-2972 AML20 4 64917595 64917595 T A SNP SRD5A2L2 NM_001010874.4 human genbank 54_36p -1 validated intronic c.286+5890 e2+5890 0.002 - - - no_errors tier3 284 1 0.35 220 166 43.01 0 0 NA 179223 TCGA-AB-2972 AML20 4 64986730 64986730 G A SNP SRD5A2L2 NM_001010874.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-29066 NULL 0.01 - - - no_errors tier3 354 0 0 178 120 40.27 0 0 NA 179223 TCGA-AB-2972 AML20 4 65036469 65036469 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 4 65404813 65404813 T G SNP LOC100133173 XM_001714474.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-11767 NULL 0 - - - no_errors tier3 698 0 0 387 336 46.47 0 0 NA 179223 TCGA-AB-2972 AML20 4 69911658 69911658 C - DEL UGT2B11 ENST00000305206 human ensembl 54_36p -1 known intronic c.1590-6601 e7-6601 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 4 70003047 70003047 C - DEL UGT2B7 NM_001074.2 human genbank 54_36p 1 validated intronic c.871-67 e3-67 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 4 71425373 71425373 T C SNP AMTN NM_212557.2 human genbank 54_36p 1 validated intronic c.294+106 e4+106 0 - - - no_errors tier3 870 4 0.46 509 409 44.55 0 0 NA 179223 TCGA-AB-2972 AML20 4 77711524 77711524 C T SNP SHROOM3 NM_020859.3 human genbank 54_36p 1 validated intronic c.320+15584 e2+15584 0.006 - - - no_errors tier3 916 1 0.11 376 277 42.35 0 0 NA 179223 TCGA-AB-2972 AML20 4 80931305 80931305 C T SNP - - - - - - - - - - - - - - - tier3 1178 3 0.25 440 357 44.74 0 0 NA 179223 TCGA-AB-2972 AML20 4 83757184 83757184 G A SNP uc010ijs.1 ENST00000354971 human ensembl 54_36p -1 known intronic c.NULL NULL 0.003 - - - no_coding_region:pseudogene tier3 888 4 0.45 358 277 43.62 0 0 NA 179223 TCGA-AB-2972 AML20 4 92903874 92903874 C A SNP - - - - - - - - - - - - - - - tier3 556 4 0.71 281 224 44.27 0 0 NA 179223 TCGA-AB-2972 AML20 4 97326410 97326410 T A SNP ENSG00000201744 ENST00000364874 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33833 NULL 0 - - - no_errors tier3 416 1 0.24 232 159 40.66 0 0 NA 179223 TCGA-AB-2972 AML20 4 100053980 100053980 G C SNP EIF4E NM_001968.1 human genbank 54_36p -1 validated intronic c.19-11824 e2-11824 0.018 - - - no_errors tier3 238 1 0.42 117 94 44.55 1 1 50 179223 TCGA-AB-2972 AML20 4 112718753 112718753 A G SNP - - - - - - - - - - - - - - - tier3 797 2 0.25 568 463 44.86 0 0 NA 179223 TCGA-AB-2972 AML20 4 115987515 115987515 G A SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.1941-913 e9-913 0 - - - no_errors tier3 625 5 0.79 274 216 44.08 0 0 NA 179223 TCGA-AB-2972 AML20 4 116545288 116545288 G A SNP - - - - - - - - - - - - - - - tier3 480 0 0 266 193 42.05 0 0 NA 179223 TCGA-AB-2972 AML20 4 120800142 120800142 T C SNP PDE5A NM_001083.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-30868 NULL 0.002 - - - no_errors tier3 574 0 0 243 171 41.2 0 0 NA 179223 TCGA-AB-2972 AML20 4 123834104 123834104 C T SNP BBS12 NM_152618.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-48394 NULL 0.004 - - - no_errors tier3 804 1 0.12 335 241 41.77 0 0 NA 179223 TCGA-AB-2972 AML20 4 125137296 125137296 C T SNP - - - - - - - - - - - - - - - tier3 231 1 0.43 185 122 39.74 0 0 NA 179223 TCGA-AB-2972 AML20 4 130306521 130306521 C G SNP - - - - - - - - - - - - - - - tier3 565 0 0 230 191 45.37 0 0 NA 179223 TCGA-AB-2972 AML20 4 136670929 136670929 G A SNP - - - - - - - - - - - - - - - tier3 702 4 0.56 257 207 44.52 0 0 NA 179223 TCGA-AB-2972 AML20 4 137704871 137704871 C G SNP - - - - - - - - - - - - - - - tier3 765 2 0.26 481 355 42.46 0 0 NA 179223 TCGA-AB-2972 AML20 4 138319143 138319143 G A SNP LOC729578 XM_001130691.2 human genbank 54_36p -1 model intronic c.69+34198 e1+34198 0 - - - no_errors tier3 891 3 0.34 587 442 42.95 0 0 NA 179223 TCGA-AB-2972 AML20 4 147362926 147362926 C T SNP LOC345051 XR_040587.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 754 2 0.26 405 300 42.49 0 0 NA 179223 TCGA-AB-2972 AML20 4 147631621 147631621 T C SNP SLC10A7 NM_001029998.3 human genbank 54_36p -1 validated intronic c.396+12830 e4+12830 0.014 - - - no_errors tier3 1002 0 0 578 510 46.88 1 2 66.67 179223 TCGA-AB-2972 AML20 4 160600470 160600470 C T SNP ENSG00000208635 ENST00000385900 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*47521 NULL 0.245 - - - pseudogene tier3 595 1 0.17 306 184 37.55 0 0 NA 179223 TCGA-AB-2972 AML20 4 161224002 161224002 G A SNP - - - - - - - - - - - - - - - tier3 758 5 0.66 350 272 43.66 0 0 NA 179223 TCGA-AB-2972 AML20 4 164133960 164133960 G A SNP - - - - - - - - - - - - - - - tier3 711 3 0.42 307 210 40.54 0 0 NA 179223 TCGA-AB-2972 AML20 4 165340867 165340867 A G SNP ANP32C NM_012403.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2554 NULL 0.053 - - - no_errors tier3 666 0 0 297 220 42.55 0 0 NA 179223 TCGA-AB-2972 AML20 4 173773226 173773226 G A SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.554-193861 e5-193861 0.766 - - - no_errors tier3 1459 4 0.27 854 625 42.2 0 0 NA 179223 TCGA-AB-2972 AML20 4 179480737 179480737 C T SNP - - - - - - - - - - - - - - - tier3 613 5 0.81 410 270 39.65 0 0 NA 179223 TCGA-AB-2972 AML20 4 179508709 179508709 T A SNP - - - - - - - - - - - - - - - tier3 1006 1 0.1 569 427 42.83 0 0 NA 179223 TCGA-AB-2972 AML20 4 183004776 183004776 C A SNP LOC728191 XM_001126817.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-16656 NULL 0 - - - no_errors tier3 445 0 0 299 205 40.67 0 0 NA 179223 TCGA-AB-2972 AML20 4 183761100 183761100 G A SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.749+1792 e3+1792 0 - - - no_errors tier3 348 1 0.29 151 109 41.92 0 0 NA 179223 TCGA-AB-2972 AML20 4 183916515 183916515 G A SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.4892+3109 e21+3109 0 - - - no_errors tier3 1000 4 0.4 405 301 42.57 0 0 NA 179223 TCGA-AB-2972 AML20 4 185002175 185002175 T C SNP - - - - - - - - - - - - - - - tier3 235 1 0.42 83 67 44.67 0 0 NA 179223 TCGA-AB-2972 AML20 4 188462246 188462247 TT - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 4 188824389 188824389 A G SNP ENSG00000203363 ENST00000366187 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14025 NULL 0 - - - no_coding_region:pseudogene tier3 821 3 0.36 247 179 42.02 0 0 NA 179223 TCGA-AB-2972 AML20 4 189263714 189263714 C A SNP TRIML1 NM_178556.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-33993 NULL 0 - - - no_errors tier3 800 3 0.37 216 165 43.31 0 0 NA 179223 TCGA-AB-2972 AML20 4 189392782 189392782 G T SNP - - - - - - - - - - - - - - - tier3 858 1 0.12 227 196 46.34 0 0 NA 179223 TCGA-AB-2972 AML20 5 1603676 1603676 G A SNP LPCAT1 NM_024830.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-26717 NULL 0 - - - no_errors tier3 353 1 0.28 122 79 38.54 0 0 NA 179223 TCGA-AB-2972 AML20 5 2101402 2101402 T A SNP - - - - - - - - - - - - - - - tier3 939 5 0.52 207 157 42.78 0 0 NA 179223 TCGA-AB-2972 AML20 5 2245233 2245233 A T SNP ENSG00000201026 ENST00000364156 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*7299 NULL 0 - - - no_errors tier3 632 4 0.62 194 147 42.61 0 0 NA 179223 TCGA-AB-2972 AML20 5 2515616 2515616 T C SNP - - - - - - - - - - - - - - - tier3 1862 1 0.05 489 345 41.22 0 0 NA 179223 TCGA-AB-2972 AML20 5 7659571 7659571 C T SNP ADCY2 NM_020546.2 human genbank 54_36p 1 reviewed intronic c.571-19709 e4-19709 0 - - - no_errors tier3 638 1 0.16 306 238 43.75 0 0 NA 179223 TCGA-AB-2972 AML20 5 12223458 12223458 G T SNP - - - - - - - - - - - - - - - tier3 844 0 0 491 369 42.91 0 0 NA 179223 TCGA-AB-2972 AML20 5 13947834 13947834 G T SNP DNAH5 NM_001369.2 human genbank 54_36p -1 validated missense c.2356 p.Q786K 1 HMMPfam_DHC_N1 "HMMSmart_AAA,HMMPfam_Dynein_heavy,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin,superfamily_SSF52540" - no_errors tier1 1142 2 0.17 577 467 44.73 NA 179223 TCGA-AB-2972 AML20 5 16074633 16074633 C T SNP MARCH11 NM_001102562.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*45947 NULL 0.001 - - - no_errors tier3 1298 1 0.08 463 350 42.84 0 0 NA 179223 TCGA-AB-2972 AML20 5 22300107 22300107 G T SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-51598 e1-51598 0 - - - no_errors tier3 309 0 0 162 139 46.18 0 0 NA 179223 TCGA-AB-2972 AML20 5 24136017 24136017 C T SNP - - - - - - - - - - - - - - - tier3 309 0 0 229 149 39.31 7 0 0 179223 TCGA-AB-2972 AML20 5 24564479 24564479 C T SNP CDH10 NM_006727.2 human genbank 54_36p -1 reviewed intronic c.814+6499 e4+6499 0 - - - no_errors tier3 1032 2 0.19 445 376 45.8 0 0 0 179223 TCGA-AB-2972 AML20 5 24606924 24606924 G A SNP CDH10 NM_006727.2 human genbank 54_36p -1 reviewed intronic c.231+22202 e1+22202 0 - - - no_errors tier3 494 1 0.2 248 153 38.06 0 0 NA 179223 TCGA-AB-2972 AML20 5 25387040 25387040 G A SNP - - - - - - - - - - - - - - - tier3 223 1 0.45 142 132 48.18 0 0 NA 179223 TCGA-AB-2972 AML20 5 27693712 27693712 G A SNP - - - - - - - - - - - - - - - tier3 180 0 0 132 99 42.86 0 0 NA 179223 TCGA-AB-2972 AML20 5 31445149 31445149 T A SNP RNASEN NM_013235.1 human genbank 54_36p -1 validated missense c.3715 p.T1239S 1 "HMMSmart_SM00535,superfamily_RNase III catalytic domain-like (Pfam 00636)" "HMMPfam_Ribonuclease_3,HMMSmart_SM00535,PatternScan_RNASE_3_1,superfamily_RNase III catalytic domain-like (Pfam 00636),HMMPfam_dsrm,HMMSmart_SM00358,superfamily_dsRNA-binding domain-like" - no_errors tier1 743 1 0.13 308 245 44.22 35 27 43.55 179223 TCGA-AB-2972 AML20 5 40151287 40151287 C T SNP - - - - - - - - - - - - - - - tier3 440 1 0.23 240 184 43.4 0 0 NA 179223 TCGA-AB-2972 AML20 5 41210445 41210445 T C SNP C6 NM_000065.2 human genbank 54_36p -1 reviewed intronic c.1168+1889 e7+1889 0.04 - - - no_errors tier3 818 4 0.49 574 416 42.02 0 0 NA 179223 TCGA-AB-2972 AML20 5 42746153 42746154 - TT INS GHR NM_000163.2 human genbank 54_36p 1 reviewed intronic c.619-913_619-912 e6-912 0.968:0.971 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 5 45678329 45678329 T C SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.849+2715 e2+2715 0.004 - - - no_errors tier3 615 1 0.16 386 314 44.79 0 0 NA 179223 TCGA-AB-2972 AML20 5 51706084 51706084 G T SNP - - - - - - - - - - - - - - - tier3 990 3 0.3 495 390 44.02 0 0 NA 179223 TCGA-AB-2972 AML20 5 53304361 53304361 A T SNP ARL15 NM_019087.2 human genbank 54_36p -1 validated intronic c.463-86061 e5-86061 0.026 - - - no_errors tier3 691 0 0 691 134 16.16 3 0 0 179223 TCGA-AB-2972 AML20 5 56773948 56773948 C T SNP ACTBL2 NM_001017992.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*39213 NULL 0.001 - - - no_errors tier3 895 3 0.33 271 259 48.68 0 0 NA 179223 TCGA-AB-2972 AML20 5 57130375 57130375 T C SNP - - - - - - - - - - - - - - - tier3 657 4 0.6 409 173 29.73 0 0 NA 179223 TCGA-AB-2972 AML20 5 57313290 57313290 A G SNP - - - - - - - - - - - - - - - tier3 1342 2 0.15 656 526 44.5 0 0 NA 179223 TCGA-AB-2972 AML20 5 58876717 58876717 G T SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.456-329166 e2-329166 0.002 - - - no_errors tier3 563 3 0.53 350 235 40.1 0 0 NA 179223 TCGA-AB-2972 AML20 5 61061522 61061522 A G SNP FLJ37543 NM_173667.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*25905 NULL 0.013 - - - no_errors tier3 873 1 0.11 294 211 41.45 0 0 NA 179223 TCGA-AB-2972 AML20 5 62797068 62797068 G A SNP - - - - - - - - - - - - - - - tier3 772 2 0.26 433 303 41.17 0 0 NA 179223 TCGA-AB-2972 AML20 5 84962428 84962428 C G SNP - - - - - - - - - - - - - - - tier3 795 1 0.13 284 224 44.09 0 0 NA 179223 TCGA-AB-2972 AML20 5 87460682 87460682 T G SNP - - - - - - - - - - - - - - - tier3 648 3 0.46 277 198 41.68 0 0 NA 179223 TCGA-AB-2972 AML20 5 88572401 88572401 T G SNP - - - - - - - - - - - - - - - tier3 835 8 0.95 294 210 41.58 0 0 NA 179223 TCGA-AB-2972 AML20 5 88663144 88663144 T C SNP - - - - - - - - - - - - - - - tier3 206 1 0.48 120 87 42.03 0 3 100 179223 TCGA-AB-2972 AML20 5 92378624 92378624 C T SNP LOC391810 XM_001723772.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-47798 NULL 0 - - - pseudogene tier3 720 0 0 356 294 45.16 0 0 NA 179223 TCGA-AB-2972 AML20 5 92614387 92614387 G A SNP LOC391811 XR_016127.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-14356 NULL 0 - - - pseudogene tier3 867 3 0.34 597 410 40.71 0 0 NA 179223 TCGA-AB-2972 AML20 5 99520193 99520193 A T SNP ENSG00000207077 ENST00000384349 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*2811 NULL 0.006 - - - no_errors tier3 400 0 0 226 197 46.57 0 0 0 179223 TCGA-AB-2972 AML20 5 101389515 101389515 A G SNP - - - - - - - - - - - - - - - tier3 874 9 1.02 519 410 44.13 0 0 NA 179223 TCGA-AB-2972 AML20 5 105613367 105613367 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 5 111760509 111760509 T C SNP EPB41L4A NM_022140.3 human genbank 54_36p -1 validated intronic c.99+22028 e1+22028 0 - - - no_errors tier3 1256 5 0.4 591 447 43.06 0 0 NA 179223 TCGA-AB-2972 AML20 5 122661336 122661336 A C SNP CEP120 NM_153223.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*48776 NULL 0 - - - no_errors tier3 556 2 0.36 386 149 27.8 0 0 NA 179223 TCGA-AB-2972 AML20 5 132360516 132360516 G A SNP AFF4 NM_014423.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-59736 NULL 0.067 - - - no_errors tier3 879 1 0.11 270 169 38.5 0 0 NA 179223 TCGA-AB-2972 AML20 5 134614890 134614890 G T SNP - - - - - - - - - - - - - - - tier3 1163 6 0.51 413 327 44.19 0 0 NA 179223 TCGA-AB-2972 AML20 5 135355528 135355528 A T SNP TGFBI NM_000358.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-37116 NULL 0 - - - no_errors tier3 1633 6 0.36 538 471 46.63 0 0 NA 179223 TCGA-AB-2972 AML20 5 136072902 136072902 A G SNP - - - - - - - - - - - - - - - tier3 286 0 0 309 67 17.82 0 0 NA 179223 TCGA-AB-2972 AML20 5 160644863 160644863 T G SNP GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*8803 NULL 0 - - - no_errors tier3 1198 18 1.48 448 351 43.88 0 0 NA 179223 TCGA-AB-2972 AML20 5 160708683 160708683 G A SNP GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed intronic c.542-12329 e6-12329 0.002 - - - no_errors tier3 418 1 0.24 270 218 44.67 0 0 NA 179223 TCGA-AB-2972 AML20 5 160794247 160794247 T A SNP GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed intronic c.459-23606 e5-23606 0.003 - - - no_errors tier3 909 3 0.33 571 426 42.64 0 0 NA 179223 TCGA-AB-2972 AML20 5 162157312 162157312 C T SNP ENSG00000208481 ENST00000385746 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13647 NULL 0.006 - - - pseudogene tier3 1054 5 0.47 474 351 42.49 0 0 NA 179223 TCGA-AB-2972 AML20 5 163457117 163457117 G A SNP - - - - - - - - - - - - - - - tier3 656 1 0.15 335 223 39.96 0 0 NA 179223 TCGA-AB-2972 AML20 5 165071474 165071474 T C SNP - - - - - - - - - - - - - - - tier3 702 2 0.28 396 325 45.01 0 0 NA 179223 TCGA-AB-2972 AML20 5 166412870 166412870 A G SNP - - - - - - - - - - - - - - - tier3 1112 1 0.09 650 419 39.2 0 0 NA 179223 TCGA-AB-2972 AML20 5 169059712 169059712 A G SNP DOCK2 NM_004946.2 human genbank 54_36p 1 validated missense c.1249 p.I417V 1 NULL "HMMSmart_SM00326,superfamily_SH3-domain,superfamily_Cytochrome c,HMMPfam_SH3_2" - no_errors tier1 877 2 0.23 451 304 40.21 50 36 41.86 179223 TCGA-AB-2972 AML20 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 179223 TCGA-AB-2972 AML20 5 171183501 171183501 C A SNP FBXW11 NM_012300.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*44743 NULL 0.817 - - - no_errors tier3 453 2 0.44 249 206 45.27 0 0 NA 179223 TCGA-AB-2972 AML20 5 180112450 180112450 G A SNP OR2Y1 NM_001001657.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-12786 NULL 0 - - - no_errors tier3 990 2 0.2 281 211 42.89 0 0 NA 179223 TCGA-AB-2972 AML20 6 3825729 3825729 G A SNP ENSG00000217135 ENST00000405321 human ensembl 54_36p 1 known 5_prime_flanking_region c.-41386 NULL 0 - - - no_coding_region:pseudogene tier3 784 1 0.13 324 260 44.37 0 0 NA 179223 TCGA-AB-2972 AML20 6 7846565 7846565 C T SNP TXNDC5 NM_030810.1 human genbank 54_36p -1 reviewed intronic c.414-1652 e3-1652 0.001 - - - no_errors tier3 764 2 0.26 355 293 45.15 3 0 0 179223 TCGA-AB-2972 AML20 6 14256859 14256859 T C SNP CD83 NM_004233.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*13413 NULL 0 - - - no_errors tier3 956 5 0.52 501 427 45.96 0 0 NA 179223 TCGA-AB-2972 AML20 6 17014657 17014657 A G SNP - - - - - - - - - - - - - - - tier3 757 1 0.13 395 303 43.41 0 0 NA 179223 TCGA-AB-2972 AML20 6 19120315 19120315 T C SNP - - - - - - - - - - - - - - - tier3 884 1 0.11 330 287 46.37 0 0 NA 179223 TCGA-AB-2972 AML20 6 24626100 24626100 C A SNP ALDH5A1 NM_170740.3 human genbank 54_36p 1 reviewed intronic c.910-2508 e7-2508 0.015 - - - no_errors tier3 531 0 0 177 109 38.11 1 1 50 179223 TCGA-AB-2972 AML20 6 25006498 25006498 A G SNP FAM65B ENST00000259698 human ensembl 54_36p -1 known intronic c.1+12527 e0+12527 0 - - - no_errors tier3 1011 3 0.3 458 301 39.55 0 3 100 179223 TCGA-AB-2972 AML20 6 42905665 42905665 G A SNP KIAA0240 NM_015349.1 human genbank 54_36p 1 validated missense c.1616 p.R539Q 0.988 NULL NULL - no_errors tier1 794 4 0.5 312 243 43.63 19 12 38.71 179223 TCGA-AB-2972 AML20 6 45706438 45706438 A G SNP ENSG00000210937 ENST00000388202 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-15381 NULL 0.006 - - - pseudogene tier3 912 1 0.11 235 168 41.48 0 0 NA 179223 TCGA-AB-2972 AML20 6 47012224 47012224 C T SNP GPR116 NM_015234.1 human genbank 54_36p -1 validated intronic c.1+18206 e0+18206 0 - - - no_errors tier3 969 2 0.21 526 168 24.17 0 0 NA 179223 TCGA-AB-2972 AML20 6 47376829 47376829 G A SNP TNFRSF21 NM_014452.3 human genbank 54_36p -1 reviewed intronic c.96+8282 e1+8282 0.001 - - - no_errors tier3 1279 3 0.23 415 311 42.84 0 0 0 179223 TCGA-AB-2972 AML20 6 48423917 48423917 C T SNP - - - - - - - - - - - - - - - tier3 681 3 0.44 357 238 39.87 0 0 NA 179223 TCGA-AB-2972 AML20 6 49907641 49907641 T C SNP PGK2 NM_138733.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-44782 NULL 0 - - - no_errors tier3 496 0 0 406 158 28.01 0 0 NA 179223 TCGA-AB-2972 AML20 6 63217097 63217097 A T SNP ENSG00000216859 ENST00000406944 human ensembl 54_36p -1 known 3_prime_flanking_region c.*11707 NULL 0.001 - - - no_coding_region:pseudogene tier3 989 4 0.4 493 448 47.61 0 0 NA 179223 TCGA-AB-2972 AML20 6 66603202 66603202 C T SNP RCADH5 XM_001714398.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*342 NULL 0.015 - - - pseudogene tier3 1099 5 0.45 578 401 40.88 0 0 NA 179223 TCGA-AB-2972 AML20 6 68935783 68935783 C T SNP - - - - - - - - - - - - - - - tier3 839 2 0.24 437 369 45.72 0 0 NA 179223 TCGA-AB-2972 AML20 6 72800929 72800929 T C SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated intronic c.246-62444 e3-62444 0 - - - no_errors tier3 599 0 0 355 306 46.29 0 0 NA 179223 TCGA-AB-2972 AML20 6 72863575 72863575 C T SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated missense c.448 p.R150W 1 superfamily_FYVE/PHD zinc finger "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FYVE/PHD zinc finger,PatternScan_GLYCOSYL_HYDROL_F1_1" - no_errors tier1 685 0 522 130 19.85 NA 179223 TCGA-AB-2972 AML20 6 75248714 75248714 G A SNP - - - - - - - - - - - - - - - tier3 1342 4 0.3 350 269 43.46 0 0 NA 179223 TCGA-AB-2972 AML20 6 79763507 79763507 T C SNP PHIP NM_017934.5 human genbank 54_36p -1 validated intronic c.2201+343 e19+343 0.011 - - - no_errors tier3 169 0 0 182 184 50.14 1 0 0 179223 TCGA-AB-2972 AML20 6 84460018 84460018 C T SNP SNAP91 NM_014841.2 human genbank 54_36p -1 validated intronic c.130+14218 e1+14218 0.001 - - - no_errors tier3 670 1 0.15 337 46 11.95 0 0 NA 179223 TCGA-AB-2972 AML20 6 85347362 85347362 A T SNP - - - - - - - - - - - - - - - tier3 157 0 0 155 25 13.89 0 0 NA 179223 TCGA-AB-2972 AML20 6 87849950 87849950 T C SNP ENSG00000217776 ENST00000402666 human ensembl 54_36p -1 known 5_prime_flanking_region c.-13052 NULL 0 - - - no_coding_region:pseudogene tier3 754 2 0.26 318 252 44.13 0 0 NA 179223 TCGA-AB-2972 AML20 6 88741900 88741900 G A SNP - - - - - - - - - - - - - - - tier3 1811 2 0.11 907 312 25.55 0 0 NA 179223 TCGA-AB-2972 AML20 6 89256857 89256857 C T SNP - - - - - - - - - - - - - - - tier3 1355 4 0.29 509 415 44.86 0 0 NA 179223 TCGA-AB-2972 AML20 6 91485948 91485948 T C SNP - - - - - - - - - - - - - - - tier3 865 1 0.12 434 395 47.65 0 0 NA 179223 TCGA-AB-2972 AML20 6 94082375 94082375 C T SNP EPHA7 NM_004440.3 human genbank 54_36p -1 reviewed intronic c.1324+40781 e5+40781 0.001 - - - no_errors tier3 534 0 0 293 175 37.31 0 0 NA 179223 TCGA-AB-2972 AML20 6 95433322 95433322 C T SNP - - - - - - - - - - - - - - - tier3 306 1 0.32 182 130 41.67 0 0 NA 179223 TCGA-AB-2972 AML20 6 98603174 98603174 G A SNP - - - - - - - - - - - - - - - tier3 564 3 0.53 410 173 29.67 0 0 NA 179223 TCGA-AB-2972 AML20 6 99197909 99197909 T A SNP - - - - - - - - - - - - - - - tier3 583 0 0 268 204 43.22 0 0 NA 179223 TCGA-AB-2972 AML20 6 101962350 101962350 A G SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.115+8361 e1+8361 0.195 - - - no_errors tier3 685 2 0.29 293 230 43.98 0 0 NA 179223 TCGA-AB-2972 AML20 6 102751469 102751469 G A SNP - - - - - - - - - - - - - - - tier3 191 1 0.52 118 96 44.86 0 0 NA 179223 TCGA-AB-2972 AML20 6 105573200 105573200 G A SNP LIN28B NM_001004317.2 human genbank 54_36p 1 provisional intronic c.199-7666 e3-7666 0 - - - no_errors tier3 1092 0 0 383 262 40.62 0 0 NA 179223 TCGA-AB-2972 AML20 6 113776936 113776936 G A SNP - - - - - - - - - - - - - - - tier3 886 1 0.11 701 140 16.65 0 0 NA 179223 TCGA-AB-2972 AML20 6 121388109 121388109 C T SNP - - - - - - - - - - - - - - - tier3 766 0 0 524 346 39.72 0 0 NA 179223 TCGA-AB-2972 AML20 6 122087165 122087165 A G SNP ENSG00000219135 ENST00000406913 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43861 NULL 0.015 - - - no_coding_region:pseudogene tier3 319 0 0 157 96 37.94 0 0 NA 179223 TCGA-AB-2972 AML20 6 122295456 122295456 A C SNP - - - - - - - - - - - - - - - tier3 1113 1 0.09 750 593 44.12 0 0 NA 179223 TCGA-AB-2972 AML20 6 126048882 126048882 C T SNP LOC643623 XR_041849.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 677 8 1.17 238 170 41.56 0 0 NA 179223 TCGA-AB-2972 AML20 6 128454496 128454496 G A SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.1163-1666 e8-1666 0 - - - no_errors tier3 687 5 0.72 426 352 45.19 0 0 NA 179223 TCGA-AB-2972 AML20 6 131949506 131949507 TC - DEL MED23 NM_015979.2 human genbank 54_36p -1 reviewed intronic c.4095+1035_4095+1034 e30+1035 0.001:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 6 144696266 144696266 T C SNP UTRN NM_007124.2 human genbank 54_36p 1 reviewed intronic c.79+41530 e1+41530 0.008 - - - no_errors tier3 1772 3 0.17 890 301 25.27 6 0 0 179223 TCGA-AB-2972 AML20 6 147911557 147911557 C G SNP SAMD5 NM_001030060.1 human genbank 54_36p 1 provisional intronic c.460-15666 e2-15666 0.167 - - - no_errors tier3 874 1 0.11 357 274 43.29 0 0 NA 179223 TCGA-AB-2972 AML20 6 148360389 148360389 C T SNP - - - - - - - - - - - - - - - tier3 614 1 0.16 308 166 34.95 0 0 NA 179223 TCGA-AB-2972 AML20 6 148587814 148587814 G T SNP SASH1 ENST00000367469 human ensembl 54_36p 1 known 5_prime_flanking_region c.-47372 NULL 0 - - - no_errors tier3 750 0 0 331 234 41.42 0 0 NA 179223 TCGA-AB-2972 AML20 6 150630691 150630691 C T SNP PPP1R14C NM_030949.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*19042 NULL 0 - - - no_errors tier3 439 1 0.23 205 149 41.97 0 0 NA 179223 TCGA-AB-2972 AML20 6 151514713 151514713 C T SNP ENSG00000208509 ENST00000385774 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-49456 NULL 0.001 - - - pseudogene tier3 812 0 0 287 267 47.94 0 0 NA 179223 TCGA-AB-2972 AML20 6 153628754 153628754 C A SNP ENSG00000218426 ENST00000406898 human ensembl 54_36p -1 known 3_prime_flanking_region c.*16358 NULL 0.002 - - - no_coding_region:pseudogene tier3 456 1 0.22 289 234 44.74 0 0 NA 179223 TCGA-AB-2972 AML20 6 156325784 156325784 C T SNP MIRN1202 ENST00000408529 human ensembl 54_36p 1 known 3_prime_flanking_region c.*16079 NULL 0 - - - no_errors tier3 795 2 0.25 405 277 40.62 4 2 33.33 179223 TCGA-AB-2972 AML20 6 159531187 159531187 C T SNP FNDC1 NM_032532.2 human genbank 54_36p 1 validated intronic c.110-7264 e2-7264 0.001 - - - no_errors tier3 674 1 0.15 196 193 49.36 0 0 NA 179223 TCGA-AB-2972 AML20 6 162314286 162314286 G A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.734+38 e6+38 0.004 - - - no_errors tier3 972 3 0.31 481 356 42.43 0 0 NA 179223 TCGA-AB-2972 AML20 6 164660915 164660915 T C SNP LOC728275 XM_001127046.2 human genbank 54_36p 1 model intronic c.545-17076 e3-17076 0 - - - no_errors tier3 393 0 0 346 94 21.32 0 0 NA 179223 TCGA-AB-2972 AML20 6 164780435 164780435 T C SNP - - - - - - - - - - - - - - - tier3 1277 5 0.39 688 488 41.46 0 0 NA 179223 TCGA-AB-2972 AML20 6 168240249 168240249 G A SNP FRMD1 NM_024919.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-17626 NULL 0.002 - - - no_errors tier3 158 0 0 38 29 43.28 0 0 NA 179223 TCGA-AB-2972 AML20 7 9320989 9320989 C A SNP - - - - - - - - - - - - - - - tier3 1736 3 0.17 974 359 26.93 0 0 NA 179223 TCGA-AB-2972 AML20 7 12053541 12053541 G A SNP - - - - - - - - - - - - - - - tier3 747 0 0 407 230 36.11 0 0 NA 179223 TCGA-AB-2972 AML20 7 14408529 14408529 G A SNP DGKB NM_004080.2 human genbank 54_36p -1 reviewed intronic c.1839-56988 e21-56988 0 - - - no_errors tier3 776 1 0.13 451 366 44.74 0 0 NA 179223 TCGA-AB-2972 AML20 7 15472968 15472968 G T SNP TMEM195 NM_001004320.1 human genbank 54_36p -1 provisional intronic c.410-35710 e4-35710 0 - - - no_errors tier3 963 0 0 401 286 41.63 0 0 NA 179223 TCGA-AB-2972 AML20 7 16500263 16500263 A G SNP SOSTDC1 ENST00000396652 human ensembl 54_36p -1 known intronic c.1+2267 e0+2267 0.001 - - - no_errors tier3 588 3 0.51 258 223 46.36 0 0 NA 179223 TCGA-AB-2972 AML20 7 20358337 20358337 A G SNP ITGB8 NM_002214.2 human genbank 54_36p 1 reviewed intronic c.128-11448 e2-11448 0.011 - - - no_errors tier3 697 1 0.14 443 343 43.53 0 0 NA 179223 TCGA-AB-2972 AML20 7 20832198 20832198 C T SNP SP8 NM_182700.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-39256 NULL 0 - - - no_errors tier3 520 3 0.57 274 125 31.25 0 0 NA 179223 TCGA-AB-2972 AML20 7 31108789 31108789 C T SNP ADCYAP1R1 NM_001118.3 human genbank 54_36p 1 reviewed intronic c.1047-587 e13-587 0 - - - no_errors tier3 396 0 0 184 134 42.14 0 0 NA 179223 TCGA-AB-2972 AML20 7 41091253 41091253 A G SNP - - - - - - - - - - - - - - - tier3 533 1 0.19 313 257 45.09 0 0 NA 179223 TCGA-AB-2972 AML20 7 42413648 42413648 G A SNP - - - - - - - - - - - - - - - tier3 890 3 0.34 406 285 41.24 0 0 NA 179223 TCGA-AB-2972 AML20 7 53157308 53157308 G A SNP LOC100134550 XR_039785.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37292 NULL 0.009 - - - pseudogene tier3 417 0 0 373 130 25.69 0 0 NA 179223 TCGA-AB-2972 AML20 7 53648848 53648848 A G SNP ENSG00000205628 ENST00000380970 human ensembl 54_36p -1 known 3_prime_flanking_region c.*152551 NULL 0.004 - - - no_errors tier3 838 5 0.59 346 282 44.76 0 0 NA 179223 TCGA-AB-2972 AML20 7 62267623 62267623 T A SNP ENSG00000199231 ENST00000362361 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*6130 NULL 0.002 - - - no_errors tier3 780 0 0 363 246 40.33 0 0 NA 179223 TCGA-AB-2972 AML20 7 63025719 63025719 A T SNP ENSG00000213645 ENST00000395415 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-3380 NULL 0 - - - no_coding_region:pseudogene tier3 913 2 0.22 275 229 45.44 0 0 NA 179223 TCGA-AB-2972 AML20 7 68338568 68338568 G A SNP - - - - - - - - - - - - - - - tier3 1365 6 0.44 499 335 40.12 0 0 NA 179223 TCGA-AB-2972 AML20 7 83219130 83219130 T C SNP - - - - - - - - - - - - - - - tier3 328 0 0 270 61 18.43 0 0 NA 179223 TCGA-AB-2972 AML20 7 83454644 83454644 T C SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed intronic c.1453-1915 e13-1915 0.001 - - - no_errors tier3 753 1 0.13 333 268 44.44 0 0 NA 179223 TCGA-AB-2972 AML20 7 83773328 83773328 A G SNP - - - - - - - - - - - - - - - tier3 253 0 0 152 133 46.67 0 0 NA 179223 TCGA-AB-2972 AML20 7 84492239 84492239 G A SNP SEMA3D NM_152754.2 human genbank 54_36p -1 validated intronic c.1192-2374 e11-2374 0 - - - no_errors tier3 383 2 0.52 217 161 42.48 0 0 NA 179223 TCGA-AB-2972 AML20 7 85565001 85565001 T C SNP - - - - - - - - - - - - - - - tier3 997 3 0.3 447 340 43.09 0 0 NA 179223 TCGA-AB-2972 AML20 7 94325538 94325538 T A SNP PPP1R9A NM_017650.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-51824 NULL 0.003 - - - no_errors tier3 239 2 0.83 116 94 44.76 0 0 NA 179223 TCGA-AB-2972 AML20 7 95176280 95176280 G T SNP - - - - - - - - - - - - - - - tier3 1779 1 0.06 692 446 39.12 0 0 NA 179223 TCGA-AB-2972 AML20 7 98088232 98088232 C T SNP NPTX2 NM_002523.2 human genbank 54_36p 1 reviewed intronic c.643+1125 e2+1125 0 - - - no_errors tier3 491 1 0.2 164 130 44.22 0 0 NA 179223 TCGA-AB-2972 AML20 7 106275494 106275494 C T SNP PIK3CG NM_002649.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19749 NULL 0 - - - no_errors tier3 1801 7 0.39 632 433 40.66 0 0 NA 179223 TCGA-AB-2972 AML20 7 111800301 111800301 A G SNP ZNF277 NM_021994.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*30281 NULL 0 - - - no_errors tier3 2018 9 0.44 739 560 43.04 0 0 NA 179223 TCGA-AB-2972 AML20 7 117900776 117900776 G C SNP ENSG00000222226 ENST00000410294 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*10892 NULL 0.001 - - - no_errors tier3 842 4 0.47 417 317 43.19 0 0 NA 179223 TCGA-AB-2972 AML20 7 121163606 121163606 A T SNP ENSG00000208616 ENST00000385881 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-127 NULL 0.924 - - - pseudogene tier3 344 0 0 206 140 40.46 0 0 NA 179223 TCGA-AB-2972 AML20 7 123276380 123276380 C T SNP HYAL4 NM_012269.2 human genbank 54_36p 1 reviewed intronic c.1+932 e0+932 0 - - - no_errors tier3 511 0 0 334 272 44.88 0 0 NA 179223 TCGA-AB-2972 AML20 7 123904903 123904903 G A SNP ENSG00000213296 ENST00000393351 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2911 NULL 0 - - - no_coding_region:pseudogene tier3 57 0 0 37 30 44.78 0 0 NA 179223 TCGA-AB-2972 AML20 7 132410904 132410904 A T SNP CHCHD3 NM_017812.2 human genbank 54_36p -1 provisional intronic c.82-5375 e2-5375 0 - - - no_errors tier3 1170 2 0.17 494 370 42.14 0 0 0 179223 TCGA-AB-2972 AML20 7 134264058 134264058 A C SNP CALD1 NM_033138.5 human genbank 54_36p 1 reviewed silent c.85 p.R29 1 HMMPfam_Caldesmon "HMMPfam_Caldesmon,PatternScan_PHOSPHOPANTETHEINE" - no_errors tier1 790 8 1 264 224 45.9 3 0 179223 TCGA-AB-2972 AML20 7 153788348 153788348 C G SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.358+14002 e2+14002 0.006 - - - no_errors tier3 1121 4 0.36 618 498 44.54 0 0 NA 179223 TCGA-AB-2972 AML20 7 156531411 156531411 C A SNP MNX1 NM_005515.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35606 NULL 0 - - - no_errors tier3 822 0 0 254 220 46.32 0 0 NA 179223 TCGA-AB-2972 AML20 7 157509661 157509661 G A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1723+57090 e11+57090 0.003 - - - no_errors tier3 428 2 0.46 64 55 46.22 0 2 100 179223 TCGA-AB-2972 AML20 8 2842745 2842745 T A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.8381+195 e55+195 0.004 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 838 4 0.47 434 317 42.04 0 0 NA 179223 TCGA-AB-2972 AML20 8 3093319 3093319 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.4158-18159 e28-18159 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1152 4 0.35 664 475 41.63 0 0 NA 179223 TCGA-AB-2972 AML20 8 4227902 4227902 A G SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.415+36981 e3+36981 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1632 8 0.49 816 587 41.84 0 0 NA 179223 TCGA-AB-2972 AML20 8 4322111 4322111 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.303-57116 e3-57116 0.007 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 943 6 0.63 400 286 41.63 0 0 NA 179223 TCGA-AB-2972 AML20 8 6290602 6290602 A G SNP MCPH1 NM_024596.2 human genbank 54_36p 1 validated intronic c.1825+126 e8+126 0.001 - - - no_errors tier3 710 0 0 404 126 23.77 2 4 66.67 179223 TCGA-AB-2972 AML20 8 10479637 10479637 G A SNP LOC346702 XM_001721174.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-86019 NULL 0.001 - - - no_errors tier3 500 1 0.2 105 92 46.7 0 0 NA 179223 TCGA-AB-2972 AML20 8 11335831 11335831 A G SNP FAM167A NM_053279.2 human genbank 54_36p -1 validated intronic c.381+3119 e1+3119 0.011 - - - no_errors tier3 619 2 0.32 180 133 42.22 0 0 NA 179223 TCGA-AB-2972 AML20 8 14416755 14416755 G A SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.234+39857 e2+39857 0.002 - - - no_errors tier3 275 0 0 245 82 25.08 0 0 NA 179223 TCGA-AB-2972 AML20 8 16269780 16269780 A C SNP - - - - - - - - - - - - - - - tier3 849 1 0.12 675 223 24.83 0 0 NA 179223 TCGA-AB-2972 AML20 8 16413627 16413627 C T SNP - - - - - - - - - - - - - - - tier3 641 0 0 289 245 45.79 0 0 NA 179223 TCGA-AB-2972 AML20 8 25454756 25454756 A G SNP CDCA2 NM_152562.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*33585 NULL 0 - - - no_errors tier3 437 0 0 311 65 17.24 0 0 NA 179223 TCGA-AB-2972 AML20 8 28210771 28210771 C T SNP LOC100129848 XM_001717438.1 human genbank 54_36p -1 model intronic c.464+41691 e1+41691 0 - - - no_errors tier3 575 1 0.17 250 161 39.08 0 0 NA 179223 TCGA-AB-2972 AML20 8 32171433 32171433 C T SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.746-401455 e2-401455 0 - - - overly_large_intron tier3 752 0 0 453 355 43.88 0 0 NA 179223 TCGA-AB-2972 AML20 8 35274471 35274471 G A SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.103+61524 e1+61524 0.002 - - - no_errors tier3 720 0 0 388 329 45.89 0 0 NA 179223 TCGA-AB-2972 AML20 8 35764668 35764668 C T SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.2643-2751 e17-2751 0.012 - - - no_errors tier3 483 1 0.21 256 216 45.76 0 0 NA 179223 TCGA-AB-2972 AML20 8 36743280 36743280 T C SNP KCNU1 NM_001031836.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17807 NULL 0.005 - - - no_errors tier3 457 1 0.22 250 175 40.98 0 0 NA 179223 TCGA-AB-2972 AML20 8 38137753 38137753 A C SNP BAG4 NM_004874.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15792 NULL 0 - - - no_errors tier3 1137 11 0.96 296 246 45.39 0 0 NA 179223 TCGA-AB-2972 AML20 8 42318086 42318086 A G SNP POLB NM_002690.1 human genbank 54_36p 1 provisional intronic c.119+2342 e2+2342 0.037 - - - no_errors tier3 789 5 0.63 291 220 42.97 0 1 100 179223 TCGA-AB-2972 AML20 8 50006648 50006648 C T SNP SNAI2 NM_003068.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-10271 NULL 0 - - - no_errors tier3 821 0 0 357 295 45.18 0 0 NA 179223 TCGA-AB-2972 AML20 8 51626229 51626229 C A SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.681-1934 e10-1934 0 - - - no_errors tier3 423 1 0.24 249 190 43.28 0 0 NA 179223 TCGA-AB-2972 AML20 8 52521382 52521382 G A SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.1525+735 e12+735 0.001 - - - no_errors tier3 804 1 0.12 512 171 24.96 0 0 NA 179223 TCGA-AB-2972 AML20 8 54745291 54745291 G C SNP LOC100129667 XR_037850.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-42519 NULL 0.001 - - - pseudogene tier3 1087 3 0.27 343 235 40.59 0 0 NA 179223 TCGA-AB-2972 AML20 8 55969456 55969456 C T SNP - - - - - - - - - - - - - - - tier3 832 5 0.6 261 226 46.41 0 0 NA 179223 TCGA-AB-2972 AML20 8 56286570 56286570 C T SNP XKR4 NM_052898.1 human genbank 54_36p 1 provisional intronic c.806+108162 e1+108162 0 - - - no_errors tier3 530 0 0 555 146 20.83 0 0 NA 179223 TCGA-AB-2972 AML20 8 62506556 62506556 C T SNP RLBP1L1 NM_173519.2 human genbank 54_36p 1 validated intronic c.631-22698 e3-22698 0.001 - - - no_errors tier3 918 1 0.11 422 330 43.77 0 0 NA 179223 TCGA-AB-2972 AML20 8 62997828 62997828 C T SNP - - - - - - - - - - - - - - - tier3 1033 2 0.19 454 422 48.12 0 0 NA 179223 TCGA-AB-2972 AML20 8 65039929 65039929 T A SNP - - - - - - - - - - - - - - - tier3 942 0 0 642 215 25.06 0 0 NA 179223 TCGA-AB-2972 AML20 8 69031936 69031936 T C SNP PREX2 NM_024870.2 human genbank 54_36p 1 validated intronic c.141+4612 e1+4612 0 - - - no_errors tier3 606 3 0.49 256 162 38.76 0 0 NA 179223 TCGA-AB-2972 AML20 8 69186707 69186707 G T SNP PREX2 NM_024870.2 human genbank 54_36p 1 validated intronic c.3146+2295 e25+2295 0.003 - - - no_errors tier3 859 0 0 421 334 44.24 0 0 NA 179223 TCGA-AB-2972 AML20 8 71168074 71168074 A G SNP PRDM14 NM_024504.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23425 NULL 0.003 - - - no_errors tier3 560 1 0.18 177 119 40.2 0 0 NA 179223 TCGA-AB-2972 AML20 8 76532978 76532978 C T SNP HNF4G ENST00000354370 human ensembl 54_36p 1 known intronic c.1-31901 e1-31901 0.001 - - - no_errors tier3 914 4 0.44 475 367 43.59 0 0 NA 179223 TCGA-AB-2972 AML20 8 76827099 76827099 A G SNP ENSG00000221029 ENST00000408102 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*34056 NULL 0.01 - - - no_errors tier2 858 1 0.12 303 265 46.65 0 0 NA 179223 TCGA-AB-2972 AML20 8 77366316 77366316 C T SNP ENSG00000222231 ENST00000410299 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-25794 NULL 0.002 - - - no_errors tier3 810 5 0.61 488 356 42.13 0 0 NA 179223 TCGA-AB-2972 AML20 8 79691209 79691209 C G SNP FAM164A NM_016010.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49730 NULL 0.003 - - - no_errors tier3 918 4 0.43 394 316 44.44 1 0 0 179223 TCGA-AB-2972 AML20 8 79691345 79691345 C T SNP FAM164A NM_016010.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49594 NULL 0.001 - - - no_errors tier3 356 8 2.2 205 192 48.24 0 0 NA 179223 TCGA-AB-2972 AML20 8 81427751 81427751 T C SNP ENSG00000206649 ENST00000383922 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35892 NULL 0.068 - - - no_errors tier3 611 1 0.16 227 200 46.73 0 0 NA 179223 TCGA-AB-2972 AML20 8 86988220 86988220 C T SNP - - - - - - - - - - - - - - - tier3 776 2 0.26 510 372 42.18 0 1 100 179223 TCGA-AB-2972 AML20 8 87148920 87148920 G A SNP PSKH2 NM_033126.1 human genbank 54_36p -1 provisional intronic c.185+1863 e1+1863 0 - - - no_errors tier3 687 2 0.29 252 167 39.86 0 0 NA 179223 TCGA-AB-2972 AML20 8 87884857 87884857 A G SNP - - - - - - - - - - - - - - - tier3 722 0 0 299 212 41.49 0 0 NA 179223 TCGA-AB-2972 AML20 8 90477756 90477756 A C SNP ENSG00000213771 ENST00000396270 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*16458 NULL 0 - - - no_coding_region:pseudogene tier3 892 3 0.33 667 253 27.44 0 0 NA 179223 TCGA-AB-2972 AML20 8 91649292 91649293 - A INS ENSG00000209319 ENST00000386584 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*28076 NULL 0.004:0.004 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 8 92846180 92846180 C T SNP - - - - - - - - - - - - - - - tier3 695 2 0.28 371 309 45.37 0 0 NA 179223 TCGA-AB-2972 AML20 8 94685992 94685992 C T SNP - - - - - - - - - - - - - - - tier3 1213 1 0.08 486 394 44.72 0 0 NA 179223 TCGA-AB-2972 AML20 8 95357694 95357694 G C SNP GEM NM_005261.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15787 NULL 0.001 - - - no_errors tier3 1141 2 0.17 330 270 45 0 0 NA 179223 TCGA-AB-2972 AML20 8 96274430 96274430 G A SNP PLEKHF2 NM_024613.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*38232 NULL 0 - - - no_errors tier3 746 1 0.13 304 275 47.33 0 0 NA 179223 TCGA-AB-2972 AML20 8 97102484 97102485 - A INS ENSG00000183663 ENST00000331024 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*47649 NULL 0.998:0.993 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 8 105402404 105402404 G C SNP TM7SF4 NM_030788.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27553 NULL 0 - - - no_errors tier3 1067 4 0.37 445 292 39.57 0 0 NA 179223 TCGA-AB-2972 AML20 8 109490655 109490655 A T SNP LOC100128549 XM_001724332.1 human genbank 54_36p -1 model intronic c.199+12747 e2+12747 0.095 - - - no_errors tier3 167 0 0 115 63 35.39 0 0 NA 179223 TCGA-AB-2972 AML20 8 110765573 110765573 C T SNP GOLSYN NM_001099744.1 human genbank 54_36p -1 validated intronic c.1+7165 e0+7165 0 - - - no_errors tier3 1011 3 0.3 365 252 40.78 0 0 NA 179223 TCGA-AB-2972 AML20 8 111954415 111954415 T A SNP - - - - - - - - - - - - - - - tier3 365 2 0.54 152 122 44.36 0 0 NA 179223 TCGA-AB-2972 AML20 8 117644799 117644799 T C SNP - - - - - - - - - - - - - - - tier3 1311 5 0.38 545 490 47.3 0 0 NA 179223 TCGA-AB-2972 AML20 8 118068400 118068400 C T SNP SLC30A8 ENST00000297345 human ensembl 54_36p 1 known intronic c.1+35861 e0+35861 0 - - - no_errors tier3 853 0 0 333 252 43 0 0 NA 179223 TCGA-AB-2972 AML20 8 118216974 118216974 A G SNP SLC30A8 NM_173851.2 human genbank 54_36p 1 validated intronic c.71+156 e1+156 0.001 - - - no_errors tier3 659 3 0.45 407 309 43.1 0 0 NA 179223 TCGA-AB-2972 AML20 8 132296489 132296489 G A SNP - - - - - - - - - - - - - - - tier3 1623 4 0.25 748 240 24.29 0 0 NA 179223 TCGA-AB-2972 AML20 8 135630346 135630346 G A SNP ZFAT NM_020863.1 human genbank 54_36p -1 validated intronic c.2977-15949 e12-15949 0 - - - no_errors tier3 817 0 0 568 102 15.22 0 0 0 179223 TCGA-AB-2972 AML20 8 138061986 138061986 C A SNP - - - - - - - - - - - - - - - tier3 768 0 0 324 265 44.99 0 0 NA 179223 TCGA-AB-2972 AML20 8 138772824 138772824 A T SNP - - - - - - - - - - - - - - - tier3 352 0 0 239 188 44.03 0 0 NA 179223 TCGA-AB-2972 AML20 8 140449159 140449159 C A SNP - - - - - - - - - - - - - - - tier3 979 1 0.1 427 345 44.63 0 0 NA 179223 TCGA-AB-2972 AML20 8 140665444 140665444 C A SNP KCNK9 NM_016601.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*34239 NULL 0.026 - - - no_errors tier3 584 0 0 263 207 44.04 0 0 NA 179223 TCGA-AB-2972 AML20 9 10532561 10532561 G T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1+69837 e0+69837 0 - - - no_errors tier3 216 0 0 215 133 38.22 0 0 NA 179223 TCGA-AB-2972 AML20 9 22076681 22076681 C A SNP CDKN2BAS NR_003529.3 human genbank 54_36p 1 validated intronic c.NULL NULL 0 - - - no_errors tier3 589 1 0.17 386 280 42.04 0 0 NA 179223 TCGA-AB-2972 AML20 9 25186323 25186323 G A SNP - - - - - - - - - - - - - - - tier3 817 2 0.24 380 303 44.3 0 0 NA 179223 TCGA-AB-2972 AML20 9 31737558 31737558 G C SNP - - - - - - - - - - - - - - - tier3 451 0 0 345 75 17.86 0 0 NA 179223 TCGA-AB-2972 AML20 9 70391661 70391661 G T SNP C9orf71 NM_153237.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-46111 NULL 0.99 - - - no_errors tier3 1128 4 0.35 532 287 35.04 0 0 NA 179223 TCGA-AB-2972 AML20 9 70748179 70748179 C T SNP PIP5K1B NM_003558.2 human genbank 54_36p 1 validated intronic c.1502+2653 e11+2653 0.006 - - - no_errors tier3 738 1 0.14 515 182 26.04 6 16 72.73 179223 TCGA-AB-2972 AML20 9 72927283 72927283 C G SNP TRPM3 ENST00000357533 human ensembl 54_36p -1 known intronic c.184-258036 e2-258036 0.001 - - - no_errors tier3 922 4 0.43 469 291 38.24 0 0 NA 179223 TCGA-AB-2972 AML20 9 74046236 74046236 G C SNP GDA NM_004293.3 human genbank 54_36p 1 validated intronic c.1135+202 e11+202 0.001 - - - no_errors tier3 1022 4 0.39 457 330 41.83 0 0 NA 179223 TCGA-AB-2972 AML20 9 77726341 77726341 G A SNP PCSK5 NM_006200.3 human genbank 54_36p 1 reviewed intronic c.193-10774 e2-10774 0.004 - - - no_errors tier3 769 0 0 429 282 39.66 0 0 0 179223 TCGA-AB-2972 AML20 9 78071799 78071799 C T SNP PCSK5 ENST00000376754 human ensembl 54_36p 1 known intronic c.2252-25170 e19-25170 0.996 - - - no_errors tier3 1450 2 0.14 724 542 42.71 0 0 NA 179223 TCGA-AB-2972 AML20 9 79660334 79660334 G A SNP GNAQ NM_002072.2 human genbank 54_36p -1 provisional intronic c.322-39828 e3-39828 0 - - - no_errors tier3 905 1 0.11 365 250 40.58 22 13 37.14 179223 TCGA-AB-2972 AML20 9 82520580 82520580 T C SNP ENSG00000221581 ENST00000408654 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*18397 NULL 0.047 - - - no_errors tier3 731 3 0.41 430 271 38.49 0 0 NA 179223 TCGA-AB-2972 AML20 9 85981230 85981230 G A SNP - - - - - - - - - - - - - - - tier3 737 2 0.27 302 219 42.03 0 0 NA 179223 TCGA-AB-2972 AML20 9 86162610 86162610 A T SNP SLC28A3 NM_022127.1 human genbank 54_36p -1 provisional intronic c.1+10577 e0+10577 0.003 - - - no_errors tier3 1019 1 0.1 372 289 43.52 0 0 NA 179223 TCGA-AB-2972 AML20 9 90096246 90096246 G T SNP LOC401537 XR_017028.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-32892 NULL 0.002 - - - pseudogene tier3 974 3 0.31 370 346 48.32 0 0 NA 179223 TCGA-AB-2972 AML20 9 100743482 100743482 T C SNP COL15A1 NM_001855.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2683 NULL 0.014 - - - no_errors tier3 412 3 0.72 147 136 48.06 0 0 NA 179223 TCGA-AB-2972 AML20 9 105000462 105000462 C T SNP - - - - - - - - - - - - - - - tier3 513 0 0 308 184 37.4 0 0 NA 179223 TCGA-AB-2972 AML20 9 111633048 111633048 C T SNP PALM2-AKAP2 NM_007203.3 human genbank 54_36p 1 validated intronic c.46-36544 e2-36544 0.003 - - - no_errors tier3 899 1 0.11 315 236 42.83 0 0 NA 179223 TCGA-AB-2972 AML20 9 117987336 117987336 G A SNP PAPPA NM_002581.3 human genbank 54_36p 1 reviewed intronic c.416-1918 e2-1918 0.001 - - - no_errors tier3 1274 4 0.31 326 261 44.46 0 0 NA 179223 TCGA-AB-2972 AML20 9 121826932 121826932 C T SNP - - - - - - - - - - - - - - - tier3 976 4 0.41 454 364 44.5 0 0 NA 179223 TCGA-AB-2972 AML20 9 123092499 123092499 G A SNP GSN NM_198252.4 human genbank 54_36p 1 reviewed intronic c.1+8838 e0+8838 0.002 - - - no_errors tier3 529 1 0.19 184 121 39.54 0 2 100 179223 TCGA-AB-2972 AML20 9 124235582 124235582 C A SNP PTGS1 NM_000962.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*40938 NULL 0.127 - - - no_errors tier3 824 2 0.24 332 218 39.49 0 0 NA 179223 TCGA-AB-2972 AML20 9 125787886 125787886 C T SNP LHX2 NM_004789.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26563 NULL 0 - - - no_errors tier3 732 4 0.54 273 213 43.74 0 0 NA 179223 TCGA-AB-2972 AML20 9 125939913 125939913 C T SNP - - - - - - - - - - - - - - - tier3 976 2 0.2 328 244 42.36 0 0 NA 179223 TCGA-AB-2972 AML20 9 134471760 134471760 C T SNP DDX31 NM_022779.7 human genbank 54_36p -1 reviewed intronic c.2309+5535 e19+5535 0 - - - no_errors tier3 861 2 0.23 340 239 41.14 2 3 60 179223 TCGA-AB-2972 AML20 10 861204 861204 G A SNP LARP5 NM_015155.1 human genbank 54_36p -1 provisional missense c.1285 p.P429S 0.992 NULL "HMMPfam_La,HMMSmart_SM00715,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 561 1 0.18 285 106 27.04 56 55 49.55 179223 TCGA-AB-2972 AML20 10 8980520 8980520 G T SNP - - - - - - - - - - - - - - - tier3 1105 2 0.18 529 434 45.02 1 0 0 179223 TCGA-AB-2972 AML20 10 9660101 9660101 A C SNP - - - - - - - - - - - - - - - tier3 751 3 0.4 373 281 42.97 0 0 NA 179223 TCGA-AB-2972 AML20 10 13492377 13492377 C T SNP BEND7 NM_152751.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*28801 NULL 0.002 - - - no_errors tier3 1155 6 0.51 385 302 43.9 0 0 NA 179223 TCGA-AB-2972 AML20 10 26209581 26209581 A G SNP - - - - - - - - - - - - - - - tier3 1165 2 0.17 733 545 42.58 0 0 NA 179223 TCGA-AB-2972 AML20 10 27987964 27987964 G A SNP MKX NM_173576.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*16200 NULL 0 - - - no_errors tier3 1358 2 0.15 505 353 41.05 0 0 NA 179223 TCGA-AB-2972 AML20 10 33758378 33758378 G A SNP - - - - - - - - - - - - - - - tier3 610 7 1.11 496 377 42.17 0 0 NA 179223 TCGA-AB-2972 AML20 10 34302477 34302477 C T SNP - - - - - - - - - - - - - - - tier3 294 2 0.68 186 104 35.74 0 0 NA 179223 TCGA-AB-2972 AML20 10 49989697 49989697 C T SNP C10orf72 NM_001031746.3 human genbank 54_36p -1 validated intronic c.56-3651 e2-3651 0 - - - no_errors tier3 333 5 1.47 212 181 45.82 0 0 NA 179223 TCGA-AB-2972 AML20 10 51811202 51811202 T C SNP SGMS1 NM_147156.3 human genbank 54_36p -1 reviewed intronic c.1-37091 e1-37091 0.001 - - - no_errors tier3 890 3 0.34 401 277 40.86 2 0 0 179223 TCGA-AB-2972 AML20 10 55684730 55684730 T G SNP PCDH15 NM_033056.1 human genbank 54_36p -1 reviewed intronic c.877-18033 e8-18033 0 - - - no_errors tier3 690 1 0.14 325 276 45.85 0 0 NA 179223 TCGA-AB-2972 AML20 10 56253837 56253837 C T SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+73379 e0+73379 0.014 - - - no_errors tier3 506 0 0 340 115 25.11 0 0 NA 179223 TCGA-AB-2972 AML20 10 56803960 56803960 A T SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1-207543 e1-207543 0.009 - - - no_errors tier3 683 1 0.15 301 247 44.99 0 0 NA 179223 TCGA-AB-2972 AML20 10 56834426 56834426 C T SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+222965 e0+222965 0 - - - no_errors tier3 446 3 0.67 168 123 42.12 0 0 NA 179223 TCGA-AB-2972 AML20 10 57692166 57692166 T A SNP - - - - - - - - - - - - - - - tier3 644 3 0.46 372 275 42.5 0 0 NA 179223 TCGA-AB-2972 AML20 10 58806188 58806188 G A SNP - - - - - - - - - - - - - - - tier3 853 2 0.23 677 126 15.67 0 0 NA 179223 TCGA-AB-2972 AML20 10 61477818 61477818 G A SNP ANK3 NM_020987.2 human genbank 54_36p -1 reviewed intronic c.13066-5295 e43-5295 0.003 - - - no_errors tier3 777 1 0.13 371 279 42.79 1 0 0 179223 TCGA-AB-2972 AML20 10 78313538 78313538 A G SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.3524+3517 e28+3517 0 - - - no_errors tier3 488 0 0 233 141 37.7 0 0 NA 179223 TCGA-AB-2972 AML20 10 82296693 82296693 G A SNP SH2D4B NM_207372.1 human genbank 54_36p 1 validated intronic c.184+8442 e1+8442 0.442 - - - no_errors tier3 315 1 0.32 129 95 42.41 0 0 NA 179223 TCGA-AB-2972 AML20 10 83607982 83607982 A T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17095 NULL 0 - - - no_errors tier3 381 0 0 206 134 39.41 0 0 NA 179223 TCGA-AB-2972 AML20 10 106987918 106987918 A G SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.2869-7372 e21-7372 0.002 - - - no_errors tier3 982 7 0.71 428 316 42.36 0 0 NA 179223 TCGA-AB-2972 AML20 10 108952437 108952437 C T SNP SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-38163 NULL 0.005 - - - no_errors tier3 1194 1 0.08 409 337 44.87 0 0 NA 179223 TCGA-AB-2972 AML20 10 115234387 115234387 T C SNP ENSG00000220780 ENST00000406661 human ensembl 54_36p 1 known 3_prime_flanking_region c.*1525 NULL 0.001 - - - no_coding_region:pseudogene tier3 1319 7 0.53 489 385 44.05 0 0 NA 179223 TCGA-AB-2972 AML20 10 115881891 115881891 A C SNP C10orf118 NM_018017.2 human genbank 54_36p -1 validated missense c.1698 p.S566R 1 superfamily_Prefoldin superfamily_Prefoldin - no_errors tier1 514 2 0.39 230 216 48.43 15 8 34.78 179223 TCGA-AB-2972 AML20 10 116177274 116177274 G A SNP AFAP1L2 NM_001001936.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23070 NULL 0.007 - - - no_errors tier3 604 2 0.33 316 105 24.88 1 0 0 179223 TCGA-AB-2972 AML20 10 119504106 119504106 G C SNP - - - - - - - - - - - - - - - tier3 989 0 0 490 181 26.93 0 0 NA 179223 TCGA-AB-2972 AML20 10 119704768 119704768 T C SNP RAB11FIP2 NM_014904.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*53731 NULL 0 - - - no_errors tier3 944 0 0 301 258 46.07 0 0 NA 179223 TCGA-AB-2972 AML20 10 120391230 120391230 G A SNP PRLHR NM_004248.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-46484 NULL 0.025 - - - no_errors tier3 670 2 0.3 352 273 43.68 0 0 NA 179223 TCGA-AB-2972 AML20 11 5544695 5544695 C T SNP OR52T1P ENST00000402016 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-5544695 NULL 0.984 - - - no_coding_region:pseudogene tier3 2078 9 0.43 549 696 55.86 0 0 NA 179223 TCGA-AB-2972 AML20 11 6749288 6749288 T C SNP OR2AG1 NM_001004489.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-13557 NULL 0 - - - no_errors tier3 1818 6 0.33 484 772 61.42 0 0 NA 179223 TCGA-AB-2972 AML20 11 10356700 10356700 C T SNP LOC100130460 XM_001721426.1 human genbank 54_36p 1 model intronic c.195-32180 e3-32180 0.009 - - - no_errors tier3 1050 1 0.1 532 183 25.49 0 0 NA 179223 TCGA-AB-2972 AML20 11 24175338 24175338 T C SNP - - - - - - - - - - - - - - - tier3 629 4 0.63 270 387 58.9 0 0 NA 179223 TCGA-AB-2972 AML20 11 27256537 27256537 C T SNP - - - - - - - - - - - - - - - tier3 497 1 0.2 466 148 24.1 0 0 NA 179223 TCGA-AB-2972 AML20 11 27631200 27631200 T A SNP BDNFOS NR_002832.1 human genbank 54_36p 1 provisional intronic c.NULL NULL 0.003 - - - no_errors tier3 1324 7 0.52 863 325 27.31 0 1 100 179223 TCGA-AB-2972 AML20 11 28903976 28903976 C T SNP - - - - - - - - - - - - - - - tier3 1147 4 0.35 465 687 59.53 0 0 NA 179223 TCGA-AB-2972 AML20 11 31017680 31017680 A G SNP uc001msu.1 ENST00000342355 human ensembl 54_36p -1 known intronic c.1448+24912 e12+24912 0 - - - no_errors tier3 579 1 0.17 236 373 61.15 0 0 NA 179223 TCGA-AB-2972 AML20 11 33798024 33798024 T C SNP FBXO3 NM_012175.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-45405 NULL 0.035 - - - no_errors tier3 1663 14 0.83 414 640 60.66 0 0 NA 179223 TCGA-AB-2972 AML20 11 40996810 40996810 T G SNP - - - - - - - - - - - - - - - tier3 1250 4 0.32 621 224 26.51 0 0 NA 179223 TCGA-AB-2972 AML20 11 42908915 42908915 C A SNP - - - - - - - - - - - - - - - tier3 684 7 1.01 195 269 57.97 0 0 NA 179223 TCGA-AB-2972 AML20 11 46240390 46240390 A G SNP CREB3L1 ENST00000288400 human ensembl 54_36p 1 known 5_prime_flanking_region c.-15849 NULL 0.008 - - - no_errors tier3 1538 1 0.06 270 223 45.23 0 0 NA 179223 TCGA-AB-2972 AML20 11 47591922 47591922 A T SNP KBTBD4 NM_016506.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35795 NULL 0.004 - - - no_errors tier3 1185 4 0.34 308 230 42.59 1 3 75 179223 TCGA-AB-2972 AML20 11 47800011 47800011 C T SNP NUP160 NM_015231.1 human genbank 54_36p -1 validated intronic c.1180-62 e9-62 0 - - - no_errors tier3 809 1 0.12 350 268 43.37 3 6 66.67 179223 TCGA-AB-2972 AML20 11 59023087 59023087 C T SNP ENSG00000209815 ENST00000387080 human ensembl 54_36p 1 novel rna NULL NULL 0 - - - pseudogene tier1 662 0 426 73 14.6 NA 179223 TCGA-AB-2972 AML20 11 64917675 64917675 G A SNP FRMD8 NM_031904.3 human genbank 54_36p 1 validated silent c.309 p.E103 0.999 HMMSmart_SM00295 "HMMPfam_FERM_M,superfamily_Second domain of FERM,HMMSmart_SM00295" - no_errors tier1 793 2 0.25 136 168 54.9 8 8 50 179223 TCGA-AB-2972 AML20 11 65120148 65120148 A C SNP SIPA1 ENST00000308755 human ensembl 54_36p 1 known intronic c.1+10683 e0+10683 0 - - - no_errors tier3 290 0 0 100 62 38.27 0 0 NA 179223 TCGA-AB-2972 AML20 11 70498189 70498189 C T SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.592+446 e4+446 0.003 - - - no_errors tier3 606 3 0.49 175 126 41.72 0 0 NA 179223 TCGA-AB-2972 AML20 11 79342136 79342136 C T SNP - - - - - - - - - - - - - - - tier3 1090 3 0.27 479 323 40.22 0 0 NA 179223 TCGA-AB-2972 AML20 11 79764419 79764419 C A SNP - - - - - - - - - - - - - - - tier3 1752 3 0.17 807 309 27.69 0 0 NA 179223 TCGA-AB-2972 AML20 11 80140681 80140681 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 11 80367009 80367009 G C SNP - - - - - - - - - - - - - - - tier3 1145 2 0.17 734 284 27.84 0 0 NA 179223 TCGA-AB-2972 AML20 11 84425416 84425416 T C SNP DLG2 ENST00000376104 human ensembl 54_36p -1 known intronic c.357+74937 e4+74937 0.271 - - - no_errors tier3 730 3 0.41 526 158 23.1 0 0 NA 179223 TCGA-AB-2972 AML20 11 88693693 88693693 G A SNP ENSG00000197692 ENST00000360462 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26631 NULL 0 - - - no_coding_region:pseudogene tier3 579 0 0 298 202 40.4 0 0 NA 179223 TCGA-AB-2972 AML20 11 94615046 94615046 A G SNP SESN3 NM_144665.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-11374 NULL 0.989 - - - no_errors tier3 1235 2 0.16 283 238 45.68 0 1 100 179223 TCGA-AB-2972 AML20 11 99003639 99003639 G A SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.55+71429 e1+71429 0.001 - - - no_errors tier3 1255 1 0.08 516 371 41.83 0 0 NA 179223 TCGA-AB-2972 AML20 11 99218743 99218743 T C SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.278-2051 e3-2051 0.003 - - - no_errors tier3 99 0 0 64 59 47.97 0 0 NA 179223 TCGA-AB-2972 AML20 11 100057270 100057270 A C SNP ENSG00000223242 ENST00000411310 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-39056 NULL 0.001 - - - no_errors tier3 1012 4 0.39 261 254 49.13 0 0 NA 179223 TCGA-AB-2972 AML20 11 102250408 102250408 G T SNP MMP12 ENST00000326227 human ensembl 54_36p -1 known intronic c.102+368 e1+368 0.005 - - - no_errors tier3 834 3 0.36 450 341 43.06 0 0 NA 179223 TCGA-AB-2972 AML20 11 102726908 102726908 C T SNP DYNC2H1 NM_001080463.1 human genbank 54_36p 1 provisional intronic c.12061-7273 e84-7273 0.067 - - - no_errors tier3 701 1 0.14 352 267 43.13 0 0 0 179223 TCGA-AB-2972 AML20 11 103079646 103079646 A G SNP - - - - - - - - - - - - - - - tier3 1444 5 0.34 489 372 43.11 0 0 NA 179223 TCGA-AB-2972 AML20 11 104742040 104742040 T A SNP ENSG00000211026 ENST00000388291 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13137 NULL 0 - - - pseudogene tier3 1015 4 0.39 562 405 41.8 0 0 NA 179223 TCGA-AB-2972 AML20 11 105439979 105439979 A G SNP KBTBD3 NM_152433.3 human genbank 54_36p -1 validated intronic c.1-4933 e1-4933 0.007 - - - no_errors tier3 776 1 0.13 260 209 44.47 3 0 0 179223 TCGA-AB-2972 AML20 11 105883991 105883991 C A SNP - - - - - - - - - - - - - - - tier3 1107 2 0.18 585 454 43.65 0 0 NA 179223 TCGA-AB-2972 AML20 11 106117406 106117406 G A SNP GUCY1A2 NM_000855.1 human genbank 54_36p -1 validated intronic c.1837-32804 e7-32804 0 - - - no_errors tier3 931 3 0.32 435 274 38.65 0 0 NA 179223 TCGA-AB-2972 AML20 11 109422988 109422988 A G SNP ZC3H12C NM_033390.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46360 NULL 0 - - - no_errors tier3 1634 0 0 894 133 12.95 0 0 NA 179223 TCGA-AB-2972 AML20 11 112156279 112156279 C A SNP - - - - - - - - - - - - - - - tier3 373 4 1.06 217 218 49.89 0 0 NA 179223 TCGA-AB-2972 AML20 11 115865937 115865937 C T SNP - - - - - - - - - - - - - - - tier3 700 0 0 330 231 41.18 0 0 NA 179223 TCGA-AB-2972 AML20 11 120895825 120895825 C T SNP SORL1 NM_003105.4 human genbank 54_36p 1 reviewed intronic c.1212-751 e9-751 0 - - - no_errors tier3 927 9 0.96 554 428 43.54 5 0 0 179223 TCGA-AB-2972 AML20 11 130784335 130784335 A C SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.82+38342 e1+38342 0 - - - no_errors tier3 889 5 0.56 353 240 40.47 0 0 NA 179223 TCGA-AB-2972 AML20 11 132365168 132365168 G A SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.62-47053 e2-47053 0 - - - no_errors tier3 2177 7 0.32 402 343 45.92 0 0 NA 179223 TCGA-AB-2972 AML20 12 1839278 1839278 T C SNP CACNA2D4 NM_172364.4 human genbank 54_36p -1 reviewed intronic c.1940+294 e19+294 0.004 - - - no_errors tier3 637 5 0.78 172 125 42.09 1 4 80 179223 TCGA-AB-2972 AML20 12 7586642 7586642 A G SNP CD163 NM_004244.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-39089 NULL 0.006 - - - no_errors tier3 1045 3 0.29 547 432 44.08 0 0 NA 179223 TCGA-AB-2972 AML20 12 14252596 14252596 T C SNP ENSG00000209525 ENST00000386790 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*41840 NULL 0.003 - - - pseudogene tier3 1324 6 0.45 712 471 39.71 0 0 NA 179223 TCGA-AB-2972 AML20 12 15507318 15507318 G A SNP PTPRO NM_030667.2 human genbank 54_36p 1 reviewed intronic c.76-20857 e2-20857 0 - - - no_errors tier3 347 1 0.29 191 141 42.47 0 0 NA 179223 TCGA-AB-2972 AML20 12 16241090 16241090 C T SNP LOC729025 XM_001129090.1 human genbank 54_36p -1 model intronic c.1484-2436 e8-2436 0 - - - no_errors tier3 1228 2 0.16 551 438 44.24 0 0 NA 179223 TCGA-AB-2972 AML20 12 17862176 17862176 A G SNP - - - - - - - - - - - - - - - tier3 345 2 0.58 219 216 49.66 0 0 NA 179223 TCGA-AB-2972 AML20 12 23343253 23343253 A T SNP - - - - - - - - - - - - - - - tier3 1056 6 0.56 427 337 44.05 0 0 NA 179223 TCGA-AB-2972 AML20 12 25323275 25323275 C T SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33690 NULL 0.001 - - - no_errors tier3 859 1 0.12 401 303 42.86 0 1 100 179223 TCGA-AB-2972 AML20 12 25866601 25866601 C T SNP ENSG00000222950 ENST00000411018 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42831 NULL 0 - - - no_errors tier3 1018 2 0.2 525 444 45.82 0 0 NA 179223 TCGA-AB-2972 AML20 12 26019106 26019106 A G SNP RASSF8 NM_007211.3 human genbank 54_36p 1 provisional intronic c.1+15758 e0+15758 0 - - - no_errors tier3 998 6 0.6 300 249 45.27 0 0 NA 179223 TCGA-AB-2972 AML20 12 33615656 33615656 C G SNP ENSG00000212475 ENST00000391173 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-4641 NULL 0.269 - - - no_errors tier3 640 1 0.16 397 299 42.96 0 0 NA 179223 TCGA-AB-2972 AML20 12 37656968 37656968 G T SNP - - - - - - - - - - - - - - - tier3 608 0 0 440 129 22.67 0 0 NA 179223 TCGA-AB-2972 AML20 12 40612784 40612784 C A SNP - - - - - - - - - - - - - - - tier3 322 2 0.62 100 57 35.85 0 0 NA 179223 TCGA-AB-2972 AML20 12 43277883 43277883 G C SNP NELL2 NM_006159.1 human genbank 54_36p -1 reviewed intronic c.1663+9336 e15+9336 0.022 - - - no_errors tier3 1301 3 0.23 479 438 47.76 1 0 0 179223 TCGA-AB-2972 AML20 12 51486322 51486322 C T SNP KRT3 NM_057088.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-10229 NULL 0.001 - - - no_errors tier3 744 4 0.53 242 182 42.92 0 0 NA 179223 TCGA-AB-2972 AML20 12 59864266 59864266 C T SNP - - - - - - - - - - - - - - - tier3 335 0 0 379 59 13.41 0 0 NA 179223 TCGA-AB-2972 AML20 12 69593523 69593523 G A SNP PTPRR NM_002849.2 human genbank 54_36p -1 reviewed intronic c.58+6857 e1+6857 0 - - - no_errors tier3 627 2 0.32 481 178 26.97 0 0 NA 179223 TCGA-AB-2972 AML20 12 75381659 75381659 G C SNP OSBPL8 NM_020841.1 human genbank 54_36p -1 reviewed intronic c.43-3853 e2-3853 0.001 - - - no_errors tier3 1357 3 0.22 859 658 43.38 5 3 37.5 179223 TCGA-AB-2972 AML20 12 80871050 80871050 C T SNP - - - - - - - - - - - - - - - tier3 455 3 0.66 207 151 42.18 0 0 NA 179223 TCGA-AB-2972 AML20 12 83014857 83014857 C T SNP - - - - - - - - - - - - - - - tier3 833 3 0.36 417 302 41.94 0 0 NA 179223 TCGA-AB-2972 AML20 12 91488621 91488621 T C SNP - - - - - - - - - - - - - - - tier3 1785 0 0 1141 436 27.65 0 0 NA 179223 TCGA-AB-2972 AML20 12 93295731 93295731 G C SNP CCDC41 NM_001042399.1 human genbank 54_36p -1 validated intronic c.801+967 e5+967 0 - - - no_errors tier3 1558 2 0.13 1035 691 40.01 2 0 0 179223 TCGA-AB-2972 AML20 12 96412621 96412621 C T SNP MIRN1251 ENST00000408552 human ensembl 54_36p 1 known 3_prime_flanking_region c.*2734 NULL 0 - - - no_errors tier3 502 1 0.2 231 184 44.34 0 0 NA 179223 TCGA-AB-2972 AML20 12 99774987 99774987 C G SNP ANO4 NM_178826.3 human genbank 54_36p 1 validated intronic c.1-44568 e1-44568 0 - - - no_errors tier3 1323 2 0.15 529 414 43.86 0 0 NA 179223 TCGA-AB-2972 AML20 12 100085962 100085962 G A SNP SLC5A8 NM_145913.3 human genbank 54_36p -1 validated intronic c.1320+43 e11+43 0 - - - no_errors tier3 658 2 0.3 391 307 43.98 0 0 NA 179223 TCGA-AB-2972 AML20 12 106528309 106528310 - GT INS BTBD11 NM_001018072.1 human genbank 54_36p 1 validated intronic c.1809+47_1809+46 e5+47 0.000:0.000 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 12 111411267 111411267 T C SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed missense c.1504 p.S502P 1 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain" - no_errors tier1 1221 1 0.08 570 192 25.16 20 13 39.39 179223 TCGA-AB-2972 AML20 12 117609210 117609210 A G SNP - - - - - - - - - - - - - - - tier3 819 3 0.36 378 310 44.99 0 0 NA 179223 TCGA-AB-2972 AML20 12 117822674 117822674 C T SNP ENSG00000201042 ENST00000364172 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-11922 NULL 0.005 - - - no_errors tier3 1883 6 0.32 698 576 45.14 0 0 NA 179223 TCGA-AB-2972 AML20 12 122260757 122260757 G A SNP MPHOSPH9 NM_022782.2 human genbank 54_36p -1 validated intronic c.632-95 e4-95 0 - - - no_errors tier3 315 0 0 153 108 41.38 3 3 50 179223 TCGA-AB-2972 AML20 12 127434483 127434483 C T SNP - - - - - - - - - - - - - - - tier3 992 2 0.2 352 312 46.92 0 0 NA 179223 TCGA-AB-2972 AML20 12 128672455 128672455 T A SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.968+77853 e2+77853 0.002 - - - no_errors tier3 1167 1 0.09 525 318 37.63 0 0 NA 179223 TCGA-AB-2972 AML20 12 129562356 129562356 T G SNP RIMBP2 NM_015347.4 human genbank 54_36p -1 validated intronic c.1-5088 e1-5088 0.001 - - - no_errors tier3 390 5 1.26 64 42 39.62 0 0 NA 179223 TCGA-AB-2972 AML20 12 131126362 131126362 T - DEL EP400 NM_015409.3 human genbank 54_36p 1 validated intronic c.9019-652 e51-652 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 12 131365083 131365083 C T SNP GALNT9 ENST00000328957 human ensembl 54_36p -1 known intronic c.419+7826 e2+7826 0.131 - - - no_errors tier3 146 0 0 52 32 38.1 0 0 NA 179223 TCGA-AB-2972 AML20 13 21943149 21943149 G A SNP - - - - - - - - - - - - - - - tier3 953 2 0.21 387 298 43.5 0 0 NA 179223 TCGA-AB-2972 AML20 13 22218171 22218171 T A SNP ENSG00000218515 ENST00000405171 human ensembl 54_36p -1 known 5_prime_flanking_region c.-49458 NULL 0 - - - no_coding_region:pseudogene tier3 442 2 0.45 215 134 38.4 0 0 NA 179223 TCGA-AB-2972 AML20 13 25496684 25496684 G C SNP ATP8A2 ENST00000381655 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*4561 NULL 0.009 - - - no_errors tier3 1038 3 0.29 269 217 44.56 0 0 NA 179223 TCGA-AB-2972 AML20 13 29008907 29008907 C T SNP SLC7A1 NM_003045.4 human genbank 54_36p -1 validated intronic c.1-568 e1-568 0 - - - no_errors tier3 297 1 0.34 128 97 43.11 1 1 50 179223 TCGA-AB-2972 AML20 13 33904986 33904986 C T SNP - - - - - - - - - - - - - - - tier3 454 1 0.22 303 192 38.71 0 0 NA 179223 TCGA-AB-2972 AML20 13 41020839 41020839 A T SNP ENSG00000221194 ENST00000408267 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3931 NULL 0 - - - no_errors tier3 255 2 0.78 121 115 48.73 0 0 NA 179223 TCGA-AB-2972 AML20 13 43695387 43695387 C T SNP - - - - - - - - - - - - - - - tier3 664 2 0.3 254 158 38.35 0 0 NA 179223 TCGA-AB-2972 AML20 13 47911865 47911865 A G SNP RB1 NM_000321.2 human genbank 54_36p 1 reviewed intronic c.1696-13265 e18-13265 0.007 - - - no_errors tier3 690 3 0.43 301 291 49.16 1 0 0 179223 TCGA-AB-2972 AML20 13 49080120 49080120 T C SNP RCBTB1 NM_018191.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-40704 NULL 0.01 - - - no_errors tier3 784 2 0.25 207 187 47.34 0 0 NA 179223 TCGA-AB-2972 AML20 13 50336622 50336622 T C SNP RNASEH2B NM_024570.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45592 NULL 0.007 - - - no_errors tier3 261 2 0.75 148 123 45.22 0 0 NA 179223 TCGA-AB-2972 AML20 13 52537533 52537533 G A SNP OLFM4 NM_006418.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*14626 NULL 0.001 - - - no_errors tier3 642 6 0.93 306 188 38.06 0 0 NA 179223 TCGA-AB-2972 AML20 13 54503486 54503486 T C SNP - - - - - - - - - - - - - - - tier3 632 1 0.16 427 195 31.35 0 0 NA 179223 TCGA-AB-2972 AML20 13 56079022 56079022 T A SNP - - - - - - - - - - - - - - - tier3 597 1 0.17 365 318 46.56 0 0 NA 179223 TCGA-AB-2972 AML20 13 63221289 63221289 G T SNP ENSG00000202478 ENST00000365608 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-34646 NULL 0 - - - no_errors tier3 276 0 0 159 110 40.74 0 0 NA 179223 TCGA-AB-2972 AML20 13 64233830 64233830 G A SNP - - - - - - - - - - - - - - - tier3 1779 7 0.39 1170 902 43.45 0 0 NA 179223 TCGA-AB-2972 AML20 13 65739625 65739625 G A SNP ENSG00000219045 ENST00000404591 human ensembl 54_36p 1 known 5_prime_flanking_region c.-1505 NULL 0 - - - no_coding_region:pseudogene tier3 973 1 0.1 652 229 25.96 0 0 NA 179223 TCGA-AB-2972 AML20 13 71554801 71554801 G A SNP - - - - - - - - - - - - - - - tier3 736 3 0.41 422 316 42.82 0 0 NA 179223 TCGA-AB-2972 AML20 13 71559307 71559307 T C SNP - - - - - - - - - - - - - - - tier3 1348 2 0.15 797 565 41.45 0 0 NA 179223 TCGA-AB-2972 AML20 13 72147365 72147365 T G SNP ENSG00000217840 ENST00000402327 human ensembl 54_36p 1 known 5_prime_flanking_region c.-28467 NULL 0.001 - - - no_coding_region:pseudogene tier3 668 0 0 303 230 42.99 0 0 NA 179223 TCGA-AB-2972 AML20 13 74957504 74957504 A G SNP TBC1D4 NM_014832.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-3600 NULL 0.002 - - - no_errors tier3 389 2 0.51 177 121 40.6 0 0 NA 179223 TCGA-AB-2972 AML20 13 84517011 84517012 AT - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 13 88585220 88585220 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 13 95833415 95833415 G C SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+291591 e1+291591 0.012 - - - no_errors tier3 675 5 0.74 335 273 44.83 0 0 NA 179223 TCGA-AB-2972 AML20 13 97271948 97271948 T C SNP - - - - - - - - - - - - - - - tier3 953 2 0.21 1042 338 24.44 0 0 NA 179223 TCGA-AB-2972 AML20 13 98555399 98555399 A G SNP DOCK9 NM_015296.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-18793 NULL 0 - - - no_errors tier3 549 0 0 152 143 48.31 0 0 NA 179223 TCGA-AB-2972 AML20 13 99621814 99621814 A T SNP PCCA NM_000282.2 human genbank 54_36p 1 reviewed intronic c.468+14219 e6+14219 0.008 - - - no_errors tier3 889 0 0 360 285 44.19 1 2 66.67 179223 TCGA-AB-2972 AML20 13 101182663 101182663 A G SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.424-5502 e4-5502 0 - - - no_errors tier3 672 3 0.44 377 283 42.88 2 6 75 179223 TCGA-AB-2972 AML20 13 102945933 102945934 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 13 103867336 103867336 T - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 13 103911689 103911689 A G SNP - - - - - - - - - - - - - - - tier3 484 3 0.62 335 266 44.19 0 0 NA 179223 TCGA-AB-2972 AML20 13 105289279 105289279 C G SNP - - - - - - - - - - - - - - - tier3 1138 3 0.26 436 305 40.94 0 0 NA 179223 TCGA-AB-2972 AML20 13 106981565 106981565 G T SNP MIRN1267 ENST00000408723 human ensembl 54_36p -1 known rna NULL NULL 0.023 - - - no_errors tier1 300 4 1.32 239 162 40.4 NA 179223 TCGA-AB-2972 AML20 13 108405627 108405627 A G SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.1860-2410 e16-2410 0.002 - - - no_errors tier3 1553 3 0.19 729 532 42.12 0 1 100 179223 TCGA-AB-2972 AML20 13 108976413 108976413 C T SNP - - - - - - - - - - - - - - - tier3 1927 5 0.26 670 437 39.48 11 11 50 179223 TCGA-AB-2972 AML20 13 109287128 109287128 G A SNP LOC728767 XM_001714911.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*28721 NULL 0 - - - no_errors tier3 938 5 0.53 400 340 45.88 0 0 NA 179223 TCGA-AB-2972 AML20 13 112529959 112529959 A G SNP ATP11A NM_032189.2 human genbank 54_36p 1 reviewed intronic c.1221+753 e12+753 0 - - - no_errors tier3 654 1 0.15 153 119 43.43 1 0 0 179223 TCGA-AB-2972 AML20 14 27249503 27249503 C T SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-37288 NULL 0 - - - no_errors tier3 371 0 0 376 42 10 0 0 NA 179223 TCGA-AB-2972 AML20 14 35756011 35756011 C T SNP ENSG00000212071 ENST00000390782 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20486 NULL 0 - - - no_errors tier3 1064 6 0.56 472 409 46.32 0 0 NA 179223 TCGA-AB-2972 AML20 14 42127554 42127554 G A SNP - - - - - - - - - - - - - - - tier3 429 0 0 270 176 39.46 0 0 NA 179223 TCGA-AB-2972 AML20 14 42348364 42348364 C T SNP - - - - - - - - - - - - - - - tier3 393 1 0.25 310 201 39.26 0 0 NA 179223 TCGA-AB-2972 AML20 14 44927779 44927779 A C SNP - - - - - - - - - - - - - - - tier3 400 1 0.25 186 157 45.77 0 0 NA 179223 TCGA-AB-2972 AML20 14 47668403 47668403 G A SNP - - - - - - - - - - - - - - - tier3 683 4 0.58 353 288 44.86 0 0 NA 179223 TCGA-AB-2972 AML20 14 48045087 48045087 C T SNP - - - - - - - - - - - - - - - tier3 464 6 1.28 302 218 41.92 0 0 NA 179223 TCGA-AB-2972 AML20 14 51743278 51743278 G T SNP - - - - - - - - - - - - - - - tier3 1091 1 0.09 572 313 35.33 0 0 NA 179223 TCGA-AB-2972 AML20 14 55459497 55459497 G T SNP - - - - - - - - - - - - - - - tier3 1394 1 0.07 454 324 41.65 0 0 NA 179223 TCGA-AB-2972 AML20 14 58018135 58018135 T - DEL KIAA0586 NM_014749.3 human genbank 54_36p 1 validated intronic c.2717-849 e20-849 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 14 60716502 60716502 G C SNP - - - - - - - - - - - - - - - tier3 1908 10 0.52 480 396 45.15 0 0 NA 179223 TCGA-AB-2972 AML20 14 64702659 64702659 T C SNP ENSG00000222985 ENST00000411053 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41646 NULL 0 - - - no_errors tier3 1069 4 0.37 300 231 43.5 0 0 NA 179223 TCGA-AB-2972 AML20 14 66033321 66033321 A G SNP C14orf53 ENST00000389594 human ensembl 54_36p 1 known intronic c.674-1259 e7-1259 0.128 - - - no_errors tier3 1122 5 0.44 337 255 43.07 0 1 100 179223 TCGA-AB-2972 AML20 14 68828511 68828511 G A SNP GALNTL1 NM_020692.1 human genbank 54_36p 1 provisional intronic c.178-28670 e2-28670 0 - - - no_errors tier3 798 3 0.37 348 310 47.11 0 0 NA 179223 TCGA-AB-2972 AML20 14 75466228 75466228 T C SNP TTLL5 NM_015072.3 human genbank 54_36p 1 validated intronic c.3824-24292 e31-24292 0 - - - no_errors tier3 902 0 0 398 141 26.11 0 0 0 179223 TCGA-AB-2972 AML20 14 80226971 80226971 C T SNP C14orf145 NM_152446.3 human genbank 54_36p -1 validated intronic c.2806+52201 e17+52201 0.003 - - - no_errors tier3 138 0 0 146 123 45.72 3 0 0 179223 TCGA-AB-2972 AML20 14 83333691 83333691 A G SNP ENSG00000210408 ENST00000387673 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47095 NULL 0 - - - pseudogene tier3 932 2 0.21 669 121 15.32 0 0 NA 179223 TCGA-AB-2972 AML20 14 85872680 85872680 C T SNP - - - - - - - - - - - - - - - tier3 634 3 0.47 357 272 43.17 0 0 NA 179223 TCGA-AB-2972 AML20 14 87071694 87071694 C A SNP - - - - - - - - - - - - - - - tier3 955 1 0.1 609 180 22.78 0 0 NA 179223 TCGA-AB-2972 AML20 14 87223409 87223409 T C SNP LOC730121 XM_001132513.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-32043 NULL 0.001 - - - no_errors tier3 919 9 0.97 453 349 43.41 0 0 NA 179223 TCGA-AB-2972 AML20 14 91978635 91978635 C T SNP SLC24A4 NM_153646.2 human genbank 54_36p 1 validated intronic c.428-175 e6-175 0 - - - no_errors tier3 762 4 0.52 378 269 41.58 0 0 NA 179223 TCGA-AB-2972 AML20 14 93520574 93520574 C T SNP ASB2 NM_016150.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27543 NULL 0.001 - - - no_errors tier3 128 1 0.78 43 20 31.75 0 0 NA 179223 TCGA-AB-2972 AML20 14 97675442 97675442 C G SNP - - - - - - - - - - - - - - - tier3 1069 1 0.09 433 311 41.63 2 0 0 179223 TCGA-AB-2972 AML20 14 97706200 97706200 A G SNP - - - - - - - - - - - - - - - tier3 122 0 0 86 65 43.05 0 0 NA 179223 TCGA-AB-2972 AML20 14 99101903 99101903 A T SNP CCDC85C ENST00000380243 human ensembl 54_36p -1 known intronic c.794-29725 e2-29725 0 - - - no_errors tier3 318 1 0.31 97 78 44.32 0 0 NA 179223 TCGA-AB-2972 AML20 14 101448338 101448338 A G SNP PPP2R5C NM_002719.2 human genbank 54_36p 1 reviewed intronic c.1254-153 e12-153 0 - - - no_errors tier3 331 3 0.9 42 49 53.85 3 1 25 179223 TCGA-AB-2972 AML20 15 20716794 20716794 G T SNP LOC100133165 XM_001716939.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-6691 NULL 0.014 - - - no_errors tier3 356 0 0 119 71 37.37 0 0 0 179223 TCGA-AB-2972 AML20 15 22453504 22453504 G - DEL C15orf2 NM_018958.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-18604 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 15 23629662 23629662 A G SNP ATP10A NM_024490.3 human genbank 54_36p -1 reviewed intronic c.449+29226 e1+29226 0.001 - - - no_errors tier3 798 3 0.37 389 319 45.06 0 0 NA 179223 TCGA-AB-2972 AML20 15 24601667 24601667 G A SNP GABRB3 ENST00000383015 human ensembl 54_36p -1 known intronic c.248+10940 e2+10940 0 - - - no_errors tier3 725 0 0 238 159 39.95 0 0 NA 179223 TCGA-AB-2972 AML20 15 25508168 25508168 G T SNP - - - - - - - - - - - - - - - tier3 1071 5 0.46 274 205 42.8 0 0 NA 179223 TCGA-AB-2972 AML20 15 32026701 32026701 C T SNP AVEN NM_020371.2 human genbank 54_36p -1 validated intronic c.445+55824 e2+55824 0 - - - no_errors tier3 1309 3 0.23 495 340 40.52 2 0 0 179223 TCGA-AB-2972 AML20 15 36657979 36657980 - T INS RASGRP1 NM_005739.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-13858 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 15 37001229 37001229 C T SNP - - - - - - - - - - - - - - - tier3 597 1 0.17 393 298 43.13 0 0 NA 179223 TCGA-AB-2972 AML20 15 38248640 38248640 G T SNP BUB1B NM_001211.5 human genbank 54_36p 1 validated intronic c.180-915 e3-915 0.006 - - - no_errors tier3 683 3 0.44 412 334 44.71 0 0 0 179223 TCGA-AB-2972 AML20 15 49350988 49350988 T C SNP CYP19A1 NM_000103.3 human genbank 54_36p -1 reviewed intronic c.1-28549 e1-28549 0 - - - no_errors tier3 1055 1 0.09 350 231 39.76 0 0 NA 179223 TCGA-AB-2972 AML20 15 51367611 51367611 A G SNP - - - - - - - - - - - - - - - tier3 1050 4 0.38 502 372 42.51 0 0 NA 179223 TCGA-AB-2972 AML20 15 59809520 59809520 G A SNP - - - - - - - - - - - - - - - tier3 870 4 0.46 459 338 42.36 0 0 NA 179223 TCGA-AB-2972 AML20 15 77590847 77590847 C A SNP KIAA1024 NM_015206.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*43066 NULL 0.002 - - - no_errors tier3 732 3 0.41 311 267 46.19 0 0 NA 179223 TCGA-AB-2972 AML20 15 84218290 84218290 C A SNP - - - - - - - - - - - - - - - tier3 780 0 0 290 214 42.38 0 0 NA 179223 TCGA-AB-2972 AML20 15 87648123 87648123 T A SNP FANCI NM_018193.1 human genbank 54_36p 1 reviewed missense c.2851 p.S951T 0.084 NULL NULL - no_errors tier1 605 5 0.82 225 178 43.95 17 32 65.31 179223 TCGA-AB-2972 AML20 15 88115022 88115022 G A SNP MESP2 NM_001039958.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-5571 NULL 0 - - - no_errors tier3 387 1 0.26 96 93 49.21 0 0 NA 179223 TCGA-AB-2972 AML20 15 95386126 95386126 T C SNP ENSG00000215948 ENST00000401129 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*49370 NULL 0.004 - - - no_errors tier3 490 0 0 286 164 36.44 0 0 NA 179223 TCGA-AB-2972 AML20 16 4555299 4555299 G A SNP ENSG00000205832 ENST00000382019 human ensembl 54_36p 1 known intronic c.421-6264 e2-6264 0.002 - - - no_stop_codon tier3 549 1 0.18 123 106 46.29 0 0 NA 179223 TCGA-AB-2972 AML20 16 7605890 7605890 C T SNP A2BP1 NM_145891.1 human genbank 54_36p 1 reviewed intronic c.736+8549 e7+8549 0 - - - no_errors tier3 646 0 0 408 163 28.55 0 0 NA 179223 TCGA-AB-2972 AML20 16 20901558 20901558 G C SNP DNAH3 NM_017539.1 human genbank 54_36p -1 provisional missense c.7845 p.D2615E 0.829 superfamily_P-loop containing nucleoside triphosphate hydrolases "HMMSmart_SM00382,HMMPfam_Dynein_heavy,superfamily_Prefoldin,HMMPfam_AAA_5,HMMPfam_DHC_N2,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 600 0 195 174 47.15 0 179223 TCGA-AB-2972 AML20 16 26419731 26419731 A T SNP - - - - - - - - - - - - - - - tier3 475 1 0.21 238 163 40.65 0 0 NA 179223 TCGA-AB-2972 AML20 16 47510799 47510799 G A SNP - - - - - - - - - - - - - - - tier3 675 1 0.15 282 248 46.7 0 0 NA 179223 TCGA-AB-2972 AML20 16 49654125 49654125 T C SNP LOC728654 XM_001128037.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-23985 NULL 0 - - - no_errors tier3 1301 3 0.23 663 195 22.67 0 0 NA 179223 TCGA-AB-2972 AML20 16 49767605 49767605 G A SNP SALL1 NM_002968.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24952 NULL 0 - - - no_errors tier3 676 2 0.29 270 237 46.65 0 0 NA 179223 TCGA-AB-2972 AML20 16 56881992 56881992 G A SNP KLKBL4 NM_001080492.1 human genbank 54_36p -1 provisional intronic c.263+372 e2+372 0 - - - no_errors tier3 989 2 0.2 379 243 38.94 0 0 NA 179223 TCGA-AB-2972 AML20 16 62090900 62090900 C T SNP - - - - - - - - - - - - - - - tier3 1012 4 0.39 431 330 43.25 0 0 NA 179223 TCGA-AB-2972 AML20 16 63062058 63062058 C T SNP - - - - - - - - - - - - - - - tier3 1111 3 0.27 368 315 45.99 0 0 NA 179223 TCGA-AB-2972 AML20 16 63415199 63415199 C T SNP - - - - - - - - - - - - - - - tier3 796 0 0 598 219 26.77 0 0 NA 179223 TCGA-AB-2972 AML20 16 64278913 64278913 C T SNP - - - - - - - - - - - - - - - tier3 931 0 0 423 331 43.84 0 0 NA 179223 TCGA-AB-2972 AML20 16 76479156 76479156 T A SNP VAT1L NM_020927.1 human genbank 54_36p 1 provisional intronic c.1077+2956 e7+2956 0.001 - - - no_errors tier3 1721 5 0.29 568 376 39.83 0 0 NA 179223 TCGA-AB-2972 AML20 16 78236248 78236248 A C SNP MAF NM_005360.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44948 NULL 0 - - - no_errors tier3 1079 2 0.19 531 395 42.56 0 0 NA 179223 TCGA-AB-2972 AML20 16 81578086 81578086 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.158-45030 e3-45030 0.001 - - - no_errors tier3 1049 1 0.1 362 311 46.21 0 0 NA 179223 TCGA-AB-2972 AML20 16 82701171 82701171 C T SNP MBTPS1 NM_003791.2 human genbank 54_36p -1 reviewed intronic c.1+6670 e0+6670 0.001 - - - no_errors tier3 970 5 0.51 349 259 42.53 3 1 25 179223 TCGA-AB-2972 AML20 16 87216191 87216191 C T SNP ZC3H18 NM_144604.2 human genbank 54_36p 1 provisional nonsense c.1561 p.R521* 1 NULL "HMMPfam_zf-CCCH,HMMSmart_SM00356" - no_errors tier1 299 0 83 63 43.15 26 6 18.75 179223 TCGA-AB-2972 AML20 17 9049928 9049928 G T SNP NTN1 NM_004822.2 human genbank 54_36p 1 reviewed intronic c.1412-15282 e5-15282 0.001 - - - no_errors tier3 1492 1 0.07 365 284 43.76 0 3 100 179223 TCGA-AB-2972 AML20 17 14214146 14214146 T C SNP HS3ST3B1 NM_006041.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*24458 NULL 0 - - - no_errors tier3 1087 3 0.27 443 369 45.22 0 0 NA 179223 TCGA-AB-2972 AML20 17 17608169 17608169 G A SNP RAI1 NM_030665.3 human genbank 54_36p 1 reviewed intronic c.1-28803 e1-28803 0 - - - no_errors tier3 513 1 0.19 92 71 43.56 4 0 0 179223 TCGA-AB-2972 AML20 17 18856843 18856843 A G SNP SLC5A10 NM_152351.1 human genbank 54_36p 1 validated intronic c.983-557 e10-557 0.001 - - - no_errors tier3 1368 4 0.29 267 214 44.4 0 2 100 179223 TCGA-AB-2972 AML20 17 22713731 22713731 A G SNP LOC100132972 XR_039130.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-9982 NULL 0.002 - - - pseudogene tier3 716 0 0 248 179 41.72 0 0 NA 179223 TCGA-AB-2972 AML20 17 28669905 28669905 T C SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.556-206707 e2-206707 0.002 - - - overly_large_intron tier3 847 1 0.12 264 239 47.51 0 0 NA 179223 TCGA-AB-2972 AML20 17 29284811 29284811 A G SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.555+222299 e1+222299 0 - - - overly_large_intron tier3 1152 1 0.09 722 110 13.22 0 0 NA 179223 TCGA-AB-2972 AML20 17 32963095 32963095 T C SNP AP1GBP1 NM_007247.3 human genbank 54_36p -1 reviewed intronic c.3666+7099 e19+7099 0.518 - - - no_errors tier3 779 3 0.38 319 239 42.68 3 1 25 179223 TCGA-AB-2972 AML20 17 34477868 34477868 C T SNP PLXDC1 NM_020405.4 human genbank 54_36p -1 validated intronic c.1384-130 e14-130 0 - - - no_errors tier3 439 1 0.23 189 149 43.82 0 1 100 179223 TCGA-AB-2972 AML20 17 45025412 45025412 G A SNP SPOP NM_001007226.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*7327 NULL 0.022 - - - no_errors tier3 517 7 1.34 164 145 46.93 0 0 NA 179223 TCGA-AB-2972 AML20 17 46027808 46027808 G A SNP CACNA1G NM_018896.3 human genbank 54_36p 1 validated intronic c.2979+387 e14+387 0 - - - no_errors tier3 162 0 0 55 48 46.6 0 0 NA 179223 TCGA-AB-2972 AML20 17 47283288 47283288 G A SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.279+80061 e3+80061 0.001 - - - no_errors tier3 750 4 0.53 424 292 40.67 0 0 NA 179223 TCGA-AB-2972 AML20 17 50118668 50118668 A T SNP - - - - - - - - - - - - - - - tier3 747 5 0.66 297 241 44.8 0 0 NA 179223 TCGA-AB-2972 AML20 17 53256697 53256697 C T SNP LOC100128440 XM_001726725.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37365 NULL 0 - - - no_errors tier3 426 1 0.23 198 158 44.38 0 0 NA 179223 TCGA-AB-2972 AML20 17 58211634 58211634 G A SNP MARCH10 NM_001100875.1 human genbank 54_36p -1 validated intronic c.210+7939 e2+7939 0.012 - - - no_errors tier3 1112 1 0.09 321 260 44.75 0 0 NA 179223 TCGA-AB-2972 AML20 17 58848167 58848167 A G SNP TANC2 NM_025185.3 human genbank 54_36p 1 validated intronic c.3916-1233 e24-1233 0.001 - - - no_errors tier3 964 1 0.1 393 222 36.04 0 5 100 179223 TCGA-AB-2972 AML20 17 59325426 59325426 A G SNP CSH1 ENST00000316193 human ensembl 54_36p -1 known intronic c.654+579 e5+579 0.094 - - - no_errors tier3 612 3 0.49 127 127 49.8 0 0 NA 179223 TCGA-AB-2972 AML20 17 61918770 61918770 A T SNP PRKCA NM_002737.2 human genbank 54_36p 1 reviewed intronic c.206-4011 e3-4011 0 - - - no_errors tier3 957 2 0.21 321 214 39.93 0 0 0 179223 TCGA-AB-2972 AML20 17 62470918 62470918 C G SNP CACNG1 NM_000727.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-321 NULL 0.005 - - - no_errors tier3 455 1 0.22 139 101 42.08 0 0 NA 179223 TCGA-AB-2972 AML20 17 66218243 66218243 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 17 66890870 66890870 C T SNP - - - - - - - - - - - - - - - tier3 1143 7 0.61 609 444 42.13 0 0 NA 179223 TCGA-AB-2972 AML20 18 1081550 1081550 G A SNP - - - - - - - - - - - - - - - tier3 735 5 0.67 379 232 37.97 0 0 NA 179223 TCGA-AB-2972 AML20 18 2230180 2230180 C T SNP LOC100131655 XM_001732884.1 human genbank 54_36p -1 model intronic c.3477+8324 e15+8324 0 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1695 9 0.53 690 521 42.95 0 0 NA 179223 TCGA-AB-2972 AML20 18 3623014 3623014 G A SNP DLGAP1 NM_004746.1 human genbank 54_36p -1 provisional intronic c.1592-50768 e5-50768 0.014 - - - no_errors tier3 732 1 0.14 237 165 40.84 0 0 NA 179223 TCGA-AB-2972 AML20 18 8124680 8124680 C T SNP PTPRM NM_001105244.1 human genbank 54_36p 1 reviewed intronic c.2168-8965 e14-8965 0 - - - no_errors tier3 1319 5 0.38 805 607 42.99 1 0 0 179223 TCGA-AB-2972 AML20 18 25839667 25839667 C T SNP - - - - - - - - - - - - - - - tier3 1574 4 0.25 728 527 41.99 0 0 NA 179223 TCGA-AB-2972 AML20 18 26658740 26658740 C T SNP - - - - - - - - - - - - - - - tier3 1070 6 0.56 401 325 44.58 0 0 NA 179223 TCGA-AB-2972 AML20 18 27100235 27100235 A T SNP - - - - - - - - - - - - - - - tier3 528 5 0.94 250 170 40.28 0 0 NA 179223 TCGA-AB-2972 AML20 18 29592807 29592807 T C SNP ASXL3 NM_030632.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*12250 NULL 0.006 - - - no_errors tier3 646 1 0.15 349 236 40.14 0 0 NA 179223 TCGA-AB-2972 AML20 18 42249042 42249042 G C SNP RNF165 NM_152470.2 human genbank 54_36p 1 validated intronic c.62-18109 e2-18109 0.001 - - - no_errors tier3 890 6 0.67 262 212 44.63 0 0 NA 179223 TCGA-AB-2972 AML20 18 46855693 46855693 A G SNP SMAD4 NM_005359.5 human genbank 54_36p 1 validated intronic c.1309-1313 e10-1313 0.368 - - - no_errors tier3 658 1 0.15 376 254 40.25 0 0 0 179223 TCGA-AB-2972 AML20 18 51226811 51226811 T G SNP TCF4 NM_001083962.1 human genbank 54_36p -1 reviewed intronic c.305-5064 e5-5064 0.001 - - - no_errors tier3 1783 18 1 596 454 43.24 7 2 22.22 179223 TCGA-AB-2972 AML20 18 54333922 54333922 C A SNP ALPK2 NM_052947.3 human genbank 54_36p -1 validated intronic c.5941-629 e9-629 0.001 - - - no_errors tier3 1413 6 0.42 551 421 43.31 0 0 NA 179223 TCGA-AB-2972 AML20 18 56009956 56009956 G A SNP ENSG00000202468 ENST00000365598 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*28036 NULL 0 - - - no_errors tier3 836 1 0.12 391 281 41.69 0 0 NA 179223 TCGA-AB-2972 AML20 18 60356744 60356744 G C SNP - - - - - - - - - - - - - - - tier3 1115 1 0.09 566 386 40.38 0 0 NA 179223 TCGA-AB-2972 AML20 18 60569748 60569748 A G SNP - - - - - - - - - - - - - - - tier3 757 1 0.13 352 263 42.63 0 0 NA 179223 TCGA-AB-2972 AML20 18 60625197 60625197 C T SNP - - - - - - - - - - - - - - - tier3 958 4 0.42 502 332 39.71 0 0 NA 179223 TCGA-AB-2972 AML20 18 61097923 61097923 A G SNP - - - - - - - - - - - - - - - tier3 1749 13 0.74 691 580 45.56 0 0 NA 179223 TCGA-AB-2972 AML20 18 68864349 68864349 C T SNP - - - - - - - - - - - - - - - tier3 868 2 0.23 351 258 42.36 0 0 NA 179223 TCGA-AB-2972 AML20 18 70338310 70338310 A G SNP CNDP2 NM_018235.1 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*27 NULL 0 - - - no_errors tier3 893 4 0.45 303 244 44.53 45 30 40 179223 TCGA-AB-2972 AML20 18 72369050 72369050 G A SNP LOC100132894 XM_001715252.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-847 NULL 0 - - - no_errors tier3 495 2 0.4 138 104 42.98 0 0 NA 179223 TCGA-AB-2972 AML20 18 74517510 74517510 G C SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*34749 NULL 0 - - - no_errors tier3 153 2 1.29 53 39 42.39 0 0 NA 179223 TCGA-AB-2972 AML20 19 3315276 3315276 A C SNP NFIC NM_205843.2 human genbank 54_36p 1 validated intronic c.3+4593 e1+4593 0 - - - no_errors tier3 422 1 0.24 95 76 44.44 1 0 0 179223 TCGA-AB-2972 AML20 19 8986831 8986831 G T SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-34017 NULL 0.002 - - - no_errors tier3 664 0 0 228 99 30.28 0 0 NA 179223 TCGA-AB-2972 AML20 19 13231431 13231431 C T SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known silent c.4338 p.V1446 1 "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels" - no_errors tier1 1009 9 0.88 295 214 41.72 0 179223 TCGA-AB-2972 AML20 19 13484203 13484203 T C SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known 5_prime_flanking_region c.-6165 NULL 0 - - - no_errors tier3 1219 3 0.24 292 236 44.36 0 0 NA 179223 TCGA-AB-2972 AML20 19 15600592 15600592 G A SNP CYP4F8 ENST00000325723 human ensembl 54_36p 1 known missense c.1333 p.D445N 0.996 "HMMPfam_p450,superfamily_Cytochrome P450" "HMMPfam_p450,superfamily_Cytochrome P450,PatternScan_CYTOCHROME_P450" - no_errors tier1 466 0 131 96 42.11 NA 179223 TCGA-AB-2972 AML20 19 16859226 16859226 C T SNP F2RL3 NM_003950.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1775 NULL 0.001 - - - no_errors tier3 137 1 0.72 49 37 43.02 0 0 NA 179223 TCGA-AB-2972 AML20 19 16876651 16876651 C G SNP CPAMD8 NM_015692.2 human genbank 54_36p -1 validated intronic c.4169-289 e31-289 0 - - - no_errors tier3 485 0 0 98 73 42.69 0 0 NA 179223 TCGA-AB-2972 AML20 19 18196163 18196163 C - DEL PDE4C NM_001098819.3 human genbank 54_36p -1 validated 5_prime_untranslated_region c.-2106 NULL 0.059 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 19 21110119 21110119 G A SNP ZNF431 NM_133473.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-6708 NULL 0 - - - no_errors tier3 570 1 0.17 313 252 44.44 0 0 0 179223 TCGA-AB-2972 AML20 19 21783552 21783552 C T SNP ZNF43 NM_003423.2 human genbank 54_36p -1 validated missense c.1127 p.G376D 0.636 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 785 0 235 225 48.91 25 33 56.9 179223 TCGA-AB-2972 AML20 19 36451741 36451741 C T SNP TSHZ3 NM_020856.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*7552 NULL 0 - - - no_errors tier3 507 0 0 198 164 45.05 0 0 NA 179223 TCGA-AB-2972 AML20 19 40518771 40518771 T C SNP CD22 NM_001771.2 human genbank 54_36p 1 validated splice_region c.413-8 e3-8 0.001 - - - no_errors tier3 1065 4 0.37 303 219 41.87 2 0 0 179223 TCGA-AB-2972 AML20 19 43070188 43070188 C T SNP SIPA1L3 NM_015073.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-193858 NULL 0 - - - no_errors tier3 952 1 0.1 607 75 10.96 0 0 NA 179223 TCGA-AB-2972 AML20 19 55880946 55880946 G A SNP SHANK1 NM_016148.2 human genbank 54_36p -1 validated intronic c.2577+360 e20+360 0.003 - - - no_errors tier3 481 0 0 108 61 36.09 0 0 0 179223 TCGA-AB-2972 AML20 20 7682134 7682134 G A SNP - - - - - - - - - - - - - - - tier3 1113 3 0.27 554 434 43.84 0 0 NA 179223 TCGA-AB-2972 AML20 20 9095781 9095781 G T SNP PLCB4 NM_000933.2 human genbank 54_36p 1 reviewed intronic c.1-50256 e1-50256 0 - - - no_errors tier3 502 0 0 356 249 41.09 0 0 NA 179223 TCGA-AB-2972 AML20 20 11982877 11982877 C T SNP - - - - - - - - - - - - - - - tier3 344 2 0.58 127 156 54.93 0 2 100 179223 TCGA-AB-2972 AML20 20 12569323 12569323 T G SNP - - - - - - - - - - - - - - - tier3 589 0 0 314 211 40.11 0 0 NA 179223 TCGA-AB-2972 AML20 20 13112139 13112139 A T SNP ISM1 NM_080826.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38285 NULL 0.052 - - - no_errors tier3 330 0 0 189 168 47.06 0 0 0 179223 TCGA-AB-2972 AML20 20 22147757 22147757 G A SNP - - - - - - - - - - - - - - - tier3 485 1 0.2 454 108 19.22 0 0 NA 179223 TCGA-AB-2972 AML20 20 37378001 37378001 G A SNP ENSG00000210455 ENST00000387720 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36909 NULL 0 - - - pseudogene tier3 927 0 0 498 381 43.3 0 0 NA 179223 TCGA-AB-2972 AML20 20 39484966 39484966 T C SNP CHD6 NM_032221.3 human genbank 54_36p -1 reviewed intronic c.4555+580 e29+580 0 - - - no_errors tier3 991 2 0.2 384 296 43.34 1 0 0 179223 TCGA-AB-2972 AML20 20 39602983 39602983 T C SNP CHD6 NM_032221.3 human genbank 54_36p -1 reviewed intronic c.34-7360 e2-7360 0.079 - - - no_errors tier3 452 1 0.22 277 189 40.47 2 1 33.33 179223 TCGA-AB-2972 AML20 20 41521935 41521935 T A SNP SFRS6 NM_006275.5 human genbank 54_36p 1 reviewed missense c.367 p.W123R 1 "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 571 1 0.17 226 80 26.14 136 179 56.47 179223 TCGA-AB-2972 AML20 20 44726522 44726522 C T SNP SLC13A3 NM_001011554.1 human genbank 54_36p -1 reviewed intronic c.1+5567 e0+5567 0.001 - - - no_errors tier3 902 6 0.66 210 165 44 0 0 NA 179223 TCGA-AB-2972 AML20 20 49084883 49084883 C A SNP KCNG1 NM_002237.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24601 NULL 0.001 - - - no_errors tier3 980 9 0.91 349 243 41.05 0 0 NA 179223 TCGA-AB-2972 AML20 20 56714161 56714161 T C SNP NPEPL1 ENST00000356091 human ensembl 54_36p 1 known intronic c.820-1425 e8-1425 0 - - - no_errors tier3 296 1 0.33 122 90 42.45 0 0 0 179223 TCGA-AB-2972 AML20 20 58966372 58966372 A C SNP - - - - - - - - - - - - - - - tier3 750 0 0 210 186 46.97 0 0 NA 179223 TCGA-AB-2972 AML20 21 17758838 17758838 A T SNP CXADR NM_001338.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48481 NULL 0.015 - - - no_errors tier3 667 2 0.3 268 191 41.61 0 0 NA 179223 TCGA-AB-2972 AML20 21 19309795 19309795 G A SNP LOC100134323 XM_001724941.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-26159 NULL 0 - - - pseudogene:no_stop_codon tier3 501 2 0.4 264 229 46.45 0 0 NA 179223 TCGA-AB-2972 AML20 21 31038178 31038178 C T SNP ENSG00000216730 ENST00000405417 human ensembl 54_36p -1 known 5_prime_flanking_region c.-1394 NULL 0 - - - no_coding_region:pseudogene tier3 829 0 0 416 325 43.8 0 0 NA 179223 TCGA-AB-2972 AML20 21 31137638 31137639 - T INS KRTAP8-1 NM_175857.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-30229 NULL 0.039:0.037 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 179223 TCGA-AB-2972 AML20 21 36633035 36633035 T C SNP MORC3 NM_015358.2 human genbank 54_36p 1 reviewed missense c.554 p.L185P 1 superfamily_ATP_bd_ATPase "HMMPfam_HATPase_c,superfamily_ATP_bd_ATPase,HMMPfam_zf-CW" - no_errors tier1 1179 1 0.08 290 231 44.25 59 43 42.16 179223 TCGA-AB-2972 AML20 21 37900368 37900368 C A SNP KCNJ6 NM_002240.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*18963 NULL 0.019 - - - no_errors tier3 633 0 0 187 133 41.56 0 0 NA 179223 TCGA-AB-2972 AML20 21 37971039 37971039 C T SNP KCNJ6 NM_002240.2 human genbank 54_36p -1 reviewed intronic c.946+37345 e2+37345 0 - - - no_errors tier3 590 1 0.17 282 45 13.68 0 0 NA 179223 TCGA-AB-2972 AML20 21 38129185 38129185 G A SNP KCNJ6 NM_002240.2 human genbank 54_36p -1 reviewed intronic c.25+5645 e1+5645 0 - - - no_errors tier3 1257 9 0.71 477 340 41.56 0 0 NA 179223 TCGA-AB-2972 AML20 21 38436951 38436951 T A SNP DSCR8 ENST00000357704 human ensembl 54_36p 1 known intronic c.81-11428 e2-11428 0.001 - - - no_errors tier3 1151 3 0.26 509 355 40.99 0 0 NA 179223 TCGA-AB-2972 AML20 21 38632114 38632114 G A SNP LOC100131955 XM_001715532.1 human genbank 54_36p 1 model intronic c.459+3070 e3+3070 0.003 - - - no_errors tier3 1034 4 0.38 425 289 40.42 0 0 NA 179223 TCGA-AB-2972 AML20 21 44892418 44892418 C T SNP C21orf29 NM_144991.2 human genbank 54_36p -1 provisional intronic c.82+63358 e1+63358 0 - - - no_errors tier3 306 1 0.32 118 98 45.16 0 0 NA 179223 TCGA-AB-2972 AML20 22 24464708 24464708 C T SNP MYO18B NM_032608.5 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-22352 NULL 0.019 - - - no_errors tier3 496 3 0.6 163 89 35.18 0 0 NA 179223 TCGA-AB-2972 AML20 22 30778773 30778773 C T SNP SLC5A1 NM_000343.2 human genbank 54_36p 1 validated intronic c.207+2772 e2+2772 0.091 - - - no_errors tier3 1493 4 0.27 435 331 42.93 0 0 NA 179223 TCGA-AB-2972 AML20 22 42010952 42010952 C T SNP SCUBE1 NM_173050.2 human genbank 54_36p -1 validated intronic c.484+6044 e4+6044 0.001 - - - no_errors tier3 459 0 0 147 94 39 0 0 0 179223 TCGA-AB-2972 AML20 22 44422865 44422865 G A SNP ATXN10 NM_013236.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-23743 NULL 0 - - - no_errors tier3 1027 7 0.68 238 184 43.6 0 0 NA 179223 TCGA-AB-2972 AML20 22 44818232 44818232 A T SNP uc003bgr.2 ENST00000381051 human ensembl 54_36p 1 known 5_prime_flanking_region c.-54239 NULL 0 - - - no_errors tier3 194 1 0.51 49 35 41.67 0 0 NA 179223 TCGA-AB-2972 AML20 22 47166185 47166185 G T SNP - - - - - - - - - - - - - - - tier3 657 2 0.3 325 309 48.66 0 0 NA 573988 TCGA-AB-2973 AML35 X 37907322 37907322 T A SNP SRPX NM_006307.3 human genbank 54_36p -1 provisional intronic c.653+1644 e5+1644 0 - - - no_errors tier3 896 194 17.8 604 539 47.12 0 0 0 573988 TCGA-AB-2973 AML35 X 55700094 55700094 G A SNP ENSG00000169164 ENST00000347911 human ensembl 54_36p -1 known silent c.28 p.L10 0 HMMPfam_GAGE HMMPfam_GAGE - no_start_codon:no_stop_codon tier1 498 59 10.57 404 355 46.77 NA 573988 TCGA-AB-2973 AML35 X 121434334 121434334 G A SNP ENSG00000221317 ENST00000408390 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-982 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 X 152730397 152730397 C T SNP PDZD4 NM_032512.2 human genbank 54_36p -1 provisional intronic c.61-3153 e2-3153 0.001 - - - no_errors tier3 145 21 12.65 101 90 47.12 0 0 0 573988 TCGA-AB-2973 AML35 1 2047105 2047105 A G SNP PRKCZ NM_002744.1 human genbank 54_36p 1 reviewed intronic c.335-9456 e5-9456 0.153 - - - no_errors tier3 76 11 12.36 80 91 52.3 0 0 NA 573988 TCGA-AB-2973 AML35 1 26357620 26357620 G A SNP CNKSR1 NM_006314.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19006 NULL 0.025 - - - no_errors tier3 155 41 20.81 139 123 46.77 0 0 NA 573988 TCGA-AB-2973 AML35 1 50546418 50546418 C G SNP LOC343184 XR_016832.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-17973 NULL 0.001 - - - pseudogene tier3 931 137 12.78 651 482 42.47 0 0 NA 573988 TCGA-AB-2973 AML35 1 68010042 68010042 A T SNP GNG12 NM_018841.4 human genbank 54_36p -1 validated intronic c.1+5687 e0+5687 0.007 - - - no_errors tier3 683 105 13.29 468 377 44.51 0 0 NA 573988 TCGA-AB-2973 AML35 1 95228406 95228406 G A SNP ALG14 NM_144988.3 human genbank 54_36p -1 validated intronic c.421-6956 e4-6956 0 - - - no_errors tier2 692 123 15.06 555 439 44.12 0 0 0 573988 TCGA-AB-2973 AML35 1 97371514 97371514 T C SNP DPYD NM_000110.3 human genbank 54_36p -1 reviewed intronic c.2623-34738 e21-34738 0.003 - - - no_errors tier3 40 13 24.53 41 30 42.25 14 10 41.67 573988 TCGA-AB-2973 AML35 1 152866077 152866077 A G SNP ADAR NM_001025107.1 human genbank 54_36p -1 reviewed intronic c.1+878 e0+878 0 - - - no_errors tier2 657 92 12.28 372 240 39.22 0 0 0 573988 TCGA-AB-2973 AML35 1 156065861 156065861 G T SNP FCRL1 NM_052938.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-9410 NULL 0.193 - - - no_errors tier3 346 69 16.59 307 188 37.83 0 0 NA 573988 TCGA-AB-2973 AML35 1 157079521 157079521 A G SNP MNDA NM_002432.1 human genbank 54_36p 1 reviewed intronic c.266-172 e2-172 0 - - - no_errors tier2 913 132 12.62 627 428 40.57 5 10 66.67 573988 TCGA-AB-2973 AML35 1 170659983 170659983 A G SNP C1orf105 NM_139240.2 human genbank 54_36p 1 predicted intronic c.21+3314 e1+3314 0 - - - no_errors tier3 880 125 12.44 562 393 41.07 1 0 0 573988 TCGA-AB-2973 AML35 1 232727616 232727616 C G SNP TARBP1 NM_005646.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-46144 NULL 0.025 - - - no_errors tier2 557 116 17.13 265 251 48.64 0 0 NA 573988 TCGA-AB-2973 AML35 1 246890786 246890786 T C SNP OR2T35 NM_001001827.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-21604 NULL 0.005 - - - no_errors tier3 169 37 17.96 147 116 43.77 0 0 NA 573988 TCGA-AB-2973 AML35 2 1119223 1119223 T G SNP SNTG2 ENST00000308624 human ensembl 54_36p 1 known intronic c.326-4085 e5-4085 0.007 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 2 1780321 1780321 G A SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.3270+4154 e18+4154 0 - - - no_errors tier2 112 12 9.6 82 65 43.92 0 0 NA 573988 TCGA-AB-2973 AML35 2 9847540 9847540 C T SNP ENSG00000200034 ENST00000363164 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49177 NULL 0.006 - - - no_errors tier2 184 37 16.74 138 87 38.67 0 0 NA 573988 TCGA-AB-2973 AML35 2 80360257 80360257 C T SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1060-113590 e7-113590 0.052 - - - no_errors tier3 526 97 15.54 413 282 40.46 0 0 NA 573988 TCGA-AB-2973 AML35 2 84363515 84363515 G A SNP uc010ffz.1 ENST00000331369 human ensembl 54_36p 1 known 5_prime_flanking_region c.-7939 NULL 0.001 - - - no_errors tier2 475 72 13.04 361 299 45.3 0 0 NA 573988 TCGA-AB-2973 AML35 2 120945152 120945152 C T SNP - - - - - - - - - - - - - - - tier2 565 112 16.49 507 465 47.84 0 0 NA 573988 TCGA-AB-2973 AML35 2 132308722 132308722 A G SNP MGC50273 NM_214461.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-33742 NULL 0.492 - - - no_errors tier3 44 6 12 23 25 52.08 0 0 NA 573988 TCGA-AB-2973 AML35 2 177039562 177039562 G T SNP - - - - - - - - - - - - - - - tier3 371 46 11 305 240 44.04 0 0 NA 573988 TCGA-AB-2973 AML35 2 185954519 185954519 A G SNP - - - - - - - - - - - - - - - tier3 356 46 11.44 274 223 44.87 0 0 NA 573988 TCGA-AB-2973 AML35 2 226037120 226037120 T C SNP KIAA1486 NM_020864.1 human genbank 54_36p 1 validated intronic c.222-49211 e2-49211 0 - - - no_errors tier3 502 79 13.6 401 299 42.65 0 0 NA 573988 TCGA-AB-2973 AML35 3 1897326 1897326 G A SNP ENSG00000214073 ENST00000397467 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-25105 NULL 0 - - - no_coding_region:pseudogene tier3 347 48 12.09 334 242 42.01 0 0 NA 573988 TCGA-AB-2973 AML35 3 8381350 8381350 A G SNP ENSG00000209729 ENST00000386994 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15 NULL 0.001 - - - pseudogene tier3 951 149 13.55 743 566 43.24 0 0 NA 573988 TCGA-AB-2973 AML35 3 22074772 22074772 T C SNP - - - - - - - - - - - - - - - tier3 393 65 14.19 267 202 43.07 2 0 0 573988 TCGA-AB-2973 AML35 3 38494675 38494675 C T SNP ACVR2B NM_001106.3 human genbank 54_36p 1 reviewed missense c.410 p.T137M 1 NULL "HMMPfam_Activin_recp,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase,superfamily_Snake toxin-like" - no_errors tier1 331 62 15.78 240 183 43.26 NA 573988 TCGA-AB-2973 AML35 3 38926801 38926801 C T SNP SCN11A NM_014139.2 human genbank 54_36p -1 validated intronic c.960-99 e8-99 0.001 - - - no_errors tier2 490 69 12.32 428 280 39.44 0 0 NA 573988 TCGA-AB-2973 AML35 3 52815055 52815055 C T SNP ITIH3 NM_002217.3 human genbank 54_36p 1 validated intronic c.1907-104 e17-104 0 - - - no_errors tier3 179 48 20.87 190 111 36.39 0 0 NA 573988 TCGA-AB-2973 AML35 3 72131662 72131662 T A SNP - - - - - - - - - - - - - - - tier2 530 76 12.54 523 376 41.82 0 1 100 573988 TCGA-AB-2973 AML35 3 160308918 160308918 T A SNP IQCJ NM_001042705.1 human genbank 54_36p 1 provisional intronic c.9+38994 e1+38994 0.003 - - - no_errors tier2 477 80 14.36 385 372 48.88 0 0 NA 573988 TCGA-AB-2973 AML35 3 162939745 162939745 G A SNP - - - - - - - - - - - - - - - tier3 157 28 15.14 247 177 41.75 0 0 NA 573988 TCGA-AB-2973 AML35 3 183065520 183065520 C G SNP ENSG00000199839 ENST00000362969 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42048 NULL 0.466 - - - no_errors tier3 NA NA NA NA NA NA 1 0 0 573988 TCGA-AB-2973 AML35 4 5560977 5560977 A G SNP C4orf6 NM_005750.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-16982 NULL 0 - - - no_errors tier3 327 47 12.57 289 228 44.02 0 0 NA 573988 TCGA-AB-2973 AML35 4 7221259 7221259 G A SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-24466 NULL 0 - - - no_errors tier3 540 83 13.3 495 331 40.07 0 0 NA 573988 TCGA-AB-2973 AML35 4 27805501 27805501 T C SNP - - - - - - - - - - - - - - - tier3 419 52 11.02 429 174 28.86 0 0 NA 573988 TCGA-AB-2973 AML35 4 31876103 31876103 T C SNP LOC100130644 XM_001717608.1 human genbank 54_36p -1 model intronic c.334-6696 e3-6696 0.003 - - - pseudogene:no_stop_codon tier3 170 21 10.99 177 146 44.92 0 0 NA 573988 TCGA-AB-2973 AML35 4 46928184 46928184 T C SNP GABRB1 NM_000812.3 human genbank 54_36p 1 reviewed intronic c.461+69941 e4+69941 0.001 - - - no_errors tier3 759 100 11.64 529 344 39.27 0 0 NA 573988 TCGA-AB-2973 AML35 4 60624348 60624348 T C SNP - - - - - - - - - - - - - - - tier3 380 77 16.85 332 262 44.03 0 0 NA 573988 TCGA-AB-2973 AML35 4 156523033 156523033 C T SNP MAP9 NM_001039580.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-6581 NULL 0.946 - - - no_errors tier2 410 76 15.64 319 274 46.05 0 0 NA 573988 TCGA-AB-2973 AML35 4 162187617 162187617 G A SNP ENSG00000221362 ENST00000408435 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43057 NULL 0 - - - no_errors tier2 435 61 12.27 497 413 45.33 0 0 NA 573988 TCGA-AB-2973 AML35 4 175013857 175013857 G A SNP - - - - - - - - - - - - - - - tier2 313 71 18.44 229 193 45.52 0 0 NA 573988 TCGA-AB-2973 AML35 4 185168709 185168709 C G SNP STOX2 NM_020225.1 human genbank 54_36p 1 provisional missense c.1724 p.P575R 1 NULL HMMPfam_Stork_head - no_errors tier1 NA NA NA NA NA NA NA 573988 TCGA-AB-2973 AML35 5 1297678 1297678 A G SNP SLC6A18 NM_182632.2 human genbank 54_36p 1 validated intronic c.1497-45 e11-45 0.002 - - - no_errors tier3 149 29 16.11 148 136 47.89 0 0 NA 573988 TCGA-AB-2973 AML35 5 5040012 5040012 G A SNP - - - - - - - - - - - - - - - tier2 139 23 14.2 190 116 37.91 0 0 NA 573988 TCGA-AB-2973 AML35 5 15576863 15576863 G A SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.37+23041 e1+23041 0 - - - no_errors tier3 623 80 11.36 508 371 42.11 0 0 NA 573988 TCGA-AB-2973 AML35 5 17555650 17555650 C T SNP LOC646066 XM_116384.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-22694 NULL 0.513 - - - no_errors tier3 429 80 15.66 402 185 31.52 0 0 NA 573988 TCGA-AB-2973 AML35 5 41469819 41469819 C T SNP PLCXD3 NM_001005473.2 human genbank 54_36p -1 validated intronic c.104-51426 e2-51426 0 - - - no_errors tier2 458 81 15 416 355 45.92 0 0 NA 573988 TCGA-AB-2973 AML35 5 59661304 59661304 T C SNP LOC653198 XR_039820.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.014 - - - no_errors tier2 121 16 11.59 74 49 39.84 0 0 NA 573988 TCGA-AB-2973 AML35 5 81433358 81433358 A G SNP ATG10 NM_031482.1 human genbank 54_36p 1 validated intronic c.216+43181 e2+43181 0 - - - no_errors tier2 324 41 11.23 219 166 43.12 2 6 75 573988 TCGA-AB-2973 AML35 5 162177435 162177435 G A SNP ENSG00000208481 ENST00000385746 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33770 NULL 0.001 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 5 170770148 170770149 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.859_860 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 573988 TCGA-AB-2973 AML35 6 70909420 70909420 C T SNP COL19A1 NM_001858.4 human genbank 54_36p 1 reviewed missense c.1613 p.P538L 1 HMMPfam_Collagen "HMMSmart_TSPN,HMMPfam_Collagen,superfamily_ConA_like_lec_gl" - no_errors tier1 266 45 14.24 330 240 41.96 4 0 573988 TCGA-AB-2973 AML35 6 73006165 73006165 C T SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated intronic c.1957+1819 e9+1819 0 - - - no_errors tier2 417 87 17.19 260 208 44.44 0 0 NA 573988 TCGA-AB-2973 AML35 6 93462438 93462438 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 6 102924538 102924538 G A SNP - - - - - - - - - - - - - - - tier3 598 91 13.19 498 342 40.67 0 0 NA 573988 TCGA-AB-2973 AML35 7 1129516 1129516 G A SNP C7orf50 NM_032350.1 human genbank 54_36p -1 validated intronic c.129+3903 e1+3903 0.032 - - - no_errors tier2 152 28 15.47 127 84 39.81 0 0 0 573988 TCGA-AB-2973 AML35 7 9411942 9411942 C T SNP - - - - - - - - - - - - - - - tier3 426 87 16.89 465 344 42.31 0 0 NA 573988 TCGA-AB-2973 AML35 7 27335064 27335064 C A SNP ENSG00000219101 ENST00000401976 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-27335064 NULL 0.653 - - - no_coding_region:pseudogene tier2 505 114 18.42 401 341 45.96 0 0 NA 573988 TCGA-AB-2973 AML35 7 126904338 126904338 C T SNP - - - - - - - - - - - - - - - tier3 293 66 18.28 330 255 43.59 0 0 NA 573988 TCGA-AB-2973 AML35 7 137742937 137742937 A G SNP ENSG00000202072 ENST00000365202 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7828 NULL 0.058 - - - no_errors tier3 416 65 13.51 310 231 42.7 0 0 NA 573988 TCGA-AB-2973 AML35 8 3293986 3293986 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1564+19656 e13+19656 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 8 4506706 4506706 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.86-24218 e2-24218 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 464 36 7.2 371 226 37.79 0 0 NA 573988 TCGA-AB-2973 AML35 8 35385446 35385446 C T SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.104-140906 e2-140906 0.01 - - - no_errors tier3 276 27 8.85 296 162 35.29 0 0 NA 573988 TCGA-AB-2973 AML35 8 69990778 69990778 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 8 72014233 72014233 G C SNP - - - - - - - - - - - - - - - tier2 356 50 12.32 298 183 37.97 0 0 NA 573988 TCGA-AB-2973 AML35 8 73668443 73668443 T G SNP KCNB2 NM_004770.2 human genbank 54_36p 1 reviewed intronic c.579+25341 e1+25341 0.001 - - - no_errors tier2 578 77 11.76 455 348 43.34 0 0 NA 573988 TCGA-AB-2973 AML35 8 90168004 90168004 C T SNP - - - - - - - - - - - - - - - tier3 372 58 13.49 341 269 44.1 0 0 NA 573988 TCGA-AB-2973 AML35 9 18413175 18413175 T G SNP - - - - - - - - - - - - - - - tier2 144 23 13.77 94 90 48.65 0 0 NA 573988 TCGA-AB-2973 AML35 9 80646169 80646169 C T SNP - - - - - - - - - - - - - - - tier3 271 22 7.48 132 71 34.98 0 0 NA 573988 TCGA-AB-2973 AML35 9 88474278 88474278 G A SNP - - - - - - - - - - - - - - - tier3 415 57 12.08 273 209 43.36 0 0 NA 573988 TCGA-AB-2973 AML35 9 108822289 108822289 T C SNP ENSG00000219771 ENST00000404350 human ensembl 54_36p -1 known 5_prime_flanking_region c.-40632 NULL 0.004 - - - no_coding_region:pseudogene tier2 1455 221 13.19 1220 855 41.2 0 0 NA 573988 TCGA-AB-2973 AML35 9 128606555 128606555 C T SNP ZBTB43 NM_014007.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28055 NULL 0.446 - - - no_errors tier3 382 77 16.67 382 250 39.37 0 0 NA 573988 TCGA-AB-2973 AML35 9 133385754 133385754 G A SNP POMT1 NM_007171.1 human genbank 54_36p 1 reviewed intronic c.1764+353 e16+353 0 - - - no_errors tier3 121 16 11.59 85 61 41.78 0 0 0 573988 TCGA-AB-2973 AML35 9 133675566 133675566 T C SNP ENSG00000212395 ENST00000391093 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27362 NULL 0 - - - no_errors tier3 242 40 14.18 197 135 40.3 0 0 NA 573988 TCGA-AB-2973 AML35 10 42920506 42920506 G T SNP RET NM_020975.4 human genbank 54_36p 1 reviewed silent c.726 p.V242 0.006 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,HMMPfam_Cadherin,HMMSmart_CA,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,superfamily_Cadherin,PatternScan_PROTEIN_KINASE_ATP" - no_errors tier1 269 45 14.29 142 123 46.42 1 0 573988 TCGA-AB-2973 AML35 10 56298782 56298782 C T SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+28434 e0+28434 0 - - - no_errors tier3 498 74 12.91 347 245 41.39 0 0 NA 573988 TCGA-AB-2973 AML35 10 72563148 72563148 G A SNP - - - - - - - - - - - - - - - tier3 361 41 10.17 318 243 43.32 0 0 NA 573988 TCGA-AB-2973 AML35 10 78837968 78837968 C T SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.379-4181 e2-4181 0 - - - no_errors tier3 478 68 12.41 536 446 45.28 0 0 NA 573988 TCGA-AB-2973 AML35 10 82764687 82764687 G T SNP - - - - - - - - - - - - - - - tier3 631 65 9.34 593 338 36.31 0 0 NA 573988 TCGA-AB-2973 AML35 10 83666211 83666211 T A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.823+40312 e1+40312 0.021 - - - no_errors tier3 544 77 12.36 466 318 40.56 0 0 NA 573988 TCGA-AB-2973 AML35 10 84453341 84453341 G A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.954-34972 e3-34972 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 10 84911614 84911614 G A SNP - - - - - - - - - - - - - - - tier3 534 98 15.48 634 464 42.22 0 0 NA 573988 TCGA-AB-2973 AML35 10 90685089 90685089 C T SNP ACTA2 NM_001613.1 human genbank 54_36p -1 reviewed silent c.1005 p.P335 1 "HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain" "HMMPfam_Actin,HMMSmart_SM00268,PatternScan_ACTINS_ACT_LIKE,PatternScan_ACTINS_1,PatternScan_ACTINS_2,superfamily_Actin-like ATPase domain" - no_errors tier1 NA NA NA NA NA NA 23 0 573988 TCGA-AB-2973 AML35 10 93750121 93750121 G A SNP BTAF1 NM_003972.2 human genbank 54_36p 1 validated intronic c.3660+2633 e25+2633 0.19 - - - no_errors tier3 331 59 15.09 145 83 36.24 0 2 100 573988 TCGA-AB-2973 AML35 10 124028666 124028666 G T SNP BTBD16 NM_144587.2 human genbank 54_36p 1 validated intronic c.167+2222 e2+2222 0.003 - - - no_errors tier3 277 30 9.77 325 185 36.13 0 0 NA 573988 TCGA-AB-2973 AML35 10 128285031 128285031 A C SNP ENSG00000221717 ENST00000408790 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49408 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 10 131080284 131080284 C A SNP - - - - - - - - - - - - - - - tier3 241 44 15.44 261 179 40.68 0 0 NA 573988 TCGA-AB-2973 AML35 10 132586707 132586707 C T SNP - - - - - - - - - - - - - - - tier3 303 46 13.14 354 246 40.93 0 0 NA 573988 TCGA-AB-2973 AML35 11 14216860 14216860 G T SNP SPON1 ENST00000310358 human ensembl 54_36p 1 known intronic c.823-4594 e8-4594 0 - - - no_errors tier3 868 142 14.06 533 343 39.07 0 0 NA 573988 TCGA-AB-2973 AML35 11 81630181 81630181 G A SNP - - - - - - - - - - - - - - - tier3 79 8 9.2 37 30 44.78 0 0 NA 573988 TCGA-AB-2973 AML35 11 88630487 88630487 A C SNP TYR NM_000372.4 human genbank 54_36p 1 reviewed intronic c.1185-27102 e4-27102 0.046 - - - no_errors tier3 366 98 21.12 554 478 46.23 0 0 NA 573988 TCGA-AB-2973 AML35 11 88961314 88961314 G A SNP - - - - - - - - - - - - - - - tier3 321 36 10.08 287 242 45.75 0 0 NA 573988 TCGA-AB-2973 AML35 11 98926049 98926049 A G SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-6037 e1-6037 0 - - - no_errors tier3 300 55 15.49 283 197 41.04 0 0 NA 573988 TCGA-AB-2973 AML35 11 108348426 108348426 G A SNP ENSG00000201243 ENST00000364373 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33028 NULL 0.002 - - - no_errors tier3 344 77 18.29 401 334 45.44 0 0 NA 573988 TCGA-AB-2973 AML35 11 114932108 114932108 G A SNP - - - - - - - - - - - - - - - tier3 330 78 19.12 146 118 44.53 0 0 NA 573988 TCGA-AB-2973 AML35 11 126873995 126873995 A C SNP - - - - - - - - - - - - - - - tier3 345 64 15.65 331 296 47.21 0 0 NA 573988 TCGA-AB-2973 AML35 11 133036355 133036355 C T SNP - - - - - - - - - - - - - - - tier3 571 90 13.57 541 362 40.04 0 0 NA 573988 TCGA-AB-2973 AML35 12 2855556 2855556 G C SNP FOXM1 NM_202002.2 human genbank 54_36p -1 validated intronic c.1+791 e0+791 0.002 - - - no_errors tier3 188 45 19.31 161 110 40.29 9 0 0 573988 TCGA-AB-2973 AML35 12 5932819 5932819 C T SNP VWF NM_000552.3 human genbank 54_36p -1 reviewed intronic c.7986+104 e47+104 0 - - - no_errors tier3 258 48 15.69 93 118 55.66 0 0 0 573988 TCGA-AB-2973 AML35 12 13526038 13526038 C T SNP ENSG00000201476 ENST00000364606 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40836 NULL 0.179 - - - no_errors tier2 175 29 14.22 156 106 40.3 0 0 NA 573988 TCGA-AB-2973 AML35 12 44251466 44251466 A G SNP - - - - - - - - - - - - - - - tier3 523 57 9.83 377 225 37.31 0 0 NA 573988 TCGA-AB-2973 AML35 12 61886315 61886315 A G SNP - - - - - - - - - - - - - - - tier2 495 79 13.76 523 368 41.26 0 0 NA 573988 TCGA-AB-2973 AML35 12 104589528 104589528 C T SNP - - - - - - - - - - - - - - - tier2 406 56 12.02 347 251 41.97 0 0 NA 573988 TCGA-AB-2973 AML35 12 130082682 130082682 G A SNP GPR133 NM_198827.3 human genbank 54_36p 1 validated intronic c.1473+17844 e13+17844 0.002 - - - no_errors tier3 257 37 12.59 238 216 47.37 0 0 NA 573988 TCGA-AB-2973 AML35 13 24101719 24101719 T C SNP LOC100134060 XM_001715254.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-6727 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 331 47 12.43 255 161 38.7 0 0 NA 573988 TCGA-AB-2973 AML35 13 27245431 27245431 A G SNP GSX1 NM_145657.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-19397 NULL 0.786 - - - no_errors tier3 348 80 18.69 284 216 43.11 0 0 NA 573988 TCGA-AB-2973 AML35 13 49600060 49600060 G A SNP FLJ31945 XM_001716811.1 human genbank 54_36p 1 model 3_prime_untranslated_region c.*1616 NULL 0.003 - - - no_errors tier2 47 12 20.34 41 44 51.76 1 1 50 573988 TCGA-AB-2973 AML35 13 57310496 57310496 G T SNP ENSG00000209790 ENST00000387055 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46055 NULL 0.003 - - - pseudogene tier3 654 96 12.78 522 295 36.06 0 0 NA 573988 TCGA-AB-2973 AML35 13 60387178 60387178 T C SNP - - - - - - - - - - - - - - - tier3 628 113 15.25 578 427 42.49 0 0 NA 573988 TCGA-AB-2973 AML35 13 86024201 86024201 A T SNP - - - - - - - - - - - - - - - tier2 274 38 12.18 262 156 37.32 0 0 NA 573988 TCGA-AB-2973 AML35 14 28970786 28970786 T C SNP ENSG00000212518 ENST00000391216 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44955 NULL 0.001 - - - no_errors tier3 169 26 13.33 168 140 45.31 0 0 NA 573988 TCGA-AB-2973 AML35 14 31945736 31945736 A G SNP AKAP6 NM_004274.4 human genbank 54_36p 1 reviewed intronic c.1-26681 e1-26681 0 - - - no_errors tier3 356 67 15.84 347 275 44.07 0 0 NA 573988 TCGA-AB-2973 AML35 14 35243261 35243261 C G SNP GARNL1 NM_194301.1 human genbank 54_36p -1 provisional intronic c.2267-14301 e17-14301 0.051 - - - no_errors tier3 397 74 15.68 302 280 48.03 2 0 0 573988 TCGA-AB-2973 AML35 14 60101057 60101057 T A SNP ENSG00000209837 ENST00000387102 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18075 NULL 0 - - - pseudogene tier3 349 50 12.53 368 254 40.77 0 0 NA 573988 TCGA-AB-2973 AML35 14 71404121 71404121 G A SNP - - - - - - - - - - - - - - - tier3 408 73 15.18 439 332 43.01 0 0 NA 573988 TCGA-AB-2973 AML35 14 81981587 81981587 G A SNP ENSG00000210376 ENST00000387641 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16598 NULL 0.062 - - - pseudogene tier3 175 25 12.5 163 98 37.55 0 0 NA 573988 TCGA-AB-2973 AML35 14 99144574 99144574 G A SNP HHIPL1 NM_032425.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36724 NULL 0.001 - - - no_errors tier3 235 44 15.77 179 138 43.53 0 0 NA 573988 TCGA-AB-2973 AML35 15 27568855 27568855 C T SNP - - - - - - - - - - - - - - - tier3 532 85 13.78 481 294 37.74 0 0 NA 573988 TCGA-AB-2973 AML35 15 50800477 50800489 CGTCAGTAGACAA - DEL KIAA1370 NM_019600.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42967 NULL 0.147:0.148:0.148:0.148:0.148:0.148:0.147:0.146:0.145:0.144:0.143:0.141:0.139 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 15 84235152 84235152 G A SNP - - - - - - - - - - - - - - - tier3 527 80 13.11 537 373 40.94 0 0 NA 573988 TCGA-AB-2973 AML35 15 88432938 88432938 C T SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140Q 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 136 18 11.69 125 87 40.85 82 54 39.42 573988 TCGA-AB-2973 AML35 15 94979771 94979771 G A SNP - - - - - - - - - - - - - - - tier3 282 52 15.48 235 169 41.73 0 0 NA 573988 TCGA-AB-2973 AML35 16 27557842 27557842 A T SNP KIAA0556 NM_015202.2 human genbank 54_36p 1 validated intronic c.408+7858 e5+7858 0.002 - - - no_errors tier3 414 109 20.84 387 329 45.95 0 3 100 573988 TCGA-AB-2973 AML35 16 48157810 48157810 G A SNP ZNF423 NM_015069.2 human genbank 54_36p -1 reviewed intronic c.3578-40904 e6-40904 0 - - - no_errors tier2 267 42 13.55 231 175 43.1 0 0 NA 573988 TCGA-AB-2973 AML35 16 61747374 61747374 T G SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 16 62989048 62989048 G T SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 16 63862579 63862579 G A SNP LOC283867 NM_001101346.1 human genbank 54_36p -1 inferred 3_prime_flanking_region c.*14240 NULL 0 - - - no_errors tier3 84 14 14.29 133 136 50.56 0 0 NA 573988 TCGA-AB-2973 AML35 16 75786717 75786717 G A SNP MON1B NM_014940.2 human genbank 54_36p 1 validated intronic c.1295+165 e3+165 0.047 - - - no_errors tier3 832 139 14.3 678 446 39.64 2 2 50 573988 TCGA-AB-2973 AML35 17 11469777 11469777 C T SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed intronic c.1351-3682 e7-3682 0 - - - no_errors tier3 264 64 19.51 238 163 40.65 0 0 NA 573988 TCGA-AB-2973 AML35 17 22045352 22045352 T A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 17 45384285 45384285 G A SNP DLX4 NM_138281.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17547 NULL 0.002 - - - no_errors tier2 277 58 17.21 170 167 49.55 0 0 NA 573988 TCGA-AB-2973 AML35 17 74901938 74901938 C T SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1-86437 e1-86437 0 - - - no_errors tier3 185 23 11.06 157 92 36.95 0 0 NA 573988 TCGA-AB-2973 AML35 18 4240996 4240996 A G SNP LOC284215 XM_001127273.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-13843 NULL 0.006 - - - no_errors tier3 199 33 14.22 159 137 46.28 0 0 NA 573988 TCGA-AB-2973 AML35 18 42887822 42887822 G C SNP HDHD2 NM_032124.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1229 NULL 0.017 - - - no_errors tier3 NA NA NA NA NA NA 15 0 0 573988 TCGA-AB-2973 AML35 18 49631152 49631152 A T SNP - - - - - - - - - - - - - - - tier3 132 17 11.41 37 47 55.95 0 0 NA 573988 TCGA-AB-2973 AML35 18 74358793 74358793 C T SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-408 NULL 0.001 - - - no_errors tier2 218 32 12.8 164 156 48.6 0 0 NA 573988 TCGA-AB-2973 AML35 19 9190702 9190702 T G SNP OR7E24 NM_001079935.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-32018 NULL 0.001 - - - no_errors tier3 435 55 11.2 371 312 45.68 0 0 NA 573988 TCGA-AB-2973 AML35 20 7083263 7083263 T C SNP - - - - - - - - - - - - - - - tier3 61 22 26.51 82 47 36.43 0 0 NA 573988 TCGA-AB-2973 AML35 20 9688020 9688020 A G SNP PAK7 NM_020341.3 human genbank 54_36p -1 reviewed intronic c.1+24986 e0+24986 0 - - - no_errors tier3 433 78 15.23 384 331 46.23 0 0 NA 573988 TCGA-AB-2973 AML35 20 21151872 21151872 A G SNP NCRNA00153 ENST00000246027 human ensembl 54_36p 1 known intronic c.1676-5777 e11-5777 0.002 - - - no_errors tier3 353 48 11.94 278 195 41.14 0 2 100 573988 TCGA-AB-2973 AML35 20 50693129 50693129 C A SNP ENSG00000210771 ENST00000388036 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41307 NULL 0 - - - pseudogene tier3 476 85 15.12 415 328 44.03 0 0 NA 573988 TCGA-AB-2973 AML35 20 50997947 50997947 C A SNP TSHZ2 NM_173485.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25293 NULL 0 - - - no_errors tier3 83 16 16.16 71 22 23.4 0 0 NA 573988 TCGA-AB-2973 AML35 21 20668697 20668697 T C SNP FDPSP ENST00000407411 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13820 NULL 0.024 - - - no_coding_region:pseudogene tier3 68 7 9.33 86 61 41.5 0 0 NA 573988 TCGA-AB-2973 AML35 21 23407971 23407971 G A SNP ZNF299P ENST00000406845 human ensembl 54_36p -1 known 5_prime_flanking_region c.-21947 NULL 0 - - - no_coding_region:pseudogene tier3 305 51 14.29 260 222 46.06 0 0 NA 573988 TCGA-AB-2973 AML35 22 34566545 34566545 C T SNP RBM9 NM_001031695.2 human genbank 54_36p -1 reviewed 5_prime_untranslated_region c.-334 NULL 1 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 573988 TCGA-AB-2973 AML35 22 46051725 46051725 C T SNP - - - - - - - - - - - - - - - tier3 195 22 10.09 248 143 36.48 0 0 NA 573988 TCGA-AB-2973 AML35 22 48636061 48636061 A G SNP ZBED4 NM_014838.2 human genbank 54_36p 1 validated intronic c.1+2420 e0+2420 0.002 - - - no_errors tier2 145 26 15.2 142 93 39.57 5 2 28.57 335640 TCGA-AB-2974 AML26 X 11376575 11376575 T C SNP ARHGAP6 NM_013427.2 human genbank 54_36p -1 reviewed intronic c.589-193827 e2-193827 0.002 - - - no_errors tier3 802 124 13.36 888 716 44.56 NA NA NA 335640 TCGA-AB-2974 AML26 X 49650876 49650876 C T SNP CLCN5 ENST00000376088 human ensembl 54_36p 1 known intronic c.1-42789 e1-42789 0.03 - - - no_errors tier3 1113 170 13.21 1945 1185 37.76 NA NA NA 335640 TCGA-AB-2974 AML26 X 94095604 94095604 G A SNP - - - - - - - - - - - - - - - tier3 64 2 3.03 517 372 41.84 NA NA NA 335640 TCGA-AB-2974 AML26 X 126810801 126810801 T A SNP - - - - - - - - - - - - - - - tier3 157 24 13.26 214 206 49.05 NA NA NA 335640 TCGA-AB-2974 AML26 X 150949899 150949899 C T SNP ENSG00000220524 ENST00000405190 human ensembl 54_36p -1 known 3_prime_flanking_region c.*14543 NULL 0.002 - - - no_coding_region:pseudogene tier3 186 25 11.85 537 369 40.68 NA NA NA 335640 TCGA-AB-2974 AML26 1 4709049 4709049 G A SNP AJAP1 NM_001042478.1 human genbank 54_36p 1 validated intronic c.830-20724 e3-20724 0 - - - no_errors tier3 458 68 12.9 449 438 49.38 NA NA NA 335640 TCGA-AB-2974 AML26 1 50124839 50124839 C T SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.35-35062 e2-35062 0.006 - - - no_errors tier3 418 63 13.1 752 599 44.34 NA NA NA 335640 TCGA-AB-2974 AML26 1 163459093 163459093 C T SNP LMX1A NM_177398.1 human genbank 54_36p -1 provisional intronic c.497-9419 e4-9419 0.008 - - - no_errors tier3 378 42 10 857 671 43.88 NA NA NA 335640 TCGA-AB-2974 AML26 1 178320998 178320998 T A SNP CEP350 NM_014810.4 human genbank 54_36p 1 reviewed intronic c.6282+1062 e30+1062 0.002 - - - no_errors tier3 553 93 14.4 785 605 43.49 NA NA NA 335640 TCGA-AB-2974 AML26 1 193478304 193478304 T A SNP - - - - - - - - - - - - - - - tier3 317 18 5.37 551 434 44.06 NA NA NA 335640 TCGA-AB-2974 AML26 1 193529946 193529946 A T SNP - - - - - - - - - - - - - - - tier3 148 19 11.38 570 407 41.57 NA NA NA 335640 TCGA-AB-2974 AML26 1 207201373 207201373 C T SNP - - - - - - - - - - - - - - - tier3 1048 161 13.27 1328 1091 45.03 NA NA NA 335640 TCGA-AB-2974 AML26 1 212537626 212537626 C T SNP SMYD2 NM_020197.2 human genbank 54_36p 1 validated intronic c.174-7527 e2-7527 0.001 - - - no_errors tier3 452 88 16.27 459 369 44.46 NA NA NA 335640 TCGA-AB-2974 AML26 1 230867332 230867332 G T SNP LOC729336 XM_001129978.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-23601 NULL 0.001 - - - no_errors tier3 392 51 11.49 521 433 45.39 NA NA NA 335640 TCGA-AB-2974 AML26 2 5434519 5434519 G T SNP - - - - - - - - - - - - - - - tier3 633 94 12.93 935 759 44.78 NA NA NA 335640 TCGA-AB-2974 AML26 2 13816510 13816510 C T SNP - - - - - - - - - - - - - - - tier3 468 76 13.97 918 776 45.81 NA NA NA 335640 TCGA-AB-2974 AML26 2 25310747 25310747 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2644 p.R882C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 NA NA NA NA NA NA NA 335640 TCGA-AB-2974 AML26 2 52037749 52037749 G A SNP ENSG00000220786 ENST00000404352 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29745 NULL 0 - - - no_coding_region:pseudogene tier3 478 76 13.67 910 735 44.68 NA NA NA 335640 TCGA-AB-2974 AML26 2 55946470 55946470 C A SNP EFEMP1 NM_001039348.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*1242 NULL 0.022 - - - no_errors tier3 194 34 14.91 720 361 33.4 NA NA NA 335640 TCGA-AB-2974 AML26 2 56109888 56109888 T C SNP MIRN217 ENST00000384817 human ensembl 54_36p -1 known 5_prime_flanking_region c.-46173 NULL 1 - - - no_errors tier3 608 84 12.14 835 700 45.57 NA NA NA 335640 TCGA-AB-2974 AML26 2 56268530 56268530 C T SNP CCDC85A NM_001080433.1 human genbank 54_36p 1 provisional intronic c.276+2991 e1+2991 0.001 - - - no_errors tier3 389 80 17.06 452 378 45.38 NA NA NA 335640 TCGA-AB-2974 AML26 2 63028048 63028048 A G SNP EHBP1 NM_015252.1 human genbank 54_36p 1 validated intronic c.1519-851 e13-851 0 - - - no_errors tier3 151 29 16.11 822 636 43.62 NA NA NA 335640 TCGA-AB-2974 AML26 2 68105380 68105380 C T SNP ENSG00000219288 ENST00000402149 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-68105380 NULL 0 - - - no_coding_region:pseudogene tier3 117 14 10.69 207 174 45.43 NA NA NA 335640 TCGA-AB-2974 AML26 2 116515735 116515735 G A SNP - - - - - - - - - - - - - - - tier3 125 16 11.27 500 388 43.69 NA NA NA 335640 TCGA-AB-2974 AML26 2 155733179 155733179 G A SNP - - - - - - - - - - - - - - - tier3 487 66 11.93 1054 773 42.31 NA NA NA 335640 TCGA-AB-2974 AML26 2 160891471 160891471 A G SNP RBMS1 NM_016836.4 human genbank 54_36p -1 reviewed intronic c.252-8487 e3-8487 0 - - - no_errors tier3 397 67 14.44 681 530 43.73 NA NA NA 335640 TCGA-AB-2974 AML26 2 167700352 167700352 T C SNP XIRP2 NM_152381.2 human genbank 54_36p 1 validated intronic c.409-313 e2-313 1 - - - no_errors tier3 324 36 10 757 425 35.9 NA NA NA 335640 TCGA-AB-2974 AML26 2 171548597 171548597 G A SNP GORASP2 NM_015530.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*17711 NULL 0.002 - - - no_errors tier3 215 27 11.16 990 711 41.77 NA NA NA 335640 TCGA-AB-2974 AML26 2 189710308 189710308 G A SNP COL5A2 NM_000393.3 human genbank 54_36p -1 reviewed intronic c.98-26888 e2-26888 0 - - - no_errors tier3 380 56 12.84 1024 883 46.3 NA NA NA 335640 TCGA-AB-2974 AML26 2 215677305 215677305 G A SNP ABCA12 NM_173076.3 human genbank 54_36p -1 reviewed intronic c.163+7260 e2+7260 0 - - - no_errors tier3 572 68 10.62 513 394 43.44 NA NA NA 335640 TCGA-AB-2974 AML26 2 217166092 217166092 C T SNP IGFBP2 NM_000597.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40400 NULL 0.002 - - - no_errors tier3 1466 241 14.09 1725 1511 46.69 NA NA NA 335640 TCGA-AB-2974 AML26 2 227574486 227574486 C T SNP ENSG00000212391 ENST00000391089 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32404 NULL 0.024 - - - no_errors tier3 277 54 16.27 432 312 41.82 NA NA NA 335640 TCGA-AB-2974 AML26 2 241864512 241864512 A G SNP HDLBP NM_005336.3 human genbank 54_36p -1 validated intronic c.1-7883 e1-7883 0.036 - - - no_errors tier3 230 23 9.06 556 331 37.32 NA NA NA 335640 TCGA-AB-2974 AML26 3 1276797 1276797 G A SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.359-18300 e4-18300 0.601 - - - no_errors tier3 588 56 8.7 1348 832 38.15 NA NA NA 335640 TCGA-AB-2974 AML26 3 37977251 37977251 T A SNP CTDSPL NM_001008392.1 human genbank 54_36p 1 validated intronic c.267+3613 e3+3613 0.006 - - - no_errors tier3 301 63 17.31 579 453 43.81 NA NA NA 335640 TCGA-AB-2974 AML26 3 61697756 61697756 T A SNP PTPRG NM_002841.3 human genbank 54_36p 1 reviewed intronic c.86-11836 e2-11836 0.004 - - - no_errors tier3 747 128 14.6 897 760 45.81 NA NA NA 335640 TCGA-AB-2974 AML26 3 80461028 80461028 C T SNP - - - - - - - - - - - - - - - tier3 241 22 8.33 772 657 45.94 NA NA NA 335640 TCGA-AB-2974 AML26 3 84375641 84375641 C A SNP ENSG00000221380 ENST00000408453 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46312 NULL 0 - - - no_errors tier3 181 25 12.14 816 588 41.82 NA NA NA 335640 TCGA-AB-2974 AML26 3 86563012 86563012 G A SNP - - - - - - - - - - - - - - - tier3 356 46 11.44 561 405 41.84 NA NA NA 335640 TCGA-AB-2974 AML26 3 98752502 98752502 A G SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.2386+18425 e11+18425 0 - - - no_errors tier3 485 69 12.45 1367 1037 43.14 NA NA NA 335640 TCGA-AB-2974 AML26 3 118240309 118240309 C G SNP LOC728873 XR_015679.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*11733 NULL 0 - - - pseudogene tier3 194 28 12.61 461 407 46.89 NA NA NA 335640 TCGA-AB-2974 AML26 3 163900252 163900252 G A SNP - - - - - - - - - - - - - - - tier3 43 5 10.42 198 170 46.2 NA NA NA 335640 TCGA-AB-2974 AML26 3 184030305 184030305 G A SNP ATP11B NM_014616.1 human genbank 54_36p 1 validated intronic c.315+71 e4+71 0 - - - no_errors tier3 261 36 12.08 840 677 44.6 NA NA NA 335640 TCGA-AB-2974 AML26 4 20788231 20788231 A T SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.100+126297 e1+126297 0.003 - - - no_errors tier3 463 72 13.43 1314 967 42.39 NA NA NA 335640 TCGA-AB-2974 AML26 4 23709854 23709854 G A SNP - - - - - - - - - - - - - - - tier3 233 30 11.36 440 443 50.11 NA NA NA 335640 TCGA-AB-2974 AML26 4 34924831 34924831 T C SNP - - - - - - - - - - - - - - - tier3 182 39 17.65 757 681 47.32 NA NA NA 335640 TCGA-AB-2974 AML26 4 59276581 59276581 A G SNP - - - - - - - - - - - - - - - tier3 341 69 16.79 636 541 45.89 NA NA NA 335640 TCGA-AB-2974 AML26 4 79628785 79628785 G T SNP FRAS1 ENST00000380674 human ensembl 54_36p 1 known intronic c.8756-268 e60-268 0.004 - - - no_errors tier3 709 117 14.13 1181 924 43.87 NA NA NA 335640 TCGA-AB-2974 AML26 4 132327481 132327481 G A SNP - - - - - - - - - - - - - - - tier3 767 153 16.61 843 624 42.48 NA NA NA 335640 TCGA-AB-2974 AML26 4 166414895 166414895 C T SNP KLHL2 NM_007246.2 human genbank 54_36p 1 provisional intronic c.544+10934 e5+10934 0.001 - - - no_errors tier3 489 67 11.92 651 548 45.63 NA NA NA 335640 TCGA-AB-2974 AML26 4 190366722 190366722 G A SNP - - - - - - - - - - - - - - - tier3 966 122 11.19 1119 845 42.98 NA NA NA 335640 TCGA-AB-2974 AML26 5 23950788 23950788 C T SNP - - - - - - - - - - - - - - - tier3 257 36 12.2 651 514 44.08 NA NA NA 335640 TCGA-AB-2974 AML26 5 105159709 105159709 G C SNP - - - - - - - - - - - - - - - tier3 162 13 7.43 606 386 38.91 NA NA NA 335640 TCGA-AB-2974 AML26 5 155325552 155325552 A G SNP - - - - - - - - - - - - - - - tier3 352 74 17.37 733 586 44.43 NA NA NA 335640 TCGA-AB-2974 AML26 5 158605623 158605623 G A SNP UBLCP1 NM_145049.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22879 NULL 0.001 - - - no_errors tier3 622 96 13.35 647 524 44.75 NA NA NA 335640 TCGA-AB-2974 AML26 5 161268978 161268978 C G SNP GABRA1 NM_000806.5 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*11972 NULL 0.001 - - - no_errors tier3 607 102 14.35 1033 832 44.56 NA NA NA 335640 TCGA-AB-2974 AML26 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 335640 TCGA-AB-2974 AML26 6 19817321 19817321 T G SNP - - - - - - - - - - - - - - - tier3 497 88 15.04 1055 931 46.85 NA NA NA 335640 TCGA-AB-2974 AML26 6 25839368 25839368 C T SNP LOC100129474 XM_001717559.1 human genbank 54_36p 1 model intronic c.68-79 e2-79 0.015 - - - no_errors tier3 496 80 13.89 676 616 47.6 NA NA NA 335640 TCGA-AB-2974 AML26 6 57523079 57523079 C T SNP PRIM2 ENST00000389488 human ensembl 54_36p 1 known intronic c.1020+16803 e9+16803 0 - - - no_errors tier3 663 27 3.91 3749 469 11.09 NA NA NA 335640 TCGA-AB-2974 AML26 6 84581814 84581814 A C SNP CYB5R4 NM_016230.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44407 NULL 0.002 - - - no_errors tier3 425 44 9.38 617 501 44.81 NA NA NA 335640 TCGA-AB-2974 AML26 6 85047854 85047854 A G SNP - - - - - - - - - - - - - - - tier3 1407 227 13.88 2030 1586 43.81 NA NA NA 335640 TCGA-AB-2974 AML26 6 85882211 85882211 G A SNP ENSG00000220291 ENST00000403057 human ensembl 54_36p 1 known 5_prime_flanking_region c.-39893 NULL 0 - - - no_coding_region:pseudogene tier3 547 66 10.77 893 757 45.82 NA NA NA 335640 TCGA-AB-2974 AML26 6 155816248 155816248 C T SNP NOX3 NM_015718.1 human genbank 54_36p -1 provisional missense c.322 p.G108R 1 HMMPfam_Ferric_reduct "HMMPfam_FAD_binding_8,HMMPfam_NAD_binding_6,HMMPfam_Ferric_reduct,superfamily_Riboflavin_synthase_like_b-brl,superfamily_SSF52343" - no_errors tier1 469 85 15.21 1019 886 46.48 NA NA NA 335640 TCGA-AB-2974 AML26 6 155824189 155824189 G A SNP NOX3 NM_015718.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-5563 NULL 0.001 - - - no_errors tier3 304 45 12.82 802 739 47.96 NA NA NA 335640 TCGA-AB-2974 AML26 6 161482804 161482804 A G SNP AGPAT4 NM_020133.2 human genbank 54_36p -1 reviewed intronic c.844-2162 e7-2162 0.002 - - - no_errors tier3 364 40 9.9 515 458 46.97 NA NA NA 335640 TCGA-AB-2974 AML26 7 9512782 9512782 C T SNP - - - - - - - - - - - - - - - tier3 363 47 11.41 644 529 45.06 NA NA NA 335640 TCGA-AB-2974 AML26 7 39004543 39004543 A C SNP POU6F2 ENST00000403058 human ensembl 54_36p 1 known intronic c.1-8339 e1-8339 0.008 - - - no_errors tier3 709 72 9.22 856 470 35.42 NA NA NA 335640 TCGA-AB-2974 AML26 7 57472617 57472617 C G SNP ZNF716 XM_001714654.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-41320 NULL 0.017 - - - no_errors tier3 360 43 10.67 227 203 47.1 NA NA NA 335640 TCGA-AB-2974 AML26 7 97464989 97464989 C T SNP OCM2 NM_006188.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7637 NULL 0 - - - no_errors tier3 873 100 10.22 579 468 44.66 NA NA NA 335640 TCGA-AB-2974 AML26 7 103715963 103715963 A G SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40501 NULL 0.62 - - - no_errors tier3 557 98 14.96 1133 910 44.48 NA NA NA 335640 TCGA-AB-2974 AML26 7 119673900 119673900 C T SNP KCND2 NM_012281.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28023 NULL 0.018 - - - no_errors tier3 589 56 8.67 839 482 36.49 NA NA NA 335640 TCGA-AB-2974 AML26 7 121334358 121334358 A G SNP PTPRZ1 NM_002851.2 human genbank 54_36p 1 reviewed intronic c.59-21088 e2-21088 0.05 - - - no_errors tier3 55 15 21.43 300 313 51.06 NA NA NA 335640 TCGA-AB-2974 AML26 7 125960615 125960615 G A SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed missense c.2057 p.A686V 1 HMMPfam_7tm_3 "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_Periplasmic binding protein-like I" - no_errors tier1 744 79 9.59 947 597 38.62 NA NA NA 335640 TCGA-AB-2974 AML26 7 144984290 144984290 G A SNP - - - - - - - - - - - - - - - tier3 464 62 11.79 672 564 45.56 NA NA NA 335640 TCGA-AB-2974 AML26 8 3323084 3323084 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1452-9330 e13-9330 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 761 116 13.23 875 690 44.09 NA NA NA 335640 TCGA-AB-2974 AML26 8 50010412 50010412 C T SNP SNAI2 NM_003068.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14035 NULL 0.001 - - - no_errors tier3 272 47 14.69 508 322 38.7 NA NA NA 335640 TCGA-AB-2974 AML26 8 63574203 63574203 G A SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.55-80449 e2-80449 0 - - - no_errors tier3 1202 156 11.45 2017 1136 36.01 NA NA NA 335640 TCGA-AB-2974 AML26 8 97251191 97251191 G C SNP GDF6 NM_001001557.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-9095 NULL 0 - - - no_errors tier3 642 89 12.16 823 611 42.43 NA NA NA 335640 TCGA-AB-2974 AML26 8 123155457 123155457 A C SNP - - - - - - - - - - - - - - - tier3 286 34 10.62 585 530 47.53 NA NA NA 335640 TCGA-AB-2974 AML26 8 123686487 123686487 G A SNP - - - - - - - - - - - - - - - tier3 570 71 11.08 923 731 44.17 NA NA NA 335640 TCGA-AB-2974 AML26 9 30790783 30790783 G A SNP ENSG00000221111 ENST00000408184 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-29586 NULL 0.039 - - - no_errors tier3 297 30 9.15 439 349 44.23 NA NA NA 335640 TCGA-AB-2974 AML26 9 36912162 36912162 G A SNP PAX5 NM_016734.1 human genbank 54_36p -1 reviewed intronic c.910+1190 e7+1190 0.085 - - - no_errors tier3 492 79 13.72 525 390 42.58 NA NA NA 335640 TCGA-AB-2974 AML26 9 89859944 89859944 C T SNP ENSG00000218944 ENST00000402090 human ensembl 54_36p 1 known 5_prime_flanking_region c.-11324 NULL 0.003 - - - no_coding_region:pseudogene tier3 756 113 12.96 743 573 43.34 NA NA NA 335640 TCGA-AB-2974 AML26 9 132787460 132787460 G A SNP FIBCD1 NM_032843.1 human genbank 54_36p -1 validated intronic c.849+1492 e4+1492 0.001 - - - no_errors tier3 68 10 12.82 46 60 56.6 NA NA NA 335640 TCGA-AB-2974 AML26 9 136553556 136553556 C T SNP - - - - - - - - - - - - - - - tier3 236 40 14.44 220 191 46.02 NA NA NA 335640 TCGA-AB-2974 AML26 10 100620943 100620943 T C SNP HPSE2 NM_021828.3 human genbank 54_36p -1 validated intronic c.611-127140 e4-127140 0.004 - - - no_errors tier3 848 147 14.77 1162 1072 47.94 NA NA NA 335640 TCGA-AB-2974 AML26 10 102044717 102044717 C T SNP PKD2L1 NM_016112.2 human genbank 54_36p -1 reviewed missense c.1510 p.E504K 1 "HMMPfam_PKD_channel,superfamily_Voltage-gated potassium channels" "HMMPfam_PKD_channel,superfamily_Voltage-gated potassium channels" - no_errors tier1 770 102 11.64 369 278 42.84 NA NA NA 335640 TCGA-AB-2974 AML26 10 107448481 107448481 G A SNP ENSG00000218440 ENST00000402674 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12868 NULL 0.001 - - - no_coding_region:pseudogene tier3 651 75 10.33 921 761 45.22 NA NA NA 335640 TCGA-AB-2974 AML26 11 12373900 12373900 A C SNP PARVA NM_018222.3 human genbank 54_36p 1 provisional intronic c.136+17994 e1+17994 0 - - - no_errors tier3 685 92 11.84 759 611 44.6 NA NA NA 335640 TCGA-AB-2974 AML26 11 12728055 12728055 G A SNP TEAD1 NM_021961.4 human genbank 54_36p 1 validated intronic c.1-14247 e1-14247 0.001 - - - no_errors tier3 798 134 14.3 1068 758 41.4 NA NA NA 335640 TCGA-AB-2974 AML26 11 28285235 28285235 A G SNP - - - - - - - - - - - - - - - tier3 360 45 11.11 701 586 45.5 NA NA NA 335640 TCGA-AB-2974 AML26 11 72055292 72055292 G A SNP - - - - - - - - - - - - - - - tier3 572 105 15.49 416 383 47.93 NA NA NA 335640 TCGA-AB-2974 AML26 11 73574314 73574314 A G SNP - - - - - - - - - - - - - - - tier3 75 10 11.63 321 245 43.06 NA NA NA 335640 TCGA-AB-2974 AML26 11 129904299 129904299 G A SNP ENSG00000175730 ENST00000317045 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17602 NULL 0 - - - no_coding_region:pseudogene tier3 823 131 13.65 750 593 44.12 NA NA NA 335640 TCGA-AB-2974 AML26 11 134440250 134440250 G T SNP - - - - - - - - - - - - - - - tier3 200 35 14.83 195 160 45.07 NA NA NA 335640 TCGA-AB-2974 AML26 12 39872843 39872843 T C SNP PDZRN4 ENST00000402685 human ensembl 54_36p 1 known intronic c.735+1230 e2+1230 0.001 - - - no_errors tier3 125 15 10.71 353 276 43.6 NA NA NA 335640 TCGA-AB-2974 AML26 12 43123898 43123898 G A SNP - - - - - - - - - - - - - - - tier3 481 51 9.57 1183 1085 47.84 NA NA NA 335640 TCGA-AB-2974 AML26 12 72099552 72099552 C T SNP - - - - - - - - - - - - - - - tier3 548 86 13.56 1308 987 42.97 NA NA NA 335640 TCGA-AB-2974 AML26 12 93709482 93709482 C T SNP MIRN492 ENST00000385303 human ensembl 54_36p 1 known 5_prime_flanking_region c.-42823 NULL 0.007 - - - no_errors tier3 677 91 11.85 1337 751 35.93 NA NA NA 335640 TCGA-AB-2974 AML26 13 27490642 27490642 C A SNP FLT3 NM_004119.2 human genbank 54_36p -1 reviewed missense c.2503 p.D835Y 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 910 135 12.92 667 573 46.14 NA NA NA 335640 TCGA-AB-2974 AML26 13 63664270 63664270 A G SNP - - - - - - - - - - - - - - - tier3 99 27 21.26 523 437 45.52 NA NA NA 335640 TCGA-AB-2974 AML26 13 92079185 92079185 C T SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1562-237351 e8-237351 0.001 - - - no_errors tier3 526 72 12.04 935 715 43.28 NA NA NA 335640 TCGA-AB-2974 AML26 14 48461800 48461800 C T SNP - - - - - - - - - - - - - - - tier3 650 98 13.1 1189 970 44.93 NA NA NA 335640 TCGA-AB-2974 AML26 14 79333229 79333229 A G SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2806-7979 e14-7979 0 - - - no_errors tier3 249 67 21.2 732 613 45.58 NA NA NA 335640 TCGA-AB-2974 AML26 14 79767976 79767976 G A SNP DIO2 ENST00000388841 human ensembl 54_36p -1 known 5_prime_flanking_region c.-20408 NULL 0 - - - no_errors tier3 284 18 5.96 766 401 34.3 NA NA NA 335640 TCGA-AB-2974 AML26 14 95228941 95228941 C T SNP TCL6 NM_020554.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*21423 NULL 0.015 - - - no_errors tier3 326 51 13.39 280 206 41.04 NA NA NA 335640 TCGA-AB-2974 AML26 14 100083243 100083243 G A SNP BEGAIN NM_020836.2 human genbank 54_36p -1 provisional intronic c.15-491 e2-491 0.013 - - - no_errors tier3 179 33 15.57 211 201 48.79 NA NA NA 335640 TCGA-AB-2974 AML26 15 22619883 22619883 C T SNP SNRPN NM_022805.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-150811 NULL 0.002 - - - no_errors tier3 284 47 14.2 254 162 38.94 NA NA NA 335640 TCGA-AB-2974 AML26 15 41232436 41232436 T C SNP TMEM62 NM_024956.3 human genbank 54_36p 1 provisional intronic c.1022+1001 e8+1001 0.017 - - - no_errors tier3 53 15 22.06 388 316 44.89 NA NA NA 335640 TCGA-AB-2974 AML26 15 57383214 57383214 C T SNP MYO1E NM_004998.2 human genbank 54_36p -1 validated intronic c.4-31274 e2-31274 0.003 - - - no_errors tier3 592 84 12.43 581 500 46.25 NA NA NA 335640 TCGA-AB-2974 AML26 15 57476077 57476077 C T SNP MYO1E NM_004998.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-24086 NULL 0 - - - no_errors tier3 715 76 9.61 1031 808 43.82 NA NA NA 335640 TCGA-AB-2974 AML26 15 95123843 95123843 G A SNP SPATA8 NM_173499.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-4047 NULL 0 - - - no_errors tier3 448 46 9.27 443 334 42.93 NA NA NA 335640 TCGA-AB-2974 AML26 16 7687431 7687431 G T SNP A2BP1 NM_145891.1 human genbank 54_36p 1 reviewed intronic c.1059-11628 e12-11628 0 - - - no_errors tier3 1297 170 11.59 1305 1052 44.63 NA NA NA 335640 TCGA-AB-2974 AML26 16 7875445 7875445 G A SNP ENSG00000222109 ENST00000410177 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13896 NULL 0.001 - - - no_errors tier3 363 60 14.18 557 458 45.08 NA NA NA 335640 TCGA-AB-2974 AML26 16 25891961 25891961 G A SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.735-162473 e2-162473 0.004 - - - no_errors tier3 665 113 14.51 824 716 46.43 NA NA NA 335640 TCGA-AB-2974 AML26 16 75416930 75416930 A T SNP - - - - - - - - - - - - - - - tier3 96 11 10.28 513 343 39.98 NA NA NA 335640 TCGA-AB-2974 AML26 16 76984904 76984904 T A SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.605+6558 e6+6558 0.001 - - - no_errors tier3 344 54 13.57 606 581 48.95 NA NA NA 335640 TCGA-AB-2974 AML26 17 12423115 12423115 C T SNP ENSG00000179136 ENST00000313495 human ensembl 54_36p 1 known intronic c.1-5487 e1-5487 0 - - - no_errors tier3 865 153 15.03 754 662 46.75 NA NA NA 335640 TCGA-AB-2974 AML26 17 21750328 21750328 C T SNP FAM27L NM_203392.2 human genbank 54_36p 1 predicted silent c.180 p.H60 0 NULL NULL - no_errors tier1 276 39 12.34 196 155 44.16 NA NA NA 335640 TCGA-AB-2974 AML26 17 22747216 22747216 T A SNP LOC440419 XR_040504.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21859 NULL 0.083 - - - no_errors tier3 664 80 10.75 1020 805 44.09 NA NA NA 335640 TCGA-AB-2974 AML26 17 52326058 52326058 C A SNP TRIM25 NM_005082.4 human genbank 54_36p -1 reviewed intronic c.1364-1469 e9-1469 0 - - - no_errors tier3 435 58 11.76 463 241 34.23 NA NA NA 335640 TCGA-AB-2974 AML26 17 76101424 76101424 C A SNP NPTX1 NM_002522.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-36583 NULL 0.006 - - - no_errors tier3 576 92 13.73 345 224 39.3 NA NA NA 335640 TCGA-AB-2974 AML26 18 18159583 18159583 G A SNP - - - - - - - - - - - - - - - tier3 748 125 14.29 1047 873 45.3 NA NA NA 335640 TCGA-AB-2974 AML26 18 37214043 37214043 G T SNP - - - - - - - - - - - - - - - tier3 763 94 10.97 1494 885 37.2 NA NA NA 335640 TCGA-AB-2974 AML26 18 42655683 42655683 C A SNP PIAS2 NM_004671.2 human genbank 54_36p -1 validated intronic c.1509-650 e12-650 0.005 - - - no_errors tier3 190 19 9.05 663 483 42.15 NA NA NA 335640 TCGA-AB-2974 AML26 18 65639480 65639480 A G SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.857-19980 e8-19980 0 - - - no_errors tier3 706 124 14.94 1073 867 44.62 NA NA NA 335640 TCGA-AB-2974 AML26 18 74396426 74396426 C A SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model intronic c.1757+14219 e10+14219 0.001 - - - no_errors tier3 185 27 12.68 314 184 36.95 NA NA NA 335640 TCGA-AB-2974 AML26 19 6636422 6636422 G A SNP C3 NM_000064.2 human genbank 54_36p -1 reviewed intronic c.3811-265 e30-265 0 - - - no_errors tier3 1280 191 12.98 729 599 45.07 NA NA NA 335640 TCGA-AB-2974 AML26 19 47928897 47928897 G A SNP PSG3 NM_021016.3 human genbank 54_36p -1 validated silent c.588 p.S196 0.001 "HMMSmart_IG,HMMPfam_ig,superfamily_SSF48726" "HMMSmart_IGc2,HMMSmart_IG,HMMPfam_V-set,HMMPfam_ig,superfamily_SSF48726" - no_errors tier1 723 102 12.35 957 854 47.13 NA NA NA 335640 TCGA-AB-2974 AML26 20 7233863 7233863 G A SNP - - - - - - - - - - - - - - - tier3 435 73 14.37 720 642 47.1 NA NA NA 335640 TCGA-AB-2974 AML26 21 17854304 17854304 C T SNP CXADR NM_001338.3 human genbank 54_36p 1 reviewed intronic c.572-587 e5-587 0 - - - no_errors tier3 325 46 12.4 1011 606 37.43 NA NA NA 335640 TCGA-AB-2974 AML26 22 24549599 24549599 G A SNP MYO18B NM_032608.5 human genbank 54_36p 1 reviewed silent c.2649 p.T883 0 "HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_IQ,HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 768 80 9.4 318 309 49.13 NA NA NA 335640 TCGA-AB-2974 AML26 22 25966734 25966734 C G SNP - - - - - - - - - - - - - - - tier3 571 98 14.65 681 545 44.34 NA NA NA 335640 TCGA-AB-2974 AML26 22 31245563 31245563 G A SNP SYN3 NM_003490.1 human genbank 54_36p -1 reviewed intronic c.1319-1242 e12-1242 0.001 - - - no_errors tier3 609 89 12.73 562 472 45.6 NA NA NA 817156 TCGA-AB-2975 AML42 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 28 16 36.36 10 21 65.62 25 28 52.83 817156 TCGA-AB-2975 AML42 8 117938116 117938116 A T SNP RAD21 NM_006265.2 human genbank 54_36p -1 reviewed nonsense c.764 p.L255* 1 NULL "HMMPfam_Rad21_Rec8,HMMPfam_Rad21_Rec8_N" - no_errors tier1 24 4 14.29 12 10 45.45 27 9 25 804168 TCGA-AB-2976 AML40 X 2702186 2702186 C T SNP XG NM_175569.1 human genbank 54_36p 1 reviewed intronic c.104-571 e3-571 0 - - - no_errors tier3 1165 82 6.57 581 531 47.71 0 0 NA 804168 TCGA-AB-2976 AML40 Y 14043637 14043637 A G SNP UTY NM_007125.3 human genbank 54_36p -1 reviewed intronic c.376-7570 e5-7570 0.377 - - - no_errors tier2 975 134 12.07 60 854 93.33 1 6 85.71 804168 TCGA-AB-2976 AML40 Y 16113990 16113990 T C SNP ENSG00000218564 ENST00000406219 human ensembl 54_36p -1 known 5_prime_flanking_region c.-36642 NULL 0 - - - no_coding_region:pseudogene tier3 511 83 13.97 52 659 92.69 0 0 NA 804168 TCGA-AB-2976 AML40 Y 20078640 20078640 C A SNP BCORL2 ENST00000400605 human ensembl 54_36p -1 known intronic c.438-249 e3-249 0.003 - - - no_errors tier3 1506 186 10.97 133 1602 92.28 0 1 100 804168 TCGA-AB-2976 AML40 X 38008716 38008716 T A SNP SRPX NM_006307.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-43727 NULL 0.017 - - - no_errors tier3 367 51 12.2 28 506 94.76 0 0 NA 804168 TCGA-AB-2976 AML40 X 40416092 40416092 T C SNP MED14 NM_004229.3 human genbank 54_36p -1 reviewed missense c.3098 p.N1033S 0.797 NULL HMMPfam_MED14 - no_errors tier1 885 121 12.03 86 1241 93.52 1 58 98.31 804168 TCGA-AB-2976 AML40 X 48690748 48690748 G A SNP OTUD5 NM_017602.1 human genbank 54_36p -1 reviewed intronic c.595-4260 e2-4260 0.005 - - - no_errors tier3 459 47 9.29 34 390 91.98 0 11 100 804168 TCGA-AB-2976 AML40 X 57963125 57963125 G T SNP ZXDA NM_007156.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9546 NULL 0.001 - - - no_errors tier3 493 75 13.18 39 584 93.74 0 0 NA 804168 TCGA-AB-2976 AML40 X 78698656 78698656 C T SNP - - - - - - - - - - - - - - - tier3 814 133 14.04 68 814 92.29 0 0 NA 804168 TCGA-AB-2976 AML40 X 104681903 104681903 C T SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.772+66868 e5+66868 0.003 - - - no_errors tier3 730 57 7.23 157 643 80.27 0 0 NA 804168 TCGA-AB-2976 AML40 X 111801908 111801908 G A SNP LHFPL1 NM_178175.3 human genbank 54_36p -1 reviewed intronic c.1-620 e1-620 0 - - - no_errors tier3 644 72 10.06 36 627 94.57 0 0 NA 804168 TCGA-AB-2976 AML40 X 122157809 122157809 C A SNP GRIA3 NM_000828.4 human genbank 54_36p 1 reviewed intronic c.268+10286 e2+10286 0.001 - - - no_errors tier3 1060 174 14.08 66 981 93.7 0 0 NA 804168 TCGA-AB-2976 AML40 X 133375658 133375658 G A SNP PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed missense c.725 p.C242Y 1 NULL "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger" - no_errors tier1 334 44 11.64 48 571 92.25 1 25 96.15 804168 TCGA-AB-2976 AML40 X 140908119 140908119 T C SNP - - - - - - - - - - - - - - - tier3 754 115 13.19 82 1125 93.05 0 0 NA 804168 TCGA-AB-2976 AML40 X 141555307 141555307 G A SNP - - - - - - - - - - - - - - - tier3 617 66 9.65 64 758 92.21 0 0 NA 804168 TCGA-AB-2976 AML40 X 146216741 146216741 G A SNP MIRN514-3 ENST00000385131 human ensembl 54_36p -1 known 5_prime_flanking_region c.-45501 NULL 0.001 - - - no_errors tier3 339 57 14.39 29 352 92.15 0 0 NA 804168 TCGA-AB-2976 AML40 1 4391034 4391034 C T SNP LOC100134231 XM_001718209.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*47683 NULL 0.53 - - - no_start_codon:pseudogene:no_stop_codon tier3 1182 59 4.75 626 552 46.86 0 0 NA 804168 TCGA-AB-2976 AML40 1 5822320 5822320 A C SNP NPHP4 NM_015102.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*23592 NULL 0.002 - - - no_errors tier3 435 31 6.65 245 225 47.87 0 0 NA 804168 TCGA-AB-2976 AML40 1 7458084 7458084 C T SNP CAMTA1 NM_015215.1 human genbank 54_36p 1 validated intronic c.510+7536 e6+7536 0.003 - - - no_errors tier3 454 31 6.39 253 233 47.94 0 0 NA 804168 TCGA-AB-2976 AML40 1 10885089 10885089 G A SNP C1orf127 NM_173507.1 human genbank 54_36p -1 predicted 3_prime_flanking_region c.*45218 NULL 0 - - - no_errors tier3 1028 71 6.45 272 284 50.81 0 0 NA 804168 TCGA-AB-2976 AML40 1 17739084 17739084 G A SNP ARHGEF10L NM_018125.2 human genbank 54_36p 1 validated intronic c.1+52 e0+52 0 - - - no_errors tier2 174 7 3.87 48 45 48.39 0 0 NA 804168 TCGA-AB-2976 AML40 1 26254970 26254970 G A SNP TRIM63 NM_032588.2 human genbank 54_36p -1 reviewed intronic c.979+1311 e7+1311 0.002 - - - no_errors tier2 620 49 7.32 287 236 45.04 0 0 NA 804168 TCGA-AB-2976 AML40 1 38451053 38451053 A G SNP - - - - - - - - - - - - - - - tier3 1026 87 7.82 793 660 45.36 0 0 NA 804168 TCGA-AB-2976 AML40 1 40001674 40001674 C T SNP BMP8B NM_001720.3 human genbank 54_36p -1 reviewed intronic c.949-213 e6-213 0 - - - no_errors tier3 61 5 7.46 7 61 89.71 0 2 100 804168 TCGA-AB-2976 AML40 1 51547674 51547674 C A SNP TTC39A ENST00000371750 human ensembl 54_36p -1 known missense c.443 p.G148V 0 HMMPfam_Deme6 "HMMPfam_Deme6,HMMSmart_SM00028,superfamily_TPR-like" - no_errors tier1 1137 54 4.53 415 385 48.06 NA 804168 TCGA-AB-2976 AML40 1 61323152 61323152 G A SNP NFIA NM_005595.3 human genbank 54_36p 1 reviewed intronic c.27+2074 e1+2074 0.006 - - - no_errors tier2 741 20 2.62 355 237 40.03 0 0 NA 804168 TCGA-AB-2976 AML40 1 71800138 71800138 A - DEL NEGR1 NM_173808.2 human genbank 54_36p -1 validated intronic c.940+30950 e6+30950 1 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 1 72797149 72797149 G T SNP - - - - - - - - - - - - - - - tier2 749 52 6.48 653 588 47.34 0 0 NA 804168 TCGA-AB-2976 AML40 1 74274350 74274350 G A SNP LRRIQ3 NM_001105659.1 human genbank 54_36p -1 inferred intronic c.1718+5135 e6+5135 0.059 - - - no_errors tier3 1573 97 5.81 1171 1030 46.8 0 0 NA 804168 TCGA-AB-2976 AML40 1 76675710 76675710 A G SNP ST6GALNAC3 NM_152996.1 human genbank 54_36p 1 provisional intronic c.623+25020 e3+25020 0 - - - no_errors tier3 1117 52 4.45 904 773 46.07 0 0 NA 804168 TCGA-AB-2976 AML40 1 79923952 79923952 G A SNP - - - - - - - - - - - - - - - tier3 1169 64 5.19 660 561 45.87 0 0 NA 804168 TCGA-AB-2976 AML40 1 85893519 85893519 C T SNP ZNHIT6 NM_017953.2 human genbank 54_36p -1 provisional intronic c.1373-1150 e10-1150 0 - - - no_errors tier3 908 60 6.19 862 766 47.05 5 5 50 804168 TCGA-AB-2976 AML40 1 109740325 109740325 C T SNP SORT1 NM_002959.4 human genbank 54_36p -1 reviewed intronic c.306+1407 e1+1407 0 - - - no_errors tier3 691 55 7.31 431 457 51.35 3 0 0 804168 TCGA-AB-2976 AML40 1 112653995 112653995 C G SNP - - - - - - - - - - - - - - - tier3 2054 100 4.63 1215 995 45.02 0 0 NA 804168 TCGA-AB-2976 AML40 1 150584992 150584992 G A SNP FLG NM_002016.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-30436 NULL 0.048 - - - no_errors tier3 1330 85 6 789 720 47.71 0 0 NA 804168 TCGA-AB-2976 AML40 1 152057953 152057953 G A SNP GATAD2B NM_020699.2 human genbank 54_36p -1 validated nonsense c.535 p.R179* 1 NULL "HMMPfam_GATA,PatternScan_GATA_ZN_FINGER_1,superfamily_SSF57716" - no_errors tier1 1286 68 5.02 651 552 45.89 41 20 32.79 804168 TCGA-AB-2976 AML40 1 166672520 166672520 A G SNP ENSG00000215833 ENST00000400977 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13012 NULL 0 - - - no_coding_region:pseudogene tier3 1102 70 5.97 575 479 45.45 0 0 NA 804168 TCGA-AB-2976 AML40 1 169888177 169888177 C T SNP MYOC NM_000261.1 human genbank 54_36p -1 reviewed silent c.198 p.Q66 0.45 NULL "HMMPfam_OLF,HMMSmart_SM00284" - no_errors tier1 1293 70 5.13 603 525 46.54 NA 804168 TCGA-AB-2976 AML40 1 171107134 171107134 G A SNP ENSG00000220611 ENST00000403493 human ensembl 54_36p -1 known 3_prime_flanking_region c.*14576 NULL 0.276 - - - no_coding_region:pseudogene tier3 2373 131 5.23 1867 1765 48.56 0 0 NA 804168 TCGA-AB-2976 AML40 1 173615438 173615438 G A SNP TNR NM_003285.2 human genbank 54_36p -1 validated silent c.1836 p.L612 0.635 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III" "HMMPfam_Fibrinogen_C,HMMSmart_SM00186,superfamily_Fibrinogen C-terminal domain-like,HMMPfam_fn3,HMMSmart_SM00060,HMMSmart_SM00181,superfamily_Fibronectin type III,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_EGF/Laminin" - no_errors tier1 1564 96 5.78 913 791 46.42 NA 804168 TCGA-AB-2976 AML40 1 184998422 184998422 G T SNP - - - - - - - - - - - - - - - tier3 1170 66 5.34 888 754 45.92 0 0 NA 804168 TCGA-AB-2976 AML40 1 185612033 185612033 G A SNP - - - - - - - - - - - - - - - tier3 1075 69 6.03 759 595 43.94 0 0 NA 804168 TCGA-AB-2976 AML40 1 185928523 185928523 T G SNP ENSG00000217712 ENST00000407861 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13792 NULL 0.001 - - - no_coding_region:pseudogene tier3 1171 43 3.54 620 411 39.86 0 0 NA 804168 TCGA-AB-2976 AML40 1 188517385 188517385 T A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional missense c.355 p.T119S 1 "HMMPfam_MACPF,HMMSmart_SM00457" "HMMPfam_MACPF,HMMSmart_SM00457" - no_errors tier1 772 49 5.95 616 498 44.62 NA 804168 TCGA-AB-2976 AML40 1 199603019 199603019 C T SNP TNNT2 NM_000364.2 human genbank 54_36p -1 reviewed intronic c.200-397 e7-397 0.001 - - - no_errors tier2 594 17 2.77 346 251 41.83 0 0 NA 804168 TCGA-AB-2976 AML40 1 209220288 209220288 T A SNP KCNH1 NM_172362.3 human genbank 54_36p -1 reviewed intronic c.1032+38460 e6+38460 0.001 - - - no_errors tier3 1074 70 6.1 631 612 49.12 0 0 NA 804168 TCGA-AB-2976 AML40 1 209581055 209581055 C G SNP TRAF5 NM_001033910.2 human genbank 54_36p 1 reviewed intronic c.1-12149 e1-12149 0.003 - - - no_errors tier2 1900 114 5.65 944 890 48.4 1 0 0 804168 TCGA-AB-2976 AML40 1 211721326 211721326 T C SNP LOC643330 XM_926662.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-6122 NULL 0.002 - - - no_errors tier3 967 43 4.25 600 495 45.12 0 0 NA 804168 TCGA-AB-2976 AML40 1 212507817 212507817 G A SNP LOC100131420 XM_001714661.1 human genbank 54_36p -1 model intronic c.574-2876 e3-2876 0.002 - - - no_errors tier3 1065 53 4.74 518 462 47.09 0 0 NA 804168 TCGA-AB-2976 AML40 1 214318465 214318465 C T SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.5299-138 e26-138 0.011 - - - no_errors tier3 700 34 4.63 800 659 45.17 0 0 NA 804168 TCGA-AB-2976 AML40 1 218552672 218552672 C T SNP RAB3GAP2 NM_012414.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-40370 NULL 0.001 - - - no_errors tier3 881 46 4.95 624 467 42.8 0 0 NA 804168 TCGA-AB-2976 AML40 1 223794404 223794404 G A SNP ENAH NM_001008493.1 human genbank 54_36p -1 validated intronic c.350-9441 e4-9441 0.012 - - - no_errors tier3 533 32 5.65 374 299 44.43 1 0 0 804168 TCGA-AB-2976 AML40 1 231187565 231187565 G T SNP PCNXL2 ENST00000344698 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*758 NULL 0 - - - no_errors tier3 814 54 6.22 417 377 47.48 0 0 NA 804168 TCGA-AB-2976 AML40 1 231529190 231529190 C T SNP KIAA1804 NM_032435.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-1208 NULL 0.018 - - - no_errors tier3 308 22 6.67 296 256 46.38 0 0 NA 804168 TCGA-AB-2976 AML40 1 239744232 239744232 C T SNP FH NM_000143.2 human genbank 54_36p -1 reviewed intronic c.268-596 e3-596 0.002 - - - no_errors tier3 1072 42 3.77 618 511 45.26 0 0 0 804168 TCGA-AB-2976 AML40 2 7955772 7955772 T A SNP LOC100129581 XM_001718835.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-48286 NULL 0.103 - - - no_errors tier3 2219 153 6.44 1240 1094 46.85 0 0 NA 804168 TCGA-AB-2976 AML40 2 12925647 12925647 C T SNP - - - - - - - - - - - - - - - tier3 812 47 5.47 413 363 46.78 0 0 NA 804168 TCGA-AB-2976 AML40 2 13004617 13004617 C T SNP - - - - - - - - - - - - - - - tier3 2124 144 6.35 1419 1395 49.57 0 0 NA 804168 TCGA-AB-2976 AML40 2 22189743 22189743 T C SNP - - - - - - - - - - - - - - - tier3 1478 88 5.62 916 731 44.36 0 0 NA 804168 TCGA-AB-2976 AML40 2 23779620 23779620 T G SNP KLHL29 XM_001717454.1 human genbank 54_36p 1 model missense c.2975 p.L992R 0.898 HMMSmart_SM00612 "HMMSmart_SM00225,HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain,superfamily_POZ domain,HMMPfam_Kelch_2,HMMPfam_BACK,HMMPfam_BTB" - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 NA NA NA NA NA NA NA 804168 TCGA-AB-2976 AML40 2 26780566 26780566 C A SNP KCNK3 NM_002246.2 human genbank 54_36p 1 reviewed intronic c.283+11036 e1+11036 0.001 - - - no_errors tier3 500 32 6.02 199 154 43.63 0 0 NA 804168 TCGA-AB-2976 AML40 2 32055198 32055198 T G SNP MEMO1 NM_015955.1 human genbank 54_36p -1 validated intronic c.62-33242 e2-33242 0.023 - - - no_errors tier3 654 48 6.84 437 357 44.96 4 6 60 804168 TCGA-AB-2976 AML40 2 33469395 33469395 G A SNP LTBP1 NM_206943.2 human genbank 54_36p 1 reviewed intronic c.4837+1518 e32+1518 0 - - - no_errors tier3 1611 87 5.11 888 811 47.68 0 0 0 804168 TCGA-AB-2976 AML40 2 36083297 36083297 G A SNP - - - - - - - - - - - - - - - tier2 752 74 8.96 705 563 44.4 0 0 NA 804168 TCGA-AB-2976 AML40 2 36547137 36547137 C T SNP CRIM1 NM_016441.1 human genbank 54_36p 1 provisional intronic c.991+1835 e5+1835 0.007 - - - no_errors tier3 2345 178 7.05 1596 1267 44.25 0 0 NA 804168 TCGA-AB-2976 AML40 2 40229236 40229237 - T INS SLC8A1 NM_021097.1 human genbank 54_36p -1 validated intronic c.2270-8917_2270-8916 e9-8916 0.451:0.461 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 2 40590204 40590204 C T SNP SLC8A1 ENST00000403092 human ensembl 54_36p -1 known intronic c.1+2789 e0+2789 0.026 - - - no_errors tier3 1495 77 4.9 953 668 41.16 0 0 NA 804168 TCGA-AB-2976 AML40 2 56255977 56255977 T C SNP LOC100129434 XM_001725163.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*686 NULL 0 - - - no_errors tier2 963 84 8.02 494 354 41.7 0 0 NA 804168 TCGA-AB-2976 AML40 2 57822803 57822803 T G SNP - - - - - - - - - - - - - - - tier3 805 61 7.04 545 501 47.9 0 0 NA 804168 TCGA-AB-2976 AML40 2 67016596 67016596 G A SNP - - - - - - - - - - - - - - - tier3 1118 66 5.57 776 669 46.3 0 0 NA 804168 TCGA-AB-2976 AML40 2 77397977 77397977 T G SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+200975 e2+200975 0.027 - - - no_errors tier3 795 57 6.68 360 288 44.44 0 0 NA 804168 TCGA-AB-2976 AML40 2 96528883 96528883 A G SNP NEURL3 ENST00000310865 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*1059 NULL 0 - - - no_errors tier3 357 35 8.93 179 114 38.91 0 0 NA 804168 TCGA-AB-2976 AML40 2 107911554 107911554 G A SNP RGPD4 ENST00000354986 human ensembl 54_36p 1 known 3_prime_flanking_region c.*45470 NULL 0.001 - - - no_errors tier3 1325 59 4.26 732 651 47.07 0 0 NA 804168 TCGA-AB-2976 AML40 2 113100668 113100668 G A SNP SLC20A1 NM_005415.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-20209 NULL 0 - - - no_errors tier2 697 60 7.93 290 298 50.59 0 0 NA 804168 TCGA-AB-2976 AML40 2 117989368 117989368 C T SNP - - - - - - - - - - - - - - - tier3 1084 77 6.63 603 469 43.75 0 0 NA 804168 TCGA-AB-2976 AML40 2 126632556 126632556 C T SNP - - - - - - - - - - - - - - - tier2 1210 71 5.53 696 622 47.16 0 0 NA 804168 TCGA-AB-2976 AML40 2 134194471 134194471 G A SNP - - - - - - - - - - - - - - - tier3 1499 111 6.89 971 813 45.55 0 0 NA 804168 TCGA-AB-2976 AML40 2 134728095 134728095 A G SNP MGAT5 ENST00000409645 human ensembl 54_36p 1 known intronic c.1-208 e1-208 0.01 - - - no_errors tier2 2309 105 4.35 1217 869 41.64 2 4 66.67 804168 TCGA-AB-2976 AML40 2 138533941 138533941 C A SNP HNMT NM_006895.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45771 NULL 0.003 - - - no_errors tier3 1008 45 4.27 1017 728 41.72 0 0 NA 804168 TCGA-AB-2976 AML40 2 142698138 142698138 G A SNP - - - - - - - - - - - - - - - tier3 1369 67 4.66 951 760 44.42 0 0 NA 804168 TCGA-AB-2976 AML40 2 145358586 145358586 T C SNP - - - - - - - - - - - - - - - tier3 921 59 6.02 577 508 46.82 0 0 NA 804168 TCGA-AB-2976 AML40 2 149244556 149244556 A G SNP EPC2 NM_015630.3 human genbank 54_36p 1 validated intronic c.1099-275 e9-275 0.003 - - - no_errors tier3 622 42 6.33 442 371 45.63 2 0 0 804168 TCGA-AB-2976 AML40 2 151741023 151741023 A G SNP LOC344332 XM_001125944.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-954 NULL 0.003 - - - pseudogene tier3 898 52 5.47 575 508 46.91 0 0 NA 804168 TCGA-AB-2976 AML40 2 155526504 155526504 G A SNP ENSG00000219170 ENST00000406411 human ensembl 54_36p -1 known 5_prime_flanking_region c.-20679 NULL 0 - - - no_coding_region:pseudogene tier2 1493 109 6.8 710 712 50.07 0 0 NA 804168 TCGA-AB-2976 AML40 2 162056438 162056438 C A SNP ENSG00000174470 ENST00000312302 human ensembl 54_36p -1 known 3_prime_flanking_region c.*14216 NULL 1 - - - no_coding_region:pseudogene tier2 727 45 5.81 486 492 50.26 0 0 NA 804168 TCGA-AB-2976 AML40 2 162376985 162376985 G A SNP SLC4A10 NM_022058.3 human genbank 54_36p 1 validated intronic c.277+7634 e3+7634 0.005 - - - no_errors tier3 1868 118 5.94 1014 773 43.23 0 0 NA 804168 TCGA-AB-2976 AML40 2 163839660 163839660 G A SNP ENSG00000200902 ENST00000364032 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-14091 NULL 0.003 - - - no_errors tier3 1314 79 5.67 787 724 47.92 0 0 NA 804168 TCGA-AB-2976 AML40 2 170553191 170553191 G C SNP UBR3 NM_172070.3 human genbank 54_36p 1 validated intronic c.343+1641 e3+1641 0.031 - - - no_errors tier3 1961 76 3.73 863 613 41.53 1 0 0 804168 TCGA-AB-2976 AML40 2 170590308 170590308 G A SNP UBR3 NM_172070.3 human genbank 54_36p 1 validated intronic c.1013-3794 e9-3794 0.012 - - - no_errors tier2 1131 68 5.67 964 824 46.09 4 0 0 804168 TCGA-AB-2976 AML40 2 170601120 170601120 G A SNP UBR3 NM_172070.3 human genbank 54_36p 1 validated intronic c.1116-4518 e10-4518 0.001 - - - no_errors tier3 1184 39 3.19 1069 733 40.65 0 0 0 804168 TCGA-AB-2976 AML40 2 174223167 174223167 C T SNP - - - - - - - - - - - - - - - tier3 1381 90 6.12 1098 978 47.02 0 0 NA 804168 TCGA-AB-2976 AML40 2 174599527 174599527 G A SNP LOC100128905 XM_001721845.1 human genbank 54_36p 1 model 3_prime_untranslated_region c.*461 NULL 0 - - - no_errors tier2 980 57 5.49 454 358 43.93 0 0 NA 804168 TCGA-AB-2976 AML40 2 175187625 175187625 T A SNP WIPF1 NM_001077269.1 human genbank 54_36p -1 reviewed intronic c.1-29040 e1-29040 0.001 - - - no_errors tier3 941 88 8.55 842 676 44.53 3 3 50 804168 TCGA-AB-2976 AML40 2 175972420 175972420 G T SNP - - - - - - - - - - - - - - - tier3 981 79 7.45 767 742 49.17 0 0 NA 804168 TCGA-AB-2976 AML40 2 177107365 177107365 A G SNP - - - - - - - - - - - - - - - tier3 1029 55 5.07 672 641 48.82 0 0 NA 804168 TCGA-AB-2976 AML40 2 184048578 184048578 G A SNP - - - - - - - - - - - - - - - tier3 865 55 5.97 646 520 44.56 0 2 100 804168 TCGA-AB-2976 AML40 2 185694329 185694329 G T SNP - - - - - - - - - - - - - - - tier3 1849 92 4.74 917 748 44.92 0 0 NA 804168 TCGA-AB-2976 AML40 2 194988978 194988978 C A SNP - - - - - - - - - - - - - - - tier3 1097 52 4.53 608 501 45.18 0 0 NA 804168 TCGA-AB-2976 AML40 2 198812651 198812651 G A SNP - - - - - - - - - - - - - - - tier3 940 49 4.95 887 801 47.45 0 0 NA 804168 TCGA-AB-2976 AML40 2 199366589 199366589 T C SNP - - - - - - - - - - - - - - - tier3 1183 79 6.25 854 681 44.36 0 0 NA 804168 TCGA-AB-2976 AML40 2 204063074 204063074 A C SNP RAPH1 NM_213589.2 human genbank 54_36p -1 validated intronic c.227-17 e3-17 0.02 - - - no_errors tier2 1142 86 7 888 731 45.15 0 0 NA 804168 TCGA-AB-2976 AML40 2 207836658 207836659 AT - DEL LOC729607 XM_001130776.1 human genbank 54_36p -1 model intronic c.352+3061_352+3060 e3+3061 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 2 209806414 209806414 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 2 211606619 211606619 A T SNP - - - - - - - - - - - - - - - tier3 1273 80 5.91 671 690 50.7 0 0 NA 804168 TCGA-AB-2976 AML40 2 211950370 211950370 C T SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*6215 NULL 0.053 - - - no_errors tier2 1059 31 2.84 703 580 45.14 0 0 NA 804168 TCGA-AB-2976 AML40 2 222379753 222379753 T C SNP - - - - - - - - - - - - - - - tier3 1471 74 4.79 949 805 45.87 0 0 NA 804168 TCGA-AB-2976 AML40 2 223355668 223355668 G A SNP - - - - - - - - - - - - - - - tier3 850 32 3.62 560 337 37.57 0 0 NA 804168 TCGA-AB-2976 AML40 2 226124657 226124657 C T SNP KIAA1486 NM_020864.1 human genbank 54_36p 1 validated intronic c.524-30244 e3-30244 0 - - - no_errors tier3 1284 78 5.73 686 518 42.99 0 0 NA 804168 TCGA-AB-2976 AML40 2 228709267 228709267 G A SNP SPHKAP NM_030623.1 human genbank 54_36p -1 validated intronic c.33-4222 e2-4222 0.049 - - - no_errors tier2 1942 92 4.52 1388 1213 46.6 0 0 NA 804168 TCGA-AB-2976 AML40 2 232588697 232588697 G A SNP DIS3L2 NM_152383.4 human genbank 54_36p 1 validated intronic c.210+72 e2+72 0 - - - no_errors tier3 2022 128 5.95 953 841 46.88 2 2 50 804168 TCGA-AB-2976 AML40 3 1214870 1214870 A T SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.56-22501 e2-22501 0.066 - - - no_errors tier3 947 85 8.23 452 406 47.32 0 0 NA 804168 TCGA-AB-2976 AML40 3 1593164 1593164 A T SNP LOC391504 XR_016281.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*19257 NULL 0 - - - pseudogene tier3 1111 54 4.62 569 435 43.15 0 0 NA 804168 TCGA-AB-2976 AML40 3 7744284 7744284 G A SNP GRM7 NM_181874.2 human genbank 54_36p 1 reviewed intronic c.2769-12760 e11-12760 0.106 - - - no_errors tier3 1441 109 7.03 867 754 46.51 0 0 NA 804168 TCGA-AB-2976 AML40 3 10613530 10613530 G A SNP ATP2B2 ENST00000397077 human ensembl 54_36p -1 known intronic c.1+23072 e0+23072 0.053 - - - no_errors tier3 1595 119 6.94 735 611 45.36 0 0 NA 804168 TCGA-AB-2976 AML40 3 12173873 12173873 G A SNP TIMP4 NM_003256.2 human genbank 54_36p -1 reviewed intronic c.237+12 e2+12 0.065 - - - no_errors tier3 697 43 5.79 490 402 44.92 0 0 0 804168 TCGA-AB-2976 AML40 3 26667767 26667767 A G SNP LRRC3B NM_052953.2 human genbank 54_36p 1 provisional intronic c.1+28035 e0+28035 0 - - - no_errors tier3 1325 80 5.69 671 635 48.62 0 0 NA 804168 TCGA-AB-2976 AML40 3 26879029 26879029 A G SNP - - - - - - - - - - - - - - - tier3 1670 105 5.91 894 645 41.88 0 0 NA 804168 TCGA-AB-2976 AML40 3 29917464 29917464 T - DEL RBMS3 NM_001003793.1 human genbank 54_36p 1 reviewed intronic c.939+1214 e10+1214 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 3 38713408 38713408 G A SNP SCN5A NM_001099404.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-63606 NULL 1 - - - no_errors tier3 1501 109 6.77 937 969 50.81 0 0 NA 804168 TCGA-AB-2976 AML40 3 41001684 41001684 T A SNP - - - - - - - - - - - - - - - tier3 1125 72 6.01 841 680 44.65 0 0 NA 804168 TCGA-AB-2976 AML40 3 43928562 43928562 G A SNP - - - - - - - - - - - - - - - tier3 867 58 6.27 517 471 47.67 0 0 NA 804168 TCGA-AB-2976 AML40 3 54627493 54627493 G C SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.964-9361 e10-9361 0.012 - - - no_errors tier3 295 13 4.21 151 125 45.29 0 0 NA 804168 TCGA-AB-2976 AML40 3 58516597 58516597 T C SNP ACOX2 NM_003500.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20724 NULL 0.021 - - - no_errors tier3 355 21 5.59 192 106 35.57 0 0 NA 804168 TCGA-AB-2976 AML40 3 61372165 61372165 G A SNP - - - - - - - - - - - - - - - tier3 694 45 6.09 463 444 48.95 0 0 NA 804168 TCGA-AB-2976 AML40 3 61429642 61429642 T A SNP - - - - - - - - - - - - - - - tier3 883 45 4.84 540 500 48.08 0 0 NA 804168 TCGA-AB-2976 AML40 3 65299751 65299751 T A SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*17342 NULL 0.016 - - - no_errors tier3 985 54 5.2 574 498 46.46 0 0 NA 804168 TCGA-AB-2976 AML40 3 68982050 68982050 T C SNP FAM19A4 NM_001005527.1 human genbank 54_36p -1 reviewed intronic c.130+30521 e2+30521 0.003 - - - no_errors tier3 1563 98 5.9 948 842 46.99 0 0 NA 804168 TCGA-AB-2976 AML40 3 70355775 70355775 C A SNP LOC100128160 XM_001714107.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-8608 NULL 0.002 - - - no_errors tier3 1096 104 8.64 833 796 48.77 0 0 NA 804168 TCGA-AB-2976 AML40 3 70426028 70426028 C - DEL ENSG00000222615 ENST00000410683 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42442 NULL 0.022 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 3 70705960 70705960 A G SNP ENSG00000196732 ENST00000360030 human ensembl 54_36p -1 known 3_prime_flanking_region c.*41035 NULL 0 - - - no_coding_region:pseudogene tier3 1486 94 5.95 947 827 46.59 0 0 NA 804168 TCGA-AB-2976 AML40 3 71707904 71707904 T C SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.1+5486 e0+5486 0 - - - no_errors tier2 1153 72 5.87 571 512 47.28 11 14 56 804168 TCGA-AB-2976 AML40 3 76089380 76089380 C G SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.109+19937 e1+19937 0.002 - - - no_stop_codon:overly_large_intron tier3 406 23 5.35 336 266 44.19 0 0 NA 804168 TCGA-AB-2976 AML40 3 77822159 77822159 G A SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*44263 NULL 0.474 - - - no_errors tier2 1180 103 8.03 628 645 50.67 0 0 NA 804168 TCGA-AB-2976 AML40 3 80089123 80089124 GC - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 3 83746577 83746577 C A SNP - - - - - - - - - - - - - - - tier3 802 48 5.65 690 620 47.33 0 0 NA 804168 TCGA-AB-2976 AML40 3 86549928 86549928 C T SNP - - - - - - - - - - - - - - - tier3 1172 78 6.24 970 705 42.09 0 0 NA 804168 TCGA-AB-2976 AML40 3 96664353 96664353 G T SNP - - - - - - - - - - - - - - - tier3 557 38 6.39 392 401 50.44 0 0 NA 804168 TCGA-AB-2976 AML40 3 100708493 100708493 G A SNP - - - - - - - - - - - - - - - tier3 528 50 8.65 668 585 46.65 0 0 NA 804168 TCGA-AB-2976 AML40 3 114482133 114482133 C T SNP BOC NM_033254.2 human genbank 54_36p 1 validated silent c.2241 p.G747 0.996 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III" "PatternScan_N6_MTASE,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_CYTOCHROME_P450,superfamily_Immunoglobulin" - no_errors tier1 683 71 9.4 546 354 39.33 3 100 804168 TCGA-AB-2976 AML40 3 117330222 117330222 T A SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.156-42129 e2-42129 0 - - - no_errors tier3 1484 83 5.3 1152 965 45.58 0 0 NA 804168 TCGA-AB-2976 AML40 3 119077681 119077681 T C SNP - - - - - - - - - - - - - - - tier3 1296 89 6.43 1159 988 46 0 0 NA 804168 TCGA-AB-2976 AML40 3 119409962 119409962 C A SNP - - - - - - - - - - - - - - - tier2 857 49 5.41 499 377 43.04 0 0 NA 804168 TCGA-AB-2976 AML40 3 119584064 119584064 C T SNP - - - - - - - - - - - - - - - tier3 1321 108 7.56 904 771 46 0 0 NA 804168 TCGA-AB-2976 AML40 3 123211720 123211720 G C SNP ILDR1 NM_175924.2 human genbank 54_36p -1 provisional intronic c.59-3022 e2-3022 0 - - - no_errors tier3 693 65 8.58 299 269 47.36 0 0 NA 804168 TCGA-AB-2976 AML40 3 127618916 127618916 G T SNP CCDC37 NM_182628.2 human genbank 54_36p 1 validated intronic c.418+875 e4+875 0.013 - - - no_errors tier3 342 26 7.07 199 169 45.92 0 0 NA 804168 TCGA-AB-2976 AML40 3 129545959 129545959 C T SNP EEFSEC NM_021937.3 human genbank 54_36p 1 validated intronic c.1443+2537 e5+2537 0 - - - no_errors tier3 471 30 5.98 188 148 44.05 1 0 0 804168 TCGA-AB-2976 AML40 3 135434803 135434803 T - DEL RYK NM_001005861.2 human genbank 54_36p -1 reviewed intronic c.231-10730 e2-10730 0.97 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 3 148790700 148790700 G C SNP - - - - - - - - - - - - - - - tier3 1321 75 5.37 879 700 44.3 0 0 NA 804168 TCGA-AB-2976 AML40 3 155616427 155616427 T A SNP GPR149 NM_001038705.1 human genbank 54_36p -1 provisional intronic c.1623+5095 e3+5095 0.003 - - - no_errors tier2 647 16 2.41 431 323 42.78 0 0 NA 804168 TCGA-AB-2976 AML40 3 166457428 166457428 A T SNP - - - - - - - - - - - - - - - tier3 1152 100 7.99 1092 1010 48.05 0 0 NA 804168 TCGA-AB-2976 AML40 3 171675662 171675662 C T SNP SLC7A14 NM_020949.2 human genbank 54_36p -1 validated intronic c.1993+5110 e6+5110 0.005 - - - no_errors tier2 1024 85 7.66 517 473 47.78 0 0 NA 804168 TCGA-AB-2976 AML40 3 177883735 177883735 G A SNP - - - - - - - - - - - - - - - tier3 1262 92 6.79 1126 952 45.79 0 0 NA 804168 TCGA-AB-2976 AML40 3 186069932 186069932 T A SNP VPS8 NM_001009921.2 human genbank 54_36p 1 validated intronic c.1598-32 e19-32 0.001 - - - no_errors tier3 1048 54 4.9 1120 879 43.95 3 2 40 804168 TCGA-AB-2976 AML40 3 187605648 187605648 G A SNP DGKG NM_001346.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-84706 NULL 0.003 - - - no_errors tier3 1189 72 5.71 733 697 48.37 0 0 NA 804168 TCGA-AB-2976 AML40 3 189465626 189465626 C T SNP LPP NM_005578.2 human genbank 54_36p 1 validated intronic c.1+39617 e0+39617 0 - - - no_errors tier3 1988 131 6.17 867 700 44.61 3 0 0 804168 TCGA-AB-2976 AML40 3 193663399 193663399 G A SNP FGF12 NM_004113.4 human genbank 54_36p -1 reviewed intronic c.14-102378 e2-102378 0.214 - - - no_errors tier3 875 67 7.1 761 632 45.37 0 0 NA 804168 TCGA-AB-2976 AML40 3 194260045 194260045 G C SNP - - - - - - - - - - - - - - - tier3 783 49 5.89 397 300 43.04 0 0 NA 804168 TCGA-AB-2976 AML40 4 5256393 5256393 C T SNP STK32B NM_018401.1 human genbank 54_36p 1 provisional intronic c.260+35315 e3+35315 0.002 - - - no_errors tier3 1264 60 4.53 739 599 44.73 1 0 0 804168 TCGA-AB-2976 AML40 4 20622587 20622587 T - DEL KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.101-161199 e2-161199 0.932 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 4 26348426 26348426 G A SNP TBC1D19 NM_018317.2 human genbank 54_36p 1 validated intronic c.1118-2158 e17-2158 0.008 - - - no_errors tier3 935 60 6.03 749 616 45.13 2 0 0 804168 TCGA-AB-2976 AML40 4 27322546 27322546 G A SNP - - - - - - - - - - - - - - - tier2 1354 81 5.64 759 697 47.87 0 0 NA 804168 TCGA-AB-2976 AML40 4 29671519 29671519 G A SNP - - - - - - - - - - - - - - - tier3 968 33 3.3 667 553 45.33 0 0 NA 804168 TCGA-AB-2976 AML40 4 30936847 30936847 G C SNP - - - - - - - - - - - - - - - tier3 962 73 7.05 525 536 50.52 0 0 NA 804168 TCGA-AB-2976 AML40 4 32406119 32406119 T C SNP - - - - - - - - - - - - - - - tier3 419 23 5.2 417 372 47.15 0 0 NA 804168 TCGA-AB-2976 AML40 4 32648103 32648103 G T SNP LOC642305 XR_042368.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*40612 NULL 0 - - - pseudogene tier2 1554 91 5.53 1415 878 38.29 0 0 NA 804168 TCGA-AB-2976 AML40 4 33033308 33033308 T C SNP - - - - - - - - - - - - - - - tier3 1028 86 7.71 802 668 45.41 0 0 NA 804168 TCGA-AB-2976 AML40 4 33460727 33460727 G A SNP - - - - - - - - - - - - - - - tier3 695 35 4.79 506 475 48.42 0 0 NA 804168 TCGA-AB-2976 AML40 4 34614695 34614695 G T SNP ENSG00000210088 ENST00000387353 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*29563 NULL 0.005 - - - pseudogene tier3 1081 61 5.34 803 723 47.38 0 0 NA 804168 TCGA-AB-2976 AML40 4 43289838 43289838 C T SNP ENSG00000222933 ENST00000411001 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*5474 NULL 0.003 - - - no_errors tier3 364 25 6.43 290 191 39.63 0 0 NA 804168 TCGA-AB-2976 AML40 4 43766916 43766916 C A SNP - - - - - - - - - - - - - - - tier3 501 30 5.65 519 398 43.4 0 0 NA 804168 TCGA-AB-2976 AML40 4 43929949 43929949 A G SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated intronic c.962-57925 e2-57925 0.001 - - - no_errors tier3 776 24 3 589 342 36.73 0 0 NA 804168 TCGA-AB-2976 AML40 4 44399958 44399958 T C SNP GNPDA2 NM_138335.1 human genbank 54_36p -1 provisional intronic c.770-42 e6-42 0.849 - - - no_errors tier2 689 39 5.36 459 391 45.95 3 4 57.14 804168 TCGA-AB-2976 AML40 4 45425271 45425271 A G SNP - - - - - - - - - - - - - - - tier3 1114 71 5.99 1066 997 48.3 0 0 NA 804168 TCGA-AB-2976 AML40 4 57033214 57033214 A T SNP SRP72 NM_006947.3 human genbank 54_36p 1 validated intronic c.354+448 e3+448 0.005 - - - no_errors tier3 813 51 5.9 332 271 44.94 0 1 100 804168 TCGA-AB-2976 AML40 4 60674007 60674007 G A SNP - - - - - - - - - - - - - - - tier2 438 24 5.18 365 296 44.78 0 0 NA 804168 TCGA-AB-2976 AML40 4 64297194 64297194 G T SNP - - - - - - - - - - - - - - - tier3 872 50 5.42 567 473 45.44 0 0 NA 804168 TCGA-AB-2976 AML40 4 70908682 70908682 C A SNP HTN3 NM_000200.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-22365 NULL 0.001 - - - no_errors tier3 1017 55 5.13 719 627 46.58 0 0 NA 804168 TCGA-AB-2976 AML40 4 78407748 78407748 C G SNP - - - - - - - - - - - - - - - tier3 705 51 6.75 635 518 44.89 0 0 NA 804168 TCGA-AB-2976 AML40 4 79998292 79998292 T G SNP BMP2K NM_198892.3 human genbank 54_36p 1 reviewed intronic c.884-1470 e8-1470 0.009 - - - no_errors tier3 488 27 5.22 367 309 45.71 3 6 66.67 804168 TCGA-AB-2976 AML40 4 87888195 87888195 T A SNP PTPN13 NM_080685.2 human genbank 54_36p 1 reviewed intronic c.2651-2452 e17-2452 0.005 - - - no_errors tier2 1569 90 5.42 864 748 46.32 4 0 0 804168 TCGA-AB-2976 AML40 4 97422140 97422140 C T SNP - - - - - - - - - - - - - - - tier3 1599 94 5.55 751 604 44.58 0 0 NA 804168 TCGA-AB-2976 AML40 4 102222433 102222433 G A SNP PPP3CA NM_000944.4 human genbank 54_36p -1 validated intronic c.860+933 e7+933 0 - - - no_errors tier3 847 59 6.51 668 581 46.48 0 1 100 804168 TCGA-AB-2976 AML40 4 105638488 105638488 A T SNP LOC728847 XM_001128619.1 human genbank 54_36p -1 model intronic c.65+953 e1+953 0 - - - no_errors tier3 916 79 7.93 759 612 44.57 0 0 NA 804168 TCGA-AB-2976 AML40 4 106213224 106213224 G A SNP LOC643675 XR_041865.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.004 - - - no_errors tier3 1087 37 3.29 699 456 39.48 0 0 NA 804168 TCGA-AB-2976 AML40 4 127372675 127372675 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 4 131446209 131446209 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 4 135294719 135294719 A C SNP - - - - - - - - - - - - - - - tier3 871 47 5.12 425 382 47.34 0 0 NA 804168 TCGA-AB-2976 AML40 4 144623658 144623658 A G SNP SMARCA5 NM_003601.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30870 NULL 0.018 - - - no_errors tier3 1863 91 4.66 1238 1126 47.63 3 1 25 804168 TCGA-AB-2976 AML40 4 146963640 146963640 T C SNP ZNF827 NM_178835.3 human genbank 54_36p -1 validated intronic c.2383+384 e8+384 0 - - - no_errors tier3 1047 55 4.99 796 705 46.97 2 2 50 804168 TCGA-AB-2976 AML40 4 149100761 149100761 G A SNP ARHGAP10 NM_024605.3 human genbank 54_36p 1 validated intronic c.1450+4786 e16+4786 0.002 - - - no_errors tier3 1836 108 5.55 937 723 43.55 1 0 0 804168 TCGA-AB-2976 AML40 4 151749822 151749822 T C SNP LRBA NM_006726.2 human genbank 54_36p -1 validated intronic c.5922-10089 e37-10089 0.003 - - - no_errors tier3 1208 75 5.85 735 636 46.36 5 1 16.67 804168 TCGA-AB-2976 AML40 4 155602163 155602163 T C SNP DCHS2 ENST00000339452 human ensembl 54_36p -1 known intronic c.2052+27743 e1+27743 0.002 - - - no_errors tier3 550 22 3.85 301 191 38.74 0 0 NA 804168 TCGA-AB-2976 AML40 4 166654234 166654234 A G SNP CPE NM_001873.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*16022 NULL 0.143 - - - no_errors tier3 1017 50 4.68 730 679 48.16 0 0 NA 804168 TCGA-AB-2976 AML40 4 168488170 168488170 C T SNP - - - - - - - - - - - - - - - tier3 217 14 6.06 104 102 49.28 0 0 NA 804168 TCGA-AB-2976 AML40 4 172620653 172620653 C T SNP - - - - - - - - - - - - - - - tier3 576 41 6.65 362 319 46.84 0 0 NA 804168 TCGA-AB-2976 AML40 4 173742874 173742874 A T SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.554-224213 e5-224213 0.004 - - - no_errors tier3 1614 112 6.48 908 842 47.95 0 0 NA 804168 TCGA-AB-2976 AML40 4 177658050 177658050 T A SNP - - - - - - - - - - - - - - - tier3 2537 130 4.87 1887 1157 38.01 0 0 NA 804168 TCGA-AB-2976 AML40 4 179536441 179536441 T C SNP ENSG00000201727 ENST00000364857 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-28402 NULL 0.009 - - - no_errors tier2 962 54 5.31 907 699 43.52 0 0 NA 804168 TCGA-AB-2976 AML40 4 187856479 187856479 C G SNP FAT1 NM_005245.3 human genbank 54_36p -1 reviewed intronic c.3265+8232 e1+8232 0.004 - - - no_errors tier3 1179 84 6.62 495 491 49.75 0 0 NA 804168 TCGA-AB-2976 AML40 4 190264978 190264978 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 5 4657658 4657658 A G SNP - - - - - - - - - - - - - - - tier3 1622 126 7.21 721 576 44.38 0 0 NA 804168 TCGA-AB-2976 AML40 5 8368772 8368772 C T SNP - - - - - - - - - - - - - - - tier3 1338 60 4.29 818 690 45.76 0 0 NA 804168 TCGA-AB-2976 AML40 5 10790593 10790593 A - DEL DAP NM_004394.2 human genbank 54_36p -1 reviewed intronic c.152+10694 e2+10694 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 5 11011404 11011404 G A SNP CTNND2 NM_001332.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*15161 NULL 0 - - - no_errors tier3 1367 87 5.98 872 822 48.5 0 0 NA 804168 TCGA-AB-2976 AML40 5 25946394 25946394 C T SNP LOC100133558 XM_001716419.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*10974 NULL 0.992 - - - no_start_codon:pseudogene:no_stop_codon tier2 1934 120 5.77 807 647 43.69 14 0 0 804168 TCGA-AB-2976 AML40 5 29890034 29890034 C A SNP - - - - - - - - - - - - - - - tier3 1770 93 4.99 721 665 47.91 0 0 NA 804168 TCGA-AB-2976 AML40 5 30118829 30118829 T C SNP - - - - - - - - - - - - - - - tier3 1168 87 6.93 617 523 45.88 0 0 NA 804168 TCGA-AB-2976 AML40 5 35272873 35272873 T - DEL PRLR NM_000949.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-147394 NULL 0.181 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 5 50559759 50559759 G C SNP ENSG00000213950 ENST00000396982 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-47070 NULL 0 - - - no_coding_region:pseudogene tier3 1752 130 6.91 1322 980 42.55 0 0 NA 804168 TCGA-AB-2976 AML40 5 54085558 54085558 C T SNP - - - - - - - - - - - - - - - tier3 1018 82 7.45 576 516 47.25 0 0 NA 804168 TCGA-AB-2976 AML40 5 59821760 59821760 G C SNP ENSG00000152931 ENST00000362001 human ensembl 54_36p 1 known 3_prime_flanking_region c.*2043 NULL 0 - - - no_errors tier3 1488 85 5.4 1166 948 44.84 0 0 NA 804168 TCGA-AB-2976 AML40 5 60905114 60905114 T C SNP ENSG00000223200 ENST00000411268 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*16163 NULL 0 - - - no_errors tier3 1041 82 7.3 469 402 46.1 0 0 NA 804168 TCGA-AB-2976 AML40 5 62962549 62962549 T C SNP - - - - - - - - - - - - - - - tier3 1889 115 5.74 1172 980 45.5 0 0 NA 804168 TCGA-AB-2976 AML40 5 66984919 66984919 A T SNP - - - - - - - - - - - - - - - tier3 1532 100 6.13 1346 1056 43.93 0 0 NA 804168 TCGA-AB-2976 AML40 5 72501813 72501813 C T SNP TMEM174 NM_153217.2 human genbank 54_36p 1 validated intronic c.1+1963 e0+1963 0.011 - - - no_errors tier3 674 51 7.03 509 408 44.44 0 0 NA 804168 TCGA-AB-2976 AML40 5 77980950 77980950 A C SNP LHFPL2 NM_005779.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-139158 NULL 0.001 - - - no_errors tier2 620 10 1.58 208 59 21.61 0 0 NA 804168 TCGA-AB-2976 AML40 5 80359649 80359649 G T SNP RASGRF2 NM_006909.1 human genbank 54_36p 1 validated intronic c.289-14803 e2-14803 0.107 - - - no_errors tier3 670 56 7.71 638 539 45.79 0 0 NA 804168 TCGA-AB-2976 AML40 5 85146323 85146323 T A SNP - - - - - - - - - - - - - - - tier3 1070 42 3.77 748 600 44.48 0 0 NA 804168 TCGA-AB-2976 AML40 5 89232964 89232964 A G SNP LOC729011 XM_001132729.1 human genbank 54_36p 1 model intronic c.14+190 e1+190 0.682 - - - no_errors tier2 1379 88 5.99 1134 982 46.41 0 0 NA 804168 TCGA-AB-2976 AML40 5 95051120 95051120 T C SNP RHOBTB3 NM_014899.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-42023 NULL 0.001 - - - no_errors tier3 808 33 3.92 428 336 43.98 0 0 NA 804168 TCGA-AB-2976 AML40 5 97908635 97908635 A T SNP LOC642909 XR_016221.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-23531 NULL 0.019 - - - pseudogene tier3 2467 139 5.33 1303 1070 45.05 0 0 NA 804168 TCGA-AB-2976 AML40 5 98984803 98984803 T C SNP - - - - - - - - - - - - - - - tier3 1331 52 3.75 907 912 50.11 0 0 NA 804168 TCGA-AB-2976 AML40 5 106134513 106134513 G A SNP - - - - - - - - - - - - - - - tier3 803 68 7.81 708 469 39.81 0 0 NA 804168 TCGA-AB-2976 AML40 5 129560241 129560241 C T SNP CHSY3 NM_175856.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*10858 NULL 0 - - - no_errors tier3 861 32 3.58 672 578 46.2 0 0 NA 804168 TCGA-AB-2976 AML40 5 136620525 136620525 C T SNP SPOCK1 NM_004598.3 human genbank 54_36p -1 reviewed intronic c.232+10073 e2+10073 0.007 - - - no_errors tier3 1230 74 5.67 735 636 46.36 0 0 NA 804168 TCGA-AB-2976 AML40 5 143073237 143073237 C T SNP - - - - - - - - - - - - - - - tier3 1208 70 5.47 946 755 44.39 0 0 NA 804168 TCGA-AB-2976 AML40 5 144024078 144024078 C T SNP - - - - - - - - - - - - - - - tier2 1326 72 5.15 1000 806 44.63 0 0 NA 804168 TCGA-AB-2976 AML40 5 155277328 155277328 T G SNP - - - - - - - - - - - - - - - tier3 1307 74 5.36 767 691 47.39 0 0 NA 804168 TCGA-AB-2976 AML40 5 158909817 158909817 G T SNP - - - - - - - - - - - - - - - tier3 2104 153 6.78 1478 1253 45.86 0 0 NA 804168 TCGA-AB-2976 AML40 5 162253309 162253309 C A SNP - - - - - - - - - - - - - - - tier3 975 63 6.06 510 417 44.98 0 0 NA 804168 TCGA-AB-2976 AML40 5 164085587 164085587 C G SNP - - - - - - - - - - - - - - - tier3 962 53 5.22 656 556 45.87 0 0 NA 804168 TCGA-AB-2976 AML40 5 166663641 166663641 G A SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.226+18995 e1+18995 0 - - - no_errors tier3 1652 98 5.6 1126 884 43.96 0 0 NA 804168 TCGA-AB-2976 AML40 5 170770152 170770153 - CATG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 804168 TCGA-AB-2976 AML40 5 172379965 172379965 T C SNP ATP6V0E1 NM_003945.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*25 NULL 0.002 - - - no_errors tier3 1599 95 5.61 824 749 47.62 95 78 44.83 804168 TCGA-AB-2976 AML40 6 760755 760755 G T SNP LOC100132810 XM_001723739.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-22577 NULL 0.035 - - - no_start_codon:pseudogene:no_stop_codon tier3 1799 113 5.91 1078 882 44.95 0 0 NA 804168 TCGA-AB-2976 AML40 6 6270551 6270551 C G SNP F13A1 NM_000129.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-6655 NULL 0.001 - - - no_errors tier2 839 43 4.88 504 367 42.14 0 0 NA 804168 TCGA-AB-2976 AML40 6 6797368 6797368 G T SNP - - - - - - - - - - - - - - - tier3 1388 71 4.86 763 600 44.02 3 0 0 804168 TCGA-AB-2976 AML40 6 9879721 9879721 A G SNP OFCC1 ENST00000336327 human ensembl 54_36p -1 known intronic c.565-2447 e7-2447 0.002 - - - no_start_codon:no_stop_codon tier3 916 68 6.91 936 759 44.75 0 0 NA 804168 TCGA-AB-2976 AML40 6 12879500 12879500 G A SNP PHACTR1 NM_030948.1 human genbank 54_36p 1 validated intronic c.250+21492 e2+21492 0 - - - no_errors tier2 982 78 7.36 777 637 45.02 0 0 NA 804168 TCGA-AB-2976 AML40 6 25158617 25158617 A G SNP ENSG00000222540 ENST00000410608 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19128 NULL 0 - - - no_errors tier3 1118 59 5.01 610 397 39.38 0 0 NA 804168 TCGA-AB-2976 AML40 6 29047696 29047696 T C SNP TRIM27 NM_006510.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-48308 NULL 0.008 - - - no_errors tier2 941 50 5.05 472 375 44.27 0 0 NA 804168 TCGA-AB-2976 AML40 6 41242986 41242986 C T SNP TREM2 NM_018965.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4188 NULL 0.008 - - - no_errors tier3 1335 76 5.38 1117 920 45.16 0 0 NA 804168 TCGA-AB-2976 AML40 6 50085720 50085720 A G SNP DEFB110 NM_001037728.1 human genbank 54_36p -1 provisional intronic c.56-777 e2-777 0.01 - - - no_errors tier3 577 30 4.94 434 411 48.64 0 0 NA 804168 TCGA-AB-2976 AML40 6 51664683 51664683 C T SNP PKHD1 NM_138694.3 human genbank 54_36p -1 reviewed intronic c.10157-31957 e60-31957 0 - - - no_errors tier3 3304 183 5.25 1993 1745 46.67 0 0 NA 804168 TCGA-AB-2976 AML40 6 67101402 67101402 C A SNP ENSG00000221281 ENST00000408354 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24637 NULL 0 - - - no_errors tier3 1015 62 5.76 568 405 41.58 0 0 NA 804168 TCGA-AB-2976 AML40 6 71700473 71700473 C T SNP B3GAT2 NM_080742.2 human genbank 54_36p -1 reviewed intronic c.591+21790 e1+21790 0 - - - no_errors tier3 997 64 6.03 893 840 48.41 0 0 NA 804168 TCGA-AB-2976 AML40 6 95656550 95656550 T A SNP - - - - - - - - - - - - - - - tier2 1097 64 5.51 503 432 46.2 0 0 NA 804168 TCGA-AB-2976 AML40 6 100964840 100964840 G T SNP SIM1 NM_005068.2 human genbank 54_36p -1 reviewed intronic c.1167+10547 e9+10547 0.011 - - - no_errors tier3 823 25 2.95 589 264 30.88 0 0 NA 804168 TCGA-AB-2976 AML40 6 103679228 103679228 G T SNP - - - - - - - - - - - - - - - tier3 2023 129 5.99 1079 932 46.3 0 0 NA 804168 TCGA-AB-2976 AML40 6 103829836 103829836 T C SNP - - - - - - - - - - - - - - - tier3 626 32 4.86 479 348 42.08 0 0 NA 804168 TCGA-AB-2976 AML40 6 120201343 120201343 T G SNP LOC728727 XM_001128292.2 human genbank 54_36p 1 model intronic c.226-4568 e4-4568 0.135 - - - no_errors tier3 2471 170 6.43 1076 1001 48.17 0 0 NA 804168 TCGA-AB-2976 AML40 6 125941858 125941858 C A SNP - - - - - - - - - - - - - - - tier3 1643 98 5.63 1009 830 45.13 0 0 NA 804168 TCGA-AB-2976 AML40 6 128556820 128556820 A G SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.869-9257 e7-9257 0 - - - no_errors tier3 833 26 3.03 470 323 40.73 0 0 NA 804168 TCGA-AB-2976 AML40 6 145464261 145464261 C A SNP - - - - - - - - - - - - - - - tier3 1388 92 6.21 929 782 45.68 0 0 NA 804168 TCGA-AB-2976 AML40 6 152466599 152466599 A G SNP SYNE1 NM_182961.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*18665 NULL 0 - - - no_errors tier3 1585 88 5.26 688 611 47.04 0 0 NA 804168 TCGA-AB-2976 AML40 6 160834989 160834989 G A SNP LPAL2 NM_024492.2 human genbank 54_36p -1 validated intronic c.210-1005 e3-1005 0.005 - - - no_errors tier3 1089 62 5.39 588 474 44.55 0 0 0 804168 TCGA-AB-2976 AML40 6 164206563 164206563 C A SNP ENSG00000222470 ENST00000410538 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24691 NULL 0.997 - - - no_errors tier2 1146 78 6.37 664 542 44.9 0 0 NA 804168 TCGA-AB-2976 AML40 7 4036784 4036784 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.2602+13274 e17+13274 0.009 - - - no_errors tier3 1836 130 6.61 834 727 46.57 0 0 NA 804168 TCGA-AB-2976 AML40 7 6427925 6427925 C T SNP DAGLB NM_139179.1 human genbank 54_36p -1 validated silent c.1176 p.V392 0.092 "HMMPfam_Lipase_3,superfamily_alpha/beta-Hydrolases" "HMMPfam_Lipase_3,superfamily_alpha/beta-Hydrolases" - no_errors tier1 317 35 9.94 153 159 50.96 19 14 42.42 804168 TCGA-AB-2976 AML40 7 9315187 9315187 A T SNP - - - - - - - - - - - - - - - tier3 362 54 12.98 241 178 42.38 0 0 NA 804168 TCGA-AB-2976 AML40 7 12126246 12126246 C T SNP - - - - - - - - - - - - - - - tier2 972 63 6.08 713 607 45.95 0 0 NA 804168 TCGA-AB-2976 AML40 7 18705925 18705925 T A SNP HDAC9 NM_178425.1 human genbank 54_36p 1 reviewed intronic c.1732-27803 e12-27803 0.003 - - - no_errors tier3 684 43 5.91 518 438 45.82 0 0 NA 804168 TCGA-AB-2976 AML40 7 22672103 22672103 G A SNP ENSG00000179460 ENST00000325349 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31309 NULL 0 - - - no_coding_region:pseudogene tier2 816 31 3.66 359 274 43.15 1 0 0 804168 TCGA-AB-2976 AML40 7 29252234 29252234 G C SNP CHN2 NM_004067.1 human genbank 54_36p 1 reviewed intronic c.49+51103 e1+51103 0.003 - - - no_errors tier3 1377 63 4.38 822 649 44.06 2 0 0 804168 TCGA-AB-2976 AML40 7 41326642 41326642 C T SNP - - - - - - - - - - - - - - - tier3 910 16 1.73 930 165 15.07 0 0 NA 804168 TCGA-AB-2976 AML40 7 43464046 43464046 C G SNP HECW1 NM_015052.3 human genbank 54_36p 1 validated intronic c.2651+1475 e11+1475 0.015 - - - no_errors tier2 1364 95 6.5 661 610 47.96 0 0 NA 804168 TCGA-AB-2976 AML40 7 46307899 46307899 G T SNP - - - - - - - - - - - - - - - tier3 1515 72 4.54 731 644 46.84 0 0 NA 804168 TCGA-AB-2976 AML40 7 50496712 50496712 C T SNP DDC NM_000790.3 human genbank 54_36p -1 reviewed intronic c.1443+1693 e13+1693 0 - - - no_errors tier3 455 38 7.71 325 290 47.15 0 0 NA 804168 TCGA-AB-2976 AML40 7 50688673 50688673 C T SNP GRB10 NM_005311.2 human genbank 54_36p -1 reviewed intronic c.504+16240 e4+16240 0 - - - no_errors tier3 815 60 6.85 702 596 45.88 9 5 35.71 804168 TCGA-AB-2976 AML40 7 51623845 51623845 C T SNP LOC100134540 XR_039782.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*38133 NULL 0.002 - - - pseudogene tier3 1105 68 5.77 1065 848 44.14 0 0 NA 804168 TCGA-AB-2976 AML40 7 52356663 52356663 G A SNP - - - - - - - - - - - - - - - tier3 1398 65 4.44 784 521 39.92 0 0 NA 804168 TCGA-AB-2976 AML40 7 65216367 65216367 A G SNP CRCP ENST00000395326 human ensembl 54_36p 1 known intronic c.8+19 e1+19 0.019 - - - no_start_codon tier2 1247 115 8.44 397 280 41.36 4 1 20 804168 TCGA-AB-2976 AML40 7 66462325 66462325 A C SNP STAG3L4 NM_022906.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*39792 NULL 0.013 - - - no_errors tier3 1179 60 4.84 354 314 47.01 0 2 100 804168 TCGA-AB-2976 AML40 7 70603061 70603061 G A SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.963-71145 e6-71145 0.006 - - - no_errors tier3 3248 182 5.31 1966 1571 44.39 0 0 NA 804168 TCGA-AB-2976 AML40 7 70978440 70978440 T C SNP CALN1 NM_031468.2 human genbank 54_36p -1 validated intronic c.502-65027 e5-65027 0.001 - - - no_errors tier3 975 64 6.14 709 609 46.21 0 2 100 804168 TCGA-AB-2976 AML40 7 71113423 71113423 G A SNP CALN1 NM_031468.2 human genbank 54_36p -1 validated intronic c.501+13155 e4+13155 0 - - - no_errors tier3 700 38 5.15 631 630 49.96 0 2 100 804168 TCGA-AB-2976 AML40 7 71598329 71598329 G A SNP CALN1 ENST00000395276 human ensembl 54_36p -1 known 5_prime_flanking_region c.-216605 NULL 0.001 - - - no_errors tier3 1186 81 6.39 619 662 51.6 0 0 NA 804168 TCGA-AB-2976 AML40 7 72791334 72791334 G A SNP ABHD11 NM_148912.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-271 NULL 0.022 - - - no_errors tier2 373 35 8.58 130 118 47.58 1 0 0 804168 TCGA-AB-2976 AML40 7 75670321 75670321 C T SNP uc003uer.2 ENST00000388802 human ensembl 54_36p 1 known intronic c.1+1000 e0+1000 0 - - - no_stop_codon tier2 2363 111 4.48 596 461 43.61 0 0 NA 804168 TCGA-AB-2976 AML40 7 75860727 75860727 C T SNP SRCRB4D NM_080744.1 human genbank 54_36p -1 provisional missense c.1264 p.D422N 1 "HMMPfam_SRCR,HMMSmart_SM00202,superfamily_SRCR-like" "HMMPfam_SRCR,PatternScan_SRCR_1,HMMSmart_SM00202,superfamily_SRCR-like" - no_errors tier1 326 20 5.78 132 135 50.37 NA 804168 TCGA-AB-2976 AML40 7 92370959 92370959 C T SNP LOC100128994 XM_001717849.1 human genbank 54_36p 1 model intronic c.438-13128 e4-13128 0 - - - no_errors tier3 1077 79 6.83 801 684 46.06 8 4 33.33 804168 TCGA-AB-2976 AML40 7 97325261 97325261 C A SNP ASNS NM_001673.3 human genbank 54_36p -1 reviewed intronic c.903+265 e5+265 0.007 - - - no_errors tier3 682 40 5.54 310 217 41.18 0 0 0 804168 TCGA-AB-2976 AML40 7 115210833 115210833 A G SNP ENSG00000199224 ENST00000362354 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*49729 NULL 1 - - - no_errors tier2 525 34 6.08 270 235 46.53 0 0 NA 804168 TCGA-AB-2976 AML40 7 119521788 119521788 G A SNP - - - - - - - - - - - - - - - tier3 1058 59 5.28 659 445 40.31 0 0 NA 804168 TCGA-AB-2976 AML40 7 126601885 126601885 C A SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.511-67883 e2-67883 0.001 - - - no_errors tier3 933 35 3.61 963 712 42.51 0 0 NA 804168 TCGA-AB-2976 AML40 7 131565950 131565950 C A SNP PLXNA4 NM_020911.1 human genbank 54_36p -1 validated intronic c.1605-2182 e5-2182 1 - - - no_errors tier2 1198 69 5.44 611 577 48.49 0 0 0 804168 TCGA-AB-2976 AML40 7 134214919 134214919 G A SNP CALD1 NM_033138.5 human genbank 54_36p 1 reviewed intronic c.71+11824 e1+11824 0.012 - - - no_errors tier3 663 42 5.95 483 364 42.98 0 0 NA 804168 TCGA-AB-2976 AML40 7 142327817 142327817 C T SNP TRPV5 NM_019841.4 human genbank 54_36p -1 reviewed intronic c.1122+4929 e8+4929 0.011 - - - no_errors tier3 1149 67 5.51 575 584 50.39 0 0 NA 804168 TCGA-AB-2976 AML40 7 149471862 149471862 C A SNP - - - - - - - - - - - - - - - tier3 801 37 4.41 699 216 23.61 0 0 NA 804168 TCGA-AB-2976 AML40 7 157069965 157069965 G A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.2497-6372 e18-6372 0.001 - - - no_errors tier3 280 25 8.2 141 109 43.6 0 0 NA 804168 TCGA-AB-2976 AML40 8 4303191 4303192 - G INS CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.303-38197_303-38196 e3-38196 0.010:0.008 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier2 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 8 10005611 10005611 C T SNP MSRA NM_012331.1 human genbank 54_36p 1 reviewed intronic c.142+56033 e1+56033 0 - - - no_errors tier3 1234 77 5.87 692 618 47.18 0 1 100 804168 TCGA-AB-2976 AML40 8 10238566 10238566 C T SNP MSRA NM_012331.1 human genbank 54_36p 1 reviewed intronic c.543+23657 e5+23657 0.001 - - - no_errors tier2 1021 75 6.84 593 451 43.16 1 2 66.67 804168 TCGA-AB-2976 AML40 8 14429813 14429813 A - DEL SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.234+26799 e2+26799 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 8 20049776 20049776 T G SNP SLC18A1 NM_003053.2 human genbank 54_36p -1 validated intronic c.1210+22 e12+22 0.001 - - - no_errors tier3 1594 112 6.56 918 896 49.34 0 0 NA 804168 TCGA-AB-2976 AML40 8 20086729 20086729 C T SNP LOC100133494 XM_001717636.1 human genbank 54_36p -1 model intronic c.220+5735 e3+5735 0.048 - - - no_start_codon:pseudogene:no_stop_codon tier3 852 71 7.68 568 550 49.15 0 0 NA 804168 TCGA-AB-2976 AML40 8 20387407 20387407 T C SNP - - - - - - - - - - - - - - - tier2 2631 153 5.5 1449 1309 47.46 0 0 NA 804168 TCGA-AB-2976 AML40 8 25577832 25577832 C T SNP - - - - - - - - - - - - - - - tier2 1400 80 5.41 660 571 46.39 0 0 NA 804168 TCGA-AB-2976 AML40 8 35119219 35119219 G T SNP - - - - - - - - - - - - - - - tier3 1152 65 5.34 803 639 44.31 0 0 NA 804168 TCGA-AB-2976 AML40 8 36327505 36327505 G A SNP ENSG00000206871 ENST00000384144 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40757 NULL 0.008 - - - no_errors tier3 1106 65 5.55 811 694 46.08 0 0 NA 804168 TCGA-AB-2976 AML40 8 41276618 41276618 G A SNP SFRP1 NM_003012.3 human genbank 54_36p -1 reviewed intronic c.622+3519 e2+3519 0 - - - no_errors tier3 1069 75 6.56 408 379 48.16 0 0 NA 804168 TCGA-AB-2976 AML40 8 51018701 51018701 C T SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1+31357 e0+31357 0.003 - - - no_errors tier3 727 43 5.58 590 460 43.77 0 0 NA 804168 TCGA-AB-2976 AML40 8 51162090 51162090 A G SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1-85584 e1-85584 0 - - - no_errors tier3 1887 116 5.79 646 589 47.69 0 0 NA 804168 TCGA-AB-2976 AML40 8 51935996 51935996 C T SNP - - - - - - - - - - - - - - - tier3 1324 51 3.71 1075 600 35.82 0 0 NA 804168 TCGA-AB-2976 AML40 8 56681917 56681917 A G SNP - - - - - - - - - - - - - - - tier3 1145 84 6.83 770 689 47.22 0 0 NA 804168 TCGA-AB-2976 AML40 8 59052455 59052455 T C SNP FAM110B NM_147189.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-168889 NULL 0.004 - - - no_errors tier3 845 53 5.9 393 347 46.89 0 0 NA 804168 TCGA-AB-2976 AML40 8 62360428 62360428 G A SNP RLBP1L1 NM_173519.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14513 NULL 0.009 - - - no_errors tier2 2254 142 5.93 985 726 42.43 0 0 NA 804168 TCGA-AB-2976 AML40 8 65351175 65351175 C A SNP - - - - - - - - - - - - - - - tier3 914 67 6.83 738 640 46.44 0 0 NA 804168 TCGA-AB-2976 AML40 8 66999241 66999241 A G SNP - - - - - - - - - - - - - - - tier3 994 61 5.78 872 716 45.09 0 0 NA 804168 TCGA-AB-2976 AML40 8 70656631 70656631 G A SNP SULF1 NM_015170.1 human genbank 54_36p 1 validated intronic c.413-4515 e3-4515 0 - - - no_errors tier3 741 38 4.88 621 519 45.45 0 0 NA 804168 TCGA-AB-2976 AML40 8 76968843 76968843 A T SNP ENSG00000211417 ENST00000388682 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1149 NULL 0.402 - - - pseudogene tier3 1518 94 5.83 877 762 46.46 0 0 NA 804168 TCGA-AB-2976 AML40 8 80063473 80063473 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 8 80648545 80648545 G A SNP STMN2 NM_007029.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-37441 NULL 0 - - - no_errors tier3 739 38 4.89 664 521 43.89 0 0 NA 804168 TCGA-AB-2976 AML40 8 80849786 80849786 G T SNP HEY1 NM_001040708.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7333 NULL 0.428 - - - no_errors tier3 308 22 6.67 145 141 49.3 0 0 NA 804168 TCGA-AB-2976 AML40 8 82622315 82622315 C T SNP FABP12 NM_001105281.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-16210 NULL 0.941 - - - no_errors tier3 1415 71 4.77 714 619 46.44 0 0 NA 804168 TCGA-AB-2976 AML40 8 99365402 99365402 T C SNP NIPAL2 NM_024759.1 human genbank 54_36p -1 provisional intronic c.135+10005 e1+10005 0 - - - no_errors tier3 1711 134 7.26 925 746 44.64 4 0 0 804168 TCGA-AB-2976 AML40 8 101685643 101685643 C T SNP SNX31 NM_152628.3 human genbank 54_36p -1 validated intronic c.682-3798 e9-3798 0.445 - - - no_errors tier3 507 40 7.31 711 675 48.67 0 0 NA 804168 TCGA-AB-2976 AML40 8 110694461 110694461 G T SNP GOLSYN NM_001099744.1 human genbank 54_36p -1 validated intronic c.427+5786 e3+5786 0.001 - - - no_errors tier3 1189 65 5.18 925 773 45.52 0 0 NA 804168 TCGA-AB-2976 AML40 8 112015668 112015668 C G SNP ENSG00000208698 ENST00000385963 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-539 NULL 0.998 - - - pseudogene tier2 865 59 6.36 758 719 48.58 0 0 NA 804168 TCGA-AB-2976 AML40 8 113428346 113428346 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.6326-728 e41-728 0.007 - - - no_errors tier3 660 28 4.06 394 324 45.13 0 0 NA 804168 TCGA-AB-2976 AML40 8 124103559 124103559 G C SNP DERL1 NM_024295.1 human genbank 54_36p -1 validated intronic c.453+546 e5+546 0 - - - no_errors tier3 1311 58 4.23 919 619 40.25 14 10 41.67 804168 TCGA-AB-2976 AML40 8 131978742 131978742 G A SNP ADCY8 NM_001115.2 human genbank 54_36p -1 reviewed intronic c.1911+6458 e7+6458 0.001 - - - no_errors tier3 4252 290 6.38 1674 1388 45.33 0 0 NA 804168 TCGA-AB-2976 AML40 8 133251847 133251847 C T SNP KCNQ3 NM_004519.2 human genbank 54_36p -1 reviewed missense c.1151 p.R384K 1 NULL "HMMPfam_Ion_trans,HMMPfam_KCNQ_channel,superfamily_SSF81324" - no_errors tier1 634 35 5.23 435 413 48.7 NA 804168 TCGA-AB-2976 AML40 8 134800215 134800215 T G SNP ENSG00000208504 ENST00000385769 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36664 NULL 0.006 - - - pseudogene tier3 838 50 5.63 656 483 42.37 0 0 NA 804168 TCGA-AB-2976 AML40 8 137478771 137478771 C A SNP - - - - - - - - - - - - - - - tier3 1004 62 5.82 691 569 45.16 0 0 NA 804168 TCGA-AB-2976 AML40 8 137478943 137478943 T C SNP - - - - - - - - - - - - - - - tier3 689 45 6.13 446 400 47.28 0 0 NA 804168 TCGA-AB-2976 AML40 8 137885795 137885795 A G SNP - - - - - - - - - - - - - - - tier3 716 40 5.29 458 373 44.89 0 0 NA 804168 TCGA-AB-2976 AML40 8 138296068 138296068 A G SNP - - - - - - - - - - - - - - - tier3 1812 140 7.16 1376 1103 44.49 0 0 NA 804168 TCGA-AB-2976 AML40 8 139453829 139453829 G A SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.1-4402 e1-4402 0 - - - no_errors tier3 1101 81 6.85 783 671 46.15 0 0 NA 804168 TCGA-AB-2976 AML40 8 140046412 140046412 T A SNP - - - - - - - - - - - - - - - tier3 897 57 5.97 515 455 46.76 0 0 NA 804168 TCGA-AB-2976 AML40 8 140883225 140883225 C T SNP TRAPPC9 NM_031466.4 human genbank 54_36p -1 provisional intronic c.3350-69598 e22-69598 0.901 - - - no_errors tier3 741 46 5.84 167 106 38.83 8 1 11.11 804168 TCGA-AB-2976 AML40 9 3109415 3109415 C T SNP - - - - - - - - - - - - - - - tier3 1591 124 7.23 1183 1046 46.93 0 0 NA 804168 TCGA-AB-2976 AML40 9 4330530 4330530 T C SNP GLIS3 NM_001042413.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-54105 NULL 0.026 - - - no_errors tier3 408 33 7.48 116 99 46.05 0 0 NA 804168 TCGA-AB-2976 AML40 9 8965173 8965173 T C SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1+43524 e0+43524 0.001 - - - no_errors tier3 1355 64 4.51 742 649 46.56 0 0 NA 804168 TCGA-AB-2976 AML40 9 22642860 22642860 G A SNP - - - - - - - - - - - - - - - tier2 1361 84 5.81 678 522 43.5 0 0 NA 804168 TCGA-AB-2976 AML40 9 23949362 23949362 G A SNP LOC100133655 XM_001716507.1 human genbank 54_36p 1 model missense c.1672 p.A558T 0 NULL NULL - no_start_codon:pseudogene tier1 NA NA NA NA NA NA NA 804168 TCGA-AB-2976 AML40 9 27203572 27203572 G A SNP TEK NM_000459.3 human genbank 54_36p 1 reviewed missense c.2968 p.E990K 1 "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like" "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,HMMPfam_fn3,HMMSmart_FN3,HMMSmart_EGF,PatternScan_PROTEIN_KINASE_TYR,superfamily_FN_III-like,superfamily_Kinase_like,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Ig_Tie2_1,superfamily_SSF48726" - no_errors tier1 1650 109 6.2 910 877 48.99 NA 804168 TCGA-AB-2976 AML40 9 34289662 34289662 G A SNP KIF24 NM_194313.2 human genbank 54_36p -1 validated intronic c.814-2550 e3-2550 0.002 - - - no_errors tier2 876 68 7.2 533 420 44.07 0 0 0 804168 TCGA-AB-2976 AML40 9 38249524 38249524 C T SNP - - - - - - - - - - - - - - - tier2 720 47 6.13 364 250 40.45 0 0 NA 804168 TCGA-AB-2976 AML40 9 73432413 73432413 G A SNP TMEM2 ENST00000377044 human ensembl 54_36p -1 known intronic c.4152+55890 e23+55890 0 - - - no_errors tier3 1882 106 5.33 1258 1011 44.54 0 0 NA 804168 TCGA-AB-2976 AML40 9 74779346 74779346 G T SNP ALDH1A1 NM_000689.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-21610 NULL 0.013 - - - no_errors tier3 1492 89 5.63 1062 944 47.06 0 0 NA 804168 TCGA-AB-2976 AML40 9 79485413 79485413 C T SNP GNA14 NM_004297.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-32884 NULL 0.003 - - - no_errors tier3 918 80 8.02 776 643 45.31 2 0 0 804168 TCGA-AB-2976 AML40 9 86458473 86458473 A G SNP NTRK2 NM_006180.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17011 NULL 0 - - - no_errors tier3 940 32 3.29 508 412 44.78 0 0 NA 804168 TCGA-AB-2976 AML40 9 88744001 88744001 G A SNP GAS1 NM_002048.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*6476 NULL 0.001 - - - no_errors tier3 1028 56 5.17 864 770 47.12 0 0 NA 804168 TCGA-AB-2976 AML40 9 92915429 92915429 C T SNP LOC100128909 XM_001723661.1 human genbank 54_36p -1 model intronic c.70-6655 e2-6655 0.002 - - - no_errors tier3 1009 44 4.17 458 352 43.4 0 1 100 804168 TCGA-AB-2976 AML40 9 101888917 101888917 C T SNP ERP44 NM_015051.1 human genbank 54_36p -1 validated intronic c.57+11970 e1+11970 0.025 - - - no_errors tier3 1029 69 6.28 611 546 47.19 0 0 0 804168 TCGA-AB-2976 AML40 9 104856161 104856161 A T SNP ENSG00000217435 ENST00000402842 human ensembl 54_36p 1 known 5_prime_flanking_region c.-11358 NULL 0.049 - - - no_coding_region:pseudogene tier3 2290 158 6.45 858 762 47.01 0 0 NA 804168 TCGA-AB-2976 AML40 9 119179309 119179309 G C SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.442+37287 e1+37287 0.997 - - - no_errors tier3 829 41 4.71 476 486 50.47 0 0 NA 804168 TCGA-AB-2976 AML40 9 121245312 121245312 C T SNP - - - - - - - - - - - - - - - tier3 1476 105 6.64 972 916 48.49 0 0 NA 804168 TCGA-AB-2976 AML40 9 127538437 127538437 G C SNP MAPKAP1 NM_001006617.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-63763 NULL 0.003 - - - no_errors tier3 1191 81 6.37 453 355 43.88 0 0 0 804168 TCGA-AB-2976 AML40 9 135482492 135482492 G A SNP DBH NM_000787.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8823 NULL 0 - - - no_errors tier3 455 36 7.33 156 157 50.16 0 0 NA 804168 TCGA-AB-2976 AML40 9 137642727 137642727 G A SNP LOC100130969 XM_001714620.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-3180 NULL 0 - - - no_errors tier3 826 25 2.94 232 163 41.27 0 0 NA 804168 TCGA-AB-2976 AML40 10 24796595 24796595 G C SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated intronic c.847-5568 e6-5568 0.001 - - - no_errors tier3 1453 69 4.53 654 601 47.89 0 0 NA 804168 TCGA-AB-2976 AML40 10 34395147 34395147 A G SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*44956 NULL 0 - - - no_errors tier3 886 64 6.74 465 437 48.39 0 0 NA 804168 TCGA-AB-2976 AML40 10 35097999 35097999 G A SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional intronic c.120+45811 e1+45811 0.012 - - - no_errors tier3 1680 136 7.38 1006 904 47.06 0 0 NA 804168 TCGA-AB-2976 AML40 10 44234877 44234877 A G SNP CXCL12 NM_001033886.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-34418 NULL 0.016 - - - no_errors tier3 1227 71 5.46 696 605 46.36 0 0 NA 804168 TCGA-AB-2976 AML40 10 49751447 49751447 G A SNP WDFY4 ENST00000325239 human ensembl 54_36p 1 known intronic c.3129-95 e18-95 0.005 - - - no_errors tier3 630 37 5.55 474 446 48.48 0 1 100 804168 TCGA-AB-2976 AML40 10 52900815 52900815 T A SNP PRKG1 NM_006258.1 human genbank 54_36p 1 validated intronic c.592+3213 e3+3213 0.008 - - - no_errors tier2 988 49 4.72 695 519 42.75 0 0 NA 804168 TCGA-AB-2976 AML40 10 57900843 57900843 G A SNP - - - - - - - - - - - - - - - tier3 849 47 5.25 611 606 49.75 0 0 NA 804168 TCGA-AB-2976 AML40 10 58707998 58707998 C G SNP - - - - - - - - - - - - - - - tier3 560 31 5.25 368 285 43.64 0 0 NA 804168 TCGA-AB-2976 AML40 10 59813586 59813586 A C SNP TFAM NM_003201.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1728 NULL 0.001 - - - no_errors tier3 703 46 6.14 314 221 41.31 1 0 0 804168 TCGA-AB-2976 AML40 10 59929878 59929878 G A SNP BICC1 NM_001080512.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-13032 NULL 0.025 - - - no_errors tier3 1611 58 3.47 976 722 42.5 0 0 NA 804168 TCGA-AB-2976 AML40 10 60797293 60797293 G A SNP FAM13C NM_198215.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5067 NULL 0 - - - no_errors tier2 783 34 4.16 407 448 52.4 0 0 NA 804168 TCGA-AB-2976 AML40 10 66044462 66044462 G A SNP ENSG00000216248 ENST00000405829 human ensembl 54_36p -1 known 3_prime_flanking_region c.*5675 NULL 0 - - - no_coding_region:pseudogene tier3 1291 52 3.87 735 592 44.58 0 0 NA 804168 TCGA-AB-2976 AML40 10 69405514 69405514 T C SNP HERC4 NM_022079.3 human genbank 54_36p -1 validated intronic c.1807-8949 e14-8949 0.325 - - - no_errors tier3 1080 96 8.16 829 727 46.72 0 1 100 804168 TCGA-AB-2976 AML40 10 78632491 78632491 G C SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.603-17811 e4-17811 0 - - - no_errors tier3 1764 119 6.32 1663 1264 43.18 0 0 NA 804168 TCGA-AB-2976 AML40 10 79386002 79386002 G A SNP DLG5 NM_004747.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29718 NULL 0.002 - - - no_errors tier3 1520 96 5.94 570 503 46.88 0 0 NA 804168 TCGA-AB-2976 AML40 10 83023330 83023330 C T SNP - - - - - - - - - - - - - - - tier3 1657 72 4.16 708 590 45.38 0 0 NA 804168 TCGA-AB-2976 AML40 10 89337464 89337464 T A SNP ENSG00000222192 ENST00000410260 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-24541 NULL 0.018 - - - no_errors tier3 824 65 7.24 591 538 47.48 0 0 NA 804168 TCGA-AB-2976 AML40 10 106149282 106149282 G T SNP CCDC147 NM_001008723.1 human genbank 54_36p 1 validated intronic c.1815+34 e12+34 0 - - - no_errors tier3 1141 81 6.63 848 759 47.2 0 0 NA 804168 TCGA-AB-2976 AML40 10 108206310 108206310 G C SNP - - - - - - - - - - - - - - - tier3 821 45 5.2 482 456 48.61 0 0 NA 804168 TCGA-AB-2976 AML40 10 109089653 109089653 G T SNP - - - - - - - - - - - - - - - tier3 1339 85 5.97 684 669 49.45 0 0 NA 804168 TCGA-AB-2976 AML40 10 109474382 109474382 C T SNP - - - - - - - - - - - - - - - tier3 1162 94 7.48 935 783 45.58 0 0 NA 804168 TCGA-AB-2976 AML40 10 111614680 111614680 C T SNP XPNPEP1 NM_020383.2 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*252 NULL 0 - - - no_errors tier3 860 49 5.39 843 692 45.08 32 39 54.93 804168 TCGA-AB-2976 AML40 10 118521897 118521897 C A SNP HSPA12A NM_025015.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-29927 NULL 0.01 - - - no_errors tier3 1286 88 6.4 609 564 48.04 0 0 NA 804168 TCGA-AB-2976 AML40 10 123046446 123046446 C T SNP - - - - - - - - - - - - - - - tier3 819 67 7.55 677 544 44.52 0 0 NA 804168 TCGA-AB-2976 AML40 10 123240826 123240826 C A SNP FGFR2 NM_022970.4 human genbank 54_36p -1 reviewed intronic c.1867-3209 e13-3209 0.048 - - - no_errors tier3 906 86 8.67 734 662 47.35 0 0 NA 804168 TCGA-AB-2976 AML40 10 130239575 130239575 C T SNP - - - - - - - - - - - - - - - tier3 871 41 4.49 358 312 46.15 0 0 NA 804168 TCGA-AB-2976 AML40 10 131811648 131811648 A T SNP GLRX3 NM_006541.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-13027 NULL 0.002 - - - no_errors tier3 755 50 6.21 461 389 45.71 0 0 NA 804168 TCGA-AB-2976 AML40 10 132961953 132961953 C T SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated intronic c.671-13256 e4-13256 0 - - - no_errors tier3 330 11 3.22 353 221 38.43 0 0 NA 804168 TCGA-AB-2976 AML40 11 8041241 8041241 G A SNP TUB NM_003320.4 human genbank 54_36p 1 reviewed intronic c.203+23426 e2+23426 0 - - - no_errors tier3 989 72 6.78 602 468 43.45 0 0 NA 804168 TCGA-AB-2976 AML40 11 11557702 11557702 G A SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated intronic c.235+41780 e1+41780 0 - - - no_errors tier3 782 64 7.57 518 489 48.42 0 0 NA 804168 TCGA-AB-2976 AML40 11 13312571 13312571 C T SNP ARNTL NM_001030272.1 human genbank 54_36p 1 reviewed intronic c.1-15497 e1-15497 0 - - - no_errors tier3 2225 82 3.55 1442 1284 47.05 0 2 100 804168 TCGA-AB-2976 AML40 11 15314145 15314145 G A SNP - - - - - - - - - - - - - - - tier3 964 59 5.76 757 563 42.62 0 0 NA 804168 TCGA-AB-2976 AML40 11 25549437 25549437 T C SNP - - - - - - - - - - - - - - - tier3 1070 61 5.39 525 459 46.6 0 0 NA 804168 TCGA-AB-2976 AML40 11 25964150 25964150 C A SNP - - - - - - - - - - - - - - - tier3 1438 58 3.88 1515 1073 41.46 0 0 NA 804168 TCGA-AB-2976 AML40 11 32374485 32374486 - GACCG INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1143_1142 p.A382fs 0.771:0.996 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA 804168 TCGA-AB-2976 AML40 11 40201299 40201299 C T SNP LRRC4C NM_020929.1 human genbank 54_36p -1 validated intronic c.1+69020 e0+69020 0 - - - no_errors tier3 973 74 7.05 817 770 48.43 0 0 NA 804168 TCGA-AB-2976 AML40 11 41448094 41448094 G A SNP - - - - - - - - - - - - - - - tier3 709 35 4.7 525 474 47.45 0 0 NA 804168 TCGA-AB-2976 AML40 11 49589473 49589473 T A SNP ENSG00000205035 ENST00000357667 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*34434 NULL 0.001 - - - no_start_codon:no_stop_codon tier3 937 62 6.21 632 575 47.56 0 0 NA 804168 TCGA-AB-2976 AML40 11 50074658 50074658 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 11 55079244 55079244 C T SNP OR4C15 NM_001001920.1 human genbank 54_36p 1 provisional missense c.886 p.H296Y 0.975 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,PatternScan_LECTIN_LEGUME_ALPHA,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 1914 108 5.34 1564 1401 47.25 NA 804168 TCGA-AB-2976 AML40 11 64909362 64909362 T C SNP FRMD8 NM_031904.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-1722 NULL 0 - - - no_errors tier3 241 20 7.66 133 120 47.24 0 0 NA 804168 TCGA-AB-2976 AML40 11 70737752 70737752 G T SNP - - - - - - - - - - - - - - - tier3 1310 78 5.61 494 376 43.22 0 0 NA 804168 TCGA-AB-2976 AML40 11 86377427 86377427 C T SNP FZD4 NM_012193.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33652 NULL 0.001 - - - no_errors tier3 988 66 6.26 521 492 48.57 0 0 NA 804168 TCGA-AB-2976 AML40 11 88642511 88642511 G A SNP TYR NM_000372.4 human genbank 54_36p 1 reviewed intronic c.1185-15078 e4-15078 0.006 - - - no_errors tier3 923 59 6.01 988 785 44.28 0 0 NA 804168 TCGA-AB-2976 AML40 11 91791298 91791298 C T SNP FAT3 NM_001008781.2 human genbank 54_36p 1 validated intronic c.3292+63080 e1+63080 0 - - - no_errors tier3 502 41 7.55 334 377 52.95 0 0 NA 804168 TCGA-AB-2976 AML40 11 95802521 95802521 A G SNP CCDC82 NM_024725.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44962 NULL 0.002 - - - no_errors tier3 2034 85 4.01 686 643 48.38 0 0 NA 804168 TCGA-AB-2976 AML40 11 98849470 98849470 G T SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-82616 e1-82616 0.001 - - - no_errors tier3 896 61 6.37 533 467 46.7 0 0 NA 804168 TCGA-AB-2976 AML40 11 99822559 99822559 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 11 100333298 100333298 C T SNP ENSG00000165895 ENST00000389873 human ensembl 54_36p 1 known intronic c.797-2526 e9-2526 0.005 - - - no_start_codon tier3 1163 62 5.06 767 568 42.55 1 0 0 804168 TCGA-AB-2976 AML40 11 121559230 121559230 A C SNP MIRNLET7A2 ENST00000362105 human ensembl 54_36p -1 known 5_prime_flanking_region c.-36719 NULL 0.002 - - - no_errors tier3 1086 53 4.65 730 612 45.6 0 0 NA 804168 TCGA-AB-2976 AML40 11 121572463 121572463 G A SNP MIRNLET7A2 ENST00000362105 human ensembl 54_36p -1 known 5_prime_flanking_region c.-49952 NULL 0.003 - - - no_errors tier3 989 68 6.43 719 635 46.83 0 0 NA 804168 TCGA-AB-2976 AML40 11 123267557 123267557 C T SNP OR4D5 NM_001001965.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-47977 NULL 0.002 - - - no_errors tier3 1082 58 5.09 672 566 45.72 0 0 NA 804168 TCGA-AB-2976 AML40 11 123747677 123747677 G A SNP OR8B3 NM_001005467.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*23839 NULL 0 - - - no_errors tier2 1472 94 5.99 950 725 43.26 0 0 NA 804168 TCGA-AB-2976 AML40 11 126858772 126858772 A G SNP - - - - - - - - - - - - - - - tier3 1152 88 7.1 559 427 43.26 0 0 NA 804168 TCGA-AB-2976 AML40 11 128690570 128690570 G A SNP ENSG00000166080 ENST00000299101 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19986 NULL 0 - - - no_coding_region:pseudogene tier2 992 57 5.43 654 563 46.26 0 0 NA 804168 TCGA-AB-2976 AML40 11 134002987 134002987 C T SNP LOC729302 XM_001133304.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*43763 NULL 0.01 - - - no_errors tier3 935 68 6.77 465 355 43.24 0 0 NA 804168 TCGA-AB-2976 AML40 12 10136538 10136538 A G SNP CLEC1A NM_016511.2 human genbank 54_36p -1 reviewed intronic c.116-3450 e2-3450 0 - - - no_errors tier3 1370 62 4.33 821 758 47.97 0 0 NA 804168 TCGA-AB-2976 AML40 12 11962884 11962884 C T SNP ETV6 NM_001987.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*27637 NULL 0.001 - - - no_errors tier3 1454 89 5.76 1287 1047 44.84 0 0 NA 804168 TCGA-AB-2976 AML40 12 22264699 22264699 C T SNP ST8SIA1 NM_003034.3 human genbank 54_36p -1 reviewed intronic c.585-18460 e5-18460 0 - - - no_errors tier3 1779 92 4.91 1339 1135 45.82 0 0 NA 804168 TCGA-AB-2976 AML40 12 22700579 22700579 T A SNP ETNK1 NM_018638.1 human genbank 54_36p 1 reviewed intronic c.684-2636 e3-2636 0.001 - - - no_errors tier3 863 47 5.16 596 516 46.32 4 2 33.33 804168 TCGA-AB-2976 AML40 12 31014363 31014363 T C SNP TSPAN11 NM_001080509.2 human genbank 54_36p 1 validated intronic c.276+6144 e2+6144 0.002 - - - no_errors tier3 1101 44 3.84 396 336 45.9 0 1 100 804168 TCGA-AB-2976 AML40 12 51724502 51724502 C - DEL TENC1 NM_015319.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-4693 NULL 0.949 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 12 52126095 52126095 C T SNP PRR13 NM_018457.2 human genbank 54_36p 1 validated silent c.432 p.S144 1 NULL NULL - no_errors tier1 422 37 8.06 163 186 53.14 86 84 49.41 804168 TCGA-AB-2976 AML40 12 56811832 56811832 G A SNP - - - - - - - - - - - - - - - tier2 1280 74 5.46 990 752 43.17 0 0 NA 804168 TCGA-AB-2976 AML40 12 60277805 60277805 G A SNP - - - - - - - - - - - - - - - tier3 1157 53 4.38 820 705 46.17 0 0 NA 804168 TCGA-AB-2976 AML40 12 68965071 68965071 G A SNP CNOT2 NM_014515.4 human genbank 54_36p 1 provisional intronic c.48+6750 e1+6750 0 - - - no_errors tier3 1135 31 2.66 899 525 36.87 8 4 33.33 804168 TCGA-AB-2976 AML40 12 70655871 70655871 G A SNP TPH2 NM_173353.3 human genbank 54_36p 1 reviewed intronic c.805+3109 e6+3109 0 - - - no_errors tier3 1187 77 6.09 856 706 45.14 0 0 NA 804168 TCGA-AB-2976 AML40 12 74609574 74609574 A G SNP ENSG00000198923 ENST00000361500 human ensembl 54_36p 1 known 5_prime_flanking_region c.-34505 NULL 0 - - - no_errors tier3 1724 115 6.25 666 622 48.25 0 0 NA 804168 TCGA-AB-2976 AML40 12 80648841 80648841 G C SNP PPFIA2 NM_003625.2 human genbank 54_36p -1 reviewed intronic c.249+23042 e1+23042 0 - - - no_errors tier3 1216 63 4.92 456 297 39.39 0 0 NA 804168 TCGA-AB-2976 AML40 12 85138336 85138336 A C SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+113638 e0+113638 0 - - - no_errors tier3 1274 61 4.57 683 671 49.56 0 0 NA 804168 TCGA-AB-2976 AML40 12 86295165 86295165 G T SNP - - - - - - - - - - - - - - - tier3 1034 51 4.7 636 494 43.72 0 0 NA 804168 TCGA-AB-2976 AML40 12 106007689 106007689 A G SNP CRY1 NM_004075.3 human genbank 54_36p -1 validated intronic c.158+3023 e1+3023 0 - - - no_errors tier3 1208 72 5.62 610 510 45.54 0 1 100 804168 TCGA-AB-2976 AML40 12 108956068 108956068 G A SNP ANKRD13A NM_033121.1 human genbank 54_36p 1 validated missense c.1432 p.V478M 0.364 NULL "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,HMMPfam_UIM,HMMSmart_SM00726" - no_errors tier1 1762 119 6.33 724 594 45.03 39 38 49.35 804168 TCGA-AB-2976 AML40 12 117762123 117762123 T G SNP ENSG00000199809 ENST00000362939 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*10139 NULL 0.001 - - - no_errors tier2 953 44 4.41 573 413 41.84 0 0 NA 804168 TCGA-AB-2976 AML40 12 125520708 125520708 C A SNP ENSG00000214043 ENST00000397346 human ensembl 54_36p 1 known intronic c.516+324 e5+324 0.014 - - - no_errors tier3 1205 81 6.3 841 955 53.17 0 0 NA 804168 TCGA-AB-2976 AML40 12 126711072 126711072 C T SNP LOC644489 XM_932212.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-24617 NULL 0.007 - - - no_errors tier3 758 48 5.96 372 340 47.75 0 0 NA 804168 TCGA-AB-2976 AML40 12 127357651 127357651 C G SNP - - - - - - - - - - - - - - - tier3 1824 82 4.3 693 579 45.52 0 0 NA 804168 TCGA-AB-2976 AML40 12 130098775 130098775 G T SNP GPR133 NM_198827.3 human genbank 54_36p 1 validated intronic c.1474-28524 e14-28524 0.001 - - - no_errors tier3 300 21 6.52 165 146 46.95 0 0 NA 804168 TCGA-AB-2976 AML40 13 27506256 27506257 - TCATATTCATATTCATATTCATAT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1800_1799 p.600in_frame_insEYEYEYEY 0.998:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 804168 TCGA-AB-2976 AML40 13 34007876 34007876 C T SNP ENSG00000220002 ENST00000407757 human ensembl 54_36p -1 known 3_prime_flanking_region c.*38465 NULL 0.001 - - - no_coding_region:pseudogene tier3 928 60 6.07 513 416 44.78 0 0 NA 804168 TCGA-AB-2976 AML40 13 34100881 34100881 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 13 54855092 54855092 G A SNP - - - - - - - - - - - - - - - tier3 980 50 4.85 512 364 41.51 0 0 NA 804168 TCGA-AB-2976 AML40 13 54857596 54857596 C A SNP - - - - - - - - - - - - - - - tier3 1273 75 5.56 600 474 44.13 0 0 NA 804168 TCGA-AB-2976 AML40 13 54895439 54895439 A C SNP - - - - - - - - - - - - - - - tier3 992 57 5.43 593 586 49.7 0 0 NA 804168 TCGA-AB-2976 AML40 13 55195249 55195249 T C SNP - - - - - - - - - - - - - - - tier3 942 41 4.16 781 646 45.21 0 0 NA 804168 TCGA-AB-2976 AML40 13 55195288 55195288 G C SNP - - - - - - - - - - - - - - - tier3 853 37 4.15 745 629 45.75 0 0 NA 804168 TCGA-AB-2976 AML40 13 58677514 58677514 A T SNP - - - - - - - - - - - - - - - tier3 1488 73 4.68 969 834 46.23 0 0 NA 804168 TCGA-AB-2976 AML40 13 65790842 65790842 C T SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed intronic c.3341-13681 e4-13681 0 - - - no_errors tier3 797 44 5.23 585 527 47.39 0 0 NA 804168 TCGA-AB-2976 AML40 13 65819875 65819875 C T SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed intronic c.3341-42714 e4-42714 0.002 - - - no_errors tier3 1689 112 6.22 1212 1064 46.71 0 0 NA 804168 TCGA-AB-2976 AML40 13 68080775 68080775 T C SNP ENSG00000218340 ENST00000402052 human ensembl 54_36p 1 known 5_prime_flanking_region c.-25548 NULL 0.001 - - - no_coding_region:pseudogene tier3 684 45 6.16 613 629 50.6 0 0 NA 804168 TCGA-AB-2976 AML40 13 88627192 88627192 C G SNP - - - - - - - - - - - - - - - tier3 316 23 6.78 207 199 49.01 0 0 NA 804168 TCGA-AB-2976 AML40 13 89964903 89964903 C T SNP - - - - - - - - - - - - - - - tier3 830 49 5.55 723 480 39.83 0 0 NA 804168 TCGA-AB-2976 AML40 13 92632214 92632214 C T SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45497 NULL 0 - - - no_errors tier2 769 53 6.44 524 414 44.04 0 0 NA 804168 TCGA-AB-2976 AML40 13 93513959 93513959 C T SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.877+35810 e4+35810 0.163 - - - no_errors tier3 1025 103 9.13 944 761 44.63 0 0 NA 804168 TCGA-AB-2976 AML40 13 93555335 93555335 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.877+77186 e4+77186 0 - - - no_errors tier3 330 20 5.71 152 119 43.91 0 0 NA 804168 TCGA-AB-2976 AML40 13 95096598 95096598 G A SNP DNAJC3 NM_006260.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30913 NULL 0.012 - - - no_errors tier2 1221 28 2.24 660 423 39.06 0 0 0 804168 TCGA-AB-2976 AML40 13 107421802 107421802 G A SNP - - - - - - - - - - - - - - - tier2 683 25 3.53 1046 820 43.94 0 0 NA 804168 TCGA-AB-2976 AML40 13 108417114 108417114 C A SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.2303+1863 e19+1863 0.001 - - - no_errors tier3 843 78 8.47 566 485 46.15 0 0 NA 804168 TCGA-AB-2976 AML40 13 111072379 111072379 G A SNP ENSG00000204398 ENST00000375713 human ensembl 54_36p 1 known intronic c.1-3956 e1-3956 0 - - - no_errors tier3 1173 81 6.44 488 442 47.48 0 0 NA 804168 TCGA-AB-2976 AML40 14 29397936 29397936 C T SNP PRKD1 NM_002742.2 human genbank 54_36p -1 validated intronic c.264+68270 e1+68270 0 - - - no_errors tier3 1708 87 4.85 1182 833 41.26 0 0 NA 804168 TCGA-AB-2976 AML40 14 48690637 48690637 T C SNP - - - - - - - - - - - - - - - tier3 821 56 6.39 575 468 44.87 0 0 NA 804168 TCGA-AB-2976 AML40 14 52599500 52599500 C T SNP DDHD1 NM_030637.1 human genbank 54_36p -1 provisional silent c.1677 p.L559 1 NULL HMMPfam_DDHD - no_errors tier1 1050 78 6.91 924 818 46.96 25 11 30.56 804168 TCGA-AB-2976 AML40 14 56274859 56274859 C T SNP - - - - - - - - - - - - - - - tier2 1200 85 6.61 886 715 44.58 0 0 NA 804168 TCGA-AB-2976 AML40 14 61937789 61937789 A C SNP - - - - - - - - - - - - - - - tier3 777 46 5.59 501 503 50.05 0 0 NA 804168 TCGA-AB-2976 AML40 14 62593389 62593389 C T SNP KCNH5 NM_172376.3 human genbank 54_36p -1 reviewed intronic c.1-39964 e1-39964 0.001 - - - no_errors tier3 773 57 6.87 324 279 46.19 0 0 NA 804168 TCGA-AB-2976 AML40 14 64969508 64969508 C T SNP FUT8 NM_178154.3 human genbank 54_36p 1 reviewed intronic c.1+19823 e0+19823 0 - - - no_errors tier2 448 27 5.68 222 200 47.28 2 0 0 804168 TCGA-AB-2976 AML40 14 73015343 73015343 T A SNP HEATR4 NM_203309.1 human genbank 54_36p -1 provisional intronic c.2704-43 e16-43 0 - - - no_errors tier3 1352 90 6.24 394 312 44.13 0 0 NA 804168 TCGA-AB-2976 AML40 14 76162153 76162153 C A SNP - - - - - - - - - - - - - - - tier3 775 46 5.6 567 534 48.5 0 0 NA 804168 TCGA-AB-2976 AML40 14 79736807 79736807 T C SNP DIO2 ENST00000388841 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*2401 NULL 0.006 - - - no_errors tier3 1003 72 6.69 840 759 47.44 0 0 NA 804168 TCGA-AB-2976 AML40 14 79918273 79918273 C T SNP - - - - - - - - - - - - - - - tier3 1433 120 7.73 1138 963 45.84 0 0 NA 804168 TCGA-AB-2976 AML40 14 83367514 83367514 T A SNP - - - - - - - - - - - - - - - tier3 972 78 7.43 803 682 45.93 0 0 NA 804168 TCGA-AB-2976 AML40 14 83809609 83809609 G T SNP - - - - - - - - - - - - - - - tier3 1743 134 7.14 1250 1053 45.72 0 0 NA 804168 TCGA-AB-2976 AML40 14 85694731 85694731 G A SNP - - - - - - - - - - - - - - - tier3 351 29 7.61 308 265 46.25 0 0 NA 804168 TCGA-AB-2976 AML40 14 99386453 99386453 G T SNP EML1 NM_001008707.1 human genbank 54_36p 1 reviewed intronic c.68-490 e2-490 0.004 - - - no_errors tier3 842 52 5.82 593 464 43.86 0 0 NA 804168 TCGA-AB-2976 AML40 14 100761804 100761804 G A SNP - - - - - - - - - - - - - - - tier3 117 15 11.28 70 158 69.3 0 0 NA 804168 TCGA-AB-2976 AML40 14 101028995 101028995 G A SNP - - - - - - - - - - - - - - - tier3 529 36 6.3 134 102 42.32 0 0 NA 804168 TCGA-AB-2976 AML40 15 48279128 48279128 A G SNP SLC27A2 NM_003645.2 human genbank 54_36p 1 reviewed intronic c.688+1930 e2+1930 0.004 - - - no_errors tier3 547 34 5.85 313 284 47.57 1 0 0 804168 TCGA-AB-2976 AML40 15 49763040 49763040 C T SNP SCG3 NM_013243.2 human genbank 54_36p 1 reviewed intronic c.397+117 e4+117 0 - - - no_errors tier2 1133 40 3.41 670 485 41.99 0 0 NA 804168 TCGA-AB-2976 AML40 15 56133363 56133363 G A SNP ALDH1A2 NM_003888.2 human genbank 54_36p -1 reviewed intronic c.117+11661 e1+11661 0.996 - - - no_errors tier2 1233 103 7.71 714 606 45.91 0 0 NA 804168 TCGA-AB-2976 AML40 15 65905590 65905590 G T SNP LBXCOR1 NM_001031807.1 human genbank 54_36p 1 provisional missense c.343 p.G115C 1 "HMMPfam_Ski_Sno,superfamily_Putativ_DNA_bind" "HMMPfam_Ski_Sno,superfamily_Putativ_DNA_bind,superfamily_SAND_like,HMMPfam_c-SKI_SMAD_bind" - no_errors tier1 233 13 5.28 134 112 45.53 NA 804168 TCGA-AB-2976 AML40 15 68596723 68596723 C T SNP - - - - - - - - - - - - - - - tier3 1116 90 7.46 582 507 46.51 0 0 NA 804168 TCGA-AB-2976 AML40 15 72494038 72494038 C T SNP SEMA7A NM_003612.1 human genbank 54_36p -1 reviewed silent c.1197 p.T399 0.001 "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema" "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema,HMMPfam_PSI,HMMSmart_IG,HMMSmart_PSI,superfamily_Plexin-like_fold,superfamily_SSF48726" - no_errors tier1 649 62 8.71 196 156 44.19 10 8 44.44 804168 TCGA-AB-2976 AML40 15 76282691 76282691 C T SNP ACSBG1 NM_015162.3 human genbank 54_36p -1 reviewed intronic c.232+4708 e2+4708 0 - - - no_errors tier3 693 40 5.46 476 411 46.34 0 0 NA 804168 TCGA-AB-2976 AML40 15 76344956 76344957 - T INS DNAJA4 NM_018602.1 human genbank 54_36p 1 validated intronic c.132+664_132+663 e1+664 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 15 78642023 78642023 A G SNP ARNT2 NM_014862.3 human genbank 54_36p 1 reviewed intronic c.1165-461 e12-461 0 - - - no_errors tier3 1430 72 4.79 690 489 41.48 0 0 NA 804168 TCGA-AB-2976 AML40 15 78892039 78892039 C T SNP KIAA1199 NM_018689.1 human genbank 54_36p 1 validated intronic c.1+33029 e0+33029 0 - - - no_errors tier2 1389 91 6.14 848 709 45.54 0 0 NA 804168 TCGA-AB-2976 AML40 15 91557562 91557562 G A SNP UNQ9370 XR_041834.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*6590 NULL 0.007 - - - no_errors tier3 1012 47 4.43 879 592 39.89 0 0 NA 804168 TCGA-AB-2976 AML40 15 93993689 93993689 C T SNP - - - - - - - - - - - - - - - tier3 955 65 6.37 549 443 44.66 0 0 NA 804168 TCGA-AB-2976 AML40 15 99983562 99983562 C T SNP TM2D3 NM_078474.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*16643 NULL 0.001 - - - no_errors tier3 1160 64 5.23 610 506 45.26 0 0 NA 804168 TCGA-AB-2976 AML40 16 5741425 5741425 C T SNP ENSG00000221257 ENST00000408330 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9264 NULL 0.001 - - - no_errors tier3 1363 97 6.64 845 739 46.62 0 0 NA 804168 TCGA-AB-2976 AML40 16 6649061 6649061 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+4409 e0+4409 0.004 - - - no_errors tier3 1062 70 6.17 561 505 47.28 0 0 NA 804168 TCGA-AB-2976 AML40 16 6807899 6807899 C A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+163247 e0+163247 0 - - - no_errors tier2 1439 112 7.22 881 714 44.65 0 0 NA 804168 TCGA-AB-2976 AML40 16 7213109 7213109 T A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.27+171009 e1+171009 0 - - - no_errors tier3 1105 74 6.26 653 555 45.87 0 0 NA 804168 TCGA-AB-2976 AML40 16 11634104 11634104 C T SNP LITAF NM_004862.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-76017 NULL 0 - - - no_errors tier2 546 59 9.74 180 201 52.76 0 0 NA 804168 TCGA-AB-2976 AML40 16 19233525 19233525 C T SNP ENSG00000209734 ENST00000386999 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-10824 NULL 0.052 - - - pseudogene tier2 1251 65 4.94 953 728 43.28 0 0 NA 804168 TCGA-AB-2976 AML40 16 53595367 53595367 A G SNP - - - - - - - - - - - - - - - tier3 558 46 7.62 266 254 48.75 0 0 NA 804168 TCGA-AB-2976 AML40 16 58910650 58910650 G A SNP LOC729159 XM_001129515.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*39210 NULL 0.001 - - - no_errors tier3 1644 56 3.28 1221 793 39.34 0 0 NA 804168 TCGA-AB-2976 AML40 16 76077228 76077228 C A SNP ENSG00000216131 ENST00000401312 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49728 NULL 0 - - - no_errors tier3 1579 94 5.62 888 769 46.41 0 0 NA 804168 TCGA-AB-2976 AML40 16 76107813 76107813 G T SNP - - - - - - - - - - - - - - - tier3 1012 47 4.43 765 667 46.55 0 0 NA 804168 TCGA-AB-2976 AML40 16 76385589 76385589 G A SNP VAT1L NM_020927.1 human genbank 54_36p 1 provisional intronic c.233+5276 e1+5276 0.058 - - - no_errors tier3 2602 167 6.02 1217 1120 47.88 0 0 NA 804168 TCGA-AB-2976 AML40 16 77995390 77995390 G A SNP - - - - - - - - - - - - - - - tier3 1450 100 6.44 968 988 50.51 0 0 NA 804168 TCGA-AB-2976 AML40 16 86629993 86629993 T C SNP BANP NM_079837.3 human genbank 54_36p 1 reviewed intronic c.1194+875 e9+875 0 - - - no_errors tier3 579 40 6.46 302 246 44.89 6 9 60 804168 TCGA-AB-2976 AML40 17 8395824 8395824 C T SNP MYH10 NM_005964.1 human genbank 54_36p -1 validated intronic c.889+265 e7+265 0 - - - no_errors tier3 314 12 3.68 210 104 33.12 0 0 0 804168 TCGA-AB-2976 AML40 17 8989445 8989445 C T SNP NTN1 NM_004822.2 human genbank 54_36p 1 reviewed intronic c.1019-17410 e2-17410 0.003 - - - no_errors tier3 809 49 5.71 336 263 43.91 0 0 NA 804168 TCGA-AB-2976 AML40 17 13675592 13675592 G T SNP - - - - - - - - - - - - - - - tier3 1096 78 6.64 650 549 45.75 0 0 NA 804168 TCGA-AB-2976 AML40 17 16358142 16358142 A G SNP C17orf76 NM_207387.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22254 NULL 0 - - - no_errors tier3 1701 117 6.43 923 789 46.03 0 0 NA 804168 TCGA-AB-2976 AML40 17 17469948 17469948 C A SNP PEMT NM_148172.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-34283 NULL 0.036 - - - no_errors tier3 2017 129 6.01 809 713 46.85 0 0 NA 804168 TCGA-AB-2976 AML40 17 21466743 21466743 T C SNP ENSG00000205203 ENST00000324949 human ensembl 54_36p 1 known 5_prime_flanking_region c.-9860 NULL 0.072 - - - no_stop_codon tier3 685 17 2.42 545 151 21.7 0 0 NA 804168 TCGA-AB-2976 AML40 17 23027134 23027134 C T SNP LOC729562 XM_001723827.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-3406 NULL 0 - - - no_errors tier3 69 3 4.17 53 42 44.21 0 0 0 804168 TCGA-AB-2976 AML40 17 27401222 27401223 - T INS LRRC37B NM_052888.2 human genbank 54_36p 1 validated frame_shift_ins c.2764_2765 p.C924fs 0.201:0.224 NULL "HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like" - no_errors tier1 NA NA NA NA NA NA NA 804168 TCGA-AB-2976 AML40 17 36333913 36333913 C T SNP KRT23 NM_015515.3 human genbank 54_36p -1 reviewed intronic c.1174+337 e7+337 0 - - - no_errors tier3 1070 93 8 794 597 42.77 0 0 NA 804168 TCGA-AB-2976 AML40 17 38835868 38835868 C T SNP uc010czf.1 ENST00000341011 human ensembl 54_36p -1 known 5_prime_flanking_region c.-21643 NULL 0.697 - - - no_errors tier3 1006 56 5.27 341 262 43.45 0 0 NA 804168 TCGA-AB-2976 AML40 17 40050083 40050083 G A SNP LOC728675 XM_001128122.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-28222 NULL 0.009 - - - no_errors tier3 1658 115 6.48 539 442 45.06 0 0 NA 804168 TCGA-AB-2976 AML40 17 40442905 40442905 G A SNP C1QL1 NM_006688.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-41963 NULL 0.016 - - - no_errors tier3 326 39 10.68 112 114 50.44 1 0 0 804168 TCGA-AB-2976 AML40 17 48566688 48566688 T A SNP - - - - - - - - - - - - - - - tier2 1231 66 5.08 944 840 47.01 0 0 NA 804168 TCGA-AB-2976 AML40 17 59595878 59595878 G A SNP TEX2 NM_018469.3 human genbank 54_36p -1 validated intronic c.2693-3853 e7-3853 0 - - - no_errors tier3 612 54 8.11 428 368 46.23 0 0 0 804168 TCGA-AB-2976 AML40 17 66541218 66541218 G T SNP ENSG00000211252 ENST00000388517 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26401 NULL 1 - - - pseudogene tier2 1045 69 6.19 745 638 46.06 0 0 NA 804168 TCGA-AB-2976 AML40 17 66623767 66623767 G T SNP - - - - - - - - - - - - - - - tier3 1263 94 6.93 912 776 45.94 0 0 NA 804168 TCGA-AB-2976 AML40 17 68908757 68908757 G T SNP SDK2 ENST00000334543 human ensembl 54_36p -1 known missense c.2005 p.P669T 1 superfamily_FN_III-like "HMMSmart_IGc2,HMMSmart_IG,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,HMMPfam_ig,superfamily_SSF48726" - no_errors tier1 778 61 7.27 258 263 50.38 1 100 804168 TCGA-AB-2976 AML40 17 69104075 69104075 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 17 77816725 77816725 T G SNP CSNK1D NM_001893.3 human genbank 54_36p -1 reviewed intronic c.187+126 e2+126 0.001 - - - no_errors tier3 790 39 4.7 232 252 52.07 1 3 75 804168 TCGA-AB-2976 AML40 18 6741538 6741538 T - DEL ARHGAP28 ENST00000262227 human ensembl 54_36p 1 known 5_prime_flanking_region c.-73224 NULL 0.006 - - - no_start_codon tier3 NA NA NA NA NA NA 0 0 NA 804168 TCGA-AB-2976 AML40 18 7273835 7273835 A G SNP ENSG00000212626 ENST00000391324 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17183 NULL 0.004 - - - no_errors tier3 1203 80 6.24 903 771 46.06 0 0 NA 804168 TCGA-AB-2976 AML40 18 13357053 13357053 G A SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.1-20287 e1-20287 0.258 - - - no_errors tier3 843 46 5.17 509 395 43.69 0 0 NA 804168 TCGA-AB-2976 AML40 18 18043891 18043891 C T SNP LOC100131966 XM_001714344.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21964 NULL 0.001 - - - no_errors tier3 947 78 7.57 457 338 42.52 0 0 NA 804168 TCGA-AB-2976 AML40 18 24510358 24510358 C A SNP ENSG00000221268 ENST00000408341 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*10511 NULL 0 - - - no_errors tier3 1107 69 5.87 689 564 44.94 0 0 NA 804168 TCGA-AB-2976 AML40 18 26790827 26790827 A G SNP ENSG00000209893 ENST00000387158 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-27243 NULL 0.132 - - - pseudogene tier3 617 28 4.34 348 359 50.78 0 0 NA 804168 TCGA-AB-2976 AML40 18 26874395 26874395 A G SNP DSC3 NM_001941.3 human genbank 54_36p -1 reviewed intronic c.69+2161 e1+2161 0.003 - - - no_errors tier3 1148 83 6.74 680 542 44.32 0 0 NA 804168 TCGA-AB-2976 AML40 18 31407153 31407153 C T SNP GALNT1 ENST00000392829 human ensembl 54_36p 1 known 5_prime_flanking_region c.-81472 NULL 0.001 - - - no_errors tier3 1119 86 7.13 774 604 43.83 0 0 NA 804168 TCGA-AB-2976 AML40 18 35462584 35462584 C T SNP ENSG00000212354 ENST00000391052 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*49898 NULL 0.523 - - - no_errors tier3 1992 118 5.58 780 621 44.33 0 4 100 804168 TCGA-AB-2976 AML40 18 38565791 38565791 T G SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*11665 NULL 0.569 - - - no_errors tier3 1112 79 6.63 1096 955 46.52 0 0 NA 804168 TCGA-AB-2976 AML40 18 50651208 50651208 A G SNP RAB27B NM_004163.3 human genbank 54_36p 1 provisional intronic c.1+4279 e0+4279 0.021 - - - no_errors tier3 788 54 6.41 327 275 45.68 0 0 0 804168 TCGA-AB-2976 AML40 18 56626116 56626116 C T SNP LOC728111 XM_001126567.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-12999 NULL 0 - - - no_errors tier3 1515 75 4.72 697 548 44.02 0 0 NA 804168 TCGA-AB-2976 AML40 18 61573340 61573340 T A SNP CDH7 NM_004361.2 human genbank 54_36p 1 reviewed intronic c.1+3974 e0+3974 0.008 - - - no_errors tier3 1148 74 6.05 664 491 42.51 0 0 NA 804168 TCGA-AB-2976 AML40 18 69785377 69785377 C T SNP - - - - - - - - - - - - - - - tier3 1714 78 4.35 1033 804 43.74 0 0 NA 804168 TCGA-AB-2976 AML40 18 71180486 71180486 G A SNP TSHZ1 NM_005786.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*50902 NULL 0.002 - - - no_errors tier3 1108 75 6.33 513 504 49.56 3 0 0 804168 TCGA-AB-2976 AML40 18 73779976 73779976 C G SNP - - - - - - - - - - - - - - - tier3 1184 85 6.69 536 493 47.91 0 0 NA 804168 TCGA-AB-2976 AML40 18 74251612 74251612 G A SNP - - - - - - - - - - - - - - - tier2 477 43 8.24 199 143 41.81 0 0 NA 804168 TCGA-AB-2976 AML40 19 1995081 1995081 A G SNP MKNK2 NM_199054.3 human genbank 54_36p -1 validated intronic c.340-500 e5-500 0.535 - - - no_errors tier2 319 28 7.63 160 145 47.08 2 0 0 804168 TCGA-AB-2976 AML40 19 6928811 6928811 C T SNP EMR4P ENST00000359590 human ensembl 54_36p -1 known intronic c.542-445 e7-445 0.006 - - - no_errors tier3 758 30 3.8 389 335 46.27 1 0 0 804168 TCGA-AB-2976 AML40 19 7817120 7817120 C T SNP EVI5L NM_145245.2 human genbank 54_36p 1 provisional intronic c.1-262 e1-262 0 - - - no_errors tier3 528 36 6.37 240 190 44.19 1 0 0 804168 TCGA-AB-2976 AML40 19 34247995 34247995 C A SNP - - - - - - - - - - - - - - - tier3 746 47 5.93 485 420 46.41 0 0 NA 804168 TCGA-AB-2976 AML40 19 35106340 35106340 T A SNP C19orf2 NM_003796.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-18955 NULL 0.013 - - - no_errors tier3 1416 99 6.53 532 471 46.87 0 0 NA 804168 TCGA-AB-2976 AML40 19 43895312 43895312 T G SNP ACTN4 NM_004924.3 human genbank 54_36p 1 reviewed intronic c.820-1637 e9-1637 0 - - - no_errors tier3 446 30 6.28 232 215 47.99 15 11 42.31 804168 TCGA-AB-2976 AML40 19 56767177 56767177 G A SNP ZNF175 NM_007147.2 human genbank 54_36p 1 validated intronic c.1+637 e0+637 0 - - - no_errors tier3 1122 83 6.89 858 765 47.13 0 2 100 804168 TCGA-AB-2976 AML40 20 4681021 4681021 A G SNP LOC100131517 XM_001717950.1 human genbank 54_36p -1 model intronic c.401+5137 e3+5137 0.006 - - - no_start_codon:pseudogene:no_stop_codon tier3 856 61 6.65 615 529 46.16 0 0 NA 804168 TCGA-AB-2976 AML40 20 8347993 8347993 G T SNP PLCB1 NM_015192.2 human genbank 54_36p 1 reviewed intronic c.246+47896 e3+47896 0.001 - - - no_errors tier3 1062 51 4.58 875 698 44.32 5 7 58.33 804168 TCGA-AB-2976 AML40 20 10715758 10715758 A G SNP - - - - - - - - - - - - - - - tier3 1474 107 6.75 896 812 47.54 0 0 NA 804168 TCGA-AB-2976 AML40 20 11865626 11865626 G C SNP BTBD3 NM_014962.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*13312 NULL 0 - - - no_errors tier3 1183 106 8.22 715 661 48.04 0 0 NA 804168 TCGA-AB-2976 AML40 20 14794162 14794162 C T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.418+180557 e5+180557 0.001 - - - no_errors tier3 916 43 4.48 656 471 41.76 0 0 NA 804168 TCGA-AB-2976 AML40 20 14840849 14840849 C T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.418+227244 e5+227244 0.001 - - - no_errors tier3 1155 70 5.71 718 661 47.93 0 1 100 804168 TCGA-AB-2976 AML40 20 20346418 20346418 T G SNP C20orf74 NM_020343.2 human genbank 54_36p -1 validated intronic c.5496-5626 e38-5626 0.002 - - - no_errors tier3 443 37 7.71 248 264 51.56 7 2 22.22 804168 TCGA-AB-2976 AML40 20 38705572 38705572 G A SNP MAFB NM_005461.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*44361 NULL 0.001 - - - no_errors tier3 1555 97 5.87 631 515 44.94 0 0 NA 804168 TCGA-AB-2976 AML40 20 40233548 40233548 C T SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.2549-9952 e18-9952 0.002 - - - no_errors tier3 1568 82 4.97 1004 907 47.46 0 0 NA 804168 TCGA-AB-2976 AML40 20 42302696 42302696 A T SNP GDAP1L1 NM_024034.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6693 NULL 0 - - - no_errors tier3 1731 100 5.46 450 389 46.25 0 0 NA 804168 TCGA-AB-2976 AML40 20 50407501 50407501 G A SNP - - - - - - - - - - - - - - - tier3 1844 112 5.73 1652 1546 48.31 0 0 NA 804168 TCGA-AB-2976 AML40 20 51030183 51030183 C T SNP TSHZ2 NM_173485.4 human genbank 54_36p 1 validated intronic c.40+6904 e1+6904 0.037 - - - no_errors tier3 1194 93 7.23 552 471 46.04 0 0 NA 804168 TCGA-AB-2976 AML40 20 53745770 53745770 G T SNP - - - - - - - - - - - - - - - tier3 1322 58 4.19 910 568 38.43 0 0 NA 804168 TCGA-AB-2976 AML40 20 54963861 54963861 G A SNP - - - - - - - - - - - - - - - tier2 938 54 5.44 604 504 45.45 0 0 NA 804168 TCGA-AB-2976 AML40 20 60230226 60230226 C A SNP OSBPL2 NM_144498.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34410 NULL 0 - - - no_errors tier3 87 2 2.22 49 46 48.42 0 0 NA 804168 TCGA-AB-2976 AML40 21 18186691 18186691 C G SNP CHODL ENST00000400131 human ensembl 54_36p 1 known 5_prime_flanking_region c.-364050 NULL 0.021 - - - no_errors tier3 1106 60 5.14 667 643 49.01 0 0 NA 804168 TCGA-AB-2976 AML40 21 22404855 22404855 A T SNP C21orf74 ENST00000333482 human ensembl 54_36p 1 known intronic c.87-1106 e2-1106 0 - - - no_errors tier3 1770 125 6.59 853 705 45.22 0 0 NA 804168 TCGA-AB-2976 AML40 21 24117145 24117145 T C SNP - - - - - - - - - - - - - - - tier3 1418 90 5.96 851 769 47.44 0 0 NA 804168 TCGA-AB-2976 AML40 21 25100372 25100372 C T SNP - - - - - - - - - - - - - - - tier3 1146 79 6.44 866 731 45.74 0 0 NA 804168 TCGA-AB-2976 AML40 21 34742474 34742474 C T SNP KCNE1 NM_000219.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*939 NULL 0 - - - no_errors tier2 986 54 5.19 506 456 47.35 0 3 100 804168 TCGA-AB-2976 AML40 21 35242561 35242561 G T SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed intronic c.59-55431 e2-55431 0 - - - no_errors tier3 618 33 5.07 487 391 44.53 43 25 36.76 804168 TCGA-AB-2976 AML40 22 26191695 26191695 G T SNP - - - - - - - - - - - - - - - tier3 1350 73 5.13 563 523 48.16 0 0 NA 804168 TCGA-AB-2976 AML40 22 30694329 30694329 C T SNP C22orf24 NM_015372.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-30277 NULL 0 - - - no_errors tier2 569 33 5.47 203 165 44.72 0 0 NA 804168 TCGA-AB-2976 AML40 22 33530064 33530064 T G SNP - - - - - - - - - - - - - - - tier3 1960 139 6.62 1304 1002 43.4 0 0 NA 804168 TCGA-AB-2976 AML40 22 40878648 40878648 G A SNP ENSG00000218093 ENST00000402963 human ensembl 54_36p -1 known intronic c.NULL NULL 0.001 - - - no_coding_region:pseudogene tier2 183 5 2.65 87 69 41.57 0 0 0 804168 TCGA-AB-2976 AML40 22 43816898 43816898 T C SNP PHF21B NM_138415.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-32804 NULL 0.002 - - - no_errors tier3 696 40 5.43 577 478 45.31 0 0 NA 804168 TCGA-AB-2976 AML40 22 44307388 44307388 C T SNP FBLN1 NM_006486.2 human genbank 54_36p 1 reviewed intronic c.545-219 e6-219 0 - - - no_errors tier3 487 25 4.87 221 162 41.97 0 0 NA 804168 TCGA-AB-2976 AML40 22 46399434 46399434 C T SNP ENSG00000205634 ENST00000380990 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*413 NULL 0 - - - no_errors tier3 565 22 3.74 216 193 46.84 0 0 NA 804168 TCGA-AB-2976 AML40 22 47922920 47922920 G A SNP - - - - - - - - - - - - - - - tier3 583 40 6.38 193 195 49.24 0 0 NA 804168 TCGA-AB-2976 AML40 22 48085867 48085867 G A SNP - - - - - - - - - - - - - - - tier3 355 28 7.31 196 191 49.23 0 0 NA 225373 TCGA-AB-2977 AML22 X 2153565 2153565 T C SNP DHRSX NM_145177.2 human genbank 54_36p -1 validated intronic c.805-4295 e7-4295 0 - - - no_errors tier3 33 34 50.75 29 3 9.38 0 0 0 225373 TCGA-AB-2977 AML22 X 13791780 13791780 G A SNP GPM6B NM_001001994.1 human genbank 54_36p -1 validated intronic c.4+74767 e1+74767 0.991 - - - no_errors tier3 284 216 43.03 223 32 12.55 0 0 NA 225373 TCGA-AB-2977 AML22 X 15751360 15751360 C T SNP ZRSR2 ENST00000307771 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*74 NULL 0 - - - no_errors tier3 78 64 44.76 267 33 11 1 0 0 225373 TCGA-AB-2977 AML22 X 32319465 32319465 A C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.4234-1246 e31-1246 0.002 - - - no_errors tier3 505 142 21.95 213 6 2.74 0 0 NA 225373 TCGA-AB-2977 AML22 X 32906972 32906972 A C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.93+41205 e2+41205 0 - - - no_errors tier3 503 386 43.42 290 27 8.52 0 0 NA 225373 TCGA-AB-2977 AML22 X 36086087 36086087 G A SNP CXorf59 NM_173695.1 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*13240 NULL 0.012 - - - no_errors tier3 393 317 44.59 165 27 14.06 0 0 NA 225373 TCGA-AB-2977 AML22 X 37633654 37633654 A C SNP DYNLT3 NM_006520.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41947 NULL 0.001 - - - no_errors tier3 236 177 42.86 249 24 8.79 0 0 NA 225373 TCGA-AB-2977 AML22 X 39680417 39680417 C T SNP - - - - - - - - - - - - - - - tier3 310 263 45.9 227 43 15.81 0 0 NA 225373 TCGA-AB-2977 AML22 X 39718243 39718243 G A SNP - - - - - - - - - - - - - - - tier3 211 161 43.16 160 26 13.98 0 0 NA 225373 TCGA-AB-2977 AML22 X 44177383 44177383 G A SNP ENSG00000218348 ENST00000402107 human ensembl 54_36p 1 known 5_prime_flanking_region c.-33498 NULL 0.082 - - - no_coding_region:pseudogene tier3 382 300 43.99 249 48 16.16 0 0 NA 225373 TCGA-AB-2977 AML22 X 49036244 49036244 T C SNP FOXP3 NM_014009.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-34338 NULL 0.013 - - - no_errors tier3 173 158 47.02 137 21 13.29 0 0 NA 225373 TCGA-AB-2977 AML22 X 85755540 85755540 A G SNP DACH2 NM_053281.1 human genbank 54_36p 1 reviewed intronic c.641-37155 e4-37155 0.495 - - - no_errors tier3 194 175 47.43 179 17 8.67 0 0 NA 225373 TCGA-AB-2977 AML22 X 101001139 101001139 C A SNP NXF5 NM_032946.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-16719 NULL 0 - - - no_errors tier3 337 280 45.38 210 34 13.93 0 0 NA 225373 TCGA-AB-2977 AML22 X 103551388 103551388 G C SNP - - - - - - - - - - - - - - - tier3 528 451 46.07 261 24 8.42 0 0 NA 225373 TCGA-AB-2977 AML22 X 104964196 104964196 A T SNP NRK ENST00000243300 human ensembl 54_36p 1 known intronic c.123+2428 e2+2428 0.041 - - - no_errors tier3 390 336 46.22 504 40 7.35 0 0 NA 225373 TCGA-AB-2977 AML22 X 106767504 106767504 C A SNP PRPS1 NM_002764.3 human genbank 54_36p 1 reviewed intronic c.123-1677 e2-1677 0 - - - no_errors tier3 279 257 47.86 250 21 7.75 1 0 0 225373 TCGA-AB-2977 AML22 X 122814575 122814575 G A SNP XIAP NM_001167.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32619 NULL 0.003 - - - no_errors tier3 271 199 42.07 374 43 10.31 0 0 NA 225373 TCGA-AB-2977 AML22 X 138337952 138337952 A T SNP ENSG00000217296 ENST00000405662 human ensembl 54_36p 1 known 5_prime_flanking_region c.-18764 NULL 0 - - - no_coding_region:pseudogene tier3 475 367 43.53 438 58 11.69 0 0 NA 225373 TCGA-AB-2977 AML22 X 138600499 138600499 T A SNP MCF2 NM_001099855.1 human genbank 54_36p -1 validated intronic c.1+17432 e0+17432 0.001 - - - no_errors tier3 181 143 44 233 19 7.54 0 0 NA 225373 TCGA-AB-2977 AML22 X 143919554 143919554 T G SNP ENSG00000201912 ENST00000365042 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-26766 NULL 0.008 - - - no_errors tier3 264 214 44.77 170 30 14.93 0 0 NA 225373 TCGA-AB-2977 AML22 X 144024047 144024047 G A SNP ENSG00000218657 ENST00000403711 human ensembl 54_36p 1 known 5_prime_flanking_region c.-41747 NULL 0 - - - no_coding_region:pseudogene tier3 527 416 43.79 332 24 6.69 0 0 NA 225373 TCGA-AB-2977 AML22 X 144917082 144917082 G T SNP MIRN891A ENST00000401237 human ensembl 54_36p -1 known rna NULL NULL 0.001 - - - no_errors tier1 312 41 11.61 376 280 42.62 NA 225373 TCGA-AB-2977 AML22 X 145739548 145739548 T C SNP LOC100132556 XM_001716020.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-26924 NULL 0.002 - - - no_start_codon tier3 332 296 47.06 454 71 13.52 0 0 NA 225373 TCGA-AB-2977 AML22 X 153656391 153656391 G T SNP DKC1 NM_001363.1 human genbank 54_36p 1 reviewed intronic c.1259+217 e12+217 0 - - - no_errors tier3 128 91 41.55 193 33 14.6 0 4 100 225373 TCGA-AB-2977 AML22 1 2408210 2408210 C T SNP PLCH2 NM_014638.2 human genbank 54_36p 1 provisional missense c.821 p.A274V 0 "HMMPfam_efhand_like,superfamily_EF-hand" "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_PH,HMMSmart_SM00233,HMMSmart_SM00054,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_EF-hand,superfamily_PH domain-like" - no_errors tier1 67 7 9.46 39 38 49.35 4 0 225373 TCGA-AB-2977 AML22 1 5210032 5210032 T C SNP - - - - - - - - - - - - - - - tier3 222 156 41.27 161 25 13.44 0 0 NA 225373 TCGA-AB-2977 AML22 1 11150058 11150058 G T SNP FRAP1 NM_004958.3 human genbank 54_36p -1 reviewed intronic c.4329+28 e28+28 0.001 - - - no_errors tier3 345 230 40 163 29 15.1 0 0 0 225373 TCGA-AB-2977 AML22 1 24294468 24294468 G C SNP MYOM3 NM_152372.3 human genbank 54_36p -1 validated intronic c.790+51 e7+51 0 - - - no_errors tier3 67 63 48.46 81 12 12.9 0 0 NA 225373 TCGA-AB-2977 AML22 1 41778058 41778058 G T SNP HIVEP3 NM_024503.1 human genbank 54_36p -1 validated intronic c.5208-14890 e3-14890 0.001 - - - no_errors tier3 80 43 34.96 89 11 11 0 0 NA 225373 TCGA-AB-2977 AML22 1 54865988 54865988 G A SNP ACOT11 NM_015547.2 human genbank 54_36p 1 reviewed intronic c.1630-3007 e16-3007 0 - - - no_errors tier3 397 250 38.64 281 37 11.64 0 0 NA 225373 TCGA-AB-2977 AML22 1 76552896 76552896 G A SNP ST6GALNAC3 NM_152996.1 human genbank 54_36p 1 provisional intronic c.213+624 e2+624 0 - - - no_errors tier3 352 295 45.52 254 23 8.3 0 0 NA 225373 TCGA-AB-2977 AML22 1 90069453 90069453 C T SNP LRRC8D NM_018103.1 human genbank 54_36p 1 validated intronic c.1+9121 e0+9121 0 - - - no_errors tier3 196 147 42.86 298 36 10.78 0 5 100 225373 TCGA-AB-2977 AML22 1 96230959 96230959 C T SNP - - - - - - - - - - - - - - - tier3 609 503 45.23 318 39 10.92 0 0 NA 225373 TCGA-AB-2977 AML22 1 98719420 98719420 C A SNP - - - - - - - - - - - - - - - tier3 388 205 34.57 333 26 7.24 0 0 NA 225373 TCGA-AB-2977 AML22 1 99467561 99467561 A G SNP LPPR4 NM_014839.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35033 NULL 0.005 - - - no_errors tier3 316 305 49.11 376 52 12.15 0 0 NA 225373 TCGA-AB-2977 AML22 1 110883195 110883195 G A SNP KCNA10 NM_005549.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20263 NULL 0.109 - - - no_errors tier3 207 164 44.09 240 36 13.04 0 0 NA 225373 TCGA-AB-2977 AML22 1 115232296 115232296 G A SNP SYCP1 NM_003176.2 human genbank 54_36p 1 validated intronic c.1258+459 e14+459 0 - - - no_errors tier3 306 211 40.81 274 50 15.43 0 0 NA 225373 TCGA-AB-2977 AML22 1 159186710 159186710 T C SNP ITLN2 NM_080878.2 human genbank 54_36p -1 validated intronic c.601-130 e6-130 0 - - - no_errors tier3 102 100 49.5 141 31 18.02 0 0 NA 225373 TCGA-AB-2977 AML22 1 173943223 173943223 T G SNP TNR NM_003285.2 human genbank 54_36p -1 validated intronic c.1+35762 e0+35762 0 - - - no_errors tier3 527 464 46.82 407 36 8.13 0 0 NA 225373 TCGA-AB-2977 AML22 1 175491552 175491552 G A SNP FAM5B NM_021165.2 human genbank 54_36p 1 provisional intronic c.270-126 e2-126 0 - - - no_errors tier3 292 256 46.63 191 22 10.33 0 0 NA 225373 TCGA-AB-2977 AML22 1 175974409 175974409 G A SNP - - - - - - - - - - - - - - - tier3 1130 855 42.96 633 55 7.99 0 0 NA 225373 TCGA-AB-2977 AML22 1 187367433 187367433 A C SNP ENSG00000219973 ENST00000401817 human ensembl 54_36p -1 known 3_prime_flanking_region c.*671 NULL 0 - - - no_coding_region:pseudogene tier3 272 107 28.23 301 12 3.83 0 0 NA 225373 TCGA-AB-2977 AML22 1 239028780 239028780 A T SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.1413+2598 e16+2598 0 - - - no_errors tier3 214 176 44.9 381 50 11.6 0 0 0 225373 TCGA-AB-2977 AML22 2 5795833 5795833 G A SNP SOX11 NM_003108.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*44203 NULL 0 - - - no_errors tier3 646 601 48.16 395 62 13.54 0 0 NA 225373 TCGA-AB-2977 AML22 2 10552402 10552402 C T SNP ODC1 NM_002539.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49793 NULL 0.005 - - - no_errors tier3 133 99 42.67 228 36 13.64 0 0 NA 225373 TCGA-AB-2977 AML22 2 12112496 12112496 C T SNP LOC729992 XR_038318.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*30473 NULL 0.01 - - - pseudogene tier3 436 336 43.41 231 37 13.81 0 0 NA 225373 TCGA-AB-2977 AML22 2 20155308 20155308 G A SNP LAPTM4A NM_014713.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-40546 NULL 0.089 - - - no_errors tier3 145 108 42.52 188 20 9.62 0 0 NA 225373 TCGA-AB-2977 AML22 2 21787609 21787609 T A SNP LOC645949 XR_040569.1 human genbank 54_36p -1 model rna NULL NULL 0.001 - - - no_errors tier1 217 37 14.51 364 345 48.66 NA 225373 TCGA-AB-2977 AML22 2 22526963 22526963 T A SNP - - - - - - - - - - - - - - - tier3 392 300 43.35 211 27 11.34 0 0 NA 225373 TCGA-AB-2977 AML22 2 23685717 23685717 G A SNP KLHL29 XM_001717454.1 human genbank 54_36p 1 model intronic c.1096-29797 e6-29797 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 167 146 46.65 209 12 5.43 0 0 NA 225373 TCGA-AB-2977 AML22 2 31197464 31197464 T A SNP GALNT14 NM_024572.2 human genbank 54_36p -1 validated intronic c.129+16864 e1+16864 0.001 - - - no_errors tier3 394 319 44.68 263 33 11.15 0 0 0 225373 TCGA-AB-2977 AML22 2 35373318 35373318 G A SNP - - - - - - - - - - - - - - - tier3 451 395 46.69 235 29 10.98 0 0 NA 225373 TCGA-AB-2977 AML22 2 59198415 59198415 G A SNP - - - - - - - - - - - - - - - tier3 354 299 45.58 241 26 9.74 0 0 NA 225373 TCGA-AB-2977 AML22 2 83810700 83810700 G A SNP - - - - - - - - - - - - - - - tier3 652 579 46.92 569 84 12.84 0 0 NA 225373 TCGA-AB-2977 AML22 2 100180890 100180890 C T SNP LOC150577 XR_041753.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-10258 NULL 0.248 - - - no_errors tier3 420 299 41.3 289 42 12.61 0 0 NA 225373 TCGA-AB-2977 AML22 2 102508559 102508559 G A SNP SLC9A4 NM_001011552.3 human genbank 54_36p 1 validated intronic c.1950+513 e10+513 0 - - - no_errors tier3 405 286 41.39 208 19 8.37 0 0 NA 225373 TCGA-AB-2977 AML22 2 114299453 114299453 G A SNP ENSG00000208621 ENST00000385886 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*22729 NULL 0.003 - - - pseudogene tier3 299 239 44.42 239 25 9.47 0 0 NA 225373 TCGA-AB-2977 AML22 2 116495939 116495939 G A SNP - - - - - - - - - - - - - - - tier3 398 328 45.05 242 38 13.57 0 0 NA 225373 TCGA-AB-2977 AML22 2 125881353 125881353 C T SNP - - - - - - - - - - - - - - - tier3 130 100 43.48 210 19 8.3 0 0 NA 225373 TCGA-AB-2977 AML22 2 153488837 153488837 G A SNP - - - - - - - - - - - - - - - tier3 320 307 48.96 126 27 17.65 0 0 NA 225373 TCGA-AB-2977 AML22 2 167568737 167568737 C T SNP XIRP2 NM_152381.2 human genbank 54_36p 1 validated intronic c.408+100091 e1+100091 0 - - - no_errors tier3 120 100 45.45 229 22 8.76 0 0 NA 225373 TCGA-AB-2977 AML22 2 179110367 179110367 C T SNP TTN NM_133378.3 human genbank 54_36p -1 reviewed missense c.92108 p.S30703N 0.999 NULL "superfamily_Ypt/Rab-GAP domain of gyp1p,PatternScan_RCC1_2,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_PPAK,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_beta-sandwich domain of Sec23/24" - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier1 219 45 17.05 348 354 50.43 NA 225373 TCGA-AB-2977 AML22 2 192230765 192230765 T C SNP LOC729245 XM_001129743.1 human genbank 54_36p 1 model intronic c.73+9759 e1+9759 0.096 - - - no_errors tier3 456 308 40.26 241 41 14.54 0 0 NA 225373 TCGA-AB-2977 AML22 2 202157819 202157819 A G SNP ALS2CR11 NM_152525.4 human genbank 54_36p -1 validated intronic c.517-2634 e5-2634 0 - - - no_errors tier3 257 201 43.79 345 51 12.88 0 0 NA 225373 TCGA-AB-2977 AML22 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 270 38 12.34 197 141 41.59 22 30 57.69 225373 TCGA-AB-2977 AML22 2 212013470 212013470 G A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.2488-9400 e21-9400 0.005 - - - no_errors tier3 728 623 46.08 554 100 15.29 0 0 NA 225373 TCGA-AB-2977 AML22 2 213725769 213725769 T C SNP IKZF2 NM_016260.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4171 NULL 0.914 - - - no_errors tier3 104 83 44.39 195 20 9.3 0 0 NA 225373 TCGA-AB-2977 AML22 2 229556271 229556271 A T SNP PID1 NM_017933.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*42321 NULL 0.002 - - - no_errors tier3 349 253 41.89 322 38 10.56 0 0 NA 225373 TCGA-AB-2977 AML22 3 533278 533278 C G SNP - - - - - - - - - - - - - - - tier3 262 219 45.53 249 41 14.14 0 0 NA 225373 TCGA-AB-2977 AML22 3 3570989 3570989 C T SNP - - - - - - - - - - - - - - - tier3 305 223 42 213 30 12.35 1 0 0 225373 TCGA-AB-2977 AML22 3 14315433 14315433 G A SNP - - - - - - - - - - - - - - - tier3 185 168 47.59 326 58 15.1 0 0 NA 225373 TCGA-AB-2977 AML22 3 26436677 26436677 C T SNP - - - - - - - - - - - - - - - tier3 602 497 45.14 334 67 16.71 0 0 NA 225373 TCGA-AB-2977 AML22 3 27447642 27447642 A G SNP SLC4A7 NM_003615.3 human genbank 54_36p -1 validated intronic c.1123+151 e7+151 0 - - - no_errors tier3 246 223 47.55 151 26 14.69 0 0 NA 225373 TCGA-AB-2977 AML22 3 29030194 29030194 G T SNP - - - - - - - - - - - - - - - tier3 519 355 40.62 334 43 11.41 0 0 NA 225373 TCGA-AB-2977 AML22 3 63571210 63571210 G A SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated intronic c.540+1178 e4+1178 0.033 - - - no_errors tier3 593 491 45.3 449 44 8.92 0 0 NA 225373 TCGA-AB-2977 AML22 3 66712761 66712761 G A SNP - - - - - - - - - - - - - - - tier3 596 490 45.04 423 56 11.69 0 0 NA 225373 TCGA-AB-2977 AML22 3 73661269 73661269 C T SNP PDZRN3 NM_015009.1 human genbank 54_36p -1 provisional intronic c.918+72926 e3+72926 0 - - - no_errors tier3 386 329 45.89 227 35 13.36 0 0 NA 225373 TCGA-AB-2977 AML22 3 78109483 78109483 A G SNP - - - - - - - - - - - - - - - tier3 518 363 41.11 223 22 8.98 0 0 NA 225373 TCGA-AB-2977 AML22 3 80232671 80232671 G C SNP - - - - - - - - - - - - - - - tier3 436 415 48.77 293 63 17.7 0 0 NA 225373 TCGA-AB-2977 AML22 3 105006962 105006962 T C SNP - - - - - - - - - - - - - - - tier3 196 215 52.31 360 54 13.04 0 0 NA 225373 TCGA-AB-2977 AML22 3 107918521 107918521 C G SNP ENSG00000200361 ENST00000363491 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*28205 NULL 0.019 - - - no_errors tier3 318 284 47.1 244 29 10.62 0 0 NA 225373 TCGA-AB-2977 AML22 3 112838065 112838065 T C SNP CD96 NM_198196.4 human genbank 54_36p 1 reviewed intronic c.1370-668 e12-668 0 - - - no_errors tier3 493 418 45.73 269 25 8.5 1 0 0 225373 TCGA-AB-2977 AML22 3 118682809 118682809 C T SNP - - - - - - - - - - - - - - - tier3 350 296 45.68 283 28 9 0 0 NA 225373 TCGA-AB-2977 AML22 3 128031799 128031799 G A SNP CHCHD6 NM_032343.1 human genbank 54_36p 1 provisional intronic c.412-22381 e5-22381 0.007 - - - no_errors tier3 254 220 46.22 258 17 6.18 0 0 0 225373 TCGA-AB-2977 AML22 3 152417421 152417421 C G SNP P2RY14 NM_001081455.1 human genbank 54_36p -1 reviewed intronic c.1+2592 e0+2592 0.002 - - - no_errors tier3 311 247 44.19 160 20 11.05 0 0 NA 225373 TCGA-AB-2977 AML22 3 165389940 165389940 G T SNP MIRN1263 ENST00000408324 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17902 NULL 0.721 - - - no_errors tier3 195 130 40 184 13 6.6 0 0 NA 225373 TCGA-AB-2977 AML22 3 172991750 172991750 C T SNP PLD1 ENST00000351298 human ensembl 54_36p -1 known intronic c.1+19133 e0+19133 0 - - - no_errors tier3 562 483 46.13 328 61 15.64 0 0 NA 225373 TCGA-AB-2977 AML22 3 174513835 174513835 C T SNP - - - - - - - - - - - - - - - tier3 420 346 45.05 239 47 16.43 0 0 NA 225373 TCGA-AB-2977 AML22 3 176218398 176218398 A T SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated intronic c.44-78876 e2-78876 0.106 - - - no_errors tier3 456 325 41.56 224 15 6.28 0 0 NA 225373 TCGA-AB-2977 AML22 3 180873636 180873636 G A SNP USP13 NM_003940.2 human genbank 54_36p 1 validated intronic c.169-8724 e2-8724 0 - - - no_errors tier3 223 182 44.61 192 36 15.79 0 0 NA 225373 TCGA-AB-2977 AML22 4 427878 427878 T C SNP ZNF721 NM_133474.2 human genbank 54_36p -1 validated silent c.378 p.Q126 0.017 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 260 19 6.79 267 220 45.17 3 0 225373 TCGA-AB-2977 AML22 4 14413763 14413763 A G SNP - - - - - - - - - - - - - - - tier3 704 572 44.79 393 65 14.19 0 0 NA 225373 TCGA-AB-2977 AML22 4 24018127 24018127 C A SNP ENSG00000222262 ENST00000410330 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13770 NULL 0 - - - no_errors tier3 452 306 40.37 312 28 8.24 0 0 NA 225373 TCGA-AB-2977 AML22 4 29383994 29383994 G C SNP ENSG00000212045 ENST00000390756 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22964 NULL 0.001 - - - no_errors tier3 149 95 38.93 205 33 13.87 0 0 NA 225373 TCGA-AB-2977 AML22 4 31185101 31185101 G A SNP - - - - - - - - - - - - - - - tier3 395 328 45.18 190 37 16.3 0 0 NA 225373 TCGA-AB-2977 AML22 4 44914241 44914241 G A SNP - - - - - - - - - - - - - - - tier3 229 188 44.98 219 27 10.98 0 0 NA 225373 TCGA-AB-2977 AML22 4 48001743 48001743 C T SNP TEC NM_003215.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-76355 NULL 0.013 - - - no_errors tier3 145 109 42.91 218 28 11.38 0 0 NA 225373 TCGA-AB-2977 AML22 4 65023393 65023393 T C SNP - - - - - - - - - - - - - - - tier3 122 95 43.78 72 9 11.11 0 0 NA 225373 TCGA-AB-2977 AML22 4 73471131 73471131 T A SNP ADAMTS3 NM_014243.1 human genbank 54_36p -1 reviewed intronic c.661+28265 e4+28265 0.01 - - - no_errors tier3 558 500 47.21 295 39 11.64 0 0 NA 225373 TCGA-AB-2977 AML22 4 84843406 84843406 G T SNP - - - - - - - - - - - - - - - tier3 110 91 45.27 136 11 7.48 0 0 NA 225373 TCGA-AB-2977 AML22 4 113943114 113943114 G T SNP ENSG00000202536 ENST00000365666 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-46592 NULL 0.041 - - - no_errors tier3 143 112 43.92 227 24 9.56 0 0 NA 225373 TCGA-AB-2977 AML22 4 116801311 116801311 C T SNP - - - - - - - - - - - - - - - tier3 370 333 47.37 312 43 12.11 0 0 NA 225373 TCGA-AB-2977 AML22 4 132052903 132052903 C T SNP - - - - - - - - - - - - - - - tier3 516 435 45.74 352 39 9.97 0 0 NA 225373 TCGA-AB-2977 AML22 4 142218533 142218533 C T SNP RNF150 NM_020724.1 human genbank 54_36p -1 validated intronic c.484+54396 e1+54396 0.091 - - - no_errors tier3 462 371 44.38 364 42 10.32 0 0 NA 225373 TCGA-AB-2977 AML22 4 144192664 144192664 G C SNP LOC729675 XM_001130993.1 human genbank 54_36p -1 model intronic c.570-111816 e3-111816 0.002 - - - no_errors tier3 383 269 41.26 279 46 14.15 0 0 NA 225373 TCGA-AB-2977 AML22 4 145689067 145689067 T A SNP - - - - - - - - - - - - - - - tier3 421 363 46.12 230 31 11.79 0 0 NA 225373 TCGA-AB-2977 AML22 4 148998110 148998110 A C SNP ARHGAP10 NM_024605.3 human genbank 54_36p 1 validated intronic c.385-44 e5-44 0 - - - no_errors tier3 211 150 41.55 221 40 15.33 0 0 0 225373 TCGA-AB-2977 AML22 4 151918745 151918745 A G SNP LRBA NM_006726.2 human genbank 54_36p -1 validated intronic c.5581-16296 e34-16296 0.588 - - - no_errors tier3 561 464 45.22 621 77 11.03 0 0 0 225373 TCGA-AB-2977 AML22 4 180869076 180869076 G A SNP - - - - - - - - - - - - - - - tier3 219 195 47.1 180 17 8.59 0 0 NA 225373 TCGA-AB-2977 AML22 4 190202540 190202540 G A SNP - - - - - - - - - - - - - - - tier3 430 359 45.33 217 44 16.86 0 0 NA 225373 TCGA-AB-2977 AML22 5 3450258 3450258 C A SNP - - - - - - - - - - - - - - - tier3 122 44 26.51 110 6 5.17 0 0 NA 225373 TCGA-AB-2977 AML22 5 4423157 4423157 T C SNP - - - - - - - - - - - - - - - tier3 350 260 42.62 253 37 12.76 0 0 NA 225373 TCGA-AB-2977 AML22 5 15989890 15989890 C T SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed silent c.1071 p.I357 1 "HMMSmart_SM00367,superfamily_RNI-like" "HMMPfam_F-box,HMMSmart_SM00256,HMMSmart_SM00367,superfamily_RNI-like" - no_errors tier1 184 25 11.85 206 169 44.47 NA 225373 TCGA-AB-2977 AML22 5 25769921 25769921 T C SNP ENSG00000201016 ENST00000364146 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32733 NULL 0 - - - no_errors tier3 380 346 47.59 243 44 15.22 0 0 NA 225373 TCGA-AB-2977 AML22 5 27122035 27122035 T A SNP CDH9 NM_016279.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-97838 NULL 0.004 - - - no_errors tier3 257 198 43.52 266 23 7.96 0 0 NA 225373 TCGA-AB-2977 AML22 5 29520602 29520602 G A SNP - - - - - - - - - - - - - - - tier3 156 103 39.77 214 20 8.55 0 0 NA 225373 TCGA-AB-2977 AML22 5 50690001 50690001 G A SNP ISL1 NM_002202.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25262 NULL 0.475 - - - no_errors tier3 377 296 43.85 244 35 12.54 0 0 NA 225373 TCGA-AB-2977 AML22 5 50894075 50894075 A G SNP - - - - - - - - - - - - - - - tier3 205 198 49.13 230 23 9.09 0 0 NA 225373 TCGA-AB-2977 AML22 5 83710508 83710508 T C SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.67+5374 e1+5374 0 - - - no_errors tier3 267 205 43.34 353 27 7.09 0 0 NA 225373 TCGA-AB-2977 AML22 5 89961074 89961074 G A SNP GPR98 NM_032119.3 human genbank 54_36p 1 reviewed missense c.1801 p.D601N 1 NULL "HMMPfam_GPS,PatternScan_LIPOYL,HMMPfam_Calx-beta,HMMSmart_SM00237,HMMPfam_EPTP,PatternScan_A_DEAMINASE,superfamily_Concanavalin A-like lectins/glucanases" - no_errors tier1 232 31 11.79 334 226 40.36 NA 225373 TCGA-AB-2977 AML22 5 96354987 96354987 C T SNP LNPEP NM_005575.2 human genbank 54_36p 1 reviewed intronic c.1253-290 e6-290 0 - - - no_errors tier3 536 378 41.36 347 42 10.77 0 0 NA 225373 TCGA-AB-2977 AML22 5 97765285 97765285 C T SNP ENSG00000211351 ENST00000388616 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8492 NULL 0 - - - pseudogene tier3 290 273 47.98 233 35 13.06 0 0 NA 225373 TCGA-AB-2977 AML22 5 106301239 106301239 T C SNP - - - - - - - - - - - - - - - tier3 144 106 42.4 203 34 14.35 0 0 NA 225373 TCGA-AB-2977 AML22 5 122082261 122082261 C G SNP - - - - - - - - - - - - - - - tier3 205 195 48.51 204 27 11.69 0 0 NA 225373 TCGA-AB-2977 AML22 5 160769353 160769353 G A SNP GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed intronic c.541+1206 e5+1206 0 - - - no_errors tier3 473 423 47.21 455 77 14.47 0 0 NA 225373 TCGA-AB-2977 AML22 5 164219533 164219533 A T SNP - - - - - - - - - - - - - - - tier3 589 440 42.72 376 54 12.56 0 0 NA 225373 TCGA-AB-2977 AML22 6 13806282 13806282 A C SNP RANBP9 NM_005493.2 human genbank 54_36p -1 reviewed intronic c.572-1175 e2-1175 0.063 - - - no_errors tier3 335 288 46.23 375 50 11.76 0 0 0 225373 TCGA-AB-2977 AML22 6 37735685 37735685 C T SNP MDGA1 NM_153487.3 human genbank 54_36p -1 validated intronic c.208-1512 e3-1512 0.014 - - - no_errors tier3 202 141 41.11 348 46 11.68 0 0 NA 225373 TCGA-AB-2977 AML22 6 41788611 41788611 C T SNP TFEB NM_007162.1 human genbank 54_36p -1 provisional intronic c.1+19754 e0+19754 0.002 - - - no_errors tier3 80 115 58.67 132 27 16.98 3 0 0 225373 TCGA-AB-2977 AML22 6 49767768 49767768 A T SNP CRISP2 NM_003296.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*677 NULL 0.002 - - - no_errors tier3 217 174 44.39 194 13 6.28 0 0 NA 225373 TCGA-AB-2977 AML22 6 62398543 62398543 C A SNP LOC727798 XM_001125736.1 human genbank 54_36p -1 model intronic c.104-178 e4-178 0.002 - - - no_errors tier3 442 377 45.86 204 20 8.93 0 0 NA 225373 TCGA-AB-2977 AML22 6 75891214 75891214 G A SNP COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed intronic c.6607+349 e39+349 0.001 - - - no_errors tier3 383 248 39.24 304 23 7.03 0 0 NA 225373 TCGA-AB-2977 AML22 6 77476027 77476027 A G SNP ENSG00000216473 ENST00000373528 human ensembl 54_36p 1 known 3_prime_flanking_region c.*46821 NULL 0 - - - no_coding_region:pseudogene tier3 577 559 49.21 384 52 11.93 0 0 NA 225373 TCGA-AB-2977 AML22 6 78291471 78291471 C G SNP ENSG00000219253 ENST00000406279 human ensembl 54_36p 1 known 3_prime_flanking_region c.*28364 NULL 0 - - - no_coding_region:pseudogene tier3 260 231 47.05 210 27 11.39 0 0 NA 225373 TCGA-AB-2977 AML22 6 86942574 86942574 A G SNP ENSG00000217272 ENST00000401856 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5119 NULL 0.014 - - - no_coding_region:pseudogene tier3 336 283 45.65 212 33 13.47 0 0 NA 225373 TCGA-AB-2977 AML22 6 90274967 90274967 G A SNP ANKRD6 NM_014942.3 human genbank 54_36p 1 validated intronic c.1-58305 e1-58305 0 - - - no_errors tier3 334 277 45.34 195 31 13.72 0 0 NA 225373 TCGA-AB-2977 AML22 6 94792093 94792093 A C SNP - - - - - - - - - - - - - - - tier3 287 217 42.97 227 20 8.1 0 0 NA 225373 TCGA-AB-2977 AML22 6 110372917 110372917 C T SNP GPR6 NM_005284.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-34092 NULL 0.066 - - - no_errors tier3 171 89 34.23 80 6 6.98 0 0 NA 225373 TCGA-AB-2977 AML22 6 122467592 122467592 C G SNP - - - - - - - - - - - - - - - tier3 189 125 39.81 207 14 6.33 0 0 NA 225373 TCGA-AB-2977 AML22 6 127802849 127802849 C T SNP ENSG00000220522 ENST00000406554 human ensembl 54_36p -1 known 5_prime_flanking_region c.-23068 NULL 0 - - - no_coding_region:pseudogene tier3 249 212 45.59 231 40 14.71 0 0 NA 225373 TCGA-AB-2977 AML22 6 164667986 164667986 C T SNP LOC728275 XM_001127046.2 human genbank 54_36p 1 model intronic c.545-10005 e3-10005 0 - - - no_errors tier3 298 224 42.91 211 32 13.17 0 0 NA 225373 TCGA-AB-2977 AML22 6 170254752 170254752 C T SNP - - - - - - - - - - - - - - - tier3 105 42 28.57 80 7 8.05 0 0 NA 225373 TCGA-AB-2977 AML22 7 851331 851331 T C SNP UNC84A NM_025154.1 human genbank 54_36p 1 reviewed intronic c.508+1648 e4+1648 0 - - - no_errors tier3 88 90 50.56 156 25 13.81 0 0 0 225373 TCGA-AB-2977 AML22 7 34202814 34202814 G A SNP BMPER NM_133468.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*43404 NULL 0 - - - no_errors tier3 448 296 39.78 275 30 9.8 0 0 NA 225373 TCGA-AB-2977 AML22 7 34498529 34498529 C T SNP ENSG00000197085 ENST00000357959 human ensembl 54_36p -1 known intronic c.189-74720 e4-74720 0 - - - no_errors tier3 556 458 45.12 373 52 12.24 0 0 NA 225373 TCGA-AB-2977 AML22 7 42578607 42578607 C A SNP - - - - - - - - - - - - - - - tier3 890 573 39.09 432 43 9.05 0 0 NA 225373 TCGA-AB-2977 AML22 7 51922223 51922223 G A SNP - - - - - - - - - - - - - - - tier3 282 230 44.83 381 58 13.21 0 0 NA 225373 TCGA-AB-2977 AML22 7 118237845 118237845 G A SNP - - - - - - - - - - - - - - - tier3 585 415 41.33 378 42 10 0 0 NA 225373 TCGA-AB-2977 AML22 7 144682602 144682602 C T SNP - - - - - - - - - - - - - - - tier3 83 63 43.15 212 26 10.92 0 0 NA 225373 TCGA-AB-2977 AML22 7 156782537 156782537 C T SNP DNAJB6 NM_058246.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-61491 NULL 0.031 - - - no_errors tier3 97 53 35.33 217 20 8.44 0 0 NA 225373 TCGA-AB-2977 AML22 8 3718893 3718893 G C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.819-119921 e6-119921 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 294 246 45.47 149 14 8.59 0 0 NA 225373 TCGA-AB-2977 AML22 8 23433598 23433598 G A SNP SLC25A37 NM_016612.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-8863 NULL 0.971 - - - no_errors tier3 175 135 43.55 225 19 7.79 0 0 NA 225373 TCGA-AB-2977 AML22 8 32319974 32319974 C T SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.746-252914 e2-252914 0 - - - overly_large_intron tier3 494 390 44.12 250 47 15.77 0 0 NA 225373 TCGA-AB-2977 AML22 8 34445592 34445592 G A SNP - - - - - - - - - - - - - - - tier3 426 333 43.87 266 42 13.64 0 0 NA 225373 TCGA-AB-2977 AML22 8 38949937 38949937 T C SNP PLEKHA2 ENST00000388745 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*3509 NULL 0 - - - no_errors tier3 131 98 42.79 249 38 13.24 59 32 35.16 225373 TCGA-AB-2977 AML22 8 39765016 39765016 A G SNP ADAM2 NM_001464.3 human genbank 54_36p -1 reviewed intronic c.643-89 e9-89 0.001 - - - no_errors tier3 91 109 54.5 167 19 10.22 0 0 NA 225373 TCGA-AB-2977 AML22 8 49745362 49745362 T C SNP - - - - - - - - - - - - - - - tier3 166 127 43.2 214 33 13.36 0 0 NA 225373 TCGA-AB-2977 AML22 8 51265839 51265839 A G SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1+18091 e0+18091 0.003 - - - no_errors tier3 447 382 45.97 264 39 12.87 0 0 NA 225373 TCGA-AB-2977 AML22 8 62339147 62339147 G A SNP RLBP1L1 NM_173519.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-35794 NULL 0 - - - no_errors tier3 685 574 45.56 417 59 12.37 0 0 NA 225373 TCGA-AB-2977 AML22 8 67477909 67477909 G A SNP ADHFE1 NM_144650.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29397 NULL 0.002 - - - no_errors tier3 430 327 43.2 409 43 9.49 0 0 NA 225373 TCGA-AB-2977 AML22 8 94792623 94792623 G A SNP FAM92A1 NM_145269.3 human genbank 54_36p 1 predicted intronic c.543+1344 e6+1344 0.001 - - - no_errors tier3 164 126 43.3 276 24 8 0 0 NA 225373 TCGA-AB-2977 AML22 8 99443905 99443905 C T SNP - - - - - - - - - - - - - - - tier3 515 383 42.6 296 47 13.7 0 0 NA 225373 TCGA-AB-2977 AML22 8 117545368 117545368 C T SNP - - - - - - - - - - - - - - - tier3 494 336 40.48 168 32 16 0 0 NA 225373 TCGA-AB-2977 AML22 8 130784770 130784770 T C SNP GSDMC NM_031415.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*45159 NULL 0 - - - no_errors tier3 586 410 41.04 340 49 12.6 0 0 NA 225373 TCGA-AB-2977 AML22 8 132001792 132001792 G A SNP ADCY8 NM_001115.2 human genbank 54_36p -1 reviewed intronic c.1482-10498 e6-10498 0 - - - no_errors tier3 643 475 42.49 419 51 10.85 0 0 NA 225373 TCGA-AB-2977 AML22 8 140162454 140162454 G A SNP - - - - - - - - - - - - - - - tier3 467 437 48.18 348 49 12.34 0 0 NA 225373 TCGA-AB-2977 AML22 8 140706842 140706842 G A SNP KCNK9 NM_016601.2 human genbank 54_36p -1 reviewed intronic c.284-6318 e2-6318 0.005 - - - no_errors tier3 222 169 43.22 215 33 13.31 0 0 NA 225373 TCGA-AB-2977 AML22 9 6927100 6927100 A T SNP JMJD2C NM_015061.2 human genbank 54_36p 1 reviewed intronic c.922-43825 e8-43825 0.003 - - - no_errors tier3 181 143 44.14 286 35 10.9 0 0 NA 225373 TCGA-AB-2977 AML22 9 34946678 34946678 G A SNP KIAA1045 NM_015297.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14618 NULL 0 - - - no_errors tier3 160 116 42.03 177 22 11.06 0 0 NA 225373 TCGA-AB-2977 AML22 9 104805993 104805993 G A SNP CYLC2 NM_001340.2 human genbank 54_36p 1 reviewed intronic c.180+627 e3+627 0 - - - no_errors tier3 385 296 43.47 260 25 8.71 0 0 NA 225373 TCGA-AB-2977 AML22 9 106049538 106049538 A G SNP LOC347281 XR_016664.2 human genbank 54_36p 1 model intronic c.NULL NULL 0.003 - - - pseudogene tier3 213 151 41.48 359 31 7.95 0 0 NA 225373 TCGA-AB-2977 AML22 9 111605566 111605566 C T SNP PALM2-AKAP2 NM_007203.3 human genbank 54_36p 1 validated intronic c.45+22932 e1+22932 0.013 - - - no_errors tier3 242 210 46.36 265 42 13.68 0 0 NA 225373 TCGA-AB-2977 AML22 9 114609976 114609976 C T SNP SNX30 NM_001012994.1 human genbank 54_36p 1 validated intronic c.348+2908 e2+2908 0.001 - - - no_errors tier3 270 200 42.55 222 15 6.33 0 0 NA 225373 TCGA-AB-2977 AML22 9 127405605 127405605 T C SNP MAPKAP1 NM_001006617.1 human genbank 54_36p -1 reviewed intronic c.499-17778 e4-17778 0.002 - - - no_errors tier3 228 176 43.46 207 28 11.81 0 0 0 225373 TCGA-AB-2977 AML22 9 135681190 135681190 G A SNP VAV2 NM_003371.1 human genbank 54_36p -1 reviewed intronic c.449+8025 e4+8025 0.001 - - - no_errors tier3 26 18 40.91 47 5 9.62 0 0 NA 225373 TCGA-AB-2977 AML22 10 7824846 7824846 G T SNP ITIH2 NM_002216.2 human genbank 54_36p 1 validated intronic c.2096-269 e17-269 0.004 - - - no_errors tier3 245 168 40.68 191 27 12.39 0 0 NA 225373 TCGA-AB-2977 AML22 10 11158168 11158168 C T SNP CUGBP2 NM_006561.2 human genbank 54_36p 1 reviewed intronic c.74+58036 e1+58036 0 - - - no_errors tier3 423 348 45.14 255 32 11.15 0 0 NA 225373 TCGA-AB-2977 AML22 10 17599919 17599919 A T SNP ENSG00000202091 ENST00000365221 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35205 NULL 0.009 - - - no_errors tier3 326 313 48.83 265 50 15.82 0 0 NA 225373 TCGA-AB-2977 AML22 10 33424928 33424928 C A SNP LOC401640 XR_017380.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-37585 NULL 0.341 - - - pseudogene tier3 390 222 36.27 238 22 8.46 2 0 0 225373 TCGA-AB-2977 AML22 10 58293144 58293144 C T SNP - - - - - - - - - - - - - - - tier3 361 247 40.62 186 17 8.37 0 0 NA 225373 TCGA-AB-2977 AML22 10 58903685 58903685 C G SNP ENSG00000218583 ENST00000403728 human ensembl 54_36p 1 known 5_prime_flanking_region c.-39238 NULL 0.001 - - - no_coding_region:pseudogene tier3 169 142 45.66 85 10 10.31 0 0 NA 225373 TCGA-AB-2977 AML22 10 68459866 68459866 A T SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1047+150215 e6+150215 0.011 - - - no_errors tier3 283 209 42.48 253 28 9.96 0 0 NA 225373 TCGA-AB-2977 AML22 10 84212249 84212249 T A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.953+103645 e2+103645 0 - - - no_errors tier3 172 147 45.94 138 14 9.15 0 0 NA 225373 TCGA-AB-2977 AML22 10 115711593 115711593 T C SNP - - - - - - - - - - - - - - - tier3 290 237 44.97 193 36 15.72 0 0 NA 225373 TCGA-AB-2977 AML22 11 11326771 11326771 C T SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated intronic c.1093-7644 e7-7644 0 - - - no_errors tier3 810 670 45.27 490 73 12.97 0 0 NA 225373 TCGA-AB-2977 AML22 11 39333264 39333264 G A SNP - - - - - - - - - - - - - - - tier3 201 147 42.24 203 17 7.73 0 0 NA 225373 TCGA-AB-2977 AML22 11 41211709 41211709 T C SNP LOC387753 XM_001724792.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*49456 NULL 0.006 - - - no_start_codon:pseudogene:no_stop_codon tier3 221 174 44.05 272 40 12.82 0 0 NA 225373 TCGA-AB-2977 AML22 11 41245712 41245712 C T SNP LOC387753 XM_001724792.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*15453 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 535 422 44.1 339 32 8.6 0 0 NA 225373 TCGA-AB-2977 AML22 11 56188275 56188275 G A SNP OR5AR1 NM_001004730.1 human genbank 54_36p 1 provisional missense c.538 p.E180K 1 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 214 34 13.71 539 426 44.05 NA 225373 TCGA-AB-2977 AML22 11 65859692 65859692 G A SNP RIN1 NM_004292.2 human genbank 54_36p -1 validated silent c.420 p.D140 1 "HMMSmart_SM00252,superfamily_SH2 domain" "HMMPfam_RA,HMMSmart_SM00314,HMMSmart_SM00252,HMMPfam_VPS9,HMMSmart_SM00167,superfamily_VPS9 domain (Pfam 02204),superfamily_SH2 domain" - no_errors tier1 199 37 15.68 86 79 47.88 5 1 16.67 225373 TCGA-AB-2977 AML22 11 68369437 68369437 A G SNP CPT1A NM_001876.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29919 NULL 0 - - - no_errors tier3 109 75 40.76 161 22 11.89 4 0 0 225373 TCGA-AB-2977 AML22 11 77594995 77594995 C T SNP USP35 NM_020798.1 human genbank 54_36p 1 validated intronic c.1391+266 e6+266 0.018 - - - no_errors tier3 167 121 42.01 155 14 8.28 0 0 NA 225373 TCGA-AB-2977 AML22 11 90157477 90157477 A G SNP - - - - - - - - - - - - - - - tier3 844 707 45.58 482 75 13.44 0 0 NA 225373 TCGA-AB-2977 AML22 11 114461036 114461036 C T SNP - - - - - - - - - - - - - - - tier3 377 286 43.07 179 23 11.33 0 0 NA 225373 TCGA-AB-2977 AML22 11 132614950 132614950 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+292419 e1+292419 0.003 - - - no_errors tier3 417 341 44.99 322 38 10.56 0 0 NA 225373 TCGA-AB-2977 AML22 12 44270109 44270109 T C SNP - - - - - - - - - - - - - - - tier3 152 126 45.16 198 27 11.95 0 0 NA 225373 TCGA-AB-2977 AML22 12 47785081 47785081 G A SNP LMBR1L NM_018113.2 human genbank 54_36p -1 validated intronic c.192-146 e4-146 0 - - - no_errors tier3 58 53 47.75 114 21 15.56 2 6 75 225373 TCGA-AB-2977 AML22 12 60724273 60724273 T G SNP FAM19A2 NM_178539.3 human genbank 54_36p -1 reviewed intronic c.1+147034 e0+147034 0 - - - no_errors tier3 354 213 37.5 371 41 9.95 0 0 NA 225373 TCGA-AB-2977 AML22 12 62733462 62733462 T C SNP SRGAP1 NM_020762.2 human genbank 54_36p 1 validated intronic c.802-9502 e7-9502 0 - - - no_errors tier3 661 551 45.39 436 72 14.15 0 0 NA 225373 TCGA-AB-2977 AML22 12 62770951 62770951 G A SNP SRGAP1 NM_020762.2 human genbank 54_36p 1 validated intronic c.1437-372 e12-372 0.001 - - - no_errors tier3 506 431 45.95 272 44 13.92 0 0 NA 225373 TCGA-AB-2977 AML22 12 71785732 71785732 T C SNP - - - - - - - - - - - - - - - tier3 64 48 42.86 121 15 11.03 0 0 NA 225373 TCGA-AB-2977 AML22 12 77926892 77926892 T A SNP SYT1 ENST00000261205 human ensembl 54_36p 1 known intronic c.1+31050 e0+31050 0 - - - no_errors tier3 383 302 44.09 393 43 9.86 0 0 NA 225373 TCGA-AB-2977 AML22 12 93058231 93058231 C T SNP LOC441644 XM_001714973.1 human genbank 54_36p 1 model missense c.158 p.T53M 1 HMMPfam_ELM2 HMMPfam_ELM2 - no_errors tier1 101 14 12.17 149 95 38.93 NA 225373 TCGA-AB-2977 AML22 12 97194829 97194829 C A SNP - - - - - - - - - - - - - - - tier3 418 385 47.83 309 42 11.97 0 0 NA 225373 TCGA-AB-2977 AML22 12 105658994 105658994 A C SNP RFX4 NM_213594.3 human genbank 54_36p 1 reviewed intronic c.1634-6351 e16-6351 0.003 - - - no_errors tier3 555 458 45.17 334 67 16.71 0 0 NA 225373 TCGA-AB-2977 AML22 12 125444249 125444249 A C SNP LOC728173 XM_001129061.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-32422 NULL 0 - - - no_errors tier3 428 348 44.67 266 26 8.87 0 0 NA 225373 TCGA-AB-2977 AML22 12 125872553 125872553 C A SNP LOC121296 XR_016630.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-42822 NULL 0.004 - - - no_errors tier3 513 465 47.5 397 80 16.77 0 0 NA 225373 TCGA-AB-2977 AML22 12 126129519 126129519 T A SNP - - - - - - - - - - - - - - - tier3 288 243 45.59 200 35 14.89 0 0 NA 225373 TCGA-AB-2977 AML22 13 28628026 28628026 G A SNP KIAA0774 NM_001033602.2 human genbank 54_36p 1 validated intronic c.2674+54919 e3+54919 0 - - - no_errors tier3 378 213 35.92 264 32 10.81 0 0 NA 225373 TCGA-AB-2977 AML22 13 34824155 34824155 T C SNP NBEA NM_015678.3 human genbank 54_36p 1 reviewed intronic c.6013-139 e38-139 0.025 - - - no_errors tier3 285 240 45.71 305 44 12.61 0 0 NA 225373 TCGA-AB-2977 AML22 13 36927214 36927214 C T SNP - - - - - - - - - - - - - - - tier3 737 557 42.95 372 45 10.79 0 0 NA 225373 TCGA-AB-2977 AML22 13 41672446 41672446 G A SNP DGKH NM_178009.3 human genbank 54_36p 1 reviewed intronic c.2493+401 e20+401 0.002 - - - no_errors tier3 91 36 28.35 217 14 6.06 0 0 NA 225373 TCGA-AB-2977 AML22 13 45844149 45844149 C T SNP C13orf18 NM_025113.2 human genbank 54_36p -1 validated missense c.463 p.A155T 0.001 NULL NULL - no_errors tier1 282 35 10.97 387 309 44.21 NA 225373 TCGA-AB-2977 AML22 13 52847824 52847824 G A SNP ENSG00000220990 ENST00000408063 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-7732 NULL 0.001 - - - no_errors tier3 317 269 45.83 211 28 11.72 0 0 NA 225373 TCGA-AB-2977 AML22 13 56155065 56155065 T G SNP - - - - - - - - - - - - - - - tier3 176 130 42.48 123 19 13.38 0 0 NA 225373 TCGA-AB-2977 AML22 13 58746434 58746434 A G SNP - - - - - - - - - - - - - - - tier3 358 324 47.51 362 54 12.98 0 0 NA 225373 TCGA-AB-2977 AML22 13 83696129 83696129 A G SNP - - - - - - - - - - - - - - - tier3 583 582 49.83 499 80 13.82 0 0 NA 225373 TCGA-AB-2977 AML22 13 105346854 105346854 A T SNP - - - - - - - - - - - - - - - tier3 402 295 42.2 258 20 7.19 0 0 NA 225373 TCGA-AB-2977 AML22 14 25458820 25458820 C T SNP - - - - - - - - - - - - - - - tier3 475 323 40.48 326 32 8.94 0 0 NA 225373 TCGA-AB-2977 AML22 14 33155388 33155388 G A SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.519+56221 e5+56221 0 - - - no_errors tier3 383 331 46.29 225 36 13.79 0 0 NA 225373 TCGA-AB-2977 AML22 14 48525872 48525872 C T SNP - - - - - - - - - - - - - - - tier3 235 147 38.48 209 25 10.68 0 0 NA 225373 TCGA-AB-2977 AML22 14 48831472 48831472 C T SNP - - - - - - - - - - - - - - - tier3 359 322 47.08 264 39 12.83 0 0 NA 225373 TCGA-AB-2977 AML22 14 78068846 78068846 T C SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.1-112370 e1-112370 0.004 - - - no_errors tier3 1251 870 41.02 669 90 11.84 0 0 NA 225373 TCGA-AB-2977 AML22 14 79829775 79829775 G A SNP - - - - - - - - - - - - - - - tier3 182 164 47.4 304 24 7.32 0 0 NA 225373 TCGA-AB-2977 AML22 14 80859964 80859964 C T SNP STON2 NM_033104.2 human genbank 54_36p -1 provisional intronic c.572-45128 e4-45128 0.978 - - - no_errors tier3 159 133 45.55 215 26 10.79 0 0 NA 225373 TCGA-AB-2977 AML22 15 34104520 34104520 G A SNP - - - - - - - - - - - - - - - tier3 237 193 44.88 263 37 12.33 0 0 NA 225373 TCGA-AB-2977 AML22 15 43977706 43977706 C T SNP - - - - - - - - - - - - - - - tier3 243 212 46.49 163 24 12.77 0 0 NA 225373 TCGA-AB-2977 AML22 15 44567954 44567954 A T SNP - - - - - - - - - - - - - - - tier3 575 378 39.62 305 39 11.34 2 0 0 225373 TCGA-AB-2977 AML22 15 95730799 95730799 C T SNP ENSG00000208890 ENST00000386155 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*32839 NULL 0.001 - - - pseudogene tier3 754 620 44.99 494 53 9.69 0 0 NA 225373 TCGA-AB-2977 AML22 15 96743142 96743142 C G SNP - - - - - - - - - - - - - - - tier3 507 436 46.14 339 56 14.18 0 0 NA 225373 TCGA-AB-2977 AML22 16 20877502 20877502 T G SNP DNAH3 NM_017539.1 human genbank 54_36p -1 provisional intronic c.10826+500 e54+500 0 - - - no_errors tier3 429 315 42.34 316 63 16.62 0 0 NA 225373 TCGA-AB-2977 AML22 16 34405373 34405373 A G SNP ENSG00000221532 ENST00000408605 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36908 NULL 0 - - - no_errors tier3 158 120 43.17 104 16 13.33 0 0 NA 225373 TCGA-AB-2977 AML22 16 51341604 51341604 G A SNP LOC100132440 XM_001719251.1 human genbank 54_36p -1 model intronic c.663+3733 e3+3733 0.012 - - - no_errors tier3 326 217 39.82 294 42 12.5 0 0 NA 225373 TCGA-AB-2977 AML22 16 60108617 60108617 A T SNP - - - - - - - - - - - - - - - tier3 202 151 42.78 141 25 14.97 0 0 NA 225373 TCGA-AB-2977 AML22 17 8285599 8285599 A T SNP NDEL1 NM_030808.1 human genbank 54_36p 1 reviewed intronic c.1-2704 e1-2704 0.01 - - - no_errors tier3 107 73 40.56 227 28 10.98 0 5 100 225373 TCGA-AB-2977 AML22 17 43076480 43076480 C A SNP LOC728896 XM_001719193.1 human genbank 54_36p -1 model intronic c.56+5281 e1+5281 0 - - - no_errors tier3 140 122 46.56 340 54 13.67 0 0 0 225373 TCGA-AB-2977 AML22 17 51683142 51683142 G A SNP ANKFN1 NM_153228.2 human genbank 54_36p 1 validated intronic c.62+22825 e2+22825 0.001 - - - no_errors tier3 316 249 44.07 234 19 7.51 0 0 NA 225373 TCGA-AB-2977 AML22 17 60650080 60650080 C A SNP RGS9 NM_003835.1 human genbank 54_36p 1 validated intronic c.1408-1502 e18-1502 0.001 - - - no_errors tier3 262 218 45.42 254 44 14.72 0 0 NA 225373 TCGA-AB-2977 AML22 17 67119234 67119234 C G SNP LOC124685 XR_040247.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.035 - - - no_errors tier3 145 110 42.97 111 8 6.67 0 0 NA 225373 TCGA-AB-2977 AML22 18 12026347 12026347 T G SNP IMPA2 NM_014214.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*5890 NULL 0 - - - no_errors tier3 103 76 42.22 165 19 10.33 0 0 NA 225373 TCGA-AB-2977 AML22 18 27310273 27310273 G T SNP DSG3 NM_001944.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*52 NULL 0 - - - no_errors tier3 352 307 46.59 249 37 12.94 0 0 NA 225373 TCGA-AB-2977 AML22 18 35636903 35636903 A C SNP - - - - - - - - - - - - - - - tier3 440 273 38.29 346 32 8.47 0 0 NA 225373 TCGA-AB-2977 AML22 18 39078545 39078545 C T SNP SYT4 NM_020783.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*25759 NULL 0 - - - no_errors tier3 295 227 43.49 198 15 7.04 0 0 NA 225373 TCGA-AB-2977 AML22 18 44681476 44681476 G A SNP KIAA0427 NM_014772.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*41548 NULL 0.006 - - - no_errors tier3 249 208 45.51 230 32 12.21 0 0 NA 225373 TCGA-AB-2977 AML22 18 65346073 65346073 C G SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.67-36630 e2-36630 0 - - - no_errors tier3 226 152 40.21 149 20 11.83 0 0 NA 225373 TCGA-AB-2977 AML22 18 73900315 73900315 C A SNP ENSG00000199728 ENST00000362858 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*2482 NULL 0.002 - - - no_errors tier3 326 244 42.81 381 53 12.21 0 0 NA 225373 TCGA-AB-2977 AML22 19 2509558 2509558 T C SNP GNG7 NM_052847.2 human genbank 54_36p -1 validated intronic c.1-3372 e1-3372 0.025 - - - no_errors tier3 70 66 48.18 98 13 11.71 7 0 0 225373 TCGA-AB-2977 AML22 19 8409046 8409046 G A SNP MARCH2 NM_001005415.1 human genbank 54_36p 1 validated intronic c.583-226 e4-226 0 - - - no_errors tier3 64 68 51.52 169 24 12.44 12 7 36.84 225373 TCGA-AB-2977 AML22 19 15625527 15625527 G A SNP CYP4F3 NM_000896.2 human genbank 54_36p 1 reviewed intronic c.1115+765 e8+765 0 - - - no_errors tier3 225 189 45.32 176 27 13.3 0 0 NA 225373 TCGA-AB-2977 AML22 19 21752534 21752534 C G SNP ZNF100 NM_173531.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-10463 NULL 0.002 - - - no_errors tier3 97 53 35.33 111 7 5.93 0 0 NA 225373 TCGA-AB-2977 AML22 19 33904390 33904390 G A SNP ENSG00000205243 ENST00000379371 human ensembl 54_36p -1 known intronic c.117+311 e2+311 0 - - - no_errors tier3 157 129 45.1 133 9 6.29 0 0 NA 225373 TCGA-AB-2977 AML22 19 47960929 47960929 G C SNP PSG8 NM_182707.1 human genbank 54_36p -1 validated intronic c.64+581 e1+581 0 - - - no_errors tier3 386 326 45.79 279 49 14.8 0 0 NA 225373 TCGA-AB-2977 AML22 20 9223964 9223964 C T SNP PLCB4 NM_000933.2 human genbank 54_36p 1 reviewed intronic c.1-12483 e1-12483 0.001 - - - no_errors tier3 1350 1147 45.94 707 97 12.06 0 0 NA 225373 TCGA-AB-2977 AML22 20 25916550 25916550 C T SNP uc002wvh.2 ENST00000376399 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21921 NULL 0 - - - no_coding_region:pseudogene tier3 249 175 41.08 237 32 11.9 0 0 NA 225373 TCGA-AB-2977 AML22 20 30822749 30822749 T G SNP DNMT3B NM_006892.3 human genbank 54_36p 1 reviewed intronic c.1+8583 e0+8583 0.045 - - - no_errors tier3 87 68 43.87 107 11 9.32 0 0 NA 225373 TCGA-AB-2977 AML22 20 41460146 41460146 A G SNP ENSG00000201021 ENST00000364151 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7381 NULL 0.045 - - - no_errors tier3 241 250 50.81 237 36 13.19 0 0 NA 225373 TCGA-AB-2977 AML22 20 41794518 41794518 A T SNP GTSF1L NM_176791.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5770 NULL 0 - - - no_errors tier3 253 213 45.71 247 27 9.85 0 0 NA 225373 TCGA-AB-2977 AML22 21 35012138 35012138 C T SNP CLIC6 NM_053277.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*1488 NULL 0 - - - no_errors tier3 390 334 46.07 321 61 15.97 0 0 NA 225373 TCGA-AB-2977 AML22 21 35225067 35225067 A T SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed intronic c.59-37937 e2-37937 0 - - - no_errors tier3 634 480 42.48 403 51 11.16 0 0 0 225373 TCGA-AB-2977 AML22 21 35942715 35942715 C T SNP ENSG00000217521 ENST00000404239 human ensembl 54_36p -1 known 5_prime_flanking_region c.-48525 NULL 0 - - - no_coding_region:pseudogene tier3 366 267 41.92 274 34 11.04 0 0 NA 225373 TCGA-AB-2977 AML22 22 23954856 23954856 A T SNP CRYBB2 NM_000496.2 human genbank 54_36p 1 reviewed intronic c.307-547 e4-547 0 - - - no_errors tier3 83 60 41.96 117 16 11.94 0 0 NA 225373 TCGA-AB-2977 AML22 22 34105603 34105603 C T SNP MCM5 NM_006739.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20829 NULL 0 - - - no_errors tier3 46 42 47.73 156 17 9.77 0 0 NA 103342 TCGA-AB-2978 AML17 X 6505670 6505670 T C SNP VCX3A NM_016379.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43132 NULL 0.003 - - - no_errors tier3 1303 43 3.19 59 39 39.8 0 0 NA 103342 TCGA-AB-2978 AML17 X 10295297 10295297 A C SNP - - - - - - - - - - - - - - - tier3 636 24 3.62 49 24 32.88 0 0 NA 103342 TCGA-AB-2978 AML17 X 11470643 11470643 A G SNP ARHGAP6 NM_013427.2 human genbank 54_36p -1 reviewed intronic c.588+121639 e1+121639 0.006 - - - no_errors tier3 481 20 3.99 27 33 55 0 0 NA 103342 TCGA-AB-2978 AML17 X 14113921 14113921 G A SNP - - - - - - - - - - - - - - - tier3 935 27 2.8 56 30 34.88 0 0 NA 103342 TCGA-AB-2978 AML17 X 15691166 15691166 C - DEL CA5B NM_007220.3 human genbank 54_36p 1 reviewed intronic c.143-1456 e2-1456 0.061 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 X 17527849 17527849 T A SNP NHS NM_198270.2 human genbank 54_36p 1 reviewed intronic c.566-87934 e2-87934 0.007 - - - no_errors tier3 652 19 2.83 57 34 37.36 0 0 NA 103342 TCGA-AB-2978 AML17 X 19772820 19772820 T C SNP SH3KBP1 NM_031892.2 human genbank 54_36p -1 validated intronic c.5-8499 e2-8499 0 - - - no_errors tier3 272 9 3.2 28 16 36.36 0 0 0 103342 TCGA-AB-2978 AML17 X 22447165 22447165 G T SNP ENSG00000201095 ENST00000364225 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8708 NULL 0.003 - - - no_errors tier3 679 5 0.73 65 34 34.34 0 0 NA 103342 TCGA-AB-2978 AML17 X 40341789 40341789 C T SNP ATP6AP2 NM_005765.2 human genbank 54_36p 1 reviewed missense c.463 p.R155C 1 NULL HMMPfam_Renin_r - no_errors tier1 810 30 3.57 36 13 26.53 130 0 103342 TCGA-AB-2978 AML17 X 41663430 41663430 A G SNP CASK NM_003688.2 human genbank 54_36p -1 validated intronic c.59+3697 e1+3697 0.998 - - - no_errors tier3 507 17 3.24 66 34 34 0 0 0 103342 TCGA-AB-2978 AML17 X 79487059 79487059 G A SNP ENSG00000215104 ENST00000399581 human ensembl 54_36p -1 known 5_prime_flanking_region c.-34722 NULL 0 - - - no_start_codon tier3 806 25 3 40 17 29.82 0 0 NA 103342 TCGA-AB-2978 AML17 X 83288308 83288308 C T SNP RPS6KA6 NM_014496.2 human genbank 54_36p -1 provisional intronic c.421+334 e5+334 0 - - - no_errors tier3 774 7 0.9 72 20 21.74 0 0 NA 103342 TCGA-AB-2978 AML17 X 99822888 99822888 C T SNP SYTL4 NM_080737.1 human genbank 54_36p -1 validated missense c.1550 p.R517Q 0.989 superfamily_C2 domain (Calcium/lipid-binding domain CaLB) "HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RPH3A_effector,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FYVE/PHD zinc finger" - no_errors tier1 640 2 0.31 105 51 32.69 2 0 103342 TCGA-AB-2978 AML17 X 103703330 103703330 T C SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.1+4942 e0+4942 0.003 - - - no_errors tier3 782 26 3.22 45 29 39.19 0 0 NA 103342 TCGA-AB-2978 AML17 X 111101307 111101307 C T SNP TRPC5 NM_012471.2 human genbank 54_36p -1 validated intronic c.1-18982 e1-18982 0.001 - - - no_errors tier3 783 21 2.61 75 69 47.59 0 0 NA 103342 TCGA-AB-2978 AML17 X 112764392 112764392 G A SNP - - - - - - - - - - - - - - - tier3 1059 13 1.21 129 33 20.37 2 0 0 103342 TCGA-AB-2978 AML17 X 115498866 115498866 C T SNP SLC6A14 NM_007231.2 human genbank 54_36p 1 validated intronic c.1285+531 e9+531 0.037 - - - no_errors tier3 857 33 3.71 112 90 44.33 0 0 NA 103342 TCGA-AB-2978 AML17 X 123014734 123014734 G A SNP STAG2 NM_001042749.1 human genbank 54_36p 1 validated intronic c.1196+1809 e11+1809 0.001 - - - no_errors tier3 337 7 2.03 26 11 29.73 2 0 0 103342 TCGA-AB-2978 AML17 X 123048157 123048157 C T SNP STAG2 NM_001042749.1 human genbank 54_36p 1 validated nonsense c.3133 p.R1045* 1 superfamily_ARM-type_fold "HMMPfam_STAG,superfamily_ARM-type_fold" - no_errors tier1 989 14 1.4 145 37 20.33 6 10 62.5 103342 TCGA-AB-2978 AML17 X 128023297 128023297 C T SNP TJAP1 ENST00000393940 human ensembl 54_36p -1 known 5_prime_flanking_region c.-18456 NULL 0.001 - - - no_coding_region:pseudogene tier3 856 26 2.95 70 57 44.88 0 0 NA 103342 TCGA-AB-2978 AML17 X 130257513 130257513 C T SNP IGSF1 ENST00000370904 human ensembl 54_36p -1 known intronic c.1+3793 e0+3793 0 - - - no_errors tier3 822 23 2.72 70 15 17.65 0 0 NA 103342 TCGA-AB-2978 AML17 X 132115303 132115303 C T SNP ENSG00000220625 ENST00000402273 human ensembl 54_36p -1 known 5_prime_flanking_region c.-9669 NULL 0.011 - - - no_coding_region:pseudogene tier3 832 36 4.15 86 35 28.93 0 0 NA 103342 TCGA-AB-2978 AML17 X 136553100 136553100 G A SNP ENSG00000218923 ENST00000287722 human ensembl 54_36p 1 known 5_prime_flanking_region c.-17244 NULL 0 - - - no_coding_region:pseudogene tier3 910 18 1.94 157 40 20.3 0 0 NA 103342 TCGA-AB-2978 AML17 X 139570580 139570580 C T SNP uc004fbe.1 ENST00000370535 human ensembl 54_36p 1 known 5_prime_flanking_region c.-49048 NULL 0 - - - no_errors tier3 954 31 3.14 44 34 43.59 0 0 NA 103342 TCGA-AB-2978 AML17 X 142886610 142886610 C G SNP - - - - - - - - - - - - - - - tier3 803 13 1.59 206 58 21.97 0 0 NA 103342 TCGA-AB-2978 AML17 X 146840986 146840986 T G SNP FMR1NB NM_152578.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-29629 NULL 0.015 - - - no_errors tier3 479 14 2.84 58 41 41.41 0 0 NA 103342 TCGA-AB-2978 AML17 X 149239267 149239267 G A SNP MAMLD1 ENST00000370401 human ensembl 54_36p 1 known 5_prime_flanking_region c.-125174 NULL 0.001 - - - no_errors tier3 603 15 2.43 55 40 42.11 0 0 NA 103342 TCGA-AB-2978 AML17 1 4304366 4304366 C T SNP - - - - - - - - - - - - - - - tier3 651 17 2.53 63 30 32.26 0 0 NA 103342 TCGA-AB-2978 AML17 1 49686281 49686281 G T SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.283-202158 e4-202158 0 - - - no_errors tier3 1002 13 1.28 234 65 21.74 0 0 NA 103342 TCGA-AB-2978 AML17 1 49782597 49782597 T C SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.282+152975 e3+152975 0.01 - - - no_errors tier3 379 13 3.31 28 25 47.17 0 0 NA 103342 TCGA-AB-2978 AML17 1 56934311 56934311 C T SNP PRKAA2 NM_006252.3 human genbank 54_36p 1 validated nonsense c.679 p.R227* 1 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 838 25 2.9 194 192 49.74 NA 103342 TCGA-AB-2978 AML17 1 65962167 65962167 G A SNP ENSG00000222443 ENST00000410511 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*37164 NULL 0 - - - no_errors tier3 910 12 1.29 159 47 22.71 0 0 NA 103342 TCGA-AB-2978 AML17 1 83155045 83155045 C G SNP - - - - - - - - - - - - - - - tier3 552 5 0.9 143 34 19.21 0 0 NA 103342 TCGA-AB-2978 AML17 1 94565289 94565289 G T SNP ENSG00000178596 ENST00000332534 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24120 NULL 0.001 - - - no_coding_region:pseudogene tier3 610 11 1.77 92 37 28.68 0 0 NA 103342 TCGA-AB-2978 AML17 1 95747780 95747780 C A SNP ENSG00000216037 ENST00000401218 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4573 NULL 0 - - - no_errors tier3 760 27 3.43 148 37 20 0 0 NA 103342 TCGA-AB-2978 AML17 1 114378927 114378927 A G SNP ENSG00000216343 ENST00000406779 human ensembl 54_36p -1 known 5_prime_flanking_region c.-32544 NULL 0.822 - - - no_coding_region:pseudogene tier3 765 19 2.42 48 35 42.17 0 0 NA 103342 TCGA-AB-2978 AML17 1 115058052 115058052 T G SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.182 p.Q61P 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 749 9 1.19 69 23 25 23 15 39.47 103342 TCGA-AB-2978 AML17 1 119242794 119242794 G A SNP TBX15 NM_152380.2 human genbank 54_36p -1 validated intronic c.706+380 e6+380 0.019 - - - no_errors tier3 675 18 2.59 56 39 41.05 0 0 NA 103342 TCGA-AB-2978 AML17 1 148496324 148496324 C T SNP CA14 NM_012113.1 human genbank 54_36p 1 reviewed intronic c.1-520 e1-520 0 - - - no_errors tier3 612 23 3.62 18 14 43.75 0 0 NA 103342 TCGA-AB-2978 AML17 1 150045896 150045896 C T SNP RORC NM_005060.1 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*676 NULL 0 - - - no_errors tier3 753 26 3.34 31 17 35.42 0 0 NA 103342 TCGA-AB-2978 AML17 1 151432693 151432693 C T SNP SPRR2G NM_001014291.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-43483 NULL 0.002 - - - no_errors tier3 675 29 4.12 73 42 36.52 0 0 NA 103342 TCGA-AB-2978 AML17 1 168956654 168956654 C T SNP PRRX1 NM_022716.3 human genbank 54_36p 1 reviewed intronic c.417+988 e2+988 0 - - - no_errors tier3 1180 23 1.91 235 76 24.44 0 0 NA 103342 TCGA-AB-2978 AML17 1 170357068 170357068 C T SNP DNM3 NM_015569.1 human genbank 54_36p 1 validated intronic c.1546-9870 e14-9870 0.143 - - - no_errors tier3 688 33 4.56 75 46 38.02 0 0 0 103342 TCGA-AB-2978 AML17 1 176189281 176189281 C T SNP SEC16B NM_033127.2 human genbank 54_36p -1 validated intronic c.1463+756 e10+756 0 - - - no_errors tier3 952 24 2.46 86 49 36.3 0 0 0 103342 TCGA-AB-2978 AML17 1 178006822 178006822 C T SNP FAM163A NM_173509.2 human genbank 54_36p 1 provisional intronic c.1+27641 e0+27641 0.015 - - - no_errors tier3 605 24 3.82 128 61 32.28 0 0 NA 103342 TCGA-AB-2978 AML17 1 182831018 182831018 C G SNP C1orf21 NM_030806.3 human genbank 54_36p 1 validated intronic c.267-3140 e4-3140 0.001 - - - no_errors tier3 516 8 1.53 33 18 35.29 9 14 60.87 103342 TCGA-AB-2978 AML17 1 183661048 183661048 G A SNP - - - - - - - - - - - - - - - tier3 1089 25 2.24 85 41 32.54 0 0 NA 103342 TCGA-AB-2978 AML17 1 195166431 195166431 T C SNP CFHR5 NM_030787.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46987 NULL 0 - - - no_errors tier3 464 13 2.73 36 9 20 0 0 NA 103342 TCGA-AB-2978 AML17 1 199088535 199088535 A G SNP CAMSAP1L1 NM_203459.1 human genbank 54_36p 1 validated intronic c.3602+107 e12+107 0.003 - - - no_errors tier3 395 18 4.36 21 15 41.67 0 0 NA 103342 TCGA-AB-2978 AML17 1 206426190 206426190 C T SNP PLXNA2 NM_025179.3 human genbank 54_36p -1 reviewed intronic c.1371+24058 e2+24058 0.002 - - - no_errors tier3 681 23 3.27 22 11 33.33 0 0 NA 103342 TCGA-AB-2978 AML17 1 207803245 207803245 C T SNP CAMK1G NM_020439.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-31707 NULL 0.004 - - - no_errors tier3 1602 56 3.37 55 40 42.11 0 0 NA 103342 TCGA-AB-2978 AML17 1 214230449 214230449 C T SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.6805+2536 e34+2536 0.004 - - - no_errors tier3 768 11 1.41 76 29 27.62 0 0 NA 103342 TCGA-AB-2978 AML17 1 214907111 214907111 C T SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.472+9930 e2+9930 0 - - - no_errors tier3 550 9 1.61 160 62 27.93 0 0 NA 103342 TCGA-AB-2978 AML17 1 216000908 216000908 C T SNP SPATA17 NM_138796.2 human genbank 54_36p 1 provisional intronic c.520-13391 e7-13391 0.048 - - - no_errors tier3 1257 16 1.25 105 52 33.12 0 0 NA 103342 TCGA-AB-2978 AML17 1 223724858 223724858 G A SNP LBR NM_002296.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-46458 NULL 0.015 - - - no_errors tier3 295 7 2.32 19 21 52.5 0 0 NA 103342 TCGA-AB-2978 AML17 1 240999674 240999674 G A SNP ENSG00000215800 ENST00000400938 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2872 NULL 0.002 - - - no_coding_region:pseudogene tier3 687 21 2.96 34 23 40.35 0 0 NA 103342 TCGA-AB-2978 AML17 1 243829614 243829614 C T SNP KIF26B NM_018012.3 human genbank 54_36p 1 provisional intronic c.1351-2888 e6-2888 0.012 - - - no_errors tier3 559 24 4.12 77 51 39.84 0 0 NA 103342 TCGA-AB-2978 AML17 2 1937038 1937038 G A SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.153-10925 e4-10925 0 - - - no_errors tier3 173 4 2.26 43 14 24.56 0 0 NA 103342 TCGA-AB-2978 AML17 2 4554718 4554718 T A SNP ENSG00000216435 ENST00000402611 human ensembl 54_36p -1 known 5_prime_flanking_region c.-14197 NULL 0.007 - - - no_coding_region:pseudogene tier3 529 12 2.21 32 22 40.74 0 0 NA 103342 TCGA-AB-2978 AML17 2 4735473 4735473 G T SNP - - - - - - - - - - - - - - - tier3 736 10 1.34 63 16 20.25 0 0 NA 103342 TCGA-AB-2978 AML17 2 7991060 7991060 C T SNP - - - - - - - - - - - - - - - tier3 954 25 2.55 70 45 39.13 0 0 NA 103342 TCGA-AB-2978 AML17 2 13173532 13173532 A T SNP ENSG00000210742 ENST00000388007 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-31089 NULL 0.003 - - - pseudogene tier3 938 27 2.8 105 107 50.23 0 0 NA 103342 TCGA-AB-2978 AML17 2 41566159 41566159 T A SNP - - - - - - - - - - - - - - - tier3 529 16 2.94 34 17 33.33 0 0 NA 103342 TCGA-AB-2978 AML17 2 43018909 43018909 G A SNP - - - - - - - - - - - - - - - tier3 603 29 4.59 28 22 44 0 0 NA 103342 TCGA-AB-2978 AML17 2 52781366 52781366 T A SNP - - - - - - - - - - - - - - - tier3 713 11 1.52 42 19 31.15 0 0 NA 103342 TCGA-AB-2978 AML17 2 57969346 57969346 C T SNP - - - - - - - - - - - - - - - tier3 662 8 1.19 97 22 18.49 0 2 100 103342 TCGA-AB-2978 AML17 2 58055985 58055985 A G SNP - - - - - - - - - - - - - - - tier3 751 27 3.47 54 47 46.08 0 0 NA 103342 TCGA-AB-2978 AML17 2 80289277 80289277 T C SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1060-184570 e7-184570 0 - - - no_errors tier3 1171 35 2.9 147 86 36.91 0 0 NA 103342 TCGA-AB-2978 AML17 2 104430955 104430955 A G SNP - - - - - - - - - - - - - - - tier3 909 30 3.19 59 39 39.8 0 0 NA 103342 TCGA-AB-2978 AML17 2 118429864 118429864 A G SNP CCDC93 NM_019044.3 human genbank 54_36p -1 validated intronic c.1005+2547 e12+2547 0.002 - - - no_errors tier3 470 20 4.08 21 14 40 0 0 0 103342 TCGA-AB-2978 AML17 2 119590590 119590590 C T SNP C1QL2 NM_182528.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*40258 NULL 0.002 - - - no_errors tier3 493 20 3.9 104 83 44.39 0 0 NA 103342 TCGA-AB-2978 AML17 2 133969470 133969470 C T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.69+22029 e1+22029 0.003 - - - no_errors tier3 641 27 4.04 159 66 29.33 0 0 NA 103342 TCGA-AB-2978 AML17 2 134034242 134034242 G A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.1-1084 e1-1084 0 - - - no_errors tier3 459 11 2.34 78 53 40.46 0 0 NA 103342 TCGA-AB-2978 AML17 2 139102700 139102700 C T SNP NXPH2 NM_007226.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*42262 NULL 0.001 - - - no_errors tier3 543 18 3.21 73 26 26.26 0 0 NA 103342 TCGA-AB-2978 AML17 2 162456880 162456880 C T SNP SLC4A10 NM_022058.3 human genbank 54_36p 1 validated intronic c.1105-2555 e10-2555 0.004 - - - no_errors tier3 558 20 3.46 23 14 37.84 0 0 NA 103342 TCGA-AB-2978 AML17 2 181307542 181307542 G T SNP - - - - - - - - - - - - - - - tier3 716 25 3.37 118 57 32.57 0 0 NA 103342 TCGA-AB-2978 AML17 2 193292180 193292180 A - DEL PCGEM1 NR_002769.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-30636 NULL 0.033 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 2 217744369 217744369 T C SNP - - - - - - - - - - - - - - - tier3 699 22 3.05 118 47 28.48 0 0 NA 103342 TCGA-AB-2978 AML17 2 222655641 222655641 G A SNP - - - - - - - - - - - - - - - tier3 840 24 2.77 62 24 27.91 0 0 NA 103342 TCGA-AB-2978 AML17 2 230594491 230594491 C T SNP ENSG00000221271 ENST00000408344 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27610 NULL 0 - - - no_errors tier3 1110 33 2.88 105 103 49.52 0 0 NA 103342 TCGA-AB-2978 AML17 2 235425282 235425282 A G SNP - - - - - - - - - - - - - - - tier3 1152 38 3.19 64 23 26.44 0 0 NA 103342 TCGA-AB-2978 AML17 3 1542076 1542076 T C SNP - - - - - - - - - - - - - - - tier3 458 18 3.78 39 30 43.48 0 0 NA 103342 TCGA-AB-2978 AML17 3 10645205 10645205 C T SNP ATP2B2 ENST00000397077 human ensembl 54_36p -1 known intronic c.1-8559 e1-8559 0.024 - - - no_errors tier3 1519 48 3.06 162 118 42.14 0 0 NA 103342 TCGA-AB-2978 AML17 3 18839814 18839814 C A SNP - - - - - - - - - - - - - - - tier3 707 21 2.88 16 15 48.39 0 0 NA 103342 TCGA-AB-2978 AML17 3 24294117 24294117 C G SNP THRB NM_000461.4 human genbank 54_36p -1 reviewed intronic c.1-48621 e1-48621 0.005 - - - no_errors tier3 566 7 1.22 22 8 26.67 0 0 NA 103342 TCGA-AB-2978 AML17 3 26365975 26365975 G A SNP - - - - - - - - - - - - - - - tier3 543 11 1.99 45 28 37.84 0 0 NA 103342 TCGA-AB-2978 AML17 3 26659803 26659803 G A SNP LRRC3B NM_052953.2 human genbank 54_36p 1 provisional intronic c.1+20071 e0+20071 0 - - - no_errors tier3 399 5 1.24 17 13 43.33 0 0 NA 103342 TCGA-AB-2978 AML17 3 38723001 38723001 C T SNP SCN10A NM_006514.2 human genbank 54_36p -1 validated intronic c.4386+773 e25+773 0.004 - - - no_errors tier3 653 3 0.46 60 12 16.67 0 0 NA 103342 TCGA-AB-2978 AML17 3 40669650 40669650 G A SNP LOC729505 XM_001130480.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*45911 NULL 0.002 - - - no_errors tier3 733 43 5.53 108 77 41.62 0 0 NA 103342 TCGA-AB-2978 AML17 3 56156162 56156162 C T SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.1305+1883 e4+1883 0.002 - - - no_errors tier3 489 13 2.59 49 40 44.94 0 0 NA 103342 TCGA-AB-2978 AML17 3 62611965 62611965 T C SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.970-170 e5-170 0.003 - - - no_errors tier3 586 20 3.3 100 39 28.06 0 0 NA 103342 TCGA-AB-2978 AML17 3 64041118 64041118 G T SNP ENSG00000189196 ENST00000339674 human ensembl 54_36p -1 known intronic c.387-395 e3-395 0.001 - - - no_errors tier3 1096 34 3.01 73 55 42.97 0 0 NA 103342 TCGA-AB-2978 AML17 3 65627353 65627353 G A SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.314-44550 e2-44550 0.003 - - - no_errors tier3 515 23 4.28 53 22 29.33 0 0 0 103342 TCGA-AB-2978 AML17 3 68864336 68864336 C T SNP FAM19A4 NM_001005527.1 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*647 NULL 0 - - - no_errors tier3 541 12 2.17 36 11 23.4 0 0 NA 103342 TCGA-AB-2978 AML17 3 74503631 74503631 A G SNP CNTN3 NM_020872.1 human genbank 54_36p -1 validated intronic c.455-391 e5-391 0.002 - - - no_errors tier3 805 28 3.36 118 60 33.71 0 0 NA 103342 TCGA-AB-2978 AML17 3 77598771 77598771 A C SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.389-10484 e3-10484 0.962 - - - no_errors tier3 1319 41 3.01 317 191 37.6 1 0 0 103342 TCGA-AB-2978 AML17 3 82474596 82474596 G A SNP - - - - - - - - - - - - - - - tier3 889 29 3.16 61 33 35.11 0 0 NA 103342 TCGA-AB-2978 AML17 3 83926842 83926842 C T SNP - - - - - - - - - - - - - - - tier3 595 4 0.67 44 5 10.2 0 0 NA 103342 TCGA-AB-2978 AML17 3 85284135 85284135 G A SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+192626 e1+192626 0 - - - no_errors tier3 758 20 2.57 29 24 45.28 0 0 NA 103342 TCGA-AB-2978 AML17 3 96436602 96436602 C T SNP - - - - - - - - - - - - - - - tier3 401 11 2.67 26 22 45.83 0 0 NA 103342 TCGA-AB-2978 AML17 3 100095335 100095335 A C SNP DCBLD2 NM_080927.3 human genbank 54_36p -1 validated intronic c.205+7321 e1+7321 0 - - - no_errors tier3 757 30 3.81 25 17 40.48 3 0 0 103342 TCGA-AB-2978 AML17 3 107128001 107128001 G C SNP - - - - - - - - - - - - - - - tier3 609 20 3.18 29 17 36.96 0 0 NA 103342 TCGA-AB-2978 AML17 3 117117709 117117709 C T SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.515-63555 e4-63555 0 - - - no_errors tier3 809 36 4.26 80 43 34.96 0 0 NA 103342 TCGA-AB-2978 AML17 3 119870788 119870788 C G SNP - - - - - - - - - - - - - - - tier3 926 32 3.34 38 35 47.95 0 0 NA 103342 TCGA-AB-2978 AML17 3 123484153 123484153 T C SNP CASR NM_000388.3 human genbank 54_36p 1 reviewed intronic c.1732+380 e5+380 0.002 - - - no_errors tier3 557 17 2.96 62 52 45.61 0 0 NA 103342 TCGA-AB-2978 AML17 3 144015008 144015008 A G SNP TRPC1 NM_003304.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*7241 NULL 0.001 - - - no_errors tier3 626 25 3.83 31 26 45.61 0 0 NA 103342 TCGA-AB-2978 AML17 3 152367673 152367673 A G SNP MED12L NM_053002.3 human genbank 54_36p 1 validated intronic c.1494+1214 e10+1214 0 - - - no_errors tier3 569 19 3.23 28 19 40.43 3 4 57.14 103342 TCGA-AB-2978 AML17 3 183102139 183102139 A T SNP ENSG00000213155 ENST00000392635 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-34503 NULL 0 - - - no_coding_region:pseudogene tier3 631 9 1.4 34 19 35.85 0 0 NA 103342 TCGA-AB-2978 AML17 3 193442112 193442112 A T SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed intronic c.415-70973 e4-70973 0.002 - - - no_errors tier3 443 26 5.54 21 10 32.26 0 0 NA 103342 TCGA-AB-2978 AML17 3 194761357 194761357 A T SNP OPA1 NM_130837.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32504 NULL 0.068 - - - no_errors tier3 598 18 2.91 87 52 37.41 0 0 NA 103342 TCGA-AB-2978 AML17 4 3682723 3682723 T C SNP - - - - - - - - - - - - - - - tier3 314 10 3.09 25 15 37.5 0 0 NA 103342 TCGA-AB-2978 AML17 4 5922932 5922932 C - DEL CRMP1 NM_001014809.1 human genbank 54_36p -1 reviewed intronic c.382-3548 e2-3548 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 4 6064533 6064533 G T SNP FLJ46481 NM_207405.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-23556 NULL 0 - - - no_errors tier2 212 8 3.62 17 17 50 0 0 NA 103342 TCGA-AB-2978 AML17 4 7674369 7674369 G C SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.199-16586 e4-16586 0.001 - - - no_errors tier3 562 19 3.27 20 12 37.5 0 0 NA 103342 TCGA-AB-2978 AML17 4 9915959 9915959 G A SNP - - - - - - - - - - - - - - - tier3 507 17 3.24 44 30 40.54 0 0 NA 103342 TCGA-AB-2978 AML17 4 19659910 19659910 C T SNP - - - - - - - - - - - - - - - tier3 1048 44 4.02 92 96 51.06 0 0 NA 103342 TCGA-AB-2978 AML17 4 19668594 19668594 T A SNP - - - - - - - - - - - - - - - tier3 1025 15 1.44 74 29 28.16 0 0 NA 103342 TCGA-AB-2978 AML17 4 22876782 22876782 A G SNP - - - - - - - - - - - - - - - tier3 915 26 2.76 103 82 44.32 0 0 NA 103342 TCGA-AB-2978 AML17 4 29452231 29452231 G A SNP - - - - - - - - - - - - - - - tier3 620 30 4.62 24 25 51.02 0 0 0 103342 TCGA-AB-2978 AML17 4 62079564 62079564 G A SNP LPHN3 NM_015236.4 human genbank 54_36p 1 reviewed intronic c.55+33903 e1+33903 0.002 - - - no_errors tier3 764 26 3.29 75 56 42.75 0 0 NA 103342 TCGA-AB-2978 AML17 4 72326882 72326882 A G SNP SLC4A4 NM_001098484.2 human genbank 54_36p 1 reviewed intronic c.73+5652 e1+5652 0.147 - - - no_errors tier3 551 9 1.61 34 20 37.04 0 0 NA 103342 TCGA-AB-2978 AML17 4 72527099 72527099 G C SNP SLC4A4 NM_001098484.2 human genbank 54_36p 1 reviewed intronic c.965+1745 e7+1745 0.002 - - - no_errors tier3 655 35 5.07 30 25 45.45 0 0 0 103342 TCGA-AB-2978 AML17 4 106402456 106402457 - T INS TET2 ENST00000265149 human ensembl 54_36p 1 known splice_site_ins c.450+2_450+1 e3+2 1.000:0.991 - - - no_start_codon tier1 NA NA NA NA NA NA NA 103342 TCGA-AB-2978 AML17 4 106415662 106415662 C T SNP TET2 ENST00000265149 human ensembl 54_36p 1 known nonsense c.952 p.R318* 0.992 NULL NULL - no_start_codon tier1 881 34 3.72 360 248 40.79 12 15 55.56 103342 TCGA-AB-2978 AML17 4 111511951 111511951 C T SNP - - - - - - - - - - - - - - - tier3 337 14 3.99 40 30 42.86 0 0 NA 103342 TCGA-AB-2978 AML17 4 114551671 114551671 C T SNP ENSG00000206820 ENST00000384093 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-9257 NULL 0.001 - - - no_errors tier3 663 18 2.64 148 121 44.98 0 0 NA 103342 TCGA-AB-2978 AML17 4 127710779 127710779 C T SNP - - - - - - - - - - - - - - - tier3 924 41 4.25 111 50 31.06 0 0 NA 103342 TCGA-AB-2978 AML17 4 134870340 134870340 T C SNP ENSG00000222681 ENST00000410749 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21400 NULL 0 - - - no_errors tier3 653 18 2.68 24 25 51.02 0 0 NA 103342 TCGA-AB-2978 AML17 4 138676360 138676360 G C SNP PCDH18 NM_019035.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3668 NULL 0 - - - no_errors tier3 364 5 1.36 50 19 27.54 0 0 NA 103342 TCGA-AB-2978 AML17 4 141141074 141141074 G A SNP MAML3 NM_018717.4 human genbank 54_36p -1 validated intronic c.469-109503 e2-109503 0.064 - - - no_errors tier3 879 34 3.72 82 65 44.22 1 0 0 103342 TCGA-AB-2978 AML17 4 161916726 161916726 G A SNP - - - - - - - - - - - - - - - tier3 507 14 2.69 41 13 24.07 0 0 NA 103342 TCGA-AB-2978 AML17 4 166147871 166147871 G A SNP TRIM60 NM_152620.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32804 NULL 0.004 - - - no_errors tier3 641 15 2.29 65 52 44.44 0 0 NA 103342 TCGA-AB-2978 AML17 4 169283209 169283209 C T SNP ANXA10 NM_007193.3 human genbank 54_36p 1 reviewed intronic c.19-2601 e2-2601 0.006 - - - no_errors tier3 1242 42 3.27 158 74 31.9 0 0 NA 103342 TCGA-AB-2978 AML17 4 171648308 171648308 G T SNP - - - - - - - - - - - - - - - tier3 1166 40 3.32 34 34 50 0 0 NA 103342 TCGA-AB-2978 AML17 4 177659372 177659372 G T SNP - - - - - - - - - - - - - - - tier3 1075 12 1.1 43 17 28.33 0 0 NA 103342 TCGA-AB-2978 AML17 4 183195617 183195618 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 5 470689 470689 G A SNP AHRR NM_020731.3 human genbank 54_36p 1 reviewed intronic c.453+4141 e5+4141 0 - - - no_errors tier3 397 23 5.48 41 45 52.33 0 0 NA 103342 TCGA-AB-2978 AML17 5 3022248 3022248 C A SNP - - - - - - - - - - - - - - - tier3 450 22 4.66 52 14 21.21 0 0 NA 103342 TCGA-AB-2978 AML17 5 4949485 4949485 C G SNP - - - - - - - - - - - - - - - tier3 869 35 3.87 82 81 49.69 0 0 NA 103342 TCGA-AB-2978 AML17 5 5407115 5407115 G A SNP ENSG00000209891 ENST00000387156 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-42403 NULL 0 - - - pseudogene tier3 1251 46 3.55 91 26 22.22 0 1 100 103342 TCGA-AB-2978 AML17 5 6958979 6958979 G A SNP - - - - - - - - - - - - - - - tier3 483 14 2.73 70 52 41.6 0 0 NA 103342 TCGA-AB-2978 AML17 5 9084612 9084612 G A SNP LOC646916 XM_943571.2 human genbank 54_36p -1 model 3_prime_untranslated_region c.*681 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 453 13 2.78 27 16 37.21 0 0 NA 103342 TCGA-AB-2978 AML17 5 44745933 44745933 G - DEL ENSG00000222995 ENST00000411063 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6116 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 5 51137102 51137102 C T SNP - - - - - - - - - - - - - - - tier3 728 38 4.96 114 93 44.93 0 0 NA 103342 TCGA-AB-2978 AML17 5 58211228 58211228 T A SNP RAB3C NM_138453.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*28293 NULL 0.01 - - - no_errors tier3 1144 46 3.86 138 110 44.35 0 0 NA 103342 TCGA-AB-2978 AML17 5 75238808 75238808 C A SNP - - - - - - - - - - - - - - - tier3 985 38 3.71 33 23 41.07 0 0 NA 103342 TCGA-AB-2978 AML17 5 80263116 80263116 T C SNP RASGRF2 NM_006909.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29198 NULL 0.002 - - - no_errors tier3 588 27 4.39 42 14 25 0 0 NA 103342 TCGA-AB-2978 AML17 5 81973323 81973324 - TT INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 5 84566058 84566058 C A SNP - - - - - - - - - - - - - - - tier3 552 19 3.33 29 17 36.17 0 0 NA 103342 TCGA-AB-2978 AML17 5 110537669 110537669 C T SNP WDR36 NM_139281.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*47189 NULL 0.111 - - - no_errors tier3 1508 62 3.94 128 88 40.74 0 0 NA 103342 TCGA-AB-2978 AML17 5 116541436 116541436 G A SNP - - - - - - - - - - - - - - - tier2 390 20 4.88 65 28 30.11 0 0 NA 103342 TCGA-AB-2978 AML17 5 147491522 147491522 T A SNP SPINK5 NM_006846.1 human genbank 54_36p 1 reviewed intronic c.3095+377 e31+377 0 - - - no_errors tier3 676 25 3.55 55 51 48.11 0 0 NA 103342 TCGA-AB-2978 AML17 5 155363662 155363662 G A SNP - - - - - - - - - - - - - - - tier3 406 11 2.64 21 15 41.67 0 0 NA 103342 TCGA-AB-2978 AML17 5 157894679 157894679 C T SNP - - - - - - - - - - - - - - - tier3 1145 32 2.72 65 53 44.92 0 0 NA 103342 TCGA-AB-2978 AML17 5 173716775 173716775 T G SNP - - - - - - - - - - - - - - - tier3 699 28 3.85 115 41 26.28 0 0 NA 103342 TCGA-AB-2978 AML17 5 178515144 178515144 C T SNP ADAMTS2 NM_014244.2 human genbank 54_36p -1 reviewed intronic c.1133-618 e7-618 0 - - - no_errors tier3 193 5 2.51 22 11 33.33 0 0 0 103342 TCGA-AB-2978 AML17 6 10522553 10522553 C A SNP TFAP2A NM_003220.2 human genbank 54_36p -1 validated intronic c.45+607 e1+607 0 - - - no_errors tier3 1036 26 2.45 93 32 25.6 0 0 NA 103342 TCGA-AB-2978 AML17 6 10718150 10718150 G C SNP GCNT2 NM_145649.2 human genbank 54_36p 1 reviewed intronic c.926-11420 e2-11420 0.001 - - - no_errors tier3 502 20 3.83 36 18 33.33 0 0 0 103342 TCGA-AB-2978 AML17 6 17985631 17985631 C T SNP KIF13A NM_022113.1 human genbank 54_36p -1 validated intronic c.160-3984 e4-3984 0.712 - - - no_errors tier3 597 14 2.29 60 17 22.08 3 0 0 103342 TCGA-AB-2978 AML17 6 40602729 40602729 A G SNP LRFN2 NM_020737.1 human genbank 54_36p -1 provisional intronic c.1+59929 e0+59929 0.021 - - - no_errors tier3 1245 42 3.26 106 55 34.16 0 0 NA 103342 TCGA-AB-2978 AML17 6 46030840 46030840 C T SNP CLIC5 NM_016929.1 human genbank 54_36p -1 validated splice_region c.173+10 e2+10 0 - - - no_errors tier3 1564 53 3.28 205 125 37.88 0 0 0 103342 TCGA-AB-2978 AML17 6 47280625 47280625 C T SNP TNFRSF21 NM_014452.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*27835 NULL 0.021 - - - no_errors tier3 1198 41 3.31 58 26 30.95 0 0 NA 103342 TCGA-AB-2978 AML17 6 56945399 56945399 A T SNP BEND6 NM_152731.2 human genbank 54_36p 1 validated intronic c.1-9069 e1-9069 0.268 - - - no_errors tier3 505 12 2.32 26 9 25.71 0 0 0 103342 TCGA-AB-2978 AML17 6 62587805 62587805 T G SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.810+74694 e6+74694 0 - - - no_errors tier3 695 26 3.61 60 42 41.18 0 0 NA 103342 TCGA-AB-2978 AML17 6 66429800 66429800 C T SNP EYS ENST00000393380 human ensembl 54_36p -1 known intronic c.1-23294 e1-23294 0.006 - - - no_errors tier3 676 21 3.01 36 31 46.27 0 0 NA 103342 TCGA-AB-2978 AML17 6 67360210 67360210 C T SNP - - - - - - - - - - - - - - - tier3 1098 32 2.83 80 36 31.03 0 0 NA 103342 TCGA-AB-2978 AML17 6 77306934 77306934 G A SNP LOC643281 XM_931461.1 human genbank 54_36p -1 model intronic c.280-17694 e4-17694 0 - - - no_errors tier3 746 17 2.23 31 10 24.39 0 0 NA 103342 TCGA-AB-2978 AML17 6 85320807 85320807 A G SNP - - - - - - - - - - - - - - - tier3 682 9 1.3 39 17 30.36 0 0 NA 103342 TCGA-AB-2978 AML17 6 85430272 85430272 C T SNP ENSG00000219604 ENST00000405071 human ensembl 54_36p -1 known 3_prime_flanking_region c.*25457 NULL 0.494 - - - no_coding_region:pseudogene tier3 970 35 3.48 37 22 37.29 0 0 NA 103342 TCGA-AB-2978 AML17 6 88561579 88561579 G A SNP ENSG00000207131 ENST00000384402 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*31031 NULL 0.001 - - - no_errors tier3 820 38 4.43 133 51 27.72 0 0 NA 103342 TCGA-AB-2978 AML17 6 88736665 88736665 G A SNP - - - - - - - - - - - - - - - tier3 823 21 2.49 123 70 36.27 0 0 NA 103342 TCGA-AB-2978 AML17 6 89524849 89524849 C A SNP RNGTT NM_003800.3 human genbank 54_36p -1 validated intronic c.1439+11363 e13+11363 0 - - - no_errors tier3 946 36 3.67 51 24 32 0 0 NA 103342 TCGA-AB-2978 AML17 6 91900972 91900972 G A SNP - - - - - - - - - - - - - - - tier3 1043 17 1.6 109 67 38.07 0 0 NA 103342 TCGA-AB-2978 AML17 6 92341751 92341751 C T SNP - - - - - - - - - - - - - - - tier3 498 10 1.96 76 40 34.48 0 0 NA 103342 TCGA-AB-2978 AML17 6 99286423 99286423 G A SNP LOC100129158 XR_038602.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*48457 NULL 0 - - - pseudogene tier3 462 18 3.75 53 25 32.05 0 0 NA 103342 TCGA-AB-2978 AML17 6 102636954 102636954 A T SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*13875 NULL 0.036 - - - no_errors tier3 634 35 5.23 29 18 38.3 0 0 NA 103342 TCGA-AB-2978 AML17 6 103810644 103810644 G C SNP - - - - - - - - - - - - - - - tier3 560 14 2.43 36 15 29.41 0 0 NA 103342 TCGA-AB-2978 AML17 6 122111264 122111264 C A SNP - - - - - - - - - - - - - - - tier3 909 22 2.36 39 19 32.76 0 0 NA 103342 TCGA-AB-2978 AML17 6 126672682 126672682 T A SNP C6orf173 NM_001012507.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30431 NULL 0.827 - - - no_errors tier3 508 16 3.04 41 23 35.94 0 0 NA 103342 TCGA-AB-2978 AML17 6 128826940 128826940 C T SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.100+56157 e1+56157 0.003 - - - no_errors tier3 501 5 0.99 53 42 44.21 0 0 NA 103342 TCGA-AB-2978 AML17 6 138479701 138479701 T C SNP KIAA1244 NM_020340.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45216 NULL 0 - - - no_errors tier3 663 26 3.77 65 27 29.35 0 0 NA 103342 TCGA-AB-2978 AML17 6 141499609 141499609 C T SNP - - - - - - - - - - - - - - - tier3 481 17 3.41 30 19 38.78 0 0 NA 103342 TCGA-AB-2978 AML17 6 145772070 145772070 T C SNP - - - - - - - - - - - - - - - tier3 468 7 1.47 81 31 27.68 0 0 NA 103342 TCGA-AB-2978 AML17 6 146636206 146636206 T G SNP GRM1 NM_000838.3 human genbank 54_36p 1 reviewed intronic c.951-31234 e3-31234 0 - - - no_errors tier3 464 22 4.53 36 25 40.98 0 0 NA 103342 TCGA-AB-2978 AML17 6 149585586 149585586 G C SNP - - - - - - - - - - - - - - - tier3 460 13 2.74 106 60 36.14 0 0 NA 103342 TCGA-AB-2978 AML17 6 161315709 161315709 C A SNP MAP3K4 NM_005922.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17245 NULL 0.004 - - - no_errors tier3 752 29 3.71 82 56 40.58 0 0 NA 103342 TCGA-AB-2978 AML17 6 164842395 164842395 A T SNP - - - - - - - - - - - - - - - tier3 461 17 3.56 52 26 33.33 0 0 NA 103342 TCGA-AB-2978 AML17 6 169084742 169084742 C T SNP - - - - - - - - - - - - - - - tier3 770 16 2.03 123 45 26.79 0 0 NA 103342 TCGA-AB-2978 AML17 7 2573215 2573215 C T SNP IQCE NM_152558.1 human genbank 54_36p 1 validated intronic c.37-61 e2-61 0 - - - no_errors tier3 723 16 2.17 27 10 27.03 0 0 0 103342 TCGA-AB-2978 AML17 7 3476084 3476084 A C SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.299-149154 e2-149154 0 - - - no_errors tier3 857 41 4.56 81 47 36.72 0 0 NA 103342 TCGA-AB-2978 AML17 7 6367227 6367227 C T SNP LOC100134557 XM_001716011.1 human genbank 54_36p -1 model intronic c.1241-5712 e9-5712 0.004 - - - no_start_codon:pseudogene:no_stop_codon tier3 422 15 3.43 32 8 20 0 0 NA 103342 TCGA-AB-2978 AML17 7 11060650 11060650 G A SNP PHF14 NM_001007157.1 human genbank 54_36p 1 validated intronic c.2481+2718 e14+2718 0.975 - - - no_errors tier3 461 19 3.96 45 25 35.71 2 0 0 103342 TCGA-AB-2978 AML17 7 19390718 19390718 C T SNP - - - - - - - - - - - - - - - tier3 818 32 3.76 78 55 41.35 0 0 NA 103342 TCGA-AB-2978 AML17 7 37679496 37679496 G A SNP - - - - - - - - - - - - - - - tier3 622 38 5.76 26 24 48 0 0 NA 103342 TCGA-AB-2978 AML17 7 49220826 49220826 C T SNP - - - - - - - - - - - - - - - tier3 1170 21 1.76 85 25 22.73 0 0 NA 103342 TCGA-AB-2978 AML17 7 66709285 66709285 C T SNP - - - - - - - - - - - - - - - tier3 418 10 2.34 30 8 21.05 0 0 NA 103342 TCGA-AB-2978 AML17 7 82344014 82344014 A C SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.13654+2575 e10+2575 0.046 - - - no_errors tier3 504 29 5.43 19 21 52.5 0 0 NA 103342 TCGA-AB-2978 AML17 7 86137082 86137082 T A SNP GRM3 NM_000840.2 human genbank 54_36p 1 reviewed intronic c.1+24958 e0+24958 0 - - - no_errors tier3 1312 13 0.98 64 13 16.88 0 0 NA 103342 TCGA-AB-2978 AML17 7 104033968 104033968 C T SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed intronic c.446-130390 e2-130390 0 - - - no_errors tier3 464 18 3.73 122 76 38.38 0 0 NA 103342 TCGA-AB-2978 AML17 7 105829105 105829105 A G SNP - - - - - - - - - - - - - - - tier3 529 22 3.99 33 18 35.29 0 0 NA 103342 TCGA-AB-2978 AML17 7 106243254 106243254 C G SNP PIK3CG NM_002649.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-51989 NULL 0.001 - - - no_errors tier3 464 10 2.11 30 17 36.17 0 0 NA 103342 TCGA-AB-2978 AML17 7 110792932 110792932 C G SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional intronic c.239+121598 e2+121598 0.008 - - - no_errors tier3 409 4 0.97 26 22 45.83 0 0 NA 103342 TCGA-AB-2978 AML17 7 114786358 114786358 A G SNP - - - - - - - - - - - - - - - tier3 408 9 2.15 54 30 35.71 0 0 NA 103342 TCGA-AB-2978 AML17 7 120389377 120389377 A G SNP ING3 NM_019071.2 human genbank 54_36p 1 reviewed intronic c.268-2655 e5-2655 0 - - - no_errors tier3 978 53 5.14 101 51 33.55 2 0 0 103342 TCGA-AB-2978 AML17 7 141406790 141406790 C - DEL MGAM NM_004668.2 human genbank 54_36p 1 reviewed intronic c.4122+148 e33+148 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 7 154526439 154526439 C T SNP uc003wlt.1 ENST00000395731 human ensembl 54_36p -1 known 5_prime_flanking_region c.-32493 NULL 0 - - - no_errors tier3 581 10 1.69 45 19 29.69 0 0 NA 103342 TCGA-AB-2978 AML17 7 155877096 155877096 T C SNP - - - - - - - - - - - - - - - tier3 444 20 4.31 47 38 44.71 0 0 NA 103342 TCGA-AB-2978 AML17 8 4101012 4101012 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.415+163871 e3+163871 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 244 9 3.56 22 17 43.59 0 0 NA 103342 TCGA-AB-2978 AML17 8 4313854 4313854 C G SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.303-48859 e3-48859 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 690 32 4.43 52 17 24.64 0 0 NA 103342 TCGA-AB-2978 AML17 8 4483441 4483441 C G SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.86-953 e2-953 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 650 23 3.42 73 29 28.43 0 0 NA 103342 TCGA-AB-2978 AML17 8 20501567 20501567 T C SNP ENSG00000210340 ENST00000387605 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48575 NULL 0.002 - - - pseudogene tier3 754 16 2.08 53 51 49.04 0 0 NA 103342 TCGA-AB-2978 AML17 8 34202754 34202754 G A SNP - - - - - - - - - - - - - - - tier3 814 26 3.09 74 20 21.28 0 0 NA 103342 TCGA-AB-2978 AML17 8 37121022 37121023 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 8 40886733 40886733 C T SNP ZMAT4 NM_024645.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-84381 NULL 0.006 - - - no_errors tier3 663 31 4.47 75 36 32.43 0 0 NA 103342 TCGA-AB-2978 AML17 8 42942444 42942444 C G SNP HOOK3 NM_032410.3 human genbank 54_36p 1 validated missense c.1052 p.T351S 1 HMMPfam_HOOK HMMPfam_HOOK - no_errors tier1 758 33 4.17 65 49 42.98 15 13 46.43 103342 TCGA-AB-2978 AML17 8 52484186 52484186 C T SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated missense c.2551 p.D851N 0.996 "HMMPfam_An_peroxidase,superfamily_Heme-dependent peroxidases" "HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_LRR_1,HMMPfam_An_peroxidase,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Heme-dependent peroxidases,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_L domain-like" - no_errors tier1 249 4 1.58 40 21 34.43 NA 103342 TCGA-AB-2978 AML17 8 56084127 56084127 C T SNP - - - - - - - - - - - - - - - tier3 488 27 5.23 31 20 39.22 0 0 NA 103342 TCGA-AB-2978 AML17 8 62410914 62410914 G A SNP RLBP1L1 NM_173519.2 human genbank 54_36p 1 validated intronic c.455+35519 e1+35519 0.001 - - - no_errors tier3 672 12 1.75 19 14 42.42 0 0 NA 103342 TCGA-AB-2978 AML17 8 68846640 68846640 C T SNP CPA6 NM_020361.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-25722 NULL 0 - - - no_errors tier3 1058 34 3.11 81 51 38.64 0 0 NA 103342 TCGA-AB-2978 AML17 8 74589938 74589938 T G SNP STAU2 ENST00000343268 human ensembl 54_36p -1 known intronic c.1530+36863 e10+36863 0.005 - - - no_errors tier3 386 5 1.27 24 8 25 7 0 0 103342 TCGA-AB-2978 AML17 8 81231445 81231445 A C SNP TPD52 NM_001025253.1 human genbank 54_36p -1 validated intronic c.19+14770 e1+14770 0.005 - - - no_errors tier3 707 24 3.28 39 26 40 3 0 0 103342 TCGA-AB-2978 AML17 8 87258203 87258203 G T SNP LOC100128962 XM_001722280.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-3687 NULL 0.098 - - - no_errors tier3 706 21 2.88 192 115 37.46 0 0 NA 103342 TCGA-AB-2978 AML17 8 96484222 96484222 T C SNP - - - - - - - - - - - - - - - tier3 505 14 2.69 19 21 52.5 0 0 NA 103342 TCGA-AB-2978 AML17 8 118297769 118297769 T C SNP SLC30A8 NM_173851.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*43668 NULL 0 - - - no_errors tier3 686 27 3.79 25 19 43.18 0 0 NA 103342 TCGA-AB-2978 AML17 8 124134713 124134713 G A SNP WDR67 NM_145647.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-19478 NULL 0 - - - no_errors tier3 1163 41 3.41 96 33 25.58 0 0 NA 103342 TCGA-AB-2978 AML17 8 127027458 127027458 A G SNP LOC100130231 XM_001725273.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*72 NULL 0.001 - - - no_errors tier3 702 23 3.17 54 23 29.87 25 0 0 103342 TCGA-AB-2978 AML17 8 131243568 131243568 A G SNP ASAP1 NM_018482.2 human genbank 54_36p -1 validated intronic c.910-2176 e11-2176 0.001 - - - no_errors tier3 749 17 2.22 40 15 27.27 2 0 0 103342 TCGA-AB-2978 AML17 8 140319652 140319652 C T SNP - - - - - - - - - - - - - - - tier3 458 3 0.65 40 11 21.57 0 0 NA 103342 TCGA-AB-2978 AML17 8 142795581 142795581 C T SNP - - - - - - - - - - - - - - - tier3 1091 27 2.41 41 17 29.31 0 0 NA 103342 TCGA-AB-2978 AML17 9 7612190 7612190 C T SNP LOC392285 XR_017134.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*23596 NULL 0 - - - pseudogene tier3 547 12 2.15 34 15 30.61 0 0 NA 103342 TCGA-AB-2978 AML17 9 9430836 9430836 T C SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-43354 e1-43354 0.005 - - - no_errors tier3 499 7 1.38 49 23 31.94 0 0 NA 103342 TCGA-AB-2978 AML17 9 13371273 13371273 G A SNP FLJ41200 XM_379623.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*27071 NULL 0.001 - - - no_errors tier3 891 34 3.68 105 57 35.19 0 0 NA 103342 TCGA-AB-2978 AML17 9 14551900 14551900 A G SNP uc003zlg.1 ENST00000399884 human ensembl 54_36p -1 known intronic c.106-6166 e3-6166 0.974 - - - no_start_codon tier3 743 22 2.87 43 27 38.57 0 0 NA 103342 TCGA-AB-2978 AML17 9 18546114 18546114 G A SNP ADAMTSL1 NM_001040272.4 human genbank 54_36p 1 validated intronic c.238-17914 e4-17914 0 - - - no_errors tier3 639 17 2.59 28 29 50.88 0 0 NA 103342 TCGA-AB-2978 AML17 9 21576777 21576777 C T SNP ENSG00000171889 ENST00000304425 human ensembl 54_36p -1 known 5_prime_flanking_region c.-130840 NULL 0.001 - - - no_errors tier3 604 26 4.13 84 49 36.84 0 0 NA 103342 TCGA-AB-2978 AML17 9 21726868 21726868 T C SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 3_prime_flanking_region c.*39920 NULL 0.072 - - - no_coding_region:pseudogene tier3 728 10 1.36 26 24 48 0 0 NA 103342 TCGA-AB-2978 AML17 9 23675524 23675524 C T SNP ELAVL2 NM_004432.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*7031 NULL 0.001 - - - no_errors tier3 894 11 1.22 121 30 19.87 0 0 NA 103342 TCGA-AB-2978 AML17 9 24904417 24904417 T C SNP ENSG00000216088 ENST00000401269 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41621 NULL 0 - - - no_errors tier3 798 21 2.56 35 19 35.19 0 0 NA 103342 TCGA-AB-2978 AML17 9 27386035 27386035 G A SNP MOBKL2B NM_024761.3 human genbank 54_36p -1 reviewed intronic c.419-36801 e2-36801 0.001 - - - no_errors tier3 836 43 4.89 51 48 48.48 0 0 NA 103342 TCGA-AB-2978 AML17 9 74870910 74870910 C T SNP ENSG00000220631 ENST00000407176 human ensembl 54_36p 1 known 3_prime_flanking_region c.*9646 NULL 0 - - - no_coding_region:pseudogene tier3 593 15 2.47 29 15 34.09 0 0 NA 103342 TCGA-AB-2978 AML17 9 86142482 86142482 T C SNP SLC28A3 NM_022127.1 human genbank 54_36p -1 provisional intronic c.60+2827 e1+2827 0.005 - - - no_errors tier3 730 29 3.82 29 29 50 0 0 NA 103342 TCGA-AB-2978 AML17 9 87066002 87066002 G A SNP - - - - - - - - - - - - - - - tier3 766 35 4.37 108 67 38.29 0 0 NA 103342 TCGA-AB-2978 AML17 9 100421513 100421513 T C SNP GABBR2 NM_005458.6 human genbank 54_36p -1 validated intronic c.322-41338 e2-41338 0.019 - - - no_errors tier3 674 21 3.02 50 10 16.67 0 0 NA 103342 TCGA-AB-2978 AML17 9 108536588 108536588 A T SNP LOC644620 XM_001718226.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*36310 NULL 0.005 - - - no_errors tier3 554 24 4.15 51 36 41.38 0 0 NA 103342 TCGA-AB-2978 AML17 9 111213500 111213500 C T SNP PTPN3 NM_002829.1 human genbank 54_36p -1 reviewed intronic c.1314-984 e14-984 0 - - - no_errors tier3 553 28 4.82 47 31 39.74 0 0 NA 103342 TCGA-AB-2978 AML17 9 113704077 113704077 A G SNP UGCG NM_003358.1 human genbank 54_36p 1 reviewed intronic c.98+4663 e1+4663 0.067 - - - no_errors tier3 980 34 3.35 29 27 48.21 0 0 0 103342 TCGA-AB-2978 AML17 9 127166206 127166206 G A SNP GAPVD1 NM_015635.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*1360 NULL 0.042 - - - no_errors tier3 585 23 3.78 26 13 33.33 3 12 80 103342 TCGA-AB-2978 AML17 9 135349469 135349469 C T SNP ADAMTSL2 NM_014694.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-42187 NULL 0.021 - - - no_errors tier3 709 18 2.48 35 18 33.96 0 0 NA 103342 TCGA-AB-2978 AML17 10 18750750 18750750 C A SNP CACNB2 NM_201596.3 human genbank 54_36p 1 validated intronic c.333+19772 e3+19772 0 - - - no_errors tier3 499 16 3.1 16 14 46.67 0 0 NA 103342 TCGA-AB-2978 AML17 10 24557697 24557697 T G SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated intronic c.354+8853 e2+8853 0 - - - no_errors tier3 414 3 0.72 28 26 48.15 0 0 NA 103342 TCGA-AB-2978 AML17 10 28919390 28919390 A T SNP WAC NM_016628.3 human genbank 54_36p 1 reviewed intronic c.498-265 e6-265 0.003 - - - no_errors tier3 571 23 3.87 41 21 33.87 0 0 0 103342 TCGA-AB-2978 AML17 10 30419032 30419032 G A SNP LOC729663 XM_001130940.1 human genbank 54_36p 1 model intronic c.557-18690 e4-18690 0 - - - no_errors tier3 982 41 4 103 50 32.68 0 0 NA 103342 TCGA-AB-2978 AML17 10 38671209 38671209 G A SNP LOC100131082 XM_001723927.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-7724 NULL 0.001 - - - no_errors tier3 606 23 3.65 180 68 27.42 0 0 NA 103342 TCGA-AB-2978 AML17 10 48182415 48182415 G A SNP ENSG00000221361 ENST00000408434 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*35177 NULL 0.002 - - - no_errors tier3 417 3 0.71 52 12 18.75 0 0 NA 103342 TCGA-AB-2978 AML17 10 50215699 50215699 C T SNP C10orf71 NM_199459.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*10632 NULL 0 - - - no_errors tier3 439 5 1.13 25 6 19.35 0 0 NA 103342 TCGA-AB-2978 AML17 10 60907948 60907948 T C SNP - - - - - - - - - - - - - - - tier3 882 34 3.71 204 160 43.96 0 0 NA 103342 TCGA-AB-2978 AML17 10 65466428 65466428 T C SNP - - - - - - - - - - - - - - - tier3 683 19 2.7 80 46 36.51 0 0 NA 103342 TCGA-AB-2978 AML17 10 86251945 86251945 T - DEL KIAA1128 NM_018999.2 human genbank 54_36p 1 validated intronic c.2410+2250 e9+2250 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 10 93919856 93919856 T C SNP CPEB3 NM_014912.3 human genbank 54_36p -1 validated intronic c.1222+10844 e3+10844 0.002 - - - no_errors tier3 543 21 3.72 37 23 38.33 4 3 42.86 103342 TCGA-AB-2978 AML17 10 95589309 95589309 C T SNP LGI1 NM_005097.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*41759 NULL 0.003 - - - no_errors tier3 769 26 3.27 20 20 50 0 0 NA 103342 TCGA-AB-2978 AML17 10 101525778 101525778 A G SNP ABCC2 NM_000392.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6814 NULL 0.165 - - - no_errors tier3 1013 16 1.55 68 14 17.07 0 4 100 103342 TCGA-AB-2978 AML17 10 107397912 107397912 A G SNP ENSG00000213260 ENST00000393174 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38158 NULL 0 - - - no_coding_region:pseudogene tier3 748 30 3.85 79 45 36.29 0 0 NA 103342 TCGA-AB-2978 AML17 10 108608389 108608389 G A SNP SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed intronic c.627-28968 e3-28968 0.002 - - - no_errors tier3 586 15 2.48 34 44 56.41 0 0 NA 103342 TCGA-AB-2978 AML17 10 109025864 109025864 T C SNP - - - - - - - - - - - - - - - tier3 606 23 3.66 29 20 40.82 0 0 NA 103342 TCGA-AB-2978 AML17 10 133248608 133248608 G A SNP - - - - - - - - - - - - - - - tier3 500 11 2.15 31 20 39.22 0 0 NA 103342 TCGA-AB-2978 AML17 11 4977503 4977503 G A SNP OR51L1 NM_001004755.1 human genbank 54_36p 1 provisional missense c.715 p.A239T 0.995 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 902 35 3.74 210 82 28.08 NA 103342 TCGA-AB-2978 AML17 11 12185634 12185634 G A SNP MICAL2 NM_014632.2 human genbank 54_36p 1 provisional intronic c.473-512 e3-512 0.004 - - - no_errors tier3 612 24 3.77 74 53 41.73 0 0 0 103342 TCGA-AB-2978 AML17 11 21895710 21895710 A G SNP - - - - - - - - - - - - - - - tier3 571 23 3.87 49 19 27.94 0 0 NA 103342 TCGA-AB-2978 AML17 11 24639625 24639625 C T SNP LUZP2 NM_001009909.2 human genbank 54_36p 1 validated intronic c.63-67666 e2-67666 0.018 - - - no_errors tier3 1015 46 4.34 402 166 29.23 0 0 NA 103342 TCGA-AB-2978 AML17 11 26280137 26280137 C T SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30262 NULL 0 - - - no_errors tier3 1100 36 3.17 156 124 44.29 0 0 NA 103342 TCGA-AB-2978 AML17 11 35030151 35030151 C T SNP - - - - - - - - - - - - - - - tier3 806 27 3.24 24 13 35.14 0 0 NA 103342 TCGA-AB-2978 AML17 11 37023647 37023647 T C SNP - - - - - - - - - - - - - - - tier3 792 15 1.86 97 34 25.95 0 0 NA 103342 TCGA-AB-2978 AML17 11 42098260 42098260 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 11 42334634 42334634 T A SNP - - - - - - - - - - - - - - - tier3 1105 40 3.49 39 37 48.68 0 0 NA 103342 TCGA-AB-2978 AML17 11 56137457 56137457 G A SNP OR5M1 NM_001004740.1 human genbank 54_36p -1 provisional missense c.98 p.A33V 0.053 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 811 9 1.1 114 37 24.5 NA 103342 TCGA-AB-2978 AML17 11 56454413 56454413 C A SNP OR5AK3P ENST00000326876 human ensembl 54_36p 1 known 5_prime_flanking_region c.-40688 NULL 0.02 - - - no_errors tier3 1092 32 2.85 149 86 36.6 0 0 NA 103342 TCGA-AB-2978 AML17 11 65856009 65856009 C T SNP CD248 NM_020404.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14935 NULL 0 - - - no_errors tier3 177 4 2.21 19 12 38.71 0 0 NA 103342 TCGA-AB-2978 AML17 11 79998921 79998921 A T SNP - - - - - - - - - - - - - - - tier3 649 17 2.55 69 37 34.91 0 0 NA 103342 TCGA-AB-2978 AML17 11 81798677 81798677 G A SNP - - - - - - - - - - - - - - - tier3 552 15 2.65 49 21 30 0 0 NA 103342 TCGA-AB-2978 AML17 11 98691674 98691674 G A SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-9613 e1-9613 0.002 - - - no_errors tier3 492 23 4.47 21 10 32.26 0 0 NA 103342 TCGA-AB-2978 AML17 11 112791193 112791193 C T SNP DRD2 NM_000795.3 human genbank 54_36p -1 reviewed intronic c.723+160 e4+160 0.016 - - - no_errors tier3 1246 37 2.88 42 20 32.26 0 0 NA 103342 TCGA-AB-2978 AML17 11 117870121 117870121 G C SNP MLL NM_005933.2 human genbank 54_36p 1 validated intronic c.5170-92 e17-92 0.003 - - - no_errors tier3 701 28 3.84 34 20 37.04 0 0 0 103342 TCGA-AB-2978 AML17 11 118673340 118673340 G A SNP CBL NM_005188.2 human genbank 54_36p 1 reviewed silent c.2190 p.T730 0.666 NULL "HMMPfam_UBA,HMMSmart_RING,HMMPfam_Cbl_N,superfamily_Adaptor_Cbl_N,HMMPfam_Cbl_N2,HMMPfam_Cbl_N3,HMMSmart_UBA,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,superfamily_SSF47473,superfamily_SSF55550,superfamily_SSF57850" - no_errors tier1 528 11 2.04 90 35 28 17 9 34.62 103342 TCGA-AB-2978 AML17 11 118908684 118908684 C T SNP LOC100130353 XM_001719137.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*34105 NULL 0 - - - no_errors tier3 693 28 3.88 54 36 40 0 0 NA 103342 TCGA-AB-2978 AML17 11 131199858 131199858 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.83-86810 e2-86810 0.018 - - - no_errors tier3 906 40 4.22 114 87 43.28 0 0 NA 103342 TCGA-AB-2978 AML17 11 131237121 131237121 G A SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.83-49547 e2-49547 0 - - - no_errors tier3 941 15 1.57 125 57 31.32 0 0 NA 103342 TCGA-AB-2978 AML17 11 132144161 132144161 G T SNP OPCML NM_002545.1 human genbank 54_36p -1 reviewed intronic c.168-111737 e2-111737 0.366 - - - no_errors tier3 674 22 3.16 88 50 36.23 0 0 NA 103342 TCGA-AB-2978 AML17 12 15718148 15718148 G C SNP EPS8 NM_004447.5 human genbank 54_36p -1 reviewed intronic c.137-3024 e3-3024 0.001 - - - no_errors tier3 362 10 2.68 22 13 37.14 0 0 0 103342 TCGA-AB-2978 AML17 12 17143286 17143286 G A SNP ENSG00000212358 ENST00000391056 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27580 NULL 0.008 - - - no_errors tier3 818 27 3.2 102 32 23.88 0 0 NA 103342 TCGA-AB-2978 AML17 12 17741834 17741834 G A SNP ENSG00000206662 ENST00000383935 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13301 NULL 0.003 - - - no_errors tier3 359 7 1.91 34 13 27.66 0 0 NA 103342 TCGA-AB-2978 AML17 12 21922546 21922546 G A SNP ABCC9 NM_005691.2 human genbank 54_36p -1 reviewed intronic c.2020-2619 e15-2619 0.062 - - - no_errors tier3 686 9 1.29 96 62 39.24 0 0 NA 103342 TCGA-AB-2978 AML17 12 27767413 27767413 G C SNP MRPS35 NM_021821.2 human genbank 54_36p 1 reviewed intronic c.383-834 e5-834 0 - - - no_errors tier3 645 24 3.59 118 62 34.44 0 0 0 103342 TCGA-AB-2978 AML17 12 29472820 29472820 A G SNP OVCH1 NM_183378.2 human genbank 54_36p -1 validated intronic c.3330-974 e29-974 0 - - - no_errors tier3 579 23 3.82 40 47 54.02 0 0 NA 103342 TCGA-AB-2978 AML17 12 30120498 30120498 C T SNP - - - - - - - - - - - - - - - tier3 913 33 3.49 135 76 36.02 0 0 NA 103342 TCGA-AB-2978 AML17 12 42665634 42665634 T A SNP TMEM117 NM_032256.1 human genbank 54_36p 1 provisional intronic c.410+41222 e2+41222 0.005 - - - no_errors tier3 324 8 2.41 16 16 50 0 0 NA 103342 TCGA-AB-2978 AML17 12 54605162 54605162 G T SNP WIBG NM_032345.1 human genbank 54_36p -1 validated intronic c.37+2614 e1+2614 0.053 - - - no_errors tier3 649 22 3.27 70 31 30.69 0 0 0 103342 TCGA-AB-2978 AML17 12 55696299 55696299 C A SNP TAC3 NM_013251.2 human genbank 54_36p -1 validated intronic c.1+139 e0+139 0.001 - - - no_errors tier3 756 22 2.82 23 14 37.84 0 0 NA 103342 TCGA-AB-2978 AML17 12 57485891 57485891 G A SNP - - - - - - - - - - - - - - - tier3 505 8 1.56 42 27 39.13 0 0 NA 103342 TCGA-AB-2978 AML17 12 64310871 64310871 C T SNP LOC729298 XR_015503.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*14681 NULL 0 - - - pseudogene tier3 1876 18 0.95 138 86 38.39 0 0 NA 103342 TCGA-AB-2978 AML17 12 70245741 70245741 C T SNP LGR5 NM_003667.2 human genbank 54_36p 1 provisional intronic c.858-710 e9-710 0.001 - - - no_errors tier3 562 18 3.1 33 18 35.29 0 0 NA 103342 TCGA-AB-2978 AML17 12 79118851 79118851 G A SNP C12orf64 ENST00000298820 human ensembl 54_36p 1 known 5_prime_flanking_region c.-155926 NULL 0.004 - - - no_errors tier3 665 9 1.34 97 28 22.4 0 0 NA 103342 TCGA-AB-2978 AML17 12 84723327 84723327 G T SNP RASSF9 NM_005447.3 human genbank 54_36p -1 reviewed missense c.592 p.H198N 1 NULL HMMSmart_SM00314 - no_errors tier1 535 4 0.74 110 32 22.54 NA 103342 TCGA-AB-2978 AML17 12 87695736 87695736 G A SNP - - - - - - - - - - - - - - - tier3 1123 33 2.85 184 91 33.09 0 0 NA 103342 TCGA-AB-2978 AML17 12 100011886 100011886 G A SNP ANO4 NM_178826.3 human genbank 54_36p 1 validated intronic c.1597-279 e16-279 0.012 - - - no_errors tier3 516 11 2.08 111 58 34.32 0 0 NA 103342 TCGA-AB-2978 AML17 12 101723306 101723306 T C SNP PAH NM_000277.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*33777 NULL 0 - - - no_errors tier3 486 6 1.22 39 5 11.36 0 0 NA 103342 TCGA-AB-2978 AML17 12 105020053 105020053 C T SNP NUAK1 NM_014840.2 human genbank 54_36p -1 validated intronic c.361+4260 e2+4260 0.006 - - - no_errors tier3 810 16 1.94 23 11 32.35 0 0 NA 103342 TCGA-AB-2978 AML17 12 108461589 108461589 G A SNP MVK NM_000431.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35422 NULL 0.003 - - - no_errors tier3 254 10 3.79 63 33 34.38 0 0 NA 103342 TCGA-AB-2978 AML17 12 114306103 114306103 G A SNP - - - - - - - - - - - - - - - tier3 1143 38 3.22 134 85 38.81 0 0 NA 103342 TCGA-AB-2978 AML17 12 128903799 128903799 G A SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.79+49960 e1+49960 0 - - - no_errors tier3 302 8 2.58 20 13 39.39 0 0 NA 103342 TCGA-AB-2978 AML17 13 18433830 18433830 G T SNP ENSG00000218236 ENST00000405207 human ensembl 54_36p -1 known intronic c.NULL NULL 0.023 - - - no_coding_region:pseudogene tier3 123 1 0.81 37 14 27.45 0 0 NA 103342 TCGA-AB-2978 AML17 13 32917293 32917293 G T SNP - - - - - - - - - - - - - - - tier3 483 18 3.59 18 17 48.57 0 0 NA 103342 TCGA-AB-2978 AML17 13 55084959 55084959 C T SNP - - - - - - - - - - - - - - - tier3 854 17 1.95 50 17 25.37 0 0 NA 103342 TCGA-AB-2978 AML17 13 56558415 56558415 A G SNP - - - - - - - - - - - - - - - tier3 476 21 4.23 41 37 47.44 0 0 0 103342 TCGA-AB-2978 AML17 13 60501628 60501628 T C SNP - - - - - - - - - - - - - - - tier3 1788 76 4.08 105 70 39.77 0 0 NA 103342 TCGA-AB-2978 AML17 13 69583212 69583212 C T SNP ATXN8OS NR_002717.2 human genbank 54_36p 1 reviewed intronic c.NULL NULL 0 - - - no_errors tier3 658 6 0.9 43 8 15.69 0 0 NA 103342 TCGA-AB-2978 AML17 13 76082573 76082573 C T SNP - - - - - - - - - - - - - - - tier3 771 8 1.03 141 44 23.78 0 0 NA 103342 TCGA-AB-2978 AML17 13 77414667 77414667 C T SNP EDNRB NM_000115.2 human genbank 54_36p -1 reviewed intronic c.1-23907 e1-23907 0.175 - - - no_errors tier3 1353 18 1.31 272 126 31.66 0 0 NA 103342 TCGA-AB-2978 AML17 13 81045362 81045362 A T SNP - - - - - - - - - - - - - - - tier3 481 26 5.13 33 26 44.07 0 0 NA 103342 TCGA-AB-2978 AML17 13 95757177 95757177 A T SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+215353 e1+215353 0.001 - - - no_errors tier3 886 19 2.09 232 109 31.96 0 0 NA 103342 TCGA-AB-2978 AML17 13 95946531 95946531 G A SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.708-336214 e2-336214 0.001 - - - no_errors tier3 687 25 3.51 51 50 49.5 0 0 NA 103342 TCGA-AB-2978 AML17 13 96190990 96190990 G A SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.708-91755 e2-91755 0 - - - no_errors tier3 784 39 4.74 69 14 16.87 0 0 NA 103342 TCGA-AB-2978 AML17 13 97710291 97710291 C G SNP FARP1 NM_005766.2 human genbank 54_36p 1 reviewed intronic c.171+46623 e1+46623 0.053 - - - no_errors tier3 611 9 1.45 29 8 21.62 0 0 NA 103342 TCGA-AB-2978 AML17 13 98255269 98255269 G A SNP DOCK9 NM_015296.1 human genbank 54_36p -1 validated missense c.5755 p.R1919C 1 HMMPfam_Ded_cyto "HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Ded_cyto,superfamily_PH domain-like" - no_errors tier1 531 25 4.49 85 51 37.5 1 0 103342 TCGA-AB-2978 AML17 13 101313020 101313020 T C SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.423+6056 e3+6056 0 - - - no_errors tier3 503 5 0.98 50 14 21.88 0 0 NA 103342 TCGA-AB-2978 AML17 13 102898291 102898291 C T SNP ENSG00000219505 ENST00000407214 human ensembl 54_36p -1 known 5_prime_flanking_region c.-2972 NULL 0 - - - no_coding_region:pseudogene tier3 728 29 3.83 28 9 24.32 0 0 NA 103342 TCGA-AB-2978 AML17 13 111881824 111881824 C A SNP - - - - - - - - - - - - - - - tier3 350 5 1.41 97 42 30.22 0 0 NA 103342 TCGA-AB-2978 AML17 13 113555543 113555543 T G SNP GAS6 NM_000820.2 human genbank 54_36p 1 reviewed intronic c.256-7377 e3-7377 0.006 - - - no_errors tier3 324 12 3.57 32 27 45.76 0 0 0 103342 TCGA-AB-2978 AML17 14 19298443 19298443 G A SNP OR4H12P ENST00000316004 human ensembl 54_36p 1 known missense c.535 p.A179T 0.012 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 743 17 2.23 129 37 22.29 NA 103342 TCGA-AB-2978 AML17 14 23139363 23139363 C G SNP AP1G2 NM_003917.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33000 NULL 0.008 - - - no_errors tier3 752 10 1.31 40 15 26.79 0 0 NA 103342 TCGA-AB-2978 AML17 14 25182712 25182712 T A SNP - - - - - - - - - - - - - - - tier3 556 7 1.24 40 11 21.57 0 0 NA 103342 TCGA-AB-2978 AML17 14 28743670 28743670 T - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 14 29029673 29029673 G T SNP ENSG00000212518 ENST00000391216 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13801 NULL 0 - - - no_errors tier3 544 25 4.39 63 47 42.73 0 0 NA 103342 TCGA-AB-2978 AML17 14 29059536 29059536 C T SNP ENSG00000212518 ENST00000391216 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*43664 NULL 0 - - - no_errors tier3 817 43 5 38 16 29.63 0 0 NA 103342 TCGA-AB-2978 AML17 14 40994734 40994734 T G SNP - - - - - - - - - - - - - - - tier3 488 9 1.81 25 9 26.47 0 0 NA 103342 TCGA-AB-2978 AML17 14 41114723 41114723 G A SNP LRFN5 NM_152447.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-310856 NULL 0.004 - - - no_errors tier3 589 7 1.17 56 24 30 0 0 NA 103342 TCGA-AB-2978 AML17 14 62443767 62443767 G T SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed intronic c.1369+42837 e7+42837 0.512 - - - no_errors tier3 902 17 1.85 105 44 29.53 0 0 NA 103342 TCGA-AB-2978 AML17 14 69492807 69492807 T G SNP SMOC1 NM_001034852.1 human genbank 54_36p 1 validated intronic c.378+2805 e3+2805 0.997 - - - no_errors tier3 1067 35 3.16 241 124 33.97 0 0 0 103342 TCGA-AB-2978 AML17 14 81806925 81806925 C T SNP - - - - - - - - - - - - - - - tier3 483 14 2.82 55 22 28.57 0 0 NA 103342 TCGA-AB-2978 AML17 14 86616776 86616776 G C SNP - - - - - - - - - - - - - - - tier3 570 18 3.05 45 33 42.31 0 0 NA 103342 TCGA-AB-2978 AML17 15 40087702 40087702 C T SNP PLA2G4E NM_001080490.1 human genbank 54_36p -1 provisional intronic c.170-347 e2-347 0 - - - no_errors tier3 1030 44 4.09 18 16 47.06 0 0 NA 103342 TCGA-AB-2978 AML17 15 46668368 46668368 C T SNP FBN1 NM_000138.3 human genbank 54_36p -1 reviewed intronic c.538+7404 e5+7404 0.001 - - - no_errors tier3 871 24 2.68 157 71 31.14 2 0 0 103342 TCGA-AB-2978 AML17 15 58031269 58031269 C - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 15 67178372 67178372 C T SNP NOX5 NM_024505.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*42282 NULL 0.398 - - - no_errors tier3 956 38 3.82 147 61 29.19 0 0 NA 103342 TCGA-AB-2978 AML17 15 86423802 86423802 G A SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed intronic c.1397-46522 e12-46522 0 - - - no_errors tier3 802 22 2.67 127 100 44.05 0 0 NA 103342 TCGA-AB-2978 AML17 15 86444702 86444702 G A SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed intronic c.1396+25804 e11+25804 0 - - - no_errors tier3 1162 21 1.78 269 118 30.49 0 0 NA 103342 TCGA-AB-2978 AML17 16 3123148 3123148 A G SNP ZNF213 NM_004220.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-4135 NULL 0 - - - no_errors tier3 328 4 1.2 20 13 39.39 7 1 12.5 103342 TCGA-AB-2978 AML17 16 6197403 6197403 C T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-109594 e1-109594 0.472 - - - no_errors tier3 501 5 0.99 93 35 27.34 0 0 NA 103342 TCGA-AB-2978 AML17 16 8064944 8064944 G A SNP - - - - - - - - - - - - - - - tier3 1036 29 2.72 60 23 27.71 0 0 NA 103342 TCGA-AB-2978 AML17 16 9381914 9381914 C T SNP - - - - - - - - - - - - - - - tier3 866 31 3.45 50 21 29.58 0 0 NA 103342 TCGA-AB-2978 AML17 16 13852875 13852875 C T SNP - - - - - - - - - - - - - - - tier3 439 3 0.68 33 11 25 0 0 NA 103342 TCGA-AB-2978 AML17 16 20688461 20688461 A T SNP ACSM3 NM_005622.3 human genbank 54_36p 1 validated intronic c.1-346 e1-346 0.025 - - - no_errors tier3 858 26 2.94 65 32 32.99 0 0 0 103342 TCGA-AB-2978 AML17 16 45195378 45195378 C T SNP SHCBP1 NM_024745.4 human genbank 54_36p -1 validated splice_region c.1092+10 e7+10 0.015 - - - no_errors tier3 487 13 2.6 18 16 47.06 0 0 0 103342 TCGA-AB-2978 AML17 16 45240262 45240262 A G SNP ORC6L NM_014321.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40857 NULL 0.043 - - - no_errors tier3 548 18 3.17 48 34 41.46 0 0 NA 103342 TCGA-AB-2978 AML17 16 46179685 46179685 C T SNP PHKB NM_000293.2 human genbank 54_36p 1 validated intronic c.870+510 e9+510 0 - - - no_errors tier3 545 9 1.62 23 9 28.12 0 0 0 103342 TCGA-AB-2978 AML17 16 47282732 47282732 T C SNP ENSG00000210206 ENST00000387471 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32837 NULL 0.001 - - - pseudogene tier3 809 11 1.34 56 66 54.1 0 0 NA 103342 TCGA-AB-2978 AML17 16 50565984 50565984 T C SNP - - - - - - - - - - - - - - - tier3 697 7 0.99 28 9 24.32 0 0 NA 103342 TCGA-AB-2978 AML17 16 81389884 81389884 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.46-59584 e2-59584 0 - - - no_errors tier3 512 12 2.29 28 19 40.43 0 0 NA 103342 TCGA-AB-2978 AML17 17 10721138 10721138 G A SNP PIRT NM_001101387.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-51451 NULL 0.001 - - - no_errors tier3 404 15 3.57 17 16 48.48 0 0 NA 103342 TCGA-AB-2978 AML17 17 11582982 11582982 G A SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed missense c.5875 p.E1959K 1 "HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00382,HMMPfam_Dynein_heavy,PatternScan_CPSASE_2,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 814 19 2.28 190 167 46.78 NA 103342 TCGA-AB-2978 AML17 17 21737781 21737782 - A INS LOC100128559 XM_001723707.1 human genbank 54_36p 1 model 3_prime_untranslated_region c.*123 NULL 0.748:0.718 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 103342 TCGA-AB-2978 AML17 17 23132416 23132416 C G SNP NOS2 NM_000625.4 human genbank 54_36p -1 reviewed intronic c.723-86 e7-86 0 - - - no_errors tier3 1076 48 4.27 70 49 41.18 0 0 NA 103342 TCGA-AB-2978 AML17 17 42703362 42703362 C T SNP ITGB3 NM_000212.2 human genbank 54_36p 1 reviewed intronic c.80-3422 e2-3422 0 - - - no_errors tier3 636 22 3.34 29 23 44.23 0 0 0 103342 TCGA-AB-2978 AML17 17 43054846 43054846 A G SNP NPEPPS NM_006310.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*561 NULL 1 - - - no_errors tier3 802 17 2.08 52 25 32.47 35 40 53.33 103342 TCGA-AB-2978 AML17 17 48459939 48459939 G A SNP LOC339209 XM_294854.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*40259 NULL 0.006 - - - no_errors tier3 914 32 3.38 86 28 24.56 0 0 NA 103342 TCGA-AB-2978 AML17 17 48927268 48927268 G A SNP ENSG00000221534 ENST00000408607 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-42605 NULL 0 - - - no_errors tier3 914 32 3.38 94 37 28.24 0 0 NA 103342 TCGA-AB-2978 AML17 17 68080833 68080833 C T SNP - - - - - - - - - - - - - - - tier3 1309 9 0.68 86 51 37.23 0 0 NA 103342 TCGA-AB-2978 AML17 18 8424101 8424101 C T SNP ENSG00000222891 ENST00000410959 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-37728 NULL 0.004 - - - no_errors tier3 682 16 2.29 28 9 24.32 0 0 NA 103342 TCGA-AB-2978 AML17 18 27110994 27110994 G A SNP DSG1 NM_001942.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-41268 NULL 0 - - - no_errors tier3 967 29 2.91 199 100 33.44 0 0 NA 103342 TCGA-AB-2978 AML17 18 38894825 38894825 G A SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional intronic c.104-26995 e2-26995 0 - - - no_errors tier3 875 25 2.78 61 29 32.22 0 0 NA 103342 TCGA-AB-2978 AML17 18 47959882 47959882 A C SNP - - - - - - - - - - - - - - - tier3 756 10 1.31 192 97 33.56 0 0 NA 103342 TCGA-AB-2978 AML17 18 48709388 48709388 C T SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.985+3650 e5+3650 0.002 - - - no_errors tier3 515 25 4.63 48 25 34.25 0 0 NA 103342 TCGA-AB-2978 AML17 18 50692294 50692294 C T SNP RAB27B NM_004163.3 human genbank 54_36p 1 provisional intronic c.1-3502 e1-3502 0.138 - - - no_errors tier3 1148 46 3.85 83 46 35.66 0 2 100 103342 TCGA-AB-2978 AML17 18 67672197 67672197 G A SNP - - - - - - - - - - - - - - - tier3 591 10 1.66 61 14 18.67 0 0 NA 103342 TCGA-AB-2978 AML17 19 40195782 40195782 G A SNP GRAMD1A NM_020895.1 human genbank 54_36p 1 validated intronic c.607-218 e8-218 0.172 - - - no_errors tier3 379 16 4.05 20 24 54.55 5 3 37.5 103342 TCGA-AB-2978 AML17 19 40926605 40926605 G T SNP U2AF1L4 NM_144987.1 human genbank 54_36p -1 validated nonsense c.348 p.C116* 0.996 NULL "HMMPfam_zf-CCCH,HMMSmart_RRM_1,superfamily_SSF54928" - no_errors tier1 309 10 3.13 49 30 37.97 3 5 62.5 103342 TCGA-AB-2978 AML17 19 48233651 48233651 A G SNP CEACAMP8 ENST00000406672 human ensembl 54_36p -1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 321 15 4.46 43 23 34.85 0 0 NA 103342 TCGA-AB-2978 AML17 19 49876379 49876379 C A SNP CEACAM19 NM_020219.1 human genbank 54_36p 1 validated silent c.747 p.L249 0.676 NULL superfamily_Immunoglobulin - no_errors tier1 729 24 3.18 59 39 39.8 2 3 60 103342 TCGA-AB-2978 AML17 19 56772253 56772253 C T SNP ZNF175 NM_007147.2 human genbank 54_36p 1 validated intronic c.72+3787 e1+3787 0 - - - no_errors tier3 920 33 3.46 74 61 44.85 0 1 100 103342 TCGA-AB-2978 AML17 20 12193256 12193256 T G SNP - - - - - - - - - - - - - - - tier3 759 31 3.92 128 62 32.63 0 0 NA 103342 TCGA-AB-2978 AML17 20 14684398 14684398 A G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.418+70793 e5+70793 0.009 - - - no_errors tier3 451 16 3.43 18 15 45.45 0 0 NA 103342 TCGA-AB-2978 AML17 20 15239212 15239212 T A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.540+80505 e6+80505 0 - - - no_errors tier3 739 25 3.27 82 83 50.3 0 0 NA 103342 TCGA-AB-2978 AML17 20 15610695 15610695 C G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.646-180695 e9-180695 0.003 - - - no_errors tier3 731 23 3.05 31 28 47.46 0 0 NA 103342 TCGA-AB-2978 AML17 20 23650471 23650471 A T SNP CST4 NM_001899.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-32865 NULL 0.003 - - - no_errors tier3 1026 29 2.75 225 161 41.71 0 0 NA 103342 TCGA-AB-2978 AML17 20 34955241 34955241 C T SNP C20orf118 NM_080628.1 human genbank 54_36p 1 predicted 3_prime_untranslated_region c.*4038 NULL 0 - - - no_errors tier3 1148 29 2.46 73 28 27.72 10 4 28.57 103342 TCGA-AB-2978 AML17 20 43810172 43810172 T C SNP WFDC10B NM_172131.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43128 NULL 0.298 - - - no_errors tier3 483 16 3.21 63 19 23.17 2 0 0 103342 TCGA-AB-2978 AML17 20 59394477 59394477 C T SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.169+131089 e2+131089 0 - - - no_errors tier3 763 27 3.42 293 155 34.6 0 6 100 103342 TCGA-AB-2978 AML17 21 14948956 14948956 A G SNP ENSG00000215552 ENST00000400562 human ensembl 54_36p -1 known intronic c.24+3984 e1+3984 0.005 - - - no_errors tier3 727 27 3.58 69 59 46.09 0 0 NA 103342 TCGA-AB-2978 AML17 21 17171911 17171911 C T SNP - - - - - - - - - - - - - - - tier3 291 13 4.26 21 24 53.33 0 0 NA 103342 TCGA-AB-2978 AML17 21 17754741 17754741 C T SNP ENSG00000220521 ENST00000407779 human ensembl 54_36p -1 known 3_prime_flanking_region c.*40127 NULL 0.002 - - - no_coding_region:pseudogene tier3 1008 45 4.27 29 17 36.96 0 0 NA 103342 TCGA-AB-2978 AML17 21 25260560 25260560 T G SNP - - - - - - - - - - - - - - - tier3 675 19 2.74 51 21 29.17 0 0 NA 103342 TCGA-AB-2978 AML17 21 35153653 35153653 G A SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed nonsense c.601 p.R201* 1 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 519 8 1.52 25 22 46.81 216 53 19.63 103342 TCGA-AB-2978 AML17 21 36240900 36240900 T G SNP - - - - - - - - - - - - - - - tier3 823 21 2.49 87 69 44.23 0 0 NA 103342 TCGA-AB-2978 AML17 21 40140122 40140122 G A SNP PCP4 NM_006198.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21176 NULL 0.008 - - - no_errors tier3 1115 23 2.02 117 39 25 0 0 NA 103342 TCGA-AB-2978 AML17 21 42541559 42541559 C G SNP ABCG1 NM_004915.3 human genbank 54_36p 1 reviewed intronic c.286+22466 e2+22466 0 - - - no_errors tier3 534 16 2.91 39 36 48 1 0 0 103342 TCGA-AB-2978 AML17 22 31724414 31724414 C T SNP SYN3 NM_003490.1 human genbank 54_36p -1 reviewed intronic c.311+7923 e1+7923 0 - - - no_errors tier3 403 21 4.95 28 26 48.15 0 0 NA 103342 TCGA-AB-2978 AML17 22 36786434 36786434 A C SNP PICK1 NM_001039583.1 human genbank 54_36p 1 reviewed intronic c.153+1136 e2+1136 0.385 - - - no_errors tier3 1003 56 5.29 54 23 29.87 2 0 0 103342 TCGA-AB-2978 AML17 22 36990440 36990440 C G SNP TMEM184B NM_012264.3 human genbank 54_36p -1 validated intronic c.1+8396 e0+8396 0 - - - no_errors tier3 745 24 3.12 45 56 55.45 3 0 0 103342 TCGA-AB-2978 AML17 22 41487232 41487232 G C SNP A4GALT NM_017436.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-67331 NULL 0.033 - - - no_errors tier3 332 8 2.35 20 20 50 0 2 100 545259 TCGA-AB-2979 AML33 X 3972184 3972184 G A SNP ENSG00000210180 ENST00000387445 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*15445 NULL 0.007 - - - pseudogene tier2 1093 37 3.27 1015 804 44.18 0 0 NA 545259 TCGA-AB-2979 AML33 X 8230710 8230710 G A SNP - - - - - - - - - - - - - - - tier3 1238 32 2.52 1250 975 43.8 2 0 0 545259 TCGA-AB-2979 AML33 X 22893124 22893124 T G SNP DDX53 NM_182699.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-34972 NULL 0.999 - - - no_errors tier2 1882 49 2.54 1818 1291 41.51 0 0 NA 545259 TCGA-AB-2979 AML33 X 26422235 26422235 G A SNP ENSG00000218955 ENST00000402392 human ensembl 54_36p 1 known 5_prime_flanking_region c.-2739 NULL 0 - - - no_coding_region:pseudogene tier3 1438 31 2.11 1209 882 42.18 0 0 NA 545259 TCGA-AB-2979 AML33 X 28178504 28178504 T G SNP - - - - - - - - - - - - - - - tier3 1068 16 1.47 1022 764 42.78 0 0 NA 545259 TCGA-AB-2979 AML33 X 36690523 36690523 C T SNP ENSG00000220231 ENST00000406375 human ensembl 54_36p 1 known 3_prime_flanking_region c.*42304 NULL 0.003 - - - no_coding_region:pseudogene tier3 805 14 1.71 1028 884 46.21 0 0 NA 545259 TCGA-AB-2979 AML33 X 37105004 37105004 G T SNP PRRG1 ENST00000378628 human ensembl 54_36p 1 known intronic c.1+11435 e0+11435 0.309 - - - no_errors tier3 1277 26 1.99 1303 1131 46.43 0 0 NA 545259 TCGA-AB-2979 AML33 X 40264207 40264207 G A SNP ENSG00000206677 ENST00000383950 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*27071 NULL 0.003 - - - no_errors tier3 314 6 1.88 264 224 45.81 0 0 NA 545259 TCGA-AB-2979 AML33 X 41718474 41718474 G C SNP - - - - - - - - - - - - - - - tier3 964 29 2.92 904 612 40.37 0 0 NA 545259 TCGA-AB-2979 AML33 X 42469685 42469685 G A SNP - - - - - - - - - - - - - - - tier2 1508 38 2.46 1465 1166 44.3 0 0 NA 545259 TCGA-AB-2979 AML33 X 102147620 102147620 G A SNP ENSG00000219659 ENST00000406951 human ensembl 54_36p 1 known 5_prime_flanking_region c.-1425 NULL 0 - - - no_coding_region:pseudogene tier3 1526 41 2.61 1737 1277 42.37 0 0 NA 545259 TCGA-AB-2979 AML33 X 104117916 104117916 C T SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.83-208897 e2-208897 0 - - - no_errors tier2 797 35 4.21 845 587 40.99 0 0 NA 545259 TCGA-AB-2979 AML33 X 105946476 105946476 G T SNP TBC1D8B NM_017752.2 human genbank 54_36p 1 validated intronic c.131-2073 e2-2073 0 - - - no_errors tier3 880 18 2 813 650 44.4 0 0 NA 545259 TCGA-AB-2979 AML33 X 109136888 109136888 C T SNP TMEM164 NM_032227.2 human genbank 54_36p 1 provisional intronic c.390+2840 e1+2840 0.008 - - - no_errors tier3 1344 43 3.1 1086 774 41.57 2 0 0 545259 TCGA-AB-2979 AML33 X 110794523 110794523 A - DEL ALG13 ENST00000394780 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16580 NULL 0.019 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 X 124955812 124955812 G A SNP - - - - - - - - - - - - - - - tier3 1004 27 2.62 974 673 40.79 0 0 NA 545259 TCGA-AB-2979 AML33 X 125677731 125677731 C T SNP ENSG00000219741 ENST00000404361 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13037 NULL 0.031 - - - no_coding_region:pseudogene tier3 1231 27 2.15 1548 1311 45.86 0 0 0 545259 TCGA-AB-2979 AML33 X 129657044 129657044 A C SNP ENOX2 NM_182314.2 human genbank 54_36p -1 reviewed intronic c.185-6371 e3-6371 0.025 - - - no_errors tier3 998 19 1.87 1172 885 43 0 0 0 545259 TCGA-AB-2979 AML33 X 130098472 130098472 C T SNP ENSG00000222814 ENST00000410882 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2427 NULL 0.969 - - - no_errors tier2 55 3 5.17 20 20 50 0 0 NA 545259 TCGA-AB-2979 AML33 X 132836393 132836393 G A SNP GPC3 NM_004484.2 human genbank 54_36p -1 reviewed intronic c.337+78350 e2+78350 0.691 - - - no_errors tier3 1021 27 2.57 976 782 44.48 0 0 NA 545259 TCGA-AB-2979 AML33 X 143862804 143862804 C T SNP - - - - - - - - - - - - - - - tier3 917 20 2.13 1079 813 42.97 0 0 NA 545259 TCGA-AB-2979 AML33 X 144439408 144439408 C T SNP - - - - - - - - - - - - - - - tier3 784 21 2.61 911 758 45.33 0 0 NA 545259 TCGA-AB-2979 AML33 X 144749651 144749651 G A SNP SLITRK2 NM_032539.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*35478 NULL 0 - - - no_errors tier3 1250 26 2.04 1171 755 39.2 0 0 NA 545259 TCGA-AB-2979 AML33 1 11759565 11759565 G A SNP C1orf167 XM_209234.1 human genbank 54_36p 1 model intronic c.242+283 e2+283 0.002 - - - no_errors tier3 573 19 3.21 425 268 38.67 0 0 NA 545259 TCGA-AB-2979 AML33 1 11866308 11866308 G T SNP KIAA2013 ENST00000376576 human ensembl 54_36p -1 known intronic c.2193+38657 e2+38657 0.001 - - - no_start_codon tier2 336 8 2.32 256 212 45.3 0 0 NA 545259 TCGA-AB-2979 AML33 1 53102280 53102280 C T SNP ZYG11A XM_001133615.1 human genbank 54_36p 1 model nonsense c.1189 p.R397* 0.996 NULL "superfamily_ARM repeat,superfamily_RNI-like" - no_errors tier1 578 6 1.03 534 104 16.3 NA 545259 TCGA-AB-2979 AML33 1 58106297 58106297 G C SNP DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.1+15962 e0+15962 0.699 - - - no_errors tier3 859 13 1.49 1185 1008 45.96 0 0 NA 545259 TCGA-AB-2979 AML33 1 66038259 66038259 C T SNP PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.1+7358 e0+7358 0 - - - no_errors tier3 374 11 2.86 313 254 44.64 0 0 NA 545259 TCGA-AB-2979 AML33 1 89424735 89424735 C T SNP GBP4 NM_052941.4 human genbank 54_36p -1 validated missense c.1576 p.E526K 0.53 "HMMPfam_GBP_C,superfamily_GBP" "HMMPfam_GBP_C,HMMPfam_GBP,superfamily_GBP,superfamily_SSF52540" - no_errors tier1 1470 24 1.6 1485 717 32.53 8 8 50 545259 TCGA-AB-2979 AML33 1 99294130 99294130 G A SNP LOC100129620 XM_001726877.1 human genbank 54_36p 1 model intronic c.9+51341 e1+51341 0 - - - no_errors tier3 289 5 1.7 170 114 40.14 0 0 NA 545259 TCGA-AB-2979 AML33 1 106344265 106344265 A - DEL LOC727933 XM_001128972.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-47547 NULL 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 1 111018259 111018259 C T SNP KCNA3 NM_002232.3 human genbank 54_36p -1 reviewed silent c.696 p.P232 0.967 superfamily_SSF81324 "HMMSmart_BTB,HMMPfam_K_tetra,HMMPfam_Ion_trans,superfamily_BTB/POZ_fold,superfamily_SSF81324" - no_errors tier1 214 8 3.57 275 272 49.45 15 9 37.5 545259 TCGA-AB-2979 AML33 1 150937320 150937320 A G SNP LCE2A NM_178428.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-682 NULL 0.001 - - - no_errors tier2 506 12 2.31 491 412 45.63 0 0 NA 545259 TCGA-AB-2979 AML33 1 153195085 153195085 T C SNP PBXIP1 NM_020524.2 human genbank 54_36p -1 provisional intronic c.1+84 e0+84 0.001 - - - no_errors tier2 221 5 2.21 89 93 51.1 5 10 66.67 545259 TCGA-AB-2979 AML33 1 161312343 161312343 C G SNP RGS4 NM_001102445.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*1369 NULL 0 - - - no_errors tier3 711 15 2.06 539 398 42.48 0 0 NA 545259 TCGA-AB-2979 AML33 1 169890872 169890872 T G SNP MYOC NM_000261.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2498 NULL 0.001 - - - no_errors tier3 583 11 1.85 476 337 41.4 0 0 NA 545259 TCGA-AB-2979 AML33 1 178459251 178459251 A - DEL LHX4 NM_033343.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-7037 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 1 186387689 186387689 G C SNP ENSG00000222240 ENST00000410308 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*3904 NULL 0 - - - no_errors tier2 1003 22 2.14 918 765 45.45 0 0 NA 545259 TCGA-AB-2979 AML33 1 189423996 189423996 T C SNP ENSG00000217637 ENST00000405368 human ensembl 54_36p -1 known 5_prime_flanking_region c.-41282 NULL 0.004 - - - no_coding_region:pseudogene tier3 679 16 2.3 619 560 47.5 0 0 NA 545259 TCGA-AB-2979 AML33 1 193610731 193610731 A T SNP - - - - - - - - - - - - - - - tier3 739 20 2.64 731 551 42.95 0 0 NA 545259 TCGA-AB-2979 AML33 1 208188589 208188589 C T SNP SYT14 NM_153262.2 human genbank 54_36p 1 validated intronic c.14-4088 e2-4088 0.002 - - - no_errors tier3 817 32 3.77 446 324 42.08 0 0 NA 545259 TCGA-AB-2979 AML33 1 230383299 230383299 G C SNP ENSG00000223209 ENST00000411277 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41936 NULL 0 - - - no_errors tier3 796 23 2.81 844 661 43.92 0 0 NA 545259 TCGA-AB-2979 AML33 1 241351860 241351860 C - DEL LOC284701 XM_934038.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-24727 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 2 2632621 2632621 G A SNP - - - - - - - - - - - - - - - tier3 703 14 1.95 473 428 47.4 0 0 NA 545259 TCGA-AB-2979 AML33 2 8302156 8302156 G A SNP - - - - - - - - - - - - - - - tier3 662 16 2.36 811 633 43.84 0 0 NA 545259 TCGA-AB-2979 AML33 2 14941757 14941757 C T SNP - - - - - - - - - - - - - - - tier3 1143 24 2.06 1230 964 43.88 0 0 NA 545259 TCGA-AB-2979 AML33 2 23423900 23423900 A G SNP KLHL29 XM_001717454.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-35303 NULL 0.003 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 845 15 1.74 521 417 44.46 0 0 NA 545259 TCGA-AB-2979 AML33 2 31652060 31652060 C G SNP SRD5A2 ENST00000233139 human ensembl 54_36p -1 known intronic c.278+7134 e2+7134 0.001 - - - no_errors tier2 976 12 1.21 830 688 45.26 0 0 NA 545259 TCGA-AB-2979 AML33 2 35528726 35528726 G T SNP ENSG00000207255 ENST00000384525 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21449 NULL 0 - - - no_errors tier3 771 13 1.66 687 494 41.76 0 0 NA 545259 TCGA-AB-2979 AML33 2 46895000 46895000 C A SNP LOC388948 XM_373985.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-2468 NULL 0.002 - - - no_errors tier2 597 12 1.97 790 593 42.85 0 0 NA 545259 TCGA-AB-2979 AML33 2 50960432 50960432 A T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.832+42079 e4+42079 0 - - - no_errors tier3 668 13 1.91 692 557 44.6 0 0 NA 545259 TCGA-AB-2979 AML33 2 52445675 52445675 T A SNP - - - - - - - - - - - - - - - tier3 1208 33 2.66 1314 1180 47.31 0 0 NA 545259 TCGA-AB-2979 AML33 2 59270520 59270520 G T SNP ENSG00000222030 ENST00000409590 human ensembl 54_36p 1 known 5_prime_flanking_region c.-65309 NULL 0.55 - - - no_errors tier2 859 20 2.28 667 485 42.06 0 0 NA 545259 TCGA-AB-2979 AML33 2 77291118 77291118 C T SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+307834 e2+307834 0 - - - no_errors tier3 768 16 2.04 694 570 45.09 0 0 NA 545259 TCGA-AB-2979 AML33 2 79957454 79957454 A G SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.852+2478 e5+2478 0 - - - no_errors tier3 882 32 3.5 915 728 44.28 0 0 NA 545259 TCGA-AB-2979 AML33 2 80556386 80556386 C A SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1293+56149 e8+56149 0.001 - - - no_errors tier3 1296 36 2.7 1184 943 44.33 0 0 NA 545259 TCGA-AB-2979 AML33 2 81331458 81331458 A G SNP - - - - - - - - - - - - - - - tier2 1098 29 2.57 1152 875 43.15 0 0 NA 545259 TCGA-AB-2979 AML33 2 103842692 103842692 C T SNP - - - - - - - - - - - - - - - tier3 736 15 1.99 1078 732 40.42 0 0 NA 545259 TCGA-AB-2979 AML33 2 108496531 108496531 G C SNP ENSG00000214184 ENST00000397737 human ensembl 54_36p -1 known intronic c.1-1631 e1-1631 0.286 - - - no_errors tier3 184 7 3.66 158 129 44.95 1 2 66.67 545259 TCGA-AB-2979 AML33 2 123299629 123299629 C A SNP - - - - - - - - - - - - - - - tier3 840 5 0.59 1390 237 14.56 0 0 NA 545259 TCGA-AB-2979 AML33 2 125394077 125394077 C T SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*5742 NULL 0 - - - no_errors tier3 825 16 1.9 941 762 44.74 0 0 NA 545259 TCGA-AB-2979 AML33 2 126452831 126452831 G A SNP - - - - - - - - - - - - - - - tier3 745 19 2.49 861 752 46.62 0 0 NA 545259 TCGA-AB-2979 AML33 2 134115510 134115510 G A SNP ENSG00000200708 ENST00000363838 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*45063 NULL 0.001 - - - no_errors tier3 1064 29 2.65 1366 986 41.89 0 0 NA 545259 TCGA-AB-2979 AML33 2 142124872 142124872 G A SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.205+159446 e2+159446 0 - - - no_errors tier3 933 31 3.21 702 522 42.47 0 0 NA 545259 TCGA-AB-2979 AML33 2 146331485 146331485 C A SNP - - - - - - - - - - - - - - - tier3 875 23 2.56 861 701 44.88 0 0 NA 545259 TCGA-AB-2979 AML33 2 147462420 147462420 G C SNP - - - - - - - - - - - - - - - tier3 989 20 1.98 1012 750 42.54 0 0 NA 545259 TCGA-AB-2979 AML33 2 176136875 176136875 T C SNP - - - - - - - - - - - - - - - tier2 1005 28 2.71 1022 836 44.99 0 0 NA 545259 TCGA-AB-2979 AML33 2 180191770 180191770 A G SNP ZNF385B NM_152520.1 human genbank 54_36p -1 validated intronic c.254-73829 e2-73829 0.006 - - - no_errors tier3 1007 27 2.61 1274 985 43.6 0 0 NA 545259 TCGA-AB-2979 AML33 2 184773736 184773736 C G SNP - - - - - - - - - - - - - - - tier3 359 8 2.18 260 232 47.06 0 0 NA 545259 TCGA-AB-2979 AML33 2 204676418 204676418 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 2 219361508 219361508 A C SNP CYP27A1 NM_000784.3 human genbank 54_36p 1 reviewed intronic c.255+6104 e1+6104 0.01 - - - no_errors tier3 847 15 1.74 665 545 45.04 0 0 0 545259 TCGA-AB-2979 AML33 2 220122163 220122163 G A SNP TMEM198 NM_001005209.1 human genbank 54_36p 1 provisional missense c.788 p.R263Q 0.998 NULL NULL - no_errors tier1 265 13 4.68 235 181 43.51 NA 545259 TCGA-AB-2979 AML33 2 229611041 229611041 C A SNP PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.271-11973 e3-11973 0.001 - - - no_errors tier3 728 17 2.28 1176 831 41.41 0 0 NA 545259 TCGA-AB-2979 AML33 2 237028898 237028898 T A SNP IQCA1 NM_024726.3 human genbank 54_36p -1 provisional intronic c.926+9989 e6+9989 0 - - - no_errors tier3 472 7 1.45 559 481 45.55 0 0 NA 545259 TCGA-AB-2979 AML33 3 19298678 19298678 T A SNP KCNH8 NM_144633.2 human genbank 54_36p 1 reviewed intronic c.442+853 e3+853 0.006 - - - no_errors tier3 888 28 3.06 740 565 43.3 0 0 NA 545259 TCGA-AB-2979 AML33 3 26435365 26435365 T C SNP - - - - - - - - - - - - - - - tier3 1082 29 2.61 1244 1098 46.86 0 0 NA 545259 TCGA-AB-2979 AML33 3 31893390 31893390 C T SNP OSBPL10 NM_017784.3 human genbank 54_36p -1 reviewed intronic c.458-382 e3-382 0.001 - - - no_errors tier3 648 22 3.24 399 313 43.72 0 0 0 545259 TCGA-AB-2979 AML33 3 35215606 35215606 C A SNP - - - - - - - - - - - - - - - tier3 1307 32 2.39 1243 943 43.1 0 0 NA 545259 TCGA-AB-2979 AML33 3 39866988 39866988 T C SNP MYRIP NM_015460.2 human genbank 54_36p 1 validated intronic c.1+40577 e0+40577 0.013 - - - no_errors tier3 750 13 1.7 654 501 43.38 0 0 NA 545259 TCGA-AB-2979 AML33 3 44238581 44238581 C T SNP uc003cmz.1 ENST00000309765 human ensembl 54_36p 1 known 5_prime_flanking_region c.-19969 NULL 0.003 - - - no_stop_codon tier3 521 14 2.61 427 304 41.47 0 0 NA 545259 TCGA-AB-2979 AML33 3 44907266 44907266 G C SNP TGM4 NM_003241.3 human genbank 54_36p 1 validated intronic c.430+38 e4+38 0.004 - - - no_errors tier2 1267 28 2.16 912 612 40.05 0 0 NA 545259 TCGA-AB-2979 AML33 3 50514542 50514542 C A SNP CACNA2D2 NM_001005505.1 human genbank 54_36p -1 reviewed intronic c.206+1111 e1+1111 0.847 - - - no_errors tier3 161 4 2.42 104 112 51.38 0 0 NA 545259 TCGA-AB-2979 AML33 3 69334116 69334116 G - DEL FRMD4B NM_015123.1 human genbank 54_36p -1 validated intronic c.877-3501 e12-3501 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 3 86224776 86224776 A T SNP ENSG00000201410 ENST00000364540 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32280 NULL 0.006 - - - no_errors tier3 399 5 1.24 248 176 41.51 0 0 NA 545259 TCGA-AB-2979 AML33 3 104636692 104636692 T C SNP - - - - - - - - - - - - - - - tier3 654 15 2.24 339 290 46.1 0 0 NA 545259 TCGA-AB-2979 AML33 3 129184551 129184551 C T SNP KLHDC6 NM_207335.2 human genbank 54_36p 1 validated intronic c.1691-1079 e5-1079 0 - - - no_errors tier2 576 14 2.37 713 538 43.01 0 0 NA 545259 TCGA-AB-2979 AML33 3 138708617 138708617 A T SNP ENSG00000201325 ENST00000364455 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*11055 NULL 0.571 - - - no_errors tier3 884 18 2 908 726 44.43 0 0 NA 545259 TCGA-AB-2979 AML33 3 145297034 145297034 C T SNP - - - - - - - - - - - - - - - tier3 907 16 1.73 814 628 43.52 0 0 NA 545259 TCGA-AB-2979 AML33 3 149224034 149224034 T C SNP - - - - - - - - - - - - - - - tier3 569 15 2.57 745 572 43.43 0 0 NA 545259 TCGA-AB-2979 AML33 3 178895267 178895267 G C SNP - - - - - - - - - - - - - - - tier3 1077 24 2.18 817 591 41.86 0 0 NA 545259 TCGA-AB-2979 AML33 3 179527412 179527412 C T SNP - - - - - - - - - - - - - - - tier2 1001 27 2.63 1106 847 43.3 0 0 NA 545259 TCGA-AB-2979 AML33 3 192547080 192547080 C T SNP CCDC50 NM_178335.3 human genbank 54_36p 1 reviewed intronic c.50-10491 e2-10491 0 - - - no_errors tier3 827 17 2.01 604 426 41.36 0 0 0 545259 TCGA-AB-2979 AML33 3 194515101 194515101 G T SNP ATP13A5 NM_198505.2 human genbank 54_36p -1 provisional intronic c.2158+354 e18+354 0 - - - no_errors tier3 1125 17 1.49 1627 1236 43.14 0 0 NA 545259 TCGA-AB-2979 AML33 3 196065924 196065924 C A SNP - - - - - - - - - - - - - - - tier3 482 8 1.63 387 341 46.84 0 0 NA 545259 TCGA-AB-2979 AML33 4 2989115 2989115 A G SNP GRK4 NM_182982.1 human genbank 54_36p 1 reviewed intronic c.742-2051 e9-2051 0.002 - - - no_errors tier3 453 10 2.16 332 268 44.59 0 0 0 545259 TCGA-AB-2979 AML33 4 7741443 7741443 G A SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.1039-670 e11-670 0.005 - - - no_errors tier3 156 3 1.89 78 50 39.06 0 0 NA 545259 TCGA-AB-2979 AML33 4 23774277 23774277 A G SNP - - - - - - - - - - - - - - - tier3 863 21 2.37 872 653 42.79 0 0 NA 545259 TCGA-AB-2979 AML33 4 27598394 27598394 G A SNP - - - - - - - - - - - - - - - tier3 1058 41 3.73 465 390 45.61 0 0 NA 545259 TCGA-AB-2979 AML33 4 29846646 29846646 T G SNP - - - - - - - - - - - - - - - tier3 1323 32 2.36 1200 891 42.61 0 0 NA 545259 TCGA-AB-2979 AML33 4 32241380 32241380 C T SNP - - - - - - - - - - - - - - - tier3 1088 26 2.33 962 703 42.17 0 0 NA 545259 TCGA-AB-2979 AML33 4 34989015 34989015 G T SNP - - - - - - - - - - - - - - - tier3 1199 33 2.68 917 679 42.54 0 0 NA 545259 TCGA-AB-2979 AML33 4 42688413 42688413 G C SNP GRXCR1 NM_001080476.1 human genbank 54_36p 1 inferred intronic c.627+28505 e2+28505 0.003 - - - no_errors tier3 834 18 2.11 725 565 43.8 0 0 NA 545259 TCGA-AB-2979 AML33 4 43118590 43118590 G A SNP LOC441013 XR_016299.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-10879 NULL 0.001 - - - pseudogene tier2 1066 29 2.65 1017 858 45.76 0 0 NA 545259 TCGA-AB-2979 AML33 4 44917740 44917740 A G SNP - - - - - - - - - - - - - - - tier3 403 7 1.71 274 193 41.33 0 0 NA 545259 TCGA-AB-2979 AML33 4 63908366 63908366 T A SNP LOC644578 XM_927694.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*9156 NULL 0.005 - - - no_errors tier3 457 13 2.76 317 262 45.17 0 0 NA 545259 TCGA-AB-2979 AML33 4 69873291 69873291 G A SNP UGT2A3 NM_024743.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-21224 NULL 0.009 - - - no_errors tier2 827 10 1.19 736 555 42.86 0 0 0 545259 TCGA-AB-2979 AML33 4 71035490 71035490 C T SNP CSN1S2B NR_003721.1 human genbank 54_36p -1 provisional intronic c.NULL NULL 0 - - - pseudogene tier3 572 8 1.38 619 533 46.19 0 0 NA 545259 TCGA-AB-2979 AML33 4 79990248 79990248 T C SNP BMP2K NM_198892.3 human genbank 54_36p 1 reviewed intronic c.751-854 e7-854 0.014 - - - no_errors tier3 531 10 1.85 461 379 45.07 0 0 0 545259 TCGA-AB-2979 AML33 4 81762875 81762875 A G SNP C4orf22 NM_152770.1 human genbank 54_36p 1 predicted intronic c.333+39514 e3+39514 0 - - - no_errors tier3 835 27 3.13 709 637 47.33 0 0 NA 545259 TCGA-AB-2979 AML33 4 88871542 88871542 T C SNP ENSG00000200024 ENST00000363154 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*12586 NULL 0.006 - - - no_errors tier3 1193 30 2.45 868 688 44.13 0 0 NA 545259 TCGA-AB-2979 AML33 4 101856228 101856228 T A SNP - - - - - - - - - - - - - - - tier3 941 11 1.16 861 677 43.96 0 0 NA 545259 TCGA-AB-2979 AML33 4 111541124 111541124 G A SNP ENSG00000199894 ENST00000363024 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*32590 NULL 0.456 - - - no_errors tier3 1715 32 1.83 1461 1045 41.68 0 0 NA 545259 TCGA-AB-2979 AML33 4 116067646 116067646 T A SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.1536+8165 e5+8165 0 - - - no_errors tier3 1089 29 2.59 827 549 39.9 0 0 NA 545259 TCGA-AB-2979 AML33 4 120614663 120614664 - T INS LOC645513 XM_001717939.1 human genbank 54_36p 1 model intronic c.843+11081_11082 e7+11081 0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 4 120885301 120885301 C T SNP - - - - - - - - - - - - - - - tier3 992 18 1.78 1229 976 44.2 0 0 NA 545259 TCGA-AB-2979 AML33 4 121152634 121152634 G T SNP MAD2L1 NM_002358.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*48087 NULL 0.001 - - - no_errors tier3 1108 32 2.81 857 673 43.9 0 0 NA 545259 TCGA-AB-2979 AML33 4 123520075 123520075 G A SNP ADAD1 ENST00000388724 human ensembl 54_36p 1 known 5_prime_untranslated_region c.-600 NULL 0.19 - - - no_errors tier2 272 6 2.16 341 253 42.59 0 0 NA 545259 TCGA-AB-2979 AML33 4 125889947 125889947 A G SNP ANKRD50 NM_020337.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-38831 NULL 0.001 - - - no_errors tier3 513 14 2.66 182 263 59.1 0 0 NA 545259 TCGA-AB-2979 AML33 4 126347429 126347429 T A SNP - - - - - - - - - - - - - - - tier3 815 20 2.4 396 258 39.45 0 0 NA 545259 TCGA-AB-2979 AML33 4 132190986 132190986 C G SNP - - - - - - - - - - - - - - - tier3 627 6 0.95 300 237 44.05 0 0 NA 545259 TCGA-AB-2979 AML33 4 132439054 132439054 A T SNP ENSG00000206782 ENST00000384055 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*25101 NULL 0.001 - - - no_errors tier2 559 10 1.76 499 377 43.04 0 0 NA 545259 TCGA-AB-2979 AML33 4 132719705 132719705 C T SNP - - - - - - - - - - - - - - - tier3 668 12 1.76 766 593 43.51 0 0 NA 545259 TCGA-AB-2979 AML33 4 141460051 141460051 T C SNP SCOC NM_032547.1 human genbank 54_36p 1 provisional intronic c.1-24174 e1-24174 0.003 - - - no_errors tier2 999 34 3.29 1177 1021 46.43 0 0 NA 545259 TCGA-AB-2979 AML33 4 143105849 143105849 C T SNP - - - - - - - - - - - - - - - tier3 965 20 2.03 1115 769 40.82 0 0 NA 545259 TCGA-AB-2979 AML33 4 158726618 158726618 T C SNP ENSG00000221618 ENST00000408691 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*2132 NULL 0 - - - no_errors tier2 735 13 1.74 666 530 44.31 0 0 NA 545259 TCGA-AB-2979 AML33 4 162588583 162588583 T G SNP FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.1841+7023 e14+7023 0 - - - no_errors tier3 755 14 1.82 828 658 44.25 0 0 NA 545259 TCGA-AB-2979 AML33 4 168984416 168984416 G A SNP - - - - - - - - - - - - - - - tier3 821 14 1.67 1010 854 45.82 0 0 NA 545259 TCGA-AB-2979 AML33 4 173517320 173517320 C T SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.553+10905 e4+10905 0.044 - - - no_errors tier3 834 12 1.42 660 463 41.23 0 0 NA 545259 TCGA-AB-2979 AML33 4 178325620 178325620 G A SNP ENSG00000222859 ENST00000410927 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13970 NULL 0 - - - no_errors tier3 506 18 3.36 407 325 43.86 0 0 NA 545259 TCGA-AB-2979 AML33 4 186498786 186498786 G - DEL SNX25 NM_031953.2 human genbank 54_36p 1 validated intronic c.1554+1128 e10+1128 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 5 2196451 2196451 C T SNP ENSG00000201026 ENST00000364156 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41373 NULL 0.001 - - - no_errors tier3 536 9 1.65 570 171 23.01 0 0 NA 545259 TCGA-AB-2979 AML33 5 3044293 3044293 G A SNP - - - - - - - - - - - - - - - tier3 376 7 1.82 370 280 43.08 0 0 NA 545259 TCGA-AB-2979 AML33 5 5184128 5184128 C T SNP ADAMTS16 NM_139056.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-9453 NULL 0 - - - no_errors tier2 921 21 2.23 645 516 44.44 0 0 NA 545259 TCGA-AB-2979 AML33 5 7059938 7059938 A G SNP ENSG00000212258 ENST00000390956 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-40402 NULL 0 - - - no_errors tier3 1350 31 2.24 1336 1039 43.75 0 0 NA 545259 TCGA-AB-2979 AML33 5 8122918 8122918 T C SNP - - - - - - - - - - - - - - - tier3 1271 37 2.83 1421 1204 45.83 0 0 NA 545259 TCGA-AB-2979 AML33 5 8961234 8961234 G A SNP - - - - - - - - - - - - - - - tier2 991 26 2.56 941 735 43.85 0 0 NA 545259 TCGA-AB-2979 AML33 5 9164127 9164127 T C SNP SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.1926-2728 e14-2728 0 - - - no_errors tier3 921 20 2.13 723 509 41.28 0 0 NA 545259 TCGA-AB-2979 AML33 5 38905016 38905016 G A SNP OSMR NM_003999.1 human genbank 54_36p 1 reviewed intronic c.73+40 e1+40 0 - - - no_errors tier3 816 12 1.45 592 353 37.35 0 0 0 545259 TCGA-AB-2979 AML33 5 39664791 39664791 G C SNP - - - - - - - - - - - - - - - tier3 1236 26 2.06 953 810 45.87 0 0 NA 545259 TCGA-AB-2979 AML33 5 39664793 39664793 A G SNP - - - - - - - - - - - - - - - tier3 1238 27 2.13 952 809 45.91 0 0 NA 545259 TCGA-AB-2979 AML33 5 41215168 41215168 G A SNP C6 NM_000065.2 human genbank 54_36p -1 reviewed intronic c.927+2050 e6+2050 0.055 - - - no_errors tier3 876 16 1.79 983 704 41.73 0 0 NA 545259 TCGA-AB-2979 AML33 5 41573911 41573911 A G SNP PLCXD3 NM_001005473.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-27526 NULL 0 - - - no_errors tier2 525 13 2.42 433 305 41.33 0 0 NA 545259 TCGA-AB-2979 AML33 5 42567840 42567840 G A SNP GHR NM_000163.2 human genbank 54_36p 1 reviewed intronic c.1-33883 e1-33883 0 - - - no_errors tier3 1236 44 3.43 1408 1225 46.19 0 0 NA 545259 TCGA-AB-2979 AML33 5 50437676 50437676 G A SNP - - - - - - - - - - - - - - - tier3 932 30 3.12 1120 864 43.55 0 0 NA 545259 TCGA-AB-2979 AML33 5 51713973 51713973 C T SNP - - - - - - - - - - - - - - - tier2 868 23 2.58 1003 888 46.93 0 0 NA 545259 TCGA-AB-2979 AML33 5 55953232 55953232 G C SNP - - - - - - - - - - - - - - - tier3 771 15 1.91 606 391 39.18 0 0 NA 545259 TCGA-AB-2979 AML33 5 58813420 58813421 - A INS PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.456-265870_456-265869 e2-265869 0.017:0.021 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 5 60388022 60388022 C T SNP NDUFAF2 NM_174889.4 human genbank 54_36p 1 reviewed intronic c.128-16687 e2-16687 0.02 - - - no_errors tier2 1035 30 2.82 921 839 47.64 0 0 NA 545259 TCGA-AB-2979 AML33 5 72075871 72075871 G T SNP ENSG00000206770 ENST00000384043 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24414 NULL 0.001 - - - no_errors tier3 1282 9 0.7 1429 573 28.61 0 0 NA 545259 TCGA-AB-2979 AML33 5 91788922 91788922 G A SNP - - - - - - - - - - - - - - - tier3 481 4 0.82 333 255 43.37 0 0 NA 545259 TCGA-AB-2979 AML33 5 92269523 92269523 C A SNP LOC391810 XM_001723772.1 human genbank 54_36p -1 model intronic c.715+14168 e5+14168 1 - - - pseudogene tier2 921 23 2.44 913 677 42.58 0 0 NA 545259 TCGA-AB-2979 AML33 5 95676801 95676801 G A SNP - - - - - - - - - - - - - - - tier2 825 17 2.02 1110 879 44.17 0 0 NA 545259 TCGA-AB-2979 AML33 5 100243115 100243115 T C SNP ST8SIA4 NM_005668.4 human genbank 54_36p -1 reviewed intronic c.503+6831 e3+6831 0.68 - - - no_errors tier3 348 9 2.51 268 202 42.98 0 0 0 545259 TCGA-AB-2979 AML33 5 100719983 100719983 C T SNP - - - - - - - - - - - - - - - tier3 1452 32 2.15 1690 1204 41.57 0 0 NA 545259 TCGA-AB-2979 AML33 5 104573698 104573698 A C SNP - - - - - - - - - - - - - - - tier3 1264 19 1.48 1548 1187 43.34 0 0 NA 545259 TCGA-AB-2979 AML33 5 106820334 106820334 G T SNP EFNA5 NM_001962.2 human genbank 54_36p -1 reviewed intronic c.126-29225 e2-29225 0.001 - - - no_errors tier3 1104 29 2.56 1169 945 44.64 0 0 NA 545259 TCGA-AB-2979 AML33 5 114534278 114534278 A G SNP LOC100131040 XM_001715034.1 human genbank 54_36p 1 model missense c.73 p.S25G 0.001 NULL NULL - no_errors tier1 239 9 3.61 260 191 42.35 NA 545259 TCGA-AB-2979 AML33 5 114779724 114779724 A C SNP ENSG00000177962 ENST00000317782 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-24276 NULL 0.019 - - - no_coding_region:pseudogene tier3 1397 32 2.24 1316 1109 45.68 0 0 NA 545259 TCGA-AB-2979 AML33 5 121298698 121298698 A G SNP SRFBP1 NM_152546.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26929 NULL 0.083 - - - no_errors tier3 836 22 2.56 522 404 43.63 0 0 NA 545259 TCGA-AB-2979 AML33 5 125401893 125401893 C T SNP - - - - - - - - - - - - - - - tier3 654 13 1.95 660 582 46.82 0 0 NA 545259 TCGA-AB-2979 AML33 5 129031493 129031493 A G SNP ADAMTS19 NM_133638.3 human genbank 54_36p 1 reviewed intronic c.2488+2322 e16+2322 0 - - - no_errors tier2 1007 28 2.7 992 797 44.5 0 0 NA 545259 TCGA-AB-2979 AML33 5 133161352 133161352 T C SNP - - - - - - - - - - - - - - - tier3 1122 15 1.32 783 529 40.29 0 0 NA 545259 TCGA-AB-2979 AML33 5 144461356 144461356 C G SNP - - - - - - - - - - - - - - - tier3 1021 20 1.92 1299 902 40.98 0 0 NA 545259 TCGA-AB-2979 AML33 5 155476757 155476757 A G SNP ENSG00000208554 ENST00000385819 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32634 NULL 0.001 - - - pseudogene tier3 807 21 2.54 898 759 45.81 0 0 NA 545259 TCGA-AB-2979 AML33 5 155992807 155992807 T A SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.503-14245 e6-14245 0.001 - - - no_errors tier3 785 18 2.24 1235 907 42.34 0 0 NA 545259 TCGA-AB-2979 AML33 5 156250002 156250002 G A SNP TIMD4 NM_138379.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*29044 NULL 0 - - - no_errors tier3 1833 48 2.55 1667 1267 43.17 0 0 NA 545259 TCGA-AB-2979 AML33 5 160874859 160874860 - T INS GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed intronic c.237+29951_237+29950 e3+29951 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 5 169974342 169974342 T A SNP KCNIP1 NM_001034837.1 human genbank 54_36p 1 reviewed intronic c.62-98094 e2-98094 0 - - - no_errors tier3 712 15 2.05 393 377 48.96 0 0 NA 545259 TCGA-AB-2979 AML33 5 176108331 176108331 G A SNP LOC729378 XM_001130104.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*4955 NULL 0.004 - - - no_errors tier3 114 3 2.56 76 80 51.28 0 0 NA 545259 TCGA-AB-2979 AML33 5 176229496 176229496 G A SNP UNC5A NM_133369.2 human genbank 54_36p 1 validated intronic c.722-481 e6-481 0.003 - - - no_errors tier2 70 1 1.41 85 48 36.09 0 0 NA 545259 TCGA-AB-2979 AML33 6 3414030 3414030 G A SNP SLC22A23 NM_021945.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-58540 NULL 0 - - - no_errors tier3 955 19 1.95 822 694 45.78 0 0 NA 545259 TCGA-AB-2979 AML33 6 5978933 5978933 G A SNP NRN1 NM_016588.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-26952 NULL 0 - - - no_errors tier3 2312 67 2.82 2381 1943 44.9 0 0 NA 545259 TCGA-AB-2979 AML33 6 10283788 10283788 G C SNP ENSG00000221583 ENST00000408656 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46467 NULL 0.035 - - - no_errors tier3 1624 40 2.4 1292 1164 47.34 0 0 NA 545259 TCGA-AB-2979 AML33 6 17326578 17326578 A C SNP ENSG00000209103 ENST00000386368 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*6651 NULL 0 - - - pseudogene tier3 1021 23 2.2 716 515 41.77 0 0 NA 545259 TCGA-AB-2979 AML33 6 21142749 21142749 T A SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated intronic c.1056-30509 e10-30509 0.012 - - - no_errors tier3 1064 22 2.03 881 827 48.39 0 0 0 545259 TCGA-AB-2979 AML33 6 35282744 35282744 G A SNP SCUBE3 NM_152753.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-7430 NULL 0.001 - - - no_errors tier3 413 9 2.13 235 147 38.48 0 0 NA 545259 TCGA-AB-2979 AML33 6 48974097 48974097 C T SNP ENSG00000221175 ENST00000408248 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48499 NULL 0.005 - - - no_errors tier3 1153 24 2.04 1078 719 39.99 0 0 NA 545259 TCGA-AB-2979 AML33 6 51632140 51632140 G C SNP PKHD1 NM_138694.3 human genbank 54_36p -1 reviewed silent c.10743 p.L3581 0.391 NULL "HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00710,superfamily_Pectin lyase-like,superfamily_E set domains,HMMPfam_G8" - no_errors tier1 968 20 2.02 1292 1083 45.56 NA 545259 TCGA-AB-2979 AML33 6 66942135 66942135 A G SNP - - - - - - - - - - - - - - - tier3 1076 7 0.65 2039 520 20.32 0 0 NA 545259 TCGA-AB-2979 AML33 6 79538263 79538263 C T SNP - - - - - - - - - - - - - - - tier3 1221 26 2.08 1501 1166 43.65 0 0 NA 545259 TCGA-AB-2979 AML33 6 83372275 83372275 T C SNP - - - - - - - - - - - - - - - tier3 1377 31 2.2 1426 1223 46.15 0 0 NA 545259 TCGA-AB-2979 AML33 6 83516808 83516808 C T SNP - - - - - - - - - - - - - - - tier3 1000 16 1.57 802 600 42.8 0 0 NA 545259 TCGA-AB-2979 AML33 6 91939541 91939541 G T SNP - - - - - - - - - - - - - - - tier3 1277 28 2.15 1269 1068 45.7 0 0 NA 545259 TCGA-AB-2979 AML33 6 94135050 94135050 T G SNP EPHA7 NM_004440.3 human genbank 54_36p -1 reviewed intronic c.833-10200 e4-10200 0 - - - no_errors tier3 530 13 2.39 367 354 49.1 0 0 NA 545259 TCGA-AB-2979 AML33 6 99102451 99102451 C T SNP - - - - - - - - - - - - - - - tier2 815 13 1.57 1415 1087 43.41 0 0 NA 545259 TCGA-AB-2979 AML33 6 104162192 104162192 T A SNP ENSG00000202283 ENST00000365413 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24356 NULL 0.069 - - - no_errors tier3 1202 34 2.75 1275 1040 44.89 0 0 NA 545259 TCGA-AB-2979 AML33 6 104515766 104515766 C T SNP - - - - - - - - - - - - - - - tier3 1135 35 2.99 1143 847 42.52 0 0 NA 545259 TCGA-AB-2979 AML33 6 122631270 122631270 C T SNP - - - - - - - - - - - - - - - tier3 827 24 2.82 478 342 41.71 0 0 NA 545259 TCGA-AB-2979 AML33 6 123403173 123403173 G A SNP RLBP1L2 NM_001010852.2 human genbank 54_36p 1 provisional intronic c.565-8293 e3-8293 0.008 - - - no_errors tier2 607 14 2.25 693 582 45.65 0 0 NA 545259 TCGA-AB-2979 AML33 6 125246381 125246381 A G SNP - - - - - - - - - - - - - - - tier3 1197 26 2.13 1060 848 44.44 0 0 NA 545259 TCGA-AB-2979 AML33 6 128469573 128469573 T C SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.1163-16743 e8-16743 0.407 - - - no_errors tier3 500 15 2.91 497 448 47.36 0 0 NA 545259 TCGA-AB-2979 AML33 6 152190346 152190346 G A SNP ESR1 NM_000125.3 human genbank 54_36p 1 reviewed intronic c.453-15079 e2-15079 0.002 - - - no_errors tier3 1199 17 1.4 732 543 42.55 0 0 NA 545259 TCGA-AB-2979 AML33 6 156862423 156862423 A T SNP ENSG00000208442 ENST00000385707 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*48315 NULL 0.002 - - - pseudogene tier2 690 10 1.43 604 441 42.16 0 0 NA 545259 TCGA-AB-2979 AML33 6 157504045 157504045 G A SNP ARID1B NM_017519.1 human genbank 54_36p 1 validated intronic c.2339-7405 e8-7405 0.004 - - - no_errors tier3 424 9 2.08 202 164 44.81 0 2 100 545259 TCGA-AB-2979 AML33 6 165954719 165954719 G C SNP PDE10A NM_006661.1 human genbank 54_36p -1 validated intronic c.1+40706 e0+40706 0 - - - no_errors tier2 579 12 2.02 329 302 47.71 0 0 NA 545259 TCGA-AB-2979 AML33 7 7047316 7047316 G A SNP LOC100131257 XM_001716696.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*37135 NULL 0.012 - - - no_errors tier3 1109 36 3.14 1431 1147 44.46 0 1 100 545259 TCGA-AB-2979 AML33 7 40887265 40887265 G A SNP C7orf10 NM_024728.1 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*20662 NULL 0.001 - - - no_errors tier3 741 28 3.64 869 650 42.79 0 0 NA 545259 TCGA-AB-2979 AML33 7 75704159 75704159 G T SNP uc003uer.2 ENST00000326382 human ensembl 54_36p 1 known intronic c.233+1606 e1+1606 0.001 - - - no_errors tier3 1533 41 2.6 455 429 48.53 0 0 NA 545259 TCGA-AB-2979 AML33 7 82353930 82353930 T C SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.13529-7216 e10-7216 0.002 - - - no_errors tier3 916 2 0.22 1247 139 10.03 0 0 NA 545259 TCGA-AB-2979 AML33 7 90546660 90546660 A T SNP PFTK1 NM_012395.2 human genbank 54_36p 1 validated intronic c.1052-23 e11-23 0.007 - - - no_errors tier3 1328 26 1.92 1179 964 44.96 0 0 0 545259 TCGA-AB-2979 AML33 7 108719518 108719518 G C SNP - - - - - - - - - - - - - - - tier3 580 12 2.03 534 396 42.53 0 0 NA 545259 TCGA-AB-2979 AML33 7 119400605 119400605 A T SNP ENSG00000194647 ENST00000350695 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*32619 NULL 0.002 - - - no_errors tier3 678 13 1.88 473 379 44.48 0 0 NA 545259 TCGA-AB-2979 AML33 7 121113252 121113252 A T SNP - - - - - - - - - - - - - - - tier2 1103 38 3.33 753 530 41.28 0 0 NA 545259 TCGA-AB-2979 AML33 7 125980860 125980860 A C SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.1495-19683 e8-19683 0.013 - - - no_errors tier3 541 9 1.64 748 657 46.76 0 0 NA 545259 TCGA-AB-2979 AML33 7 133189161 133189161 G A SNP EXOC4 NM_021807.1 human genbank 54_36p 1 reviewed intronic c.1734+36324 e11+36324 0 - - - no_errors tier2 1272 36 2.75 1111 1019 47.84 0 0 0 545259 TCGA-AB-2979 AML33 7 137916991 137916991 C T SNP TRIM24 NM_015905.3 human genbank 54_36p 1 reviewed missense c.2728 p.R910C 0.998 "HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain" "HMMPfam_zf-B_box,HMMSmart_SM00336,HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain,HMMSmart_SM00184,HMMSmart_SM00249,HMMSmart_SM00502,superfamily_FYVE/PHD zinc finger,PatternScan_ZF_RING_1,PatternScan_BROMODOMAIN_1,HMMPfam_zf-C3HC4,PatternScan_ZF_PHD_1,HMMPfam_PHD,superfamily_RING/U-box" - no_errors tier1 1009 22 2.13 697 483 40.9 49 37 43.02 545259 TCGA-AB-2979 AML33 7 152952453 152952453 T A SNP - - - - - - - - - - - - - - - tier3 806 12 1.46 873 666 43.27 0 0 NA 545259 TCGA-AB-2979 AML33 7 157391146 157391146 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1724-6956 e12-6956 0.98 - - - no_errors tier2 460 10 2.13 292 229 43.95 0 0 NA 545259 TCGA-AB-2979 AML33 8 4131170 4131170 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.415+133713 e3+133713 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier2 477 11 2.25 657 464 41.39 0 0 NA 545259 TCGA-AB-2979 AML33 8 14927315 14927315 C A SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.39+212150 e1+212150 0.59 - - - no_errors tier3 720 17 2.31 742 483 39.4 0 0 NA 545259 TCGA-AB-2979 AML33 8 15673338 15673338 C T SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*13649 NULL 0.248 - - - no_errors tier3 527 8 1.5 391 276 41.26 0 0 NA 545259 TCGA-AB-2979 AML33 8 25914229 25914229 C T SNP EBF2 NM_022659.2 human genbank 54_36p -1 validated intronic c.551+32289 e6+32289 0.868 - - - no_errors tier2 525 13 2.42 451 366 44.74 0 0 NA 545259 TCGA-AB-2979 AML33 8 26583997 26583997 G T SNP DPYSL2 NM_001386.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*14858 NULL 0 - - - no_errors tier3 1107 17 1.51 739 549 42.62 0 0 NA 545259 TCGA-AB-2979 AML33 8 27334366 27334366 T G SNP PTK2B NM_004103.3 human genbank 54_36p 1 reviewed intronic c.471+188 e3+188 0 - - - no_errors tier3 1099 31 2.74 1032 887 46.15 1 0 0 545259 TCGA-AB-2979 AML33 8 27384663 27384663 G A SNP CHRNA2 NM_000742.3 human genbank 54_36p -1 validated intronic c.1-35 e1-35 0.001 - - - no_errors tier3 735 10 1.34 612 515 45.7 0 0 NA 545259 TCGA-AB-2979 AML33 8 40300527 40300527 G A SNP - - - - - - - - - - - - - - - tier2 396 8 1.98 529 388 42.31 0 0 NA 545259 TCGA-AB-2979 AML33 8 53254395 53254395 T C SNP ST18 NM_014682.2 human genbank 54_36p -1 validated intronic c.277+840 e3+840 0 - - - no_errors tier3 378 10 2.58 427 347 44.83 0 0 NA 545259 TCGA-AB-2979 AML33 8 73212789 73212789 T - DEL LOC392232 XR_037363.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*16912 NULL 0.007 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 8 74169189 74169189 C T SNP C8orf84 ENST00000360973 human ensembl 54_36p -1 known intronic c.220-13187 e2-13187 0.004 - - - no_errors tier3 243 3 1.22 124 117 48.35 0 0 NA 545259 TCGA-AB-2979 AML33 8 77427820 77427820 T A SNP - - - - - - - - - - - - - - - tier3 717 7 0.97 461 370 44.52 0 0 NA 545259 TCGA-AB-2979 AML33 8 89047922 89047922 G A SNP - - - - - - - - - - - - - - - tier3 437 10 2.24 361 273 42.92 0 0 NA 545259 TCGA-AB-2979 AML33 8 107894546 107894546 T A SNP ABRA NM_139166.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42952 NULL 0.009 - - - no_errors tier2 678 12 1.74 755 596 44.08 0 0 NA 545259 TCGA-AB-2979 AML33 8 120951856 120951856 G T SNP TAF2 NM_003184.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37871 NULL 0 - - - no_errors tier3 389 11 2.74 162 125 43.55 0 0 NA 545259 TCGA-AB-2979 AML33 8 123131322 123131322 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 8 139400112 139400112 C T SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.78-7767 e2-7767 0 - - - no_errors tier2 1228 30 2.38 1106 821 42.58 0 0 NA 545259 TCGA-AB-2979 AML33 8 142930427 142930427 G T SNP - - - - - - - - - - - - - - - tier3 889 17 1.88 657 520 44.14 0 0 NA 545259 TCGA-AB-2979 AML33 9 22033438 22033438 G C SNP CDKN2BAS NR_003529.3 human genbank 54_36p 1 validated intronic c.NULL NULL 0.022 - - - no_errors tier3 849 24 2.75 842 596 41.36 1 2 66.67 545259 TCGA-AB-2979 AML33 9 23279375 23279375 A G SNP - - - - - - - - - - - - - - - tier3 1260 26 2.02 1437 1089 43.11 0 0 NA 545259 TCGA-AB-2979 AML33 9 24131322 24131322 C A SNP - - - - - - - - - - - - - - - tier3 454 9 1.94 368 263 41.61 0 0 NA 545259 TCGA-AB-2979 AML33 9 27366157 27366157 T A SNP MOBKL2B NM_024761.3 human genbank 54_36p -1 reviewed intronic c.419-16923 e2-16923 0.008 - - - no_errors tier3 720 15 2.04 875 702 44.49 0 0 0 545259 TCGA-AB-2979 AML33 9 31531183 31531184 - A INS ENSG00000218562 ENST00000401640 human ensembl 54_36p 1 known 3_prime_flanking_region c.*34570 NULL 0.000:0.001 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 9 40591637 40591637 G A SNP LOC642406 XR_036855.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.002 - - - pseudogene tier3 721 21 2.83 619 477 43.52 0 0 NA 545259 TCGA-AB-2979 AML33 9 74554010 74554010 G A SNP TMC1 NM_138691.2 human genbank 54_36p 1 reviewed intronic c.536-2576 e7-2576 0 - - - no_errors tier3 848 15 1.74 889 598 40.22 0 0 NA 545259 TCGA-AB-2979 AML33 9 80809708 80809708 G A SNP KRT18P24 XR_016865.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*29764 NULL 0.026 - - - pseudogene tier3 543 6 1.09 350 223 38.85 0 0 NA 545259 TCGA-AB-2979 AML33 9 82300766 82300766 C T SNP - - - - - - - - - - - - - - - tier3 834 15 1.76 837 698 45.44 0 0 NA 545259 TCGA-AB-2979 AML33 9 84041810 84041810 C T SNP - - - - - - - - - - - - - - - tier3 640 21 3.18 759 592 43.82 0 0 NA 545259 TCGA-AB-2979 AML33 9 95563803 95563803 G A SNP - - - - - - - - - - - - - - - tier3 739 16 2.12 573 402 41.19 0 0 NA 545259 TCGA-AB-2979 AML33 9 99551950 99551950 T G SNP KRT18P13 XM_001726959.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*49113 NULL 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 847 21 2.42 878 645 42.21 0 0 NA 545259 TCGA-AB-2979 AML33 9 112258857 112258857 C T SNP SVEP1 NM_153366.3 human genbank 54_36p -1 validated intronic c.3673+500 e21+500 0.01 - - - no_errors tier3 729 16 2.14 709 462 39.45 0 0 NA 545259 TCGA-AB-2979 AML33 9 118194560 118194560 G C SNP PAPPA NM_002581.3 human genbank 54_36p 1 reviewed intronic c.4777-4049 e22-4049 0.001 - - - no_errors tier3 620 18 2.82 745 582 43.86 0 0 NA 545259 TCGA-AB-2979 AML33 9 120052667 120052667 C A SNP - - - - - - - - - - - - - - - tier3 896 22 2.4 1037 433 29.44 0 0 NA 545259 TCGA-AB-2979 AML33 9 120263664 120263664 T C SNP - - - - - - - - - - - - - - - tier3 1221 28 2.24 1129 954 45.71 0 0 NA 545259 TCGA-AB-2979 AML33 9 125350410 125350410 C G SNP DENND1A NM_020946.1 human genbank 54_36p -1 validated intronic c.993+9260 e13+9260 0.003 - - - no_errors tier3 672 19 2.75 762 647 45.89 0 0 0 545259 TCGA-AB-2979 AML33 9 130692744 130692744 C T SNP LRRC8A NM_019594.1 human genbank 54_36p 1 reviewed intronic c.1+4523 e0+4523 0 - - - no_errors tier3 287 11 3.68 135 124 47.88 0 2 100 545259 TCGA-AB-2979 AML33 9 137349581 137349581 G A SNP LOC100131900 XM_001719692.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-34785 NULL 0 - - - no_errors tier3 477 10 2.05 203 153 42.86 0 0 NA 545259 TCGA-AB-2979 AML33 9 137725072 137725072 G A SNP KCNT1 NM_020822.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-8854 NULL 0 - - - no_errors tier3 299 14 4.47 106 99 48.29 0 0 NA 545259 TCGA-AB-2979 AML33 9 140154787 140154787 C T SNP ENSG00000218926 ENST00000405180 human ensembl 54_36p 1 known intronic c.NULL NULL 0.006 - - - no_coding_region:pseudogene tier3 675 20 2.88 374 295 44.1 0 0 NA 545259 TCGA-AB-2979 AML33 10 1204129 1204129 C T SNP ADARB2 NM_018702.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*15004 NULL 0.001 - - - no_errors tier2 433 7 1.59 353 313 47 0 0 NA 545259 TCGA-AB-2979 AML33 10 1461848 1461848 C T SNP ADARB2 NM_018702.2 human genbank 54_36p -1 reviewed intronic c.101-50493 e2-50493 0.073 - - - no_errors tier3 901 26 2.8 869 655 42.98 0 0 NA 545259 TCGA-AB-2979 AML33 10 10244807 10244807 G T SNP TCEB1P3 XM_927664.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-11392 NULL 0 - - - pseudogene tier2 705 13 1.81 559 416 42.62 0 0 NA 545259 TCGA-AB-2979 AML33 10 15658241 15658241 G A SNP ITGA8 NM_003638.1 human genbank 54_36p -1 provisional intronic c.2373-642 e24-642 0 - - - no_errors tier3 1053 28 2.59 971 745 43.41 0 0 NA 545259 TCGA-AB-2979 AML33 10 24902028 24902028 C A SNP ARHGAP21 NM_020824.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*11319 NULL 0.002 - - - no_errors tier3 791 19 2.35 560 458 44.99 0 0 NA 545259 TCGA-AB-2979 AML33 10 37522616 37522616 T - DEL ANKRD30A NM_052997.2 human genbank 54_36p 1 validated intronic c.2446+424 e27+424 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 10 57024040 57024040 G A SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+33351 e0+33351 0 - - - no_errors tier2 564 9 1.57 577 340 37.08 0 0 NA 545259 TCGA-AB-2979 AML33 10 58267498 58267498 C T SNP - - - - - - - - - - - - - - - tier3 1070 28 2.55 749 575 43.43 0 0 NA 545259 TCGA-AB-2979 AML33 10 58401765 58401765 G A SNP - - - - - - - - - - - - - - - tier3 1140 27 2.31 724 550 43.17 0 0 NA 545259 TCGA-AB-2979 AML33 10 64494269 64494269 C T SNP ENSG00000199446 ENST00000362576 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-45636 NULL 0.959 - - - no_errors tier3 1209 36 2.89 952 610 39.03 0 0 NA 545259 TCGA-AB-2979 AML33 10 65522024 65522024 A C SNP - - - - - - - - - - - - - - - tier3 897 21 2.29 1055 836 44.19 0 0 NA 545259 TCGA-AB-2979 AML33 10 84506244 84506244 C A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.1027+17858 e3+17858 0.004 - - - no_errors tier3 639 22 3.32 802 575 41.76 0 0 NA 545259 TCGA-AB-2979 AML33 10 92527824 92527824 C T SNP HTR7 NM_019859.4 human genbank 54_36p -1 reviewed intronic c.540-28493 e2-28493 0 - - - no_errors tier3 1413 33 2.28 1294 1048 44.69 0 0 NA 545259 TCGA-AB-2979 AML33 10 95843404 95843404 A G SNP PLCE1 NM_016341.3 human genbank 54_36p 1 validated intronic c.1207-38517 e2-38517 0 - - - no_errors tier3 1212 27 2.18 1302 1085 45.42 0 0 NA 545259 TCGA-AB-2979 AML33 10 122292548 122292548 C T SNP PPAPDC1A NM_001030059.1 human genbank 54_36p 1 validated intronic c.445+21951 e5+21951 0.003 - - - no_errors tier3 990 23 2.25 891 753 45.09 0 0 NA 545259 TCGA-AB-2979 AML33 10 122572543 122572543 C T SNP BRWD2 NM_018117.10 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28380 NULL 0.004 - - - no_errors tier3 817 24 2.85 724 601 45.36 0 0 NA 545259 TCGA-AB-2979 AML33 10 132377835 132377835 C T SNP - - - - - - - - - - - - - - - tier3 534 13 2.38 581 466 44.47 0 0 NA 545259 TCGA-AB-2979 AML33 11 2138649 2138649 G A SNP INS-IGF2 NM_001042376.1 human genbank 54_36p -1 reviewed silent c.129 p.C43 0.999 "HMMPfam_Insulin,HMMSmart_SM00078,superfamily_Insulin-like" "HMMPfam_Insulin,HMMSmart_SM00078,superfamily_Insulin-like" - no_errors tier1 46 0 42 51 54.84 NA 545259 TCGA-AB-2979 AML33 11 2570063 2570063 C T SNP KCNQ1 NM_000218.2 human genbank 54_36p 1 reviewed intronic c.1393+3403 e10+3403 0.005 - - - no_errors tier3 236 5 2.07 296 214 41.96 0 0 0 545259 TCGA-AB-2979 AML33 11 15577689 15577689 A T SNP - - - - - - - - - - - - - - - tier3 990 29 2.82 1106 929 45.58 0 0 NA 545259 TCGA-AB-2979 AML33 11 20060737 20060737 C T SNP NAV2 NM_182964.1 human genbank 54_36p 1 validated intronic c.5502+15 e28+15 0.227 - - - no_errors tier2 938 21 2.19 1052 808 43.42 1 0 0 545259 TCGA-AB-2979 AML33 11 87777845 87777845 T G SNP - - - - - - - - - - - - - - - tier3 1177 14 1.18 985 741 42.93 0 0 0 545259 TCGA-AB-2979 AML33 11 88753887 88753887 C T SNP NOX4 NM_016931.1 human genbank 54_36p -1 reviewed intronic c.1075-7579 e12-7579 0.97 - - - no_errors tier3 1124 31 2.68 979 845 46.33 0 0 NA 545259 TCGA-AB-2979 AML33 11 94948350 94948351 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 11 102240926 102240926 A T SNP MMP12 ENST00000326227 human ensembl 54_36p -1 known intronic c.1206-733 e9-733 0.004 - - - no_errors tier3 703 19 2.63 954 775 44.82 0 0 NA 545259 TCGA-AB-2979 AML33 11 106317289 106317289 T A SNP GUCY1A2 NM_000855.1 human genbank 54_36p -1 validated intronic c.488-1175 e4-1175 0 - - - no_errors tier3 918 12 1.28 971 806 45.18 0 0 0 545259 TCGA-AB-2979 AML33 11 108720478 108720478 G A SNP - - - - - - - - - - - - - - - tier3 1363 42 2.99 1072 969 47.48 0 0 NA 545259 TCGA-AB-2979 AML33 11 111641734 111641734 C T SNP C11orf34 ENST00000338832 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5212 NULL 0.001 - - - no_stop_codon tier2 1083 27 2.43 1132 912 44.51 0 0 NA 545259 TCGA-AB-2979 AML33 11 113943091 113943091 G A SNP FAM55A NM_152315.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-36578 NULL 0.045 - - - no_errors tier3 1595 62 3.74 1887 1603 45.89 0 1 100 545259 TCGA-AB-2979 AML33 11 117293353 117293353 T C SNP TMPRSS13 NM_001077263.1 human genbank 54_36p -1 validated intronic c.452-154 e3-154 0.001 - - - no_errors tier3 308 9 2.84 305 285 48.31 2 1 33.33 545259 TCGA-AB-2979 AML33 11 119761642 119761642 T G SNP ARHGEF12 NM_015313.1 human genbank 54_36p 1 reviewed intronic c.33-20395 e2-20395 0.928 - - - no_errors tier2 1214 26 2.1 943 709 42.89 0 0 0 545259 TCGA-AB-2979 AML33 11 120122683 120122683 G A SNP GRIK4 NM_014619.2 human genbank 54_36p 1 reviewed intronic c.83-55929 e2-55929 0.004 - - - no_errors tier3 1525 41 2.62 1653 1219 42.4 0 0 NA 545259 TCGA-AB-2979 AML33 11 133458959 133458959 C T SNP JAM3 NM_032801.3 human genbank 54_36p 1 reviewed intronic c.211+14695 e1+14695 0 - - - no_errors tier3 988 18 1.79 793 693 46.64 0 0 NA 545259 TCGA-AB-2979 AML33 11 133850557 133850557 C T SNP ENSG00000216049 ENST00000401230 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-24614 NULL 0.001 - - - no_errors tier2 424 10 2.3 401 320 44.38 0 0 NA 545259 TCGA-AB-2979 AML33 12 15362981 15362981 T C SNP PTPRO NM_030667.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3947 NULL 0 - - - no_errors tier3 1180 23 1.91 739 548 42.55 0 0 NA 545259 TCGA-AB-2979 AML33 12 18387259 18387259 G A SNP PIK3C2G ENST00000266497 human ensembl 54_36p 1 known intronic c.1396-269 e9-269 0 - - - no_errors tier2 771 28 3.5 788 612 43.65 0 0 NA 545259 TCGA-AB-2979 AML33 12 20694904 20694904 A G SNP PDE3A NM_000921.3 human genbank 54_36p 1 validated intronic c.2925+103 e14+103 0 - - - no_errors tier3 659 4 0.6 689 560 44.8 0 0 NA 545259 TCGA-AB-2979 AML33 12 28972586 28972586 C T SNP - - - - - - - - - - - - - - - tier3 867 23 2.58 1339 1009 42.95 0 0 NA 545259 TCGA-AB-2979 AML33 12 48902219 48902220 - T INS LIMA1 NM_016357.1 human genbank 54_36p -1 validated frame_shift_ins c.482_481 p.M161fs 0.998:0.974 NULL "HMMPfam_LIM,HMMSmart_SM00132,PatternScan_LIM_DOMAIN_1,superfamily_Glucocorticoid receptor-like (DNA-binding domain)" - no_errors tier1 NA NA NA NA NA NA NA 545259 TCGA-AB-2979 AML33 12 49918637 49918637 C T SNP DAZAP2 NM_014764.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-322 NULL 0.002 - - - no_errors tier2 752 22 2.84 327 278 45.95 1 0 0 545259 TCGA-AB-2979 AML33 12 57054501 57054501 T A SNP - - - - - - - - - - - - - - - tier3 1205 30 2.43 1439 1105 43.44 0 0 NA 545259 TCGA-AB-2979 AML33 12 70914822 70914822 T C SNP TRHDE NM_013381.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-38004 NULL 0.022 - - - no_errors tier3 501 13 2.53 389 395 50.38 0 0 NA 545259 TCGA-AB-2979 AML33 12 71596145 71596145 G T SNP - - - - - - - - - - - - - - - tier3 572 13 2.22 580 482 45.39 0 0 NA 545259 TCGA-AB-2979 AML33 12 74370754 74370754 G A SNP LOC100130336 XM_001726624.1 human genbank 54_36p -1 model 5_prime_untranslated_region c.-3 NULL 0 - - - no_errors tier2 979 28 2.78 1136 934 45.12 0 0 NA 545259 TCGA-AB-2979 AML33 12 78179975 78179975 G A SNP SYT1 NM_005639.1 human genbank 54_36p 1 validated intronic c.167-23723 e2-23723 0.002 - - - no_errors tier3 955 23 2.35 741 543 42.26 0 0 NA 545259 TCGA-AB-2979 AML33 12 78958560 78958560 G A SNP - - - - - - - - - - - - - - - tier3 1157 30 2.53 1855 1452 43.88 0 0 NA 545259 TCGA-AB-2979 AML33 12 96997914 96997914 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 12 112406571 112406571 C T SNP LHX5 NM_022363.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12885 NULL 0 - - - no_errors tier3 924 26 2.74 608 459 43.02 0 0 NA 545259 TCGA-AB-2979 AML33 12 115256369 115256369 C T SNP - - - - - - - - - - - - - - - tier3 1038 28 2.63 744 554 42.68 0 0 NA 545259 TCGA-AB-2979 AML33 12 125189869 125189869 C T SNP - - - - - - - - - - - - - - - tier3 1418 45 3.08 1413 1150 44.85 0 0 NA 545259 TCGA-AB-2979 AML33 12 127194720 127194720 C G SNP - - - - - - - - - - - - - - - tier3 713 14 1.93 986 688 41.1 0 0 NA 545259 TCGA-AB-2979 AML33 12 127693461 127693461 C G SNP TMEM132C ENST00000315208 human ensembl 54_36p 1 known intronic c.154-26454 e2-26454 0.001 - - - no_errors tier3 490 20 3.92 632 440 41.04 0 0 NA 545259 TCGA-AB-2979 AML33 13 18518170 18518170 G A SNP ENSG00000218236 ENST00000405207 human ensembl 54_36p -1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 511 16 3.04 449 381 45.9 0 0 0 545259 TCGA-AB-2979 AML33 13 21747707 21747707 C G SNP - - - - - - - - - - - - - - - tier3 870 23 2.57 1209 906 42.74 0 0 NA 545259 TCGA-AB-2979 AML33 13 26154030 26154030 A G SNP WASF3 NM_006646.5 human genbank 54_36p 1 reviewed intronic c.983+573 e6+573 0.001 - - - no_errors tier3 590 12 1.99 643 543 45.75 0 0 NA 545259 TCGA-AB-2979 AML33 13 52709058 52709058 T A SNP ENSG00000223329 ENST00000411397 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21155 NULL 0.001 - - - no_errors tier3 706 20 2.75 788 651 45.24 0 0 NA 545259 TCGA-AB-2979 AML33 13 53800375 53800375 G A SNP LOC387930 XR_041079.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*7720 NULL 0.517 - - - pseudogene tier3 1026 27 2.56 780 583 42.77 0 0 NA 545259 TCGA-AB-2979 AML33 13 53840594 53840594 T G SNP LOC387930 XR_041079.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - pseudogene tier3 428 13 2.95 314 169 34.92 0 0 NA 545259 TCGA-AB-2979 AML33 13 59634397 59634397 G C SNP DIAPH3 NM_001042517.1 human genbank 54_36p -1 validated intronic c.180+1325 e1+1325 0.005 - - - no_errors tier2 898 29 3.13 807 634 44 0 0 0 545259 TCGA-AB-2979 AML33 13 60296300 60296300 C T SNP ENSG00000206854 ENST00000384127 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*34504 NULL 0.001 - - - no_errors tier3 718 21 2.84 714 598 45.54 0 0 NA 545259 TCGA-AB-2979 AML33 13 71641795 71641795 C T SNP - - - - - - - - - - - - - - - tier3 482 3 0.62 586 407 40.99 0 0 NA 545259 TCGA-AB-2979 AML33 13 86634710 86634710 C T SNP ENSG00000220931 ENST00000405599 human ensembl 54_36p 1 known 5_prime_flanking_region c.-34550 NULL 0 - - - no_coding_region:pseudogene tier2 485 5 1.02 338 257 43.19 0 0 NA 545259 TCGA-AB-2979 AML33 13 110849818 110849818 G A SNP - - - - - - - - - - - - - - - tier3 910 18 1.94 538 400 42.55 0 0 NA 545259 TCGA-AB-2979 AML33 13 111068213 111068213 A G SNP ENSG00000204398 ENST00000375713 human ensembl 54_36p 1 known intronic c.1-8122 e1-8122 0.055 - - - no_errors tier3 991 21 2.08 522 433 45.34 0 0 NA 545259 TCGA-AB-2979 AML33 13 111562934 111562934 G A SNP - - - - - - - - - - - - - - - tier3 615 18 2.84 695 459 39.77 0 0 NA 545259 TCGA-AB-2979 AML33 14 25416998 25416998 G C SNP - - - - - - - - - - - - - - - tier3 703 16 2.22 617 408 39.8 0 0 NA 545259 TCGA-AB-2979 AML33 14 32635818 32635818 G T SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.51-118321 e2-118321 0.011 - - - no_errors tier3 945 26 2.67 884 747 45.74 0 0 NA 545259 TCGA-AB-2979 AML33 14 35529859 35529859 C T SNP - - - - - - - - - - - - - - - tier3 1164 26 2.18 844 583 40.83 0 0 NA 545259 TCGA-AB-2979 AML33 14 36970301 36970301 C T SNP MIPOL1 NM_138731.5 human genbank 54_36p 1 validated intronic c.1031+8396 e9+8396 0.007 - - - no_errors tier3 1700 46 2.63 1665 1224 42.37 0 0 NA 545259 TCGA-AB-2979 AML33 14 41475046 41475046 C T SNP LRFN5 NM_152447.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*31918 NULL 0.029 - - - no_errors tier3 325 5 1.52 221 144 39.45 0 0 NA 545259 TCGA-AB-2979 AML33 14 43889392 43889392 G A SNP - - - - - - - - - - - - - - - tier3 967 18 1.83 971 739 43.19 0 0 NA 545259 TCGA-AB-2979 AML33 14 43898634 43898634 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 14 44067155 44067155 C A SNP FSCB NM_032135.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-21215 NULL 0 - - - no_errors tier3 689 19 2.68 659 456 40.9 0 0 NA 545259 TCGA-AB-2979 AML33 14 47681803 47681803 G A SNP - - - - - - - - - - - - - - - tier3 1005 23 2.24 888 636 41.73 0 0 NA 545259 TCGA-AB-2979 AML33 14 51637434 51637434 C T SNP NID2 NM_007361.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31972 NULL 0.001 - - - no_errors tier3 602 17 2.75 350 251 41.76 0 0 NA 545259 TCGA-AB-2979 AML33 14 57471478 57471478 G T SNP - - - - - - - - - - - - - - - tier3 897 26 2.82 1049 769 42.21 0 0 NA 545259 TCGA-AB-2979 AML33 14 64730709 64730709 G C SNP LOC100128233 XM_001724610.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*24409 NULL 0.009 - - - no_errors tier3 993 20 1.97 982 780 44.27 0 0 NA 545259 TCGA-AB-2979 AML33 14 78907794 78907794 T A SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2144-95523 e11-95523 0 - - - no_errors tier3 928 25 2.62 577 482 45.43 0 0 NA 545259 TCGA-AB-2979 AML33 14 82308743 82308743 T A SNP LOC730105 XM_001132445.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*16086 NULL 0.004 - - - no_errors tier3 886 21 2.32 700 557 44.31 0 0 NA 545259 TCGA-AB-2979 AML33 14 87102018 87102018 G A SNP - - - - - - - - - - - - - - - tier3 1093 24 2.15 1284 880 40.65 0 0 NA 545259 TCGA-AB-2979 AML33 14 98553298 98553298 C T SNP ENSG00000218496 ENST00000405897 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43907 NULL 0.03 - - - no_coding_region:pseudogene tier3 347 14 3.88 254 220 46.41 0 0 NA 545259 TCGA-AB-2979 AML33 14 104109786 104109786 G A SNP C14orf180 NM_001008404.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-14027 NULL 0.315 - - - no_errors tier2 57 0 0 27 47 60.26 0 0 NA 545259 TCGA-AB-2979 AML33 15 19273566 19273566 G A SNP ENSG00000214319 ENST00000398098 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3392 NULL 0.013 - - - no_coding_region:pseudogene tier3 587 12 2 273 42 13.33 0 0 NA 545259 TCGA-AB-2979 AML33 15 22790120 22790120 T C SNP SNORD109A NR_001295.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-48094 NULL 0.001 - - - no_errors tier3 979 21 2.1 1043 880 45.76 0 2 100 545259 TCGA-AB-2979 AML33 15 34440139 34440139 G T SNP - - - - - - - - - - - - - - - tier3 815 20 2.4 705 494 41.2 0 0 NA 545259 TCGA-AB-2979 AML33 15 34593037 34593037 T C SNP - - - - - - - - - - - - - - - tier3 638 16 2.45 510 359 41.12 0 0 NA 545259 TCGA-AB-2979 AML33 15 34696082 34696082 C G SNP C15orf41 NM_032499.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-41265 NULL 0.005 - - - no_errors tier3 680 20 2.86 683 517 43.01 0 0 0 545259 TCGA-AB-2979 AML33 15 40226145 40226145 T C SNP PLA2G4F NM_213600.2 human genbank 54_36p -1 provisional intronic c.1420-414 e14-414 0.037 - - - no_errors tier3 350 7 1.92 404 342 45.66 0 0 NA 545259 TCGA-AB-2979 AML33 15 56293254 56293254 G A SNP AQP9 NM_020980.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*29628 NULL 0 - - - no_errors tier3 1061 18 1.67 1087 830 43.3 0 0 NA 545259 TCGA-AB-2979 AML33 15 67089532 67089532 C A SNP NOX5 NM_024505.2 human genbank 54_36p 1 provisional intronic c.1-16390 e1-16390 0.003 - - - no_errors tier3 862 21 2.38 758 555 42.27 0 0 NA 545259 TCGA-AB-2979 AML33 15 69420299 69420299 A G SNP THSD4 NM_024817.2 human genbank 54_36p 1 provisional intronic c.1016-70781 e6-70781 0.01 - - - no_errors tier3 689 21 2.95 616 394 38.97 0 0 NA 545259 TCGA-AB-2979 AML33 15 85651766 85651766 T C SNP - - - - - - - - - - - - - - - tier3 1018 36 3.42 1149 981 46.03 0 0 NA 545259 TCGA-AB-2979 AML33 15 87785888 87785888 G A SNP RHCG NM_016321.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*31082 NULL 0.002 - - - no_errors tier3 467 14 2.91 397 371 48.31 0 0 NA 545259 TCGA-AB-2979 AML33 16 1484217 1484217 C T SNP TELO2 NM_016111.3 human genbank 54_36p 1 reviewed intronic c.1-31 e1-31 0 - - - no_errors tier2 227 5 2.16 127 97 43.3 10 14 58.33 545259 TCGA-AB-2979 AML33 16 3648976 3648976 G T SNP TRAP1 NM_016292.2 human genbank 54_36p -1 validated intronic c.1941-109 e17-109 0.012 - - - no_errors tier3 368 8 2.13 291 210 41.92 7 13 65 545259 TCGA-AB-2979 AML33 16 24649417 24649417 A G SNP TNRC6A NM_014494.2 human genbank 54_36p 1 reviewed intronic c.53+295 e2+295 1 - - - no_errors tier2 483 12 2.42 258 219 45.82 3 0 0 545259 TCGA-AB-2979 AML33 16 48724848 48724848 C T SNP LOC100130390 XM_001726097.1 human genbank 54_36p -1 model intronic c.99+11139 e2+11139 0 - - - no_errors tier3 726 16 2.16 554 433 43.83 0 0 NA 545259 TCGA-AB-2979 AML33 16 60628648 60628648 C G SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15840 NULL 0.002 - - - no_errors tier3 528 13 2.4 719 325 31.07 0 0 NA 545259 TCGA-AB-2979 AML33 16 60901780 60901780 G A SNP ENSG00000218786 ENST00000405014 human ensembl 54_36p 1 known 5_prime_flanking_region c.-46996 NULL 0 - - - no_coding_region:pseudogene tier2 1289 33 2.49 1193 988 45.28 0 0 NA 545259 TCGA-AB-2979 AML33 16 60918353 60918353 G A SNP ENSG00000218786 ENST00000405014 human ensembl 54_36p 1 known 5_prime_flanking_region c.-30423 NULL 0.001 - - - no_coding_region:pseudogene tier3 1115 27 2.36 1200 988 45.16 0 0 NA 545259 TCGA-AB-2979 AML33 16 62324316 62324316 G T SNP - - - - - - - - - - - - - - - tier3 1010 7 0.69 1310 221 14.44 0 0 NA 545259 TCGA-AB-2979 AML33 16 64539410 64539410 G T SNP - - - - - - - - - - - - - - - tier3 733 10 1.35 649 531 44.96 0 0 NA 545259 TCGA-AB-2979 AML33 16 68267478 68267478 G A SNP NFAT5 NM_138713.1 human genbank 54_36p 1 reviewed intronic c.1558-1129 e10-1129 0 - - - no_errors tier3 681 19 2.71 574 415 41.96 3 0 0 545259 TCGA-AB-2979 AML33 16 81260155 81260155 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.45+41912 e1+41912 0.001 - - - no_errors tier3 965 24 2.42 1173 924 43.61 0 0 NA 545259 TCGA-AB-2979 AML33 16 81349447 81349447 G T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.46-100021 e2-100021 0.001 - - - no_errors tier3 927 26 2.73 820 657 44.48 0 0 NA 545259 TCGA-AB-2979 AML33 17 10072154 10072154 G T SNP GAS7 NM_201433.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29722 NULL 0.009 - - - no_errors tier3 1312 26 1.94 1159 513 30.65 0 0 NA 545259 TCGA-AB-2979 AML33 17 23737117 23737117 C A SNP SARM1 ENST00000379061 human ensembl 54_36p 1 known intronic c.1624+696 e7+696 0 - - - no_errors tier3 527 6 1.13 169 120 41.52 1 0 0 545259 TCGA-AB-2979 AML33 17 28603367 28603367 C A SNP ACCN1 NM_183377.4 human genbank 54_36p -1 reviewed intronic c.708+39172 e1+39172 0.432 - - - no_errors tier3 2230 75 3.25 2165 1580 42.17 0 0 NA 545259 TCGA-AB-2979 AML33 17 42169315 42169315 A G SNP NSF NM_006178.2 human genbank 54_36p 1 validated intronic c.1908+7831 e17+7831 0 - - - no_errors tier3 498 9 1.78 410 316 43.53 0 0 0 545259 TCGA-AB-2979 AML33 17 42443152 42443152 G C SNP RPRML NM_203400.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31780 NULL 0 - - - no_errors tier3 285 11 3.72 239 192 44.34 2 5 71.43 545259 TCGA-AB-2979 AML33 17 44351780 44351780 T C SNP UBE2Z NM_023079.3 human genbank 54_36p 1 validated intronic c.691-1741 e5-1741 0 - - - no_errors tier3 542 11 1.99 246 158 39.11 2 2 50 545259 TCGA-AB-2979 AML33 17 47063324 47063324 T A SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*620 NULL 0.994 - - - no_errors tier2 837 17 1.99 600 475 44.14 0 0 NA 545259 TCGA-AB-2979 AML33 17 57991020 57991020 T C SNP TLK2 NM_006852.1 human genbank 54_36p 1 validated intronic c.721-89 e9-89 0.001 - - - no_errors tier3 467 4 0.85 230 174 43.07 0 0 0 545259 TCGA-AB-2979 AML33 17 62718692 62718692 G A SNP HELZ NM_014877.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-73310 NULL 0 - - - no_errors tier2 378 4 1.05 272 211 43.6 0 0 NA 545259 TCGA-AB-2979 AML33 17 67781458 67781458 A G SNP LOC727973 XR_039997.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-36513 NULL 0 - - - no_errors tier3 544 19 3.37 696 499 41.76 0 0 NA 545259 TCGA-AB-2979 AML33 17 73319353 73319353 C T SNP LOC100128106 XM_001714985.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*37886 NULL 0.003 - - - no_start_codon tier3 1790 50 2.72 1357 1109 44.92 0 0 NA 545259 TCGA-AB-2979 AML33 18 2964400 2964400 A C SNP LPIN2 NM_014646.2 human genbank 54_36p -1 reviewed intronic c.1-13553 e1-13553 0.002 - - - no_errors tier3 571 14 2.39 542 455 45.55 0 1 100 545259 TCGA-AB-2979 AML33 18 38442159 38442159 G A SNP - - - - - - - - - - - - - - - tier3 1594 44 2.68 1422 961 40.33 0 0 NA 545259 TCGA-AB-2979 AML33 18 57845047 57845047 C G SNP PIGN ENST00000357637 human ensembl 54_36p -1 known 3_prime_flanking_region c.*19022 NULL 0.089 - - - no_errors tier3 574 25 4.17 678 526 43.65 0 0 NA 545259 TCGA-AB-2979 AML33 18 63368709 63368709 C G SNP DSEL NM_032160.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35854 NULL 0 - - - no_errors tier2 690 15 2.13 421 317 42.9 0 0 NA 545259 TCGA-AB-2979 AML33 18 64833138 64833138 T C SNP CCDC102B NM_001093729.1 human genbank 54_36p 1 validated intronic c.1434+3817 e6+3817 0.018 - - - no_errors tier3 1185 35 2.87 1115 820 42.33 0 0 NA 545259 TCGA-AB-2979 AML33 18 65497727 65497727 A G SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.409+1658 e4+1658 0 - - - no_errors tier3 1157 28 2.35 874 674 43.48 0 0 NA 545259 TCGA-AB-2979 AML33 18 73670991 73670991 C A SNP - - - - - - - - - - - - - - - tier3 817 17 2.04 624 490 43.99 0 0 NA 545259 TCGA-AB-2979 AML33 18 73700270 73700270 G A SNP - - - - - - - - - - - - - - - tier3 855 21 2.39 850 720 45.8 0 0 NA 545259 TCGA-AB-2979 AML33 19 37494640 37494640 G T SNP ZNF507 NM_014910.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40937 NULL 0.001 - - - no_errors tier3 710 14 1.93 614 474 43.53 0 0 NA 545259 TCGA-AB-2979 AML33 19 38484235 38484240 TCCACG - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_del c.926_921 p.NVE307in_frame_delK 1.000:1.000:1.000:1.000:1.000:1.000 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA 545259 TCGA-AB-2979 AML33 19 38484959 38484960 TG - DEL CEBPA NM_004364.3 human genbank 54_36p -1 reviewed frame_shift_del c.202_201 p.I68fs 1.000:1.000 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 545259 TCGA-AB-2979 AML33 20 1891802 1891802 A G SNP LOC727993 XR_040002.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 1300 27 2.03 1082 875 44.71 0 0 NA 545259 TCGA-AB-2979 AML33 20 19441792 19441792 G A SNP SLC24A3 NM_020689.3 human genbank 54_36p 1 validated intronic c.272-2340 e3-2340 0.002 - - - no_errors tier3 597 18 2.93 760 555 42.17 0 0 NA 545259 TCGA-AB-2979 AML33 20 21142571 21142571 G - DEL NCRNA00153 ENST00000246027 human ensembl 54_36p 1 known intronic c.1444-602 e9-602 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 20 37086832 37086832 C G SNP DHX35 NM_021931.2 human genbank 54_36p 1 reviewed intronic c.1672-455 e18-455 0.001 - - - no_errors tier3 539 24 4.26 441 420 48.78 1 2 66.67 545259 TCGA-AB-2979 AML33 20 38640363 38640363 C A SNP - - - - - - - - - - - - - - - tier2 2548 4 0.16 4463 473 9.57 0 0 NA 545259 TCGA-AB-2979 AML33 20 39187966 39187966 G T SNP PLCG1 NM_002660.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11730 NULL 0 - - - no_errors tier3 1660 38 2.24 790 605 43.34 0 0 NA 545259 TCGA-AB-2979 AML33 20 43349032 43349032 G C SNP RBPJL NM_014276.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19945 NULL 0.56 - - - no_errors tier3 830 29 3.38 360 299 45.37 0 0 NA 545259 TCGA-AB-2979 AML33 20 51033064 51033064 C - DEL TSHZ2 NM_173485.4 human genbank 54_36p 1 validated intronic c.40+9785 e1+9785 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 20 62064879 62064879 G A SNP ZNF512B NM_020713.1 human genbank 54_36p -1 provisional intronic c.1968+13 e11+13 0.003 - - - no_errors tier2 103 1 0.96 92 48 34.29 0 0 0 545259 TCGA-AB-2979 AML33 21 13648583 13648583 T C SNP LOC100129305 XM_001714760.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*39761 NULL 0.167 - - - no_errors tier3 161 3 1.82 129 110 46.03 0 0 NA 545259 TCGA-AB-2979 AML33 21 21347250 21347250 A - DEL NCAM2 NM_004540.2 human genbank 54_36p 1 reviewed intronic c.55+54443 e1+54443 0.012 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 545259 TCGA-AB-2979 AML33 21 22058629 22058629 G A SNP - - - - - - - - - - - - - - - tier3 971 22 2.21 1308 992 43.09 0 0 NA 545259 TCGA-AB-2979 AML33 21 22144274 22144274 G A SNP - - - - - - - - - - - - - - - tier3 1138 21 1.81 940 779 45.32 0 0 NA 545259 TCGA-AB-2979 AML33 21 23323290 23323290 C T SNP - - - - - - - - - - - - - - - tier3 284 6 2.06 91 65 41.67 0 0 NA 545259 TCGA-AB-2979 AML33 21 35855587 35855587 A G SNP ENSG00000217521 ENST00000404239 human ensembl 54_36p -1 known 3_prime_flanking_region c.*38313 NULL 0.001 - - - no_coding_region:pseudogene tier2 953 28 2.85 885 738 45.47 0 0 NA 545259 TCGA-AB-2979 AML33 21 38602337 38602337 G A SNP LOC100131955 XM_001715532.1 human genbank 54_36p 1 model intronic c.63+6920 e1+6920 0.002 - - - no_errors tier3 750 22 2.84 763 593 43.51 0 0 NA 545259 TCGA-AB-2979 AML33 21 43545886 43545886 C T SNP C21orf136 XM_001722584.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*27120 NULL 0.009 - - - no_errors tier3 201 3 1.47 126 68 35.05 0 0 NA 545259 TCGA-AB-2979 AML33 22 21787340 21787340 A G SNP GNAZ NM_002073.2 human genbank 54_36p 1 reviewed intronic c.724-7934 e2-7934 0.135 - - - no_errors tier2 151 5 3.21 181 143 44.14 0 0 NA 545259 TCGA-AB-2979 AML33 22 42553862 42553862 A C SNP SULT4A1 NM_014351.3 human genbank 54_36p -1 reviewed intronic c.743-536 e7-536 0.002 - - - no_errors tier2 771 18 2.28 620 489 44.09 0 0 NA 478908 TCGA-AB-2980 AML11 X 676156 676156 G T SNP - - - - - - - - - - - - - - - tier3 1586 0 0 1366 559 29.02 0 0 NA 478908 TCGA-AB-2980 AML11 X 5252565 5252565 T G SNP ENSG00000218705 ENST00000407168 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17396 NULL 0 - - - no_coding_region:pseudogene tier3 473 0 0 247 339 57.85 0 0 NA 478908 TCGA-AB-2980 AML11 X 11884237 11884237 C T SNP LOC100130046 XM_001721046.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*41729 NULL 0 - - - no_errors tier3 1024 2 0.19 823 384 31.81 0 0 NA 478908 TCGA-AB-2980 AML11 X 91365022 91365022 C A SNP PCDH11X NM_032968.1 human genbank 54_36p 1 reviewed intronic c.3114+21912 e3+21912 0 - - - no_errors tier3 694 0 0 516 159 23.56 0 0 NA 478908 TCGA-AB-2980 AML11 X 109577945 109577945 C T SNP RGAG1 NM_020769.1 human genbank 54_36p 1 provisional intronic c.1-2506 e1-2506 0.303 - - - no_errors tier3 750 0 0 320 521 61.95 0 0 NA 478908 TCGA-AB-2980 AML11 X 114799545 114799545 G C SNP LOC642357 XR_016681.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-43842 NULL 0.105 - - - no_errors tier2 460 0 0 182 350 65.79 0 0 NA 478908 TCGA-AB-2980 AML11 X 131948619 131948619 G A SNP HS6ST2 ENST00000319809 human ensembl 54_36p -1 known 5_prime_flanking_region c.-28317 NULL 0.036 - - - no_errors tier3 394 0 0 222 270 54.77 0 0 NA 478908 TCGA-AB-2980 AML11 X 134538245 134538245 A G SNP DDX26B NM_182540.4 human genbank 54_36p 1 validated intronic c.1774-539 e14-539 0.086 - - - no_errors tier3 932 1 0.11 434 478 52.35 0 0 0 478908 TCGA-AB-2980 AML11 X 135389095 135389095 C T SNP BRS3 NM_001727.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-8845 NULL 0.001 - - - no_errors tier3 938 0 0 432 738 63.02 0 0 NA 478908 TCGA-AB-2980 AML11 X 141919216 141919216 C T SNP SPANXN4 NM_001009613.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22251 NULL 0 - - - no_errors tier2 831 1 0.12 620 128 17.11 0 0 NA 478908 TCGA-AB-2980 AML11 X 149860629 149860629 A T SNP CD99L2 NM_031462.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42910 NULL 0.001 - - - no_errors tier3 428 0 0 404 492 54.73 0 0 NA 478908 TCGA-AB-2980 AML11 1 4647818 4647818 C T SNP AJAP1 NM_001042478.1 human genbank 54_36p 1 validated intronic c.30-24002 e2-24002 0.004 - - - no_errors tier3 1036 1 0.1 1218 612 33.41 0 0 NA 478908 TCGA-AB-2980 AML11 1 4983475 4983475 C T SNP - - - - - - - - - - - - - - - tier3 1264 0 0 1080 457 29.71 0 0 NA 478908 TCGA-AB-2980 AML11 1 9131465 9131465 C T SNP GPR157 NM_024980.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19792 NULL 0 - - - no_errors tier2 760 0 0 755 315 29.44 1 0 0 478908 TCGA-AB-2980 AML11 1 12557296 12557296 G A SNP DHRS3 NM_004753.4 human genbank 54_36p -1 validated intronic c.699-1828 e5-1828 0.023 - - - no_errors tier3 740 2 0.27 759 318 29.53 0 0 0 478908 TCGA-AB-2980 AML11 1 13775829 13775829 G A SNP PDPN NM_006474.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-7059 NULL 0 - - - no_errors tier3 1048 0 0 782 294 27.27 0 0 NA 478908 TCGA-AB-2980 AML11 1 18446515 18446515 G A SNP IGSF21 NM_032880.2 human genbank 54_36p 1 provisional intronic c.183+19424 e2+19424 0.01 - - - no_errors tier3 1282 1 0.08 1446 537 27.05 0 0 NA 478908 TCGA-AB-2980 AML11 1 41644415 41644415 G A SNP FOXO6 ENST00000372591 human ensembl 54_36p 1 known 3_prime_flanking_region c.*23275 NULL 0.099 - - - no_errors tier2 1129 0 0 1077 346 24.16 0 0 NA 478908 TCGA-AB-2980 AML11 1 74522248 74522248 G A SNP TNNI3K NM_015978.1 human genbank 54_36p 1 validated intronic c.444+12268 e5+12268 0 - - - no_errors tier3 1135 0 0 709 251 26.15 0 0 NA 478908 TCGA-AB-2980 AML11 1 75319980 75319980 C T SNP LHX8 NM_001001933.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49008 NULL 0.001 - - - no_errors tier3 1610 2 0.12 1059 512 32.53 0 0 NA 478908 TCGA-AB-2980 AML11 1 77772134 77772134 C A SNP AK5 NM_174858.2 human genbank 54_36p 1 reviewed intronic c.1429-1986 e13-1986 0.029 - - - no_errors tier2 838 0 0 714 264 26.97 0 0 NA 478908 TCGA-AB-2980 AML11 1 78746805 78746805 G A SNP PTGFR NM_000959.3 human genbank 54_36p 1 reviewed intronic c.798+14991 e1+14991 0.003 - - - no_errors tier3 1441 1 0.07 959 383 28.54 0 0 NA 478908 TCGA-AB-2980 AML11 1 95909110 95909110 A C SNP - - - - - - - - - - - - - - - tier3 650 0 0 399 148 27.06 0 0 NA 478908 TCGA-AB-2980 AML11 1 111219635 111219635 C T SNP CD53 NM_000560.3 human genbank 54_36p 1 reviewed intronic c.1+2242 e0+2242 0 - - - no_errors tier3 1168 0 0 850 371 30.38 1 0 0 478908 TCGA-AB-2980 AML11 1 117905415 117905415 T G SNP FAM46C NM_017709.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-61599 NULL 0.001 - - - no_errors tier3 471 1 0.21 592 184 23.65 0 0 NA 478908 TCGA-AB-2980 AML11 1 154859787 154859787 C T SNP HAPLN2 NM_021817.2 human genbank 54_36p 1 validated intronic c.1-96 e1-96 0.007 - - - no_errors tier3 1530 0 0 1176 407 25.69 0 0 NA 478908 TCGA-AB-2980 AML11 1 160733003 160733003 C T SNP UHMK1 NM_175866.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1412 NULL 0.011 - - - no_errors tier2 1123 2 0.18 925 337 26.66 0 0 NA 478908 TCGA-AB-2980 AML11 1 181417261 181417261 G C SNP LAMC2 NM_005562.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-4850 NULL 0.005 - - - no_errors tier3 480 0 0 328 118 26.4 0 0 NA 478908 TCGA-AB-2980 AML11 1 181662183 181662183 G T SNP NMNAT2 NM_015039.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-8158 NULL 0.076 - - - no_errors tier3 1460 0 0 1060 438 29.18 0 0 NA 478908 TCGA-AB-2980 AML11 1 188435890 188435890 A T SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional intronic c.961+25945 e5+25945 0.001 - - - no_errors tier3 510 0 0 327 132 28.7 0 0 NA 478908 TCGA-AB-2980 AML11 1 200027142 200027142 G C SNP NAV1 NM_020443.3 human genbank 54_36p 1 reviewed intronic c.3321+625 e13+625 0.01 - - - no_errors tier3 765 1 0.13 765 265 25.7 2 0 0 478908 TCGA-AB-2980 AML11 1 200869222 200869222 G T SNP SYT2 NM_177402.1 human genbank 54_36p -1 validated intronic c.1-27682 e1-27682 0.001 - - - no_errors tier3 511 0 0 441 164 27.11 0 0 NA 478908 TCGA-AB-2980 AML11 1 207395307 207395307 C T SNP ENSG00000219339 ENST00000402858 human ensembl 54_36p 1 known 5_prime_flanking_region c.-17675 NULL 1 - - - no_coding_region:pseudogene tier3 900 0 0 679 284 29.49 0 0 NA 478908 TCGA-AB-2980 AML11 1 211186777 211186777 T C SNP VASH2 NM_024749.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-4731 NULL 0.003 - - - no_errors tier3 1113 2 0.18 897 333 27.03 0 0 NA 478908 TCGA-AB-2980 AML11 1 222553937 222553937 C T SNP NVL NM_002533.2 human genbank 54_36p -1 validated intronic c.1062+950 e10+950 0.025 - - - no_errors tier2 1305 2 0.15 1096 304 21.71 0 0 0 478908 TCGA-AB-2980 AML11 1 230368651 230368651 A G SNP - - - - - - - - - - - - - - - tier3 1710 0 0 1231 499 28.79 0 0 NA 478908 TCGA-AB-2980 AML11 1 239491076 239491076 G A SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.78+94546 e1+94546 0.001 - - - no_errors tier3 1407 0 0 1380 454 24.74 0 0 NA 478908 TCGA-AB-2980 AML11 2 9811138 9811138 T C SNP ENSG00000200034 ENST00000363164 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12775 NULL 0.002 - - - no_errors tier3 808 0 0 1053 136 11.42 0 0 NA 478908 TCGA-AB-2980 AML11 2 22040854 22040854 A T SNP ENSG00000222621 ENST00000410689 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41188 NULL 0.003 - - - no_errors tier3 1517 0 0 955 356 27.15 0 0 NA 478908 TCGA-AB-2980 AML11 2 27923420 27923420 A C SNP RBKS NM_022128.1 human genbank 54_36p -1 reviewed missense c.342 p.N114K 1 "HMMPfam_PfkB,superfamily_SSF53613" "PatternScan_PFKB_KINASES_1,PatternScan_PFKB_KINASES_2,HMMPfam_PfkB,superfamily_SSF53613" - no_errors tier1 1349 0 1449 514 26.18 5 3 37.5 478908 TCGA-AB-2980 AML11 2 29911343 29911343 G C SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.667+85020 e1+85020 0.113 - - - no_errors tier3 2298 0 0 1938 856 30.62 0 0 NA 478908 TCGA-AB-2980 AML11 2 56418210 56418210 C T SNP CCDC85A NM_001080433.1 human genbank 54_36p 1 provisional intronic c.1241-5308 e3-5308 0 - - - no_errors tier3 1067 1 0.09 654 272 29.37 0 0 NA 478908 TCGA-AB-2980 AML11 2 60509191 60509191 G A SNP BCL11A NM_022893.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*31852 NULL 0 - - - no_errors tier3 1647 0 0 1431 493 25.62 0 0 NA 478908 TCGA-AB-2980 AML11 2 64740072 64740072 A G SNP SERTAD2 NM_014755.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22563 NULL 0.037 - - - no_errors tier3 966 0 0 781 312 28.52 0 0 0 478908 TCGA-AB-2980 AML11 2 71594589 71594589 C G SNP DYSF NM_003494.1 human genbank 54_36p 1 reviewed intronic c.663+30 e6+30 0 - - - no_errors tier3 1488 1 0.07 1511 514 25.38 0 0 NA 478908 TCGA-AB-2980 AML11 2 80562520 80562520 A T SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1293+62283 e8+62283 0 - - - no_errors tier2 1053 0 0 618 233 27.38 0 0 NA 478908 TCGA-AB-2980 AML11 2 115292819 115292819 T C SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+375934 e1+375934 0 - - - no_errors tier3 1254 0 0 1145 402 25.97 0 0 NA 478908 TCGA-AB-2980 AML11 2 115770634 115770634 C T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.61-12651 e2-12651 0.002 - - - no_errors tier3 1402 0 0 900 354 28.18 0 0 NA 478908 TCGA-AB-2980 AML11 2 116269321 116269321 G A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.1700+3919 e19+3919 0 - - - no_errors tier3 1263 5 0.39 755 288 27.59 0 0 NA 478908 TCGA-AB-2980 AML11 2 129848228 129848228 C T SNP - - - - - - - - - - - - - - - tier3 1011 0 0 835 432 34.07 0 0 NA 478908 TCGA-AB-2980 AML11 2 130754748 130754748 G A SNP ENSG00000208411 ENST00000385676 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5183 NULL 0.953 - - - pseudogene tier3 808 1 0.12 434 57 11.61 0 0 NA 478908 TCGA-AB-2980 AML11 2 130754763 130754763 A G SNP ENSG00000208411 ENST00000385676 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5198 NULL 0.989 - - - pseudogene tier3 803 0 0 424 57 11.85 0 0 NA 478908 TCGA-AB-2980 AML11 2 133227881 133227881 C T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.5128+19978 e14+19978 0 - - - no_errors tier3 930 1 0.11 905 359 28.2 0 0 NA 478908 TCGA-AB-2980 AML11 2 133756675 133756675 G A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.143+20404 e2+20404 0.004 - - - no_errors tier3 1224 0 0 1001 351 25.96 0 0 NA 478908 TCGA-AB-2980 AML11 2 137088844 137088844 C T SNP ENSG00000221762 ENST00000408835 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*30304 NULL 0.995 - - - no_errors tier3 1761 3 0.17 1300 553 29.8 0 0 NA 478908 TCGA-AB-2980 AML11 2 139592384 139592384 G T SNP - - - - - - - - - - - - - - - tier3 1106 0 0 799 314 28.16 0 0 NA 478908 TCGA-AB-2980 AML11 2 150230555 150230555 G A SNP LOC642340 XM_930713.1 human genbank 54_36p 1 model intronic c.209-77923 e2-77923 0 - - - no_errors tier2 1159 1 0.09 744 342 31.49 0 0 NA 478908 TCGA-AB-2980 AML11 2 150988258 150988258 T A SNP RND3 NM_005168.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*46489 NULL 0.002 - - - no_errors tier3 1367 1 0.07 1090 390 26.35 0 0 NA 478908 TCGA-AB-2980 AML11 2 158735585 158735585 G A SNP UPP2 NM_173355.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*35937 NULL 0.002 - - - no_errors tier3 1486 0 0 1146 466 28.89 0 1 100 478908 TCGA-AB-2980 AML11 2 163301606 163301606 C A SNP KCNH7 NM_033272.2 human genbank 54_36p -1 reviewed intronic c.307+99687 e2+99687 0 - - - no_errors tier3 1089 0 0 754 204 21.27 0 0 NA 478908 TCGA-AB-2980 AML11 2 164546492 164546492 C T SNP - - - - - - - - - - - - - - - tier3 682 0 0 569 215 27.42 0 0 NA 478908 TCGA-AB-2980 AML11 2 172862318 172862318 G T SNP - - - - - - - - - - - - - - - tier3 985 0 0 1077 405 27.33 0 0 0 478908 TCGA-AB-2980 AML11 2 176944053 176944053 T C SNP MTX2 NM_006554.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*33415 NULL 1 - - - no_errors tier2 1814 1 0.06 1361 533 28.14 0 0 NA 478908 TCGA-AB-2980 AML11 2 177341843 177341843 T A SNP LOC100131991 XM_001722203.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*38165 NULL 0.002 - - - pseudogene tier3 1011 1 0.1 890 368 29.23 0 0 NA 478908 TCGA-AB-2980 AML11 2 184100035 184100035 C T SNP - - - - - - - - - - - - - - - tier3 1593 0 0 1015 467 31.49 0 0 NA 478908 TCGA-AB-2980 AML11 2 198942946 198942946 C G SNP - - - - - - - - - - - - - - - tier3 771 0 0 523 236 31.09 0 0 NA 478908 TCGA-AB-2980 AML11 2 202343289 202343289 C T SNP ALS2 NM_020919.1 human genbank 54_36p -1 reviewed intronic c.1-1376 e1-1376 0.001 - - - no_errors tier3 1081 0 0 848 246 22.45 10 0 0 478908 TCGA-AB-2980 AML11 2 217621089 217621089 C T SNP - - - - - - - - - - - - - - - tier3 750 2 0.27 854 373 30.35 0 0 NA 478908 TCGA-AB-2980 AML11 2 228158919 228158919 G C SNP AGFG1 NM_004504.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*31464 NULL 0.048 - - - no_errors tier3 1661 1 0.06 1263 553 30.42 0 0 NA 478908 TCGA-AB-2980 AML11 2 230259513 230259513 C T SNP DNER NM_139072.3 human genbank 54_36p -1 validated intronic c.276+27595 e1+27595 0 - - - no_errors tier3 1689 0 0 1317 618 31.89 0 0 NA 478908 TCGA-AB-2980 AML11 2 235430647 235430647 C T SNP - - - - - - - - - - - - - - - tier3 702 0 0 745 272 26.72 0 0 NA 478908 TCGA-AB-2980 AML11 2 237521413 237521413 C G SNP - - - - - - - - - - - - - - - tier3 929 0 0 846 327 27.85 0 0 NA 478908 TCGA-AB-2980 AML11 3 22235127 22235127 C G SNP - - - - - - - - - - - - - - - tier3 1060 0 0 919 337 26.83 0 0 NA 478908 TCGA-AB-2980 AML11 3 22959493 22959493 T C SNP - - - - - - - - - - - - - - - tier3 882 1 0.11 622 250 28.64 0 0 NA 478908 TCGA-AB-2980 AML11 3 23488135 23488135 G A SNP UBE2E2 NM_152653.3 human genbank 54_36p 1 validated intronic c.228-27968 e3-27968 0 - - - no_errors tier3 1489 2 0.13 897 394 30.5 0 0 0 478908 TCGA-AB-2980 AML11 3 27043554 27043554 T C SNP - - - - - - - - - - - - - - - tier3 1575 0 0 1278 561 30.49 0 0 NA 478908 TCGA-AB-2980 AML11 3 39200931 39200931 T C SNP XIRP1 NM_194293.2 human genbank 54_36p -1 provisional silent c.5010 p.P1670 0.979 NULL HMMPfam_Xin - no_errors tier1 752 2 0.26 819 359 30.09 NA 478908 TCGA-AB-2980 AML11 3 41836047 41836047 G A SNP ULK4 NM_017886.2 human genbank 54_36p -1 validated intronic c.1765-45 e18-45 0.916 - - - no_errors tier3 2883 2 0.07 2732 568 17.2 0 0 0 478908 TCGA-AB-2980 AML11 3 46682316 46682316 C T SNP LOC100134405 XM_001726032.1 human genbank 54_36p 1 model intronic c.147+11131 e3+11131 0.02 - - - no_start_codon:pseudogene:no_stop_codon tier3 1317 0 0 1461 607 29.35 0 0 NA 478908 TCGA-AB-2980 AML11 3 53459577 53459577 G T SNP CACNA1D NM_000720.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44657 NULL 0 - - - no_errors tier3 658 1 0.15 461 198 30.05 1 0 0 478908 TCGA-AB-2980 AML11 3 54908903 54908903 T C SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed missense c.2417 p.L806P 1 NULL "HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Cache_1,HMMPfam_VWA_N,superfamily_vWA-like" - no_errors tier1 1104 0 920 437 32.16 NA 478908 TCGA-AB-2980 AML11 3 62052487 62052487 A G SNP PTPRG NM_002841.3 human genbank 54_36p 1 reviewed intronic c.615+13515 e5+13515 0 - - - no_errors tier3 641 0 0 472 214 31.2 1 0 0 478908 TCGA-AB-2980 AML11 3 63132712 63132712 C T SNP - - - - - - - - - - - - - - - tier3 1260 0 0 943 306 24.48 0 0 NA 478908 TCGA-AB-2980 AML11 3 78547325 78547325 G C SNP - - - - - - - - - - - - - - - tier3 1365 0 0 932 410 30.55 0 0 NA 478908 TCGA-AB-2980 AML11 3 80216740 80216740 G T SNP - - - - - - - - - - - - - - - tier3 759 0 0 437 165 27.41 0 0 NA 478908 TCGA-AB-2980 AML11 3 117209287 117209287 G A SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.514+11765 e3+11765 0 - - - no_errors tier3 1490 0 0 1323 571 30.12 0 0 NA 478908 TCGA-AB-2980 AML11 3 121405540 121405540 T C SNP GPR156 NM_153002.1 human genbank 54_36p -1 provisional intronic c.234-10579 e3-10579 0 - - - no_errors tier3 1088 1 0.09 887 341 27.75 0 0 NA 478908 TCGA-AB-2980 AML11 3 126004412 126004412 A C SNP ITGB5 NM_002213.3 human genbank 54_36p -1 provisional intronic c.1264-6058 e10-6058 0.013 - - - no_errors tier3 809 0 0 830 296 26.24 0 0 0 478908 TCGA-AB-2980 AML11 3 132220212 132220212 G A SNP ASTE1 NM_014065.2 human genbank 54_36p -1 validated silent c.1341 p.T447 0.869 NULL "HMMPfam_XPG_N,superfamily_SSF88723" - no_errors tier1 928 1 0.11 845 316 27.17 1 3 75 478908 TCGA-AB-2980 AML11 3 135279737 135279737 G T SNP SLCO2A1 NM_005630.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-48401 NULL 0.007 - - - no_errors tier3 683 0 0 642 309 32.49 0 0 NA 478908 TCGA-AB-2980 AML11 3 144894631 144894631 T C SNP SLC9A9 NM_173653.2 human genbank 54_36p -1 validated intronic c.649+93 e5+93 0.047 - - - no_errors tier2 1360 0 0 1223 195 13.72 0 0 NA 478908 TCGA-AB-2980 AML11 3 162784395 162784395 C T SNP - - - - - - - - - - - - - - - tier3 1417 0 0 1043 456 30.42 0 0 NA 478908 TCGA-AB-2980 AML11 3 170827132 170827132 T C SNP MDS1 NM_004991.2 human genbank 54_36p -1 validated intronic c.37+36686 e1+36686 0 - - - no_errors tier3 973 2 0.21 770 277 26.46 0 0 NA 478908 TCGA-AB-2980 AML11 3 178614849 178614849 G A SNP - - - - - - - - - - - - - - - tier2 1472 0 0 844 348 29.15 0 0 NA 478908 TCGA-AB-2980 AML11 3 179957165 179957165 G A SNP KCNMB2 NM_005832.3 human genbank 54_36p 1 reviewed intronic c.1-38459 e1-38459 0.015 - - - no_errors tier3 1089 2 0.18 612 209 25.46 0 0 NA 478908 TCGA-AB-2980 AML11 3 192376612 192376612 C T SNP OSTN NM_198184.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-36404 NULL 0.664 - - - no_errors tier3 913 0 0 541 190 25.99 0 0 NA 478908 TCGA-AB-2980 AML11 4 413915 413915 T C SNP ABCA11P ENST00000400168 human ensembl 54_36p -1 known intronic c.1-3153 e1-3153 0 - - - no_errors tier3 819 0 0 480 243 33.61 4 2 33.33 478908 TCGA-AB-2980 AML11 4 9696906 9696906 C G SNP WDR1 NM_017491.4 human genbank 54_36p -1 reviewed intronic c.951+1523 e8+1523 0.004 - - - no_errors tier3 1039 0 0 1330 557 29.5 1 2 66.67 478908 TCGA-AB-2980 AML11 4 11177871 11177871 A G SNP - - - - - - - - - - - - - - - tier3 911 2 0.22 615 380 38.15 0 0 NA 478908 TCGA-AB-2980 AML11 4 19680909 19680909 A C SNP - - - - - - - - - - - - - - - tier3 1254 0 0 1139 486 29.91 0 0 NA 478908 TCGA-AB-2980 AML11 4 24369857 24369857 G A SNP SOD3 NM_003102.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40385 NULL 0.017 - - - no_errors tier3 634 0 0 549 229 29.36 0 0 NA 478908 TCGA-AB-2980 AML11 4 35470015 35470015 G T SNP - - - - - - - - - - - - - - - tier3 1049 0 0 344 161 31.88 0 0 NA 478908 TCGA-AB-2980 AML11 4 36405530 36405530 G A SNP - - - - - - - - - - - - - - - tier3 1216 0 0 685 224 24.62 0 0 NA 478908 TCGA-AB-2980 AML11 4 47886478 47886478 T C SNP TEC NM_003215.2 human genbank 54_36p -1 reviewed intronic c.139-13518 e2-13518 0.002 - - - no_errors tier3 1214 0 0 874 385 30.58 10 7 41.18 478908 TCGA-AB-2980 AML11 4 52979500 52979500 A C SNP - - - - - - - - - - - - - - - tier3 1361 4 0.29 1194 466 28.06 0 0 NA 478908 TCGA-AB-2980 AML11 4 62179814 62179814 T C SNP LPHN3 NM_015236.4 human genbank 54_36p 1 reviewed intronic c.269+44061 e2+44061 0 - - - no_errors tier3 1062 0 0 548 246 30.94 0 2 100 478908 TCGA-AB-2980 AML11 4 73186273 73186273 A T SNP NPFFR2 NM_004885.1 human genbank 54_36p 1 reviewed intronic c.300-26893 e2-26893 0.002 - - - no_errors tier3 563 0 0 391 194 33.11 0 0 NA 478908 TCGA-AB-2980 AML11 4 86224038 86224038 C G SNP ENSG00000201901 ENST00000365031 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16635 NULL 0 - - - no_errors tier2 690 1 0.14 421 153 26.66 0 0 NA 478908 TCGA-AB-2980 AML11 4 94168976 94168976 C T SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.245-56193 e3-56193 0 - - - no_errors tier2 1685 0 0 862 299 25.75 0 0 NA 478908 TCGA-AB-2980 AML11 4 100068115 100068115 C T SNP EIF4E NM_001968.1 human genbank 54_36p -1 validated intronic c.18+1154 e1+1154 0 - - - no_errors tier3 1341 0 0 813 325 28.53 4 0 0 478908 TCGA-AB-2980 AML11 4 106808430 106808430 G C SNP GSTCD NM_001031720.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49790 NULL 0.001 - - - no_errors tier3 996 1 0.1 790 267 25.24 0 0 NA 478908 TCGA-AB-2980 AML11 4 112121709 112121709 C T SNP - - - - - - - - - - - - - - - tier3 1121 1 0.09 766 294 27.74 0 0 NA 478908 TCGA-AB-2980 AML11 4 126013347 126013347 C A SNP - - - - - - - - - - - - - - - tier3 688 2 0.29 471 244 34.08 0 0 NA 478908 TCGA-AB-2980 AML11 4 130577080 130577080 A G SNP - - - - - - - - - - - - - - - tier3 828 0 0 536 245 31.37 0 0 NA 478908 TCGA-AB-2980 AML11 4 131951132 131951132 C T SNP - - - - - - - - - - - - - - - tier2 1748 1 0.06 1378 237 14.67 0 0 NA 478908 TCGA-AB-2980 AML11 4 136783113 136783113 A G SNP - - - - - - - - - - - - - - - tier3 486 0 0 283 83 22.68 0 0 NA 478908 TCGA-AB-2980 AML11 4 155090799 155090799 G A SNP - - - - - - - - - - - - - - - tier3 1328 1 0.08 1130 566 33.37 0 0 NA 478908 TCGA-AB-2980 AML11 4 158334654 158334654 C A SNP GRIA2 NM_000826.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26991 NULL 0.001 - - - no_errors tier3 1187 2 0.17 844 407 32.48 0 0 NA 478908 TCGA-AB-2980 AML11 4 164011462 164011462 A T SNP - - - - - - - - - - - - - - - tier3 1240 0 0 800 306 27.64 0 0 NA 478908 TCGA-AB-2980 AML11 4 169764798 169764798 G A SNP PALLD NM_016081.3 human genbank 54_36p 1 validated intronic c.909-61118 e2-61118 0 - - - no_errors tier3 820 0 0 612 263 29.95 0 0 NA 478908 TCGA-AB-2980 AML11 4 189770638 189770638 G A SNP - - - - - - - - - - - - - - - tier2 918 1 0.11 600 292 32.74 0 0 NA 478908 TCGA-AB-2980 AML11 5 3903250 3903250 G A SNP - - - - - - - - - - - - - - - tier3 955 0 0 606 288 32.21 0 0 NA 478908 TCGA-AB-2980 AML11 5 8017072 8017072 T C SNP ENSG00000199773 ENST00000362903 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16187 NULL 0.045 - - - no_errors tier3 1045 1 0.1 794 366 31.55 0 0 NA 478908 TCGA-AB-2980 AML11 5 9767481 9767481 C T SNP ENSG00000222054 ENST00000410122 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46547 NULL 0.001 - - - no_errors tier3 1228 2 0.16 1238 187 13.11 0 0 NA 478908 TCGA-AB-2980 AML11 5 14160066 14160066 T C SNP TRIO NM_007118.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36769 NULL 0.124 - - - no_errors tier3 1725 3 0.17 1596 800 33.39 0 0 NA 478908 TCGA-AB-2980 AML11 5 15378962 15378962 G A SNP - - - - - - - - - - - - - - - tier3 911 0 0 617 263 29.89 0 0 NA 478908 TCGA-AB-2980 AML11 5 18022045 18022045 G A SNP - - - - - - - - - - - - - - - tier3 456 0 0 341 151 30.69 0 0 NA 478908 TCGA-AB-2980 AML11 5 25101427 25101427 C T SNP - - - - - - - - - - - - - - - tier3 715 0 0 384 145 27.41 0 0 NA 478908 TCGA-AB-2980 AML11 5 35050840 35050840 G A SNP AGXT2 NM_031900.2 human genbank 54_36p -1 reviewed intronic c.964-859 e10-859 0.001 - - - no_errors tier3 1551 0 0 1085 432 28.46 0 0 NA 478908 TCGA-AB-2980 AML11 5 36780218 36780218 G A SNP - - - - - - - - - - - - - - - tier2 835 0 0 744 318 29.92 0 0 NA 478908 TCGA-AB-2980 AML11 5 49622719 49622719 G A SNP - - - - - - - - - - - - - - - tier3 1198 2 0.17 823 394 32.37 0 0 NA 478908 TCGA-AB-2980 AML11 5 53351027 53351027 G A SNP ARL15 NM_019087.2 human genbank 54_36p -1 validated intronic c.462+93762 e4+93762 0 - - - no_errors tier3 975 0 0 640 162 20.2 5 0 0 478908 TCGA-AB-2980 AML11 5 62961529 62961529 C T SNP - - - - - - - - - - - - - - - tier3 885 0 0 463 213 31.51 0 0 NA 478908 TCGA-AB-2980 AML11 5 63618324 63618324 A G SNP RNF180 ENST00000389100 human ensembl 54_36p 1 known intronic c.1228-38445 e5-38445 0.014 - - - no_errors tier3 1346 0 0 1037 442 29.86 0 0 NA 478908 TCGA-AB-2980 AML11 5 71716484 71716484 G T SNP PTCD2 NM_024754.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*26474 NULL 0.001 - - - no_errors tier3 1095 0 0 1181 496 29.56 0 0 NA 478908 TCGA-AB-2980 AML11 5 73907645 73907645 G C SNP - - - - - - - - - - - - - - - tier2 1019 0 0 938 276 22.73 0 0 NA 478908 TCGA-AB-2980 AML11 5 94527390 94527390 C T SNP MCTP1 NM_024717.2 human genbank 54_36p -1 validated intronic c.720+117926 e1+117926 0 - - - no_errors tier3 1417 0 0 978 310 24.07 0 0 NA 478908 TCGA-AB-2980 AML11 5 103807196 103807196 C T SNP - - - - - - - - - - - - - - - tier2 1221 1 0.08 801 260 24.51 0 0 NA 478908 TCGA-AB-2980 AML11 5 108201907 108201907 G A SNP FER NM_005246.2 human genbank 54_36p 1 reviewed intronic c.481+2500 e3+2500 0.003 - - - no_errors tier3 956 0 0 540 317 36.99 0 0 0 478908 TCGA-AB-2980 AML11 5 126679794 126679794 G A SNP MEGF10 NM_032446.2 human genbank 54_36p 1 validated intronic c.1-15088 e1-15088 0 - - - no_errors tier2 1608 3 0.19 1348 523 27.94 0 0 NA 478908 TCGA-AB-2980 AML11 5 131436049 131436049 G A SNP CSF2 NM_000758.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1367 NULL 0 - - - no_errors tier3 665 0 0 937 338 26.51 0 0 NA 478908 TCGA-AB-2980 AML11 5 131541176 131541176 A C SNP ENSG00000214459 ENST00000398366 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21872 NULL 0.001 - - - no_coding_region:pseudogene tier3 840 0 0 609 226 27.03 0 0 NA 478908 TCGA-AB-2980 AML11 5 143676186 143676186 C T SNP KCTD16 NM_020768.3 human genbank 54_36p 1 validated intronic c.832+108884 e1+108884 0 - - - no_errors tier3 1176 4 0.34 976 398 28.97 0 0 NA 478908 TCGA-AB-2980 AML11 5 148058909 148058909 C T SNP HTR4 NM_001040173.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-62139 NULL 0.001 - - - no_errors tier3 1051 2 0.19 733 214 22.6 0 0 NA 478908 TCGA-AB-2980 AML11 5 156316758 156316758 C G SNP TIMD4 NM_138379.1 human genbank 54_36p -1 provisional intronic c.59-2413 e2-2413 0.001 - - - no_errors tier3 562 0 0 513 300 36.9 0 0 NA 478908 TCGA-AB-2980 AML11 5 156898454 156898454 C T SNP ADAM19 NM_033274.3 human genbank 54_36p -1 reviewed intronic c.252-877 e4-877 0 - - - no_errors tier3 1163 1 0.09 1452 632 30.33 1 0 0 478908 TCGA-AB-2980 AML11 5 157782856 157782856 C T SNP - - - - - - - - - - - - - - - tier3 816 0 0 926 185 16.61 0 0 NA 478908 TCGA-AB-2980 AML11 5 158935340 158935340 C T SNP - - - - - - - - - - - - - - - tier3 1404 1 0.07 1136 522 31.48 0 0 NA 478908 TCGA-AB-2980 AML11 5 175985912 175985912 G A SNP SNCB NM_001001502.1 human genbank 54_36p -1 reviewed intronic c.282+93 e3+93 0 - - - no_errors tier3 652 1 0.15 785 462 36.96 0 0 NA 478908 TCGA-AB-2980 AML11 5 177072631 177072631 A - DEL FAM153A ENST00000360669 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*11089 NULL 0.689 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 6 9511975 9511975 G A SNP - - - - - - - - - - - - - - - tier2 874 0 0 554 276 33.21 0 0 NA 478908 TCGA-AB-2980 AML11 6 23504319 23504319 G T SNP - - - - - - - - - - - - - - - tier3 1449 1 0.07 1193 152 11.3 0 0 NA 478908 TCGA-AB-2980 AML11 6 27814053 27814053 T A SNP ENSG00000216915 ENST00000407924 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-27814053 NULL 0.998 - - - no_coding_region:pseudogene tier2 736 16 2.12 640 225 26.01 0 0 0 478908 TCGA-AB-2980 AML11 6 28577160 28577160 G T SNP GPX5 NM_001509.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-24610 NULL 0 - - - no_errors tier3 705 0 0 551 198 26.44 0 1 100 478908 TCGA-AB-2980 AML11 6 39411455 39411455 G A SNP KIF6 NM_145027.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*831 NULL 0.003 - - - no_errors tier3 1431 0 0 1155 405 25.91 1 0 0 478908 TCGA-AB-2980 AML11 6 40017275 40017275 G A SNP MOCS1 NM_005942.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-13980 NULL 0.002 - - - no_errors tier3 854 0 0 588 237 28.73 0 0 NA 478908 TCGA-AB-2980 AML11 6 44545486 44545486 A G SNP LOC100128935 XM_001725735.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-3133 NULL 0 - - - no_errors tier3 946 0 0 1057 395 27.2 0 0 NA 478908 TCGA-AB-2980 AML11 6 49546950 49546950 G A SNP CENPQ NM_018132.3 human genbank 54_36p 1 validated intronic c.157+250 e2+250 0.087 - - - no_errors tier3 1496 0 0 1087 430 28.35 0 0 0 478908 TCGA-AB-2980 AML11 6 50660075 50660075 C A SNP - - - - - - - - - - - - - - - tier2 915 0 0 729 106 12.68 0 0 NA 478908 TCGA-AB-2980 AML11 6 53883941 53883941 G A SNP LRRC1 NM_018214.4 human genbank 54_36p 1 validated intronic c.991-2670 e11-2670 0.018 - - - no_errors tier3 1084 1 0.09 1059 178 14.38 0 0 0 478908 TCGA-AB-2980 AML11 6 54347089 54347089 T A SNP TINAG NM_014464.3 human genbank 54_36p 1 validated intronic c.1251-6194 e10-6194 0.001 - - - no_errors tier3 1547 0 0 1126 431 27.68 0 0 NA 478908 TCGA-AB-2980 AML11 6 54832995 54832995 G A SNP FAM83B NM_001010872.1 human genbank 54_36p 1 validated intronic c.1-9949 e1-9949 0 - - - no_errors tier3 817 0 0 592 196 24.84 0 0 NA 478908 TCGA-AB-2980 AML11 6 55356635 55356635 T A SNP GFRAL NM_207410.2 human genbank 54_36p 1 validated intronic c.953-15302 e7-15302 0.009 - - - no_errors tier3 870 0 0 589 206 25.91 0 0 NA 478908 TCGA-AB-2980 AML11 6 55356669 55356669 A C SNP GFRAL NM_207410.2 human genbank 54_36p 1 validated intronic c.953-15268 e7-15268 0.001 - - - no_errors tier3 858 0 0 582 203 25.86 0 0 NA 478908 TCGA-AB-2980 AML11 6 55707334 55707334 C A SNP BMP5 NM_021073.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*20956 NULL 0.001 - - - no_errors tier2 772 0 0 510 234 31.45 0 0 NA 478908 TCGA-AB-2980 AML11 6 72963622 72963622 G A SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated intronic c.1678+14049 e6+14049 0.019 - - - no_errors tier3 1173 1 0.09 867 322 27.08 0 0 NA 478908 TCGA-AB-2980 AML11 6 79215236 79215236 A T SNP - - - - - - - - - - - - - - - tier3 901 0 0 499 228 31.36 0 0 NA 478908 TCGA-AB-2980 AML11 6 82538496 82538496 A G SNP FAM46A NM_017633.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19919 NULL 0.004 - - - no_errors tier3 1506 0 0 871 433 33.21 0 0 NA 478908 TCGA-AB-2980 AML11 6 84462196 84462196 C T SNP SNAP91 NM_014841.2 human genbank 54_36p -1 validated intronic c.130+12040 e1+12040 0.001 - - - no_errors tier3 1141 1 0.09 620 251 28.75 0 0 NA 478908 TCGA-AB-2980 AML11 6 93514280 93514280 C T SNP ENSG00000221455 ENST00000408528 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-42612 NULL 0.009 - - - no_errors tier3 594 0 0 384 132 25.58 0 0 NA 478908 TCGA-AB-2980 AML11 6 93862330 93862330 C T SNP ENSG00000213187 ENST00000392786 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3040 NULL 0.001 - - - no_coding_region:pseudogene tier3 776 1 0.13 673 260 27.84 0 0 NA 478908 TCGA-AB-2980 AML11 6 95642746 95642746 A G SNP - - - - - - - - - - - - - - - tier3 800 0 0 471 172 26.75 0 0 NA 478908 TCGA-AB-2980 AML11 6 100860564 100860564 A G SNP - - - - - - - - - - - - - - - tier3 1115 0 0 907 384 29.74 0 0 NA 478908 TCGA-AB-2980 AML11 6 116477050 116477050 C T SNP FRK NM_002031.2 human genbank 54_36p -1 reviewed intronic c.344+10774 e1+10774 0.19 - - - no_errors tier3 809 0 0 614 232 27.36 0 0 NA 478908 TCGA-AB-2980 AML11 6 122119716 122119716 A T SNP - - - - - - - - - - - - - - - tier3 938 0 0 659 286 30.26 0 0 NA 478908 TCGA-AB-2980 AML11 6 130164516 130164516 G A SNP ENSG00000219666 ENST00000403074 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17633 NULL 1 - - - no_coding_region:pseudogene tier2 682 0 0 488 218 30.83 0 0 NA 478908 TCGA-AB-2980 AML11 6 134046452 134046452 C T SNP ENSG00000218213 ENST00000406512 human ensembl 54_36p -1 known 5_prime_flanking_region c.-6192 NULL 0.688 - - - no_coding_region:pseudogene tier3 1106 1 0.09 600 245 28.99 0 0 NA 478908 TCGA-AB-2980 AML11 6 135242123 135242123 G A SNP LOC645175 XR_017268.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-18554 NULL 0.005 - - - pseudogene tier3 1121 0 0 1014 352 25.71 0 0 NA 478908 TCGA-AB-2980 AML11 6 149964617 149964617 T C SNP KATNA1 NM_007044.2 human genbank 54_36p -1 reviewed intronic c.730-36 e6-36 0 - - - no_errors tier3 1209 0 0 943 321 25.4 1 0 0 478908 TCGA-AB-2980 AML11 6 151000674 151000674 A T SNP PLEKHG1 NM_001029884.1 human genbank 54_36p 1 provisional intronic c.1-12883 e1-12883 0 - - - no_errors tier3 1278 0 0 895 265 22.83 0 0 NA 478908 TCGA-AB-2980 AML11 6 154294446 154294446 G A SNP ENSG00000217085 ENST00000403971 human ensembl 54_36p -1 known 3_prime_flanking_region c.*6815 NULL 0.035 - - - no_coding_region:pseudogene tier3 1305 2 0.15 984 274 21.78 0 0 NA 478908 TCGA-AB-2980 AML11 6 159918202 159918202 T C SNP - - - - - - - - - - - - - - - tier3 882 1 0.11 892 161 15.28 0 0 NA 478908 TCGA-AB-2980 AML11 7 8435910 8435910 C T SNP NXPH1 NM_152745.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-5959 NULL 0.902 - - - no_errors tier3 1859 0 0 1200 451 27.32 0 0 NA 478908 TCGA-AB-2980 AML11 7 25645223 25645223 G A SNP LOC646588 XM_933738.1 human genbank 54_36p -1 model intronic c.208+18882 e3+18882 0 - - - no_errors tier3 865 0 0 859 373 30.25 0 0 0 478908 TCGA-AB-2980 AML11 7 32102381 32102381 A G SNP PDE1C ENST00000284920 human ensembl 54_36p -1 known intronic c.309-43925 e4-43925 0.002 - - - no_errors tier3 1139 1 0.09 932 396 29.8 0 0 NA 478908 TCGA-AB-2980 AML11 7 43017635 43017635 G C SNP - - - - - - - - - - - - - - - tier3 1591 0 0 1287 520 28.76 0 0 NA 478908 TCGA-AB-2980 AML11 7 49331898 49331898 G T SNP LOC100134791 XM_001726801.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16469 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1191 0 0 811 350 30.07 0 0 NA 478908 TCGA-AB-2980 AML11 7 55532684 55532684 G A SNP ECOP NM_030796.3 human genbank 54_36p -1 validated intronic c.191+116 e3+116 0.001 - - - no_errors tier3 770 0 0 1027 328 24.14 0 0 NA 478908 TCGA-AB-2980 AML11 7 67519963 67519963 C T SNP - - - - - - - - - - - - - - - tier3 2068 0 0 1686 525 23.72 0 0 NA 478908 TCGA-AB-2980 AML11 7 67786034 67786034 C T SNP ENSG00000222428 ENST00000410496 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*40828 NULL 1 - - - no_errors tier2 1806 1 0.06 1572 569 26.58 0 0 NA 478908 TCGA-AB-2980 AML11 7 80110028 80110028 G A SNP CD36 NM_000072.3 human genbank 54_36p 1 reviewed intronic c.1-3312 e1-3312 0 - - - no_errors tier3 760 0 0 480 217 31.04 0 0 0 478908 TCGA-AB-2980 AML11 7 89533151 89533151 A G SNP - - - - - - - - - - - - - - - tier3 750 0 0 627 261 29.39 0 0 NA 478908 TCGA-AB-2980 AML11 7 95722495 95722495 G A SNP SLC25A13 NM_014251.2 human genbank 54_36p -1 validated intronic c.213-20330 e4-20330 0.008 - - - no_errors tier3 2302 3 0.13 1845 621 25.16 0 1 100 478908 TCGA-AB-2980 AML11 7 102420865 102420865 T A SNP FBXL13 NM_145032.1 human genbank 54_36p -1 validated intronic c.496-25065 e5-25065 0.973 - - - no_errors tier2 1742 1 0.06 1749 539 23.55 0 0 NA 478908 TCGA-AB-2980 AML11 7 105193632 105193632 G A SNP ATXN7L1 NM_152749.1 human genbank 54_36p -1 validated intronic c.356-4487 e4-4487 0.001 - - - no_errors tier3 1023 1 0.1 1150 256 18.19 6 0 0 478908 TCGA-AB-2980 AML11 7 117926132 117926132 T C SNP ENSG00000222226 ENST00000410294 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36248 NULL 0 - - - no_errors tier3 1392 0 0 983 437 30.77 0 0 NA 478908 TCGA-AB-2980 AML11 7 122658977 122658977 A G SNP SLC13A1 NM_022444.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31741 NULL 0.003 - - - no_errors tier2 1439 0 0 1146 428 27.19 0 0 NA 478908 TCGA-AB-2980 AML11 7 125427142 125427142 G T SNP ENSG00000221418 ENST00000408491 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-40377 NULL 0 - - - no_errors tier3 1184 1 0.08 812 327 28.71 0 0 NA 478908 TCGA-AB-2980 AML11 7 145161951 145161951 G A SNP - - - - - - - - - - - - - - - tier3 957 0 0 651 248 27.56 0 0 NA 478908 TCGA-AB-2980 AML11 7 152439459 152439459 G A SNP ENSG00000217267 ENST00000402195 human ensembl 54_36p -1 known 3_prime_flanking_region c.*32872 NULL 0 - - - no_coding_region:pseudogene tier3 976 0 0 1195 172 12.55 0 0 NA 478908 TCGA-AB-2980 AML11 7 152439464 152439464 G T SNP ENSG00000217267 ENST00000402195 human ensembl 54_36p -1 known 3_prime_flanking_region c.*32867 NULL 0.001 - - - no_coding_region:pseudogene tier3 983 0 0 1206 169 12.28 0 0 NA 478908 TCGA-AB-2980 AML11 7 153689300 153689300 T C SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.244-84932 e2-84932 0.005 - - - no_errors tier3 1087 0 0 1159 532 31.46 0 0 NA 478908 TCGA-AB-2980 AML11 7 154180321 154180321 A G SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.884-11739 e9-11739 0 - - - no_errors tier3 996 0 0 1501 207 12.12 0 0 NA 478908 TCGA-AB-2980 AML11 8 2099916 2099916 G T SNP MYOM2 NM_003970.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*19604 NULL 0 - - - no_errors tier3 904 1 0.11 765 282 26.93 0 0 NA 478908 TCGA-AB-2980 AML11 8 13491759 13491759 C T SNP C8orf48 ENST00000297324 human ensembl 54_36p 1 known 3_prime_flanking_region c.*21928 NULL 0.001 - - - no_errors tier3 1674 1 0.06 1270 532 29.52 0 0 NA 478908 TCGA-AB-2980 AML11 8 21000762 21000762 T C SNP - - - - - - - - - - - - - - - tier3 899 1 0.11 921 368 28.51 0 0 NA 478908 TCGA-AB-2980 AML11 8 23832024 23832024 A G SNP LOC100132107 XM_001717230.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-29537 NULL 0.004 - - - no_errors tier3 892 1 0.11 808 136 14.39 0 0 NA 478908 TCGA-AB-2980 AML11 8 34226043 34226043 C T SNP - - - - - - - - - - - - - - - tier3 1293 1 0.08 741 355 32.39 0 0 NA 478908 TCGA-AB-2980 AML11 8 35622555 35622555 C A SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.556-38052 e5-38052 0 - - - no_errors tier3 927 0 0 813 86 9.57 0 0 NA 478908 TCGA-AB-2980 AML11 8 40331150 40331150 C A SNP - - - - - - - - - - - - - - - tier3 657 0 0 482 149 23.61 0 0 NA 478908 TCGA-AB-2980 AML11 8 41440908 41440908 G A SNP GOLGA7 NM_001002296.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26623 NULL 0 - - - no_errors tier3 1693 1 0.06 1525 582 27.61 0 0 NA 478908 TCGA-AB-2980 AML11 8 43178820 43178821 TG - DEL HGSNAT NM_152419.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*4951 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 8 47869892 47869892 G A SNP ENSG00000210859 ENST00000388124 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-11142 NULL 0.102 - - - pseudogene tier3 981 0 0 771 72 8.54 0 0 NA 478908 TCGA-AB-2980 AML11 8 51469014 51469014 C T SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1-311 e1-311 0.001 - - - no_errors tier3 892 3 0.33 542 220 28.76 0 0 NA 478908 TCGA-AB-2980 AML11 8 56653502 56653502 A G SNP - - - - - - - - - - - - - - - tier3 1012 0 0 848 318 27.27 0 0 NA 478908 TCGA-AB-2980 AML11 8 58143431 58143431 G A SNP - - - - - - - - - - - - - - - tier3 703 0 0 504 198 28.21 0 0 NA 478908 TCGA-AB-2980 AML11 8 62795678 62795678 G A SNP ASPH NM_004318.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-6194 NULL 0 - - - no_errors tier2 1328 3 0.23 892 367 29.13 0 0 NA 478908 TCGA-AB-2980 AML11 8 63008400 63008400 G A SNP - - - - - - - - - - - - - - - tier3 1103 2 0.18 1026 149 12.68 0 0 NA 478908 TCGA-AB-2980 AML11 8 72183972 72183972 G T SNP - - - - - - - - - - - - - - - tier3 924 0 0 936 143 13.24 0 0 NA 478908 TCGA-AB-2980 AML11 8 73943658 73943658 C - DEL KCNB2 NM_004770.2 human genbank 54_36p 1 reviewed intronic c.580-67066 e2-67066 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 8 75191396 75191396 G C SNP ENSG00000212485 ENST00000391183 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36964 NULL 0.015 - - - no_errors tier3 1395 0 0 832 387 31.7 0 0 NA 478908 TCGA-AB-2980 AML11 8 85120078 85120078 A G SNP - - - - - - - - - - - - - - - tier3 563 0 0 280 109 28.02 0 0 NA 478908 TCGA-AB-2980 AML11 8 96875906 96875906 G A SNP - - - - - - - - - - - - - - - tier3 1305 0 0 953 359 27.36 0 0 NA 478908 TCGA-AB-2980 AML11 8 97637618 97637618 T A SNP SDC2 NM_002998.3 human genbank 54_36p 1 reviewed intronic c.61-37266 e2-37266 0.454 - - - no_errors tier3 700 0 0 292 91 23.76 0 0 NA 478908 TCGA-AB-2980 AML11 8 122960520 122960520 G A SNP - - - - - - - - - - - - - - - tier3 495 0 0 416 120 22.39 0 0 NA 478908 TCGA-AB-2980 AML11 8 123989450 123989450 G A SNP ZHX2 NM_014943.3 human genbank 54_36p 1 reviewed intronic c.1-43263 e1-43263 0 - - - no_errors tier2 1847 1 0.05 1930 657 25.36 0 0 0 478908 TCGA-AB-2980 AML11 8 126587890 126587890 A T SNP - - - - - - - - - - - - - - - tier3 1113 1 0.09 1054 388 26.85 0 0 NA 478908 TCGA-AB-2980 AML11 8 138649814 138649814 A C SNP - - - - - - - - - - - - - - - tier3 1797 0 0 1526 562 26.9 0 0 NA 478908 TCGA-AB-2980 AML11 8 139854920 139854920 G A SNP COL22A1 NM_152888.1 human genbank 54_36p -1 validated intronic c.1803+2471 e15+2471 0.017 - - - no_errors tier3 929 2 0.21 925 484 34.35 0 0 NA 478908 TCGA-AB-2980 AML11 9 1511562 1511563 - T INS LOC100134189 XM_001722214.1 human genbank 54_36p 1 model intronic c.348+4424_348+4423 e2+4424 0.003:0.006 - - - no_start_codon:pseudogene:no_stop_codon tier2 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 9 13363866 13363866 G C SNP FLJ41200 XM_379623.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*34478 NULL 0.002 - - - no_errors tier2 1086 0 0 982 149 13.16 0 0 NA 478908 TCGA-AB-2980 AML11 9 21307932 21307932 T G SNP IFNA5 NM_002169.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-12677 NULL 0.03 - - - no_errors tier3 763 0 0 537 189 26.03 0 0 NA 478908 TCGA-AB-2980 AML11 9 21675989 21675989 G A SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 5_prime_flanking_region c.-9186 NULL 0 - - - no_coding_region:pseudogene tier3 836 0 0 718 106 12.86 0 0 NA 478908 TCGA-AB-2980 AML11 9 23439243 23439243 G A SNP LOC100131398 XM_001716436.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-12055 NULL 0.001 - - - no_start_codon:pseudogene tier3 1506 5 0.33 915 435 32.2 0 0 NA 478908 TCGA-AB-2980 AML11 9 28745243 28745243 A T SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-804574 NULL 0.003 - - - no_errors tier3 973 0 0 740 298 28.71 0 0 NA 478908 TCGA-AB-2980 AML11 9 35800321 35800321 A T SNP SPAG8 NM_172312.1 human genbank 54_36p -1 reviewed intronic c.1201-15 e6-15 0.001 - - - no_errors tier2 681 1 0.15 613 336 35.37 0 0 0 478908 TCGA-AB-2980 AML11 9 36281451 36281451 C T SNP GNE NM_005476.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42099 NULL 0.076 - - - no_errors tier3 727 1 0.14 732 204 21.75 1 1 50 478908 TCGA-AB-2980 AML11 9 36930902 36930902 G A SNP PAX5 NM_016734.1 human genbank 54_36p -1 reviewed intronic c.781-17421 e7-17421 0.001 - - - no_errors tier3 1419 0 0 1359 434 24.19 0 0 NA 478908 TCGA-AB-2980 AML11 9 71362024 71362024 G A SNP APBA1 NM_001163.3 human genbank 54_36p -1 reviewed intronic c.1-40009 e1-40009 0.006 - - - no_errors tier3 2271 3 0.13 1866 664 26.23 0 0 NA 478908 TCGA-AB-2980 AML11 9 71856493 71856493 C T SNP MAMDC2 NM_153267.4 human genbank 54_36p 1 validated intronic c.148+7060 e2+7060 0 - - - no_errors tier3 872 0 0 651 345 34.64 2 2 50 478908 TCGA-AB-2980 AML11 9 75947701 75947701 C T SNP - - - - - - - - - - - - - - - tier3 760 1 0.13 481 121 20.1 0 0 NA 478908 TCGA-AB-2980 AML11 9 91792965 91792965 C T SNP - - - - - - - - - - - - - - - tier3 685 0 0 748 298 28.44 0 0 NA 478908 TCGA-AB-2980 AML11 9 115392813 115392813 C T SNP RGS3 NM_144488.3 human genbank 54_36p 1 reviewed intronic c.3016-621 e21-621 0.004 - - - no_errors tier3 199 0 0 204 85 29.41 1 0 0 478908 TCGA-AB-2980 AML11 9 116559817 116559817 A T SNP LOC100129633 XM_001718491.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-11520 NULL 0.004 - - - no_errors tier2 1758 0 0 1293 470 26.66 0 0 NA 478908 TCGA-AB-2980 AML11 9 117396158 117396158 T C SNP - - - - - - - - - - - - - - - tier3 1129 1 0.09 990 373 27.35 0 0 NA 478908 TCGA-AB-2980 AML11 9 123610911 123610911 C T SNP DAB2IP NM_032552.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*25266 NULL 0.001 - - - no_errors tier3 629 0 0 383 143 27.19 0 0 NA 478908 TCGA-AB-2980 AML11 9 126223674 126223674 C T SNP PSMB7 NM_002799.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-6149 NULL 0.001 - - - no_errors tier3 642 0 0 662 250 27.38 0 0 NA 478908 TCGA-AB-2980 AML11 9 128591750 128591750 G A SNP ZBTB43 NM_014007.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-42860 NULL 0.002 - - - no_errors tier3 981 1 0.1 1209 221 15.45 0 0 NA 478908 TCGA-AB-2980 AML11 9 137217296 137217296 G A SNP ENSG00000189363 ENST00000313150 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*237 NULL 0.002 - - - no_errors tier2 700 0 0 528 152 22.29 0 0 NA 478908 TCGA-AB-2980 AML11 10 9752890 9752890 G T SNP - - - - - - - - - - - - - - - tier3 938 1 0.11 602 249 29.26 0 0 NA 478908 TCGA-AB-2980 AML11 10 20351570 20351570 A G SNP PLXDC2 NM_032812.7 human genbank 54_36p 1 provisional intronic c.324+20649 e2+20649 0 - - - no_errors tier3 1019 0 0 809 291 26.45 0 2 100 478908 TCGA-AB-2980 AML11 10 49435173 49435173 T A SNP ARHGAP22 NM_021226.2 human genbank 54_36p -1 validated intronic c.235-1572 e3-1572 0.164 - - - no_errors tier3 663 0 0 732 343 31.91 0 0 NA 478908 TCGA-AB-2980 AML11 10 50321100 50321100 C A SNP LOC100128032 XM_001719050.1 human genbank 54_36p 1 model intronic c.27+23538 e1+23538 0.006 - - - no_errors tier3 1031 2 0.19 770 346 30.95 0 0 NA 478908 TCGA-AB-2980 AML11 10 56208079 56208079 C T SNP PCDH15 NM_033056.1 human genbank 54_36p -1 reviewed intronic c.1+22612 e0+22612 0.001 - - - no_errors tier3 1028 0 0 593 284 32.38 0 0 NA 478908 TCGA-AB-2980 AML11 10 60237428 60237428 A C SNP BICC1 NM_001080512.1 human genbank 54_36p 1 provisional intronic c.2376+504 e17+504 1 - - - no_errors tier2 886 1 0.11 703 248 26.08 0 0 NA 478908 TCGA-AB-2980 AML11 10 65314056 65314056 C T SNP ENSG00000213609 ENST00000395235 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*18154 NULL 0 - - - no_coding_region:pseudogene tier3 896 0 0 582 245 29.63 0 0 NA 478908 TCGA-AB-2980 AML11 10 70815156 70815156 T C SNP HK1 NM_033497.2 human genbank 54_36p 1 reviewed intronic c.1851+479 e13+479 0.001 - - - no_errors tier3 1268 2 0.16 1174 523 30.75 2 4 66.67 478908 TCGA-AB-2980 AML11 10 71862986 71862986 A G SNP NODAL NM_018055.4 human genbank 54_36p -1 reviewed intronic c.892-136 e3-136 0.948 - - - no_errors tier3 960 0 0 806 344 29.89 0 0 NA 478908 TCGA-AB-2980 AML11 10 72394880 72394880 C T SNP - - - - - - - - - - - - - - - tier3 1880 0 0 1633 582 26.22 0 0 NA 478908 TCGA-AB-2980 AML11 10 76503217 76503217 T G SNP SAMD8 NM_144660.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-77076 NULL 0.007 - - - no_errors tier2 803 0 0 752 310 29.16 0 0 NA 478908 TCGA-AB-2980 AML11 10 78749033 78749033 A T SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.541-68013 e3-68013 0.001 - - - no_errors tier3 1305 5 0.38 1089 562 33.9 0 0 NA 478908 TCGA-AB-2980 AML11 10 78934665 78934665 G A SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.379-100878 e2-100878 0.006 - - - no_errors tier3 1143 0 0 985 436 30.62 0 0 NA 478908 TCGA-AB-2980 AML11 10 78975591 78975591 G A SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.378+91438 e1+91438 0.004 - - - no_errors tier3 2179 1 0.05 1703 704 29.2 0 0 NA 478908 TCGA-AB-2980 AML11 10 92137553 92137553 C T SNP - - - - - - - - - - - - - - - tier3 1531 0 0 1282 469 26.71 0 0 NA 478908 TCGA-AB-2980 AML11 10 106478259 106478259 G T SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.627+86557 e1+86557 0 - - - no_errors tier3 1057 1 0.09 1123 432 27.76 0 0 NA 478908 TCGA-AB-2980 AML11 10 107017547 107017547 G C SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*4425 NULL 0.751 - - - no_errors tier3 1267 0 0 1268 581 31.42 0 0 NA 478908 TCGA-AB-2980 AML11 10 109814806 109814806 C T SNP - - - - - - - - - - - - - - - tier3 1283 0 0 1036 360 25.77 0 0 NA 478908 TCGA-AB-2980 AML11 10 117889160 117889160 G A SNP GFRA1 NM_005264.1 human genbank 54_36p -1 reviewed intronic c.434-14102 e5-14102 0.003 - - - no_errors tier3 754 0 0 686 288 29.51 0 0 NA 478908 TCGA-AB-2980 AML11 10 125166407 125166407 G A SNP - - - - - - - - - - - - - - - tier3 1182 3 0.25 1039 509 32.84 0 0 NA 478908 TCGA-AB-2980 AML11 10 130207067 130207067 G A SNP - - - - - - - - - - - - - - - tier3 1814 0 0 1580 561 26.2 0 0 NA 478908 TCGA-AB-2980 AML11 10 132261833 132261833 G A SNP - - - - - - - - - - - - - - - tier3 1864 0 0 1964 781 28.37 0 0 NA 478908 TCGA-AB-2980 AML11 10 133500974 133500974 G A SNP FLJ46300 XR_040360.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-42609 NULL 0.037 - - - no_errors tier3 698 1 0.14 744 322 29.84 0 0 NA 478908 TCGA-AB-2980 AML11 10 134160559 134160559 C - DEL INPP5A NM_005539.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-41032 NULL 0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 11 2098139 2098139 G T SNP IGF2AS NM_016412.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20311 NULL 0.006 - - - no_errors tier3 401 0 0 357 125 25.93 0 0 NA 478908 TCGA-AB-2980 AML11 11 21043779 21043779 G A SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1301-47932 e13-47932 0.001 - - - no_errors tier3 1575 0 0 1193 573 32.41 0 0 NA 478908 TCGA-AB-2980 AML11 11 26142671 26142671 C A SNP - - - - - - - - - - - - - - - tier3 1839 1 0.05 957 374 28.06 0 0 NA 478908 TCGA-AB-2980 AML11 11 26493623 26493623 C T SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated intronic c.592-1327 e6-1327 0 - - - no_errors tier3 932 0 0 585 201 25.57 0 0 NA 478908 TCGA-AB-2980 AML11 11 34644035 34644035 G A SNP EHF NM_012153.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*6981 NULL 0 - - - no_errors tier3 1812 1 0.06 1829 744 28.9 0 0 NA 478908 TCGA-AB-2980 AML11 11 42560719 42560719 C G SNP - - - - - - - - - - - - - - - tier3 1179 0 0 1146 332 22.43 0 0 NA 478908 TCGA-AB-2980 AML11 11 42560720 42560720 A T SNP - - - - - - - - - - - - - - - tier3 1174 1 0.09 1145 332 22.46 0 0 NA 478908 TCGA-AB-2980 AML11 11 43232102 43232102 G A SNP LOC399881 XR_040375.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*7528 NULL 0.002 - - - no_errors tier3 2248 2 0.09 2009 783 28.03 0 0 NA 478908 TCGA-AB-2980 AML11 11 44719765 44719765 A G SNP LOC652436 XM_001718120.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-19555 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 3059 2 0.07 2654 997 27.29 0 0 NA 478908 TCGA-AB-2980 AML11 11 55496634 55496634 A - DEL OR5I1 NM_006637.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-36182 NULL 0.115 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 11 55643776 55643776 G T SNP OR8H3 NM_001005201.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-2649 NULL 0.004 - - - no_errors tier3 1191 0 0 724 362 33.3 0 0 NA 478908 TCGA-AB-2980 AML11 11 61058109 61058109 G A SNP SYT7 NM_004200.2 human genbank 54_36p -1 validated intronic c.216-937 e4-937 0.776 - - - no_errors tier3 609 0 0 535 260 32.66 0 0 NA 478908 TCGA-AB-2980 AML11 11 68744896 68744896 C T SNP - - - - - - - - - - - - - - - tier3 461 0 0 318 110 25.58 0 0 NA 478908 TCGA-AB-2980 AML11 11 70528303 70528303 T G SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.207+7511 e1+7511 0.001 - - - no_errors tier3 1071 0 0 830 304 26.78 0 0 NA 478908 TCGA-AB-2980 AML11 11 91515441 91515441 A G SNP - - - - - - - - - - - - - - - tier3 1504 2 0.13 1173 419 26.29 0 0 NA 478908 TCGA-AB-2980 AML11 11 98990472 98990472 G T SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.55+58262 e1+58262 0 - - - no_errors tier3 793 0 0 635 97 13.23 0 0 NA 478908 TCGA-AB-2980 AML11 11 101173371 101173371 C T SNP - - - - - - - - - - - - - - - tier2 2122 1 0.05 1639 751 31.38 0 0 NA 478908 TCGA-AB-2980 AML11 11 104256326 104256326 T A SNP LOC643733 XM_001718827.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*27194 NULL 0 - - - no_errors tier3 1217 0 0 1274 161 11.22 1 0 0 478908 TCGA-AB-2980 AML11 11 114982184 114982184 A G SNP ENSG00000211200 ENST00000388465 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*20828 NULL 0.128 - - - pseudogene tier3 1411 0 0 1001 468 31.73 0 0 NA 478908 TCGA-AB-2980 AML11 11 124111964 124111964 G C SNP NRGN NM_006176.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3227 NULL 0.582 - - - no_errors tier3 698 1 0.14 605 117 16.18 0 0 NA 478908 TCGA-AB-2980 AML11 11 129660796 129660796 G C SNP ZBTB44 NM_014155.4 human genbank 54_36p -1 validated intronic c.1-23762 e1-23762 0 - - - no_errors tier3 1097 0 0 604 297 32.93 0 1 100 478908 TCGA-AB-2980 AML11 11 132452186 132452186 C A SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.62-134071 e2-134071 0 - - - no_errors tier3 912 0 0 475 131 21.62 0 0 NA 478908 TCGA-AB-2980 AML11 12 3271442 3271442 G A SNP LOC647546 XM_936601.3 human genbank 54_36p -1 model 5_prime_flanking_region c.-34218 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 553 0 0 813 345 29.72 0 0 NA 478908 TCGA-AB-2980 AML11 12 14928977 14928977 C T SNP MGP NM_000900.2 human genbank 54_36p -1 validated intronic c.62-531 e2-531 0.981 - - - no_errors tier2 1911 5 0.26 1465 650 30.7 0 0 0 478908 TCGA-AB-2980 AML11 12 24645615 24645615 A G SNP SOX5 NM_152989.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-705391 NULL 0.019 - - - no_errors tier3 744 1 0.13 468 208 30.77 0 0 NA 478908 TCGA-AB-2980 AML11 12 26218262 26218262 C T SNP SSPN NM_005086.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-21611 NULL 0.457 - - - no_errors tier3 1895 0 0 1315 643 32.79 0 0 NA 478908 TCGA-AB-2980 AML11 12 30527581 30527581 C G SNP - - - - - - - - - - - - - - - tier3 1009 1 0.1 672 239 26.15 0 0 NA 478908 TCGA-AB-2980 AML11 12 31279480 31279480 C T SNP uc001rka.1 ENST00000266524 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29125 NULL 0 - - - no_errors tier3 1003 2 0.2 1058 413 27.87 0 0 NA 478908 TCGA-AB-2980 AML11 12 37639117 37639117 T G SNP - - - - - - - - - - - - - - - tier3 983 1 0.1 693 236 25.29 0 0 NA 478908 TCGA-AB-2980 AML11 12 46300375 46300375 C G SNP RPAP3 NM_024604.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*43180 NULL 0 - - - no_errors tier3 1307 0 0 882 334 27.42 0 0 NA 478908 TCGA-AB-2980 AML11 12 51593516 51593516 C T SNP KRT8 NM_002273.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-8484 NULL 0 - - - no_errors tier3 1379 2 0.14 1377 503 26.74 3 0 0 478908 TCGA-AB-2980 AML11 12 51686517 51686517 C G SNP EIF4B NM_001417.4 human genbank 54_36p 1 validated 5_prime_untranslated_region c.-18 NULL 1 - - - no_errors tier2 550 0 0 503 155 23.56 0 2 100 478908 TCGA-AB-2980 AML11 12 66470787 66470787 G A SNP - - - - - - - - - - - - - - - tier3 1532 0 0 891 493 35.62 0 0 NA 478908 TCGA-AB-2980 AML11 12 68111006 68111006 C A SNP FRS2 NM_001042555.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-138072 NULL 0 - - - no_errors tier3 1488 1 0.07 1431 529 26.99 0 2 100 478908 TCGA-AB-2980 AML11 12 69034559 69034559 C T SNP CNOT2 NM_014515.4 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*597 NULL 1 - - - no_errors tier2 777 0 0 411 202 32.95 77 47 37.9 478908 TCGA-AB-2980 AML11 12 76702344 76702344 C T SNP NAV3 NM_014903.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-47029 NULL 0 - - - no_errors tier2 1794 2 0.11 1261 467 26.98 0 0 NA 478908 TCGA-AB-2980 AML11 12 78848141 78848141 G A SNP PPP1R12A NM_002480.1 human genbank 54_36p -1 reviewed intronic c.237+4465 e1+4465 0 - - - no_errors tier3 931 0 0 770 268 25.77 6 10 62.5 478908 TCGA-AB-2980 AML11 12 85209799 85209799 G T SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+42175 e0+42175 0.003 - - - no_errors tier3 913 0 0 487 83 14.56 0 0 NA 478908 TCGA-AB-2980 AML11 12 85257695 85257695 A C SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1-5659 e1-5659 0.016 - - - no_errors tier3 1318 1 0.08 956 352 26.91 0 0 NA 478908 TCGA-AB-2980 AML11 12 90458320 90458320 T C SNP - - - - - - - - - - - - - - - tier3 621 0 0 384 129 25.15 0 0 NA 478908 TCGA-AB-2980 AML11 12 97690835 97690835 A T SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.3504+116 e24+116 0.001 - - - no_errors tier3 619 0 0 407 193 32.17 0 0 NA 478908 TCGA-AB-2980 AML11 12 97921650 97921650 C T SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.2778+49416 e17+49416 0 - - - no_errors tier3 1616 3 0.19 1317 599 31.26 0 0 NA 478908 TCGA-AB-2980 AML11 12 99090423 99090423 A G SNP GOLGA2L1 NM_017600.1 human genbank 54_36p -1 provisional intronic c.1+598 e0+598 0.001 - - - no_errors tier3 515 0 0 466 236 33.57 0 1 100 478908 TCGA-AB-2980 AML11 12 113300627 113300627 G T SNP TBX5 NM_000192.3 human genbank 54_36p -1 reviewed intronic c.755+7037 e6+7037 0 - - - no_errors tier3 3185 0 0 3028 1235 28.96 0 0 NA 478908 TCGA-AB-2980 AML11 12 122034537 122034537 G C SNP PITPNM2 NM_020845.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1990 NULL 0.002 - - - no_errors tier3 557 0 0 676 284 29.52 1 2 66.67 478908 TCGA-AB-2980 AML11 12 124824046 124824046 G C SNP - - - - - - - - - - - - - - - tier2 1331 1 0.08 901 388 30.05 0 0 NA 478908 TCGA-AB-2980 AML11 12 125600984 125600984 C T SNP ENSG00000209315 ENST00000386580 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*33164 NULL 0.001 - - - pseudogene tier3 1127 1 0.09 1133 167 12.85 0 0 NA 478908 TCGA-AB-2980 AML11 12 125650472 125650472 G T SNP ENSG00000209315 ENST00000386580 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16275 NULL 0.012 - - - pseudogene tier3 1325 2 0.15 1081 382 26.08 0 0 NA 478908 TCGA-AB-2980 AML11 13 18198096 18198096 G A SNP LOC100132598 XM_001714168.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-7794 NULL 0.988 - - - no_errors tier3 316 1 0.31 201 28 12.23 0 0 NA 478908 TCGA-AB-2980 AML11 13 23370321 23370321 C T SNP uc001upa.1 ENST00000382140 human ensembl 54_36p -1 known intronic c.1-297 e1-297 0 - - - no_errors tier3 1063 0 0 660 217 24.74 0 0 NA 478908 TCGA-AB-2980 AML11 13 27431261 27431261 G - DEL FLT3 NM_004119.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*44928 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 13 27506255 27506256 - ATCATATTCATATTCTCTGAA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1801_1800 p.600in_frame_insFREYEYD 1.000:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 478908 TCGA-AB-2980 AML11 13 31536844 31536844 G A SNP FRY NM_023037.2 human genbank 54_36p 1 validated intronic c.71-14127 e2-14127 0.055 - - - no_errors tier3 923 0 0 719 310 30.13 0 0 0 478908 TCGA-AB-2980 AML11 13 34178157 34178157 C T SNP - - - - - - - - - - - - - - - tier3 781 1 0.13 640 229 26.35 0 0 NA 478908 TCGA-AB-2980 AML11 13 36191010 36191010 A C SNP ENSG00000220531 ENST00000402206 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21168 NULL 0.004 - - - no_coding_region:pseudogene tier3 1893 1 0.05 1789 837 31.86 0 0 NA 478908 TCGA-AB-2980 AML11 13 46296155 46296155 C T SNP ESD NM_001984.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-32606 NULL 0 - - - no_errors tier3 1082 1 0.09 760 299 28.21 0 0 NA 478908 TCGA-AB-2980 AML11 13 49304592 49304592 G A SNP KPNA3 NM_002267.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-39949 NULL 0.095 - - - no_errors tier3 367 1 0.27 361 97 21.13 0 0 NA 478908 TCGA-AB-2980 AML11 13 55157652 55157652 C T SNP - - - - - - - - - - - - - - - tier3 673 0 0 420 171 28.89 0 0 NA 478908 TCGA-AB-2980 AML11 13 55678582 55678582 C T SNP ENSG00000219006 ENST00000404148 human ensembl 54_36p 1 known 5_prime_flanking_region c.-7926 NULL 0 - - - no_coding_region:pseudogene tier3 987 0 0 560 231 29.2 0 0 NA 478908 TCGA-AB-2980 AML11 13 71445043 71445043 A C SNP ENSG00000200037 ENST00000363167 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-5184 NULL 0.001 - - - no_errors tier3 1107 1 0.09 789 386 32.85 0 0 NA 478908 TCGA-AB-2980 AML11 13 93919166 93919166 C T SNP DCT NM_001922.1 human genbank 54_36p -1 validated missense c.430 p.A144T 0.599 superfamily_Di-copper_centre "HMMPfam_Tyrosinase,PatternScan_TYROSINASE_1,PatternScan_TYROSINASE_2,superfamily_Di-copper_centre" - no_errors tier1 904 0 833 299 26.41 NA 478908 TCGA-AB-2980 AML11 13 108007935 108007935 T A SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-108338 NULL 0 - - - no_errors tier2 721 1 0.14 316 161 33.75 0 0 NA 478908 TCGA-AB-2980 AML11 13 108007978 108007978 A C SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-108295 NULL 0.005 - - - no_errors tier3 734 0 0 329 157 32.3 0 0 NA 478908 TCGA-AB-2980 AML11 13 108141456 108141456 C T SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.227-21554 e2-21554 0 - - - no_errors tier3 1269 0 0 956 368 27.79 0 0 NA 478908 TCGA-AB-2980 AML11 14 26624564 26624564 G A SNP - - - - - - - - - - - - - - - tier3 1360 2 0.15 990 452 31.32 0 0 NA 478908 TCGA-AB-2980 AML11 14 51176138 51176138 C T SNP FRMD6 NM_001042481.1 human genbank 54_36p 1 validated intronic c.1-50021 e1-50021 0.004 - - - no_errors tier3 1270 1 0.08 904 343 27.48 0 0 NA 478908 TCGA-AB-2980 AML11 14 86305176 86305176 C T SNP - - - - - - - - - - - - - - - tier3 774 0 0 362 235 39.36 0 0 NA 478908 TCGA-AB-2980 AML11 14 87211443 87211443 G A SNP LOC730121 XM_001132513.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-20077 NULL 0 - - - no_errors tier3 1597 0 0 1259 586 31.73 0 0 NA 478908 TCGA-AB-2980 AML11 14 89957020 89957020 C G SNP CALM1 NM_006888.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*16206 NULL 0.002 - - - no_errors tier3 594 0 0 743 316 29.81 0 0 NA 478908 TCGA-AB-2980 AML11 14 95616763 95616763 C T SNP - - - - - - - - - - - - - - - tier2 914 0 0 771 309 28.61 0 0 NA 478908 TCGA-AB-2980 AML11 14 97173516 97173516 T C SNP LOC100129345 XM_001726414.1 human genbank 54_36p -1 model intronic c.118-3735 e2-3735 0.001 - - - no_errors tier3 1949 2 0.1 2060 539 20.74 0 0 NA 478908 TCGA-AB-2980 AML11 14 97918644 97918644 G A SNP ENSG00000223045 ENST00000411113 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30890 NULL 0.002 - - - no_errors tier3 1178 1 0.08 1483 247 14.27 0 0 NA 478908 TCGA-AB-2980 AML11 14 103338909 103338909 C T SNP PPP1R13B NM_015316.2 human genbank 54_36p -1 reviewed intronic c.10-5301 e2-5301 0.023 - - - no_errors tier2 965 1 0.1 767 234 23.35 1 0 0 478908 TCGA-AB-2980 AML11 15 22203945 22203945 T C SNP - - - - - - - - - - - - - - - tier3 809 0 0 563 267 32.17 0 0 NA 478908 TCGA-AB-2980 AML11 15 23415387 23415387 C T SNP ENSG00000220571 ENST00000403285 human ensembl 54_36p 1 known 3_prime_flanking_region c.*38024 NULL 0.001 - - - no_coding_region:pseudogene tier3 890 1 0.11 670 314 31.81 0 0 NA 478908 TCGA-AB-2980 AML11 15 24464111 24464111 C T SNP GABRB3 NM_000814.4 human genbank 54_36p -1 reviewed intronic c.241-46337 e4-46337 0 - - - no_errors tier3 1169 0 0 872 422 32.59 0 0 NA 478908 TCGA-AB-2980 AML11 15 27424264 27424264 T A SNP - - - - - - - - - - - - - - - tier3 1782 1 0.06 1901 800 29.59 0 0 NA 478908 TCGA-AB-2980 AML11 15 43082291 43082291 G C SNP SORD NM_003104.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20483 NULL 0.233 - - - no_errors tier3 691 0 0 509 159 23.7 0 0 NA 478908 TCGA-AB-2980 AML11 15 57800413 57800413 T A SNP BNIP2 NM_004330.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-38465 NULL 0.001 - - - no_errors tier3 963 1 0.1 664 325 32.83 0 0 NA 478908 TCGA-AB-2980 AML11 15 59452014 59452014 C A SNP - - - - - - - - - - - - - - - tier2 760 0 0 559 159 22.14 0 0 NA 478908 TCGA-AB-2980 AML11 15 61935214 61935214 G A SNP HERC1 NM_003922.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-80339 NULL 0.001 - - - no_errors tier3 971 0 0 954 369 27.85 0 0 NA 478908 TCGA-AB-2980 AML11 15 63348950 63348950 T A SNP PARP16 NM_017851.4 human genbank 54_36p -1 provisional intronic c.312+1376 e2+1376 0 - - - no_errors tier3 784 0 0 1018 440 30.16 0 1 100 478908 TCGA-AB-2980 AML11 15 75895903 75895903 T C SNP - - - - - - - - - - - - - - - tier3 573 1 0.17 569 182 24.23 0 0 NA 478908 TCGA-AB-2980 AML11 15 81455585 81455585 C T SNP HOMER2 NM_199330.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43294 NULL 0.008 - - - no_errors tier2 1810 3 0.17 1782 662 27.05 0 3 100 478908 TCGA-AB-2980 AML11 15 86394512 86394512 C A SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed intronic c.1397-17232 e12-17232 0.005 - - - no_errors tier3 935 1 0.11 616 263 29.92 0 0 NA 478908 TCGA-AB-2980 AML11 16 923521 923521 G A SNP LMF1 NM_022773.2 human genbank 54_36p -1 validated intronic c.514+724 e3+724 0.015 - - - no_errors tier3 463 0 0 483 170 26.03 2 2 50 478908 TCGA-AB-2980 AML11 16 25811143 25811143 C T SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.734+199170 e1+199170 0 - - - no_errors tier3 1536 1 0.07 1611 514 24.13 0 0 NA 478908 TCGA-AB-2980 AML11 16 33537438 33537438 C G SNP ENSG00000198229 ENST00000354689 human ensembl 54_36p 1 known missense c.162 p.H54Q 0.984 "HMMSmart_IGv,HMMPfam_V-set,superfamily_SSF48726" "HMMSmart_IGv,HMMPfam_V-set,superfamily_SSF48726" - no_stop_codon tier1 648 0 557 110 16.49 3 1 25 478908 TCGA-AB-2980 AML11 16 56802780 56802780 C T SNP CCDC113 NM_014157.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38640 NULL 0 - - - no_errors tier3 742 0 0 473 195 29.19 0 0 NA 478908 TCGA-AB-2980 AML11 16 60645977 60645977 C T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33169 NULL 0.001 - - - no_errors tier3 2141 0 0 1480 590 28.49 0 0 NA 478908 TCGA-AB-2980 AML11 16 62815326 62815326 A T SNP LOC729217 XR_015483.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*36399 NULL 0.005 - - - pseudogene tier3 1532 2 0.13 1063 436 29.09 0 0 NA 478908 TCGA-AB-2980 AML11 16 62882464 62882464 C T SNP LOC729217 XR_015483.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-24914 NULL 0 - - - pseudogene tier3 1300 0 0 830 358 30.13 0 0 NA 478908 TCGA-AB-2980 AML11 16 63696861 63696861 C T SNP CDH11 NM_001797.2 human genbank 54_36p -1 reviewed intronic c.1+16423 e0+16423 0.439 - - - no_errors tier2 1224 0 0 863 366 29.71 0 0 0 478908 TCGA-AB-2980 AML11 16 71554233 71554233 T C SNP ZFHX3 NM_006885.3 human genbank 54_36p -1 validated intronic c.1-2639 e1-2639 0 - - - no_errors tier3 705 0 0 389 175 30.97 0 0 NA 478908 TCGA-AB-2980 AML11 16 78554920 78554920 T G SNP - - - - - - - - - - - - - - - tier2 2083 0 0 1634 638 28.07 0 0 NA 478908 TCGA-AB-2980 AML11 16 81637378 81637378 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.366+14054 e3+14054 0.001 - - - no_errors tier3 1183 0 0 918 362 28.28 0 0 NA 478908 TCGA-AB-2980 AML11 16 82023578 82023578 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.782-54005 e7-54005 0 - - - no_errors tier3 1924 0 0 1766 705 28.53 0 0 NA 478908 TCGA-AB-2980 AML11 17 1164752 1164752 G A SNP ENSG00000209456 ENST00000386721 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-8223 NULL 0 - - - pseudogene tier3 511 1 0.2 509 136 21.09 0 0 NA 478908 TCGA-AB-2980 AML11 17 12329045 12329045 C T SNP - - - - - - - - - - - - - - - tier3 1448 1 0.07 1014 488 32.43 0 0 NA 478908 TCGA-AB-2980 AML11 17 18735513 18735513 A G SNP PRPSAP2 NM_002767.2 human genbank 54_36p 1 reviewed intronic c.584+1598 e6+1598 0.006 - - - no_errors tier3 912 0 0 665 230 25.7 3 3 50 478908 TCGA-AB-2980 AML11 17 34245313 34245313 A C SNP C17orf98 NM_001080465.2 human genbank 54_36p -1 validated intronic c.308-188 e3-188 0.007 - - - no_errors tier2 950 0 0 1092 364 25 0 0 NA 478908 TCGA-AB-2980 AML11 17 36102765 36102765 G A SNP SMARCE1 NM_003079.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-47185 NULL 0 - - - no_errors tier3 1103 0 0 1080 308 22.17 0 0 NA 478908 TCGA-AB-2980 AML11 17 38204466 38204466 T C SNP CNTD1 NM_173478.2 human genbank 54_36p 1 validated 5_prime_untranslated_region c.-146 NULL 0 - - - no_errors tier2 561 1 0.18 652 200 23.47 0 0 NA 478908 TCGA-AB-2980 AML11 17 48334061 48334061 C G SNP - - - - - - - - - - - - - - - tier3 1582 0 0 1180 493 29.45 0 0 NA 478908 TCGA-AB-2980 AML11 17 60584616 60584616 C T SNP RGS9 NM_003835.1 human genbank 54_36p 1 validated intronic c.155-259 e3-259 0 - - - no_errors tier3 1530 0 0 1987 982 33.08 0 0 0 478908 TCGA-AB-2980 AML11 17 67437822 67437822 C T SNP - - - - - - - - - - - - - - - tier3 1562 2 0.13 1292 444 25.53 0 0 NA 478908 TCGA-AB-2980 AML11 17 67650354 67650354 G A SNP FLJ37644 XM_001126807.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23188 NULL 0.006 - - - no_errors tier3 950 1 0.11 750 373 33.16 0 0 NA 478908 TCGA-AB-2980 AML11 18 3097114 3097114 T C SNP MYOM1 NM_003803.3 human genbank 54_36p -1 reviewed intronic c.3419-4486 e22-4486 0.014 - - - no_errors tier3 675 0 0 622 229 26.85 0 0 0 478908 TCGA-AB-2980 AML11 18 9106183 9106183 G A SNP NDUFV2 NM_021074.3 human genbank 54_36p 1 validated intronic c.55-1653 e2-1653 0.006 - - - no_errors tier3 969 0 0 638 192 23.13 22 12 35.29 478908 TCGA-AB-2980 AML11 18 19251753 19251753 T C SNP C18orf45 NM_032933.4 human genbank 54_36p -1 validated intronic c.197+3576 e3+3576 0.001 - - - no_errors tier3 1224 0 0 924 258 21.81 0 0 0 478908 TCGA-AB-2980 AML11 18 21446007 21446007 C T SNP - - - - - - - - - - - - - - - tier3 1395 0 0 1055 432 29.01 0 0 NA 478908 TCGA-AB-2980 AML11 18 22905789 22905789 T G SNP CHST9 NM_031422.3 human genbank 54_36p -1 validated intronic c.122-23324 e2-23324 0.001 - - - no_errors tier3 811 0 0 516 227 30.55 0 0 NA 478908 TCGA-AB-2980 AML11 18 24306471 24306471 G A SNP - - - - - - - - - - - - - - - tier3 812 2 0.25 609 289 32.18 0 0 NA 478908 TCGA-AB-2980 AML11 18 26432795 26432795 C T SNP - - - - - - - - - - - - - - - tier3 964 0 0 766 263 25.53 0 0 NA 478908 TCGA-AB-2980 AML11 18 28307166 28307166 C G SNP FAM59A NM_022751.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-2777 NULL 0.006 - - - no_errors tier3 463 0 0 271 136 33.42 0 0 NA 478908 TCGA-AB-2980 AML11 18 28579062 28579062 G A SNP KLHL14 NM_020805.1 human genbank 54_36p -1 provisional intronic c.948-3052 e2-3052 0 - - - no_errors tier2 992 1 0.1 678 338 33.27 0 0 NA 478908 TCGA-AB-2980 AML11 18 29428541 29428541 T G SNP ASXL3 NM_030632.1 human genbank 54_36p 1 validated intronic c.55-13015 e2-13015 0.046 - - - no_errors tier3 884 0 0 691 84 10.81 0 0 NA 478908 TCGA-AB-2980 AML11 18 38368417 38368417 C T SNP LOC284260 XM_001720683.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*1274 NULL 0.001 - - - no_errors tier3 1094 1 0.09 818 374 31.32 0 0 NA 478908 TCGA-AB-2980 AML11 18 38764059 38764059 G T SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional intronic c.235-6333 e4-6333 0 - - - no_errors tier3 1367 0 0 981 434 30.58 0 0 NA 478908 TCGA-AB-2980 AML11 18 41250425 41250425 C A SNP - - - - - - - - - - - - - - - tier2 1029 1 0.1 932 431 31.6 0 0 NA 478908 TCGA-AB-2980 AML11 18 44177275 44177275 C T SNP LOC647055 XM_001715324.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-7851 NULL 0.001 - - - no_errors tier3 2661 1 0.04 1866 758 28.85 0 0 NA 478908 TCGA-AB-2980 AML11 18 46455371 46455371 C T SNP MAPK4 NM_002747.3 human genbank 54_36p 1 reviewed intronic c.546+10499 e1+10499 0 - - - no_errors tier3 1046 1 0.1 1090 426 28.04 0 0 NA 478908 TCGA-AB-2980 AML11 18 49506537 49506537 A G SNP - - - - - - - - - - - - - - - tier3 2041 1 0.05 1503 542 26.5 0 0 NA 478908 TCGA-AB-2980 AML11 18 60003440 60003440 T G SNP C18orf20 ENST00000397982 human ensembl 54_36p -1 known 5_prime_flanking_region c.-86616 NULL 0.002 - - - no_errors tier3 767 0 0 667 274 29.09 0 0 NA 478908 TCGA-AB-2980 AML11 18 62920295 62920295 C T SNP - - - - - - - - - - - - - - - tier3 1014 1 0.1 692 328 32.13 0 0 NA 478908 TCGA-AB-2980 AML11 19 34039122 34039122 C T SNP - - - - - - - - - - - - - - - tier3 1151 0 0 1152 375 24.54 0 0 NA 478908 TCGA-AB-2980 AML11 19 56393829 56393829 T C SNP CD33 NM_001772.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26358 NULL 0 - - - no_errors tier2 818 1 0.12 865 363 29.56 0 0 0 478908 TCGA-AB-2980 AML11 19 56864351 56864351 C T SNP SIGLEC5 NM_003830.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-38951 NULL 0.028 - - - no_errors tier3 1680 0 0 1297 437 25.16 0 0 NA 478908 TCGA-AB-2980 AML11 19 61937624 61937624 A G SNP ZIM2 NM_015363.3 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*40244 NULL 0 - - - no_errors tier3 2009 0 0 1697 519 23.4 0 0 NA 478908 TCGA-AB-2980 AML11 20 1663465 1663465 A - DEL ENSG00000220200 ENST00000407264 human ensembl 54_36p -1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 20 15328300 15328300 C A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.541-31750 e7-31750 0 - - - no_errors tier3 1195 0 0 864 334 27.86 0 0 NA 478908 TCGA-AB-2980 AML11 20 15540852 15540852 A G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.645+112360 e8+112360 0.001 - - - no_errors tier3 912 0 0 798 306 27.72 0 0 NA 478908 TCGA-AB-2980 AML11 20 16897999 16897999 G A SNP ENSG00000212165 ENST00000390863 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13478 NULL 0 - - - no_errors tier2 995 1 0.1 603 302 33.33 0 0 NA 478908 TCGA-AB-2980 AML11 20 24968198 24968198 G C SNP ACSS1 NM_032501.2 human genbank 54_36p -1 reviewed intronic c.431+8523 e2+8523 0.009 - - - no_errors tier3 815 0 0 680 329 32.57 0 0 0 478908 TCGA-AB-2980 AML11 20 38666638 38666638 C G SNP - - - - - - - - - - - - - - - tier2 1678 1 0.06 1161 429 26.95 0 0 NA 478908 TCGA-AB-2980 AML11 20 44942924 44942924 G A SNP EYA2 NM_005244.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-109133 NULL 0.013 - - - no_errors tier3 668 0 0 592 207 25.91 0 0 NA 478908 TCGA-AB-2980 AML11 21 25408024 25408024 C T SNP ENSG00000222567 ENST00000410635 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*12393 NULL 0 - - - no_errors tier3 937 0 0 684 253 27 0 0 NA 478908 TCGA-AB-2980 AML11 21 45610468 45610468 C T SNP COL18A1 NM_130445.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-39106 NULL 0.007 - - - no_errors tier2 362 0 0 414 151 26.68 0 0 NA 478908 TCGA-AB-2980 AML11 22 16668857 16668857 C T SNP MICAL3 NM_015241.1 human genbank 54_36p -1 provisional intronic c.2569+2753 e8+2753 0.002 - - - no_errors tier3 1071 1 0.09 1271 559 30.5 1 1 50 478908 TCGA-AB-2980 AML11 22 26181077 26181077 C G SNP - - - - - - - - - - - - - - - tier3 1787 0 0 1654 712 30.08 0 0 NA 478908 TCGA-AB-2980 AML11 22 31530711 31530711 G A SNP SYN3 NM_003490.1 human genbank 54_36p -1 reviewed intronic c.711+60191 e5+60191 1 - - - no_errors tier2 1149 1 0.09 848 351 29.23 0 0 0 478908 TCGA-AB-2980 AML11 22 34051961 34051961 A - DEL TOM1 NM_005488.1 human genbank 54_36p 1 reviewed intronic c.649-1303 e7-1303 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 478908 TCGA-AB-2980 AML11 22 39551836 39551836 T A SNP ST13 NM_003932.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*652 NULL 0 - - - no_errors tier3 669 1 0.15 446 162 26.56 49 39 43.33 478908 TCGA-AB-2980 AML11 22 40297750 40297750 C T SNP CSDC2 NM_014460.3 human genbank 54_36p 1 validated intronic c.1-43 e1-43 0.001 - - - no_errors tier2 738 0 0 563 272 32.57 0 0 NA 816067 TCGA-AB-2981 AML41 X 3638194 3638194 G A SNP PRKX NM_005044.3 human genbank 54_36p -1 validated intronic c.166+2935 e1+2935 0.003 - - - no_errors tier3 340 74 17.75 98 76 43.68 1 1 50 816067 TCGA-AB-2981 AML41 X 92843462 92843462 T A SNP FAM133A NM_173698.1 human genbank 54_36p 1 predicted intronic c.1+3322 e0+3322 0.004 - - - no_errors tier3 644 101 13.5 229 183 44.42 0 0 NA 816067 TCGA-AB-2981 AML41 X 147969698 147969698 T G SNP LOC100132557 XM_001720865.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*23271 NULL 0.007 - - - no_errors tier3 690 116 14.3 312 299 48.86 0 0 NA 816067 TCGA-AB-2981 AML41 1 32724447 32724447 G A SNP ENSG00000215897 ENST00000291374 human ensembl 54_36p 1 known intronic c.1402+927 e3+927 0.005 - - - no_errors tier3 403 72 15.09 104 92 46.7 0 0 NA 816067 TCGA-AB-2981 AML41 1 39921509 39921509 C T SNP HPCAL4 NM_016257.2 human genbank 54_36p -1 reviewed intronic c.379-517 e3-517 0.006 - - - no_errors tier3 390 79 16.7 134 107 44.4 0 0 NA 816067 TCGA-AB-2981 AML41 1 81102103 81102103 T C SNP - - - - - - - - - - - - - - - tier3 182 41 18.14 61 82 56.94 0 0 NA 816067 TCGA-AB-2981 AML41 1 115647987 115647987 G A SNP NGF NM_002506.2 human genbank 54_36p -1 reviewed intronic c.1-10093 e1-10093 0.017 - - - no_errors tier3 450 80 15.01 152 131 46.29 0 0 NA 816067 TCGA-AB-2981 AML41 1 192589278 192589278 C T SNP - - - - - - - - - - - - - - - tier3 172 24 12.24 34 26 43.33 0 0 NA 816067 TCGA-AB-2981 AML41 2 1356450 1356450 G A SNP TPO NM_000547.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40738 NULL 0.001 - - - no_errors tier3 667 114 14.47 310 274 46.84 0 0 NA 816067 TCGA-AB-2981 AML41 2 25310747 25310747 G A SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2644 p.R882C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 731 185 20.07 257 263 50.48 10 11 52.38 816067 TCGA-AB-2981 AML41 2 226729819 226729819 G A SNP - - - - - - - - - - - - - - - tier3 946 154 13.92 474 367 43.64 0 0 NA 816067 TCGA-AB-2981 AML41 3 35570654 35570654 G A SNP LOC100130503 XM_001717149.1 human genbank 54_36p 1 model intronic c.72+962 e1+962 0.326 - - - no_errors tier3 838 102 10.76 348 334 48.97 0 0 NA 816067 TCGA-AB-2981 AML41 3 48588501 48588501 C T SNP COL7A1 NM_000094.3 human genbank 54_36p -1 reviewed intronic c.5821-162 e71-162 0.709 - - - no_errors tier3 259 56 17.61 106 102 49.04 0 0 NA 816067 TCGA-AB-2981 AML41 3 77357044 77357044 C T SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.388+126863 e2+126863 0.001 - - - no_errors tier3 145 19 11.52 35 19 35.19 0 0 NA 816067 TCGA-AB-2981 AML41 3 86874539 86874539 C T SNP - - - - - - - - - - - - - - - tier3 522 75 12.54 148 120 44.78 0 0 NA 816067 TCGA-AB-2981 AML41 3 129109114 129109114 A T SNP LOC100128453 XM_001717848.1 human genbank 54_36p 1 model intronic c.210-7575 e2-7575 0 - - - no_errors tier3 667 127 15.97 213 214 50.12 0 0 NA 816067 TCGA-AB-2981 AML41 3 130046075 130046075 T C SNP LOC100128615 XM_001717892.1 human genbank 54_36p -1 model intronic c.1619-258 e8-258 0.077 - - - no_errors tier3 361 62 14.62 217 188 46.42 0 0 NA 816067 TCGA-AB-2981 AML41 3 158577590 158577590 C T SNP VEPH1 NM_024621.1 human genbank 54_36p -1 provisional intronic c.1127+4049 e6+4049 0.024 - - - no_errors tier3 1047 202 16.1 461 453 49.56 0 0 NA 816067 TCGA-AB-2981 AML41 3 174049689 174049689 G C SNP ECT2 NM_018098.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*28968 NULL 0.088 - - - no_errors tier3 750 165 17.88 174 155 47.11 0 0 NA 816067 TCGA-AB-2981 AML41 3 184474795 184474795 G A SNP MCF2L2 NM_015078.2 human genbank 54_36p -1 validated intronic c.1862+2559 e15+2559 0.006 - - - no_errors tier3 1177 209 15.03 323 228 41.38 0 0 NA 816067 TCGA-AB-2981 AML41 4 17148745 17148745 G T SNP QDPR NM_000320.2 human genbank 54_36p -1 reviewed intronic c.1+3649 e0+3649 0.015 - - - no_errors tier3 309 67 17.72 117 88 42.93 0 0 0 816067 TCGA-AB-2981 AML41 4 18646411 18646411 A G SNP - - - - - - - - - - - - - - - tier3 911 159 14.78 368 405 52.39 0 0 NA 816067 TCGA-AB-2981 AML41 4 19969113 19969113 A G SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.395+89511 e4+89511 0 - - - no_errors tier3 928 187 16.59 379 370 49.33 0 0 NA 816067 TCGA-AB-2981 AML41 4 101431281 101431281 C T SNP - - - - - - - - - - - - - - - tier3 1733 290 14.25 945 712 42.94 0 0 NA 816067 TCGA-AB-2981 AML41 4 123010916 123010916 C A SNP BBS7 NM_176824.2 human genbank 54_36p -1 reviewed missense c.3 p.M1I 1 NULL NULL - no_errors tier1 677 126 15.54 297 269 47.44 7 6 46.15 816067 TCGA-AB-2981 AML41 5 903655 903655 C T SNP ZDHHC11 NM_024786.2 human genbank 54_36p -1 validated silent c.63 p.K21 0.002 NULL HMMPfam_zf-DHHC - no_errors tier1 134 28 17.07 92 101 52.33 NA 816067 TCGA-AB-2981 AML41 5 71284452 71284452 G C SNP - - - - - - - - - - - - - - - tier3 789 140 14.93 276 263 48.7 0 0 NA 816067 TCGA-AB-2981 AML41 5 96488507 96488507 G C SNP LIX1 NM_153234.4 human genbank 54_36p -1 validated intronic c.83-2418 e2-2418 0.339 - - - no_errors tier3 797 150 15.77 451 329 42.18 0 0 NA 816067 TCGA-AB-2981 AML41 5 151488881 151488881 C A SNP - - - - - - - - - - - - - - - tier3 1252 214 14.54 553 473 46.1 0 0 NA 816067 TCGA-AB-2981 AML41 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 816067 TCGA-AB-2981 AML41 5 177863823 177863823 A G SNP COL23A1 NM_173465.3 human genbank 54_36p -1 validated intronic c.361+56466 e2+56466 0.001 - - - no_errors tier3 480 70 12.68 262 204 43.78 0 0 0 816067 TCGA-AB-2981 AML41 6 105073339 105073339 C T SNP - - - - - - - - - - - - - - - tier3 601 92 13.18 317 248 43.89 0 0 NA 816067 TCGA-AB-2981 AML41 6 163804678 163804678 G A SNP QKI NM_006775.1 human genbank 54_36p 1 validated intronic c.285+8235 e2+8235 0.002 - - - no_errors tier3 1064 194 15.34 374 305 44.85 9 11 55 816067 TCGA-AB-2981 AML41 7 131105126 131105126 C T SNP ENSG00000172400 ENST00000305171 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15806 NULL 0.059 - - - no_coding_region:pseudogene tier3 913 157 14.56 341 274 44.26 0 0 NA 816067 TCGA-AB-2981 AML41 8 52423313 52423313 G A SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.3902-2253 e20-2253 0.008 - - - no_errors tier3 180 14 7.14 52 34 39.53 0 0 NA 816067 TCGA-AB-2981 AML41 8 134842366 134842366 C T SNP ENSG00000208501 ENST00000385766 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5174 NULL 0.045 - - - pseudogene tier3 452 73 13.88 140 140 50 0 0 NA 816067 TCGA-AB-2981 AML41 9 14001086 14001086 G T SNP ENSG00000219127 ENST00000407278 human ensembl 54_36p 1 known 5_prime_flanking_region c.-29634 NULL 0 - - - no_coding_region:pseudogene tier3 1006 159 13.61 388 354 47.71 0 0 NA 816067 TCGA-AB-2981 AML41 9 18196401 18196401 A G SNP - - - - - - - - - - - - - - - tier3 645 99 13.18 334 290 46.47 0 0 NA 816067 TCGA-AB-2981 AML41 9 90022934 90022934 A G SNP ENSG00000216788 ENST00000407613 human ensembl 54_36p -1 known 5_prime_flanking_region c.-27997 NULL 0 - - - no_coding_region:pseudogene tier3 262 52 16.4 80 38 32.2 0 0 NA 816067 TCGA-AB-2981 AML41 10 82549072 82549072 G A SNP ENSG00000218551 ENST00000406125 human ensembl 54_36p -1 known 5_prime_flanking_region c.-21248 NULL 0 - - - no_coding_region:pseudogene tier3 1093 258 19.03 539 575 51.62 0 0 NA 816067 TCGA-AB-2981 AML41 10 86773180 86773180 G A SNP - - - - - - - - - - - - - - - tier3 1274 227 15.06 640 545 45.99 0 0 NA 816067 TCGA-AB-2981 AML41 10 114314275 114314275 G A SNP VTI1A NM_145206.2 human genbank 54_36p 1 validated intronic c.427+26196 e5+26196 0 - - - no_errors tier3 356 72 16.74 161 98 37.84 0 1 100 816067 TCGA-AB-2981 AML41 11 11681626 11681626 T C SNP - - - - - - - - - - - - - - - tier3 1018 232 18.44 572 560 49.38 0 0 NA 816067 TCGA-AB-2981 AML41 11 15870661 15870661 C A SNP - - - - - - - - - - - - - - - tier3 486 101 17.09 274 318 53.72 0 0 NA 816067 TCGA-AB-2981 AML41 11 69930952 69930952 G T SNP CTTN NM_005231.3 human genbank 54_36p 1 reviewed intronic c.1-100 e1-100 0.008 - - - no_errors tier3 330 53 13.73 103 90 46.39 0 0 NA 816067 TCGA-AB-2981 AML41 11 103903669 103903669 G A SNP LOC643718 XM_931763.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*41138 NULL 0 - - - no_errors tier3 968 215 18.11 425 354 45.44 0 0 NA 816067 TCGA-AB-2981 AML41 12 56544366 56544366 C G SNP AVIL NM_006576.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-48276 NULL 0.005 - - - no_errors tier3 1088 181 14.17 205 184 47.3 0 0 NA 816067 TCGA-AB-2981 AML41 12 87863161 87863161 G A SNP - - - - - - - - - - - - - - - tier3 1066 203 15.95 578 469 44.79 0 0 NA 816067 TCGA-AB-2981 AML41 12 115731267 115731267 C T SNP RNFT2 NM_001109903.1 human genbank 54_36p 1 validated intronic c.883-24713 e7-24713 0 - - - no_errors tier3 398 55 12.11 203 151 42.66 0 0 NA 816067 TCGA-AB-2981 AML41 12 118445871 118445871 G A SNP CCDC60 NM_178499.3 human genbank 54_36p 1 validated splice_region c.1104-10 e11-10 0.069 - - - no_errors tier3 791 127 13.79 363 308 45.9 0 0 NA 816067 TCGA-AB-2981 AML41 13 27506311 27506312 - ATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGCCA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1745_1744 p.T582in_frame_insMAGSSDNEYFYVDFREYES 0.986:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 816067 TCGA-AB-2981 AML41 14 25233582 25233582 C T SNP - - - - - - - - - - - - - - - tier3 1387 263 15.84 661 588 47.08 0 0 NA 816067 TCGA-AB-2981 AML41 14 49332385 49332385 A G SNP SDCCAG1 NM_004713.3 human genbank 54_36p -1 validated silent c.2493 p.S831 0.789 NULL "HMMPfam_DUF814,HMMPfam_FbpA" - no_errors tier1 394 59 12.94 136 103 43.1 37 33 47.14 816067 TCGA-AB-2981 AML41 14 77156130 77156130 C T SNP SPTLC2 NM_004863.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-3455 NULL 0.087 - - - no_errors tier3 718 134 15.65 213 153 41.8 0 0 NA 816067 TCGA-AB-2981 AML41 15 73623618 73623618 C T SNP LOC100128562 XM_001726845.1 human genbank 54_36p -1 model silent c.390 p.S130 0 NULL PatternScan_LECTIN_LEGUME_BETA - no_errors tier1 546 93 14.51 161 128 44.29 7 3 30 816067 TCGA-AB-2981 AML41 16 29944069 29944069 C T SNP FAM57B NM_031478.4 human genbank 54_36p -1 validated missense c.761 p.R254H 0.997 "HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724" "HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724" - no_errors tier1 91 26 22.22 31 29 48.33 NA 816067 TCGA-AB-2981 AML41 16 62671707 62671707 C T SNP - - - - - - - - - - - - - - - tier3 835 135 13.87 240 224 48.28 0 0 NA 816067 TCGA-AB-2981 AML41 16 71660750 71660750 G A SNP ZFHX3 NM_006885.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-109205 NULL 0 - - - no_errors tier3 854 180 17.32 319 350 52.24 0 0 NA 816067 TCGA-AB-2981 AML41 16 81388069 81388069 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.46-61399 e2-61399 0.002 - - - no_errors tier3 1274 195 13.19 429 415 49.17 0 0 NA 816067 TCGA-AB-2981 AML41 17 36548778 36548778 G T SNP KRTAP4-12 NM_031854.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14878 NULL 0 - - - no_errors tier3 450 91 16.79 191 148 43.66 0 0 NA 816067 TCGA-AB-2981 AML41 17 76249741 76249741 G A SNP KIAA1303 NM_020761.2 human genbank 54_36p 1 validated intronic c.348+17536 e3+17536 0 - - - no_errors tier3 1050 213 16.82 568 480 45.76 1 2 66.67 816067 TCGA-AB-2981 AML41 17 77423522 77423522 C A SNP P4HB NM_000918.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11886 NULL 0.002 - - - no_errors tier3 169 29 14.65 41 29 41.43 1 1 50 816067 TCGA-AB-2981 AML41 18 13311413 13311413 G A SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.1+43226 e0+43226 0.002 - - - no_errors tier3 581 87 12.89 248 234 48.35 0 1 100 816067 TCGA-AB-2981 AML41 18 19859882 19859882 G A SNP TTC39C NM_153211.1 human genbank 54_36p 1 validated intronic c.1+32882 e0+32882 0 - - - no_errors tier3 670 146 17.83 284 246 46.42 1 0 0 816067 TCGA-AB-2981 AML41 18 48054177 48054177 C T SNP - - - - - - - - - - - - - - - tier3 480 65 11.86 164 129 44.03 0 0 NA 816067 TCGA-AB-2981 AML41 20 26153836 26153836 C T SNP LOC284801 XM_378973.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16391 NULL 0 - - - no_errors tier3 291 11 3.63 173 25 12.63 0 0 NA 816067 TCGA-AB-2981 AML41 20 34534990 34534990 G A SNP DLGAP4 NM_014902.1 human genbank 54_36p 1 reviewed intronic c.1649-23532 e6-23532 0.96 - - - no_errors tier3 429 76 14.9 134 101 42.98 2 2 50 816067 TCGA-AB-2981 AML41 20 41030936 41030936 G A SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.89-82950 e2-82950 0 - - - no_errors tier3 1035 179 14.7 673 579 46.25 0 0 NA 816067 TCGA-AB-2981 AML41 21 14279092 14279092 C A SNP C21orf81 ENST00000400580 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4996 NULL 0 - - - no_errors tier3 744 84 10.11 369 206 35.76 0 0 NA 455499 TCGA-AB-2982 AML16 X 17614138 17614138 G A SNP NHS NM_198270.2 human genbank 54_36p 1 reviewed intronic c.566-1645 e2-1645 0.002 - - - no_errors tier3 722 158 17.95 905 548 37.69 0 0 NA 455499 TCGA-AB-2982 AML16 X 37052212 37052212 G A SNP PRRG1 ENST00000378628 human ensembl 54_36p 1 known 5_prime_flanking_region c.-98212 NULL 0.014 - - - no_errors tier3 167 13 7.22 1084 579 34.77 0 0 NA 455499 TCGA-AB-2982 AML16 X 46825408 46825408 G A SNP RGN NM_004683.4 human genbank 54_36p 1 reviewed intronic c.1-65 e1-65 0 - - - no_errors tier3 411 32 7.22 471 267 36.18 0 0 NA 455499 TCGA-AB-2982 AML16 X 70571004 70571004 C A SNP TAF1 NM_004606.3 human genbank 54_36p 1 reviewed intronic c.4813+10191 e32+10191 0.001 - - - no_errors tier3 754 40 5.04 1662 858 34.05 5 0 0 455499 TCGA-AB-2982 AML16 X 88188318 88188318 G A SNP - - - - - - - - - - - - - - - tier2 446 51 10.24 697 372 34.77 0 0 NA 455499 TCGA-AB-2982 AML16 X 92566613 92566613 T C SNP ENSG00000219191 ENST00000404417 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35972 NULL 1 - - - no_coding_region:pseudogene tier2 328 47 12.53 819 504 38.07 0 0 NA 455499 TCGA-AB-2982 AML16 X 105004850 105004850 C T SNP NRK ENST00000243300 human ensembl 54_36p 1 known intronic c.124-5998 e3-5998 0 - - - no_errors tier3 637 70 9.9 895 505 36.02 0 0 NA 455499 TCGA-AB-2982 AML16 X 105712154 105712154 A T SNP LOC100129700 XM_001718040.1 human genbank 54_36p -1 model intronic c.106+9572 e1+9572 0.087 - - - no_errors tier3 596 83 12.22 758 427 36.03 0 0 NA 455499 TCGA-AB-2982 AML16 X 126928371 126928371 G A SNP - - - - - - - - - - - - - - - tier3 133 25 15.82 612 394 39.17 0 0 NA 455499 TCGA-AB-2982 AML16 1 15391332 15391333 - AGCGTAAGTACACGGGTGG INS ENSG00000215720 ENST00000400795 human ensembl 54_36p -1 known splice_site_ins c.NULL NULL 0.994:0.991 - - - no_coding_region:pseudogene tier1 NA NA NA NA NA NA NA 455499 TCGA-AB-2982 AML16 1 85691966 85691966 C T SNP DDAH1 NM_012137.1 human genbank 54_36p -1 reviewed intronic c.303+11048 e1+11048 0.004 - - - no_errors tier3 359 60 14.29 821 488 37.25 0 1 100 455499 TCGA-AB-2982 AML16 1 111759025 111759048 TCACAGACTGATGACTCACAGGGG - DEL OVGP1 NM_002557.3 human genbank 54_36p -1 reviewed in_frame_del c.1621_1598 p.TPVSHQSV533in_frame_del 0.115:0.128:0.134:0.121:0.100:0.104:0.104:0.104:0.104:0.105:0.099:0.087:0.066:0.056:0.038:0.029:0.001:0.002:0.076:0.129:0.139:0.142:0.139:0.125 NULL "HMMPfam_Glyco_hydro_18,HMMSmart_SM00636,superfamily_(Trans)glycosidases,superfamily_Chitinase insertion domain" - no_errors tier1 NA NA NA NA NA NA NA 455499 TCGA-AB-2982 AML16 1 186890453 186890453 A C SNP ENSG00000217509 ENST00000404186 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16654 NULL 0.003 - - - no_coding_region:pseudogene tier3 221 9 3.91 602 119 16.48 0 0 NA 455499 TCGA-AB-2982 AML16 1 192573011 192573011 G A SNP - - - - - - - - - - - - - - - tier3 201 18 8.22 668 377 36.08 0 0 NA 455499 TCGA-AB-2982 AML16 1 218206228 218206228 G A SNP SLC30A10 NM_018713.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-37823 NULL 0 - - - no_errors tier3 258 22 7.86 559 282 33.41 0 0 NA 455499 TCGA-AB-2982 AML16 1 235486540 235486540 G A SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.49-13880 e2-13880 0.009 - - - no_errors tier3 432 59 12.02 544 294 35 0 0 NA 455499 TCGA-AB-2982 AML16 2 12651559 12651559 T C SNP - - - - - - - - - - - - - - - tier3 224 43 16.1 704 384 35.23 0 0 NA 455499 TCGA-AB-2982 AML16 2 21964258 21964258 G T SNP ENSG00000222621 ENST00000410689 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-35112 NULL 0 - - - no_errors tier3 374 32 7.88 701 410 36.67 0 0 NA 455499 TCGA-AB-2982 AML16 2 23112165 23112165 G T SNP - - - - - - - - - - - - - - - tier3 738 135 15.45 630 422 40.08 0 0 NA 455499 TCGA-AB-2982 AML16 2 44751579 44751579 A G SNP C2orf34 NM_024766.3 human genbank 54_36p 1 validated intronic c.377-33347 e4-33347 0.069 - - - no_errors tier3 492 49 9.06 906 562 38.26 0 0 NA 455499 TCGA-AB-2982 AML16 2 75880083 75880083 C T SNP - - - - - - - - - - - - - - - tier2 289 18 5.86 1217 635 34.27 0 0 NA 455499 TCGA-AB-2982 AML16 2 83696418 83696418 A G SNP ENSG00000199295 ENST00000362425 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41952 NULL 0.014 - - - no_errors tier3 507 38 6.97 1021 589 36.56 0 0 NA 455499 TCGA-AB-2982 AML16 2 112086761 112086761 C T SNP - - - - - - - - - - - - - - - tier3 716 66 8.44 549 304 35.64 0 0 NA 455499 TCGA-AB-2982 AML16 2 116746417 116746417 G A SNP - - - - - - - - - - - - - - - tier3 276 17 5.8 752 186 19.83 0 0 NA 455499 TCGA-AB-2982 AML16 2 124548603 124548603 G T SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.82+48824 e1+48824 0.001 - - - no_errors tier3 953 71 6.93 1346 285 17.45 0 0 NA 455499 TCGA-AB-2982 AML16 2 146986107 146986107 G A SNP - - - - - - - - - - - - - - - tier3 196 7 3.45 693 314 31.09 0 0 NA 455499 TCGA-AB-2982 AML16 2 177056721 177056721 G A SNP - - - - - - - - - - - - - - - tier3 558 29 4.94 823 400 32.71 0 0 NA 455499 TCGA-AB-2982 AML16 2 234796151 234796151 T C SNP ENSG00000220908 ENST00000404689 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*24767 NULL 0 - - - no_coding_region:pseudogene tier2 42 3 6.67 364 223 37.86 0 0 NA 455499 TCGA-AB-2982 AML16 3 29303577 29303577 G A SNP RBMS3 NM_001003793.1 human genbank 54_36p 1 reviewed intronic c.75+5326 e1+5326 0.001 - - - no_errors tier3 472 95 16.75 605 310 33.88 0 0 NA 455499 TCGA-AB-2982 AML16 3 33169319 33169319 G A SNP SUSD5 NM_015551.1 human genbank 54_36p -1 validated silent c.1809 p.H603 1 NULL "HMMSmart_CCP,HMMPfam_Xlink,HMMSmart_LINK,PatternScan_LINK_1,superfamily_Complement_control_module,superfamily_C-type_lectin_fold" - no_errors tier1 466 36 7.17 800 472 37.08 NA 455499 TCGA-AB-2982 AML16 3 35361418 35361418 A G SNP - - - - - - - - - - - - - - - tier3 646 147 18.54 874 493 36.06 0 0 NA 455499 TCGA-AB-2982 AML16 3 39275507 39275507 T G SNP CX3CR1 NM_001337.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*6430 NULL 0.001 - - - no_errors tier3 291 33 10.19 599 395 39.66 0 0 NA 455499 TCGA-AB-2982 AML16 3 58686004 58686004 C T SNP C3orf67 NM_198463.2 human genbank 54_36p -1 predicted 3_prime_flanking_region c.*17223 NULL 0.004 - - - no_errors tier3 247 47 15.99 785 450 36.41 0 0 NA 455499 TCGA-AB-2982 AML16 3 63051605 63051605 C G SNP - - - - - - - - - - - - - - - tier3 916 110 10.71 927 489 34.51 0 0 NA 455499 TCGA-AB-2982 AML16 3 114367012 114367012 C G SNP BOC NM_033254.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-84328 NULL 0 - - - no_errors tier3 441 50 10.18 1034 558 34.98 0 0 NA 455499 TCGA-AB-2982 AML16 3 157539819 157539819 T A SNP KCNAB1 NM_172160.3 human genbank 54_36p 1 reviewed intronic c.276-82280 e2-82280 0.001 - - - no_errors tier3 208 24 10.34 478 261 35.32 0 0 NA 455499 TCGA-AB-2982 AML16 3 165422183 165422183 T C SNP - - - - - - - - - - - - - - - tier3 31 1 3.12 218 116 34.73 0 0 NA 455499 TCGA-AB-2982 AML16 3 173066789 173066789 C T SNP LOC100130245 XM_001726380.1 human genbank 54_36p 1 model intronic c.585+9598 e4+9598 0 - - - no_errors tier2 327 64 16.37 1007 583 36.67 0 0 NA 455499 TCGA-AB-2982 AML16 4 20569005 20569005 A T SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.101-107617 e2-107617 0 - - - no_errors tier3 180 24 11.76 511 268 34.4 0 0 NA 455499 TCGA-AB-2982 AML16 4 22272367 22272367 C T SNP GBA3 ENST00000317327 human ensembl 54_36p 1 known 5_prime_flanking_region c.-31370 NULL 0.982 - - - no_errors tier3 527 67 11.28 681 427 38.5 0 0 NA 455499 TCGA-AB-2982 AML16 4 27754443 27754443 A C SNP - - - - - - - - - - - - - - - tier3 461 46 9.07 620 326 34.42 0 0 NA 455499 TCGA-AB-2982 AML16 4 63446963 63446963 T A SNP - - - - - - - - - - - - - - - tier3 249 38 13.24 552 323 36.91 0 0 NA 455499 TCGA-AB-2982 AML16 4 65254084 65254084 C T SNP - - - - - - - - - - - - - - - tier3 563 76 11.84 734 345 31.94 0 0 NA 455499 TCGA-AB-2982 AML16 4 132055946 132055946 C T SNP - - - - - - - - - - - - - - - tier3 233 27 10.38 960 566 37.09 0 0 NA 455499 TCGA-AB-2982 AML16 4 169162398 169162398 C T SNP - - - - - - - - - - - - - - - tier2 122 14 10.29 654 338 34.04 0 0 NA 455499 TCGA-AB-2982 AML16 4 169790613 169790613 C T SNP PALLD NM_016081.3 human genbank 54_36p 1 validated intronic c.909-35303 e2-35303 0.006 - - - no_errors tier2 417 43 9.35 678 396 36.84 0 0 NA 455499 TCGA-AB-2982 AML16 5 2513893 2513893 C A SNP - - - - - - - - - - - - - - - tier3 2436 90 3.56 1428 271 15.95 0 0 NA 455499 TCGA-AB-2982 AML16 5 29083204 29083204 A T SNP - - - - - - - - - - - - - - - tier2 108 1 0.92 724 137 15.84 0 0 NA 455499 TCGA-AB-2982 AML16 5 91000315 91000315 G A SNP - - - - - - - - - - - - - - - tier3 78 7 8.24 373 212 36.24 0 0 NA 455499 TCGA-AB-2982 AML16 5 104584443 104584443 G A SNP - - - - - - - - - - - - - - - tier3 235 35 12.92 424 237 35.85 0 0 NA 455499 TCGA-AB-2982 AML16 5 109993401 109993401 C T SNP FLJ43080 XM_001719018.2 human genbank 54_36p -1 model intronic c.496-1921 e5-1921 0.004 - - - no_errors tier3 302 27 8.21 712 434 37.84 0 0 0 455499 TCGA-AB-2982 AML16 5 153577229 153577229 G A SNP GALNT10 NM_198321.3 human genbank 54_36p 1 reviewed intronic c.159+26451 e1+26451 0.008 - - - no_errors tier2 446 56 11.13 535 260 32.58 0 1 100 455499 TCGA-AB-2982 AML16 5 160616867 160616867 G A SNP ENSG00000221002 ENST00000408075 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27135 NULL 0.274 - - - no_errors tier3 479 46 8.75 368 222 37.63 0 0 NA 455499 TCGA-AB-2982 AML16 5 165839387 165839387 A T SNP - - - - - - - - - - - - - - - tier3 587 26 4.24 674 138 16.97 0 0 NA 455499 TCGA-AB-2982 AML16 5 166874680 166874680 C T SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.502+139624 e2+139624 0 - - - no_errors tier3 317 26 7.58 1022 622 37.79 0 0 NA 455499 TCGA-AB-2982 AML16 6 22636780 22636780 A G SNP HDGFL1 NM_138574.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-41004 NULL 0 - - - no_errors tier3 94 8 7.84 591 320 35.09 0 0 NA 455499 TCGA-AB-2982 AML16 6 40234500 40234500 G T SNP - - - - - - - - - - - - - - - tier3 326 45 12.13 920 541 37.03 0 0 NA 455499 TCGA-AB-2982 AML16 6 49741293 49741293 G A SNP RHAG NM_000324.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-28809 NULL 0.001 - - - no_errors tier3 245 43 14.93 716 369 34.01 0 0 NA 455499 TCGA-AB-2982 AML16 6 50127602 50127602 G A SNP DEFB112 NM_001037498.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-3279 NULL 0.003 - - - no_errors tier2 77 6 7.23 455 237 34.25 0 0 NA 455499 TCGA-AB-2982 AML16 6 54491432 54491432 C A SNP ENSG00000213335 ENST00000393532 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32810 NULL 0.002 - - - no_coding_region:pseudogene tier3 212 16 7.02 515 175 25.33 0 0 NA 455499 TCGA-AB-2982 AML16 6 69472791 69472791 C A SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.757+66746 e1+66746 0.001 - - - no_errors tier3 465 85 15.45 852 445 34.28 0 0 NA 455499 TCGA-AB-2982 AML16 6 83397640 83397640 G A SNP - - - - - - - - - - - - - - - tier3 528 27 4.86 1447 593 29.05 0 0 NA 455499 TCGA-AB-2982 AML16 6 86928919 86928919 C G SNP ENSG00000217272 ENST00000401856 human ensembl 54_36p -1 known 3_prime_flanking_region c.*7965 NULL 0.186 - - - no_coding_region:pseudogene tier3 842 77 8.38 575 320 35.67 0 0 NA 455499 TCGA-AB-2982 AML16 6 91705397 91705397 G A SNP - - - - - - - - - - - - - - - tier3 134 10 6.94 374 199 34.73 0 0 NA 455499 TCGA-AB-2982 AML16 6 98397963 98397963 A G SNP - - - - - - - - - - - - - - - tier3 183 22 10.73 516 240 31.75 0 0 NA 455499 TCGA-AB-2982 AML16 6 112798441 112798441 T C SNP LOC100128588 XM_001723020.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-43797 NULL 0.031 - - - no_errors tier3 99 9 8.33 269 210 43.84 0 0 NA 455499 TCGA-AB-2982 AML16 6 143182392 143182392 G C SNP HIVEP2 NM_006734.3 human genbank 54_36p -1 provisional intronic c.1+17373 e0+17373 0.025 - - - no_errors tier2 88 7 7.37 985 466 32.12 0 0 0 455499 TCGA-AB-2982 AML16 6 159883472 159883472 G A SNP LOC642738 XR_017625.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-15877 NULL 0.005 - - - pseudogene tier3 235 22 8.56 805 580 41.85 0 0 NA 455499 TCGA-AB-2982 AML16 6 166168369 166168369 T G SNP - - - - - - - - - - - - - - - tier3 386 57 12.87 561 329 36.84 0 0 NA 455499 TCGA-AB-2982 AML16 7 7332585 7332585 C T SNP COL28A1 NM_001037763.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*32204 NULL 0.004 - - - no_errors tier2 402 19 4.51 1573 357 18.49 0 0 NA 455499 TCGA-AB-2982 AML16 7 76663891 76663891 C A SNP FGL2 NM_006682.2 human genbank 54_36p -1 reviewed missense c.961 p.V321L 1 "HMMPfam_Fibrinogen_C,HMMSmart_SM00186,superfamily_Fibrinogen C-terminal domain-like" "HMMPfam_Fibrinogen_C,HMMSmart_SM00186,PatternScan_FIBRIN_AG_C_DOMAIN,superfamily_Fibrinogen C-terminal domain-like" - no_errors tier1 168 17 9.19 663 360 35.19 1 3 75 455499 TCGA-AB-2982 AML16 7 109010488 109010488 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 455499 TCGA-AB-2982 AML16 7 114337500 114337500 A G SNP MDFIC ENST00000393486 human ensembl 54_36p 1 known 5_prime_flanking_region c.-12825 NULL 0.489 - - - no_errors tier3 119 6 4.8 321 223 40.92 0 0 NA 455499 TCGA-AB-2982 AML16 7 114979767 114979767 G T SNP ENSG00000202377 ENST00000365507 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*28838 NULL 0 - - - no_errors tier3 70 3 4.11 515 229 30.74 0 0 NA 455499 TCGA-AB-2982 AML16 8 48987793 48987793 T C SNP PRKDC ENST00000314191 human ensembl 54_36p -1 known intronic c.2782-118 e25-118 0 - - - no_errors tier3 54 5 8.47 349 158 31.16 2 1 33.33 455499 TCGA-AB-2982 AML16 8 51599420 51599420 T C SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.467-5870 e8-5870 0 - - - no_errors tier3 74 7 8.64 562 285 33.65 0 0 NA 455499 TCGA-AB-2982 AML16 8 63736703 63736703 C A SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.273+71796 e3+71796 0.011 - - - no_errors tier3 182 24 11.65 1101 650 37.12 0 0 NA 455499 TCGA-AB-2982 AML16 8 70650209 70650209 G A SNP SULF1 NM_015170.1 human genbank 54_36p 1 validated intronic c.173-550 e2-550 0 - - - no_errors tier3 245 18 6.84 487 283 36.75 0 0 0 455499 TCGA-AB-2982 AML16 8 94201509 94201509 C A SNP LOC389676 XM_374276.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*14190 NULL 0.001 - - - no_errors tier2 446 50 10.08 662 382 36.56 0 0 NA 455499 TCGA-AB-2982 AML16 8 105463270 105463289 ACACACACACACACACACAT - DEL ENSG00000220279 ENST00000404280 human ensembl 54_36p -1 known frame_shift_del c.155_136 p.M46fs 0.001:0.000:0.000:0.000:0.000:0.001:0.001:0.001:0.001:0.002:0.001:0.000:0.000:0.000:0.001:0.000:0.000:0.000:0.000:0.000 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA 455499 TCGA-AB-2982 AML16 8 118158426 118158426 C A SNP SLC30A8 ENST00000297345 human ensembl 54_36p 1 known intronic c.1+37748 e0+37748 0.271 - - - no_errors tier3 120 2 1.64 482 92 16.03 0 0 NA 455499 TCGA-AB-2982 AML16 8 130359543 130359543 A T SNP LOC728724 XM_001128934.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-36930 NULL 0 - - - no_errors tier3 315 26 7.6 848 417 32.94 0 0 NA 455499 TCGA-AB-2982 AML16 9 82207547 82207547 A - DEL ENSG00000218777 ENST00000404193 human ensembl 54_36p -1 known 5_prime_flanking_region c.-42474 NULL 1 - - - no_coding_region:pseudogene tier2 NA NA NA NA NA NA 0 0 NA 455499 TCGA-AB-2982 AML16 10 30239587 30239587 G A SNP ENSG00000220159 ENST00000402446 human ensembl 54_36p -1 known 5_prime_flanking_region c.-19185 NULL 0 - - - no_coding_region:pseudogene tier2 651 96 12.85 925 588 38.86 0 0 NA 455499 TCGA-AB-2982 AML16 10 57490912 57490912 A T SNP - - - - - - - - - - - - - - - tier3 158 1 0.63 733 139 15.94 0 0 NA 455499 TCGA-AB-2982 AML16 10 128460850 128460850 T G SNP ENSG00000199321 ENST00000362451 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2517 NULL 0 - - - no_errors tier3 162 15 8.47 297 168 36.13 0 0 NA 455499 TCGA-AB-2982 AML16 11 41192009 41192009 A G SNP - - - - - - - - - - - - - - - tier3 265 22 7.67 1125 601 34.8 0 0 NA 455499 TCGA-AB-2982 AML16 11 41592401 41592401 G A SNP - - - - - - - - - - - - - - - tier3 546 80 12.74 1057 603 36.22 0 0 NA 455499 TCGA-AB-2982 AML16 11 46873485 46873485 C T SNP LRP4 NM_002334.2 human genbank 54_36p -1 validated intronic c.1184-67 e11-67 0 - - - no_errors tier3 235 38 13.92 220 134 37.75 0 0 NA 455499 TCGA-AB-2982 AML16 11 88891441 88891441 G A SNP NOX4 NM_016931.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27379 NULL 0 - - - no_errors tier3 614 49 7.39 768 384 33.3 0 0 NA 455499 TCGA-AB-2982 AML16 11 104610071 104610071 T C SNP - - - - - - - - - - - - - - - tier3 143 8 5.3 477 231 32.58 0 0 NA 455499 TCGA-AB-2982 AML16 11 114159343 114159343 C A SNP - - - - - - - - - - - - - - - tier3 904 30 3.21 1853 401 17.78 0 0 NA 455499 TCGA-AB-2982 AML16 12 577213 577213 G A SNP NINJ2 NM_016533.4 human genbank 54_36p -1 validated intronic c.172-31608 e2-31608 0 - - - no_errors tier3 370 53 12.53 341 172 33.53 0 0 0 455499 TCGA-AB-2982 AML16 12 3545391 3545391 G A SNP PRMT8 NM_019854.3 human genbank 54_36p 1 validated intronic c.482-2742 e5-2742 0.183 - - - no_errors tier3 733 134 15.44 841 480 36.28 0 0 NA 455499 TCGA-AB-2982 AML16 12 5326326 5326326 G A SNP LOC100133418 XM_001714459.1 human genbank 54_36p -1 model intronic c.444+4772 e2+4772 0 - - - no_start_codon:pseudogene:no_stop_codon tier2 814 84 9.34 624 327 34.38 0 0 NA 455499 TCGA-AB-2982 AML16 12 122266308 122266308 T C SNP MPHOSPH9 NM_022782.2 human genbank 54_36p -1 validated intronic c.541-974 e3-974 0 - - - no_errors tier3 312 34 9.8 498 244 32.88 3 2 40 455499 TCGA-AB-2982 AML16 12 127653147 127653147 C A SNP TMEM132C ENST00000315208 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13534 NULL 0 - - - no_errors tier2 446 56 11.16 547 322 36.88 0 0 NA 455499 TCGA-AB-2982 AML16 13 29720439 29720439 T C SNP KATNAL1 NM_001014380.1 human genbank 54_36p -1 validated intronic c.492+7145 e3+7145 0 - - - no_errors tier3 256 30 10.49 410 248 37.63 0 0 0 455499 TCGA-AB-2982 AML16 13 72030278 72030278 T C SNP ENSG00000199282 ENST00000362412 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-28541 NULL 0.013 - - - no_errors tier2 370 42 10.19 833 442 34.67 0 0 NA 455499 TCGA-AB-2982 AML16 13 73162206 73162206 G A SNP KLF12 NM_007249.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*5422 NULL 0 - - - no_errors tier3 136 3 2.16 539 101 15.78 3 0 0 455499 TCGA-AB-2982 AML16 13 79097153 79097153 A G SNP - - - - - - - - - - - - - - - tier3 198 23 10.41 490 266 35.09 0 0 NA 455499 TCGA-AB-2982 AML16 13 85350192 85350192 G A SNP - - - - - - - - - - - - - - - tier2 82 2 2.38 474 253 34.75 0 0 NA 455499 TCGA-AB-2982 AML16 13 97856091 97856091 A T SNP FARP1 NM_005766.2 human genbank 54_36p 1 reviewed intronic c.1415-3502 e13-3502 0.003 - - - no_errors tier3 792 82 9.38 655 340 34.17 0 0 0 455499 TCGA-AB-2982 AML16 14 24990954 24990954 G A SNP - - - - - - - - - - - - - - - tier3 640 60 8.57 766 430 35.89 0 0 NA 455499 TCGA-AB-2982 AML16 14 33495271 33495271 C T SNP EGLN3 NM_022073.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5562 NULL 0.002 - - - no_errors tier3 107 13 10.83 322 191 37.23 0 0 NA 455499 TCGA-AB-2982 AML16 14 68789630 68789630 C G SNP GALNTL1 NM_020692.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-7131 NULL 0.818 - - - no_errors tier2 1152 95 7.62 522 236 31.13 0 0 NA 455499 TCGA-AB-2982 AML16 14 75092317 75092317 C T SNP FLVCR2 NM_017791.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22752 NULL 0 - - - no_errors tier3 1322 44 3.22 1118 204 15.42 0 0 NA 455499 TCGA-AB-2982 AML16 14 97700081 97700081 T A SNP - - - - - - - - - - - - - - - tier3 761 77 9.19 795 451 36.17 1 0 0 455499 TCGA-AB-2982 AML16 15 58865641 58865641 C T SNP RORA NM_134261.3 human genbank 54_36p -1 reviewed intronic c.167-107464 e2-107464 0.002 - - - no_errors tier3 303 36 10.62 495 267 35.04 0 0 NA 455499 TCGA-AB-2982 AML16 15 85490797 85490797 G A SNP - - - - - - - - - - - - - - - tier3 260 42 13.91 688 374 35.22 0 0 NA 455499 TCGA-AB-2982 AML16 15 87547224 87547224 T C SNP FANCI NM_018193.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-44659 NULL 0.011 - - - no_errors tier3 319 49 13.28 313 174 35.73 0 0 NA 455499 TCGA-AB-2982 AML16 16 7529873 7529873 C T SNP A2BP1 NM_145891.1 human genbank 54_36p 1 reviewed intronic c.330+21481 e2+21481 0.001 - - - no_errors tier3 620 107 14.7 728 384 34.5 0 0 NA 455499 TCGA-AB-2982 AML16 16 22759008 22759008 G T SNP HS3ST2 NM_006043.1 human genbank 54_36p 1 reviewed intronic c.485+25091 e1+25091 0.002 - - - no_errors tier3 1745 164 8.58 1077 633 37.02 0 0 NA 455499 TCGA-AB-2982 AML16 16 54908358 54908358 G A SNP GNAO1 NM_020988.2 human genbank 54_36p 1 validated intronic c.304-11686 e4-11686 0 - - - no_errors tier2 171 15 8.06 266 114 30 0 0 NA 455499 TCGA-AB-2982 AML16 16 59595920 59595920 G C SNP ENSG00000180019 ENST00000321498 human ensembl 54_36p -1 novel intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 251 35 12.24 928 493 34.69 0 0 NA 455499 TCGA-AB-2982 AML16 17 12082296 12082296 C T SNP - - - - - - - - - - - - - - - tier2 504 25 4.73 590 299 33.45 0 0 NA 455499 TCGA-AB-2982 AML16 18 43993856 43993856 G A SNP C18orf12 XR_040899.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-38814 NULL 0 - - - no_errors tier3 443 52 10.48 1034 619 37.33 0 0 NA 455499 TCGA-AB-2982 AML16 18 47945352 47945352 G T SNP - - - - - - - - - - - - - - - tier3 403 63 13.52 575 344 37.39 0 0 NA 455499 TCGA-AB-2982 AML16 18 69654334 69654334 G - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 455499 TCGA-AB-2982 AML16 19 9906673 9906673 G A SNP OLFM2 NM_058164.2 human genbank 54_36p -1 provisional intronic c.63+1307 e1+1307 0.013 - - - no_errors tier3 368 57 13.41 221 120 35.19 0 0 0 455499 TCGA-AB-2982 AML16 20 35783079 35783079 C G SNP CTNNBL1 NM_030877.3 human genbank 54_36p 1 reviewed intronic c.31-11616 e2-11616 0.027 - - - no_errors tier3 345 29 7.75 427 209 32.81 1 0 0 455499 TCGA-AB-2982 AML16 22 42141668 42141668 G T SNP MPPED1 ENST00000334209 human ensembl 54_36p 1 known intronic c.1+3560 e0+3560 0.001 - - - no_errors tier3 279 19 6.38 156 108 40.91 0 0 NA 700717 TCGA-AB-2983 AML36 X 3343551 3343551 A - DEL LOC100130844 XR_042509.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-20190 NULL 0.01 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 X 17756726 17756726 A - DEL RAI2 ENST00000331511 human ensembl 54_36p -1 known intronic c.1+8852 e0+8852 0.017 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 X 31924780 31924780 C T SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6439-28228 e45-28228 0 - - - no_errors tier3 831 21 2.45 310 957 75.41 0 0 NA 700717 TCGA-AB-2983 AML36 X 33978744 33978744 C A SNP - - - - - - - - - - - - - - - tier3 594 24 3.87 151 813 84.25 0 0 NA 700717 TCGA-AB-2983 AML36 X 34048632 34048632 G T SNP LOC139431 XR_017164.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-25795 NULL 0.004 - - - no_errors tier3 258 9 3.36 77 467 85.85 0 0 NA 700717 TCGA-AB-2983 AML36 X 52058443 52058443 C T SNP - - - - - - - - - - - - - - - tier3 346 11 3.07 90 602 86.74 0 0 NA 700717 TCGA-AB-2983 AML36 X 58095841 58095841 G C SNP - - - - - - - - - - - - - - - tier3 760 24 3.06 225 1048 82.07 0 0 NA 700717 TCGA-AB-2983 AML36 X 77659702 77659702 T A SNP ENSG00000218635 ENST00000406464 human ensembl 54_36p 1 known 5_prime_flanking_region c.-36861 NULL 0.002 - - - no_coding_region:pseudogene tier3 303 15 4.7 86 594 87.22 0 0 NA 700717 TCGA-AB-2983 AML36 X 94964405 94964405 T C SNP - - - - - - - - - - - - - - - tier3 208 11 5.02 73 438 85.71 0 0 NA 700717 TCGA-AB-2983 AML36 X 99319291 99319291 A - DEL ENSG00000220672 ENST00000405682 human ensembl 54_36p -1 known 5_prime_flanking_region c.-26260 NULL 0.049 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 X 115657045 115657045 G A SNP ENSG00000218675 ENST00000407812 human ensembl 54_36p 1 known 5_prime_flanking_region c.-49821 NULL 0.004 - - - no_coding_region:pseudogene tier3 371 15 3.88 141 745 83.99 0 0 NA 700717 TCGA-AB-2983 AML36 X 127601113 127601113 T C SNP ENSG00000223339 ENST00000411407 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15555 NULL 0.001 - - - no_errors tier3 823 33 3.85 122 732 85.71 0 0 NA 700717 TCGA-AB-2983 AML36 X 143588083 143588083 G A SNP - - - - - - - - - - - - - - - tier3 1221 38 3.01 192 1441 88.19 0 0 NA 700717 TCGA-AB-2983 AML36 1 2561154 2561154 G A SNP MMEL1 NM_033467.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-10398 NULL 0.112 - - - no_errors tier3 69 1 1.43 57 47 45.19 1 2 66.67 700717 TCGA-AB-2983 AML36 1 4021792 4021792 G A SNP - - - - - - - - - - - - - - - tier3 768 18 2.28 710 528 42.55 0 0 NA 700717 TCGA-AB-2983 AML36 1 11445880 11445880 G A SNP PTCHD2 NM_020780.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37757 NULL 0.004 - - - no_errors tier3 346 9 2.54 231 164 41.41 0 0 NA 700717 TCGA-AB-2983 AML36 1 44688593 44688593 G A SNP RNF220 NM_018150.2 human genbank 54_36p 1 validated intronic c.625+37612 e1+37612 0.005 - - - no_errors tier3 352 2 0.56 522 237 31.14 140 109 43.78 700717 TCGA-AB-2983 AML36 1 58194055 58194055 A - DEL DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.1-71633 e1-71633 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 1 66115022 66115022 G A SNP PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.1-36494 e1-36494 0.006 - - - no_errors tier3 508 10 1.92 594 377 38.83 2 0 0 700717 TCGA-AB-2983 AML36 1 70150230 70150230 G T SNP LRRC7 NM_020794.2 human genbank 54_36p 1 validated intronic c.534-19548 e6-19548 0.053 - - - no_errors tier3 221 3 1.34 366 222 37.76 0 0 NA 700717 TCGA-AB-2983 AML36 1 76699602 76699602 G A SNP ST6GALNAC3 NM_152996.1 human genbank 54_36p 1 provisional intronic c.623+48912 e3+48912 0.29 - - - no_errors tier3 883 23 2.53 987 703 41.57 1 0 0 700717 TCGA-AB-2983 AML36 1 101821352 101821352 G T SNP - - - - - - - - - - - - - - - tier3 1020 28 2.66 733 593 44.65 0 0 NA 700717 TCGA-AB-2983 AML36 1 105451153 105451153 G A SNP - - - - - - - - - - - - - - - tier3 884 14 1.56 926 523 36.09 0 0 NA 700717 TCGA-AB-2983 AML36 1 107329287 107329287 G T SNP - - - - - - - - - - - - - - - tier3 1618 38 2.29 1050 709 40.24 0 0 NA 700717 TCGA-AB-2983 AML36 1 109896437 109896437 A G SNP GNAI3 NM_006496.2 human genbank 54_36p 1 validated intronic c.118+3454 e1+3454 0 - - - no_errors tier3 638 12 1.85 829 596 41.8 8 0 0 700717 TCGA-AB-2983 AML36 1 115291613 115291613 C T SNP SYCP1 NM_003176.2 human genbank 54_36p 1 validated intronic c.2322+149 e26+149 0.001 - - - no_errors tier3 71 1 1.37 173 74 29.96 0 0 NA 700717 TCGA-AB-2983 AML36 1 119062662 119062662 C T SNP ENSG00000219711 ENST00000401940 human ensembl 54_36p 1 known 3_prime_flanking_region c.*4837 NULL 0 - - - no_coding_region:pseudogene tier3 246 9 3.5 431 324 42.8 0 0 NA 700717 TCGA-AB-2983 AML36 1 158352416 158352416 C T SNP ATP1A2 NM_000702.3 human genbank 54_36p 1 reviewed intronic c.12+129 e1+129 0.001 - - - no_errors tier3 642 10 1.53 342 197 36.48 0 0 NA 700717 TCGA-AB-2983 AML36 1 160367800 160367800 G A SNP NOS1AP NM_014697.1 human genbank 54_36p 1 reviewed intronic c.106-23019 e2-23019 0.004 - - - no_errors tier3 244 9 3.5 168 137 44.63 0 0 NA 700717 TCGA-AB-2983 AML36 1 164137388 164137388 G A SNP UCK2 NM_012474.3 human genbank 54_36p 1 reviewed intronic c.500-1655 e5-1655 0.064 - - - no_errors tier3 1399 24 1.68 1047 787 42.86 6 7 53.85 700717 TCGA-AB-2983 AML36 1 167241939 167241939 A G SNP - - - - - - - - - - - - - - - tier3 1642 25 1.49 1187 879 42.44 0 0 NA 700717 TCGA-AB-2983 AML36 1 168293185 168293185 A G SNP KIFAP3 NM_014970.2 human genbank 54_36p -1 reviewed intronic c.33-1984 e2-1984 0.013 - - - no_errors tier3 701 21 2.9 1221 935 43.35 0 0 0 700717 TCGA-AB-2983 AML36 1 168870961 168870961 T A SNP PRRX1 NM_022716.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29023 NULL 0 - - - no_errors tier3 871 11 1.24 472 355 42.82 0 0 NA 700717 TCGA-AB-2983 AML36 1 174814537 174814537 C G SNP PAPPA2 NM_020318.2 human genbank 54_36p 1 validated intronic c.920-15746 e2-15746 0.001 - - - no_errors tier3 1019 16 1.54 885 677 43.31 0 0 NA 700717 TCGA-AB-2983 AML36 1 181282723 181282723 A G SNP LAMC1 NM_002293.3 human genbank 54_36p 1 reviewed intronic c.418+22831 e1+22831 0 - - - no_errors tier3 547 8 1.44 773 551 41.58 0 0 0 700717 TCGA-AB-2983 AML36 1 184708070 184708070 T C SNP PDC NM_002597.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22856 NULL 0.001 - - - no_errors tier3 309 2 0.64 418 245 36.95 0 0 NA 700717 TCGA-AB-2983 AML36 1 189143308 189143308 T C SNP - - - - - - - - - - - - - - - tier3 543 11 1.98 703 527 42.85 0 0 NA 700717 TCGA-AB-2983 AML36 1 193976837 193976837 C T SNP - - - - - - - - - - - - - - - tier3 418 17 3.9 396 300 42.92 0 0 NA 700717 TCGA-AB-2983 AML36 1 201452746 201452746 C T SNP CHIT1 NM_003465.2 human genbank 54_36p -1 reviewed missense c.1295 p.R432Q 0 "HMMPfam_CBM_14,HMMSmart_SM00494,superfamily_Invertebrate chitin-binding proteins" "HMMPfam_Glyco_hydro_18,PatternScan_CHITINASE_18,HMMPfam_CBM_14,HMMSmart_SM00494,superfamily_Invertebrate chitin-binding proteins,HMMSmart_SM00636,superfamily_(Trans)glycosidases,superfamily_Chitinase insertion domain" - no_errors tier1 542 12 2.16 461 373 44.62 0 700717 TCGA-AB-2983 AML36 1 211652808 211652808 C T SNP LOC643330 XM_926662.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*15866 NULL 0.008 - - - no_errors tier3 1525 35 2.24 1080 674 38.32 0 0 NA 700717 TCGA-AB-2983 AML36 1 215611550 215611551 TG - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 1 219568668 219568668 C T SNP - - - - - - - - - - - - - - - tier3 780 24 2.98 588 392 39.96 0 0 NA 700717 TCGA-AB-2983 AML36 1 230737584 230737584 C T SNP LOC729336 XM_001129978.2 human genbank 54_36p -1 model intronic c.1318-19607 e6-19607 0 - - - no_errors tier3 1169 14 1.18 1052 769 42.21 0 0 0 700717 TCGA-AB-2983 AML36 1 243921667 243921667 A - DEL KIF26B NM_018012.3 human genbank 54_36p 1 provisional intronic c.5824+2935 e12+2935 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 2 3008478 3008478 A T SNP - - - - - - - - - - - - - - - tier3 971 12 1.22 933 643 40.72 0 0 NA 700717 TCGA-AB-2983 AML36 2 4688345 4688345 C T SNP LOC727982 XR_039999.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-6677 NULL 0.001 - - - no_errors tier3 1496 27 1.76 1000 742 42.52 0 0 NA 700717 TCGA-AB-2983 AML36 2 12705471 12705471 C T SNP - - - - - - - - - - - - - - - tier3 1392 20 1.41 1140 815 41.65 0 0 NA 700717 TCGA-AB-2983 AML36 2 13747658 13747658 C T SNP - - - - - - - - - - - - - - - tier3 1144 12 1.03 837 591 41.18 0 0 NA 700717 TCGA-AB-2983 AML36 2 15151768 15151768 C T SNP - - - - - - - - - - - - - - - tier3 715 23 3.12 508 329 39.21 0 0 NA 700717 TCGA-AB-2983 AML36 2 21804980 21804980 A G SNP LOC645949 XR_040569.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-6815 NULL 0 - - - no_errors tier3 1004 26 2.52 854 705 45.19 0 0 NA 700717 TCGA-AB-2983 AML36 2 23136226 23136226 C T SNP - - - - - - - - - - - - - - - tier3 3700 104 2.73 2109 1624 43.41 0 0 NA 700717 TCGA-AB-2983 AML36 2 29854992 29854992 C A SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.668-60925 e2-60925 0.001 - - - no_errors tier3 1281 18 1.38 820 612 42.71 0 0 NA 700717 TCGA-AB-2983 AML36 2 30504925 30504925 C T SNP LCLAT1 NM_182551.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-31058 NULL 0.013 - - - no_errors tier3 1578 30 1.86 912 679 42.6 0 0 NA 700717 TCGA-AB-2983 AML36 2 34405558 34405558 T A SNP - - - - - - - - - - - - - - - tier3 662 13 1.92 812 598 42.35 0 0 NA 700717 TCGA-AB-2983 AML36 2 35713492 35713492 C T SNP - - - - - - - - - - - - - - - tier3 1367 30 2.14 917 679 42.49 0 0 NA 700717 TCGA-AB-2983 AML36 2 36996748 36996748 A T SNP STRN NM_003162.2 human genbank 54_36p -1 validated missense c.389 p.M130K 1 HMMPfam_Striatin "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_Striatin,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 706 8 1.12 708 540 43.23 6 1 14.29 700717 TCGA-AB-2983 AML36 2 56452187 56452187 T C SNP CCDC85A NM_001080433.1 human genbank 54_36p 1 provisional intronic c.1318-796 e4-796 0.001 - - - no_errors tier3 137 2 1.44 178 126 41.45 0 0 NA 700717 TCGA-AB-2983 AML36 2 59008123 59008123 T C SNP - - - - - - - - - - - - - - - tier3 317 3 0.94 539 407 43.02 2 0 0 700717 TCGA-AB-2983 AML36 2 61663064 61663064 G T SNP XPO1 NM_003400.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-48528 NULL 0.001 - - - no_errors tier3 874 16 1.8 451 319 41.43 0 0 NA 700717 TCGA-AB-2983 AML36 2 64053557 64053557 T C SNP VPS54 NM_016516.1 human genbank 54_36p -1 reviewed intronic c.379-675 e3-675 0 - - - no_errors tier3 433 11 2.47 647 525 44.8 3 0 0 700717 TCGA-AB-2983 AML36 2 65683967 65683967 C T SNP LOC100131818 XM_001725646.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*5775 NULL 0.01 - - - no_errors tier3 646 15 2.26 427 353 44.91 0 0 NA 700717 TCGA-AB-2983 AML36 2 76119698 76119698 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 2 77478244 77478244 C T SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+120708 e2+120708 0 - - - no_errors tier3 1624 52 3.1 1435 1142 44.28 0 0 NA 700717 TCGA-AB-2983 AML36 2 98283410 98283410 G A SNP VWA3B NM_144992.4 human genbank 54_36p 1 provisional intronic c.3420+299 e24+299 0 - - - no_errors tier3 1530 34 2.16 964 702 41.69 0 0 NA 700717 TCGA-AB-2983 AML36 2 103378849 103378849 G T SNP - - - - - - - - - - - - - - - tier3 269 9 3.24 268 188 41.23 0 0 NA 700717 TCGA-AB-2983 AML36 2 104024002 104024002 C T SNP LOC728838 XM_001128590.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-11252 NULL 0.086 - - - no_errors tier3 1747 40 2.24 1264 912 41.85 0 0 NA 700717 TCGA-AB-2983 AML36 2 115454013 115454013 G T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.61-329272 e2-329272 0 - - - no_errors tier3 421 5 1.17 638 446 41.14 0 0 NA 700717 TCGA-AB-2983 AML36 2 116642889 116642889 C T SNP - - - - - - - - - - - - - - - tier3 1197 13 1.07 1441 824 36.38 0 0 NA 700717 TCGA-AB-2983 AML36 2 123017397 123017397 T A SNP - - - - - - - - - - - - - - - tier3 1145 13 1.12 611 515 45.74 0 0 NA 700717 TCGA-AB-2983 AML36 2 125176066 125176066 T C SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.2075-45210 e14-45210 0.129 - - - no_errors tier3 334 8 2.33 460 323 41.2 0 0 NA 700717 TCGA-AB-2983 AML36 2 125311673 125311673 G C SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.3215-27680 e20-27680 0 - - - no_errors tier3 935 17 1.77 1018 749 42.39 0 0 NA 700717 TCGA-AB-2983 AML36 2 141155127 141155127 C - DEL LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.6799+19162 e41+19162 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 2 146249089 146249089 G A SNP - - - - - - - - - - - - - - - tier3 705 19 2.62 615 456 42.54 0 0 NA 700717 TCGA-AB-2983 AML36 2 146267066 146267066 C A SNP - - - - - - - - - - - - - - - tier3 711 13 1.79 633 427 40.28 0 0 NA 700717 TCGA-AB-2983 AML36 2 154399765 154399765 C G SNP GALNT13 NM_052917.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-109492 NULL 0.338 - - - no_errors tier3 1082 32 2.86 837 647 43.6 0 0 NA 700717 TCGA-AB-2983 AML36 2 158397699 158397699 A T SNP ACVR1 NM_001105.4 human genbank 54_36p -1 reviewed intronic c.1+5300 e0+5300 0.484 - - - no_errors tier3 588 19 3.13 798 816 50.43 0 0 0 700717 TCGA-AB-2983 AML36 2 161020186 161020186 A G SNP RBMS1 NM_016836.4 human genbank 54_36p -1 reviewed intronic c.75+37860 e1+37860 0 - - - no_errors tier3 843 13 1.52 619 396 38.94 0 0 NA 700717 TCGA-AB-2983 AML36 2 165763526 165763526 C A SNP SCN3A NM_006922.1 human genbank 54_36p -1 reviewed intronic c.1+5053 e0+5053 0 - - - no_errors tier3 675 14 2.02 808 524 39.31 0 0 NA 700717 TCGA-AB-2983 AML36 2 169367603 169367603 C - DEL NOSTRIN NM_001039724.2 human genbank 54_36p 1 provisional intronic c.27+174 e1+174 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 2 172507510 172507510 G A SNP HAT1 NM_003642.1 human genbank 54_36p 1 reviewed intronic c.113-3964 e3-3964 0.001 - - - no_errors tier3 537 10 1.82 623 418 40.12 0 2 100 700717 TCGA-AB-2983 AML36 2 192240409 192240409 A T SNP LOC729245 XM_001129743.1 human genbank 54_36p 1 model intronic c.74-7754 e2-7754 0.789 - - - no_errors tier3 513 11 2.1 717 587 44.98 0 0 NA 700717 TCGA-AB-2983 AML36 2 194818868 194818868 T A SNP - - - - - - - - - - - - - - - tier3 456 10 2.15 414 311 42.84 0 0 NA 700717 TCGA-AB-2983 AML36 2 198960959 198960959 C T SNP - - - - - - - - - - - - - - - tier3 1670 22 1.3 1079 772 41.66 0 0 NA 700717 TCGA-AB-2983 AML36 2 210267579 210267579 G A SNP MAP2 NM_002374.1 human genbank 54_36p 1 reviewed missense c.2440 p.G814S 1 HMMPfam_MAP2_projctn "HMMPfam_Tubulin-binding,PatternScan_TAU_MAP,HMMPfam_MAP2_projctn,HMMPfam_RII_binding_1" - no_errors tier1 1054 20 1.86 764 519 40.42 NA 700717 TCGA-AB-2983 AML36 2 212664920 212664920 C A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.234+32802 e2+32802 0.004 - - - no_errors tier3 589 5 0.84 616 370 37.41 0 0 NA 700717 TCGA-AB-2983 AML36 2 216380613 216380613 A G SNP LOC646324 XR_039809.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.008 - - - no_errors tier3 568 9 1.56 560 411 42.28 0 0 NA 700717 TCGA-AB-2983 AML36 2 235739256 235739256 A G SNP - - - - - - - - - - - - - - - tier3 1271 21 1.62 757 489 39.21 0 0 NA 700717 TCGA-AB-2983 AML36 2 236095570 236095570 G A SNP AGAP1 NM_001037131.1 human genbank 54_36p 1 validated intronic c.163+27338 e1+27338 0 - - - no_errors tier3 668 13 1.9 505 375 42.61 1 0 0 700717 TCGA-AB-2983 AML36 2 236363514 236363514 T A SNP AGAP1 NM_001037131.1 human genbank 54_36p 1 validated intronic c.674-7628 e7-7628 0 - - - no_errors tier3 1584 25 1.55 1068 796 42.68 0 0 0 700717 TCGA-AB-2983 AML36 3 163781 163781 G A SNP CHL1 NM_006614.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-172679 NULL 0 - - - no_errors tier3 424 8 1.85 470 370 44.05 0 0 NA 700717 TCGA-AB-2983 AML36 3 1389403 1389403 C T SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.1669-119 e13-119 0.001 - - - no_errors tier3 452 13 2.8 587 402 40.61 0 0 NA 700717 TCGA-AB-2983 AML36 3 9099899 9099899 C A SNP SRGAP3 NM_014850.1 human genbank 54_36p -1 validated intronic c.424-3128 e4-3128 0.003 - - - no_errors tier3 852 14 1.62 653 465 41.48 0 0 0 700717 TCGA-AB-2983 AML36 3 12457779 12457779 G A SNP TSEN2 NM_025265.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48521 NULL 0 - - - no_errors tier3 204 5 2.39 187 137 42.15 0 0 NA 700717 TCGA-AB-2983 AML36 3 20008626 20008626 A G SNP C3orf48 ENST00000333083 human ensembl 54_36p -1 known intronic c.1091-7834 e3-7834 0.005 - - - no_errors tier3 1154 23 1.95 907 679 42.79 0 0 NA 700717 TCGA-AB-2983 AML36 3 31901122 31901122 G C SNP OSBPL10 NM_017784.3 human genbank 54_36p -1 reviewed intronic c.282-4796 e2-4796 0.007 - - - no_errors tier3 1268 34 2.6 824 638 43.58 0 0 0 700717 TCGA-AB-2983 AML36 3 33785660 33785660 G A SNP PDCD6IP NM_013374.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29565 NULL 0.265 - - - no_errors tier3 847 22 2.53 670 511 43.23 0 0 NA 700717 TCGA-AB-2983 AML36 3 34276630 34276630 G A SNP - - - - - - - - - - - - - - - tier3 2288 43 1.84 1583 1286 44.81 0 0 NA 700717 TCGA-AB-2983 AML36 3 38662186 38662186 C T SNP SCN5A NM_001099404.4 human genbank 54_36p -1 reviewed intronic c.1+3840 e0+3840 0.001 - - - no_errors tier3 855 14 1.6 447 290 39.35 0 0 NA 700717 TCGA-AB-2983 AML36 3 46486225 46486225 C T SNP LTF NM_002343.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4864 NULL 0.007 - - - no_errors tier3 1071 21 1.91 769 583 42.96 0 0 NA 700717 TCGA-AB-2983 AML36 3 61708104 61708104 C A SNP PTPRG NM_002841.3 human genbank 54_36p 1 reviewed intronic c.86-1488 e2-1488 0 - - - no_errors tier3 890 13 1.44 740 538 42.1 0 0 0 700717 TCGA-AB-2983 AML36 3 70613360 70613360 C A SNP - - - - - - - - - - - - - - - tier3 1214 39 3.11 877 625 41.58 0 0 NA 700717 TCGA-AB-2983 AML36 3 73520191 73520191 C T SNP PDZRN3 NM_015009.1 human genbank 54_36p -1 provisional intronic c.1417-281 e8-281 0 - - - no_errors tier3 464 13 2.73 391 274 41.14 0 0 NA 700717 TCGA-AB-2983 AML36 3 78008356 78008356 T C SNP - - - - - - - - - - - - - - - tier3 1233 29 2.29 1055 735 41.02 0 0 NA 700717 TCGA-AB-2983 AML36 3 84431586 84431586 G C SNP ENSG00000221380 ENST00000408453 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9492 NULL 0 - - - no_errors tier3 505 10 1.93 585 365 38.42 0 0 NA 700717 TCGA-AB-2983 AML36 3 90337598 90337598 C T SNP ENSG00000189002 ENST00000340162 human ensembl 54_36p -1 known intronic c.40+256 e1+256 0 - - - no_errors tier3 433 3 0.68 677 103 13.21 0 0 NA 700717 TCGA-AB-2983 AML36 3 101182283 101182283 C T SNP FILIP1L NM_182909.1 human genbank 54_36p -1 validated intronic c.1-49719 e1-49719 0 - - - no_errors tier3 2254 49 2.12 1357 987 42.11 2 1 33.33 700717 TCGA-AB-2983 AML36 3 103507991 103507991 C G SNP ZPLD1 ENST00000394046 human ensembl 54_36p 1 known intronic c.1+77116 e0+77116 0.01 - - - no_errors tier3 1160 26 2.19 1139 855 42.84 0 0 NA 700717 TCGA-AB-2983 AML36 3 106230244 106230244 C A SNP - - - - - - - - - - - - - - - tier3 604 12 1.95 559 356 38.91 0 0 NA 700717 TCGA-AB-2983 AML36 3 111779603 111779603 C T SNP ENSG00000221206 ENST00000408279 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26101 NULL 0 - - - no_errors tier3 889 28 3.04 1013 698 40.79 0 0 NA 700717 TCGA-AB-2983 AML36 3 112723014 112723014 A T SNP CD96 NM_198196.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20772 NULL 0.002 - - - no_errors tier3 538 11 1.99 557 436 43.73 0 0 NA 700717 TCGA-AB-2983 AML36 3 117525034 117525034 G A SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.155+121380 e1+121380 0 - - - no_errors tier3 1305 14 1.06 1097 795 42 0 0 NA 700717 TCGA-AB-2983 AML36 3 119640186 119640186 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 3 127315313 127315313 C T SNP ALDH1L1 NM_012190.2 human genbank 54_36p -1 reviewed intronic c.2082+777 e17+777 0.156 - - - no_errors tier3 580 14 2.35 425 329 43.52 0 0 NA 700717 TCGA-AB-2983 AML36 3 129525081 129525081 C T SNP EEFSEC NM_021937.3 human genbank 54_36p 1 validated intronic c.787-17685 e5-17685 0 - - - no_errors tier3 475 10 2.06 420 200 32.26 1 1 50 700717 TCGA-AB-2983 AML36 3 140473552 140473552 G A SNP - - - - - - - - - - - - - - - tier3 426 7 1.61 461 381 45.2 0 0 NA 700717 TCGA-AB-2983 AML36 3 141138488 141138488 T C SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.109+1473 e1+1473 0.016 - - - no_errors tier3 443 1 0.22 509 366 41.73 0 0 NA 700717 TCGA-AB-2983 AML36 3 148134496 148134496 C T SNP - - - - - - - - - - - - - - - tier3 303 4 1.29 515 354 40.64 0 0 NA 700717 TCGA-AB-2983 AML36 3 150886126 150886126 A G SNP WWTR1 NM_015472.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-28343 NULL 0.021 - - - no_errors tier3 1954 46 2.29 1495 1059 41.45 0 0 NA 700717 TCGA-AB-2983 AML36 3 165885575 165885575 C T SNP - - - - - - - - - - - - - - - tier3 1119 17 1.49 917 731 44.22 0 0 NA 700717 TCGA-AB-2983 AML36 3 169129429 169129429 G T SNP - - - - - - - - - - - - - - - tier3 322 7 2.13 502 348 40.94 0 0 NA 700717 TCGA-AB-2983 AML36 3 172201310 172201310 A C SNP SLC2A2 NM_000340.1 human genbank 54_36p -1 reviewed intronic c.1069-1661 e9-1661 0.004 - - - no_errors tier3 364 9 2.41 435 219 33.49 0 0 NA 700717 TCGA-AB-2983 AML36 3 181788129 181788129 C T SNP TTC14 NM_133462.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14615 NULL 0.025 - - - no_errors tier3 857 19 2.16 821 553 40.25 0 0 NA 700717 TCGA-AB-2983 AML36 3 188465874 188465874 G A SNP MASP1 NM_139125.1 human genbank 54_36p -1 reviewed intronic c.238-2672 e3-2672 0.001 - - - no_errors tier3 989 28 2.75 700 570 44.81 0 0 NA 700717 TCGA-AB-2983 AML36 3 198431386 198431386 C T SNP DLG1 NM_004087.1 human genbank 54_36p -1 validated intronic c.319-25529 e4-25529 0.018 - - - no_errors tier3 592 13 2.15 872 696 44.36 1 0 0 700717 TCGA-AB-2983 AML36 4 2035305 2035305 G A SNP NAT8L NM_178557.2 human genbank 54_36p 1 provisional missense c.58 p.V20M 1 "HMMPfam_Acetyltransf_1,superfamily_Acyl-CoA N-acyltransferases (Nat)" "HMMPfam_Acetyltransf_1,superfamily_Acyl-CoA N-acyltransferases (Nat)" - no_errors tier1 68 4 5.56 57 52 47.71 NA 700717 TCGA-AB-2983 AML36 4 5930274 5930274 G A SNP CRMP1 NM_001014809.1 human genbank 54_36p -1 reviewed intronic c.382-10890 e2-10890 0 - - - no_errors tier3 2223 33 1.46 838 559 39.99 0 0 NA 700717 TCGA-AB-2983 AML36 4 13148763 13148763 G A SNP NKX3-2 NM_001189.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*3952 NULL 0.001 - - - no_errors tier3 186 4 2.11 191 134 40.98 0 0 NA 700717 TCGA-AB-2983 AML36 4 18686646 18686646 C A SNP - - - - - - - - - - - - - - - tier3 2166 32 1.46 1504 781 34.16 0 0 NA 700717 TCGA-AB-2983 AML36 4 21688265 21688265 C T SNP - - - - - - - - - - - - - - - tier3 2229 44 1.93 1127 824 42.21 0 0 NA 700717 TCGA-AB-2983 AML36 4 23517964 23517964 G T SNP PPARGC1A NM_013261.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-17286 NULL 0.001 - - - no_errors tier3 1394 13 0.92 1188 613 33.94 0 0 NA 700717 TCGA-AB-2983 AML36 4 27626690 27626690 C A SNP - - - - - - - - - - - - - - - tier3 398 6 1.48 620 436 41.25 0 0 NA 700717 TCGA-AB-2983 AML36 4 27683155 27683155 G A SNP - - - - - - - - - - - - - - - tier3 315 13 3.96 433 252 36.79 0 0 NA 700717 TCGA-AB-2983 AML36 4 28546375 28546375 G T SNP - - - - - - - - - - - - - - - tier3 1116 18 1.59 1017 838 45.15 0 0 NA 700717 TCGA-AB-2983 AML36 4 31261923 31261923 G A SNP - - - - - - - - - - - - - - - tier3 729 10 1.35 798 484 37.75 0 0 NA 700717 TCGA-AB-2983 AML36 4 31983482 31983482 C A SNP - - - - - - - - - - - - - - - tier3 206 4 1.9 426 297 40.97 0 0 NA 700717 TCGA-AB-2983 AML36 4 34231273 34231273 G T SNP LOC727819 XM_001125877.2 human genbank 54_36p 1 model intronic c.128+10190 e1+10190 0.082 - - - no_errors tier3 617 11 1.75 931 329 26.11 0 0 NA 700717 TCGA-AB-2983 AML36 4 44146900 44146900 G A SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-1603 NULL 0 - - - no_errors tier3 220 2 0.9 481 277 36.54 0 0 NA 700717 TCGA-AB-2983 AML36 4 45340099 45340099 A G SNP - - - - - - - - - - - - - - - tier3 1058 15 1.4 1087 646 37.25 0 0 NA 700717 TCGA-AB-2983 AML36 4 52560609 52560609 G A SNP LRRC66 NM_001024611.1 human genbank 54_36p -1 provisional intronic c.667-1749 e3-1749 0.007 - - - no_errors tier3 337 5 1.46 458 363 44.21 0 0 NA 700717 TCGA-AB-2983 AML36 4 57943843 57943843 C T SNP - - - - - - - - - - - - - - - tier3 1113 25 2.18 971 827 45.92 0 0 NA 700717 TCGA-AB-2983 AML36 4 58404976 58404976 A T SNP - - - - - - - - - - - - - - - tier3 794 25 3.05 904 674 42.71 0 0 NA 700717 TCGA-AB-2983 AML36 4 61760950 61760950 G A SNP - - - - - - - - - - - - - - - tier3 203 2 0.97 344 204 37.16 0 0 NA 700717 TCGA-AB-2983 AML36 4 63388489 63388489 C A SNP LOC644556 XM_001719457.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*21382 NULL 0.012 - - - no_errors tier3 365 10 2.66 473 360 43.22 0 0 NA 700717 TCGA-AB-2983 AML36 4 70985815 70985815 C T SNP HTN3 NM_000200.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*52289 NULL 0.007 - - - no_errors tier3 1140 31 2.64 762 589 43.57 0 0 NA 700717 TCGA-AB-2983 AML36 4 72991134 72991134 A C SNP - - - - - - - - - - - - - - - tier3 426 8 1.84 480 355 42.41 0 0 NA 700717 TCGA-AB-2983 AML36 4 73417452 73417452 C T SNP ADAMTS3 NM_014243.1 human genbank 54_36p -1 reviewed intronic c.861+6623 e5+6623 0 - - - no_errors tier3 1179 18 1.5 1079 720 39.98 0 0 NA 700717 TCGA-AB-2983 AML36 4 93266901 93266901 A G SNP - - - - - - - - - - - - - - - tier3 449 8 1.75 703 577 45.01 0 0 NA 700717 TCGA-AB-2983 AML36 4 93979063 93979063 C A SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.245-246106 e3-246106 0 - - - no_errors tier3 1272 13 1.01 1349 863 38.98 0 0 NA 700717 TCGA-AB-2983 AML36 4 103401485 103401485 T C SNP SLC39A8 NM_022154.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*1739 NULL 0.003 - - - no_errors tier3 850 9 1.05 535 436 44.9 2 1 33.33 700717 TCGA-AB-2983 AML36 4 110324214 110324214 T C SNP COL25A1 NM_198721.2 human genbank 54_36p -1 validated intronic c.367+116974 e2+116974 0.02 - - - no_errors tier3 481 12 2.42 674 461 40.58 0 1 100 700717 TCGA-AB-2983 AML36 4 111576766 111576766 C A SNP ENPEP NM_001977.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40254 NULL 0.006 - - - no_errors tier3 459 10 2.13 526 437 45.33 0 0 NA 700717 TCGA-AB-2983 AML36 4 112040071 112040071 C T SNP MIRN297 ENST00000401142 human ensembl 54_36p -1 known 5_prime_flanking_region c.-38819 NULL 0.004 - - - no_errors tier3 481 4 0.82 510 342 40.05 0 0 NA 700717 TCGA-AB-2983 AML36 4 114780267 114780267 G A SNP CAMK2D NM_001221.3 human genbank 54_36p -1 reviewed intronic c.220+22051 e3+22051 0 - - - no_errors tier3 871 15 1.69 594 419 41.36 0 0 0 700717 TCGA-AB-2983 AML36 4 124408151 124408151 A G SNP SPATA5 NM_145207.2 human genbank 54_36p 1 validated intronic c.2505+11366 e15+11366 0.003 - - - no_errors tier3 972 16 1.62 747 536 41.74 0 0 0 700717 TCGA-AB-2983 AML36 4 128449057 128449057 G C SNP - - - - - - - - - - - - - - - tier3 934 16 1.68 698 948 57.59 0 0 NA 700717 TCGA-AB-2983 AML36 4 128485778 128485778 T A SNP - - - - - - - - - - - - - - - tier3 1117 19 1.67 1100 787 41.64 0 0 NA 700717 TCGA-AB-2983 AML36 4 128903764 128903764 A T SNP SLC25A31 NM_031291.2 human genbank 54_36p 1 validated intronic c.361-1084 e3-1084 0.823 - - - no_errors tier3 967 11 1.12 796 635 44.31 0 0 NA 700717 TCGA-AB-2983 AML36 4 130672873 130672873 A G SNP - - - - - - - - - - - - - - - tier3 497 9 1.77 417 265 38.8 0 0 NA 700717 TCGA-AB-2983 AML36 4 143990634 143990634 A G SNP INPP4B NM_001101669.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-418772 NULL 0.03 - - - no_errors tier3 764 19 2.42 628 531 45.74 0 0 NA 700717 TCGA-AB-2983 AML36 4 148076856 148076856 A G SNP TTC29 NM_031956.2 human genbank 54_36p -1 validated intronic c.176+1340 e2+1340 0 - - - no_errors tier3 633 9 1.4 794 402 33.61 0 0 NA 700717 TCGA-AB-2983 AML36 4 149913888 149913888 A T SNP - - - - - - - - - - - - - - - tier3 1611 36 2.18 1209 778 39.06 0 0 NA 700717 TCGA-AB-2983 AML36 4 150013577 150013577 G A SNP - - - - - - - - - - - - - - - tier3 973 20 2.01 810 595 42.29 0 0 NA 700717 TCGA-AB-2983 AML36 4 156621242 156621242 G A SNP ENSG00000208685 ENST00000385950 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15112 NULL 0 - - - pseudogene tier3 1346 22 1.61 1256 905 41.86 0 0 NA 700717 TCGA-AB-2983 AML36 4 157856728 157856728 C T SNP PDGFC NM_016205.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*46964 NULL 0 - - - no_errors tier3 669 9 1.32 641 457 41.58 0 0 NA 700717 TCGA-AB-2983 AML36 4 158843192 158843192 C T SNP - - - - - - - - - - - - - - - tier3 666 12 1.76 790 509 39.18 0 0 NA 700717 TCGA-AB-2983 AML36 4 164804483 164804483 G A SNP MARCH1 ENST00000274056 human ensembl 54_36p -1 known intronic c.162+36932 e2+36932 0.072 - - - no_errors tier3 334 12 3.47 645 442 40.62 0 0 NA 700717 TCGA-AB-2983 AML36 4 185880750 185880750 G A SNP MLF1IP NM_024629.2 human genbank 54_36p -1 validated intronic c.320+2355 e4+2355 0 - - - no_errors tier3 400 9 2.2 545 368 40.26 1 0 0 700717 TCGA-AB-2983 AML36 4 189475360 189475360 G A SNP LOC152663 XM_087499.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*32189 NULL 0 - - - pseudogene tier3 146 0 0 377 262 41 0 0 NA 700717 TCGA-AB-2983 AML36 5 6966341 6966341 A G SNP - - - - - - - - - - - - - - - tier3 839 15 1.75 1017 542 34.77 0 0 NA 700717 TCGA-AB-2983 AML36 5 8108237 8108237 G A SNP - - - - - - - - - - - - - - - tier3 546 11 1.97 629 395 38.42 0 0 NA 700717 TCGA-AB-2983 AML36 5 24515786 24515786 C T SNP CDH10 NM_006727.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*7743 NULL 0 - - - no_errors tier3 801 10 1.23 647 442 40.59 0 0 NA 700717 TCGA-AB-2983 AML36 5 33726201 33726201 T A SNP ADAMTS12 NM_030955.2 human genbank 54_36p -1 reviewed intronic c.635-6284 e4-6284 0.059 - - - no_errors tier3 676 8 1.17 808 608 42.91 0 0 NA 700717 TCGA-AB-2983 AML36 5 45416422 45416422 C T SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.1230+15929 e4+15929 0.01 - - - no_errors tier3 607 7 1.14 991 542 35.31 0 0 NA 700717 TCGA-AB-2983 AML36 5 51373993 51373993 T A SNP - - - - - - - - - - - - - - - tier3 525 12 2.23 606 524 46.25 0 0 NA 700717 TCGA-AB-2983 AML36 5 72588290 72588290 T C SNP - - - - - - - - - - - - - - - tier3 422 5 1.17 414 282 40.52 0 0 NA 700717 TCGA-AB-2983 AML36 5 103193419 103193419 C T SNP - - - - - - - - - - - - - - - tier3 536 9 1.65 533 433 44.55 0 0 NA 700717 TCGA-AB-2983 AML36 5 103272440 103272440 T C SNP - - - - - - - - - - - - - - - tier3 685 14 2 715 491 40.68 0 0 NA 700717 TCGA-AB-2983 AML36 5 113430705 113430705 A T SNP - - - - - - - - - - - - - - - tier3 1303 19 1.43 1310 697 34.62 0 0 NA 700717 TCGA-AB-2983 AML36 5 115433871 115433871 C T SNP COMMD10 NM_016144.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-14778 NULL 0.007 - - - no_errors tier3 1058 33 3.01 914 636 41.01 0 0 NA 700717 TCGA-AB-2983 AML36 5 118150649 118150649 A T SNP - - - - - - - - - - - - - - - tier3 665 17 2.49 747 480 39.12 0 0 NA 700717 TCGA-AB-2983 AML36 5 123396178 123396178 T C SNP - - - - - - - - - - - - - - - tier3 567 14 2.4 715 610 46 0 0 NA 700717 TCGA-AB-2983 AML36 5 134807409 134807409 C T SNP H2AFY NM_138610.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-54727 NULL 0 - - - no_errors tier3 680 12 1.72 512 325 38.78 1 2 66.67 700717 TCGA-AB-2983 AML36 5 140560654 140560654 T C SNP PCDHB11 NM_018931.2 human genbank 54_36p 1 reviewed missense c.1123 p.S375P 0.965 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin" - no_errors tier1 692 10 1.42 520 378 42.05 NA 700717 TCGA-AB-2983 AML36 5 146214737 146214738 - T INS PPP2R2B NM_181676.1 human genbank 54_36p -1 reviewed intronic c.80-153840_80-153839 e2-153839 0.013:0.019 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 5 150637552 150637552 T C SNP SLC36A3 NM_181774.1 human genbank 54_36p -1 validated intronic c.1145-137 e10-137 0.005 - - - no_errors tier3 929 23 2.38 714 505 40.79 0 0 NA 700717 TCGA-AB-2983 AML36 5 151214410 151214410 G T SNP GLRA1 NM_000171.3 human genbank 54_36p -1 reviewed intronic c.697+384 e6+384 0.039 - - - no_errors tier3 1117 56 4.77 707 565 44.35 0 0 0 700717 TCGA-AB-2983 AML36 5 164629161 164629161 T C SNP - - - - - - - - - - - - - - - tier3 784 14 1.75 1080 809 42.8 0 0 NA 700717 TCGA-AB-2983 AML36 5 165010105 165010105 G A SNP ENSG00000208461 ENST00000385726 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*40434 NULL 0 - - - pseudogene tier3 719 18 2.44 569 382 40.17 0 0 NA 700717 TCGA-AB-2983 AML36 5 165945011 165945011 G T SNP - - - - - - - - - - - - - - - tier3 689 12 1.71 913 641 41.25 0 0 NA 700717 TCGA-AB-2983 AML36 5 166240776 166240776 C T SNP - - - - - - - - - - - - - - - tier3 1170 17 1.43 928 692 42.69 0 0 NA 700717 TCGA-AB-2983 AML36 6 15056972 15056972 G A SNP LOC728961 XM_001128918.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*28523 NULL 0 - - - no_errors tier3 571 25 4.18 500 341 40.5 0 0 NA 700717 TCGA-AB-2983 AML36 6 17524306 17524307 AT - DEL CAP2 NM_006366.2 human genbank 54_36p 1 reviewed intronic c.1-5459_5458 e1-5458 0.003:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 6 19964455 19964455 A G SNP ID4 NM_001546.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*17617 NULL 0 - - - no_errors tier3 1295 22 1.67 1126 811 41.85 0 0 NA 700717 TCGA-AB-2983 AML36 6 31072909 31072909 C A SNP LOC729792 XM_001131329.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-29035 NULL 0 - - - no_errors tier3 1159 34 2.85 704 522 42.51 0 0 NA 700717 TCGA-AB-2983 AML36 6 40827760 40827760 G T SNP - - - - - - - - - - - - - - - tier3 655 10 1.5 340 279 45.07 0 0 NA 700717 TCGA-AB-2983 AML36 6 41000678 41000678 C A SNP - - - - - - - - - - - - - - - tier3 1846 31 1.65 1031 814 44.1 0 0 NA 700717 TCGA-AB-2983 AML36 6 45668137 45668137 C A SNP RUNX2 NM_001024630.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45117 NULL 0 - - - no_errors tier3 803 24 2.9 678 519 43.36 1 1 50 700717 TCGA-AB-2983 AML36 6 46544812 46544812 C T SNP RCAN2 ENST00000306764 human ensembl 54_36p -1 known intronic c.1-12138 e1-12138 0 - - - no_errors tier3 887 13 1.44 604 436 41.88 0 0 NA 700717 TCGA-AB-2983 AML36 6 56127540 56127540 G A SNP COL21A1 NM_030820.3 human genbank 54_36p -1 reviewed intronic c.1434+2104 e9+2104 0.006 - - - no_errors tier3 1366 29 2.08 862 692 44.42 0 0 0 700717 TCGA-AB-2983 AML36 6 63898992 63898992 A G SNP - - - - - - - - - - - - - - - tier3 496 14 2.75 536 392 42.2 0 0 NA 700717 TCGA-AB-2983 AML36 6 70130581 70130581 T C SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.4239+2456 e27+2456 0.001 - - - no_errors tier3 1555 28 1.77 1087 811 42.66 0 0 NA 700717 TCGA-AB-2983 AML36 6 71777785 71777785 C G SNP - - - - - - - - - - - - - - - tier3 931 23 2.41 778 511 39.64 0 0 NA 700717 TCGA-AB-2983 AML36 6 78314813 78314813 G A SNP - - - - - - - - - - - - - - - tier3 1147 21 1.79 1039 684 39.63 0 0 NA 700717 TCGA-AB-2983 AML36 6 82157187 82157187 T C SNP - - - - - - - - - - - - - - - tier3 328 10 2.96 449 383 46.03 0 0 NA 700717 TCGA-AB-2983 AML36 6 83995880 83995880 C T SNP ME1 NM_002395.3 human genbank 54_36p -1 reviewed intronic c.1027-511 e10-511 0 - - - no_errors tier3 630 11 1.71 811 681 45.55 0 0 0 700717 TCGA-AB-2983 AML36 6 93876739 93876739 T A SNP ENSG00000213187 ENST00000392786 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-17449 NULL 0.001 - - - no_coding_region:pseudogene tier3 624 1 0.16 578 486 45.63 0 0 NA 700717 TCGA-AB-2983 AML36 6 96496724 96496725 - A INS KRT18P50 XM_001716480.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-19396 NULL 0.008:0.004 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 6 96609159 96609159 C A SNP FUT9 NM_006581.3 human genbank 54_36p 1 validated intronic c.1+38350 e0+38350 0.001 - - - no_errors tier3 943 24 2.47 957 598 38.43 0 0 NA 700717 TCGA-AB-2983 AML36 6 97221075 97221075 A G SNP ENSG00000207309 ENST00000384579 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16887 NULL 0.004 - - - no_errors tier3 851 5 0.58 989 648 39.54 0 0 NA 700717 TCGA-AB-2983 AML36 6 98448036 98448036 C A SNP - - - - - - - - - - - - - - - tier3 955 7 0.73 790 432 35.32 0 0 NA 700717 TCGA-AB-2983 AML36 6 100097802 100097802 T G SNP CCNC NM_005190.1 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*350 NULL 0.062 - - - no_errors tier3 395 11 2.7 520 357 40.57 22 18 45 700717 TCGA-AB-2983 AML36 6 102226593 102226593 T A SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.542-4598 e4-4598 0.248 - - - no_errors tier3 1395 12 0.85 1355 665 32.9 0 0 NA 700717 TCGA-AB-2983 AML36 6 102226731 102226731 G A SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.542-4460 e4-4460 0.048 - - - no_errors tier3 826 7 0.84 684 525 43.39 0 0 NA 700717 TCGA-AB-2983 AML36 6 102825561 102825561 C G SNP - - - - - - - - - - - - - - - tier3 423 8 1.85 629 423 40.09 0 0 NA 700717 TCGA-AB-2983 AML36 6 105989810 105989810 C T SNP PREP NM_002726.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-32351 NULL 0.003 - - - no_errors tier3 832 12 1.42 864 613 41.47 0 0 NA 700717 TCGA-AB-2983 AML36 6 117499969 117499969 G A SNP ENSG00000217089 ENST00000402041 human ensembl 54_36p -1 known 5_prime_flanking_region c.-23275 NULL 0 - - - no_coding_region:pseudogene tier3 866 13 1.48 811 588 42 0 0 NA 700717 TCGA-AB-2983 AML36 6 121752595 121752595 G A SNP GJA1 NM_000165.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-57098 NULL 0 - - - no_errors tier3 917 15 1.61 535 402 42.9 0 0 NA 700717 TCGA-AB-2983 AML36 6 121878391 121878391 G A SNP ENSG00000219784 ENST00000406666 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35711 NULL 0.004 - - - no_coding_region:pseudogene tier3 430 2 0.46 490 251 33.83 0 0 NA 700717 TCGA-AB-2983 AML36 6 128984065 128984065 T C SNP ENSG00000213130 ENST00000392447 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40343 NULL 0.007 - - - no_coding_region:pseudogene tier3 39 0 0 160 127 44.25 0 0 NA 700717 TCGA-AB-2983 AML36 6 133699730 133699731 GA - DEL EYA4 NM_004100.4 human genbank 54_36p 1 reviewed intronic c.34-45493_34-45492 e2-45492 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 6 134374037 134374037 C T SNP SLC2A12 NM_145176.2 human genbank 54_36p -1 validated intronic c.1445-4272 e3-4272 0.003 - - - no_errors tier3 993 23 2.24 726 562 43.57 0 0 NA 700717 TCGA-AB-2983 AML36 6 141289233 141289233 T C SNP ENSG00000216548 ENST00000407538 human ensembl 54_36p -1 known 5_prime_flanking_region c.-3492 NULL 0.016 - - - no_coding_region:pseudogene tier3 719 11 1.51 571 436 43.25 0 0 NA 700717 TCGA-AB-2983 AML36 6 150217849 150217849 C G SNP LRP11 NM_032832.4 human genbank 54_36p -1 provisional intronic c.614-1860 e2-1860 0 - - - no_errors tier3 1315 22 1.64 935 631 40.27 0 0 NA 700717 TCGA-AB-2983 AML36 6 164726101 164726101 T - DEL LOC728275 XM_001127046.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*47524 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 6 166054038 166054038 T C SNP ENSG00000206681 ENST00000383954 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2222 NULL 0 - - - no_errors tier3 660 8 1.2 544 450 45.27 0 0 NA 700717 TCGA-AB-2983 AML36 6 167703048 167703048 C - DEL TCP10 ENST00000397829 human ensembl 54_36p -1 known intronic c.636+4781 e5+4781 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 7 9993676 9993676 G A SNP LOC340268 XR_041608.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 639 15 2.29 478 416 46.48 0 0 NA 700717 TCGA-AB-2983 AML36 7 22326437 22326437 C T SNP RAPGEF5 NM_012294.3 human genbank 54_36p -1 validated intronic c.1-2256 e1-2256 0 - - - no_errors tier3 1334 31 2.27 927 683 42.4 0 0 NA 700717 TCGA-AB-2983 AML36 7 41793253 41793254 - CT INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 7 45576346 45576346 T A SNP ADCY1 NM_021116.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-4322 NULL 0.001 - - - no_errors tier3 483 7 1.43 286 223 43.81 0 0 NA 700717 TCGA-AB-2983 AML36 7 51662672 51662672 G A SNP LOC100134540 XR_039782.1 human genbank 54_36p -1 model intronic c.NULL NULL 1 - - - pseudogene tier3 1115 15 1.33 881 597 40.37 0 0 NA 700717 TCGA-AB-2983 AML36 7 67572119 67572119 C T SNP - - - - - - - - - - - - - - - tier3 1171 31 2.58 760 470 38.21 0 0 NA 700717 TCGA-AB-2983 AML36 7 78236578 78236579 - T INS MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.419-142088_419-142087 e3-142087 0.003:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 7 83474648 83474648 C G SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed missense c.1097 p.W366S 1 "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema" "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema,HMMSmart_IG,HMMSmart_PSI,HMMPfam_ig,superfamily_Plexin-like_fold,superfamily_SSF48726" - no_errors tier1 842 26 2.99 571 470 45.11 NA 700717 TCGA-AB-2983 AML36 7 84542860 84542860 A - DEL SEMA3D NM_152754.2 human genbank 54_36p -1 validated intronic c.376-2527 e4-2527 0.023 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 7 92293140 92293140 C G SNP CDK6 NM_001259.1 human genbank 54_36p -1 validated intronic c.233+7201 e1+7201 0.004 - - - no_errors tier3 560 5 0.88 648 498 43.46 2 3 60 700717 TCGA-AB-2983 AML36 7 98092146 98092146 G T SNP NPTX2 NM_002523.2 human genbank 54_36p 1 reviewed intronic c.644-24 e3-24 0.055 - - - no_errors tier3 461 6 1.28 299 192 39.02 1 0 0 700717 TCGA-AB-2983 AML36 7 112101553 112101553 A G SNP - - - - - - - - - - - - - - - tier3 1541 34 2.16 1543 849 35.48 0 0 NA 700717 TCGA-AB-2983 AML36 7 116141730 116141730 C T SNP MET NM_000245.2 human genbank 54_36p 1 reviewed intronic c.1200+14156 e1+14156 0.002 - - - no_errors tier3 877 13 1.46 844 701 45.34 0 0 0 700717 TCGA-AB-2983 AML36 7 117595652 117595652 T C SNP LSM8 NM_016200.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15862 NULL 0 - - - no_errors tier3 544 17 3.02 724 494 40.56 0 0 NA 700717 TCGA-AB-2983 AML36 7 132902287 132902287 G A SNP EXOC4 NM_021807.1 human genbank 54_36p 1 reviewed intronic c.1418-63051 e10-63051 0.02 - - - no_errors tier3 750 15 1.96 782 576 42.38 1 1 50 700717 TCGA-AB-2983 AML36 7 135606173 135606173 G A SNP ENSG00000220982 ENST00000408055 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*26351 NULL 0 - - - no_errors tier3 1681 29 1.69 1501 1126 42.86 0 0 NA 700717 TCGA-AB-2983 AML36 7 136733577 136733577 C T SNP DGKI NM_004717.2 human genbank 54_36p -1 reviewed intronic c.2945-878 e32-878 0 - - - no_errors tier3 900 14 1.53 640 430 40.19 0 0 NA 700717 TCGA-AB-2983 AML36 7 152985501 152985501 G A SNP - - - - - - - - - - - - - - - tier3 538 13 2.34 407 276 40.35 0 0 NA 700717 TCGA-AB-2983 AML36 7 156089290 156089290 G A SNP RNF32 NM_030936.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40043 NULL 0 - - - no_errors tier3 550 13 2.29 587 467 44.22 0 0 NA 700717 TCGA-AB-2983 AML36 7 156966301 156966301 G A SNP LOC393078 XM_374705.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10063 NULL 0.971 - - - no_errors tier3 395 8 1.98 210 161 42.59 0 0 0 700717 TCGA-AB-2983 AML36 8 4480865 4480865 T G SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.302+1407 e2+1407 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 427 8 1.84 433 275 38.79 0 0 NA 700717 TCGA-AB-2983 AML36 8 5375579 5375579 G T SNP - - - - - - - - - - - - - - - tier3 3964 101 2.48 2528 1736 40.67 0 0 NA 700717 TCGA-AB-2983 AML36 8 7817762 7817762 A T SNP LOC100132396 XM_001720735.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24592 NULL 0.002 - - - no_errors tier3 270 3 1.1 297 263 46.96 0 0 0 700717 TCGA-AB-2983 AML36 8 20148695 20148695 G C SNP LZTS1 NM_021020.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*2818 NULL 0.005 - - - no_errors tier3 412 11 2.6 299 187 38.48 0 0 NA 700717 TCGA-AB-2983 AML36 8 25581435 25581435 C T SNP - - - - - - - - - - - - - - - tier3 847 14 1.62 761 491 39.15 0 0 NA 700717 TCGA-AB-2983 AML36 8 28198441 28198441 G A SNP LOC100129848 XM_001717438.1 human genbank 54_36p -1 model intronic c.465-34286 e2-34286 0.001 - - - no_errors tier3 1005 9 0.88 920 671 42.15 0 0 NA 700717 TCGA-AB-2983 AML36 8 29881737 29881737 C G SNP ENSG00000221003 ENST00000408076 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23926 NULL 0 - - - no_errors tier3 757 16 2.05 997 776 43.77 0 0 NA 700717 TCGA-AB-2983 AML36 8 34352235 34352235 G T SNP - - - - - - - - - - - - - - - tier3 1655 27 1.6 1535 1111 41.94 0 0 NA 700717 TCGA-AB-2983 AML36 8 35127573 35127573 G A SNP - - - - - - - - - - - - - - - tier3 994 15 1.48 883 686 43.67 0 0 NA 700717 TCGA-AB-2983 AML36 8 36036105 36036105 C T SNP - - - - - - - - - - - - - - - tier3 1343 17 1.24 1121 779 40.96 0 0 NA 700717 TCGA-AB-2983 AML36 8 53738861 53738861 C A SNP RB1CC1 NM_014781.1 human genbank 54_36p -1 validated intronic c.1174-2029 e7-2029 0.001 - - - no_errors tier3 698 20 2.78 819 568 40.95 1 1 50 700717 TCGA-AB-2983 AML36 8 53880680 53880680 T C SNP - - - - - - - - - - - - - - - tier3 689 23 3.23 605 414 40.63 0 0 NA 700717 TCGA-AB-2983 AML36 8 59121224 59121224 T - DEL FAM110B NM_147189.2 human genbank 54_36p 1 validated intronic c.1+2812 e0+2812 0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 8 59496329 59496329 C T SNP UBXN2B NM_001077619.1 human genbank 54_36p 1 validated intronic c.188+4263 e2+4263 0.056 - - - no_errors tier3 765 13 1.66 612 474 43.57 1 4 80 700717 TCGA-AB-2983 AML36 8 69150203 69150203 T A SNP PREX2 NM_024870.2 human genbank 54_36p 1 validated intronic c.1570-1983 e15-1983 0 - - - no_errors tier3 929 10 1.06 826 571 40.76 0 0 0 700717 TCGA-AB-2983 AML36 8 73394456 73394456 G - DEL ENSG00000209097 ENST00000386362 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38066 NULL 0.001 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 8 84806539 84806539 T G SNP - - - - - - - - - - - - - - - tier3 973 37 3.66 744 546 42.26 0 0 NA 700717 TCGA-AB-2983 AML36 8 88763120 88763120 G A SNP - - - - - - - - - - - - - - - tier3 1133 22 1.9 667 545 44.97 0 0 NA 700717 TCGA-AB-2983 AML36 8 104060955 104060955 A T SNP ATP6V1C1 NM_001695.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-61286 NULL 0 - - - no_errors tier3 594 14 2.3 402 293 42.16 3 3 50 700717 TCGA-AB-2983 AML36 8 118819872 118819872 C T SNP - - - - - - - - - - - - - - - tier3 2338 36 1.51 1507 1143 43.08 0 0 NA 700717 TCGA-AB-2983 AML36 8 136400204 136400204 C T SNP - - - - - - - - - - - - - - - tier3 883 19 2.1 760 543 41.61 0 0 NA 700717 TCGA-AB-2983 AML36 8 138034066 138034066 C T SNP - - - - - - - - - - - - - - - tier3 203 5 2.39 113 67 36.81 0 0 NA 700717 TCGA-AB-2983 AML36 8 138075117 138075117 T A SNP - - - - - - - - - - - - - - - tier3 1531 25 1.6 832 557 40.07 0 0 NA 700717 TCGA-AB-2983 AML36 9 26352554 26352554 C G SNP - - - - - - - - - - - - - - - tier3 523 13 2.41 562 448 44.23 0 0 NA 700717 TCGA-AB-2983 AML36 9 27196917 27196917 A G SNP TEK NM_000459.3 human genbank 54_36p 1 reviewed intronic c.2575+127 e15+127 0.003 - - - no_errors tier3 1389 17 1.21 883 635 41.75 0 1 100 700717 TCGA-AB-2983 AML36 9 28599216 28599216 T C SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1+60982 e0+60982 0.411 - - - no_errors tier3 182 4 2.15 263 219 45.44 0 0 NA 700717 TCGA-AB-2983 AML36 9 30168782 30168782 C T SNP ENSG00000210600 ENST00000387865 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-207 NULL 0.007 - - - pseudogene tier3 2128 37 1.71 1492 1142 43.34 0 0 NA 700717 TCGA-AB-2983 AML36 9 30886771 30886771 C T SNP ENSG00000214020 ENST00000397259 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38086 NULL 0 - - - no_coding_region:pseudogene tier3 54 0 0 130 86 39.81 0 0 NA 700717 TCGA-AB-2983 AML36 9 37563359 37563359 C A SNP FBXO10 NM_012166.2 human genbank 54_36p -1 validated intronic c.1+2849 e0+2849 0.064 - - - no_errors tier3 970 15 1.52 724 539 42.58 0 1 100 700717 TCGA-AB-2983 AML36 9 69120988 69120988 G C SNP ENSG00000222887 ENST00000410955 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9327 NULL 0 - - - no_errors tier3 767 7 0.9 1127 330 22.62 0 0 NA 700717 TCGA-AB-2983 AML36 9 72068067 72068067 G A SNP SMC5 NM_015110.3 human genbank 54_36p 1 validated intronic c.186-973 e2-973 0.003 - - - no_errors tier3 634 6 0.94 696 505 42.01 1 1 50 700717 TCGA-AB-2983 AML36 9 73162609 73162609 A G SNP TRPM3 ENST00000357533 human ensembl 54_36p -1 known intronic c.183+88780 e1+88780 0.002 - - - no_errors tier3 691 15 2.12 714 494 40.89 0 0 NA 700717 TCGA-AB-2983 AML36 9 76076606 76076606 A G SNP - - - - - - - - - - - - - - - tier3 1399 26 1.82 1171 616 34.45 0 0 NA 700717 TCGA-AB-2983 AML36 9 77821895 77821896 - AA INS PCSK5 NM_006200.3 human genbank 54_36p 1 reviewed intronic c.412-6579_412-6578 e4-6578 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 9 84362146 84362146 C T SNP - - - - - - - - - - - - - - - tier3 735 12 1.6 1093 769 41.3 2 0 0 700717 TCGA-AB-2983 AML36 9 93657386 93657386 C T SNP ROR2 NM_004560.2 human genbank 54_36p -1 reviewed intronic c.98-79465 e2-79465 0.001 - - - no_errors tier3 991 28 2.74 739 592 44.34 0 0 NA 700717 TCGA-AB-2983 AML36 9 96256828 96256828 A C SNP HIATL1 NM_032558.2 human genbank 54_36p 1 validated intronic c.1028+655 e9+655 0.024 - - - no_errors tier3 1393 23 1.62 1190 790 39.9 0 1 100 700717 TCGA-AB-2983 AML36 9 98694094 98694094 C T SNP ZNF782 NM_001001662.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-40030 NULL 0 - - - no_errors tier3 1436 37 2.5 915 689 42.9 24 22 47.83 700717 TCGA-AB-2983 AML36 9 100346923 100346923 C A SNP GABBR2 NM_005458.6 human genbank 54_36p -1 validated intronic c.460-2777 e3-2777 0 - - - no_errors tier3 1267 19 1.48 740 634 46.14 0 0 NA 700717 TCGA-AB-2983 AML36 9 116056676 116056676 G A SNP COL27A1 NM_032888.2 human genbank 54_36p 1 provisional intronic c.3141+1643 e27+1643 0 - - - no_errors tier3 363 11 2.94 206 124 37.46 0 0 NA 700717 TCGA-AB-2983 AML36 9 117407234 117407234 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 9 121319107 121319107 C T SNP - - - - - - - - - - - - - - - tier3 1813 41 2.21 1206 815 40.25 0 0 NA 700717 TCGA-AB-2983 AML36 9 125295333 125295333 A C SNP DENND1A NM_020946.1 human genbank 54_36p -1 validated intronic c.994-35336 e14-35336 0.007 - - - no_errors tier3 1652 31 1.84 902 725 44.51 4 2 33.33 700717 TCGA-AB-2983 AML36 9 131810872 131810872 C T SNP FNBP1 NM_015033.2 human genbank 54_36p -1 reviewed intronic c.25-13814 e2-13814 0.003 - - - no_errors tier3 1114 22 1.93 887 558 38.59 8 3 27.27 700717 TCGA-AB-2983 AML36 9 133676157 133676157 C T SNP ENSG00000212395 ENST00000391093 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27953 NULL 0.004 - - - no_errors tier3 570 17 2.89 347 271 43.78 0 0 NA 700717 TCGA-AB-2983 AML36 9 134757607 134757607 C G SNP TSC1 NM_000368.3 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*3836 NULL 0.001 - - - no_errors tier3 652 13 1.95 479 302 38.57 21 14 40 700717 TCGA-AB-2983 AML36 9 138637552 138637552 C T SNP EGFL7 NM_016215.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45004 NULL 0 - - - no_errors tier3 96 4 4 90 62 40.79 0 0 0 700717 TCGA-AB-2983 AML36 10 7240277 7240277 A C SNP SFMBT2 NM_001029880.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*5461 NULL 0.002 - - - no_errors tier3 796 20 2.44 587 480 44.99 2 1 33.33 700717 TCGA-AB-2983 AML36 10 23623269 23623269 C T SNP C10orf67 ENST00000376500 human ensembl 54_36p -1 known intronic c.556-3055 e6-3055 0 - - - no_start_codon:no_stop_codon tier3 776 23 2.87 606 415 40.61 0 0 NA 700717 TCGA-AB-2983 AML36 10 25310294 25310294 G A SNP THNSL1 NM_024838.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-41865 NULL 0.027 - - - no_errors tier3 580 10 1.69 550 432 43.95 0 0 NA 700717 TCGA-AB-2983 AML36 10 34876529 34876529 G A SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional intronic c.223-30436 e3-30436 0 - - - no_errors tier3 1048 13 1.23 748 629 45.65 0 0 NA 700717 TCGA-AB-2983 AML36 10 37310045 37310045 G A SNP ENSG00000217536 ENST00000404475 human ensembl 54_36p -1 known 5_prime_flanking_region c.-36373 NULL 0 - - - no_coding_region:pseudogene tier3 2294 46 1.96 1215 815 40.09 0 0 NA 700717 TCGA-AB-2983 AML36 10 56273934 56273934 A T SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+53282 e0+53282 0 - - - no_errors tier3 1425 32 2.2 1144 936 44.94 0 0 NA 700717 TCGA-AB-2983 AML36 10 63147418 63147418 T C SNP C10orf107 NM_173554.2 human genbank 54_36p 1 validated intronic c.288+27033 e3+27033 0.001 - - - no_errors tier3 328 8 2.37 344 276 44.52 0 0 NA 700717 TCGA-AB-2983 AML36 10 67667342 67667342 A T SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1884+42892 e12+42892 0 - - - no_errors tier3 400 5 1.22 463 310 40.05 0 0 NA 700717 TCGA-AB-2983 AML36 10 77814435 77814435 T C SNP C10orf11 NM_032024.3 human genbank 54_36p 1 provisional intronic c.517+60186 e5+60186 0 - - - no_errors tier3 522 9 1.69 494 428 46.37 4 5 55.56 700717 TCGA-AB-2983 AML36 10 89171638 89171638 A T SNP LOC118945 XR_016426.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-30605 NULL 0.004 - - - pseudogene tier3 437 9 2.02 750 590 43.96 0 0 0 700717 TCGA-AB-2983 AML36 10 92063178 92063178 C T SNP - - - - - - - - - - - - - - - tier3 584 6 1.01 538 416 42.89 0 0 NA 700717 TCGA-AB-2983 AML36 10 109752815 109752815 G A SNP - - - - - - - - - - - - - - - tier3 1152 15 1.29 1054 737 41.1 0 0 NA 700717 TCGA-AB-2983 AML36 10 119130646 119130646 G C SNP PDZD8 NM_173791.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-5918 NULL 0.112 - - - no_errors tier3 661 17 2.5 580 470 44.72 0 0 NA 700717 TCGA-AB-2983 AML36 10 122881829 122881829 G A SNP RPL19P16 ENST00000403175 human ensembl 54_36p 1 known 5_prime_flanking_region c.-691 NULL 0.002 - - - no_coding_region:pseudogene tier3 1200 24 1.96 860 704 45.01 0 0 NA 700717 TCGA-AB-2983 AML36 10 134554647 134554647 C T SNP C10orf92 ENST00000263170 human ensembl 54_36p -1 known 5_prime_flanking_region c.-33507 NULL 0.008 - - - no_errors tier3 182 6 3.19 144 110 43.31 0 0 NA 700717 TCGA-AB-2983 AML36 11 8662196 8662196 C T SNP RPL27A NM_000990.4 human genbank 54_36p 1 reviewed silent c.135 p.F45 0.79 superfamily_Ribosomal proteins L15p and L18e "HMMPfam_L15,PatternScan_RIBOSOMAL_L15,superfamily_Ribosomal proteins L15p and L18e" - no_errors tier1 684 20 2.84 126 711 84.95 1 55 98.21 700717 TCGA-AB-2983 AML36 11 10690299 10690299 G A SNP MRVI1 NM_001100163.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-78153 NULL 0.339 - - - no_errors tier3 1763 50 2.75 259 1644 86.03 0 0 NA 700717 TCGA-AB-2983 AML36 11 22800455 22800455 C T SNP SVIP NM_148893.1 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*786 NULL 0.001 - - - no_errors tier3 772 25 3.13 145 814 84.7 1 36 97.3 700717 TCGA-AB-2983 AML36 11 23065252 23065252 C T SNP - - - - - - - - - - - - - - - tier3 301 6 1.94 98 500 83.61 0 3 100 700717 TCGA-AB-2983 AML36 11 56502304 56502304 A T SNP OR5AK2 NM_001005323.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-10661 NULL 0.004 - - - no_errors tier3 874 20 2.23 1017 793 43.81 0 0 NA 700717 TCGA-AB-2983 AML36 11 56724625 56724625 A G SNP APLNR NM_005161.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*35287 NULL 0.002 - - - no_errors tier3 522 13 2.42 914 678 42.59 0 0 NA 700717 TCGA-AB-2983 AML36 11 58886912 58886912 C T SNP OR5AN1 NM_001004729.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1596 NULL 0 - - - no_errors tier3 913 16 1.72 817 549 40.19 0 0 NA 700717 TCGA-AB-2983 AML36 11 64128440 64128440 C G SNP NRXN2 NM_015080.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*2804 NULL 0 - - - no_errors tier3 304 7 2.24 252 149 37.16 2 0 0 700717 TCGA-AB-2983 AML36 11 70213993 70213993 G T SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.1856+8448 e21+8448 0 - - - no_errors tier3 324 15 3.97 228 195 42.86 0 0 NA 700717 TCGA-AB-2983 AML36 11 70524756 70524756 G A SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.207+11058 e1+11058 0.001 - - - no_errors tier3 1154 22 1.87 615 397 39.23 0 0 NA 700717 TCGA-AB-2983 AML36 11 84442142 84442142 C T SNP DLG2 ENST00000376104 human ensembl 54_36p -1 known intronic c.357+58211 e4+58211 0.048 - - - no_errors tier3 793 9 1.12 609 473 43.67 0 0 NA 700717 TCGA-AB-2983 AML36 11 97938855 97938855 C A SNP - - - - - - - - - - - - - - - tier3 1238 21 1.67 888 661 42.65 0 0 NA 700717 TCGA-AB-2983 AML36 11 99350730 99350730 T C SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.877+17779 e6+17779 0.011 - - - no_errors tier2 455 11 2.36 703 490 41 0 0 NA 700717 TCGA-AB-2983 AML36 11 101609035 101609035 G A SNP YAP1 NM_006106.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*3154 NULL 0.998 - - - no_errors tier3 1104 20 1.78 717 541 43 0 0 NA 700717 TCGA-AB-2983 AML36 11 104659576 104659576 C G SNP - - - - - - - - - - - - - - - tier3 413 3 0.72 479 417 46.54 0 0 NA 700717 TCGA-AB-2983 AML36 11 112570571 112570572 - A INS NCAM1 ENST00000404693 human ensembl 54_36p 1 known intronic c.1-7740_7739 e1-7739 0.005:0.026 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 11 113011248 113011248 G A SNP ENSG00000211180 ENST00000388445 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24569 NULL 0 - - - pseudogene tier3 1872 18 0.95 1055 754 41.54 0 0 NA 700717 TCGA-AB-2983 AML36 11 115936347 115936347 G A SNP - - - - - - - - - - - - - - - tier3 1128 10 0.88 1039 549 34.57 0 0 NA 700717 TCGA-AB-2983 AML36 11 132842559 132842559 T G SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+64810 e1+64810 0.004 - - - no_errors tier3 803 26 3.11 1115 814 42.2 0 0 NA 700717 TCGA-AB-2983 AML36 12 2156835 2156835 A G SNP CACNA1C NM_000719.6 human genbank 54_36p 1 reviewed intronic c.477+56978 e3+56978 0.728 - - - no_errors tier3 2430 86 3.42 1664 1260 43.08 1 0 0 700717 TCGA-AB-2983 AML36 12 5362676 5362676 C T SNP NTF3 NM_001102654.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49076 NULL 0.001 - - - no_errors tier3 1804 39 2.11 1350 1123 45.32 0 0 NA 700717 TCGA-AB-2983 AML36 12 15431156 15431156 C T SNP PTPRO NM_030667.2 human genbank 54_36p 1 reviewed intronic c.75+64154 e1+64154 0.01 - - - no_errors tier3 1287 31 2.35 1152 846 42.3 0 0 NA 700717 TCGA-AB-2983 AML36 12 26527092 26527092 T C SNP ITPR2 NM_002223.2 human genbank 54_36p -1 validated intronic c.6012+806 e42+806 0.017 - - - no_errors tier3 584 7 1.18 823 454 35.5 0 1 100 700717 TCGA-AB-2983 AML36 12 33179970 33179970 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 12 46666403 46666403 C A SNP COL2A1 NM_001844.4 human genbank 54_36p -1 reviewed missense c.1510 p.G504C 0.99 HMMPfam_Collagen "HMMPfam_COLFI,HMMSmart_SM00038,HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_Collagen" - no_errors tier1 317 9 2.76 222 174 43.94 NA 700717 TCGA-AB-2983 AML36 12 54867346 54867346 A G SNP SMARCC2 NM_003075.1 human genbank 54_36p -1 reviewed silent c.123 p.A41 0.915 NULL "HMMSmart_SM00298,HMMSmart_SM00717,superfamily_BRCT domain,HMMPfam_SWIRM,superfamily_Homeodomain-like,HMMPfam_Myb_DNA-binding" - no_errors tier1 456 15 3.18 454 330 42.04 62 38 38 700717 TCGA-AB-2983 AML36 12 59093392 59093392 A G SNP - - - - - - - - - - - - - - - tier3 766 18 2.3 800 584 42.2 0 0 NA 700717 TCGA-AB-2983 AML36 12 59152071 59152071 C T SNP - - - - - - - - - - - - - - - tier3 940 14 1.47 758 438 36.59 0 0 NA 700717 TCGA-AB-2983 AML36 12 68327306 68327306 G A SNP BEST3 ENST00000331471 human ensembl 54_36p -1 known intronic c.1101-3472 e9-3472 0.002 - - - no_errors tier3 1050 26 2.41 665 544 44.96 0 0 NA 700717 TCGA-AB-2983 AML36 12 72133992 72133992 A C SNP - - - - - - - - - - - - - - - tier3 578 10 1.7 732 518 41.44 0 0 NA 700717 TCGA-AB-2983 AML36 12 73178151 73178151 T C SNP ENSG00000180632 ENST00000315355 human ensembl 54_36p 1 known 5_prime_flanking_region c.-43016 NULL 0.065 - - - no_coding_region:pseudogene tier3 149 2 1.32 209 156 42.74 0 0 NA 700717 TCGA-AB-2983 AML36 12 76735451 76735452 - T INS NAV3 NM_014903.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-13922 NULL 0.001:0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 12 81009747 81009747 C T SNP - - - - - - - - - - - - - - - tier3 875 11 1.24 644 524 44.86 0 0 NA 700717 TCGA-AB-2983 AML36 12 85525786 85525786 T C SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+119331 e0+119331 0.006 - - - no_errors tier3 639 9 1.39 509 322 38.7 0 0 NA 700717 TCGA-AB-2983 AML36 12 96512625 96512625 T C SNP MIRN135A2 ENST00000384854 human ensembl 54_36p 1 known 3_prime_flanking_region c.*30805 NULL 0.002 - - - no_errors tier3 1895 37 1.91 1225 927 43.04 0 0 NA 700717 TCGA-AB-2983 AML36 12 96658721 96658721 G A SNP LOC732096 XM_001720784.1 human genbank 54_36p -1 model intronic c.1-7412 e1-7412 0.009 - - - no_errors tier3 1192 21 1.73 944 681 41.83 0 0 NA 700717 TCGA-AB-2983 AML36 12 97868039 97868039 C A SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.2778+103027 e17+103027 0.081 - - - no_errors tier3 4398 76 1.7 2774 2129 43.4 0 0 NA 700717 TCGA-AB-2983 AML36 12 101467697 101467697 G T SNP - - - - - - - - - - - - - - - tier3 3422 62 1.78 2842 2379 45.53 0 0 NA 700717 TCGA-AB-2983 AML36 12 107671875 107671875 G A SNP CORO1C NM_014325.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-52652 NULL 0.001 - - - no_errors tier3 1194 27 2.21 568 502 46.92 1 0 0 700717 TCGA-AB-2983 AML36 12 110666249 110666249 T A SNP ACAD10 NM_025247.1 human genbank 54_36p 1 reviewed intronic c.1715-581 e12-581 0.004 - - - no_errors tier3 331 9 2.64 316 238 42.81 0 1 100 700717 TCGA-AB-2983 AML36 12 118249493 118249493 C T SNP CCDC60 NM_178499.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7872 NULL 0 - - - no_errors tier3 743 29 3.75 508 430 45.79 0 0 NA 700717 TCGA-AB-2983 AML36 13 18470585 18470585 G A SNP ENSG00000218236 ENST00000405207 human ensembl 54_36p -1 known intronic c.NULL NULL 0.001 - - - no_coding_region:pseudogene tier3 1484 31 2.04 1755 1158 39.7 0 0 NA 700717 TCGA-AB-2983 AML36 13 21880239 21880239 G A SNP - - - - - - - - - - - - - - - tier3 678 12 1.73 852 507 37.31 0 0 NA 700717 TCGA-AB-2983 AML36 13 23580952 23580952 C T SNP LOC100128337 XR_037222.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*12211 NULL 0 - - - pseudogene tier3 712 21 2.85 414 425 50.42 0 0 NA 700717 TCGA-AB-2983 AML36 13 23641933 23641933 G T SNP SPATA13 NM_153023.1 human genbank 54_36p 1 provisional intronic c.1+8862 e0+8862 0.001 - - - no_errors tier3 893 9 0.99 685 480 41.03 0 0 0 700717 TCGA-AB-2983 AML36 13 28030062 28030062 A T SNP LOC341784 XR_017250.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24831 NULL 0 - - - pseudogene tier3 1829 26 1.4 1464 1196 44.89 0 0 NA 700717 TCGA-AB-2983 AML36 13 30908397 30908397 C T SNP - - - - - - - - - - - - - - - tier3 290 5 1.68 555 295 34.58 0 0 NA 700717 TCGA-AB-2983 AML36 13 31627951 31627951 G C SNP FRY NM_023037.2 human genbank 54_36p 1 validated intronic c.1651+152 e15+152 0.582 - - - no_errors tier3 365 3 0.82 726 508 41.07 4 1 20 700717 TCGA-AB-2983 AML36 13 31815354 31815354 T G SNP BRCA2 NM_000059.3 human genbank 54_36p 1 reviewed intronic c.6842-1341 e11-1341 0.172 - - - no_errors tier3 519 9 1.69 536 418 43.68 1 1 50 700717 TCGA-AB-2983 AML36 13 40406066 40406066 A G SNP ELF1 NM_172373.1 human genbank 54_36p -1 reviewed missense c.1355 p.I452T 1 NULL "HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_1,PatternScan_ETS_DOMAIN_2,superfamily_SSF46785" - no_errors tier1 1404 29 2.02 942 717 43.19 121 110 47.41 700717 TCGA-AB-2983 AML36 13 44635732 44635732 T G SNP GTF2F2 NM_004128.2 human genbank 54_36p 1 validated intronic c.304+11766 e4+11766 0.011 - - - no_errors tier3 128 1 0.78 617 507 45.11 0 0 0 700717 TCGA-AB-2983 AML36 13 46312510 46312510 G A SNP HTR2A NM_000621.2 human genbank 54_36p -1 validated intronic c.614-4735 e3-4735 0.002 - - - no_errors tier3 1188 14 1.16 987 704 41.63 0 0 NA 700717 TCGA-AB-2983 AML36 13 47778582 47778582 G A SNP RB1 NM_000321.2 human genbank 54_36p 1 reviewed intronic c.138-835 e2-835 0.511 - - - no_errors tier3 656 3 0.45 748 432 36.58 5 7 58.33 700717 TCGA-AB-2983 AML36 13 49317320 49317321 - T INS LOC220429 NR_003268.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45330 NULL 0.000:0.000 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 13 52310746 52310746 C T SNP PCDH8 NM_002590.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*5950 NULL 0.012 - - - no_errors tier3 587 14 2.31 292 220 42.8 0 0 NA 700717 TCGA-AB-2983 AML36 13 52674350 52674350 G - DEL ENSG00000218221 ENST00000401786 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*52674350 NULL 0 - - - no_coding_region:pseudogene tier2 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 13 53680319 53680319 A T SNP - - - - - - - - - - - - - - - tier3 862 19 2.16 932 690 42.54 0 0 NA 700717 TCGA-AB-2983 AML36 13 58706263 58706263 A T SNP - - - - - - - - - - - - - - - tier3 811 16 1.93 855 609 41.49 0 0 NA 700717 TCGA-AB-2983 AML36 13 61532156 61532156 T G SNP - - - - - - - - - - - - - - - tier3 794 10 1.24 654 416 38.88 0 0 NA 700717 TCGA-AB-2983 AML36 13 64632825 64632825 C T SNP - - - - - - - - - - - - - - - tier3 451 11 2.38 450 309 40.71 0 0 NA 700717 TCGA-AB-2983 AML36 13 69012231 69012231 C T SNP - - - - - - - - - - - - - - - tier3 651 11 1.66 740 522 41.36 0 0 NA 700717 TCGA-AB-2983 AML36 13 85645072 85645072 G T SNP - - - - - - - - - - - - - - - tier3 357 7 1.92 474 302 38.87 0 0 NA 700717 TCGA-AB-2983 AML36 13 91352586 91352586 A G SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1281-5606 e6-5606 0.001 - - - no_errors tier3 276 7 2.47 529 398 42.93 0 0 NA 700717 TCGA-AB-2983 AML36 13 92953523 92953523 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.161-41994 e2-41994 0 - - - no_errors tier3 1193 6 0.5 989 498 33.47 0 0 NA 700717 TCGA-AB-2983 AML36 13 93188205 93188205 C T SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.320-92203 e3-92203 0 - - - no_errors tier3 1312 17 1.28 1327 927 41.09 0 0 NA 700717 TCGA-AB-2983 AML36 13 103478013 103478013 G T SNP - - - - - - - - - - - - - - - tier3 866 7 0.8 946 507 34.87 0 0 NA 700717 TCGA-AB-2983 AML36 13 104324752 104324752 A G SNP - - - - - - - - - - - - - - - tier3 218 2 0.91 438 300 40.65 0 0 NA 700717 TCGA-AB-2983 AML36 13 107214837 107214837 G A SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.915+101194 e1+101194 0.001 - - - no_errors tier3 1601 35 2.14 985 666 40.34 0 0 NA 700717 TCGA-AB-2983 AML36 13 108625857 108625857 G T SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.5258-4034 e33-4034 0 - - - no_errors tier3 2066 30 1.43 1453 1026 41.39 0 0 NA 700717 TCGA-AB-2983 AML36 14 21049123 21049123 T C SNP METTL3 NM_019852.3 human genbank 54_36p -1 reviewed missense c.83 p.Q28R 1 NULL HMMPfam_MT-A70 - no_errors tier1 414 8 1.89 239 124 34.16 21 24 53.33 700717 TCGA-AB-2983 AML36 14 21212949 21212949 T G SNP OR10G2 NM_001005466.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-40111 NULL 0.672 - - - no_errors tier3 608 8 1.3 706 532 42.94 0 0 NA 700717 TCGA-AB-2983 AML36 14 22184068 22184068 C T SNP OR6J1 ENST00000312039 human ensembl 54_36p -1 known 5_prime_flanking_region c.-10512 NULL 0.718 - - - no_errors tier3 2280 50 2.14 1551 1022 39.7 0 0 0 700717 TCGA-AB-2983 AML36 14 26698503 26698503 G T SNP - - - - - - - - - - - - - - - tier3 649 5 0.76 851 538 38.73 0 0 NA 700717 TCGA-AB-2983 AML36 14 47012066 47012066 G A SNP MDGA2 ENST00000399232 human ensembl 54_36p -1 known intronic c.74-171563 e2-171563 0.006 - - - no_errors tier3 1745 39 2.18 1200 847 41.34 0 0 NA 700717 TCGA-AB-2983 AML36 14 55416701 55416701 C T SNP - - - - - - - - - - - - - - - tier3 747 23 2.97 628 425 40.36 0 0 NA 700717 TCGA-AB-2983 AML36 14 58859776 58859776 G A SNP DAAM1 NM_014992.1 human genbank 54_36p 1 reviewed intronic c.774+80 e5+80 0 - - - no_errors tier3 997 22 2.15 750 517 40.81 1 6 85.71 700717 TCGA-AB-2983 AML36 14 65474401 65474401 C A SNP LOC729850 XM_001131507.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*19830 NULL 0 - - - no_errors tier3 1275 27 2.07 845 611 41.91 0 0 NA 700717 TCGA-AB-2983 AML36 14 74080327 74080327 C T SNP LTBP2 NM_000428.2 human genbank 54_36p -1 reviewed intronic c.1789+5992 e8+5992 0 - - - no_errors tier3 944 29 2.97 508 387 43.14 0 0 NA 700717 TCGA-AB-2983 AML36 14 84546819 84546819 T G SNP - - - - - - - - - - - - - - - tier3 308 2 0.65 544 338 38.32 0 0 NA 700717 TCGA-AB-2983 AML36 14 86171052 86171052 T C SNP - - - - - - - - - - - - - - - tier3 120 5 4 322 223 40.92 0 1 100 700717 TCGA-AB-2983 AML36 14 88971017 88971017 C T SNP FOXN3 NM_001085471.1 human genbank 54_36p -1 reviewed intronic c.1-22430 e1-22430 0.007 - - - no_errors tier3 630 9 1.41 417 282 40.34 1 7 87.5 700717 TCGA-AB-2983 AML36 14 97400063 97400063 G T SNP - - - - - - - - - - - - - - - tier3 1013 16 1.55 721 521 41.91 0 0 NA 700717 TCGA-AB-2983 AML36 14 100142397 100142397 C T SNP BEGAIN NM_020836.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-38383 NULL 0.001 - - - no_errors tier3 373 12 3.1 209 184 46.7 0 0 NA 700717 TCGA-AB-2983 AML36 14 101522818 101522818 C T SNP DYNC1H1 NM_001376.4 human genbank 54_36p 1 reviewed missense c.2503 p.R835C 1 NULL "HMMSmart_AAA,HMMPfam_Dynein_heavy,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_SSF52540" - no_errors tier1 1623 28 1.69 1212 666 35.44 28 20 41.67 700717 TCGA-AB-2983 AML36 14 104048388 104048388 G A SNP - - - - - - - - - - - - - - - tier3 162 5 2.99 158 131 45.17 0 0 NA 700717 TCGA-AB-2983 AML36 14 105567756 105567756 G A SNP ENSG00000211937 ENST00000390597 human ensembl 54_36p -1 known 5_prime_flanking_region c.-2134 NULL 0 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 31 1 3.12 60 54 47.37 0 0 0 700717 TCGA-AB-2983 AML36 15 40417710 40417710 G A SNP GANC NM_198141.2 human genbank 54_36p 1 reviewed intronic c.1742-169 e16-169 0.003 - - - no_errors tier3 188 1 0.53 587 320 35.28 4 5 55.56 700717 TCGA-AB-2983 AML36 15 44652537 44652537 C A SNP - - - - - - - - - - - - - - - tier3 1033 18 1.71 828 511 38.16 0 0 NA 700717 TCGA-AB-2983 AML36 15 61213106 61213106 C T SNP LACTB NM_032857.2 human genbank 54_36p 1 reviewed intronic c.1118+4204 e5+4204 0.017 - - - no_errors tier3 114 0 0 357 202 36.07 3 3 50 700717 TCGA-AB-2983 AML36 15 67794112 67794112 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 15 69618692 69618692 A T SNP THSD4 NM_024817.2 human genbank 54_36p 1 provisional intronic c.1153-121231 e7-121231 0.001 - - - no_errors tier3 1007 22 2.13 823 687 45.47 0 0 NA 700717 TCGA-AB-2983 AML36 15 79735841 79735841 G A SNP - - - - - - - - - - - - - - - tier3 190 6 3.06 349 253 41.89 0 0 NA 700717 TCGA-AB-2983 AML36 15 87181945 87181945 T C SNP ACAN NM_013227.2 human genbank 54_36p 1 reviewed intronic c.71-953 e2-953 0.002 - - - no_errors tier3 935 13 1.36 524 314 37.29 0 0 NA 700717 TCGA-AB-2983 AML36 15 87792818 87792818 C T SNP RHCG NM_016321.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*24152 NULL 0 - - - no_errors tier3 557 8 1.42 434 296 40.44 0 0 NA 700717 TCGA-AB-2983 AML36 15 90740372 90740372 C T SNP ST8SIA2 NM_006011.3 human genbank 54_36p 1 reviewed intronic c.98+1976 e1+1976 0 - - - no_errors tier3 905 26 2.79 415 366 46.8 0 0 NA 700717 TCGA-AB-2983 AML36 15 92688616 92688616 G A SNP MCTP2 NM_018349.2 human genbank 54_36p 1 provisional intronic c.970-746 e7-746 0 - - - no_errors tier3 345 4 1.14 248 147 37.22 3 1 25 700717 TCGA-AB-2983 AML36 15 92737399 92737399 A T SNP MCTP2 NM_018349.2 human genbank 54_36p 1 provisional intronic c.1789-5795 e14-5795 0.001 - - - no_errors tier3 309 1 0.32 646 410 38.79 4 0 0 700717 TCGA-AB-2983 AML36 15 94414945 94414945 C T SNP - - - - - - - - - - - - - - - tier3 1386 24 1.7 778 575 42.5 0 0 NA 700717 TCGA-AB-2983 AML36 15 98655695 98655695 T C SNP ADAMTS17 NM_139057.2 human genbank 54_36p -1 reviewed intronic c.617-16566 e4-16566 0 - - - no_errors tier3 2116 47 2.17 1070 781 42.17 0 0 NA 700717 TCGA-AB-2983 AML36 16 22804662 22804662 C T SNP HS3ST2 NM_006043.1 human genbank 54_36p 1 reviewed intronic c.486-29104 e2-29104 0 - - - no_errors tier3 1165 18 1.51 768 647 45.6 0 0 NA 700717 TCGA-AB-2983 AML36 16 27129319 27129319 T G SNP JMJD5 NM_024773.1 human genbank 54_36p 1 reviewed missense c.374 p.M125R 1 NULL "HMMSmart_SM00558,superfamily_Clavaminate synthase-like" - no_errors tier1 382 8 2.05 251 178 41.3 5 1 16.67 700717 TCGA-AB-2983 AML36 16 55961732 55961732 C G SNP CCL17 NM_002987.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-43614 NULL 0.061 - - - no_errors tier3 504 11 2.13 256 120 31.83 0 0 NA 700717 TCGA-AB-2983 AML36 16 56887055 56887055 G A SNP KLKBL4 NM_001080492.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-1834 NULL 0 - - - no_errors tier3 1246 37 2.88 793 524 39.73 0 0 NA 700717 TCGA-AB-2983 AML36 16 57920627 57920627 G T SNP - - - - - - - - - - - - - - - tier3 1389 29 2.04 1055 734 40.96 0 0 NA 700717 TCGA-AB-2983 AML36 16 63961592 63961592 G A SNP LOC283867 NM_001101346.1 human genbank 54_36p -1 inferred intronic c.1-6380 e1-6380 0 - - - no_errors tier3 919 20 2.13 1273 926 42.11 0 0 NA 700717 TCGA-AB-2983 AML36 16 65631309 65631309 A G SNP CBFB NM_022845.2 human genbank 54_36p 1 reviewed intronic c.282+3150 e3+3150 0.271 - - - no_errors tier3 655 12 1.8 575 419 41.98 3 2 40 700717 TCGA-AB-2983 AML36 17 24980270 24980270 G A SNP SSH2 NM_033389.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*1715 NULL 0.019 - - - no_errors tier3 1074 18 1.65 666 456 40.61 27 22 44.9 700717 TCGA-AB-2983 AML36 17 33154189 33154189 G A SNP HNF1B NM_000458.2 human genbank 54_36p -1 validated intronic c.1046-9405 e5-9405 0.006 - - - no_errors tier3 1213 17 1.38 778 492 38.74 0 0 NA 700717 TCGA-AB-2983 AML36 17 46908576 46908576 G A SNP LOC388401 XR_016879.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*26198 NULL 0.875 - - - pseudogene tier3 338 6 1.74 598 406 40.4 0 0 NA 700717 TCGA-AB-2983 AML36 17 49370347 49370347 G T SNP - - - - - - - - - - - - - - - tier3 742 30 3.88 785 497 38.74 0 0 NA 700717 TCGA-AB-2983 AML36 17 75274643 75274643 G A SNP ENPP7 NM_178543.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44854 NULL 0.807 - - - no_errors tier3 534 10 1.83 326 226 40.87 2 0 0 700717 TCGA-AB-2983 AML36 18 9136076 9136076 A T SNP ANKRD12 NM_015208.1 human genbank 54_36p 1 validated intronic c.1+9113 e0+9113 0.132 - - - no_errors tier3 405 19 4.48 509 363 41.53 5 6 54.55 700717 TCGA-AB-2983 AML36 18 12240859 12240859 C G SNP CIDEA NM_198289.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3957 NULL 0.009 - - - no_errors tier3 391 6 1.51 300 212 41.41 0 0 NA 700717 TCGA-AB-2983 AML36 18 23310460 23310460 T C SNP FLJ45994 XR_040238.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.002 - - - no_errors tier3 1400 31 2.16 1048 832 44.14 0 0 NA 700717 TCGA-AB-2983 AML36 18 29491588 29491588 A T SNP ASXL3 NM_030632.1 human genbank 54_36p 1 validated intronic c.356-3990 e5-3990 0 - - - no_errors tier3 1277 20 1.54 1413 1117 44.12 0 0 NA 700717 TCGA-AB-2983 AML36 18 29912713 29912713 G A SNP NOL4 NM_003787.3 human genbank 54_36p -1 validated intronic c.772+14714 e5+14714 0 - - - no_errors tier3 497 8 1.58 803 579 41.9 0 0 NA 700717 TCGA-AB-2983 AML36 18 36252131 36252131 G T SNP - - - - - - - - - - - - - - - tier3 750 12 1.57 942 468 33.12 0 0 NA 700717 TCGA-AB-2983 AML36 18 48251041 48251041 C T SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.91+129795 e1+129795 0 - - - no_errors tier3 1331 11 0.82 1110 802 41.92 0 0 NA 700717 TCGA-AB-2983 AML36 18 50752017 50752017 T C SNP CCDC68 NM_025214.1 human genbank 54_36p -1 validated intronic c.600+1032 e5+1032 0.007 - - - no_errors tier3 507 16 3.06 559 407 42.09 0 0 NA 700717 TCGA-AB-2983 AML36 18 57878166 57878166 C T SNP PIGN ENST00000357637 human ensembl 54_36p -1 known intronic c.2672+12720 e27+12720 0 - - - no_errors tier3 1081 21 1.9 922 736 44.34 7 4 36.36 700717 TCGA-AB-2983 AML36 18 60879431 60879431 C T SNP - - - - - - - - - - - - - - - tier3 1476 30 1.98 724 530 42.2 0 0 NA 700717 TCGA-AB-2983 AML36 18 67976548 67976548 C T SNP - - - - - - - - - - - - - - - tier3 519 9 1.7 555 417 42.9 0 0 NA 700717 TCGA-AB-2983 AML36 19 10113242 10113242 G A SNP DNMT1 NM_001379.1 human genbank 54_36p -1 reviewed intronic c.3262-377 e30-377 0 - - - no_errors tier3 363 4 1.09 332 183 35.47 9 14 60.87 700717 TCGA-AB-2983 AML36 19 41655610 41655610 C T SNP ZNF566 NM_032838.1 human genbank 54_36p -1 validated intronic c.232+43 e3+43 0.021 - - - no_errors tier3 927 11 1.17 555 454 44.86 4 2 33.33 700717 TCGA-AB-2983 AML36 19 49164071 49164071 C T SNP ZNF155 NM_003445.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20465 NULL 0 - - - no_errors tier3 1364 25 1.79 1066 792 42.49 3 5 62.5 700717 TCGA-AB-2983 AML36 19 51109510 51109510 C T SNP NANOS2 NM_001029861.2 human genbank 54_36p -1 validated silent c.282 p.R94 0.998 HMMPfam_zf-nanos HMMPfam_zf-nanos - no_errors tier1 812 23 2.75 339 294 46.37 NA 700717 TCGA-AB-2983 AML36 19 53931602 53931602 C T SNP RASIP1 NM_017805.2 human genbank 54_36p -1 validated intronic c.824-982 e3-982 0.168 - - - no_errors tier3 738 12 1.6 465 380 44.86 0 0 NA 700717 TCGA-AB-2983 AML36 19 58089653 58089653 A G SNP ZNF320 ENST00000391781 human ensembl 54_36p -1 known intronic c.1-368 e1-368 0.004 - - - no_errors tier3 640 23 3.46 535 437 44.96 3 3 50 700717 TCGA-AB-2983 AML36 20 2504895 2504895 G A SNP TMC2 NM_080751.2 human genbank 54_36p 1 validated intronic c.646-2897 e6-2897 0.041 - - - no_errors tier3 713 16 2.19 565 361 38.98 0 0 NA 700717 TCGA-AB-2983 AML36 20 3671099 3671099 A T SNP HSPA12B NM_052970.3 human genbank 54_36p 1 reviewed intronic c.266+44 e3+44 0.002 - - - no_errors tier3 357 9 2.46 204 174 46.03 0 0 NA 700717 TCGA-AB-2983 AML36 20 29914947 29914947 G A SNP DUSP15 NM_080611.1 human genbank 54_36p -1 reviewed intronic c.263+424 e5+424 0.001 - - - no_errors tier3 783 13 1.63 561 418 42.65 0 0 NA 700717 TCGA-AB-2983 AML36 20 42844048 42844048 C T SNP RIMS4 NM_182970.2 human genbank 54_36p -1 validated intronic c.98-10580 e2-10580 0.963 - - - no_errors tier3 1584 34 2.1 754 606 44.49 0 0 NA 700717 TCGA-AB-2983 AML36 20 43250606 43250606 C T SNP SEMG2 NM_003008.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32839 NULL 0.103 - - - no_errors tier3 1437 36 2.44 1022 784 43.39 0 0 NA 700717 TCGA-AB-2983 AML36 21 20622157 20622157 G A SNP ENSG00000209746 ENST00000387011 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-28680 NULL 0.49 - - - pseudogene tier3 1029 27 2.55 1012 758 42.78 0 0 NA 700717 TCGA-AB-2983 AML36 21 28418823 28418823 C T SNP - - - - - - - - - - - - - - - tier3 264 5 1.85 610 383 38.57 0 0 NA 700717 TCGA-AB-2983 AML36 21 30401847 30401847 C T SNP - - - - - - - - - - - - - - - tier3 525 5 0.94 555 420 43.03 0 0 NA 700717 TCGA-AB-2983 AML36 21 31575012 31575012 G A SNP TIAM1 NM_003253.2 human genbank 54_36p -1 validated intronic c.1-3917 e1-3917 0 - - - no_errors tier3 206 9 4.19 161 292 64.46 0 0 NA 700717 TCGA-AB-2983 AML36 21 32528524 32528524 G A SNP C21orf45 NM_018944.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*34695 NULL 0.001 - - - no_errors tier3 1419 33 2.27 972 756 43.62 0 0 NA 700717 TCGA-AB-2983 AML36 21 34084639 34084639 T - DEL ITSN1 NM_003024.1 human genbank 54_36p 1 reviewed intronic c.1825-3876 e16-3876 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 700717 TCGA-AB-2983 AML36 21 35016653 35016653 G A SNP CLIC6 NM_053277.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*6003 NULL 0 - - - no_errors tier3 375 5 1.31 435 213 32.87 0 0 NA 700717 TCGA-AB-2983 AML36 21 35174787 35174787 C G SNP RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed missense c.445 p.A149P 0.988 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 761 16 2.05 450 312 40.78 346 328 48.66 700717 TCGA-AB-2983 AML36 21 43648836 43648836 T C SNP C21orf125 ENST00000342757 human ensembl 54_36p 1 known 5_prime_flanking_region c.-45582 NULL 0.002 - - - no_errors tier3 419 6 1.41 224 119 34.59 0 1 100 700717 TCGA-AB-2983 AML36 22 18344415 18344415 G T SNP ARVCF NM_001670.1 human genbank 54_36p -1 reviewed intronic c.1871-169 e8-169 0 - - - no_errors tier3 58 0 0 60 45 42.86 0 0 0 700717 TCGA-AB-2983 AML36 22 21888371 21888371 A G SNP BCR NM_004327.3 human genbank 54_36p 1 reviewed intronic c.1279+33945 e1+33945 0 - - - no_errors tier3 784 9 1.13 521 412 44.16 10 10 50 700717 TCGA-AB-2983 AML36 22 33346578 33346578 G A SNP ENSG00000220899 ENST00000401469 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29308 NULL 0.003 - - - no_coding_region:pseudogene tier3 630 11 1.71 607 448 42.46 0 0 NA 700717 TCGA-AB-2983 AML36 22 34357085 34357085 C T SNP LOC284912 XR_041187.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.059 - - - no_errors tier3 273 11 3.85 267 169 38.67 0 0 NA 700717 TCGA-AB-2983 AML36 22 46384169 46384169 C T SNP FLJ46257 XR_041673.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*15474 NULL 0 - - - no_errors tier3 494 8 1.59 197 174 46.52 0 0 NA 700717 TCGA-AB-2983 AML36 22 49243994 49243994 C T SNP SBF1 NM_002972.1 human genbank 54_36p -1 validated intronic c.3826+556 e28+556 0.205 - - - no_errors tier3 367 3 0.8 315 219 40.86 5 2 28.57 807970 TCGA-AB-2984 AML02 Y 22821779 22821779 C T SNP RBMY1J ENST00000382605 human ensembl 54_36p 1 known 5_prime_flanking_region c.-139204 NULL 0 - - - no_errors tier2 359 0 0 20 648 97.01 0 0 NA 807970 TCGA-AB-2984 AML02 X 28736804 28736804 A T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.82+19341 e1+19341 0.001 - - - no_errors tier2 225 0 0 10 324 97.01 0 0 NA 807970 TCGA-AB-2984 AML02 X 37475899 37475899 C T SNP XK NM_021083.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*3245 NULL 0.05 - - - no_errors tier3 544 1 0.18 19 681 97.01 0 0 NA 807970 TCGA-AB-2984 AML02 X 82476234 82476234 C T SNP - - - - - - - - - - - - - - - tier3 269 0 0 4 376 98.95 0 0 NA 807970 TCGA-AB-2984 AML02 X 85761966 85761966 T C SNP DACH2 NM_053281.1 human genbank 54_36p 1 reviewed intronic c.641-30729 e4-30729 0.051 - - - no_errors tier2 359 0 0 16 467 96.69 0 0 NA 807970 TCGA-AB-2984 AML02 X 86333261 86333261 G T SNP ENSG00000200422 ENST00000363552 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44798 NULL 0.053 - - - no_errors tier3 391 0 0 27 579 95.39 0 0 NA 807970 TCGA-AB-2984 AML02 X 107670698 107670698 G C SNP COL4A5 NM_033380.3 human genbank 54_36p 1 reviewed intronic c.141+1007 e2+1007 0.228 - - - no_errors tier3 391 0 0 26 603 95.87 0 0 0 807970 TCGA-AB-2984 AML02 X 123589037 123589037 G A SNP ODZ1 NM_014253.2 human genbank 54_36p -1 provisional intronic c.2077+14285 e11+14285 0.182 - - - no_errors tier3 463 0 0 11 712 98.48 0 0 NA 807970 TCGA-AB-2984 AML02 X 146508708 146508708 C G SNP ENSG00000219655 ENST00000405281 human ensembl 54_36p -1 known 5_prime_flanking_region c.-27589 NULL 0 - - - no_coding_region:pseudogene tier3 564 0 0 25 621 96.13 0 0 NA 807970 TCGA-AB-2984 AML02 X 148583995 148583995 G T SNP MAGEA11 NM_001011544.1 human genbank 54_36p -1 reviewed intronic c.10-5731 e2-5731 0 - - - no_errors tier3 542 0 0 19 527 96.52 0 0 0 807970 TCGA-AB-2984 AML02 1 22277647 22277647 C T SNP CDC42 NM_001039802.1 human genbank 54_36p 1 reviewed missense c.89 p.S30L 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 856 0 612 533 46.55 40 82 67.21 807970 TCGA-AB-2984 AML02 1 24868534 24868534 T A SNP SRRM1 NM_005839.3 human genbank 54_36p 1 validated silent c.2073 p.P691 0.988 NULL "HMMPfam_PWI,HMMSmart_SM00311,superfamily_PWI domain" - no_errors tier1 626 0 507 423 45.44 64 63 49.61 807970 TCGA-AB-2984 AML02 1 30221403 30221403 G A SNP - - - - - - - - - - - - - - - tier3 640 1 0.16 580 537 48.08 0 0 NA 807970 TCGA-AB-2984 AML02 1 58591900 58591900 A G SNP - - - - - - - - - - - - - - - tier3 1534 1 0.07 772 698 47.48 0 0 NA 807970 TCGA-AB-2984 AML02 1 81482160 81482160 C T SNP ENSG00000223026 ENST00000411094 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7902 NULL 0.001 - - - no_errors tier3 854 0 0 996 611 38.02 0 0 NA 807970 TCGA-AB-2984 AML02 1 90364089 90364089 C T SNP - - - - - - - - - - - - - - - tier3 610 0 0 440 399 47.56 0 0 NA 807970 TCGA-AB-2984 AML02 1 112511549 112511549 G A SNP ENSG00000209265 ENST00000386530 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-28121 NULL 0.891 - - - pseudogene tier3 1598 0 0 1126 1013 47.29 0 0 NA 807970 TCGA-AB-2984 AML02 1 115060270 115060270 C T SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.35 p.G12D 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1095 1 0.09 815 500 37.97 21 9 29.03 807970 TCGA-AB-2984 AML02 1 187232232 187232232 C T SNP - - - - - - - - - - - - - - - tier3 715 0 0 427 431 50.23 0 0 NA 807970 TCGA-AB-2984 AML02 1 205250027 205250027 C T SNP PFKFB2 NM_006212.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-44659 NULL 0.005 - - - no_errors tier2 1206 2 0.17 1353 768 36.18 0 0 NA 807970 TCGA-AB-2984 AML02 1 211344695 211344695 A G SNP RPS6KC1 NM_012424.1 human genbank 54_36p 1 validated intronic c.378+161 e4+161 0 - - - no_errors tier3 309 1 0.32 344 360 50.49 0 0 0 807970 TCGA-AB-2984 AML02 1 214543612 214543612 C T SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.1645-11277 e9-11277 0.989 - - - no_errors tier3 188 0 0 407 106 20.66 0 0 NA 807970 TCGA-AB-2984 AML02 1 222701136 222701136 G T SNP WDR26 NM_025160.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15049 NULL 0.002 - - - no_errors tier3 464 0 0 303 251 45.23 0 0 NA 807970 TCGA-AB-2984 AML02 1 238188066 238188066 C T SNP LOC645884 XR_017475.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-49381 NULL 0.01 - - - pseudogene tier3 769 0 0 378 306 44.74 0 0 NA 807970 TCGA-AB-2984 AML02 1 241429086 241429087 - ATA INS CEP170 NM_014812.1 human genbank 54_36p -1 reviewed in_frame_ins c.530_529 p.177in_frame_insL 1.000:1.000 NULL "HMMPfam_FHA,HMMSmart_SM00240,superfamily_SMAD/FHA domain" - no_errors tier1 NA NA NA NA NA NA NA 807970 TCGA-AB-2984 AML02 1 244409454 244409454 A T SNP SMYD3 NM_022743.1 human genbank 54_36p -1 provisional intronic c.354+147672 e4+147672 0 - - - no_errors tier3 824 0 0 643 570 46.99 3 4 50 807970 TCGA-AB-2984 AML02 2 11152065 11152065 G A SNP C2orf50 NM_182500.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38847 NULL 0.003 - - - no_errors tier3 152 1 0.65 135 147 51.94 0 0 NA 807970 TCGA-AB-2984 AML02 2 11264160 11264160 C T SNP ROCK2 NM_004850.3 human genbank 54_36p -1 reviewed intronic c.2549+1143 e20+1143 0 - - - no_errors tier3 1118 0 0 695 644 48.06 1 0 0 807970 TCGA-AB-2984 AML02 2 13916809 13916809 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 2 33014866 33014866 G - DEL LTBP1 NM_206943.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11030 NULL 0.013 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 2 61167607 61167607 G A SNP KIAA1841 NM_032506.1 human genbank 54_36p 1 validated intronic c.891-1191 e7-1191 0.002 - - - no_errors tier2 1062 0 0 632 600 48.7 0 2 100 807970 TCGA-AB-2984 AML02 2 70771998 70771998 G A SNP ADD2 NM_001617.2 human genbank 54_36p -1 reviewed intronic c.706-429 e6-429 0.001 - - - no_errors tier3 819 0 0 669 561 45.57 0 0 0 807970 TCGA-AB-2984 AML02 2 71793306 71793306 G A SNP DYSF NM_003494.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*26176 NULL 0.278 - - - no_errors tier3 622 0 0 377 286 43.14 0 0 NA 807970 TCGA-AB-2984 AML02 2 77282816 77282816 T G SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+316136 e2+316136 0 - - - no_errors tier3 591 0 0 525 332 38.74 0 0 NA 807970 TCGA-AB-2984 AML02 2 79609250 79609250 T A SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1+15409 e0+15409 0.119 - - - no_errors tier3 677 0 0 528 394 42.73 0 0 NA 807970 TCGA-AB-2984 AML02 2 103820742 103820742 C T SNP - - - - - - - - - - - - - - - tier3 554 0 0 756 422 35.79 0 0 NA 807970 TCGA-AB-2984 AML02 2 118739801 118739801 C T SNP - - - - - - - - - - - - - - - tier3 711 0 0 525 469 47.18 0 0 NA 807970 TCGA-AB-2984 AML02 2 119382504 119382504 C T SNP MARCO NM_006770.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33843 NULL 0.001 - - - no_errors tier3 937 1 0.11 628 615 49.4 0 0 NA 807970 TCGA-AB-2984 AML02 2 125848861 125848861 C A SNP - - - - - - - - - - - - - - - tier3 975 1 0.1 747 686 47.84 0 0 NA 807970 TCGA-AB-2984 AML02 2 130361953 130361953 G A SNP ENSG00000214100 ENST00000397540 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*35020 NULL 0 - - - no_errors tier3 560 0 0 413 425 50.66 0 0 NA 807970 TCGA-AB-2984 AML02 2 144360699 144360699 A G SNP ENSG00000200287 ENST00000363417 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-10599 NULL 0.001 - - - no_errors tier3 649 1 0.15 450 482 51.72 0 0 NA 807970 TCGA-AB-2984 AML02 2 145143586 145143586 T C SNP LOC100131409 XM_001717958.1 human genbank 54_36p 1 model intronic c.292+1441 e1+1441 0.973 - - - no_errors tier3 1084 0 0 867 934 51.86 0 0 NA 807970 TCGA-AB-2984 AML02 2 152339614 152339614 C T SNP NEB NM_004543.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-41698 NULL 0.001 - - - no_errors tier2 638 1 0.16 463 461 49.89 0 0 NA 807970 TCGA-AB-2984 AML02 2 163840921 163840921 C T SNP ENSG00000200902 ENST00000364032 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-12830 NULL 0.999 - - - no_errors tier2 780 1 0.13 577 575 49.87 0 0 NA 807970 TCGA-AB-2984 AML02 2 166315340 166315340 C A SNP GALNT3 NM_004482.3 human genbank 54_36p -1 reviewed intronic c.1627-690 e9-690 0 - - - no_errors tier3 822 0 0 722 645 47.18 0 0 0 807970 TCGA-AB-2984 AML02 2 171767703 171767703 C A SNP TLK1 NM_012290.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42519 NULL 0.004 - - - no_errors tier3 744 0 0 395 356 47.4 0 0 NA 807970 TCGA-AB-2984 AML02 2 174025207 174025207 C T SNP LOC100130171 XR_038684.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-19964 NULL 0 - - - pseudogene tier3 931 0 0 524 570 52.1 0 0 NA 807970 TCGA-AB-2984 AML02 2 205025510 205025510 G A SNP - - - - - - - - - - - - - - - tier3 510 1 0.19 535 522 49.11 0 0 NA 807970 TCGA-AB-2984 AML02 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 858 0 592 570 49.01 11 6 35.29 807970 TCGA-AB-2984 AML02 2 223059781 223059781 T C SNP SGPP2 NM_152386.2 human genbank 54_36p 1 provisional intronic c.378+12092 e2+12092 0.002 - - - no_errors tier3 682 1 0.15 518 482 48.15 0 0 NA 807970 TCGA-AB-2984 AML02 2 239589768 239589768 G T SNP ENSG00000211566 ENST00000390140 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30125 NULL 0 - - - no_errors tier3 498 1 0.2 374 335 47.18 0 0 NA 807970 TCGA-AB-2984 AML02 3 1512230 1512230 A G SNP - - - - - - - - - - - - - - - tier3 767 0 0 591 381 39.16 0 0 NA 807970 TCGA-AB-2984 AML02 3 4214634 4214634 C T SNP SUMF1 ENST00000405420 human ensembl 54_36p -1 known intronic c.1015-129205 e9-129205 0.752 - - - no_errors tier3 651 0 0 593 551 48.16 0 0 0 807970 TCGA-AB-2984 AML02 3 19003251 19003251 A - DEL ENSG00000209918 ENST00000387183 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31706 NULL 1 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 3 24908942 24908942 C T SNP - - - - - - - - - - - - - - - tier3 983 3 0.3 763 671 46.79 0 0 NA 807970 TCGA-AB-2984 AML02 3 31205180 31205180 A G SNP ENSG00000222983 ENST00000411051 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-40031 NULL 0 - - - no_errors tier3 771 0 0 649 619 48.78 0 0 0 807970 TCGA-AB-2984 AML02 3 52634438 52634438 T C SNP PBRM1 NM_018165.4 human genbank 54_36p -1 validated intronic c.1445+1891 e12+1891 0.001 - - - no_errors tier3 450 0 0 490 352 41.76 4 2 33.33 807970 TCGA-AB-2984 AML02 3 85370402 85370402 G A SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+278893 e1+278893 1 - - - no_errors tier3 315 0 0 393 321 44.9 0 0 NA 807970 TCGA-AB-2984 AML02 3 89649212 89649212 T C SNP EPHA3 NM_005233.5 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*37870 NULL 0 - - - no_errors tier2 1579 0 0 947 864 47.63 0 0 NA 807970 TCGA-AB-2984 AML02 3 98797968 98797968 G A SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.2512+3697 e12+3697 0 - - - no_errors tier3 743 0 0 500 476 48.77 0 0 NA 807970 TCGA-AB-2984 AML02 3 102445364 102445364 C T SNP IMPG2 NM_016247.2 human genbank 54_36p -1 validated missense c.2501 p.G834D 0.018 NULL "HMMPfam_SEA,HMMSmart_SM00200,PatternScan_EGF_2,superfamily_EGF/Laminin,superfamily_SEA domain" - no_errors tier1 1097 0 898 840 48.33 NA 807970 TCGA-AB-2984 AML02 3 104933735 104933735 T A SNP - - - - - - - - - - - - - - - tier3 645 0 0 427 484 52.95 0 0 NA 807970 TCGA-AB-2984 AML02 3 107008650 107008650 T C SNP CBLB NM_170662.3 human genbank 54_36p -1 validated intronic c.420-30574 e3-30574 0.007 - - - no_errors tier3 597 1 0.17 486 442 47.63 3 1 25 807970 TCGA-AB-2984 AML02 3 109061627 109061627 A G SNP - - - - - - - - - - - - - - - tier3 1100 0 0 804 732 47.66 0 0 NA 807970 TCGA-AB-2984 AML02 3 136335621 136335621 C T SNP EPHB1 NM_004441.3 human genbank 54_36p 1 reviewed intronic c.1297+1040 e5+1040 0.001 - - - no_errors tier3 1009 0 0 821 417 33.68 0 0 NA 807970 TCGA-AB-2984 AML02 3 136472243 136472243 C A SNP EPHB1 NM_004441.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*11591 NULL 0 - - - no_errors tier3 665 0 0 674 333 33.04 0 0 NA 807970 TCGA-AB-2984 AML02 3 140493992 140493992 G A SNP - - - - - - - - - - - - - - - tier2 1038 1 0.1 809 766 48.6 0 0 NA 807970 TCGA-AB-2984 AML02 3 141176619 141176619 G A SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.109+39604 e1+39604 0.001 - - - no_errors tier3 670 0 0 710 617 46.5 0 0 NA 807970 TCGA-AB-2984 AML02 3 148388711 148388711 C T SNP - - - - - - - - - - - - - - - tier3 436 0 0 440 421 48.9 0 0 NA 807970 TCGA-AB-2984 AML02 3 158356966 158356966 T C SNP CCNL1 NM_020307.2 human genbank 54_36p -1 validated intronic c.488+2383 e3+2383 0 - - - no_errors tier3 493 0 0 335 337 50.15 32 31 49.21 807970 TCGA-AB-2984 AML02 3 178119597 178119597 G T SNP - - - - - - - - - - - - - - - tier3 674 1 0.15 829 438 34.57 0 0 NA 807970 TCGA-AB-2984 AML02 3 190335390 190335390 T C SNP TPRG1 NM_198485.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-72478 NULL 0 - - - no_errors tier3 1256 6 0.47 928 828 47.15 0 0 NA 807970 TCGA-AB-2984 AML02 3 193324103 193324103 C T SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*20389 NULL 0 - - - no_errors tier3 777 0 0 481 310 39.19 0 0 NA 807970 TCGA-AB-2984 AML02 3 197298031 197298031 C T SNP TFRC NM_003234.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9664 NULL 0.993 - - - no_errors tier2 334 0 0 282 203 41.86 0 0 NA 807970 TCGA-AB-2984 AML02 4 9610143 9610143 A G SNP SLC2A9 NM_020041.1 human genbank 54_36p -1 reviewed intronic c.250-2480 e3-2480 0.005 - - - no_errors tier3 1255 0 0 695 636 47.78 0 0 NA 807970 TCGA-AB-2984 AML02 4 13760941 13760941 A T SNP LOC152742 XM_001128848.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*11684 NULL 0 - - - no_errors tier3 909 1 0.11 859 756 46.75 0 0 NA 807970 TCGA-AB-2984 AML02 4 15622492 15622492 G A SNP PROM1 NM_006017.1 human genbank 54_36p -1 reviewed intronic c.1141+1504 e10+1504 0 - - - no_errors tier3 774 2 0.26 703 694 49.68 0 0 NA 807970 TCGA-AB-2984 AML02 4 22503620 22503620 G A SNP - - - - - - - - - - - - - - - tier3 717 2 0.28 447 484 51.82 0 0 NA 807970 TCGA-AB-2984 AML02 4 23340874 23340874 T C SNP - - - - - - - - - - - - - - - tier2 758 0 0 823 865 51.24 0 0 NA 807970 TCGA-AB-2984 AML02 4 23716825 23716825 G A SNP - - - - - - - - - - - - - - - tier3 1479 6 0.4 907 942 50.43 0 0 NA 807970 TCGA-AB-2984 AML02 4 32140540 32140540 C T SNP - - - - - - - - - - - - - - - tier3 415 0 0 424 347 45.01 0 0 NA 807970 TCGA-AB-2984 AML02 4 41090401 41090401 C T SNP LIMCH1 NM_014988.1 human genbank 54_36p 1 validated intronic c.96+32691 e1+32691 0 - - - no_errors tier3 770 1 0.13 585 585 49.91 0 0 NA 807970 TCGA-AB-2984 AML02 4 42057713 42057713 G A SNP SHISA3 NM_001080505.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-37118 NULL 0 - - - no_errors tier3 802 1 0.12 814 678 45.41 0 0 NA 807970 TCGA-AB-2984 AML02 4 44225688 44225688 G A SNP - - - - - - - - - - - - - - - tier3 995 1 0.1 997 691 40.94 0 0 NA 807970 TCGA-AB-2984 AML02 4 61774313 61774313 C T SNP - - - - - - - - - - - - - - - tier3 636 2 0.31 465 429 47.67 0 1 100 807970 TCGA-AB-2984 AML02 4 63481506 63481506 A G SNP - - - - - - - - - - - - - - - tier3 473 0 0 604 403 40.02 0 0 NA 807970 TCGA-AB-2984 AML02 4 66602607 66602607 A T SNP ENSG00000210740 ENST00000388005 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-11088 NULL 0.004 - - - pseudogene tier3 1036 0 0 845 555 39.61 0 0 NA 807970 TCGA-AB-2984 AML02 4 66994326 66994326 T A SNP - - - - - - - - - - - - - - - tier2 948 1 0.11 637 534 45.52 0 0 NA 807970 TCGA-AB-2984 AML02 4 67180581 67180581 C T SNP - - - - - - - - - - - - - - - tier3 553 0 0 584 361 38.2 0 0 NA 807970 TCGA-AB-2984 AML02 4 83543103 83543103 C T SNP HNRNPD NM_031370.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29248 NULL 0.038 - - - no_errors tier2 295 0 0 217 190 46.57 0 0 NA 807970 TCGA-AB-2984 AML02 4 103493203 103493203 A C SNP SLC39A8 NM_022154.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-8361 NULL 0.001 - - - no_errors tier3 727 1 0.14 542 606 52.74 0 0 NA 807970 TCGA-AB-2984 AML02 4 105734337 105734337 C T SNP - - - - - - - - - - - - - - - tier3 785 2 0.25 680 426 38.31 0 0 NA 807970 TCGA-AB-2984 AML02 4 111792626 111792626 C T SNP PITX2 NM_000325.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29561 NULL 0.017 - - - no_errors tier3 831 0 0 647 576 47.06 0 0 NA 807970 TCGA-AB-2984 AML02 4 112026868 112026868 C T SNP MIRN297 ENST00000401142 human ensembl 54_36p -1 known 5_prime_flanking_region c.-25616 NULL 0.001 - - - no_errors tier3 751 0 0 397 412 50.86 0 0 NA 807970 TCGA-AB-2984 AML02 4 113415875 113415875 G A SNP ALPK1 NM_001102406.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-102508 NULL 0.002 - - - no_errors tier3 500 0 0 551 490 46.93 2 0 0 807970 TCGA-AB-2984 AML02 4 116344403 116344403 A T SNP - - - - - - - - - - - - - - - tier3 434 0 0 369 410 52.63 0 0 NA 807970 TCGA-AB-2984 AML02 4 128102994 128102994 A C SNP - - - - - - - - - - - - - - - tier2 1244 0 0 675 597 46.93 0 0 NA 807970 TCGA-AB-2984 AML02 4 131526720 131526720 G A SNP - - - - - - - - - - - - - - - tier2 557 0 0 427 420 49.59 0 0 NA 807970 TCGA-AB-2984 AML02 4 132345845 132345845 C G SNP - - - - - - - - - - - - - - - tier3 669 0 0 577 505 46.67 0 0 NA 807970 TCGA-AB-2984 AML02 4 137298772 137298772 T G SNP - - - - - - - - - - - - - - - tier3 537 0 0 397 389 49.43 0 0 NA 807970 TCGA-AB-2984 AML02 4 143226739 143226739 G T SNP INPP4B NM_001101669.1 human genbank 54_36p -1 reviewed splice_region c.2487+8 e21+8 0.016 - - - no_errors tier2 627 0 0 725 431 37.28 0 0 NA 807970 TCGA-AB-2984 AML02 4 147626170 147626170 C A SNP SLC10A7 NM_001029998.3 human genbank 54_36p -1 validated intronic c.396+18281 e4+18281 0.037 - - - no_errors tier3 866 0 0 703 697 49.68 1 2 66.67 807970 TCGA-AB-2984 AML02 4 150312229 150312229 C G SNP - - - - - - - - - - - - - - - tier3 596 0 0 602 523 46.45 0 0 NA 807970 TCGA-AB-2984 AML02 4 169460295 169460295 T C SNP DDX60 NM_017631.5 human genbank 54_36p -1 validated intronic c.607-153 e5-153 0 - - - no_errors tier2 466 0 0 537 568 51.4 0 0 0 807970 TCGA-AB-2984 AML02 4 178425264 178425264 C G SNP NEIL3 NM_018248.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-42838 NULL 0 - - - no_errors tier2 720 0 0 718 655 47.71 0 2 100 807970 TCGA-AB-2984 AML02 4 190306920 190306920 C T SNP - - - - - - - - - - - - - - - tier3 817 0 0 634 373 37.04 0 0 NA 807970 TCGA-AB-2984 AML02 5 2131377 2131377 G A SNP - - - - - - - - - - - - - - - tier3 366 0 0 378 333 46.84 0 0 NA 807970 TCGA-AB-2984 AML02 5 3017316 3017316 C T SNP - - - - - - - - - - - - - - - tier2 574 0 0 531 495 48.25 0 0 NA 807970 TCGA-AB-2984 AML02 5 4886494 4886494 G A SNP - - - - - - - - - - - - - - - tier2 962 1 0.1 620 538 46.46 0 0 NA 807970 TCGA-AB-2984 AML02 5 6432050 6432050 G A SNP MED10 NM_032286.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-454 NULL 0 - - - no_errors tier2 298 0 0 299 298 49.92 0 0 NA 807970 TCGA-AB-2984 AML02 5 7619838 7619838 C T SNP ADCY2 NM_020546.2 human genbank 54_36p 1 reviewed intronic c.570+45826 e3+45826 0.002 - - - no_errors tier3 555 0 0 522 477 47.75 0 0 NA 807970 TCGA-AB-2984 AML02 5 9461946 9461947 - T INS SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.1-28812_28813 e1-28811 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 5 16190037 16190037 C A SNP MARCH11 NM_001102562.1 human genbank 54_36p -1 provisional intronic c.693+40798 e2+40798 0.002 - - - no_errors tier3 565 2 0.35 749 691 47.99 0 0 NA 807970 TCGA-AB-2984 AML02 5 17495404 17495404 A G SNP LOC285697 XM_210642.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-43938 NULL 0.016 - - - no_errors tier3 750 0 0 592 593 50.04 0 0 NA 807970 TCGA-AB-2984 AML02 5 22342153 22342153 C T SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-93644 e1-93644 0.001 - - - no_errors tier3 569 1 0.18 549 528 49.03 0 0 NA 807970 TCGA-AB-2984 AML02 5 26820754 26820754 T C SNP LOC100131678 XM_001722351.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-34967 NULL 0 - - - no_errors tier3 265 0 0 269 250 48.17 0 0 NA 807970 TCGA-AB-2984 AML02 5 42531121 42531121 T C SNP GHR NM_000163.2 human genbank 54_36p 1 reviewed intronic c.1-70602 e1-70602 0 - - - no_errors tier3 1011 0 0 769 636 45.2 0 0 NA 807970 TCGA-AB-2984 AML02 5 45550440 45550440 G A SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.850-52574 e3-52574 0.003 - - - no_errors tier2 457 0 0 706 421 37.32 0 0 NA 807970 TCGA-AB-2984 AML02 5 50267241 50267241 C G SNP - - - - - - - - - - - - - - - tier3 710 0 0 552 525 48.61 0 0 NA 807970 TCGA-AB-2984 AML02 5 62406560 62406560 A G SNP - - - - - - - - - - - - - - - tier3 939 0 0 550 496 47.37 0 0 NA 807970 TCGA-AB-2984 AML02 5 74726530 74726530 C G SNP COL4A3BP NM_005713.1 human genbank 54_36p -1 reviewed intronic c.1188+4361 e11+4361 0.001 - - - no_errors tier3 340 0 0 501 497 49.8 2 4 66.67 807970 TCGA-AB-2984 AML02 5 84704058 84704058 G C SNP - - - - - - - - - - - - - - - tier2 382 1 0.26 499 404 44.74 0 0 NA 807970 TCGA-AB-2984 AML02 5 90675745 90675745 A G SNP LOC100129716 XM_001716248.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-0 NULL 0.002 - - - rna_with_coding_region tier3 751 0 0 431 481 52.68 0 0 NA 807970 TCGA-AB-2984 AML02 5 93080925 93080925 T C SNP FAM172A NM_032042.4 human genbank 54_36p -1 validated intronic c.1108+56696 e9+56696 0 - - - no_errors tier2 648 0 0 421 409 49.16 3 2 40 807970 TCGA-AB-2984 AML02 5 97577341 97577341 A G SNP - - - - - - - - - - - - - - - tier3 507 0 0 491 365 42.64 0 0 NA 807970 TCGA-AB-2984 AML02 5 102533800 102533800 A G SNP HISPPD1 NM_015216.2 human genbank 54_36p 1 provisional intronic c.2286+1902 e18+1902 0.011 - - - no_errors tier3 599 0 0 502 435 46.42 6 3 33.33 807970 TCGA-AB-2984 AML02 5 103669425 103669425 C A SNP ENSG00000222401 ENST00000410469 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-44999 NULL 0.001 - - - no_errors tier3 505 0 0 501 353 41.33 0 0 NA 807970 TCGA-AB-2984 AML02 5 107908717 107908717 A G SNP - - - - - - - - - - - - - - - tier3 634 0 0 439 414 48.53 0 0 NA 807970 TCGA-AB-2984 AML02 5 117419109 117419110 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 5 123732982 123732982 C T SNP - - - - - - - - - - - - - - - tier3 939 0 0 814 722 47.01 0 0 NA 807970 TCGA-AB-2984 AML02 5 139724859 139724859 C T SNP SLC4A9 NM_031467.2 human genbank 54_36p 1 validated intronic c.1652-430 e12-430 0.001 - - - no_errors tier3 1039 0 0 597 507 45.76 0 0 NA 807970 TCGA-AB-2984 AML02 5 140190053 140190053 G A SNP PCDHA6 NM_018909.2 human genbank 54_36p 1 reviewed silent c.2193 p.A731 0.423 NULL "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 65 0 89 76 45.78 NA 807970 TCGA-AB-2984 AML02 5 149205410 149205410 G - DEL PPARGC1B NM_133263.2 human genbank 54_36p 1 provisional intronic c.2817-106 e11-106 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 5 152683247 152683247 C T SNP - - - - - - - - - - - - - - - tier3 814 0 0 621 541 46.56 0 0 NA 807970 TCGA-AB-2984 AML02 5 154126818 154126818 C G SNP LARP1 NM_033551.3 human genbank 54_36p 1 validated intronic c.436+10872 e1+10872 0.002 - - - no_errors tier3 870 0 0 281 279 49.82 3 1 25 807970 TCGA-AB-2984 AML02 5 160524811 160524811 A G SNP - - - - - - - - - - - - - - - tier3 642 0 0 449 449 50 0 0 NA 807970 TCGA-AB-2984 AML02 5 162192390 162192390 C T SNP ENSG00000208481 ENST00000385746 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48725 NULL 0.003 - - - pseudogene tier3 855 0 0 638 563 46.8 0 0 NA 807970 TCGA-AB-2984 AML02 5 162200814 162200814 G A SNP - - - - - - - - - - - - - - - tier3 702 0 0 650 405 38.39 0 0 NA 807970 TCGA-AB-2984 AML02 5 165623531 165623531 C A SNP - - - - - - - - - - - - - - - tier3 683 0 0 593 571 49.01 0 0 NA 807970 TCGA-AB-2984 AML02 5 170014022 170014022 G A SNP KCNIP1 NM_001034837.1 human genbank 54_36p 1 reviewed intronic c.62-58414 e2-58414 0 - - - no_errors tier3 893 0 0 913 623 40.51 0 0 NA 807970 TCGA-AB-2984 AML02 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 807970 TCGA-AB-2984 AML02 6 4636929 4636929 C T SNP LOC442153 XR_016425.2 human genbank 54_36p 1 model intronic c.NULL NULL 0.208 - - - pseudogene tier3 587 1 0.17 411 377 47.72 0 0 NA 807970 TCGA-AB-2984 AML02 6 8263966 8263966 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 6 10126054 10126054 G C SNP OFCC1 NM_153003.1 human genbank 54_36p -1 provisional intronic c.1+42815 e0+42815 0 - - - no_errors tier3 1055 0 0 862 803 48.2 0 0 NA 807970 TCGA-AB-2984 AML02 6 15745887 15745887 T A SNP DTNBP1 NM_032122.3 human genbank 54_36p -1 reviewed intronic c.222+67 e4+67 0.002 - - - no_errors tier3 622 0 0 517 393 43.19 0 0 0 807970 TCGA-AB-2984 AML02 6 17161561 17161561 C T SNP - - - - - - - - - - - - - - - tier3 641 0 0 527 512 49.23 0 0 NA 807970 TCGA-AB-2984 AML02 6 18132310 18132310 G A SNP KIF13A NM_022113.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-36637 NULL 0.036 - - - no_errors tier3 1241 1 0.08 594 575 49.15 0 0 NA 807970 TCGA-AB-2984 AML02 6 18875323 18875323 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 6 23754980 23754980 G A SNP ENSG00000219453 ENST00000402635 human ensembl 54_36p 1 known 5_prime_flanking_region c.-2723 NULL 0 - - - no_coding_region:pseudogene tier3 621 1 0.16 540 518 48.96 0 0 NA 807970 TCGA-AB-2984 AML02 6 35015301 35015301 C T SNP ANKS1A NM_015245.2 human genbank 54_36p 1 validated intronic c.198-27693 e2-27693 0 - - - no_errors tier3 592 0 0 763 487 38.87 0 0 NA 807970 TCGA-AB-2984 AML02 6 54551465 54551465 G T SNP ENSG00000220773 ENST00000406712 human ensembl 54_36p 1 known 5_prime_flanking_region c.-45897 NULL 0 - - - no_coding_region:pseudogene tier3 597 0 0 786 391 33.19 0 0 NA 807970 TCGA-AB-2984 AML02 6 70166987 70166987 A T SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*11483 NULL 0 - - - no_errors tier3 1015 0 0 740 513 40.94 0 0 NA 807970 TCGA-AB-2984 AML02 6 76224363 76224363 C T SNP FILIP1 NM_015687.2 human genbank 54_36p -1 validated intronic c.1+35487 e0+35487 0.001 - - - no_errors tier3 569 0 0 473 415 46.63 0 0 NA 807970 TCGA-AB-2984 AML02 6 86512536 86512536 T C SNP LOC100127905 XM_001720540.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10179 NULL 0 - - - no_errors tier3 965 0 0 673 676 50.07 0 0 NA 807970 TCGA-AB-2984 AML02 6 95290596 95290596 G A SNP - - - - - - - - - - - - - - - tier3 130 0 0 159 100 38.61 0 0 NA 807970 TCGA-AB-2984 AML02 6 95659645 95659645 G T SNP - - - - - - - - - - - - - - - tier3 649 0 0 655 369 36.04 0 0 NA 807970 TCGA-AB-2984 AML02 6 96468528 96468528 G A SNP KRT18P50 XM_001716480.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-47592 NULL 1 - - - pseudogene tier2 601 0 0 529 458 46.4 0 0 NA 807970 TCGA-AB-2984 AML02 6 97035564 97035564 G A SNP KIAA0776 NM_015323.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40907 NULL 0.001 - - - no_errors tier3 509 0 0 716 454 38.77 0 0 NA 807970 TCGA-AB-2984 AML02 6 103080710 103080710 A G SNP LOC100132919 XM_001716737.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-31073 NULL 0.991 - - - no_errors tier3 626 0 0 496 313 38.64 0 0 NA 807970 TCGA-AB-2984 AML02 6 115966965 115966965 C T SNP - - - - - - - - - - - - - - - tier3 1027 0 0 548 498 47.56 0 0 NA 807970 TCGA-AB-2984 AML02 6 116208310 116208310 G C SNP ENSG00000217019 ENST00000401765 human ensembl 54_36p -1 known 5_prime_flanking_region c.-779 NULL 0 - - - no_coding_region:pseudogene tier3 908 0 0 590 566 48.96 0 0 NA 807970 TCGA-AB-2984 AML02 6 116400358 116400358 T C SNP FRK NM_002031.2 human genbank 54_36p -1 reviewed intronic c.467-3763 e3-3763 0 - - - no_errors tier3 708 1 0.14 542 539 49.86 0 0 NA 807970 TCGA-AB-2984 AML02 6 116729340 116729340 A G SNP DSE NM_001080976.1 human genbank 54_36p 1 reviewed intronic c.1+21224 e0+21224 0.012 - - - no_errors tier3 1564 0 0 1299 1197 47.96 3 1 25 807970 TCGA-AB-2984 AML02 6 118436511 118436511 C A SNP SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated intronic c.173+100756 e1+100756 0.046 - - - no_errors tier3 747 0 0 607 554 47.72 0 0 NA 807970 TCGA-AB-2984 AML02 6 130476764 130476764 C T SNP L3MBTL3 NM_032438.1 human genbank 54_36p 1 validated intronic c.1887-6953 e18-6953 0.014 - - - no_errors tier3 474 0 0 521 469 47.37 0 0 0 807970 TCGA-AB-2984 AML02 6 134285264 134285264 G A SNP TBPL1 NM_004865.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-57693 NULL 0 - - - no_errors tier3 666 0 0 562 475 45.76 0 0 NA 807970 TCGA-AB-2984 AML02 6 140998113 140998113 G C SNP ENSG00000221336 ENST00000408409 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*25340 NULL 0 - - - no_errors tier3 599 0 0 412 394 48.82 0 0 NA 807970 TCGA-AB-2984 AML02 6 155671288 155671288 C T SNP TFB1M NM_016020.2 human genbank 54_36p -1 validated intronic c.285+2726 e2+2726 0 - - - no_errors tier3 714 0 0 499 471 48.56 4 0 0 807970 TCGA-AB-2984 AML02 6 166111096 166111096 G A SNP - - - - - - - - - - - - - - - tier3 855 0 0 489 528 51.92 0 0 NA 807970 TCGA-AB-2984 AML02 6 168529188 168529188 A C SNP - - - - - - - - - - - - - - - tier3 643 0 0 625 298 32.29 0 0 NA 807970 TCGA-AB-2984 AML02 6 170334328 170334328 C T SNP ENSG00000218716 ENST00000405880 human ensembl 54_36p 1 known 5_prime_flanking_region c.-22590 NULL 0.011 - - - no_coding_region:pseudogene tier2 103 0 0 48 81 62.31 0 0 NA 807970 TCGA-AB-2984 AML02 7 3007085 3007085 C G SNP CARD11 NM_032415.3 human genbank 54_36p -1 validated intronic c.1-42294 e1-42294 0.08 - - - no_errors tier3 949 0 0 506 398 43.98 0 0 NA 807970 TCGA-AB-2984 AML02 7 5753393 5753393 C T SNP RNF216 NM_207111.2 human genbank 54_36p -1 reviewed intronic c.202-5421 e3-5421 0.026 - - - no_errors tier3 546 0 0 478 407 45.99 2 0 0 807970 TCGA-AB-2984 AML02 7 25593430 25593430 G A SNP LOC100134662 XM_001724856.1 human genbank 54_36p -1 model intronic c.1-1508 e1-1508 0.003 - - - no_start_codon:pseudogene:no_stop_codon tier3 653 0 0 459 427 48.14 0 0 NA 807970 TCGA-AB-2984 AML02 7 28396457 28396457 G A SNP CREB5 NM_182899.1 human genbank 54_36p 1 reviewed intronic c.1+90872 e0+90872 0.025 - - - no_errors tier3 960 2 0.21 658 465 41.37 0 0 NA 807970 TCGA-AB-2984 AML02 7 28836559 28836559 T A SNP CREB5 NM_182898.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*11138 NULL 0.001 - - - no_errors tier3 850 1 0.12 398 423 51.52 0 0 NA 807970 TCGA-AB-2984 AML02 7 29838427 29838427 A T SNP WIPF3 ENST00000409123 human ensembl 54_36p 1 known intronic c.1-2382 e1-2382 0.011 - - - no_errors tier3 787 0 0 466 460 49.68 0 0 NA 807970 TCGA-AB-2984 AML02 7 41168656 41168656 G A SNP - - - - - - - - - - - - - - - tier3 467 0 0 412 395 48.95 0 0 NA 807970 TCGA-AB-2984 AML02 7 45872376 45872376 A G SNP IGFBP1 NM_000596.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-22401 NULL 0 - - - no_errors tier3 309 0 0 291 236 44.78 0 0 NA 807970 TCGA-AB-2984 AML02 7 53971107 53971107 A C SNP LOC100134708 XM_001726848.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-12842 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 598 0 0 584 532 47.67 0 0 NA 807970 TCGA-AB-2984 AML02 7 70094939 70094939 G A SNP - - - - - - - - - - - - - - - tier2 472 1 0.21 440 443 50.17 0 0 NA 807970 TCGA-AB-2984 AML02 7 72676141 72676141 G A SNP MLXIPL NM_032951.2 human genbank 54_36p -1 reviewed intronic c.293+325 e1+325 0.001 - - - no_errors tier2 149 1 0.66 182 112 38.1 0 0 NA 807970 TCGA-AB-2984 AML02 7 77375712 77375712 G A SNP PHTF2 NM_020432.1 human genbank 54_36p 1 validated intronic c.446-334 e7-334 0.051 - - - no_errors tier3 648 1 0.15 608 538 46.95 0 3 100 807970 TCGA-AB-2984 AML02 7 77400037 77400037 A T SNP PHTF2 NM_020432.1 human genbank 54_36p 1 validated intronic c.1338+3457 e11+3457 0.005 - - - no_errors tier3 1040 0 0 1476 1095 42.56 0 1 100 807970 TCGA-AB-2984 AML02 7 82413237 82413237 C T SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.11112+3491 e6+3491 0 - - - no_errors tier3 660 0 0 745 652 46.67 0 0 NA 807970 TCGA-AB-2984 AML02 7 100548633 100548633 A T SNP AP1S1 NM_001283.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35883 NULL 0.007 - - - no_errors tier3 880 1 0.11 646 527 43.88 0 0 NA 807970 TCGA-AB-2984 AML02 7 105808701 105808701 C T SNP - - - - - - - - - - - - - - - tier3 1026 0 0 592 641 51.99 0 0 NA 807970 TCGA-AB-2984 AML02 7 110752467 110752467 A G SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional intronic c.239+162063 e2+162063 0 - - - no_errors tier3 364 0 0 469 492 51.2 4 7 63.64 807970 TCGA-AB-2984 AML02 7 112882071 112882071 G T SNP - - - - - - - - - - - - - - - tier3 690 0 0 681 424 38.34 0 0 NA 807970 TCGA-AB-2984 AML02 7 118090330 118090330 A G SNP - - - - - - - - - - - - - - - tier2 533 0 0 504 484 48.99 0 0 NA 807970 TCGA-AB-2984 AML02 7 122750486 122750486 T A SNP - - - - - - - - - - - - - - - tier3 938 0 0 703 590 45.63 0 0 NA 807970 TCGA-AB-2984 AML02 7 125791301 125791301 C T SNP - - - - - - - - - - - - - - - tier3 965 0 0 1047 934 47.01 0 0 NA 807970 TCGA-AB-2984 AML02 7 154302850 154302850 C T SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.2079-681 e21-681 0.002 - - - no_errors tier2 227 0 0 344 315 47.73 0 0 NA 807970 TCGA-AB-2984 AML02 7 154329061 154329061 G A SNP ENSG00000214106 ENST00000397551 human ensembl 54_36p 1 known 5_prime_flanking_region c.-22231 NULL 0.001 - - - no_errors tier3 377 0 0 276 293 51.49 0 0 NA 807970 TCGA-AB-2984 AML02 8 4798408 4798408 T C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+40854 e1+40854 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier2 1008 0 0 718 647 47.36 0 0 NA 807970 TCGA-AB-2984 AML02 8 5541052 5541052 G A SNP - - - - - - - - - - - - - - - tier3 447 0 0 647 537 45.32 0 0 NA 807970 TCGA-AB-2984 AML02 8 9149620 9149620 G A SNP ENSG00000207415 ENST00000384684 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*32772 NULL 0.124 - - - no_errors tier2 1675 0 0 1067 1053 49.67 0 0 NA 807970 TCGA-AB-2984 AML02 8 13919244 13919244 A G SNP - - - - - - - - - - - - - - - tier2 913 0 0 565 555 49.55 0 0 NA 807970 TCGA-AB-2984 AML02 8 23557094 23557094 G A SNP NKX3-1 NM_006167.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*37585 NULL 0.002 - - - no_errors tier3 848 0 0 503 430 46.04 0 0 NA 807970 TCGA-AB-2984 AML02 8 26775999 26775999 C A SNP ADRA1A NM_033303.2 human genbank 54_36p -1 reviewed intronic c.883+1522 e1+1522 0.003 - - - no_errors tier3 357 0 0 274 275 50 0 0 NA 807970 TCGA-AB-2984 AML02 8 31882281 31882281 G A SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.745+264494 e1+264494 0.042 - - - overly_large_intron tier3 815 0 0 501 492 49.15 0 0 NA 807970 TCGA-AB-2984 AML02 8 32104814 32104814 C T SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.746-468074 e2-468074 0.001 - - - overly_large_intron tier3 1090 0 0 545 547 50.09 0 0 NA 807970 TCGA-AB-2984 AML02 8 32516277 32516277 A C SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.746-56611 e2-56611 0.008 - - - overly_large_intron tier3 670 0 0 404 408 50.18 0 0 NA 807970 TCGA-AB-2984 AML02 8 34113728 34113728 G A SNP - - - - - - - - - - - - - - - tier3 1067 0 0 717 697 49.29 0 0 NA 807970 TCGA-AB-2984 AML02 8 38867823 38867823 C T SNP PLEKHA2 ENST00000388745 human ensembl 54_36p 1 known 5_prime_flanking_region c.-26782 NULL 0.001 - - - no_errors tier3 792 1 0.13 639 597 48.26 0 0 NA 807970 TCGA-AB-2984 AML02 8 40817734 40817734 G A SNP ZMAT4 NM_024645.1 human genbank 54_36p -1 validated intronic c.1-15378 e1-15378 0.001 - - - no_errors tier3 919 1 0.11 979 634 39.26 0 0 NA 807970 TCGA-AB-2984 AML02 8 41870797 41870797 C T SNP ANK1 ENST00000265709 human ensembl 54_36p -1 known intronic c.126+2233 e1+2233 0 - - - no_errors tier3 664 1 0.15 639 513 44.45 0 0 NA 807970 TCGA-AB-2984 AML02 8 53734442 53734443 AC - DEL RB1CC1 NM_014781.1 human genbank 54_36p -1 validated intronic c.1690-354_1690-353 e11-353 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 8 65005209 65005209 G A SNP - - - - - - - - - - - - - - - tier3 424 0 0 480 450 48.34 0 0 NA 807970 TCGA-AB-2984 AML02 8 84612250 84612250 A T SNP - - - - - - - - - - - - - - - tier3 511 0 0 410 437 51.59 0 0 NA 807970 TCGA-AB-2984 AML02 8 85216064 85216064 G A SNP RALYL NM_001100391.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-43725 NULL 0.012 - - - no_errors tier3 1364 3 0.22 859 862 50.09 0 0 NA 807970 TCGA-AB-2984 AML02 8 91528910 91528910 G A SNP - - - - - - - - - - - - - - - tier3 596 0 0 448 451 50.17 0 0 NA 807970 TCGA-AB-2984 AML02 8 96989825 96989825 C A SNP - - - - - - - - - - - - - - - tier3 751 0 0 885 598 40.32 0 0 NA 807970 TCGA-AB-2984 AML02 8 97500290 97500290 C A SNP LOC100130665 XM_001723130.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-32419 NULL 0.029 - - - no_errors tier3 1250 0 0 940 915 49.3 0 0 NA 807970 TCGA-AB-2984 AML02 8 103367734 103367734 T A SNP UBR5 NM_015902.4 human genbank 54_36p -1 reviewed intronic c.5215+30 e38+30 0 - - - no_errors tier3 1046 0 0 724 697 49.02 3 3 50 807970 TCGA-AB-2984 AML02 8 108496412 108496412 C T SNP ANGPT1 NM_001146.3 human genbank 54_36p -1 reviewed intronic c.298-67911 e2-67911 0 - - - no_errors tier3 983 1 0.1 802 769 48.95 6 0 0 807970 TCGA-AB-2984 AML02 8 111429033 111429033 C T SNP - - - - - - - - - - - - - - - tier2 725 2 0.27 597 527 46.84 0 0 NA 807970 TCGA-AB-2984 AML02 8 113299072 113299072 G A SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*7104 NULL 0.001 - - - no_errors tier3 721 0 0 671 692 50.7 0 0 NA 807970 TCGA-AB-2984 AML02 8 127015810 127015810 A T SNP LOC100130231 XM_001725273.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*11720 NULL 0.001 - - - no_errors tier3 1332 0 0 767 697 47.61 0 0 NA 807970 TCGA-AB-2984 AML02 8 132213761 132213761 C A SNP - - - - - - - - - - - - - - - tier3 762 0 0 545 520 48.83 0 0 NA 807970 TCGA-AB-2984 AML02 8 137729609 137729609 G C SNP - - - - - - - - - - - - - - - tier2 568 0 0 473 263 35.73 0 0 NA 807970 TCGA-AB-2984 AML02 8 138109924 138109924 C T SNP - - - - - - - - - - - - - - - tier3 1171 0 0 877 784 47.2 0 0 NA 807970 TCGA-AB-2984 AML02 9 525519 525519 G A SNP KANK1 NM_015158.2 human genbank 54_36p 1 reviewed intronic c.1+30765 e0+30765 0 - - - no_errors tier3 928 0 0 526 481 47.77 0 0 NA 807970 TCGA-AB-2984 AML02 9 1692880 1692880 T G SNP LOC100133954 XM_001722570.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*28766 NULL 1 - - - no_start_codon:pseudogene:no_stop_codon tier2 860 0 0 575 530 47.96 0 0 NA 807970 TCGA-AB-2984 AML02 9 9022168 9022168 C T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-13433 e1-13433 0.831 - - - no_errors tier2 1116 0 0 766 773 50.19 0 0 NA 807970 TCGA-AB-2984 AML02 9 13474943 13474943 G A SNP - - - - - - - - - - - - - - - tier3 650 0 0 458 448 49.45 0 0 NA 807970 TCGA-AB-2984 AML02 9 25794197 25794197 C T SNP - - - - - - - - - - - - - - - tier3 692 0 0 443 321 42.02 0 0 NA 807970 TCGA-AB-2984 AML02 9 25899233 25899233 G A SNP - - - - - - - - - - - - - - - tier3 1462 3 0.2 1281 869 40.32 0 0 NA 807970 TCGA-AB-2984 AML02 9 88823181 88823181 G A SNP ENSG00000197698 ENST00000359720 human ensembl 54_36p -1 known intronic c.NULL NULL 0.001 - - - no_coding_region:pseudogene tier3 1472 0 0 860 774 47.34 0 0 NA 807970 TCGA-AB-2984 AML02 9 94813406 94813406 G A SNP FGD3 NM_001083536.1 human genbank 54_36p 1 validated intronic c.1035+31 e6+31 0 - - - no_errors tier2 559 0 0 422 327 43.6 1 0 0 807970 TCGA-AB-2984 AML02 9 104889792 104889792 G A SNP ENSG00000217435 ENST00000402842 human ensembl 54_36p 1 known 3_prime_flanking_region c.*22091 NULL 0.004 - - - no_coding_region:pseudogene tier3 641 1 0.16 381 338 47.01 0 0 NA 807970 TCGA-AB-2984 AML02 9 109796180 109796180 C T SNP LOC392382 XR_016755.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-45962 NULL 0 - - - pseudogene tier3 987 1 0.1 1154 916 44.25 0 0 NA 807970 TCGA-AB-2984 AML02 9 109915621 109915621 G C SNP LOC100128657 XR_039427.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-15669 NULL 0 - - - pseudogene tier3 637 0 0 376 429 53.29 0 0 NA 807970 TCGA-AB-2984 AML02 9 120878406 120878406 G A SNP - - - - - - - - - - - - - - - tier2 1042 0 0 762 589 43.53 0 0 NA 807970 TCGA-AB-2984 AML02 10 2388611 2388611 C T SNP - - - - - - - - - - - - - - - tier3 1053 1 0.09 653 667 50.49 0 0 NA 807970 TCGA-AB-2984 AML02 10 14293722 14293722 T A SNP FRMD4A NM_018027.3 human genbank 54_36p -1 validated intronic c.45+118341 e1+118341 0 - - - no_errors tier3 738 1 0.14 607 546 47.35 0 0 NA 807970 TCGA-AB-2984 AML02 10 19828152 19828152 G A SNP C10orf112 ENST00000377265 human ensembl 54_36p 1 known intronic c.160+571 e1+571 0 - - - no_start_codon:no_stop_codon tier3 728 0 0 413 463 52.85 0 0 NA 807970 TCGA-AB-2984 AML02 10 27357859 27357859 C G SNP ANKRD26 NM_014915.2 human genbank 54_36p -1 validated missense c.3900 p.K1300N 1 NULL "HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK" - no_errors tier1 404 0 339 335 49.63 7 100 807970 TCGA-AB-2984 AML02 10 29524615 29524615 C T SNP - - - - - - - - - - - - - - - tier3 793 0 0 682 635 48.22 0 0 NA 807970 TCGA-AB-2984 AML02 10 31544255 31544255 C T SNP ENSG00000209675 ENST00000386940 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44279 NULL 0.007 - - - pseudogene tier3 911 0 0 752 645 46.17 1 0 0 807970 TCGA-AB-2984 AML02 10 35840237 35840237 C T SNP CCNY NM_145012.4 human genbank 54_36p 1 validated intronic c.265-5220 e4-5220 0.006 - - - no_errors tier3 456 1 0.22 361 287 44.09 1 2 66.67 807970 TCGA-AB-2984 AML02 10 36237607 36237607 T A SNP - - - - - - - - - - - - - - - tier3 1077 0 0 999 630 38.65 0 0 NA 807970 TCGA-AB-2984 AML02 10 37190901 37190901 C A SNP - - - - - - - - - - - - - - - tier3 577 0 0 490 307 38.47 0 0 NA 807970 TCGA-AB-2984 AML02 10 58975706 58975706 T A SNP ENSG00000218583 ENST00000403728 human ensembl 54_36p 1 known 3_prime_flanking_region c.*32515 NULL 0.004 - - - no_coding_region:pseudogene tier3 721 0 0 664 637 48.96 0 0 NA 807970 TCGA-AB-2984 AML02 10 63901627 63901627 G A SNP ZNF365 NM_199451.2 human genbank 54_36p 1 validated intronic c.981+12065 e3+12065 0 - - - no_errors tier3 924 1 0.11 549 563 50.63 0 0 NA 807970 TCGA-AB-2984 AML02 10 72682158 72682158 G A SNP UNC5B NM_170744.3 human genbank 54_36p 1 validated intronic c.80-27426 e2-27426 0 - - - no_errors tier3 835 1 0.12 442 441 49.89 0 0 NA 807970 TCGA-AB-2984 AML02 10 85680684 85680684 G C SNP - - - - - - - - - - - - - - - tier3 847 0 0 916 774 45.8 0 0 NA 807970 TCGA-AB-2984 AML02 10 87812050 87812050 G A SNP GRID1 NM_017551.2 human genbank 54_36p -1 reviewed intronic c.726+76506 e4+76506 0 - - - no_errors tier3 464 0 0 476 478 50.1 0 0 NA 807970 TCGA-AB-2984 AML02 10 95547568 95547568 C A SNP LGI1 NM_005097.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*18 NULL 0.411 - - - no_errors tier2 934 0 0 755 517 40.64 0 0 NA 807970 TCGA-AB-2984 AML02 10 102863455 102863455 C T SNP TD1 NM_001085398.1 human genbank 54_36p -1 validated intronic c.1+13252 e0+13252 0.001 - - - no_errors tier3 1042 0 0 441 347 44.04 0 0 NA 807970 TCGA-AB-2984 AML02 10 104815413 104815413 A G SNP CNNM2 NM_017649.3 human genbank 54_36p 1 validated intronic c.2074-2963 e5-2963 0.001 - - - no_errors tier2 809 0 0 672 564 45.59 0 1 100 807970 TCGA-AB-2984 AML02 10 107082733 107082733 C T SNP - - - - - - - - - - - - - - - tier3 912 0 0 636 643 50.27 0 0 NA 807970 TCGA-AB-2984 AML02 10 108115590 108115590 C T SNP - - - - - - - - - - - - - - - tier2 995 0 0 532 625 53.93 0 0 NA 807970 TCGA-AB-2984 AML02 10 111991159 111991159 C T SNP MXI1 NM_130439.1 human genbank 54_36p 1 reviewed intronic c.408-3417 e3-3417 0.294 - - - no_errors tier3 710 0 0 412 401 49.32 0 1 100 807970 TCGA-AB-2984 AML02 10 116041368 116041368 A G SNP VWA2 ENST00000392982 human ensembl 54_36p 1 known intronic c.2248+1254 e12+1254 0 - - - no_stop_codon tier3 921 0 0 498 499 50.05 0 0 NA 807970 TCGA-AB-2984 AML02 10 117496534 117496534 G T SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.3903+19679 e27+19679 1 - - - no_errors tier2 713 0 0 540 526 49.34 0 0 NA 807970 TCGA-AB-2984 AML02 10 122871676 122871676 C T SNP RPL19P16 ENST00000403175 human ensembl 54_36p 1 known 5_prime_flanking_region c.-10844 NULL 0 - - - no_coding_region:pseudogene tier3 787 0 0 607 554 47.72 0 0 NA 807970 TCGA-AB-2984 AML02 10 123458607 123458607 C T SNP RPS15AP5 ENST00000402213 human ensembl 54_36p 1 known 5_prime_flanking_region c.-4504 NULL 0.006 - - - no_coding_region:pseudogene tier3 496 0 0 343 338 49.63 0 0 NA 807970 TCGA-AB-2984 AML02 10 130615075 130615075 G A SNP LOC728327 XR_041016.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*10550 NULL 0 - - - no_errors tier2 347 0 0 504 282 35.83 0 0 NA 807970 TCGA-AB-2984 AML02 11 12237178 12237178 C T SNP MICAL2 NM_014632.2 human genbank 54_36p 1 provisional intronic c.3231+499 e23+499 0 - - - no_errors tier3 648 0 0 592 404 40.48 0 0 NA 807970 TCGA-AB-2984 AML02 11 15720833 15720833 T C SNP - - - - - - - - - - - - - - - tier2 673 0 0 514 450 46.63 0 0 NA 807970 TCGA-AB-2984 AML02 11 16831544 16831544 G A SNP PLEKHA7 NM_175058.3 human genbank 54_36p -1 provisional intronic c.523-1066 e7-1066 0.003 - - - no_errors tier3 844 0 0 808 709 46.74 0 0 NA 807970 TCGA-AB-2984 AML02 11 21050079 21050079 T G SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1301-41632 e13-41632 0 - - - no_errors tier3 848 1 0.12 659 615 48.27 0 0 NA 807970 TCGA-AB-2984 AML02 11 29313906 29313906 C T SNP LOC729560 XM_001130628.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*285 NULL 0 - - - no_errors tier3 1052 2 0.19 717 628 46.66 0 0 NA 807970 TCGA-AB-2984 AML02 11 38867621 38867621 C T SNP - - - - - - - - - - - - - - - tier3 811 0 0 549 570 50.94 0 0 NA 807970 TCGA-AB-2984 AML02 11 44973812 44973812 G A SNP TP53I11 NM_001076787.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-57350 NULL 0.004 - - - no_errors tier3 980 1 0.1 972 642 39.73 0 0 NA 807970 TCGA-AB-2984 AML02 11 56949569 56949569 G A SNP SLC43A3 NM_014096.2 human genbank 54_36p -1 validated intronic c.314+21 e2+21 0 - - - no_errors tier3 1454 0 0 835 498 37.33 0 0 0 807970 TCGA-AB-2984 AML02 11 58176934 58176934 G A SNP ENSG00000197254 ENST00000359225 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38584 NULL 0.22 - - - no_coding_region:pseudogene tier2 915 0 0 753 673 47.16 0 0 NA 807970 TCGA-AB-2984 AML02 11 79716772 79716772 C T SNP - - - - - - - - - - - - - - - tier2 1547 0 0 1064 620 36.75 0 0 NA 807970 TCGA-AB-2984 AML02 11 79769963 79769964 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 11 83496017 83496017 G A SNP DLG2 NM_001364.1 human genbank 54_36p -1 reviewed intronic c.310-8279 e5-8279 0.356 - - - no_errors tier3 1149 0 0 877 712 44.78 0 0 NA 807970 TCGA-AB-2984 AML02 11 89566685 89566685 G C SNP NAALAD2 NM_005467.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*2122 NULL 0 - - - no_errors tier3 710 0 0 538 542 50.19 3 5 62.5 807970 TCGA-AB-2984 AML02 11 92669194 92669194 C A SNP CCDC67 NM_181645.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-35880 NULL 1 - - - no_errors tier2 1152 0 0 664 690 50.96 0 0 NA 807970 TCGA-AB-2984 AML02 11 97270900 97270900 G A SNP ENSG00000216073 ENST00000401254 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18107 NULL 0 - - - no_errors tier3 687 0 0 508 356 41.11 0 0 NA 807970 TCGA-AB-2984 AML02 11 98151573 98151573 G A SNP - - - - - - - - - - - - - - - tier3 764 1 0.13 444 402 47.52 0 0 NA 807970 TCGA-AB-2984 AML02 11 100337546 100337546 C T SNP ENSG00000165895 ENST00000298815 human ensembl 54_36p 1 known intronic c.17-79 e2-79 0 - - - no_errors tier3 721 0 0 640 547 46.08 0 0 NA 807970 TCGA-AB-2984 AML02 11 115762224 115762224 C T SNP - - - - - - - - - - - - - - - tier3 347 2 0.57 365 350 48.95 0 0 NA 807970 TCGA-AB-2984 AML02 11 119965027 119965027 C T SNP - - - - - - - - - - - - - - - tier3 1622 1 0.06 1420 1374 49.14 0 0 NA 807970 TCGA-AB-2984 AML02 11 120176764 120176764 G A SNP GRIK4 NM_014619.2 human genbank 54_36p 1 reviewed intronic c.83-1848 e2-1848 0 - - - no_errors tier3 1003 0 0 989 702 41.51 0 0 NA 807970 TCGA-AB-2984 AML02 11 125969946 125969946 G T SNP KIRREL3 NM_032531.2 human genbank 54_36p -1 provisional intronic c.56-31929 e2-31929 0 - - - no_errors tier3 668 0 0 569 551 49.2 0 0 NA 807970 TCGA-AB-2984 AML02 11 129775545 129775545 G T SNP ENSG00000175773 ENST00000318117 human ensembl 54_36p 1 known intronic c.148+254 e4+254 0 - - - no_errors tier2 544 0 0 472 411 46.49 0 0 NA 807970 TCGA-AB-2984 AML02 12 9423953 9423953 G A SNP LOC731039 XM_001715876.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-44493 NULL 0 - - - no_errors tier3 735 0 0 662 553 45.48 0 0 0 807970 TCGA-AB-2984 AML02 12 31471132 31471132 G C SNP DENND5B NM_144973.3 human genbank 54_36p -1 validated intronic c.2107-507 e9-507 0 - - - no_errors tier3 1048 0 0 698 676 49.16 0 0 NA 807970 TCGA-AB-2984 AML02 12 36728917 36728917 C T SNP - - - - - - - - - - - - - - - tier3 406 3 0.73 205 203 49.39 0 0 NA 807970 TCGA-AB-2984 AML02 12 47811419 47811419 G A SNP TUBA1B NM_006082.2 human genbank 54_36p -1 validated 5_prime_untranslated_region c.-69 NULL 1 - - - no_errors tier2 114 0 0 109 117 51.77 126 110 46.61 807970 TCGA-AB-2984 AML02 12 48760185 48760185 G A SNP ACCN2 NM_020039.2 human genbank 54_36p 1 reviewed intronic c.1205+80 e7+80 0.002 - - - no_errors tier2 536 0 0 340 388 53.15 0 0 NA 807970 TCGA-AB-2984 AML02 12 64352944 64352944 A C SNP LOC729298 XR_015503.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-26439 NULL 0.002 - - - pseudogene tier3 784 2 0.25 602 548 47.49 0 0 NA 807970 TCGA-AB-2984 AML02 12 84739663 84739663 C T SNP RASSF9 NM_005447.3 human genbank 54_36p -1 reviewed intronic c.47+14401 e1+14401 0.003 - - - no_errors tier3 1180 1 0.08 1102 579 34.42 0 0 NA 807970 TCGA-AB-2984 AML02 12 85563807 85563807 T C SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+81310 e0+81310 0.001 - - - no_errors tier3 444 1 0.22 459 413 47.36 0 0 NA 807970 TCGA-AB-2984 AML02 12 94945444 94945444 A G SNP LTA4H NM_000895.1 human genbank 54_36p -1 provisional missense c.320 p.F107S 0.946 "HMMPfam_Peptidase_M1,superfamily_Leukotriene A4 hydrolase N-terminal domain" "HMMPfam_Peptidase_M1,HMMPfam_Leuk-A4-hydro_C,superfamily_ARM repeat,superfamily_Metalloproteases (""zincins"") catalytic domain,superfamily_Leukotriene A4 hydrolase N-terminal domain" - no_errors tier1 632 0 500 405 44.65 4 11 73.33 807970 TCGA-AB-2984 AML02 12 95759480 95759480 C T SNP LOC387876 XM_373543.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*18747 NULL 0.037 - - - no_errors tier3 956 1 0.1 923 786 45.91 0 0 NA 807970 TCGA-AB-2984 AML02 12 97621229 97621229 T C SNP APAF1 NM_181861.2 human genbank 54_36p 1 reviewed intronic c.2467-51 e17-51 0.004 - - - no_errors tier3 541 0 0 591 430 42.12 0 0 0 807970 TCGA-AB-2984 AML02 12 97798115 97798115 C T SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.2779-48070 e18-48070 0 - - - no_errors tier3 671 0 0 504 479 48.73 0 0 NA 807970 TCGA-AB-2984 AML02 12 113689870 113689870 C T SNP ENSG00000209253 ENST00000386518 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29867 NULL 0.001 - - - pseudogene tier3 1328 0 0 676 578 46.02 0 0 NA 807970 TCGA-AB-2984 AML02 12 113859585 113859585 C G SNP - - - - - - - - - - - - - - - tier3 1117 0 0 594 567 48.75 0 0 NA 807970 TCGA-AB-2984 AML02 12 127179803 127179803 C T SNP - - - - - - - - - - - - - - - tier3 548 2 0.36 292 295 50.17 0 0 NA 807970 TCGA-AB-2984 AML02 12 131911515 131911515 T C SNP GOLGA3 NM_005895.3 human genbank 54_36p -1 reviewed intronic c.1-2545 e1-2545 0.008 - - - no_errors tier3 663 3 0.45 359 316 46.75 1 2 66.67 807970 TCGA-AB-2984 AML02 13 25442489 25442489 G T SNP ATP8A2 NM_016529.4 human genbank 54_36p 1 validated intronic c.3377+1672 e35+1672 0 - - - no_errors tier3 603 0 0 463 372 44.55 0 0 NA 807970 TCGA-AB-2984 AML02 13 38320657 38320657 C G SNP FREM2 NM_207361.4 human genbank 54_36p 1 reviewed missense c.6229 p.Q2077E 1 "HMMPfam_Calx-beta,HMMSmart_SM00237" "HMMPfam_Calx-beta,HMMSmart_SM00237" - no_errors tier1 845 0 584 540 48 NA 807970 TCGA-AB-2984 AML02 13 57177560 57177560 A T SNP PCDH17 NM_001040429.2 human genbank 54_36p 1 reviewed intronic c.2798-19187 e4-19187 0 - - - no_errors tier3 744 0 0 680 589 46.41 0 0 NA 807970 TCGA-AB-2984 AML02 13 58788118 58788118 C T SNP - - - - - - - - - - - - - - - tier2 1010 0 0 754 784 50.84 0 0 NA 807970 TCGA-AB-2984 AML02 13 61289146 61289146 C T SNP ENSG00000217192 ENST00000407335 human ensembl 54_36p 1 known 3_prime_flanking_region c.*11336 NULL 0.115 - - - no_coding_region:pseudogene tier3 476 0 0 629 400 38.83 0 0 NA 807970 TCGA-AB-2984 AML02 13 61343056 61343056 T G SNP - - - - - - - - - - - - - - - tier3 949 1 0.11 527 524 49.86 0 0 NA 807970 TCGA-AB-2984 AML02 13 62270655 62270655 A T SNP - - - - - - - - - - - - - - - tier3 593 2 0.34 441 524 54.13 0 0 NA 807970 TCGA-AB-2984 AML02 13 64276866 64276866 A T SNP - - - - - - - - - - - - - - - tier3 585 0 0 462 471 50.32 0 0 NA 807970 TCGA-AB-2984 AML02 13 79409471 79409471 A G SNP - - - - - - - - - - - - - - - tier3 673 0 0 606 389 39.1 0 0 NA 807970 TCGA-AB-2984 AML02 13 109695454 109695454 A G SNP COL4A1 NM_001845.4 human genbank 54_36p -1 reviewed intronic c.85-2372 e2-2372 0 - - - no_errors tier3 422 0 0 399 227 36.2 0 0 NA 807970 TCGA-AB-2984 AML02 14 31465853 31465853 C T SNP - - - - - - - - - - - - - - - tier2 980 0 0 943 950 50.18 0 0 NA 807970 TCGA-AB-2984 AML02 14 36642991 36642991 G A SNP SLC25A21 NM_030631.2 human genbank 54_36p -1 provisional intronic c.70+68246 e1+68246 0 - - - no_errors tier3 731 0 0 779 443 36.25 0 0 NA 807970 TCGA-AB-2984 AML02 14 37146082 37146082 A T SNP FOXA1 NM_004496.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12154 NULL 0.062 - - - no_errors tier3 895 0 0 472 343 42.09 0 0 NA 807970 TCGA-AB-2984 AML02 14 44437885 44437885 G A SNP LOC100129788 XM_001717616.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*73 NULL 0.002 - - - no_errors tier3 479 0 0 309 333 51.87 0 0 NA 807970 TCGA-AB-2984 AML02 14 62426076 62426076 C T SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed intronic c.1370-39753 e8-39753 0.004 - - - no_errors tier3 707 0 0 581 561 49.04 0 0 NA 807970 TCGA-AB-2984 AML02 14 81997429 81997429 G A SNP ENSG00000210376 ENST00000387641 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-756 NULL 0.001 - - - pseudogene tier3 715 0 0 621 595 48.93 0 0 NA 807970 TCGA-AB-2984 AML02 14 91824301 91824301 G A SNP SLC24A4 NM_153646.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-35678 NULL 0 - - - no_errors tier3 597 0 0 411 420 50.54 0 0 NA 807970 TCGA-AB-2984 AML02 14 99070726 99070726 C A SNP CCDC85C ENST00000380243 human ensembl 54_36p -1 known intronic c.867+1379 e2+1379 0 - - - no_errors tier3 818 1 0.12 452 456 50.22 0 0 NA 807970 TCGA-AB-2984 AML02 15 22321510 22321510 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 807970 TCGA-AB-2984 AML02 15 25450184 25450184 A C SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.1123-1157 e10-1157 0 - - - no_errors tier3 982 0 0 756 562 42.61 0 0 NA 807970 TCGA-AB-2984 AML02 15 29162303 29162303 G A SNP TRPM1 NM_002420.4 human genbank 54_36p -1 reviewed intronic c.1-5824 e1-5824 0 - - - no_errors tier3 535 0 0 378 315 45.39 0 0 NA 807970 TCGA-AB-2984 AML02 15 36017020 36017020 C T SNP TMCO5A NM_152453.2 human genbank 54_36p 1 provisional intronic c.315+131 e3+131 0 - - - no_errors tier3 1430 0 0 1040 886 45.93 0 0 NA 807970 TCGA-AB-2984 AML02 15 37473901 37473901 G A SNP - - - - - - - - - - - - - - - tier3 868 0 0 507 439 46.41 0 0 NA 807970 TCGA-AB-2984 AML02 15 37934847 37934847 A G SNP GPR176 NM_007223.1 human genbank 54_36p -1 provisional intronic c.173-48096 e2-48096 0.003 - - - no_errors tier3 818 0 0 647 558 46.27 0 0 NA 807970 TCGA-AB-2984 AML02 15 59586265 59586265 C G SNP - - - - - - - - - - - - - - - tier3 1355 0 0 1129 1044 48.04 0 0 NA 807970 TCGA-AB-2984 AML02 15 85316709 85316709 G A SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.3084-15513 e22-15513 0.001 - - - no_errors tier3 400 0 0 473 273 36.6 0 0 NA 807970 TCGA-AB-2984 AML02 16 6129410 6129410 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+119416 e0+119416 0 - - - no_errors tier3 1189 0 0 950 835 46.73 0 0 NA 807970 TCGA-AB-2984 AML02 16 13459521 13459521 C T SNP - - - - - - - - - - - - - - - tier3 898 0 0 684 377 35.43 0 0 NA 807970 TCGA-AB-2984 AML02 16 23126191 23126191 C T SNP SCNN1G NM_001039.3 human genbank 54_36p 1 validated intronic c.1078-2381 e6-2381 0.002 - - - no_errors tier3 786 1 0.13 898 675 42.8 0 0 NA 807970 TCGA-AB-2984 AML02 16 25675656 25675656 G A SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.734+63683 e1+63683 0.71 - - - no_errors tier3 1194 0 0 616 576 48.32 0 0 NA 807970 TCGA-AB-2984 AML02 16 34545515 34545515 G T SNP ENSG00000214581 ENST00000398617 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5758 NULL 0.188 - - - no_stop_codon tier3 368 0 0 269 186 40.88 0 0 NA 807970 TCGA-AB-2984 AML02 16 50555432 50555432 C A SNP - - - - - - - - - - - - - - - tier3 802 2 0.25 658 680 50.78 0 0 NA 807970 TCGA-AB-2984 AML02 16 59774113 59774113 G A SNP - - - - - - - - - - - - - - - tier3 777 0 0 517 499 49.11 0 0 NA 807970 TCGA-AB-2984 AML02 16 60293394 60293394 C T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.1654+11852 e9+11852 0.065 - - - no_errors tier3 423 0 0 459 403 46.75 0 0 NA 807970 TCGA-AB-2984 AML02 16 60428193 60428193 C G SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.668-11609 e4-11609 0 - - - no_errors tier3 1031 0 0 716 687 48.93 0 0 NA 807970 TCGA-AB-2984 AML02 16 70147637 70147637 A G SNP LOC100132529 XM_001719539.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-8749 NULL 0 - - - no_errors tier3 919 0 0 764 722 48.55 0 0 NA 807970 TCGA-AB-2984 AML02 16 75125036 75125036 G A SNP CNTNAP4 NM_138994.3 human genbank 54_36p 1 validated intronic c.2537-1907 e17-1907 0.188 - - - no_errors tier3 644 2 0.31 615 532 46.38 0 0 NA 807970 TCGA-AB-2984 AML02 16 78097856 78097856 T A SNP - - - - - - - - - - - - - - - tier3 779 0 0 601 533 46.67 0 0 NA 807970 TCGA-AB-2984 AML02 16 78485636 78485636 G A SNP - - - - - - - - - - - - - - - tier3 739 0 0 660 696 51.25 0 0 NA 807970 TCGA-AB-2984 AML02 17 13204218 13204218 T A SNP - - - - - - - - - - - - - - - tier3 751 0 0 478 440 47.93 0 0 NA 807970 TCGA-AB-2984 AML02 17 21642170 21642170 C T SNP uc002gyy.2 ENST00000344561 human ensembl 54_36p 1 known 5_prime_flanking_region c.-12656 NULL 0.002 - - - no_errors tier3 561 1 0.18 412 320 43.54 0 0 NA 807970 TCGA-AB-2984 AML02 17 29358381 29358381 G A SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.555+148729 e1+148729 0.005 - - - overly_large_intron tier3 1450 0 0 917 761 45.32 0 0 NA 807970 TCGA-AB-2984 AML02 18 1563126 1563126 C T SNP - - - - - - - - - - - - - - - tier3 898 1 0.11 768 763 49.84 0 0 NA 807970 TCGA-AB-2984 AML02 18 4392754 4392754 C T SNP - - - - - - - - - - - - - - - tier3 847 1 0.12 588 549 48.28 0 0 NA 807970 TCGA-AB-2984 AML02 18 13236919 13236919 A G SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.1+27932 e0+27932 0.02 - - - no_errors tier3 820 0 0 211 211 49.76 0 0 NA 807970 TCGA-AB-2984 AML02 18 13921277 13921277 C T SNP MC2R NM_000529.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-45760 NULL 0 - - - no_errors tier3 651 2 0.3 867 573 39.74 0 0 NA 807970 TCGA-AB-2984 AML02 18 18913391 18913391 T C SNP - - - - - - - - - - - - - - - tier3 1002 2 0.2 484 476 49.58 0 0 NA 807970 TCGA-AB-2984 AML02 18 21299630 21299630 A G SNP - - - - - - - - - - - - - - - tier2 781 0 0 747 670 47.28 0 0 NA 807970 TCGA-AB-2984 AML02 18 29330494 29330494 C T SNP - - - - - - - - - - - - - - - tier3 886 1 0.11 770 426 35.59 0 0 NA 807970 TCGA-AB-2984 AML02 18 33387656 33387656 G T SNP BRUNOL4 NM_020180.1 human genbank 54_36p -1 reviewed intronic c.286+11661 e1+11661 0 - - - no_errors tier3 308 1 0.32 265 260 49.52 0 0 NA 807970 TCGA-AB-2984 AML02 18 35942769 35942769 T C SNP - - - - - - - - - - - - - - - tier3 844 0 0 827 537 39.34 0 0 NA 807970 TCGA-AB-2984 AML02 18 36766203 36766203 G A SNP - - - - - - - - - - - - - - - tier3 949 0 0 609 551 47.5 0 0 NA 807970 TCGA-AB-2984 AML02 18 48353307 48353307 C T SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.92-179115 e2-179115 1 - - - no_errors tier2 919 1 0.11 956 927 49.23 0 0 NA 807970 TCGA-AB-2984 AML02 18 49739729 49739729 A G SNP - - - - - - - - - - - - - - - tier3 943 0 0 748 637 45.96 0 0 NA 807970 TCGA-AB-2984 AML02 18 52871977 52871977 G T SNP WDR7 NM_015285.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*26541 NULL 0.003 - - - no_errors tier3 702 2 0.28 515 422 45.04 0 0 NA 807970 TCGA-AB-2984 AML02 18 54156098 54156098 C T SNP NEDD4L NM_015277.1 human genbank 54_36p 1 validated intronic c.1066-3152 e13-3152 0 - - - no_errors tier3 749 2 0.27 667 466 41.06 0 0 NA 807970 TCGA-AB-2984 AML02 18 61550415 61550415 T C SNP CDH7 NM_004361.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30644 NULL 0.001 - - - no_errors tier3 731 0 0 618 525 45.93 0 0 NA 807970 TCGA-AB-2984 AML02 18 61641107 61641107 G C SNP CDH7 NM_004361.2 human genbank 54_36p 1 reviewed intronic c.793+643 e4+643 0.005 - - - no_errors tier3 508 0 0 507 425 45.5 0 0 NA 807970 TCGA-AB-2984 AML02 18 74512893 74512893 C T SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*30132 NULL 0.001 - - - no_errors tier3 1161 1 0.09 795 848 51.61 0 0 NA 807970 TCGA-AB-2984 AML02 19 17247609 17247609 G T SNP C19orf62 NM_001033549.1 human genbank 54_36p 1 validated splice_site c.545-1 e5-1 1 - - - no_errors tier1 756 0 332 211 38.86 7 7 43.75 807970 TCGA-AB-2984 AML02 19 22492122 22492122 C T SNP ZNF729 ENST00000357491 human ensembl 54_36p 1 known intronic c.2644+45638 e5+45638 0.001 - - - no_stop_codon tier2 524 9 1.68 376 337 46.35 0 0 0 807970 TCGA-AB-2984 AML02 19 51078985 51078985 C T SNP IRF2BP1 NM_015649.1 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*133 NULL 0.947 - - - no_errors tier2 160 0 0 136 70 33.98 77 60 43.8 807970 TCGA-AB-2984 AML02 19 56142303 56142303 C T SNP KLK5 NM_001077491.1 human genbank 54_36p -1 reviewed intronic c.726+1405 e4+1405 0.001 - - - no_errors tier3 1056 0 0 431 456 51.35 0 0 NA 807970 TCGA-AB-2984 AML02 19 59583043 59583043 G T SNP ENSG00000217662 ENST00000405448 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*59583043 NULL 0 - - - no_coding_region:pseudogene tier3 825 1 0.12 562 378 40.21 0 0 NA 807970 TCGA-AB-2984 AML02 20 9473400 9473400 G C SNP PAK7 NM_020341.3 human genbank 54_36p -1 reviewed intronic c.1744-259 e6-259 0.003 - - - no_errors tier3 546 0 0 435 427 49.54 0 0 NA 807970 TCGA-AB-2984 AML02 20 9769028 9769028 G A SNP PAK7 NM_020341.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-196052 NULL 0 - - - no_errors tier3 746 0 0 533 494 48.1 0 0 NA 807970 TCGA-AB-2984 AML02 20 16296673 16296673 C T SNP KIF16B NM_024704.3 human genbank 54_36p -1 validated intronic c.3498+2558 e22+2558 0.167 - - - no_errors tier3 732 0 0 592 618 51.03 1 0 0 807970 TCGA-AB-2984 AML02 20 35999809 35999809 C T SNP VSTM2L NM_080607.2 human genbank 54_36p 1 validated intronic c.342+4404 e3+4404 0 - - - no_errors tier2 413 0 0 333 261 43.65 0 0 NA 807970 TCGA-AB-2984 AML02 20 54344611 54344611 C T SNP C20orf108 NM_080821.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22858 NULL 0.016 - - - no_errors tier3 578 0 0 634 313 33.02 0 0 NA 807970 TCGA-AB-2984 AML02 20 57352967 57352967 C T SNP EDN3 NM_000114.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*20058 NULL 0 - - - no_errors tier3 795 0 0 639 557 46.53 0 0 NA 807970 TCGA-AB-2984 AML02 20 59292352 59292352 G A SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.169+28964 e2+28964 0 - - - no_errors tier2 1774 0 0 716 709 49.65 0 0 NA 807970 TCGA-AB-2984 AML02 20 62003188 62003188 C T SNP DNAJC5 NM_025219.1 human genbank 54_36p 1 provisional intronic c.1+6068 e0+6068 0 - - - no_errors tier2 540 1 0.18 340 299 46.79 2 1 33.33 807970 TCGA-AB-2984 AML02 21 27963972 27963972 G A SNP - - - - - - - - - - - - - - - tier3 934 0 0 788 442 35.93 0 0 NA 807970 TCGA-AB-2984 AML02 21 33052262 33052262 G A SNP C21orf66 NM_016631.3 human genbank 54_36p -1 reviewed intronic c.1383+1000 e7+1000 0.002 - - - no_errors tier3 790 1 0.13 463 490 51.42 6 12 66.67 807970 TCGA-AB-2984 AML02 21 34678000 34678000 C A SNP FAM165B NM_058182.4 human genbank 54_36p 1 validated intronic c.13-1646 e2-1646 0 - - - no_errors tier3 960 2 0.21 700 660 48.46 1 0 0 807970 TCGA-AB-2984 AML02 22 29545914 29545914 G A SNP OSBP2 NM_030758.3 human genbank 54_36p 1 reviewed intronic c.854-50502 e3-50502 0.001 - - - no_errors tier3 731 0 0 414 440 51.52 0 0 NA 807970 TCGA-AB-2984 AML02 22 42557355 42557355 C T SNP SULT4A1 NM_014351.3 human genbank 54_36p -1 reviewed intronic c.604-944 e6-944 0 - - - no_errors tier3 374 0 0 448 447 49.89 0 0 NA 807970 TCGA-AB-2984 AML02 22 45145099 45145099 C A SNP CELSR1 NM_014246.1 human genbank 54_36p -1 reviewed intronic c.7760-734 e26-734 0.011 - - - no_errors tier3 734 0 0 469 443 48.57 0 0 NA 807970 TCGA-AB-2984 AML02 22 46282936 46282936 T A SNP ENSG00000218357 ENST00000405369 human ensembl 54_36p -1 known 5_prime_flanking_region c.-21744 NULL 0 - - - no_errors tier3 787 0 0 391 370 48.56 0 0 NA 807970 TCGA-AB-2984 AML02 22 47588579 47588579 G A SNP - - - - - - - - - - - - - - - tier3 303 0 0 237 194 45.01 0 0 NA 907786 TCGA-AB-2985 AML45 X 17541083 17541083 C G SNP NHS NM_198270.2 human genbank 54_36p 1 reviewed intronic c.566-74700 e2-74700 0.006 - - - no_errors tier3 1044 119 10.21 415 264 38.77 0 0 NA 907786 TCGA-AB-2985 AML45 X 43696160 43696160 G A SNP NDP NM_000266.3 human genbank 54_36p -1 reviewed intronic c.175-1944 e2-1944 0.004 - - - no_errors tier3 685 52 7.06 319 187 36.96 0 0 NA 907786 TCGA-AB-2985 AML45 X 62417619 62417619 A C SNP LOC645251 XR_037445.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*17113 NULL 0 - - - pseudogene tier3 895 71 7.33 422 192 31.27 0 0 NA 907786 TCGA-AB-2985 AML45 X 74731366 74731366 G A SNP ENSG00000217374 ENST00000405568 human ensembl 54_36p 1 known 3_prime_flanking_region c.*9300 NULL 0 - - - no_coding_region:pseudogene tier3 361 37 9.3 158 125 43.86 0 0 NA 907786 TCGA-AB-2985 AML45 X 127882257 127882257 A G SNP - - - - - - - - - - - - - - - tier3 399 65 14.01 270 190 41.21 0 0 NA 907786 TCGA-AB-2985 AML45 X 143546169 143546169 A G SNP - - - - - - - - - - - - - - - tier3 1316 140 9.62 416 372 47.21 0 0 NA 907786 TCGA-AB-2985 AML45 X 153932414 153932414 G A SNP FUNDC2 NM_023934.3 human genbank 54_36p 1 validated intronic c.361-725 e4-725 0 - - - no_errors tier3 725 55 7.04 267 185 40.93 0 0 0 907786 TCGA-AB-2985 AML45 1 6648825 6648825 T C SNP DNAJC11 NM_018198.3 human genbank 54_36p -1 validated intronic c.378+1531 e4+1531 0.095 - - - no_errors tier3 512 59 10.31 200 168 45.65 4 0 0 907786 TCGA-AB-2985 AML45 1 12065259 12065259 G A SNP TNFRSF8 NM_001243.3 human genbank 54_36p 1 reviewed intronic c.64-1849 e2-1849 0.005 - - - no_errors tier3 447 53 10.54 132 114 45.78 0 0 NA 907786 TCGA-AB-2985 AML45 1 12702744 12702744 T G SNP AADACL3 NM_001103170.1 human genbank 54_36p 1 validated intronic c.214+464 e1+464 0.021 - - - no_errors tier3 440 50 10.2 204 197 49.13 0 0 NA 907786 TCGA-AB-2985 AML45 1 49089959 49089959 G A SNP AGBL4 NM_032785.3 human genbank 54_36p -1 validated intronic c.79+15491 e2+15491 0.016 - - - no_errors tier3 677 67 9.01 319 204 38.93 0 0 NA 907786 TCGA-AB-2985 AML45 1 66141174 66141174 A C SNP PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.1-10342 e1-10342 0.003 - - - no_errors tier3 487 72 12.86 252 207 45 0 0 NA 907786 TCGA-AB-2985 AML45 1 67283022 67283022 C T SNP SLC35D1 NM_015139.1 human genbank 54_36p -1 provisional intronic c.637-2423 e8-2423 0.012 - - - no_errors tier3 653 82 11.14 403 295 42.2 0 0 0 907786 TCGA-AB-2985 AML45 1 68155870 68155870 T C SNP LOC100133029 XM_001726661.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-28547 NULL 0.017 - - - no_errors tier3 512 73 12.46 232 190 45.02 0 0 NA 907786 TCGA-AB-2985 AML45 1 79262280 79262280 G A SNP ELTD1 NM_022159.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-17353 NULL 0 - - - no_errors tier3 1016 106 9.43 476 275 36.62 0 0 NA 907786 TCGA-AB-2985 AML45 1 107654853 107654853 T A SNP NTNG1 NM_014917.1 human genbank 54_36p 1 provisional intronic c.247-13574 e2-13574 0.001 - - - no_errors tier3 487 59 10.77 225 113 33.33 0 0 NA 907786 TCGA-AB-2985 AML45 1 115060271 115060271 C A SNP NRAS NM_002524.3 human genbank 54_36p -1 reviewed missense c.34 p.G12C 1 "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1357 136 9.11 736 301 28.75 17 8 32 907786 TCGA-AB-2985 AML45 1 164974357 164974357 C T SNP LOC646688 XR_038043.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-353 NULL 0.08 - - - pseudogene tier3 524 51 8.87 218 204 48.34 0 0 NA 907786 TCGA-AB-2985 AML45 1 164974422 164974422 A C SNP LOC646688 XR_038043.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-288 NULL 0.004 - - - pseudogene tier3 442 38 7.92 212 151 41.6 0 0 NA 907786 TCGA-AB-2985 AML45 1 179893494 179893494 G C SNP CACNA1E NM_000721.2 human genbank 54_36p 1 reviewed intronic c.1055+6294 e7+6294 0.001 - - - no_errors tier3 749 91 10.83 437 301 40.68 0 0 NA 907786 TCGA-AB-2985 AML45 1 181842119 181842119 G A SNP LOC100132985 XM_001719111.1 human genbank 54_36p 1 model intronic c.168+1075 e2+1075 0.518 - - - no_errors tier3 533 60 10.12 325 207 38.84 3 0 0 907786 TCGA-AB-2985 AML45 1 208203796 208203796 G A SNP SYT14 NM_153262.2 human genbank 54_36p 1 validated intronic c.61+11072 e2+11072 0 - - - no_errors tier3 811 109 11.8 536 390 42.12 0 0 NA 907786 TCGA-AB-2985 AML45 1 212210965 212210965 C T SNP PROX1 NM_002763.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-25537 NULL 0.001 - - - no_errors tier3 1434 157 9.86 517 474 47.73 0 0 NA 907786 TCGA-AB-2985 AML45 1 214165273 214165273 A G SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.7300+9308 e37+9308 0.042 - - - no_errors tier3 170 10 5.52 137 122 46.92 0 0 NA 907786 TCGA-AB-2985 AML45 1 220179285 220179285 C T SNP LOC100129950 XM_001720733.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-8914 NULL 0 - - - no_errors tier3 1406 158 10.1 845 704 45.42 0 0 NA 907786 TCGA-AB-2985 AML45 1 224864800 224864800 T G SNP ITPKB NM_002221.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*24195 NULL 0 - - - no_errors tier3 363 36 9.02 144 112 43.75 0 0 NA 907786 TCGA-AB-2985 AML45 1 238542917 238542917 T C SNP FMN2 NM_020066.4 human genbank 54_36p 1 validated intronic c.4645-16082 e9-16082 0.01 - - - no_errors tier3 1167 150 11.38 444 356 44.39 0 0 NA 907786 TCGA-AB-2985 AML45 1 240678902 240678902 G A SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.1+75111 e0+75111 0.151 - - - no_errors tier3 807 71 8.08 408 261 38.96 0 0 NA 907786 TCGA-AB-2985 AML45 2 6256847 6256847 G A SNP - - - - - - - - - - - - - - - tier3 989 135 12.01 532 449 45.77 0 0 NA 907786 TCGA-AB-2985 AML45 2 12495972 12495972 C T SNP ENSG00000207183 ENST00000384454 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26894 NULL 0 - - - no_errors tier3 1058 122 10.33 442 310 41.06 0 0 NA 907786 TCGA-AB-2985 AML45 2 29644065 29644065 A G SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.953-35579 e4-35579 0 - - - no_errors tier3 835 111 11.71 307 233 43.07 0 0 NA 907786 TCGA-AB-2985 AML45 2 34240495 34240495 G A SNP - - - - - - - - - - - - - - - tier3 752 85 10.16 307 276 47.34 0 0 NA 907786 TCGA-AB-2985 AML45 2 83869361 83869361 C T SNP - - - - - - - - - - - - - - - tier3 506 60 10.56 190 151 44.28 0 0 NA 907786 TCGA-AB-2985 AML45 2 108404971 108404971 C T SNP GCC2 NM_181453.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27192 NULL 0.001 - - - no_errors tier3 465 34 6.81 228 71 23.75 0 0 NA 907786 TCGA-AB-2985 AML45 2 121805028 121805028 G A SNP TFCP2L1 NM_014553.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-45873 NULL 0 - - - no_errors tier3 706 98 12.17 242 161 39.95 0 2 100 907786 TCGA-AB-2985 AML45 2 126205425 126205425 G C SNP - - - - - - - - - - - - - - - tier3 740 77 9.42 337 245 42.1 0 0 NA 907786 TCGA-AB-2985 AML45 2 139786704 139786704 T G SNP - - - - - - - - - - - - - - - tier3 960 119 11.01 481 366 43.11 0 0 NA 907786 TCGA-AB-2985 AML45 2 152938084 152938084 G A SNP FMNL2 NM_052905.3 human genbank 54_36p 1 reviewed intronic c.117+37604 e1+37604 0.003 - - - no_errors tier3 475 54 10.19 163 125 43.25 0 0 NA 907786 TCGA-AB-2985 AML45 2 187792460 187792460 T C SNP - - - - - - - - - - - - - - - tier3 317 36 10.2 184 137 42.41 0 0 NA 907786 TCGA-AB-2985 AML45 2 208238522 208238522 C T SNP LOC729406 XR_037781.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - pseudogene tier3 990 110 9.96 536 370 40.79 0 0 NA 907786 TCGA-AB-2985 AML45 2 209521023 209521023 A G SNP ENSG00000202164 ENST00000365294 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27390 NULL 0.016 - - - no_errors tier3 845 112 11.7 393 296 42.96 0 0 NA 907786 TCGA-AB-2985 AML45 2 227795504 227795504 G A SNP COL4A3 NM_000091.3 human genbank 54_36p 1 reviewed intronic c.88-15424 e2-15424 0.002 - - - no_errors tier3 724 116 13.74 275 286 50.98 0 0 NA 907786 TCGA-AB-2985 AML45 2 228555719 228555719 T C SNP SPHKAP NM_030623.1 human genbank 54_36p -1 validated intronic c.4873-899 e11-899 0 - - - no_errors tier3 824 95 10.34 392 268 40.61 0 0 NA 907786 TCGA-AB-2985 AML45 3 19771388 19771388 A G SNP - - - - - - - - - - - - - - - tier3 1319 151 10.27 475 316 39.9 0 0 NA 907786 TCGA-AB-2985 AML45 3 36578755 36578755 G A SNP STAC NM_003149.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*15970 NULL 0.001 - - - no_errors tier3 852 102 10.69 370 283 43.34 0 0 NA 907786 TCGA-AB-2985 AML45 3 78591412 78591412 T C SNP - - - - - - - - - - - - - - - tier3 1007 134 11.74 529 364 40.72 0 0 NA 907786 TCGA-AB-2985 AML45 3 98563764 98563764 A G SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.1607-42920 e6-42920 0 - - - no_errors tier3 264 27 9.28 238 162 40.5 0 0 NA 907786 TCGA-AB-2985 AML45 3 112125378 112125378 C T SNP LOC151760 XR_041821.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-30479 NULL 0 - - - no_errors tier3 743 84 10.11 268 274 50.55 0 0 NA 907786 TCGA-AB-2985 AML45 3 130623213 130623213 C T SNP C3orf25 NM_207307.1 human genbank 54_36p -1 predicted missense c.173 p.R58Q 0.532 NULL "PatternScan_EF_HAND_1,superfamily_SSF47473" - no_errors tier1 1057 162 13.29 430 374 46.46 NA 907786 TCGA-AB-2985 AML45 3 157104607 157104607 C T SNP GMPS NM_003875.2 human genbank 54_36p 1 reviewed intronic c.422+164 e4+164 0 - - - no_errors tier3 706 87 10.97 354 269 43.11 0 0 0 907786 TCGA-AB-2985 AML45 3 168581494 168581494 C T SNP ZBBX NM_024687.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-8111 NULL 0 - - - no_errors tier3 996 97 8.84 521 328 38.54 0 0 NA 907786 TCGA-AB-2985 AML45 3 188243074 188243074 G A SNP ST6GAL1 NM_003032.2 human genbank 54_36p 1 reviewed intronic c.1-62 e1-62 0 - - - no_errors tier3 952 79 7.66 500 244 32.62 0 3 100 907786 TCGA-AB-2985 AML45 4 2748451 2748451 G T SNP SH3BP2 NM_003023.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-43692 NULL 0.004 - - - no_errors tier3 842 89 9.56 268 175 39.5 0 0 NA 907786 TCGA-AB-2985 AML45 4 29899270 29899270 T C SNP - - - - - - - - - - - - - - - tier3 431 36 7.71 249 133 34.82 0 0 NA 907786 TCGA-AB-2985 AML45 4 35070965 35070965 G T SNP - - - - - - - - - - - - - - - tier3 620 56 8.27 248 189 43.05 0 0 NA 907786 TCGA-AB-2985 AML45 4 89113386 89113386 A G SNP PKD2 NM_000297.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34524 NULL 0.001 - - - no_errors tier3 413 57 12.1 191 154 44.51 0 0 NA 907786 TCGA-AB-2985 AML45 4 105903090 105903090 T A SNP - - - - - - - - - - - - - - - tier3 361 43 10.64 197 111 36.04 0 0 NA 907786 TCGA-AB-2985 AML45 4 114197842 114197842 T C SNP ANK2 NM_001148.1 human genbank 54_36p 1 reviewed intronic c.84+7425 e1+7425 0.004 - - - no_errors tier3 239 38 13.67 202 153 43.1 0 0 NA 907786 TCGA-AB-2985 AML45 4 116195263 116195263 G A SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.978+21401 e1+21401 0 - - - no_errors tier3 629 66 9.5 368 302 45.01 0 0 NA 907786 TCGA-AB-2985 AML45 4 151173967 151173967 G A SNP DCLK2 NM_001040260.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45663 NULL 0.003 - - - no_errors tier3 1133 132 10.43 440 325 42.48 0 0 NA 907786 TCGA-AB-2985 AML45 4 162103807 162103807 C T SNP ENSG00000221362 ENST00000408435 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*40672 NULL 0 - - - no_errors tier3 711 114 13.8 392 263 39.91 0 0 NA 907786 TCGA-AB-2985 AML45 4 179007826 179007826 A G SNP LOC285501 NM_001085490.1 human genbank 54_36p 1 predicted intronic c.1-111079 e1-111079 0.002 - - - no_errors tier3 219 29 11.69 126 131 50.97 0 0 NA 907786 TCGA-AB-2985 AML45 4 181320430 181320430 G A SNP - - - - - - - - - - - - - - - tier3 122 18 12.86 153 110 41.83 0 0 NA 907786 TCGA-AB-2985 AML45 4 190449077 190449077 T C SNP - - - - - - - - - - - - - - - tier3 530 68 11.33 212 219 50.81 0 0 NA 907786 TCGA-AB-2985 AML45 5 9439323 9439323 G A SNP SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.1-6188 e1-6188 0.001 - - - no_errors tier3 1921 189 8.94 991 739 42.72 0 0 NA 907786 TCGA-AB-2985 AML45 5 35442851 35442851 C G SNP ENSG00000201368 ENST00000364498 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-22072 NULL 0.003 - - - no_errors tier3 1051 140 11.73 601 453 42.82 0 0 NA 907786 TCGA-AB-2985 AML45 5 40359579 40359579 G T SNP - - - - - - - - - - - - - - - tier3 494 68 12.1 219 168 43.41 0 0 NA 907786 TCGA-AB-2985 AML45 5 45550574 45550574 C - DEL HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.850-52708 e3-52708 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 907786 TCGA-AB-2985 AML45 5 54199190 54199190 T G SNP ENSG00000221073 ENST00000408146 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14657 NULL 0.013 - - - no_errors tier3 250 43 14.68 123 116 48.33 0 0 NA 907786 TCGA-AB-2985 AML45 5 57692508 57692508 T C SNP - - - - - - - - - - - - - - - tier3 962 97 9.14 453 304 40.16 0 0 NA 907786 TCGA-AB-2985 AML45 5 75874444 75874444 T C SNP IQGAP2 NM_006633.2 human genbank 54_36p 1 validated intronic c.147-19533 e3-19533 0.001 - - - no_errors tier3 1284 163 11.25 611 386 38.48 0 2 100 907786 TCGA-AB-2985 AML45 5 105684798 105684798 G A SNP - - - - - - - - - - - - - - - tier3 1148 130 10.17 512 356 40.97 0 0 NA 907786 TCGA-AB-2985 AML45 5 124515423 124515423 C T SNP - - - - - - - - - - - - - - - tier3 932 111 10.63 323 342 51.27 0 0 NA 907786 TCGA-AB-2985 AML45 5 156539363 156539363 G C SNP ITK NM_005546.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1204 NULL 0.002 - - - no_errors tier3 505 54 9.66 242 194 44.39 0 0 NA 907786 TCGA-AB-2985 AML45 5 169236601 169236601 G T SNP DOCK2 NM_004946.2 human genbank 54_36p 1 validated intronic c.2799+36167 e27+36167 0 - - - no_errors tier3 749 82 9.86 396 313 44.15 4 5 55.56 907786 TCGA-AB-2985 AML45 5 170275370 170275370 C G SNP RANBP17 NM_022897.2 human genbank 54_36p 1 provisional intronic c.835-704 e9-704 0 - - - no_errors tier3 837 91 9.75 465 329 41.18 0 0 NA 907786 TCGA-AB-2985 AML45 6 11802478 11802478 G T SNP ENSG00000207419 ENST00000384688 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-15560 NULL 0 - - - no_errors tier3 1854 203 9.86 810 607 42.81 0 0 NA 907786 TCGA-AB-2985 AML45 6 20599279 20599279 A G SNP E2F3 NM_001949.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*639 NULL 0 - - - no_errors tier3 391 46 10.53 184 137 42.68 11 15 57.69 907786 TCGA-AB-2985 AML45 6 48427319 48427319 G C SNP - - - - - - - - - - - - - - - tier3 996 122 10.91 572 442 43.59 0 0 NA 907786 TCGA-AB-2985 AML45 6 52331004 52331004 A T SNP LOC647163 XM_001725956.1 human genbank 54_36p -1 model intronic c.812-3554 e6-3554 0.167 - - - no_errors tier3 356 40 10.1 169 146 46.35 0 0 NA 907786 TCGA-AB-2985 AML45 6 52765802 52765802 C T SNP GSTA1 NM_145740.3 human genbank 54_36p -1 reviewed intronic c.415-58 e5-58 0.093 - - - no_errors tier3 1316 191 12.64 544 358 39.69 0 0 NA 907786 TCGA-AB-2985 AML45 6 95328747 95328747 T C SNP - - - - - - - - - - - - - - - tier3 868 88 9.21 525 341 39.33 0 0 NA 907786 TCGA-AB-2985 AML45 6 97174456 97174456 G C SNP ENSG00000219139 ENST00000407851 human ensembl 54_36p 1 known 5_prime_flanking_region c.-33415 NULL 0 - - - no_coding_region:pseudogene tier3 450 29 6.05 223 154 40.85 0 0 NA 907786 TCGA-AB-2985 AML45 6 104569099 104569099 C T SNP ENSG00000214428 ENST00000398310 human ensembl 54_36p -1 known 3_prime_flanking_region c.*11009 NULL 0.039 - - - no_coding_region:pseudogene tier3 987 145 12.78 463 292 38.68 0 0 NA 907786 TCGA-AB-2985 AML45 6 110452423 110452423 G A SNP GPR6 NM_005284.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*44326 NULL 0.011 - - - no_errors tier3 894 102 10.22 357 252 41.38 0 0 NA 907786 TCGA-AB-2985 AML45 6 112179063 112179063 T C SNP FYN NM_002037.3 human genbank 54_36p -1 reviewed intronic c.1+29399 e0+29399 0.988 - - - no_errors tier3 708 71 9.11 263 171 39.31 5 3 37.5 907786 TCGA-AB-2985 AML45 6 115788131 115788131 T C SNP ENSG00000219619 ENST00000404881 human ensembl 54_36p -1 known 5_prime_flanking_region c.-1522 NULL 0 - - - no_coding_region:pseudogene tier3 299 34 10.21 132 136 50.56 0 0 NA 907786 TCGA-AB-2985 AML45 6 116133054 116133054 C T SNP - - - - - - - - - - - - - - - tier3 492 45 8.38 252 196 43.46 0 0 NA 907786 TCGA-AB-2985 AML45 6 116279689 116279689 T C SNP - - - - - - - - - - - - - - - tier3 1006 110 9.84 499 392 44 0 0 NA 907786 TCGA-AB-2985 AML45 6 125189057 125189057 G A SNP NKAIN2 NM_001040214.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*2983 NULL 0 - - - no_errors tier3 911 101 9.97 404 258 38.91 0 0 NA 907786 TCGA-AB-2985 AML45 6 135743523 135743523 C G SNP AHI1 NM_017651.1 human genbank 54_36p -1 reviewed intronic c.3109+14084 e20+14084 0.001 - - - no_errors tier3 156 16 9.3 81 48 37.21 0 0 0 907786 TCGA-AB-2985 AML45 7 34149471 34149471 A C SNP BMPER NM_133468.3 human genbank 54_36p 1 validated missense c.1850 p.H617P 0.936 HMMPfam_C8 "HMMPfam_VWC,HMMSmart_VWC,PatternScan_VWFC_1,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 810 85 9.5 340 259 43.24 NA 907786 TCGA-AB-2985 AML45 7 42979156 42979156 T C SNP PSMA2 NM_002787.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-40874 NULL 0.011 - - - no_errors tier3 771 91 10.53 374 284 43.16 0 0 NA 907786 TCGA-AB-2985 AML45 7 70484792 70484792 T C SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.423-6365 e3-6365 0 - - - no_errors tier3 1117 119 9.62 699 261 27.13 0 0 NA 907786 TCGA-AB-2985 AML45 7 83692859 83692859 T C SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31021 NULL 0 - - - no_errors tier3 427 55 11.39 272 212 43.71 0 0 NA 907786 TCGA-AB-2985 AML45 7 99255262 99255262 T C SNP CYP3A43 NM_022820.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8413 NULL 0 - - - no_errors tier3 1067 225 17.4 437 311 41.41 0 0 NA 907786 TCGA-AB-2985 AML45 7 104718970 104718970 G A SNP SRPK2 NM_182692.1 human genbank 54_36p -1 validated intronic c.72-87502 e3-87502 0.039 - - - no_errors tier3 752 96 11.32 400 365 47.65 12 3 20 907786 TCGA-AB-2985 AML45 7 108126324 108126324 G A SNP - - - - - - - - - - - - - - - tier3 898 124 12.1 510 368 41.91 0 0 NA 907786 TCGA-AB-2985 AML45 7 142223304 142223304 T C SNP EPHB6 NM_004445.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47849 NULL 0.004 - - - no_errors tier3 1076 113 9.5 462 297 39.03 0 0 NA 907786 TCGA-AB-2985 AML45 7 142280210 142280210 G A SNP TRPV6 NM_018646.2 human genbank 54_36p -1 validated intronic c.1895+37 e14+37 0 - - - no_errors tier3 457 57 11.09 165 125 43.1 0 0 NA 907786 TCGA-AB-2985 AML45 8 3805350 3805350 G T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.818+37483 e5+37483 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 816 94 10.33 357 272 43.17 0 0 NA 907786 TCGA-AB-2985 AML45 8 4908171 4908171 T C SNP - - - - - - - - - - - - - - - tier3 201 26 11.45 117 86 42.36 0 0 NA 907786 TCGA-AB-2985 AML45 8 5403124 5403124 T A SNP - - - - - - - - - - - - - - - tier3 1231 185 13.06 374 331 46.88 0 0 NA 907786 TCGA-AB-2985 AML45 8 19893251 19893251 T C SNP LPL NM_000237.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*26150 NULL 0.043 - - - no_errors tier3 1383 195 12.32 700 432 37.96 0 0 NA 907786 TCGA-AB-2985 AML45 8 50652323 50652323 G T SNP - - - - - - - - - - - - - - - tier3 682 81 10.62 276 203 42.38 0 0 NA 907786 TCGA-AB-2985 AML45 8 52381085 52381085 T C SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*13919 NULL 0.083 - - - no_errors tier3 627 78 11.05 413 297 41.83 0 0 NA 907786 TCGA-AB-2985 AML45 8 58439631 58439631 T A SNP - - - - - - - - - - - - - - - tier3 399 47 10.49 212 134 38.73 0 0 NA 907786 TCGA-AB-2985 AML45 8 63791127 63791127 A G SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.274-30918 e4-30918 0.001 - - - no_errors tier3 1012 114 10.12 503 374 42.6 0 0 NA 907786 TCGA-AB-2985 AML45 8 75038063 75038063 A G SNP TCEB1 NM_005648.2 human genbank 54_36p -1 reviewed intronic c.1-3456 e1-3456 0.002 - - - no_errors tier3 328 43 11.59 217 161 42.48 2 4 66.67 907786 TCGA-AB-2985 AML45 8 76959313 76959313 C T SNP ENSG00000211417 ENST00000388682 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8289 NULL 0 - - - pseudogene tier3 441 44 9.07 272 170 38.29 0 0 NA 907786 TCGA-AB-2985 AML45 8 83389509 83389509 T G SNP HNRNPA1P4 ENST00000222956 human ensembl 54_36p -1 known 5_prime_flanking_region c.-22337 NULL 0 - - - no_start_codon tier3 452 72 13.71 203 174 45.79 0 0 NA 907786 TCGA-AB-2985 AML45 8 131746700 131746700 C A SNP - - - - - - - - - - - - - - - tier3 351 43 10.86 219 171 43.85 0 0 NA 907786 TCGA-AB-2985 AML45 8 139123019 139123019 G T SNP FLJ45872 XR_040309.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - no_errors tier3 1097 160 12.72 549 400 42.15 0 0 NA 907786 TCGA-AB-2985 AML45 9 20238324 20238324 G C SNP ENSG00000221744 ENST00000408817 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46678 NULL 0.006 - - - no_errors tier3 751 93 11.01 394 298 43.06 0 0 NA 907786 TCGA-AB-2985 AML45 9 23728520 23728520 C T SNP ELAVL2 NM_004432.2 human genbank 54_36p -1 validated intronic c.230-7397 e2-7397 1 - - - no_errors tier3 1528 167 9.85 701 402 36.35 0 0 NA 907786 TCGA-AB-2985 AML45 9 24593652 24593652 G A SNP - - - - - - - - - - - - - - - tier3 868 76 8.03 409 260 38.75 0 0 NA 907786 TCGA-AB-2985 AML45 9 102901996 102901996 T C SNP PRG-3 NM_207299.2 human genbank 54_36p 1 reviewed intronic c.1+70791 e0+70791 0 - - - no_errors tier3 1303 152 10.45 609 481 44.05 0 0 NA 907786 TCGA-AB-2985 AML45 9 113716748 113716748 T C SNP UGCG NM_003358.1 human genbank 54_36p 1 reviewed silent c.141 p.Y47 1 NULL "HMMPfam_Glycos_transf_2,superfamily_SSF53448" - no_errors tier1 429 30 6.54 189 119 38.64 NA 907786 TCGA-AB-2985 AML45 9 128840178 128840178 C T SNP RALGPS1 NM_014636.1 human genbank 54_36p 1 provisional intronic c.300+3564 e4+3564 0.082 - - - no_errors tier3 1429 155 9.75 474 394 45.29 0 0 0 907786 TCGA-AB-2985 AML45 10 48139120 48139120 C A SNP ENSG00000221361 ENST00000408434 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8003 NULL 0.036 - - - no_errors tier3 592 81 12.02 274 228 45.42 0 0 NA 907786 TCGA-AB-2985 AML45 10 50527544 50527544 G T SNP CHAT NM_020549.1 human genbank 54_36p 1 reviewed intronic c.1383-16 e10-16 0 - - - no_errors tier3 586 82 12.28 248 171 40.81 0 0 NA 907786 TCGA-AB-2985 AML45 10 57056113 57056113 C T SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+1278 e0+1278 0 - - - no_errors tier3 750 82 9.86 270 198 42.22 0 0 NA 907786 TCGA-AB-2985 AML45 10 58332292 58332292 C T SNP - - - - - - - - - - - - - - - tier3 463 48 9.36 229 193 45.63 0 0 NA 907786 TCGA-AB-2985 AML45 10 70687136 70687136 C A SNP HKDC1 NM_025130.3 human genbank 54_36p 1 validated silent c.1980 p.T660 1 "HMMPfam_Hexokinase_1,superfamily_Actin-like ATPase domain" "HMMPfam_Hexokinase_1,HMMPfam_Hexokinase_2,PatternScan_HEXOKINASES,superfamily_Actin-like ATPase domain" - no_errors tier1 1027 146 12.43 338 288 45.93 3 0 907786 TCGA-AB-2985 AML45 10 73010600 73010600 G C SNP CDH23 NM_022124.4 human genbank 54_36p 1 reviewed intronic c.832+2845 e8+2845 0 - - - no_errors tier3 540 65 10.74 194 138 41.57 0 0 0 907786 TCGA-AB-2985 AML45 10 74000426 74000426 T C SNP CBARA1 NM_006077.2 human genbank 54_36p -1 validated intronic c.1-3868 e1-3868 0 - - - no_errors tier3 540 74 12.05 190 188 49.74 5 3 37.5 907786 TCGA-AB-2985 AML45 10 103725013 103725013 A T SNP C10orf76 NM_024541.2 human genbank 54_36p -1 validated missense c.1441 p.Y481N 1 HMMPfam_DUF1741 HMMPfam_DUF1741 - no_errors tier1 1183 14 1.17 764 107 12.27 55 5 8.33 907786 TCGA-AB-2985 AML45 10 106195487 106195487 A G SNP CCDC147 NM_001008723.1 human genbank 54_36p 1 validated intronic c.2257-1959 e16-1959 0.001 - - - no_errors tier3 1119 133 10.59 381 296 43.72 0 0 NA 907786 TCGA-AB-2985 AML45 10 122932573 122932573 C T SNP LOC100129699 XM_001718711.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-198 NULL 0 - - - no_errors tier3 463 66 12.38 290 236 44.87 0 0 NA 907786 TCGA-AB-2985 AML45 10 126974206 126974206 G A SNP LOC642622 XM_001713966.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37194 NULL 0 - - - no_errors tier3 471 46 8.9 357 260 42.14 0 0 NA 907786 TCGA-AB-2985 AML45 10 132154718 132154718 G A SNP ENSG00000222997 ENST00000411065 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38642 NULL 0 - - - no_errors tier3 1114 107 8.76 560 225 28.59 0 0 NA 907786 TCGA-AB-2985 AML45 11 13666694 13666694 C T SNP FAR1 NM_032228.5 human genbank 54_36p 1 validated intronic c.1-6188 e1-6188 0.026 - - - no_errors tier3 471 53 10.11 264 190 41.67 1 0 0 907786 TCGA-AB-2985 AML45 11 70026309 70026309 C T SNP SHANK2 NM_012309.1 human genbank 54_36p -1 reviewed intronic c.433+240 e3+240 0 - - - no_errors tier3 372 47 11.22 162 123 43.16 0 0 NA 907786 TCGA-AB-2985 AML45 12 16562166 16562166 C G SNP LMO3 NM_001001395.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*33257 NULL 0 - - - no_errors tier3 1562 186 10.58 544 461 45.73 0 0 NA 907786 TCGA-AB-2985 AML45 12 37899404 37899404 C T SNP - - - - - - - - - - - - - - - tier3 286 33 10.31 242 171 41.3 0 0 NA 907786 TCGA-AB-2985 AML45 12 40217102 40217102 G A SNP PDZRN4 NM_013377.3 human genbank 54_36p 1 validated intronic c.430-15623 e4-15623 0.001 - - - no_errors tier3 773 113 12.74 411 316 43.47 0 0 0 907786 TCGA-AB-2985 AML45 12 72630389 72630389 C T SNP - - - - - - - - - - - - - - - tier3 1124 155 12.07 638 429 40.21 0 0 NA 907786 TCGA-AB-2985 AML45 12 102506038 102506038 A G SNP STAB2 NM_017564.9 human genbank 54_36p 1 reviewed intronic c.81+573 e1+573 0 - - - no_errors tier3 1342 160 10.65 663 453 40.59 0 0 0 907786 TCGA-AB-2985 AML45 12 102608282 102608282 A C SNP STAB2 NM_017564.9 human genbank 54_36p 1 reviewed intronic c.3183-50 e30-50 0 - - - no_errors tier3 229 23 9.13 114 88 43.56 0 0 NA 907786 TCGA-AB-2985 AML45 12 117531594 117531594 G C SNP - - - - - - - - - - - - - - - tier3 2122 237 10.02 676 494 42.01 0 0 NA 907786 TCGA-AB-2985 AML45 12 122816890 122816890 T C SNP DNAH10 ENST00000409039 human ensembl 54_36p 1 known intronic c.32-1216 e2-1216 0.021 - - - no_errors tier3 251 40 13.7 223 153 40.58 0 0 NA 907786 TCGA-AB-2985 AML45 13 18810524 18810524 G A SNP ENSG00000218022 ENST00000407333 human ensembl 54_36p -1 known intronic c.NULL NULL 0.008 - - - no_coding_region:pseudogene tier3 429 48 10.06 176 101 36.46 0 0 NA 907786 TCGA-AB-2985 AML45 13 21446755 21446755 C T SNP - - - - - - - - - - - - - - - tier3 401 43 9.66 206 155 42.94 0 0 NA 907786 TCGA-AB-2985 AML45 13 54073072 54073072 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 907786 TCGA-AB-2985 AML45 13 73272002 73272002 C T SNP KLF12 NM_007249.4 human genbank 54_36p -1 validated intronic c.806+13288 e4+13288 0.007 - - - no_errors tier3 753 86 10.23 325 241 42.43 0 0 0 907786 TCGA-AB-2985 AML45 13 73640745 73640745 A T SNP KLF12 NM_007249.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-173585 NULL 0.459 - - - no_errors tier3 1144 125 9.85 463 414 47.21 0 0 NA 907786 TCGA-AB-2985 AML45 13 95346878 95346878 T C SNP UGCGL2 NM_020121.2 human genbank 54_36p -1 provisional intronic c.2635-1319 e23-1319 0.001 - - - no_errors tier3 531 45 7.81 240 178 42.48 0 0 NA 907786 TCGA-AB-2985 AML45 13 108836737 108836737 C T SNP - - - - - - - - - - - - - - - tier3 450 50 10 232 155 40.05 0 0 NA 907786 TCGA-AB-2985 AML45 14 19549217 19549217 A G SNP OR4L1 NM_001004717.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-48827 NULL 0.095 - - - no_errors tier3 308 35 10.17 136 164 54.67 0 0 NA 907786 TCGA-AB-2985 AML45 14 24920893 24920893 A T SNP - - - - - - - - - - - - - - - tier3 775 95 10.89 335 237 41.43 0 0 NA 907786 TCGA-AB-2985 AML45 14 27559062 27559062 G T SNP ENSG00000223164 ENST00000411232 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29901 NULL 0 - - - no_errors tier3 696 63 8.3 334 236 41.4 0 0 NA 907786 TCGA-AB-2985 AML45 14 68941304 68941304 G A SNP SLC39A9 NM_018375.3 human genbank 54_36p 1 validated intronic c.96+5369 e1+5369 0.119 - - - no_errors tier3 366 31 7.81 241 87 26.52 0 0 0 907786 TCGA-AB-2985 AML45 14 104196474 104196474 C T SNP INF2 NM_022489.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-42274 NULL 0 - - - no_errors tier3 1646 271 14.14 642 527 45.08 0 0 NA 907786 TCGA-AB-2985 AML45 15 24439736 24439736 G A SNP GABRB3 NM_000814.4 human genbank 54_36p -1 reviewed intronic c.241-21962 e4-21962 0 - - - no_errors tier3 1266 157 11.03 422 370 46.72 0 0 NA 907786 TCGA-AB-2985 AML45 15 44460442 44460442 G A SNP - - - - - - - - - - - - - - - tier3 1100 2 0.18 707 77 9.82 0 0 NA 907786 TCGA-AB-2985 AML45 15 77686498 77686498 A G SNP LOC390617 XR_017666.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-46547 NULL 0.208 - - - pseudogene tier3 1731 153 8.12 594 396 40 0 0 NA 907786 TCGA-AB-2985 AML45 15 85841854 85841854 G A SNP ENSG00000207150 ENST00000384421 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-23330 NULL 0 - - - no_errors tier3 753 99 11.58 302 221 42.18 0 0 NA 907786 TCGA-AB-2985 AML45 16 31279758 31279758 G A SNP ITGAX NM_000887.3 human genbank 54_36p 1 reviewed intronic c.862-127 e9-127 0 - - - no_errors tier3 423 48 10.19 160 88 35.48 66 67 50.38 907786 TCGA-AB-2985 AML45 17 926324 926324 G A SNP ABR NM_021962.3 human genbank 54_36p -1 reviewed intronic c.701-2657 e7-2657 0.001 - - - no_errors tier3 489 41 7.74 188 56 22.95 0 4 100 907786 TCGA-AB-2985 AML45 17 1982638 1982638 T C SNP SMG6 NM_017575.4 human genbank 54_36p -1 validated intronic c.3357+40064 e13+40064 0.996 - - - no_errors tier3 288 29 9.15 153 106 40.77 4 2 33.33 907786 TCGA-AB-2985 AML45 17 14581334 14581334 A G SNP LOC388339 XM_371019.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-31758 NULL 0 - - - pseudogene tier3 991 117 10.55 398 321 44.65 0 0 NA 907786 TCGA-AB-2985 AML45 17 22758624 22758624 A G SNP LOC440419 XR_040504.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-10451 NULL 0.002 - - - no_errors tier3 608 96 13.64 264 192 42.11 0 0 NA 907786 TCGA-AB-2985 AML45 17 35285326 35285326 A T SNP ZPBP2 NM_199321.2 human genbank 54_36p 1 validated intronic c.889+113 e7+113 0 - - - no_errors tier3 73 5 6.41 57 60 51.28 0 0 NA 907786 TCGA-AB-2985 AML45 17 56665324 56665324 C T SNP BCAS3 NM_001099432.1 human genbank 54_36p 1 validated intronic c.2471-135146 e23-135146 0.029 - - - no_errors tier3 554 75 11.9 273 180 39.74 1 8 88.89 907786 TCGA-AB-2985 AML45 17 65845345 65845345 T C SNP - - - - - - - - - - - - - - - tier3 589 93 13.62 295 166 36.01 0 0 NA 907786 TCGA-AB-2985 AML45 18 17092154 17092154 C T SNP KIAA1772 ENST00000400483 human ensembl 54_36p 1 known intronic c.1+15802 e0+15802 0.001 - - - no_stop_codon tier3 611 82 11.83 265 181 40.58 0 0 NA 907786 TCGA-AB-2985 AML45 18 19175632 19175632 A G SNP C18orf45 NM_032933.4 human genbank 54_36p -1 validated intronic c.765+10526 e13+10526 0.17 - - - no_errors tier3 870 116 11.75 468 297 38.77 0 0 0 907786 TCGA-AB-2985 AML45 18 31073124 31073124 A G SNP ZNF397 NM_032347.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-3309 NULL 0.01 - - - no_errors tier3 903 117 11.47 376 233 38.26 0 0 NA 907786 TCGA-AB-2985 AML45 18 33235194 33235194 A G SNP BRUNOL4 NM_020180.1 human genbank 54_36p -1 reviewed intronic c.370-79352 e3-79352 0 - - - no_errors tier3 868 104 10.7 282 113 28.61 0 0 NA 907786 TCGA-AB-2985 AML45 18 37090943 37090943 G A SNP - - - - - - - - - - - - - - - tier3 1178 129 9.86 450 337 42.71 0 0 NA 907786 TCGA-AB-2985 AML45 18 42069413 42069413 T C SNP C18orf25 NM_145055.2 human genbank 54_36p 1 validated intronic c.716-4556 e2-4556 0.001 - - - no_errors tier3 981 69 6.57 669 231 25.67 0 0 0 907786 TCGA-AB-2985 AML45 18 49546623 49546623 C T SNP - - - - - - - - - - - - - - - tier3 891 111 11.08 372 299 44.43 0 0 NA 907786 TCGA-AB-2985 AML45 18 62228987 62228987 G T SNP - - - - - - - - - - - - - - - tier3 947 126 11.74 351 223 38.85 0 0 NA 907786 TCGA-AB-2985 AML45 18 73621324 73621324 T C SNP - - - - - - - - - - - - - - - tier3 1761 176 9.08 795 382 32.46 0 0 NA 907786 TCGA-AB-2985 AML45 19 18429223 18429223 G A SNP ELL NM_006532.2 human genbank 54_36p -1 validated intronic c.869+792 e6+792 0.001 - - - no_errors tier3 450 67 12.96 136 105 43.57 6 2 25 907786 TCGA-AB-2985 AML45 19 47048702 47048702 A G SNP ARHGEF1 NM_199002.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-31673 NULL 0.006 - - - no_errors tier3 1020 155 13.19 313 257 45.01 0 0 NA 907786 TCGA-AB-2985 AML45 20 16549719 16549719 C A SNP KIF16B NM_024704.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-47799 NULL 0.006 - - - no_errors tier3 1517 195 11.38 564 456 44.66 0 0 NA 907786 TCGA-AB-2985 AML45 20 56377798 56377798 T A SNP VAPB NM_004738.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20124 NULL 0 - - - no_errors tier3 731 85 10.39 422 265 38.57 0 0 NA 907786 TCGA-AB-2985 AML45 20 57419699 57419699 G A SNP LOC645605 XM_001716708.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*49370 NULL 0 - - - no_errors tier3 695 97 12.2 206 165 44.47 0 0 NA 907786 TCGA-AB-2985 AML45 20 60103602 60103602 C T SNP TAF4 NM_003185.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29341 NULL 0.045 - - - no_errors tier3 825 93 10.13 281 152 35.1 0 0 NA 907786 TCGA-AB-2985 AML45 21 31836663 31836663 C T SNP TIAM1 NM_003253.2 human genbank 54_36p -1 validated intronic c.1+16448 e0+16448 0.001 - - - no_errors tier3 1373 156 10.18 558 345 38.12 0 0 NA 907786 TCGA-AB-2985 AML45 21 46269533 46269533 T C SNP LOC100133289 XM_001716625.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-34083 NULL 0 - - - no_errors tier3 435 79 15.37 146 139 48.6 0 0 NA 907786 TCGA-AB-2985 AML45 22 18656437 18656437 G A SNP RTN4R NM_023004.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20822 NULL 0.039 - - - no_errors tier3 550 75 12 165 147 47.12 0 0 NA 907786 TCGA-AB-2985 AML45 22 26320630 26320630 C A SNP - - - - - - - - - - - - - - - tier3 2865 374 11.51 851 701 45.11 0 0 NA 254137 TCGA-AB-2986 AML24 X 22857479 22857479 C T SNP - - - - - - - - - - - - - - - tier3 1216 52 4.1 1204 1015 45.7 0 0 NA 254137 TCGA-AB-2986 AML24 X 25204509 25204509 C T SNP ENSG00000203535 ENST00000366348 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*42090 NULL 1 - - - no_coding_region:pseudogene tier3 863 49 5.36 827 660 44.21 0 0 NA 254137 TCGA-AB-2986 AML24 X 30331124 30331124 C T SNP - - - - - - - - - - - - - - - tier3 182 13 6.63 513 394 43.34 0 0 NA 254137 TCGA-AB-2986 AML24 X 37371626 37371626 G C SNP LANCL3 NM_198511.1 human genbank 54_36p 1 provisional intronic c.574-28234 e2-28234 0.001 - - - no_errors tier3 1310 53 3.89 823 623 43.05 0 0 0 254137 TCGA-AB-2986 AML24 X 73724498 73724498 C T SNP ENSG00000218877 ENST00000402081 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4392 NULL 0 - - - no_coding_region:pseudogene tier3 806 30 3.59 600 466 43.59 5 25 83.33 254137 TCGA-AB-2986 AML24 X 102047291 102047291 G A SNP RAB40AL NM_001031834.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-31612 NULL 0.001 - - - no_errors tier3 1607 62 3.71 1180 841 41.53 0 0 NA 254137 TCGA-AB-2986 AML24 X 102476041 102476041 A G SNP WBP5 NM_001006612.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23228 NULL 0.006 - - - no_errors tier3 387 18 4.44 433 359 45.27 0 0 0 254137 TCGA-AB-2986 AML24 X 106197570 106197570 A C SNP RBM41 NM_018301.2 human genbank 54_36p -1 provisional missense c.1085 p.I362R 0.636 "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" "HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD" - no_errors tier1 620 42 6.34 693 539 43.75 21 0 254137 TCGA-AB-2986 AML24 X 106728014 106728014 C A SNP FRMPD3 XM_042978.1 human genbank 54_36p 1 model missense c.2348 p.P783H 1 NULL "HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ,PatternScan_FERM_1,PatternScan_FERM_2,HMMPfam_FERM_M,superfamily_FERM_3-hlx,HMMSmart_B41" - no_errors tier1 911 64 6.56 620 593 48.89 NA 254137 TCGA-AB-2986 AML24 X 107307273 107307273 A G SNP COL4A6 NM_001847.2 human genbank 54_36p -1 reviewed intronic c.2519-376 e28-376 0.001 - - - no_errors tier3 983 39 3.82 590 509 46.31 0 0 NA 254137 TCGA-AB-2986 AML24 X 116808857 116808857 G C SNP - - - - - - - - - - - - - - - tier3 1255 64 4.84 752 647 46.12 0 0 NA 254137 TCGA-AB-2986 AML24 X 133768774 133768774 G T SNP FAM122B NM_145284.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-10873 NULL 0 - - - no_errors tier3 1048 68 6.09 569 340 37.36 0 0 NA 254137 TCGA-AB-2986 AML24 X 136656452 136656452 C T SNP - - - - - - - - - - - - - - - tier3 993 46 4.42 793 562 41.41 0 0 NA 254137 TCGA-AB-2986 AML24 X 140589245 140589245 A T SNP SPANXD NM_032417.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*24043 NULL 0.011 - - - no_errors tier3 611 18 2.86 834 601 41.88 0 0 NA 254137 TCGA-AB-2986 AML24 1 4264057 4264057 G A SNP - - - - - - - - - - - - - - - tier3 723 27 3.6 392 282 41.78 0 0 NA 254137 TCGA-AB-2986 AML24 1 37040578 37040578 G A SNP GRIK3 NM_000831.3 human genbank 54_36p -1 reviewed intronic c.2566-345 e16-345 0.603 - - - no_errors tier3 532 24 4.32 343 269 43.74 0 0 NA 254137 TCGA-AB-2986 AML24 1 61921400 61921400 A T SNP TM2D1 NM_032027.2 human genbank 54_36p -1 reviewed intronic c.624+277 e6+277 0 - - - no_errors tier3 1009 49 4.63 846 611 41.85 0 0 0 254137 TCGA-AB-2986 AML24 1 74170409 74170409 C A SNP - - - - - - - - - - - - - - - tier3 918 34 3.57 920 714 43.64 0 0 NA 254137 TCGA-AB-2986 AML24 1 102998377 102998377 C T SNP - - - - - - - - - - - - - - - tier3 979 52 5.04 1014 730 41.83 0 0 NA 254137 TCGA-AB-2986 AML24 1 113403746 113403746 G A SNP LRIG2 NM_014813.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-13806 NULL 0.004 - - - no_errors tier3 724 35 4.61 320 266 45.32 0 0 NA 254137 TCGA-AB-2986 AML24 1 214515715 214515715 C A SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.1971+13530 e10+13530 0 - - - no_errors tier3 688 26 3.64 1060 710 40.09 0 0 NA 254137 TCGA-AB-2986 AML24 1 214565630 214565630 G A SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.849-66 e5-66 0 - - - no_errors tier3 656 31 4.51 800 560 41.18 0 0 NA 254137 TCGA-AB-2986 AML24 1 232314848 232314848 G A SNP SLC35F3 NM_173508.2 human genbank 54_36p 1 provisional intronic c.284-118938 e3-118938 0.001 - - - no_errors tier3 1041 51 4.67 1034 735 41.48 0 0 NA 254137 TCGA-AB-2986 AML24 2 11399832 11399832 T A SNP ROCK2 NM_004850.3 human genbank 54_36p -1 reviewed intronic c.141+1741 e1+1741 0 - - - no_errors tier3 779 47 5.69 507 416 45.07 0 0 NA 254137 TCGA-AB-2986 AML24 2 70953763 70953763 A T SNP VAX2 NM_012476.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27497 NULL 0.002 - - - no_errors tier3 305 29 8.63 229 183 43.88 0 0 NA 254137 TCGA-AB-2986 AML24 2 88716490 88716490 G C SNP EIF2AK3 NM_004836.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-8583 NULL 0.074 - - - no_errors tier3 709 30 4.06 482 355 42.26 0 0 NA 254137 TCGA-AB-2986 AML24 2 97546269 97546269 A G SNP ANKRD36B NM_025190.2 human genbank 54_36p -1 validated intronic c.68-2514 e2-2514 0.004 - - - no_errors tier3 135 11 7.53 111 116 50.88 0 0 0 254137 TCGA-AB-2986 AML24 2 114753248 114753248 A G SNP ENSG00000208615 ENST00000385880 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*1883 NULL 0.001 - - - pseudogene tier3 757 37 4.66 818 626 43.32 0 0 NA 254137 TCGA-AB-2986 AML24 2 114946833 114946833 T A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+29948 e1+29948 0.001 - - - no_errors tier3 1087 42 3.72 770 569 42.43 0 0 NA 254137 TCGA-AB-2986 AML24 2 123363755 123363755 G A SNP - - - - - - - - - - - - - - - tier3 568 23 3.89 684 564 45.12 0 0 NA 254137 TCGA-AB-2986 AML24 2 133481518 133481518 C A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.342-13236 e5-13236 0.001 - - - no_errors tier3 689 36 4.97 634 400 38.68 0 0 NA 254137 TCGA-AB-2986 AML24 2 135261306 135261306 C T SNP - - - - - - - - - - - - - - - tier3 869 27 3 793 574 41.84 0 0 NA 254137 TCGA-AB-2986 AML24 2 144279127 144279127 C T SNP ARHGAP15 NM_018460.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*36916 NULL 0.014 - - - no_errors tier3 459 13 2.75 334 236 41.4 0 0 NA 254137 TCGA-AB-2986 AML24 2 149824494 149824494 C T SNP LYPD6B NM_177964.3 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*45024 NULL 0.013 - - - no_errors tier3 887 50 5.34 805 534 39.79 0 0 NA 254137 TCGA-AB-2986 AML24 2 162688798 162688798 T C SNP DPP4 NM_001935.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-50061 NULL 0 - - - no_errors tier3 1239 67 5.13 1687 1263 42.74 0 0 NA 254137 TCGA-AB-2986 AML24 2 185906406 185906406 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 254137 TCGA-AB-2986 AML24 2 213299697 213299697 C G SNP ENSG00000221388 ENST00000408461 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*36842 NULL 0 - - - no_errors tier3 1122 50 4.26 450 304 40.32 0 0 NA 254137 TCGA-AB-2986 AML24 2 240697203 240697203 C T SNP ENSG00000213048 ENST00000391990 human ensembl 54_36p 1 novel 3_prime_untranslated_region c.*240697203 NULL 0.02 - - - no_coding_region:pseudogene tier3 1059 74 6.53 748 637 45.93 0 0 NA 254137 TCGA-AB-2986 AML24 3 11485565 11485565 A T SNP ATG7 NM_006395.2 human genbank 54_36p 1 validated intronic c.2079+42165 e17+42165 0.034 - - - no_errors tier3 1127 66 5.53 555 464 45.53 6 2 25 254137 TCGA-AB-2986 AML24 3 26092515 26092515 C T SNP - - - - - - - - - - - - - - - tier3 1134 43 3.64 928 758 44.88 0 0 NA 254137 TCGA-AB-2986 AML24 3 33134394 33134394 A G SNP CRTAP NM_006371.4 human genbank 54_36p 1 reviewed intronic c.472-2446 e2-2446 0.068 - - - no_errors tier3 518 34 6.15 352 260 42.48 0 0 0 254137 TCGA-AB-2986 AML24 3 50729247 50729247 T A SNP DOCK3 NM_004947.3 human genbank 54_36p 1 validated intronic c.37+41512 e1+41512 0.008 - - - no_errors tier3 210 17 7.46 447 317 41.44 0 0 NA 254137 TCGA-AB-2986 AML24 3 60957386 60957386 G A SNP FHIT NM_002012.2 human genbank 54_36p -1 reviewed intronic c.1+45373 e0+45373 0.001 - - - no_errors tier3 650 34 4.97 833 592 41.54 0 0 0 254137 TCGA-AB-2986 AML24 3 77338961 77338961 C T SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.388+108780 e2+108780 0.001 - - - no_errors tier3 71 3 4.05 461 245 34.65 0 0 NA 254137 TCGA-AB-2986 AML24 3 115013863 115013863 A C SNP GRAMD1C NM_017577.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26584 NULL 0.001 - - - no_errors tier3 421 18 4.1 387 313 44.71 0 0 NA 254137 TCGA-AB-2986 AML24 3 130295939 130295939 C T SNP RAB43 NM_198490.1 human genbank 54_36p -1 validated intronic c.388+580 e2+580 0.002 - - - no_errors tier3 638 52 7.53 496 385 43.5 4 0 0 254137 TCGA-AB-2986 AML24 3 149172849 149172849 A G SNP - - - - - - - - - - - - - - - tier3 253 6 2.32 373 271 42.02 0 0 NA 254137 TCGA-AB-2986 AML24 3 170174978 170174978 C T SNP - - - - - - - - - - - - - - - tier3 247 10 3.88 539 408 42.72 0 0 NA 254137 TCGA-AB-2986 AML24 3 184804552 184804552 A T SNP KLHL6 NM_130446.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-48417 NULL 0.007 - - - no_errors tier3 913 52 5.39 406 360 46.94 0 0 NA 254137 TCGA-AB-2986 AML24 3 188041956 188041956 T G SNP RFC4 NM_002916.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-36760 NULL 0.001 - - - no_errors tier3 457 28 5.76 259 192 42.57 0 0 NA 254137 TCGA-AB-2986 AML24 3 189622754 189622754 C A SNP LPP NM_005578.2 human genbank 54_36p 1 validated intronic c.193+15959 e1+15959 0.002 - - - no_errors tier3 1261 56 4.25 1173 815 40.95 0 0 0 254137 TCGA-AB-2986 AML24 4 4356818 4356818 T G SNP ZNF509 NM_145291.3 human genbank 54_36p 1 validated intronic c.1255+1099 e2+1099 0.241 - - - no_errors tier3 425 18 4.06 547 496 47.46 0 0 0 254137 TCGA-AB-2986 AML24 4 21019202 21019202 A C SNP KCNIP4 NM_001035003.1 human genbank 54_36p -1 reviewed intronic c.88+288869 e1+288869 0.005 - - - no_errors tier3 784 49 5.86 533 434 44.88 0 0 NA 254137 TCGA-AB-2986 AML24 4 21203554 21203555 - T INS KCNIP4 NM_001035003.1 human genbank 54_36p -1 reviewed intronic c.88+104516_88+104515 e1+104516 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 254137 TCGA-AB-2986 AML24 4 68106596 68106597 - T INS CENPC1 NM_001812.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12928 NULL 0.001:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 254137 TCGA-AB-2986 AML24 4 70089108 70089108 G A SNP UGT2B11 ENST00000305206 human ensembl 54_36p -1 known intronic c.1590+11532 e6+11532 0.001 - - - no_errors tier3 474 17 3.46 739 464 38.54 0 0 NA 254137 TCGA-AB-2986 AML24 4 77666757 77666757 C T SNP SHROOM3 NM_020859.3 human genbank 54_36p 1 validated intronic c.166-29029 e2-29029 0 - - - no_errors tier3 1471 78 5.03 1051 709 40.22 0 0 NA 254137 TCGA-AB-2986 AML24 4 88510221 88510221 A G SNP HSD17B11 NM_016245.3 human genbank 54_36p -1 validated intronic c.557+2664 e4+2664 0.003 - - - no_errors tier3 158 16 9.2 337 243 41.9 0 0 0 254137 TCGA-AB-2986 AML24 4 92895524 92895524 T C SNP - - - - - - - - - - - - - - - tier3 438 26 5.6 439 372 45.81 0 0 NA 254137 TCGA-AB-2986 AML24 4 100412190 100412190 G A SNP ADH1A NM_000667.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*4614 NULL 0.004 - - - no_errors tier3 322 22 6.38 541 414 43.31 0 0 NA 254137 TCGA-AB-2986 AML24 4 128774372 128774372 G A SNP INTU NM_015693.2 human genbank 54_36p 1 provisional intronic c.146+587 e1+587 0.025 - - - no_errors tier3 252 10 3.82 546 418 43.36 0 0 NA 254137 TCGA-AB-2986 AML24 4 135878483 135878483 C T SNP - - - - - - - - - - - - - - - tier3 245 7 2.78 410 343 45.49 0 0 NA 254137 TCGA-AB-2986 AML24 4 150772999 150772999 G T SNP LOC285423 XR_041269.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.038 - - - no_errors tier3 404 20 4.72 649 480 42.44 0 0 NA 254137 TCGA-AB-2986 AML24 4 162878560 162878560 T - DEL FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.727+21453 e5+21453 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 254137 TCGA-AB-2986 AML24 4 167239037 167239037 G A SNP TLL1 NM_012464.3 human genbank 54_36p 1 reviewed intronic c.2657-842 e20-842 0 - - - no_errors tier3 164 4 2.38 357 303 45.84 0 0 NA 254137 TCGA-AB-2986 AML24 5 3446779 3446779 G A SNP - - - - - - - - - - - - - - - tier3 319 21 6.18 217 162 42.63 0 0 NA 254137 TCGA-AB-2986 AML24 5 3485950 3485950 A T SNP - - - - - - - - - - - - - - - tier3 1090 70 6.03 674 591 46.68 0 0 NA 254137 TCGA-AB-2986 AML24 5 7675003 7675003 C T SNP ADCY2 NM_020546.2 human genbank 54_36p 1 reviewed intronic c.571-4277 e4-4277 0 - - - no_errors tier3 759 45 5.6 734 567 43.55 0 0 NA 254137 TCGA-AB-2986 AML24 5 8189554 8189554 G A SNP - - - - - - - - - - - - - - - tier3 982 44 4.29 695 511 42.3 0 0 NA 254137 TCGA-AB-2986 AML24 5 8783687 8783687 G A SNP - - - - - - - - - - - - - - - tier3 606 28 4.4 597 491 45.09 0 0 NA 254137 TCGA-AB-2986 AML24 5 11889275 11889275 G T SNP CTNND2 NM_001332.2 human genbank 54_36p -1 validated intronic c.37+67654 e1+67654 0 - - - no_errors tier3 937 30 3.1 1049 810 43.52 0 0 NA 254137 TCGA-AB-2986 AML24 5 22236776 22236776 G A SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1+11588 e0+11588 0 - - - no_errors tier3 880 32 3.5 556 429 43.55 0 0 NA 254137 TCGA-AB-2986 AML24 5 29458312 29458312 G A SNP - - - - - - - - - - - - - - - tier3 549 20 3.51 338 247 42.22 0 0 NA 254137 TCGA-AB-2986 AML24 5 35051975 35051975 G A SNP AGXT2 NM_031900.2 human genbank 54_36p -1 reviewed intronic c.964-1994 e10-1994 0.009 - - - no_errors tier3 1560 67 4.12 978 710 42.04 0 0 NA 254137 TCGA-AB-2986 AML24 5 35646834 35646834 A G SNP SPEF2 NM_024867.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7023 NULL 0.002 - - - no_errors tier3 171 4 2.27 576 460 44.4 0 0 NA 254137 TCGA-AB-2986 AML24 5 44971714 44971714 G A SNP - - - - - - - - - - - - - - - tier3 811 36 4.25 457 410 47.24 0 0 NA 254137 TCGA-AB-2986 AML24 5 63839909 63839909 G A SNP RGS7BP NM_001029875.1 human genbank 54_36p 1 provisional intronic c.332+449 e2+449 0.003 - - - no_errors tier3 317 16 4.8 397 291 42.24 0 0 NA 254137 TCGA-AB-2986 AML24 5 91241336 91241336 A G SNP - - - - - - - - - - - - - - - tier3 106 2 1.83 229 158 40.83 0 0 NA 254137 TCGA-AB-2986 AML24 5 99608423 99608423 A T SNP - - - - - - - - - - - - - - - tier3 814 37 4.34 1043 716 40.68 0 0 NA 254137 TCGA-AB-2986 AML24 5 104239995 104239995 C A SNP - - - - - - - - - - - - - - - tier3 796 28 3.39 1048 611 36.81 0 0 NA 254137 TCGA-AB-2986 AML24 5 104766399 104766399 C T SNP - - - - - - - - - - - - - - - tier3 280 17 5.72 408 263 39.2 0 0 NA 254137 TCGA-AB-2986 AML24 5 107023249 107023249 C T SNP EFNA5 NM_001962.2 human genbank 54_36p -1 reviewed intronic c.125+10840 e1+10840 0.001 - - - no_errors tier3 250 13 4.94 288 230 44.4 0 0 NA 254137 TCGA-AB-2986 AML24 5 128979604 128979604 G T SNP ADAMTS19 NM_133638.3 human genbank 54_36p 1 reviewed intronic c.1461-4606 e9-4606 0 - - - no_errors tier3 760 32 4.04 620 457 42.39 0 0 NA 254137 TCGA-AB-2986 AML24 5 149559432 149559432 G A SNP SLC6A7 NM_014228.3 human genbank 54_36p 1 validated intronic c.723+310 e5+310 0 - - - no_errors tier3 625 49 7.25 280 185 39.78 0 0 NA 254137 TCGA-AB-2986 AML24 5 151284287 151284287 G A SNP GLRA1 NM_000171.3 human genbank 54_36p -1 reviewed missense c.17 p.T6I 1 NULL "HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore,HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like,PatternScan_NEUROTR_ION_CHANNEL" - no_errors tier1 1322 76 5.43 852 609 41.68 NA 254137 TCGA-AB-2986 AML24 5 162317823 162317823 C T SNP - - - - - - - - - - - - - - - tier3 391 10 2.49 676 449 39.88 0 0 NA 254137 TCGA-AB-2986 AML24 5 170770152 170770153 - CCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 254137 TCGA-AB-2986 AML24 5 171478795 171478795 G T SNP STK10 NM_005990.3 human genbank 54_36p -1 reviewed intronic c.371-1556 e4-1556 0.026 - - - no_errors tier3 769 37 4.59 347 266 43.39 0 0 0 254137 TCGA-AB-2986 AML24 6 3316022 3316022 C G SNP SLC22A23 NM_021945.1 human genbank 54_36p -1 validated intronic c.70+39399 e1+39399 0.002 - - - no_errors tier3 994 54 5.13 400 308 43.44 0 0 NA 254137 TCGA-AB-2986 AML24 6 7149846 7149846 T A SNP RREB1 NM_001003699.2 human genbank 54_36p 1 validated intronic c.426-6190 e4-6190 0 - - - no_errors tier3 833 51 5.76 398 306 43.47 0 0 0 254137 TCGA-AB-2986 AML24 6 26282362 26282362 C A SNP HIST1H2AC ENST00000396980 human ensembl 54_36p 1 known intronic c.393-10024 e2-10024 0.003 - - - no_errors tier3 177 4 2.21 447 306 40.53 12 1 7.69 254137 TCGA-AB-2986 AML24 6 65144815 65144815 G A SNP - - - - - - - - - - - - - - - tier3 1248 85 6.37 1211 807 39.97 0 0 NA 254137 TCGA-AB-2986 AML24 6 73678720 73678720 T G SNP KCNQ5 NM_019842.2 human genbank 54_36p 1 reviewed intronic c.399-91632 e2-91632 0 - - - no_errors tier3 792 56 6.58 1063 878 45.14 0 0 NA 254137 TCGA-AB-2986 AML24 6 93019046 93019046 T G SNP - - - - - - - - - - - - - - - tier3 86 2 2.27 538 439 44.8 0 0 NA 254137 TCGA-AB-2986 AML24 6 97261399 97261399 G A SNP ENSG00000216518 ENST00000402309 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44022 NULL 0.316 - - - no_coding_region:pseudogene tier3 179 1 0.56 500 321 39.1 0 0 NA 254137 TCGA-AB-2986 AML24 6 107022957 107022957 G A SNP AIM1 NM_001624.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-43953 NULL 0.003 - - - no_errors tier3 864 41 4.53 666 563 45.77 0 0 NA 254137 TCGA-AB-2986 AML24 6 163134758 163134758 T G SNP PACRG NM_152410.1 human genbank 54_36p 1 reviewed intronic c.157-20411 e2-20411 0.028 - - - no_errors tier3 1189 51 4.11 1275 795 38.39 0 0 NA 254137 TCGA-AB-2986 AML24 7 25369614 25369614 G A SNP - - - - - - - - - - - - - - - tier3 1581 54 3.3 893 680 43.15 0 0 NA 254137 TCGA-AB-2986 AML24 7 39345840 39345840 C T SNP POU6F2 NM_007252.2 human genbank 54_36p 1 validated nonsense c.586 p.Q196* 0.001 NULL "HMMPfam_Pou,HMMSmart_SM00352,PatternScan_POU_1,PatternScan_POU_2,HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like,superfamily_lambda repressor-like DNA-binding domains" - no_errors tier1 415 13 3.03 223 187 45.39 NA 254137 TCGA-AB-2986 AML24 7 45725321 45725321 T G SNP ADCY1 NM_021116.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*5202 NULL 0 - - - no_errors tier3 458 26 5.36 282 185 39.53 0 0 NA 254137 TCGA-AB-2986 AML24 7 52594302 52594302 A T SNP - - - - - - - - - - - - - - - tier3 265 10 3.62 620 451 41.99 0 0 NA 254137 TCGA-AB-2986 AML24 7 54692337 54692337 G T SNP ENSG00000200471 ENST00000363601 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36019 NULL 0.015 - - - no_errors tier3 913 38 4 633 389 38.03 0 0 NA 254137 TCGA-AB-2986 AML24 7 62925359 62925359 G A SNP - - - - - - - - - - - - - - - tier3 1059 49 4.41 599 397 39.86 0 0 NA 254137 TCGA-AB-2986 AML24 7 76893894 76893894 T A SNP PION NM_017439.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-10320 NULL 0.008 - - - no_errors tier3 651 26 3.84 427 300 41.1 0 0 NA 254137 TCGA-AB-2986 AML24 7 78407783 78407783 C G SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.418+66559 e2+66559 0.058 - - - no_errors tier3 1694 65 3.69 1462 1189 44.77 0 0 NA 254137 TCGA-AB-2986 AML24 7 84079746 84079746 C T SNP - - - - - - - - - - - - - - - tier3 589 18 2.97 1174 839 41.64 0 0 NA 254137 TCGA-AB-2986 AML24 7 85666788 85666788 G A SNP - - - - - - - - - - - - - - - tier3 189 8 4.06 204 143 40.97 0 0 NA 254137 TCGA-AB-2986 AML24 7 136651147 136651147 C T SNP PTN NM_002825.5 human genbank 54_36p -1 validated intronic c.1+27578 e0+27578 0.109 - - - no_errors tier3 1493 54 3.48 880 681 43.6 0 0 NA 254137 TCGA-AB-2986 AML24 7 140565679 140565679 G A SNP LOC100129514 XM_001716072.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*6692 NULL 0.928 - - - no_errors tier3 1530 73 4.55 836 565 40.3 0 0 NA 254137 TCGA-AB-2986 AML24 8 3440716 3440716 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1101-9526 e10-9526 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1665 90 5.12 1013 742 42.23 0 0 NA 254137 TCGA-AB-2986 AML24 8 9968910 9968910 C G SNP MSRA NM_012331.1 human genbank 54_36p 1 reviewed intronic c.142+19332 e1+19332 0.003 - - - no_errors tier3 1011 54 5.07 671 463 40.79 11 8 42.11 254137 TCGA-AB-2986 AML24 8 15804495 15804495 T C SNP - - - - - - - - - - - - - - - tier3 431 20 4.43 463 342 42.38 0 0 NA 254137 TCGA-AB-2986 AML24 8 26810148 26810148 G A SNP ADRA1A NM_033303.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31745 NULL 0.011 - - - no_errors tier3 276 17 5.78 427 302 41.43 0 0 NA 254137 TCGA-AB-2986 AML24 8 50679243 50679243 G A SNP - - - - - - - - - - - - - - - tier3 814 33 3.9 522 477 47.65 0 0 NA 254137 TCGA-AB-2986 AML24 8 51870870 51870870 G A SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*2928 NULL 0.029 - - - no_errors tier3 311 6 1.89 653 410 38.57 0 0 NA 254137 TCGA-AB-2986 AML24 8 72008017 72008017 G A SNP - - - - - - - - - - - - - - - tier3 1015 56 5.22 946 666 41.32 0 0 NA 254137 TCGA-AB-2986 AML24 8 75219919 75219919 G A SNP - - - - - - - - - - - - - - - tier3 1152 71 5.79 945 679 41.68 0 0 NA 254137 TCGA-AB-2986 AML24 8 102548069 102548069 C G SNP GRHL2 NM_024915.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26105 NULL 0.018 - - - no_errors tier3 1149 58 4.8 965 783 44.72 0 0 NA 254137 TCGA-AB-2986 AML24 8 114062101 114062101 G A SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1031-4548 e7-4548 0.001 - - - no_errors tier3 371 16 4.13 520 366 41.31 0 0 NA 254137 TCGA-AB-2986 AML24 8 117938741 117938741 C A SNP RAD21 NM_006265.2 human genbank 54_36p -1 reviewed nonsense c.634 p.E212* 1 NULL "HMMPfam_Rad21_Rec8,HMMPfam_Rad21_Rec8_N" - no_errors tier1 788 20 2.48 590 413 41.09 46 1 2.13 254137 TCGA-AB-2986 AML24 8 137706848 137706848 G C SNP - - - - - - - - - - - - - - - tier3 179 9 4.79 340 258 43.07 0 0 NA 254137 TCGA-AB-2986 AML24 8 141140511 141140511 A G SNP TRAPPC9 NM_031466.4 human genbank 54_36p -1 provisional intronic c.2851-37153 e18-37153 0.006 - - - no_errors tier3 363 18 4.72 444 337 43.15 0 0 0 254137 TCGA-AB-2986 AML24 9 1644264 1644264 G A SNP LOC100131612 XM_001715326.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-32865 NULL 0.11 - - - no_start_codon:pseudogene tier3 1128 48 4.08 902 655 42.01 0 0 NA 254137 TCGA-AB-2986 AML24 9 88142118 88142118 C G SNP ZCCHC6 ENST00000375948 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*30 NULL 0.565 - - - no_errors tier3 457 35 7.11 480 389 44.76 6 0 0 254137 TCGA-AB-2986 AML24 9 116549957 116549957 G A SNP LOC100129633 XM_001718491.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-1660 NULL 0.513 - - - no_errors tier3 743 28 3.63 591 577 49.36 0 0 NA 254137 TCGA-AB-2986 AML24 9 128473072 128473072 A G SNP LMX1B NM_002316.2 human genbank 54_36p 1 validated intronic c.258-19864 e3-19864 0 - - - no_errors tier3 1076 41 3.66 411 325 44.16 0 0 NA 254137 TCGA-AB-2986 AML24 9 136732184 136732184 C T SNP COL5A1 NM_000093.3 human genbank 54_36p 1 reviewed intronic c.491+395 e3+395 0 - - - no_errors tier3 241 14 5.45 99 88 46.81 0 0 NA 254137 TCGA-AB-2986 AML24 10 71777862 71777862 C T SNP LRRC20 NM_207119.2 human genbank 54_36p -1 validated intronic c.83-7398 e2-7398 0 - - - no_errors tier3 781 39 4.76 382 292 43.26 0 0 0 254137 TCGA-AB-2986 AML24 10 84383796 84383796 C T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.954-104517 e3-104517 0 - - - no_errors tier3 844 39 4.41 659 464 40.99 0 0 NA 254137 TCGA-AB-2986 AML24 10 111475218 111475218 C T SNP LOC100132843 XR_037957.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*44247 NULL 0 - - - pseudogene tier3 1363 77 5.34 931 727 43.85 0 0 NA 254137 TCGA-AB-2986 AML24 10 118084390 118084390 T - DEL C10orf96 NM_198515.2 human genbank 54_36p 1 validated intronic c.166-5846 e3-5846 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 254137 TCGA-AB-2986 AML24 11 4826821 4826821 C T SNP OR51S1 NM_001004758.1 human genbank 54_36p -1 provisional missense c.194 p.R65H 0 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_SPASE_I_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 2114 101 4.55 1045 810 43.32 NA 254137 TCGA-AB-2986 AML24 11 12240127 12240127 C T SNP MICAL2 NM_014632.2 human genbank 54_36p 1 provisional intronic c.3335-476 e25-476 0 - - - no_errors tier3 750 25 3.22 331 290 46.7 3 0 0 254137 TCGA-AB-2986 AML24 11 13588724 13588724 T C SNP LOC644992 XM_932569.1 human genbank 54_36p -1 model missense c.106 p.R36G 0.983 "HMMPfam_HMG14_17,HMMSmart_SM00527" "HMMPfam_HMG14_17,HMMSmart_SM00527" - no_errors tier1 709 40 5.34 426 391 47.86 NA 254137 TCGA-AB-2986 AML24 11 17752264 17752264 G A SNP ENSG00000205289 ENST00000379472 human ensembl 54_36p 1 known 5_prime_flanking_region c.-3176 NULL 0.317 - - - no_stop_codon tier3 567 32 5.33 299 240 44.36 0 0 NA 254137 TCGA-AB-2986 AML24 11 22800080 22800080 C G SNP GAS2 NM_005256.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*9942 NULL 0.003 - - - no_errors tier3 255 14 5.17 333 227 40.32 1 0 0 254137 TCGA-AB-2986 AML24 11 41464223 41464223 G A SNP - - - - - - - - - - - - - - - tier3 1283 116 8.29 865 666 43.47 0 0 NA 254137 TCGA-AB-2986 AML24 11 49565046 49565046 G A SNP ENSG00000205035 ENST00000357667 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*10007 NULL 0.162 - - - no_start_codon:no_stop_codon tier3 85 4 4.49 188 106 36.05 0 0 NA 254137 TCGA-AB-2986 AML24 11 69118826 69118826 T G SNP CCND1 NM_053056.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46437 NULL 0 - - - no_errors tier3 565 37 6.15 271 183 40.31 0 0 NA 254137 TCGA-AB-2986 AML24 11 79044999 79044999 C G SNP ENSG00000221551 ENST00000408624 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36072 NULL 0.002 - - - no_errors tier3 2238 108 4.6 1852 1297 41.16 0 0 NA 254137 TCGA-AB-2986 AML24 11 79574301 79574301 G T SNP - - - - - - - - - - - - - - - tier3 982 33 3.25 1102 810 42.3 0 0 NA 254137 TCGA-AB-2986 AML24 11 88426176 88426176 C T SNP GRM5 ENST00000393294 human ensembl 54_36p -1 known intronic c.1-5288 e1-5288 0 - - - no_errors tier3 654 8 1.21 842 181 17.66 0 0 NA 254137 TCGA-AB-2986 AML24 11 90636962 90636962 T A SNP - - - - - - - - - - - - - - - tier3 498 25 4.78 542 408 42.9 0 0 NA 254137 TCGA-AB-2986 AML24 11 98186072 98186072 C G SNP - - - - - - - - - - - - - - - tier3 158 8 4.79 325 248 43.28 0 0 NA 254137 TCGA-AB-2986 AML24 11 98523744 98523744 T C SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1+126534 e0+126534 0.441 - - - no_errors tier3 277 10 3.48 474 398 45.64 0 0 NA 254137 TCGA-AB-2986 AML24 11 105815965 105815965 T C SNP - - - - - - - - - - - - - - - tier3 278 15 5.12 373 284 43.23 0 0 NA 254137 TCGA-AB-2986 AML24 11 112785157 112785157 G A SNP DRD2 NM_000795.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*1502 NULL 0.001 - - - no_errors tier3 410 16 3.76 268 161 37.53 0 0 NA 254137 TCGA-AB-2986 AML24 11 121968955 121968955 T G SNP ENSG00000223265 ENST00000411333 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13730 NULL 0 - - - no_errors tier3 1185 54 4.36 531 426 44.51 0 0 NA 254137 TCGA-AB-2986 AML24 12 12725699 12725699 C T SNP GPR19 ENST00000332427 human ensembl 54_36p -1 known intronic c.1+2853 e0+2853 0.003 - - - no_errors tier3 1191 52 4.17 947 670 41.36 0 0 NA 254137 TCGA-AB-2986 AML24 12 25503212 25503212 T C SNP LOC100133222 XM_001723495.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-49566 NULL 0.001 - - - pseudogene tier3 276 9 3.16 361 279 43.53 0 0 NA 254137 TCGA-AB-2986 AML24 12 28910032 28910032 T C SNP - - - - - - - - - - - - - - - tier3 94 2 2.08 215 143 39.83 0 0 NA 254137 TCGA-AB-2986 AML24 12 51502047 51502047 C T SNP KRT79 NM_175834.2 human genbank 54_36p -1 validated missense c.1484 p.G495E 0.055 NULL "superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF" - no_errors tier1 803 64 7.37 272 234 46.25 NA 254137 TCGA-AB-2986 AML24 12 61599173 61599173 G A SNP PPM1H NM_020700.1 human genbank 54_36p -1 validated intronic c.245+15366 e1+15366 0.896 - - - no_errors tier3 505 23 4.34 431 309 41.7 0 6 100 254137 TCGA-AB-2986 AML24 12 105561135 105561135 A G SNP RFX4 NM_213594.3 human genbank 54_36p 1 reviewed intronic c.191+3835 e3+3835 0 - - - no_errors tier3 1165 56 4.58 520 375 41.9 0 0 NA 254137 TCGA-AB-2986 AML24 12 113338747 113338747 C T SNP TBX5 NM_000192.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12661 NULL 0.005 - - - no_errors tier3 1404 60 4.1 649 535 45 0 0 NA 254137 TCGA-AB-2986 AML24 12 127053127 127053127 C T SNP - - - - - - - - - - - - - - - tier3 1413 55 3.74 540 471 46.5 0 0 NA 254137 TCGA-AB-2986 AML24 13 27506263 27506264 - CATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGG INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1793_1792 p.598in_frame_insAGSSDNEYFYVDFREY 0.821:0.816 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 254137 TCGA-AB-2986 AML24 13 53681620 53681620 C T SNP - - - - - - - - - - - - - - - tier3 732 23 3.04 875 598 40.54 0 0 NA 254137 TCGA-AB-2986 AML24 13 55306100 55306100 T A SNP - - - - - - - - - - - - - - - tier3 882 35 3.82 1082 800 42.37 0 0 NA 254137 TCGA-AB-2986 AML24 13 105729142 105729142 C T SNP - - - - - - - - - - - - - - - tier3 434 15 3.32 470 385 44.98 0 0 NA 254137 TCGA-AB-2986 AML24 14 20095006 20095006 C T SNP RNASE9 NM_001001673.3 human genbank 54_36p -1 provisional silent c.63 p.L21 0 NULL superfamily_RNase A-like - no_errors tier1 572 33 5.45 458 370 44.58 NA 254137 TCGA-AB-2986 AML24 14 21934994 21934994 T C SNP ENSG00000211822 ENST00000390470 human ensembl 54_36p 1 known 5_prime_flanking_region c.-42385 NULL 0 - - - no_coding_region tier3 1111 69 5.85 545 498 47.66 0 0 0 254137 TCGA-AB-2986 AML24 14 22910162 22910162 G A SNP EFS NM_005864.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-6088 NULL 0 - - - no_errors tier3 519 27 4.94 247 202 44.89 0 0 NA 254137 TCGA-AB-2986 AML24 14 24113801 24113801 G T SNP CTSG NM_001911.2 human genbank 54_36p -1 reviewed missense c.259 p.Q87K 0.994 "HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys" "HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER" - no_errors tier1 1179 34 2.8 913 778 45.98 133 135 50.19 254137 TCGA-AB-2986 AML24 14 29990492 29990492 A G SNP - - - - - - - - - - - - - - - tier3 938 64 6.39 836 748 47.19 0 0 NA 254137 TCGA-AB-2986 AML24 14 56217080 56217080 C T SNP C14orf101 NM_017799.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*33112 NULL 0 - - - no_errors tier3 1940 123 5.95 1271 996 43.9 0 0 NA 254137 TCGA-AB-2986 AML24 14 66038189 66038189 A G SNP GPHN NM_020806.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6810 NULL 0.001 - - - no_errors tier3 596 39 6.13 379 246 39.23 0 0 NA 254137 TCGA-AB-2986 AML24 14 80483400 80483400 G A SNP TSHR NM_000369.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8378 NULL 0 - - - no_errors tier3 719 31 4.13 486 433 47.07 0 0 NA 254137 TCGA-AB-2986 AML24 14 83286553 83286553 G A SNP ENSG00000210408 ENST00000387673 human ensembl 54_36p 1 novel rna NULL NULL 0.971 - - - pseudogene tier1 658 41 5.87 519 408 44.01 NA 254137 TCGA-AB-2986 AML24 14 85159164 85159164 A T SNP FLRT2 NM_013231.4 human genbank 54_36p 1 reviewed missense c.1553 p.Y518F 0.501 NULL "HMMPfam_LRRNT,HMMSmart_LRRNT,HMMPfam_LRRCT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,superfamily_SSF52058" - no_errors tier1 654 40 5.75 464 360 43.64 NA 254137 TCGA-AB-2986 AML24 14 105816928 105816928 C T SNP IGHV3-25 ENST00000401890 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-105816928 NULL 0 - - - no_coding_region:pseudogene tier3 421 12 2.76 311 134 30.11 0 0 0 254137 TCGA-AB-2986 AML24 15 33920563 33920563 G C SNP - - - - - - - - - - - - - - - tier3 1434 64 4.27 777 530 40.55 0 0 NA 254137 TCGA-AB-2986 AML24 15 38422912 38422912 C T SNP DISP2 NM_033510.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-14903 NULL 0 - - - no_errors tier3 239 15 5.88 155 103 39.77 0 0 NA 254137 TCGA-AB-2986 AML24 15 55091781 55091781 G A SNP TCF12 NM_207036.3 human genbank 54_36p 1 reviewed intronic c.149-51459 e3-51459 0.084 - - - no_errors tier3 90 0 0 303 210 40.94 0 0 0 254137 TCGA-AB-2986 AML24 15 84292430 84292430 C A SNP - - - - - - - - - - - - - - - tier3 806 73 4.32 785 737 45.66 0 0 NA 254137 TCGA-AB-2986 AML24 15 84952458 84952458 G A SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.2919+51938 e20+51938 0.008 - - - no_errors tier3 788 30 3.66 473 297 38.52 0 0 NA 254137 TCGA-AB-2986 AML24 15 94951296 94951296 C T SNP - - - - - - - - - - - - - - - tier3 2612 146 5.29 1923 1801 48.31 0 0 NA 254137 TCGA-AB-2986 AML24 15 99686250 99686250 T A SNP PCSK6 ENST00000348070 human ensembl 54_36p -1 known intronic c.2075-2043 e17-2043 0 - - - no_errors tier3 846 35 3.97 253 182 41.74 0 0 NA 254137 TCGA-AB-2986 AML24 16 9828250 9828250 C T SNP GRIN2A NM_000833.3 human genbank 54_36p -1 reviewed intronic c.2007+2531 e8+2531 0 - - - no_errors tier3 1196 68 5.38 794 800 50.13 0 0 NA 254137 TCGA-AB-2986 AML24 16 50643274 50643274 C - DEL LOC388276 XR_041361.1 human genbank 54_36p -1 model rna NULL NULL 0.001 - - - no_errors tier1 NA NA NA NA NA NA NA 254137 TCGA-AB-2986 AML24 16 51192676 51192676 G T SNP LOC643714 XM_931757.1 human genbank 54_36p -1 model intronic c.1+5241 e0+5241 0.053 - - - no_errors tier3 1415 49 3.34 807 648 44.41 0 0 NA 254137 TCGA-AB-2986 AML24 16 57151067 57151067 A - DEL CNOT1 NM_016284.3 human genbank 54_36p -1 validated intronic c.2130+550 e16+550 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 254137 TCGA-AB-2986 AML24 16 63166808 63166808 G A SNP - - - - - - - - - - - - - - - tier3 824 45 5.17 754 595 44.01 0 0 NA 254137 TCGA-AB-2986 AML24 16 65414670 65414670 C T SNP NAE1 NM_003905.1 human genbank 54_36p -1 reviewed missense c.362 p.C121Y 1 "HMMPfam_ThiF,superfamily_Activating enzymes of the ubiquitin-like proteins" "HMMPfam_ThiF,superfamily_Activating enzymes of the ubiquitin-like proteins" - no_errors tier1 158 10 5.95 257 152 37.16 29 19 39.58 254137 TCGA-AB-2986 AML24 16 70539118 70539118 A G SNP PKD1L3 ENST00000335106 human ensembl 54_36p -1 known intronic c.3619-127 e22-127 0 - - - no_errors tier3 82 10 10.87 77 37 32.46 0 0 NA 254137 TCGA-AB-2986 AML24 17 49328388 49328388 C T SNP - - - - - - - - - - - - - - - tier3 817 39 4.55 1046 668 38.91 0 0 NA 254137 TCGA-AB-2986 AML24 17 49643742 49643742 C G SNP - - - - - - - - - - - - - - - tier3 1228 52 4.05 665 558 45.55 0 0 NA 254137 TCGA-AB-2986 AML24 17 52010868 52010868 G A SNP NOG NM_005450.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15716 NULL 0.998 - - - no_errors tier3 873 45 4.89 442 332 42.78 0 0 NA 254137 TCGA-AB-2986 AML24 17 58403567 58403567 T - DEL TANC2 NM_025185.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37086 NULL 0.159 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 254137 TCGA-AB-2986 AML24 17 76587088 76587088 C A SNP CHMP6 NM_024591.4 human genbank 54_36p 1 validated intronic c.550+273 e7+273 0 - - - no_errors tier3 449 31 6.46 230 194 45.75 0 5 100 254137 TCGA-AB-2986 AML24 18 1479270 1479270 G A SNP LOC100130320 XR_038508.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-5561 NULL 0.001 - - - pseudogene tier3 704 32 4.35 730 567 43.58 0 0 NA 254137 TCGA-AB-2986 AML24 18 67659249 67659249 T C SNP - - - - - - - - - - - - - - - tier3 829 29 3.38 800 690 46.22 0 0 NA 254137 TCGA-AB-2986 AML24 18 70260425 70260425 G A SNP C18orf51 NM_001044369.2 human genbank 54_36p -1 validated intronic c.1-94 e1-94 0 - - - no_errors tier3 431 12 2.7 243 192 44.14 0 0 NA 254137 TCGA-AB-2986 AML24 19 47192889 47192889 G A SNP ATP1A3 NM_152296.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2821 NULL 0 - - - no_errors tier3 722 51 6.6 287 244 45.86 0 0 NA 254137 TCGA-AB-2986 AML24 20 7988596 7988596 G T SNP TMX4 NM_021156.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-40336 NULL 0 - - - no_errors tier3 825 33 3.84 812 569 41.2 0 0 NA 254137 TCGA-AB-2986 AML24 20 12495613 12495613 G T SNP - - - - - - - - - - - - - - - tier3 1352 63 4.45 1147 900 43.97 0 0 NA 254137 TCGA-AB-2986 AML24 20 49292765 49292765 C T SNP - - - - - - - - - - - - - - - tier3 1349 65 4.59 716 476 39.87 0 0 NA 254137 TCGA-AB-2986 AML24 20 55222905 55222905 G A SNP BMP7 NM_001719.2 human genbank 54_36p -1 reviewed intronic c.612-11819 e3-11819 0.043 - - - no_errors tier3 853 66 7.18 537 417 43.66 0 0 NA 254137 TCGA-AB-2986 AML24 20 59671735 59671735 G A SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.170-80279 e3-80279 0.001 - - - no_errors tier3 166 5 2.92 54 51 48.57 0 0 NA 254137 TCGA-AB-2986 AML24 21 40051931 40051931 C T SNP IGSF5 NM_001080444.1 human genbank 54_36p 1 provisional intronic c.101-7401 e3-7401 0 - - - no_errors tier3 1221 71 5.49 584 448 43.33 0 0 NA 254137 TCGA-AB-2986 AML24 21 46192756 46192756 G A SNP COL6A1 NM_001848.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33437 NULL 0.002 - - - no_errors tier3 356 12 3.26 297 222 42.69 0 0 NA 702808 TCGA-AB-2987 AML37 X 3502419 3502419 C T SNP ENSG00000212214 ENST00000390912 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42127 NULL 0 - - - no_errors tier3 1057 74 6.54 847 395 31.7 1 0 0 702808 TCGA-AB-2987 AML37 X 11306121 11306121 G A SNP ARHGAP6 NM_013427.2 human genbank 54_36p -1 reviewed intronic c.589-123373 e2-123373 0.002 - - - no_errors tier3 1786 126 6.58 1047 506 32.56 0 0 NA 702808 TCGA-AB-2987 AML37 X 19078171 19078171 A G SNP GPR64 NM_001079858.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-81298 NULL 0.003 - - - no_errors tier3 701 51 6.75 781 327 29.49 0 0 NA 702808 TCGA-AB-2987 AML37 X 32502743 32502743 C T SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.1603-859 e14-859 0 - - - no_errors tier3 92 5 5.15 199 86 30.07 0 0 NA 702808 TCGA-AB-2987 AML37 X 34388964 34388964 C T SNP - - - - - - - - - - - - - - - tier3 1410 100 6.59 1241 550 30.69 0 0 NA 702808 TCGA-AB-2987 AML37 X 46837697 46837697 A T SNP RNU12 NR_000041.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38960 NULL 0.004 - - - no_errors tier3 1113 71 6 882 300 25.32 0 0 NA 702808 TCGA-AB-2987 AML37 X 63694736 63694736 G A SNP - - - - - - - - - - - - - - - tier3 1202 83 6.45 985 480 32.74 0 0 NA 702808 TCGA-AB-2987 AML37 X 70298097 70298097 C G SNP NLGN3 NM_018977.2 human genbank 54_36p 1 validated intronic c.668-2621 e4-2621 0.023 - - - no_errors tier3 600 38 5.92 288 162 35.92 1 2 66.67 702808 TCGA-AB-2987 AML37 X 75563707 75563707 A G SNP MAGEE1 NM_020932.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-1021 NULL 0.14 - - - no_errors tier3 865 60 6.48 949 450 32.14 0 0 NA 702808 TCGA-AB-2987 AML37 X 86362119 86362119 G T SNP - - - - - - - - - - - - - - - tier3 734 42 5.4 749 346 31.6 0 0 NA 702808 TCGA-AB-2987 AML37 X 86480728 86480728 G A SNP - - - - - - - - - - - - - - - tier3 1541 82 5.05 1169 507 30.23 0 0 NA 702808 TCGA-AB-2987 AML37 X 98822995 98822995 C T SNP ENSG00000215070 ENST00000399535 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*38014 NULL 0.006 - - - no_coding_region:pseudogene tier3 1583 98 5.83 1269 508 28.57 0 0 NA 702808 TCGA-AB-2987 AML37 X 116809146 116809146 A C SNP - - - - - - - - - - - - - - - tier3 1191 109 8.38 985 464 32.02 0 0 NA 702808 TCGA-AB-2987 AML37 X 129870851 129870851 G A SNP ENOX2 NM_182314.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-199905 NULL 0 - - - no_errors tier3 1982 120 5.7 1822 829 31.24 0 0 NA 702808 TCGA-AB-2987 AML37 X 132809399 132809399 G T SNP GPC3 NM_004484.2 human genbank 54_36p -1 reviewed intronic c.338-93530 e3-93530 0.024 - - - no_errors tier3 1635 117 6.67 1315 592 31.03 0 0 0 702808 TCGA-AB-2987 AML37 X 133352324 133352324 T G SNP PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed intronic c.241-2873 e3-2873 0.005 - - - no_errors tier3 324 25 7.14 454 268 37.12 4 0 0 702808 TCGA-AB-2987 AML37 X 135303024 135303024 C G SNP GPR112 NM_153834.3 human genbank 54_36p 1 validated intronic c.8035-336 e15-336 0 - - - no_errors tier3 1315 101 7.13 1021 470 31.5 0 0 NA 702808 TCGA-AB-2987 AML37 X 141596756 141596756 A T SNP - - - - - - - - - - - - - - - tier3 1679 93 5.25 1242 385 23.59 0 0 NA 702808 TCGA-AB-2987 AML37 X 149860372 149860372 C A SNP CD99L2 NM_031462.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42653 NULL 0 - - - no_errors tier3 789 73 8.46 577 276 32.36 0 0 NA 702808 TCGA-AB-2987 AML37 X 150156197 150156197 C T SNP LOC286456 XR_016302.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-9352 NULL 0.025 - - - pseudogene tier3 1492 120 7.43 1290 596 31.58 0 0 NA 702808 TCGA-AB-2987 AML37 X 151546046 151546046 C T SNP GABRQ NM_018558.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11267 NULL 0.016 - - - no_errors tier3 1797 112 5.87 1532 709 31.58 0 0 NA 702808 TCGA-AB-2987 AML37 1 4433646 4433646 G A SNP LOC100134231 XM_001718209.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*5071 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 733 68 8.49 684 305 30.84 0 0 NA 702808 TCGA-AB-2987 AML37 1 5217207 5217207 G A SNP - - - - - - - - - - - - - - - tier3 1659 104 5.89 1132 482 29.79 0 0 NA 702808 TCGA-AB-2987 AML37 1 33919581 33919581 A C SNP CSMD2 NM_052896.3 human genbank 54_36p -1 validated intronic c.3932+11536 e25+11536 0.333 - - - no_errors tier3 303 22 6.77 541 261 32.5 0 0 NA 702808 TCGA-AB-2987 AML37 1 34575058 34575058 C T SNP - - - - - - - - - - - - - - - tier3 632 42 6.22 574 224 28.07 0 0 NA 702808 TCGA-AB-2987 AML37 1 39746864 39746864 C T SNP BMP8A NM_181809.3 human genbank 54_36p 1 validated intronic c.335-2569 e2-2569 0 - - - no_errors tier3 698 45 6.06 380 169 30.67 0 0 NA 702808 TCGA-AB-2987 AML37 1 41835440 41835440 C T SNP HIVEP3 NM_024503.1 human genbank 54_36p -1 validated intronic c.1-11864 e1-11864 0.003 - - - no_errors tier3 1051 71 6.31 946 450 32.19 3 0 0 702808 TCGA-AB-2987 AML37 1 47710069 47710069 G A SNP ENSG00000221346 ENST00000408419 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-30694 NULL 0.003 - - - no_errors tier3 1311 99 7.02 1081 473 30.44 0 0 NA 702808 TCGA-AB-2987 AML37 1 49515250 49515250 A T SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.283-31127 e4-31127 0.001 - - - no_errors tier3 465 26 5.3 413 197 32.3 0 0 NA 702808 TCGA-AB-2987 AML37 1 73843323 73843323 A C SNP - - - - - - - - - - - - - - - tier3 1442 92 5.99 1410 615 30.37 0 0 NA 702808 TCGA-AB-2987 AML37 1 75174117 75174117 C A SNP - - - - - - - - - - - - - - - tier3 1636 88 5.1 1266 546 30.13 0 0 NA 702808 TCGA-AB-2987 AML37 1 95665346 95665346 G A SNP - - - - - - - - - - - - - - - tier3 1341 94 6.55 1486 717 32.53 0 0 NA 702808 TCGA-AB-2987 AML37 1 101878045 101878045 T C SNP - - - - - - - - - - - - - - - tier3 572 47 7.59 858 410 32.33 0 0 NA 702808 TCGA-AB-2987 AML37 1 112338987 112338987 C G SNP KCND3 NM_004980.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12116 NULL 0 - - - no_errors tier3 1499 99 6.19 948 433 31.35 0 0 NA 702808 TCGA-AB-2987 AML37 1 149873566 149873566 C T SNP SNX27 NM_030918.5 human genbank 54_36p 1 reviewed intronic c.312-4422 e2-4422 0.001 - - - no_errors tier3 730 53 6.76 664 316 32.18 15 1 6.25 702808 TCGA-AB-2987 AML37 1 161291359 161291359 C T SNP RGS4 NM_001102445.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13990 NULL 0.003 - - - no_errors tier3 1202 75 5.87 1197 540 31.02 0 0 NA 702808 TCGA-AB-2987 AML37 1 167061942 167061942 A T SNP LOC391132 XR_017287.2 human genbank 54_36p 1 model intronic c.NULL NULL 0.008 - - - pseudogene tier3 1592 107 6.29 1459 701 32.41 0 0 NA 702808 TCGA-AB-2987 AML37 1 181334260 181334260 G A SNP LAMC1 NM_002293.3 human genbank 54_36p 1 reviewed intronic c.419-4826 e2-4826 0.001 - - - no_errors tier3 1948 119 5.75 1311 553 29.67 0 0 NA 702808 TCGA-AB-2987 AML37 1 213577181 213577181 G A SNP ENSG00000217162 ENST00000401549 human ensembl 54_36p 1 known 5_prime_flanking_region c.-39269 NULL 0 - - - no_coding_region:pseudogene tier3 1493 89 5.62 1420 627 30.56 0 0 NA 702808 TCGA-AB-2987 AML37 1 214034411 214034411 C T SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.9959-4164 e50-4164 0.041 - - - no_errors tier3 1156 86 6.91 1049 476 31.11 0 0 NA 702808 TCGA-AB-2987 AML37 1 216653526 216653526 C A SNP TGFB2 NM_003238.1 human genbank 54_36p 1 validated intronic c.510+8229 e2+8229 0 - - - no_errors tier3 1058 72 6.37 852 419 32.97 0 0 0 702808 TCGA-AB-2987 AML37 1 235645384 235645384 C T SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.774-1588 e11-1588 0 - - - no_errors tier3 662 46 6.47 577 225 27.95 0 0 NA 702808 TCGA-AB-2987 AML37 1 240348716 240348716 C A SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.658-4765 e6-4765 0 - - - no_errors tier3 775 61 7.24 594 318 34.75 0 0 NA 702808 TCGA-AB-2987 AML37 1 240906564 240906564 C T SNP - - - - - - - - - - - - - - - tier3 1569 110 6.55 1052 466 30.62 0 0 NA 702808 TCGA-AB-2987 AML37 1 240957582 240957582 T A SNP ENSG00000215800 ENST00000400938 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44964 NULL 0.002 - - - no_coding_region:pseudogene tier3 1015 78 7.13 792 338 29.91 0 0 NA 702808 TCGA-AB-2987 AML37 1 245253418 245253418 T G SNP ZNF695 NM_020394.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-15585 NULL 0.018 - - - no_errors tier3 861 69 7.4 720 346 32.43 2 0 0 702808 TCGA-AB-2987 AML37 2 3818249 3818249 G A SNP LOC728597 XM_001127882.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*21931 NULL 0.001 - - - no_errors tier3 490 39 7.37 657 265 28.71 0 0 NA 702808 TCGA-AB-2987 AML37 2 19582308 19582308 G C SNP - - - - - - - - - - - - - - - tier3 2348 186 7.33 1876 842 30.96 0 0 NA 702808 TCGA-AB-2987 AML37 2 22737706 22737706 G A SNP - - - - - - - - - - - - - - - tier3 370 20 5.13 339 155 31.38 0 0 NA 702808 TCGA-AB-2987 AML37 2 24703668 24703668 A G SNP NCOA1 NM_003743.4 human genbank 54_36p 1 reviewed intronic c.1-16671 e1-16671 0.008 - - - no_errors tier3 755 50 6.21 762 360 32.06 4 0 0 702808 TCGA-AB-2987 AML37 2 25310746 25310746 C T SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2645 p.R882H 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 965 71 6.83 592 301 33.63 16 7 30.43 702808 TCGA-AB-2987 AML37 2 26281642 26281642 T A SNP HADHA NM_000182.4 human genbank 54_36p -1 reviewed intronic c.1086-1073 e12-1073 0.002 - - - no_errors tier3 524 32 5.76 486 173 26.25 0 6 100 702808 TCGA-AB-2987 AML37 2 28160207 28160207 G A SNP BRE NM_004899.3 human genbank 54_36p 1 validated intronic c.570+38037 e5+38037 0 - - - no_errors tier3 1382 104 6.99 1253 585 31.81 3 0 0 702808 TCGA-AB-2987 AML37 2 28472317 28472317 C T SNP FOSL2 NM_005253.3 human genbank 54_36p 1 reviewed intronic c.102+2124 e1+2124 0.763 - - - no_errors tier3 721 53 6.84 493 234 32.19 21 17 44.74 702808 TCGA-AB-2987 AML37 2 30101143 30101143 G A SNP ENSG00000221383 ENST00000408456 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*41351 NULL 0.001 - - - no_errors tier3 713 48 6.3 778 304 28.02 0 0 NA 702808 TCGA-AB-2987 AML37 2 33384155 33384155 C A SNP LTBP1 NM_206943.2 human genbank 54_36p 1 reviewed intronic c.3485-3850 e23-3850 0.001 - - - no_errors tier3 939 71 7.03 616 293 32.16 0 0 0 702808 TCGA-AB-2987 AML37 2 49523429 49523429 T C SNP - - - - - - - - - - - - - - - tier3 655 39 5.61 696 354 33.71 0 0 NA 702808 TCGA-AB-2987 AML37 2 83191361 83191361 A G SNP - - - - - - - - - - - - - - - tier3 1045 75 6.7 1008 448 30.77 0 0 NA 702808 TCGA-AB-2987 AML37 2 115350043 115350043 G A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+433158 e1+433158 0.135 - - - no_errors tier3 792 61 7.14 885 382 30.13 0 0 NA 702808 TCGA-AB-2987 AML37 2 117978241 117978241 C T SNP - - - - - - - - - - - - - - - tier3 998 61 5.76 871 503 36.48 0 0 NA 702808 TCGA-AB-2987 AML37 2 139968708 139968708 G T SNP ENSG00000206901 ENST00000384174 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16756 NULL 0.999 - - - no_errors tier3 1460 98 6.28 1673 743 30.75 0 0 NA 702808 TCGA-AB-2987 AML37 2 153901918 153901918 G A SNP LOC391453 XM_001717379.1 human genbank 54_36p 1 model intronic c.730+24885 e8+24885 0.875 - - - no_errors tier3 1418 87 5.78 1279 505 28.29 0 0 NA 702808 TCGA-AB-2987 AML37 2 154990552 154990552 A G SNP GALNT13 NM_052917.2 human genbank 54_36p 1 validated intronic c.1396-12798 e10-12798 0.001 - - - no_errors tier3 1429 103 6.72 1056 485 31.47 0 0 NA 702808 TCGA-AB-2987 AML37 2 187519025 187519025 G A SNP - - - - - - - - - - - - - - - tier3 824 46 5.29 750 399 34.7 0 0 NA 702808 TCGA-AB-2987 AML37 2 191328942 191328942 G T SNP - - - - - - - - - - - - - - - tier3 1413 104 6.86 1146 526 31.44 0 0 NA 702808 TCGA-AB-2987 AML37 2 193654885 193654885 A G SNP - - - - - - - - - - - - - - - tier3 568 50 8.09 703 298 29.77 0 0 NA 702808 TCGA-AB-2987 AML37 2 199170546 199170546 C T SNP - - - - - - - - - - - - - - - tier3 599 42 6.53 652 289 30.65 0 0 NA 702808 TCGA-AB-2987 AML37 2 211386117 211386117 C T SNP - - - - - - - - - - - - - - - tier3 1026 82 7.39 1149 466 28.84 0 0 NA 702808 TCGA-AB-2987 AML37 2 211917016 211917016 A G SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*39569 NULL 0 - - - no_errors tier3 699 52 6.91 511 269 34.4 0 0 NA 702808 TCGA-AB-2987 AML37 2 220583433 220583433 G A SNP - - - - - - - - - - - - - - - tier3 2071 155 6.96 1446 726 33.41 0 0 NA 702808 TCGA-AB-2987 AML37 2 221131880 221131880 C A SNP - - - - - - - - - - - - - - - tier3 2040 155 7.05 1392 657 32.03 0 0 NA 702808 TCGA-AB-2987 AML37 2 222020376 222020376 C T SNP EPHA4 NM_004438.3 human genbank 54_36p -1 reviewed intronic c.1716-1231 e9-1231 0 - - - no_errors tier3 827 76 8.4 601 312 34.14 1 0 0 702808 TCGA-AB-2987 AML37 2 224571816 224571816 A G SNP SERPINE2 NM_006216.1 human genbank 54_36p -1 validated intronic c.260-513 e2-513 0 - - - no_errors tier3 1494 98 6.16 1249 549 30.5 0 0 NA 702808 TCGA-AB-2987 AML37 3 22829998 22829998 A G SNP - - - - - - - - - - - - - - - tier3 898 74 7.61 1297 557 30.03 0 0 NA 702808 TCGA-AB-2987 AML37 3 28872511 28872511 A G SNP - - - - - - - - - - - - - - - tier3 1005 64 5.99 1126 484 30.06 0 0 NA 702808 TCGA-AB-2987 AML37 3 29061789 29061789 C T SNP ENSG00000215004 ENST00000399418 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-42097 NULL 0 - - - no_coding_region:pseudogene tier3 860 55 6 988 425 29.95 0 0 NA 702808 TCGA-AB-2987 AML37 3 29649680 29649680 A G SNP RBMS3 NM_001003793.1 human genbank 54_36p 1 reviewed intronic c.399+45980 e4+45980 0.001 - - - no_errors tier3 1265 117 8.46 1215 570 31.9 0 0 NA 702808 TCGA-AB-2987 AML37 3 34763375 34763375 G C SNP - - - - - - - - - - - - - - - tier3 1326 93 6.55 1405 645 31.37 0 0 NA 702808 TCGA-AB-2987 AML37 3 34942716 34942716 G C SNP - - - - - - - - - - - - - - - tier3 854 59 6.44 733 337 31.47 0 0 NA 702808 TCGA-AB-2987 AML37 3 40468034 40468034 C T SNP RPL14 NM_001034996.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-5933 NULL 0.064 - - - no_errors tier3 1393 96 6.44 1303 546 29.51 0 0 0 702808 TCGA-AB-2987 AML37 3 71852547 71852547 T G SNP EIF4E3 NM_173359.1 human genbank 54_36p -1 validated intronic c.1+7770 e0+7770 0 - - - no_errors tier3 740 33 4.27 535 217 28.86 11 4 26.67 702808 TCGA-AB-2987 AML37 3 78174394 78174394 A G SNP - - - - - - - - - - - - - - - tier3 180 11 5.76 246 131 34.66 0 0 NA 702808 TCGA-AB-2987 AML37 3 80734955 80734955 C T SNP ENSG00000211100 ENST00000388365 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*24864 NULL 0.001 - - - pseudogene tier3 671 53 7.3 610 253 29.32 0 0 NA 702808 TCGA-AB-2987 AML37 3 81322257 81322257 C A SNP - - - - - - - - - - - - - - - tier3 1217 66 5.14 984 363 26.95 0 0 NA 702808 TCGA-AB-2987 AML37 3 89924664 89924664 A G SNP - - - - - - - - - - - - - - - tier3 743 63 7.82 590 255 30.14 0 0 NA 702808 TCGA-AB-2987 AML37 3 101837459 101837459 A G SNP GPR128 NM_032787.1 human genbank 54_36p 1 provisional intronic c.597+99 e5+99 0 - - - no_errors tier3 603 47 7.23 680 366 34.99 0 0 NA 702808 TCGA-AB-2987 AML37 3 102554194 102554194 T A SNP SENP7 NM_020654.1 human genbank 54_36p -1 validated intronic c.1624-1009 e12-1009 0.171 - - - no_errors tier3 1217 73 5.65 1144 454 28.38 0 0 0 702808 TCGA-AB-2987 AML37 3 103248463 103248463 C T SNP ENSG00000214407 ENST00000398281 human ensembl 54_36p 1 known 3_prime_flanking_region c.*52070 NULL 0.008 - - - no_errors tier3 1122 75 6.26 1001 385 27.78 0 0 NA 702808 TCGA-AB-2987 AML37 3 105417998 105417998 G T SNP - - - - - - - - - - - - - - - tier3 1139 95 7.7 1009 474 31.96 0 0 NA 702808 TCGA-AB-2987 AML37 3 111752035 111752035 G A SNP ENSG00000221206 ENST00000408279 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*1347 NULL 0.002 - - - no_errors tier3 630 30 4.54 630 255 28.81 0 0 NA 702808 TCGA-AB-2987 AML37 3 126546415 126546415 C T SNP ZNF148 NM_021964.2 human genbank 54_36p -1 validated intronic c.1-13643 e1-13643 0.404 - - - no_errors tier3 1272 90 6.59 1041 474 31.27 1 0 0 702808 TCGA-AB-2987 AML37 3 130440620 130440620 G A SNP COPG NM_016128.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-10623 NULL 0 - - - no_errors tier3 633 54 7.86 355 200 35.71 0 4 100 702808 TCGA-AB-2987 AML37 3 132166060 132166060 A G SNP ATP2C1 NM_001001486.1 human genbank 54_36p 1 reviewed intronic c.1025-422 e13-422 0.517 - - - no_errors tier3 922 67 6.76 1016 409 28.68 0 0 0 702808 TCGA-AB-2987 AML37 3 156947360 156947360 C T SNP C3orf33 NM_173657.1 human genbank 54_36p -1 predicted 3_prime_flanking_region c.*16640 NULL 0 - - - no_errors tier3 541 41 7.02 567 267 32.01 0 0 NA 702808 TCGA-AB-2987 AML37 3 159761171 159761171 G A SNP MLF1 NM_022443.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-10613 NULL 0 - - - no_errors tier3 592 46 7.21 405 218 34.99 0 0 NA 702808 TCGA-AB-2987 AML37 3 164294605 164294605 C A SNP - - - - - - - - - - - - - - - tier3 1541 77 4.76 1233 426 25.66 0 0 NA 702808 TCGA-AB-2987 AML37 3 171492586 171492586 C T SNP PRKCI NM_002740.5 human genbank 54_36p 1 reviewed intronic c.1291+163 e13+163 0.006 - - - no_errors tier3 881 60 6.38 766 392 33.82 2 1 33.33 702808 TCGA-AB-2987 AML37 3 186314232 186314232 G C SNP C3orf70 NM_001025266.1 human genbank 54_36p -1 predicted intronic c.197-30187 e2-30187 0.002 - - - no_errors tier3 685 51 6.93 775 349 30.99 0 0 NA 702808 TCGA-AB-2987 AML37 4 6174678 6174678 A G SNP JAKMIP1 NM_001099433.1 human genbank 54_36p -1 validated intronic c.1-9053 e1-9053 0.007 - - - no_errors tier3 618 50 7.49 584 235 28.69 0 0 NA 702808 TCGA-AB-2987 AML37 4 8185191 8185191 C T SNP ABLIM2 NM_032432.1 human genbank 54_36p -1 validated intronic c.11-25927 e2-25927 0.005 - - - no_errors tier3 294 19 6.05 155 80 34.04 0 0 NA 702808 TCGA-AB-2987 AML37 4 9901779 9901779 G T SNP - - - - - - - - - - - - - - - tier3 826 42 4.83 757 302 28.52 0 0 NA 702808 TCGA-AB-2987 AML37 4 13682000 13682000 C T SNP LOC152742 XM_001128848.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-40839 NULL 0.002 - - - no_errors tier3 2421 147 5.72 2191 931 29.75 0 0 NA 702808 TCGA-AB-2987 AML37 4 13940398 13940398 G A SNP - - - - - - - - - - - - - - - tier3 317 26 7.58 317 143 31.09 0 0 NA 702808 TCGA-AB-2987 AML37 4 24198689 24198689 A G SNP DHX15 NM_001358.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3575 NULL 0 - - - no_errors tier3 967 48 4.72 649 235 26.52 0 0 NA 702808 TCGA-AB-2987 AML37 4 27518526 27518526 T C SNP - - - - - - - - - - - - - - - tier3 1284 118 8.42 1275 644 33.51 0 0 NA 702808 TCGA-AB-2987 AML37 4 54851324 54851324 G C SNP PDGFRA NM_006206.4 human genbank 54_36p 1 reviewed missense c.2968 p.G990R 0.999 NULL "HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_SM00220,HMMSmart_SM00408,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_Immunoglobulin" - no_errors tier1 1526 93 5.74 924 426 31.44 NA 702808 TCGA-AB-2987 AML37 4 57937830 57937830 T A SNP - - - - - - - - - - - - - - - tier3 1215 77 5.96 1020 468 31.41 0 0 NA 702808 TCGA-AB-2987 AML37 4 66378162 66378162 T A SNP ENSG00000222765 ENST00000410833 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-22414 NULL 0.015 - - - no_errors tier3 1000 60 5.66 965 412 29.92 0 0 NA 702808 TCGA-AB-2987 AML37 4 73608426 73608426 A G SNP ADAMTS3 NM_014243.1 human genbank 54_36p -1 reviewed intronic c.504+24633 e3+24633 0.001 - - - no_errors tier3 719 42 5.52 582 267 31.45 0 0 NA 702808 TCGA-AB-2987 AML37 4 92860012 92860012 G A SNP - - - - - - - - - - - - - - - tier3 702 34 4.61 835 358 29.98 0 0 NA 702808 TCGA-AB-2987 AML37 4 99348886 99348886 C T SNP ENSG00000200658 ENST00000363788 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*34833 NULL 0.007 - - - no_errors tier3 509 33 6.08 439 185 29.65 0 0 NA 702808 TCGA-AB-2987 AML37 4 118495793 118495793 A G SNP - - - - - - - - - - - - - - - tier3 251 25 9.06 387 249 39.15 0 0 NA 702808 TCGA-AB-2987 AML37 4 122756203 122756203 C T SNP LOC729112 XM_001132973.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*33854 NULL 0.009 - - - no_errors tier3 946 53 5.3 1069 517 32.58 0 0 NA 702808 TCGA-AB-2987 AML37 4 131745753 131745753 G C SNP - - - - - - - - - - - - - - - tier3 763 45 5.57 730 359 32.88 0 0 NA 702808 TCGA-AB-2987 AML37 4 132143378 132143378 C A SNP - - - - - - - - - - - - - - - tier3 401 19 4.51 484 221 31.26 0 0 NA 702808 TCGA-AB-2987 AML37 4 136840180 136840180 T G SNP - - - - - - - - - - - - - - - tier3 480 26 5.14 619 287 31.64 0 0 NA 702808 TCGA-AB-2987 AML37 4 147239913 147239913 A G SNP ENSG00000216055 ENST00000401236 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*22893 NULL 0.003 - - - no_errors tier3 827 57 6.45 844 327 27.92 0 0 NA 702808 TCGA-AB-2987 AML37 4 150966626 150966626 C A SNP LOC285423 XR_041269.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10196 NULL 0.011 - - - no_errors tier3 1084 94 7.97 1189 512 30.08 0 0 NA 702808 TCGA-AB-2987 AML37 4 152558852 152558852 C T SNP FAM160A1 ENST00000340515 human ensembl 54_36p 1 known intronic c.1+8785 e0+8785 0.001 - - - no_stop_codon tier3 1104 60 5.15 1013 501 33.09 1 0 0 702808 TCGA-AB-2987 AML37 4 157844949 157844949 C T SNP - - - - - - - - - - - - - - - tier3 830 62 6.95 843 377 30.88 0 0 NA 702808 TCGA-AB-2987 AML37 4 165339394 165339394 A G SNP ANP32C NM_012403.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-1081 NULL 0 - - - no_errors tier3 834 63 7.02 575 267 31.6 0 0 NA 702808 TCGA-AB-2987 AML37 4 169197406 169197406 T A SNP - - - - - - - - - - - - - - - tier3 629 32 4.83 606 237 28.01 0 0 NA 702808 TCGA-AB-2987 AML37 4 176721504 176721504 G T SNP - - - - - - - - - - - - - - - tier3 837 49 5.53 755 313 29.28 0 0 NA 702808 TCGA-AB-2987 AML37 4 189764027 189764027 G A SNP - - - - - - - - - - - - - - - tier3 671 46 6.42 709 295 29.38 0 0 NA 702808 TCGA-AB-2987 AML37 5 1997878 1997878 G A SNP - - - - - - - - - - - - - - - tier3 630 44 6.52 542 216 28.42 0 0 NA 702808 TCGA-AB-2987 AML37 5 9928882 9928882 G A SNP - - - - - - - - - - - - - - - tier3 1768 116 6.15 1288 599 31.73 0 0 NA 702808 TCGA-AB-2987 AML37 5 31108594 31108594 G A SNP LOC100128783 XM_001717030.1 human genbank 54_36p 1 model intronic c.76+7130 e1+7130 0.001 - - - no_errors tier3 1380 79 5.41 968 417 30.09 0 0 NA 702808 TCGA-AB-2987 AML37 5 39998224 39998224 T C SNP - - - - - - - - - - - - - - - tier3 1351 66 4.66 1202 483 28.65 0 0 NA 702808 TCGA-AB-2987 AML37 5 42002381 42002381 C A SNP ENSG00000199487 ENST00000362617 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2553 NULL 0.001 - - - no_errors tier3 1148 88 7.1 959 375 28.05 0 0 NA 702808 TCGA-AB-2987 AML37 5 52972719 52972719 C T SNP NDUFS4 NM_002495.2 human genbank 54_36p 1 reviewed intronic c.178-5101 e3-5101 0 - - - no_errors tier3 906 55 5.72 856 342 28.45 0 0 0 702808 TCGA-AB-2987 AML37 5 65724633 65724633 C A SNP ENSG00000205619 ENST00000380914 human ensembl 54_36p 1 known intronic c.335-73334 e4-73334 0.004 - - - no_errors tier3 1334 100 6.97 1195 447 27.21 0 0 NA 702808 TCGA-AB-2987 AML37 5 66717118 66717118 C G SNP ENSG00000210812 ENST00000388077 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43345 NULL 0.005 - - - pseudogene tier3 560 42 6.93 557 220 28.13 0 0 NA 702808 TCGA-AB-2987 AML37 5 68730037 68730037 A C SNP RAD17 NM_133339.1 human genbank 54_36p 1 reviewed intronic c.1606-1595 e14-1595 0.001 - - - no_errors tier3 825 48 5.5 634 256 28.76 0 0 0 702808 TCGA-AB-2987 AML37 5 73966654 73966654 C G SNP ENC1 NM_003633.2 human genbank 54_36p -1 validated missense c.1413 p.R471S 1 "HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain" "HMMSmart_SM00225,HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain,superfamily_POZ domain,HMMPfam_BACK,HMMPfam_BTB" - no_errors tier1 945 65 6.43 506 247 32.76 4 5 55.56 702808 TCGA-AB-2987 AML37 5 99538767 99538767 G A SNP ENSG00000207077 ENST00000384349 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21385 NULL 0.001 - - - no_errors tier3 1381 86 5.86 1344 602 30.94 0 0 NA 702808 TCGA-AB-2987 AML37 5 101112835 101112835 C T SNP - - - - - - - - - - - - - - - tier3 890 63 6.58 792 359 31.16 0 0 NA 702808 TCGA-AB-2987 AML37 5 102757902 102757902 C T SNP - - - - - - - - - - - - - - - tier3 2089 175 7.72 1582 770 32.7 0 0 NA 702808 TCGA-AB-2987 AML37 5 103977525 103977525 C T SNP - - - - - - - - - - - - - - - tier3 1398 84 5.66 1099 518 31.96 0 0 NA 702808 TCGA-AB-2987 AML37 5 105940675 105940675 C A SNP ENSG00000209177 ENST00000386442 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23557 NULL 0.001 - - - pseudogene tier3 1179 74 5.91 1150 532 31.61 0 0 NA 702808 TCGA-AB-2987 AML37 5 106874271 106874271 A G SNP EFNA5 NM_001962.2 human genbank 54_36p -1 reviewed intronic c.126-83162 e2-83162 0.004 - - - no_errors tier3 858 55 6.02 654 302 31.52 3 0 0 702808 TCGA-AB-2987 AML37 5 114627562 114627562 T C SNP PGGT1B NM_005023.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-1115 NULL 0.001 - - - no_errors tier3 1203 80 6.22 1228 572 31.78 0 1 100 702808 TCGA-AB-2987 AML37 5 121835412 121835412 C T SNP ENSG00000197462 ENST00000354541 human ensembl 54_36p -1 known intronic c.162+6768 e1+6768 0 - - - no_errors tier3 870 43 4.7 504 230 31.29 0 0 NA 702808 TCGA-AB-2987 AML37 5 132754595 132754595 T C SNP FSTL4 NM_015082.1 human genbank 54_36p -1 validated intronic c.409+9734 e3+9734 0 - - - no_errors tier3 838 43 4.88 596 243 28.86 0 0 NA 702808 TCGA-AB-2987 AML37 5 135074945 135074945 A G SNP - - - - - - - - - - - - - - - tier3 1174 82 6.52 822 371 31.07 0 0 NA 702808 TCGA-AB-2987 AML37 5 149529461 149529461 G A SNP CDX1 NM_001804.2 human genbank 54_36p 1 reviewed intronic c.445+2384 e1+2384 0.01 - - - no_errors tier3 642 63 8.92 433 208 32.4 0 0 NA 702808 TCGA-AB-2987 AML37 5 149539536 149539536 A G SNP CDX1 NM_001804.2 human genbank 54_36p 1 reviewed intronic c.446-2988 e2-2988 0.002 - - - no_errors tier3 501 37 6.83 310 150 32.47 0 0 NA 702808 TCGA-AB-2987 AML37 5 155273878 155273878 G A SNP - - - - - - - - - - - - - - - tier3 1400 102 6.79 1108 545 32.95 0 0 NA 702808 TCGA-AB-2987 AML37 5 162566729 162566729 T C SNP - - - - - - - - - - - - - - - tier3 1588 130 7.56 1516 625 29.16 0 0 NA 702808 TCGA-AB-2987 AML37 5 166301745 166301745 T A SNP - - - - - - - - - - - - - - - tier3 152 5 3.18 319 149 31.84 0 0 NA 702808 TCGA-AB-2987 AML37 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 702808 TCGA-AB-2987 AML37 5 178767822 178767822 C T SNP - - - - - - - - - - - - - - - tier3 682 30 4.21 568 214 27.33 0 0 NA 702808 TCGA-AB-2987 AML37 6 19403763 19403763 C A SNP - - - - - - - - - - - - - - - tier3 1544 125 7.48 1326 644 32.67 0 0 NA 702808 TCGA-AB-2987 AML37 6 24297852 24297852 C A SNP DCDC2 NM_016356.3 human genbank 54_36p -1 reviewed intronic c.1024-11013 e9-11013 0 - - - no_errors tier3 811 63 7.2 791 326 29.16 0 0 NA 702808 TCGA-AB-2987 AML37 6 37814866 37814866 G A SNP MDGA1 NM_153487.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42301 NULL 0 - - - no_errors tier3 2432 154 5.95 1379 667 32.57 0 0 NA 702808 TCGA-AB-2987 AML37 6 41527426 41527426 G T SNP - - - - - - - - - - - - - - - tier3 1146 97 7.8 504 249 32.98 0 0 NA 702808 TCGA-AB-2987 AML37 6 54572513 54572513 C T SNP ENSG00000220773 ENST00000406712 human ensembl 54_36p 1 known 5_prime_flanking_region c.-24849 NULL 0.012 - - - no_coding_region:pseudogene tier3 1234 77 5.86 1027 427 29.29 0 0 NA 702808 TCGA-AB-2987 AML37 6 57794751 57794751 A T SNP ENSG00000214566 ENST00000398589 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*395 NULL 0.533 - - - no_coding_region:pseudogene tier3 1134 80 6.59 874 392 30.91 0 0 NA 702808 TCGA-AB-2987 AML37 6 81672558 81672558 A G SNP - - - - - - - - - - - - - - - tier3 1776 120 6.33 1545 673 30.34 0 0 NA 702808 TCGA-AB-2987 AML37 6 92617397 92617397 T C SNP ENSG00000219867 ENST00000406314 human ensembl 54_36p -1 known 5_prime_flanking_region c.-34530 NULL 0.019 - - - no_coding_region:pseudogene tier3 1099 83 7.02 1015 496 32.8 0 0 NA 702808 TCGA-AB-2987 AML37 6 92932369 92932369 A T SNP ENSG00000200492 ENST00000363622 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46296 NULL 0.019 - - - no_errors tier3 963 37 3.7 854 365 29.94 0 0 NA 702808 TCGA-AB-2987 AML37 6 102137752 102137752 T C SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.116-38765 e2-38765 0 - - - no_errors tier3 860 49 5.39 587 304 34.04 0 0 NA 702808 TCGA-AB-2987 AML37 6 112994719 112994719 A T SNP - - - - - - - - - - - - - - - tier3 101 12 10.53 267 133 33.25 0 0 NA 702808 TCGA-AB-2987 AML37 6 113488434 113488434 G T SNP ENSG00000218490 ENST00000407590 human ensembl 54_36p 1 known 3_prime_flanking_region c.*49124 NULL 0 - - - no_coding_region:pseudogene tier3 621 33 5.04 582 238 28.99 0 0 NA 702808 TCGA-AB-2987 AML37 6 114722903 114722903 T - DEL ENSG00000221599 ENST00000408672 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-17568 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 702808 TCGA-AB-2987 AML37 6 115746985 115746985 T G SNP ENSG00000219619 ENST00000404881 human ensembl 54_36p -1 known 3_prime_flanking_region c.*39370 NULL 0 - - - no_coding_region:pseudogene tier3 954 84 8.08 977 450 31.42 0 0 NA 702808 TCGA-AB-2987 AML37 6 118067597 118067597 C G SNP ENSG00000218233 ENST00000404786 human ensembl 54_36p 1 known intronic c.NULL NULL 0.01 - - - no_coding_region:pseudogene tier3 1168 86 6.83 901 399 30.53 0 0 NA 702808 TCGA-AB-2987 AML37 6 122541758 122541758 G A SNP ENSG00000199932 ENST00000363062 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32735 NULL 0.17 - - - no_errors tier3 389 30 7.14 449 170 27.46 0 0 NA 702808 TCGA-AB-2987 AML37 6 133627045 133627045 G T SNP EYA4 NM_004100.4 human genbank 54_36p 1 reviewed intronic c.1-10502 e1-10502 0 - - - no_errors tier3 588 58 8.98 517 267 34.01 0 0 NA 702808 TCGA-AB-2987 AML37 6 142774716 142774716 G A SNP GPR126 NM_198569.2 human genbank 54_36p 1 validated intronic c.2541+475 e18+475 0.001 - - - no_errors tier3 1987 151 7.06 1958 905 31.6 0 0 NA 702808 TCGA-AB-2987 AML37 6 145848165 145848165 A G SNP ENSG00000201119 ENST00000364249 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-21937 NULL 0.064 - - - no_errors tier3 1204 70 5.49 1127 604 34.89 0 0 NA 702808 TCGA-AB-2987 AML37 6 152765472 152765472 C T SNP SYNE1 NM_182961.2 human genbank 54_36p -1 reviewed intronic c.6826-1303 e45-1303 0 - - - no_errors tier3 1170 74 5.93 898 382 29.82 0 0 0 702808 TCGA-AB-2987 AML37 6 156044921 156044921 A G SNP - - - - - - - - - - - - - - - tier3 1307 109 7.68 1131 544 32.36 0 0 NA 702808 TCGA-AB-2987 AML37 6 162933556 162933556 C T SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.7+135128 e1+135128 0 - - - no_errors tier3 634 38 5.64 513 238 31.61 0 0 NA 702808 TCGA-AB-2987 AML37 6 163051854 163051854 T A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.7+16830 e1+16830 0 - - - no_errors tier3 1124 74 6.17 960 467 32.66 0 0 NA 702808 TCGA-AB-2987 AML37 6 168645340 168645340 G A SNP SMOC2 NM_022138.1 human genbank 54_36p 1 provisional intronic c.85-8104 e2-8104 0.001 - - - no_errors tier3 734 53 6.73 612 238 27.97 0 0 0 702808 TCGA-AB-2987 AML37 7 9296950 9296950 G A SNP - - - - - - - - - - - - - - - tier3 1385 89 6.04 1103 542 32.95 0 0 NA 702808 TCGA-AB-2987 AML37 7 20963978 20963978 C A SNP LOC100134750 XM_001724010.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*45093 NULL 0.004 - - - no_start_codon:pseudogene:no_stop_codon tier3 967 84 7.98 1171 575 32.91 0 0 NA 702808 TCGA-AB-2987 AML37 7 22075749 22075749 C T SNP RAPGEF5 NM_012294.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*52800 NULL 0 - - - no_errors tier3 2362 139 5.55 1973 934 32.12 0 0 NA 702808 TCGA-AB-2987 AML37 7 28501271 28501272 - G INS CREB5 NM_182898.1 human genbank 54_36p 1 reviewed intronic c.169+129_169+128 e3+129 0.075:0.169 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 702808 TCGA-AB-2987 AML37 7 31700127 31700127 T C SNP C7orf16 NM_006658.1 human genbank 54_36p 1 validated intronic c.82+1465 e1+1465 0.047 - - - no_errors tier3 1116 107 8.73 1012 433 29.97 6 0 0 702808 TCGA-AB-2987 AML37 7 35345893 35345893 C A SNP - - - - - - - - - - - - - - - tier3 964 62 6.04 765 371 32.63 0 0 NA 702808 TCGA-AB-2987 AML37 7 49883101 49883101 G C SNP VWC2 NM_198570.2 human genbank 54_36p 1 provisional intronic c.827-39075 e3-39075 0.009 - - - no_errors tier3 85 0 0 263 89 25.21 0 0 NA 702808 TCGA-AB-2987 AML37 7 67128826 67128826 A G SNP - - - - - - - - - - - - - - - tier3 2093 145 6.48 1540 740 32.44 0 0 NA 702808 TCGA-AB-2987 AML37 7 68084277 68084277 C T SNP - - - - - - - - - - - - - - - tier3 1059 66 5.84 1131 422 27.1 0 0 NA 702808 TCGA-AB-2987 AML37 7 68906272 68906272 C T SNP AUTS2 NM_015570.1 human genbank 54_36p 1 validated intronic c.310-95936 e2-95936 0 - - - no_errors tier3 1307 63 4.58 1041 470 31 0 0 NA 702808 TCGA-AB-2987 AML37 7 112401260 112401260 C T SNP C7orf60 NM_152556.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-34219 NULL 0.013 - - - no_errors tier3 1349 83 5.78 1070 503 31.94 0 0 NA 702808 TCGA-AB-2987 AML37 7 113989016 113989016 C T SNP FOXP2 NM_148898.2 human genbank 54_36p 1 reviewed intronic c.259-9082 e3-9082 0.001 - - - no_errors tier3 1070 56 4.94 923 352 27.54 0 0 NA 702808 TCGA-AB-2987 AML37 7 114010861 114010861 C T SNP FOXP2 NM_148898.2 human genbank 54_36p 1 reviewed intronic c.333+12689 e3+12689 0 - - - no_errors tier3 1693 103 5.72 1346 577 29.96 0 0 NA 702808 TCGA-AB-2987 AML37 7 117409433 117409434 TG - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 702808 TCGA-AB-2987 AML37 7 117713525 117713525 A T SNP ANKRD7 NM_001077708.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*46274 NULL 0.003 - - - no_errors tier3 1326 98 6.87 1109 444 28.53 0 0 NA 702808 TCGA-AB-2987 AML37 7 119632486 119632486 G T SNP - - - - - - - - - - - - - - - tier3 996 58 5.5 906 429 32.11 0 0 NA 702808 TCGA-AB-2987 AML37 7 131206312 131206312 G A SNP - - - - - - - - - - - - - - - tier3 1505 103 6.4 1263 640 33.56 0 0 NA 702808 TCGA-AB-2987 AML37 7 138277705 138277705 C T SNP KIAA1549 NM_020910.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22944 NULL 0.001 - - - no_errors tier3 1581 136 7.89 1394 695 33.14 0 0 0 702808 TCGA-AB-2987 AML37 7 140448662 140448662 C T SNP LOC100129514 XM_001716072.1 human genbank 54_36p 1 model intronic c.382+27701 e1+27701 0.001 - - - no_errors tier3 997 47 4.5 810 367 31.13 0 0 NA 702808 TCGA-AB-2987 AML37 7 144276560 144276560 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 702808 TCGA-AB-2987 AML37 7 144904532 144904532 C T SNP - - - - - - - - - - - - - - - tier3 1191 68 5.4 939 426 31.14 0 0 NA 702808 TCGA-AB-2987 AML37 7 156474488 156474488 G A SNP LOC645249 XM_928291.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21481 NULL 0.001 - - - no_errors tier3 803 53 6.16 443 244 35.47 0 0 NA 702808 TCGA-AB-2987 AML37 8 10427525 10427525 A G SNP UNQ9391 NM_198464.2 human genbank 54_36p 1 validated intronic c.599-301 e4-301 0.001 - - - no_errors tier3 1030 62 5.68 813 375 31.54 0 0 NA 702808 TCGA-AB-2987 AML37 8 15487084 15487084 G A SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed intronic c.139-37876 e2-37876 0.001 - - - no_errors tier3 1018 59 5.48 936 379 28.8 0 0 NA 702808 TCGA-AB-2987 AML37 8 18190304 18190304 A G SNP ENSG00000210291 ENST00000387556 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*25752 NULL 0 - - - pseudogene tier3 1578 94 5.62 1188 566 32.25 0 0 NA 702808 TCGA-AB-2987 AML37 8 28111906 28111906 C T SNP ELP3 NM_018091.5 human genbank 54_36p 1 validated 3_prime_flanking_region c.*8745 NULL 0.004 - - - no_errors tier3 80 2 2.44 205 84 29.07 0 0 NA 702808 TCGA-AB-2987 AML37 8 31715139 31715139 C T SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.745+97352 e1+97352 0.209 - - - overly_large_intron tier3 901 69 7.1 748 330 30.58 0 0 NA 702808 TCGA-AB-2987 AML37 8 34602924 34602924 T G SNP - - - - - - - - - - - - - - - tier3 2397 159 6.22 1890 871 31.54 0 0 NA 702808 TCGA-AB-2987 AML37 8 40072543 40072543 A G SNP - - - - - - - - - - - - - - - tier3 1019 51 4.76 1031 534 34.03 0 0 NA 702808 TCGA-AB-2987 AML37 8 42657500 42657500 C T SNP CHRNB3 NM_000749.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14347 NULL 0.002 - - - no_errors tier3 855 71 7.66 762 310 28.92 0 0 NA 702808 TCGA-AB-2987 AML37 8 52255685 52255685 A G SNP - - - - - - - - - - - - - - - tier3 859 51 5.6 765 400 34.31 0 0 NA 702808 TCGA-AB-2987 AML37 8 52865749 52865749 G A SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.164+18545 e1+18545 0.002 - - - no_errors tier3 522 41 7.24 404 235 36.72 0 0 NA 702808 TCGA-AB-2987 AML37 8 76832795 76832795 T C SNP ENSG00000221029 ENST00000408102 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*28360 NULL 0.001 - - - no_errors tier3 783 72 8.42 689 300 30.3 0 0 NA 702808 TCGA-AB-2987 AML37 8 77367532 77367532 T A SNP ENSG00000222231 ENST00000410299 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27010 NULL 0.029 - - - no_errors tier3 1070 65 5.73 1131 439 27.96 0 0 NA 702808 TCGA-AB-2987 AML37 8 84732453 84732453 G A SNP - - - - - - - - - - - - - - - tier3 378 12 3.08 368 155 29.58 0 0 NA 702808 TCGA-AB-2987 AML37 8 91438048 91438048 G A SNP - - - - - - - - - - - - - - - tier3 1417 85 5.66 1178 434 26.87 0 0 NA 702808 TCGA-AB-2987 AML37 8 92882218 92882218 A T SNP - - - - - - - - - - - - - - - tier3 1441 93 6.05 1327 646 32.73 0 0 NA 702808 TCGA-AB-2987 AML37 8 134472218 134472218 T C SNP ENSG00000213627 ENST00000395327 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-17195 NULL 0.002 - - - no_coding_region:pseudogene tier3 913 69 7.03 727 323 30.73 0 0 NA 702808 TCGA-AB-2987 AML37 8 140848773 140848773 A T SNP TRAPPC9 NM_031466.4 human genbank 54_36p -1 provisional intronic c.3350-35146 e22-35146 0.126 - - - no_errors tier3 666 67 9.12 574 227 28.3 2 1 33.33 702808 TCGA-AB-2987 AML37 9 16447178 16447178 A G SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated intronic c.670-19656 e6-19656 0.016 - - - no_errors tier3 1287 86 6.26 927 444 32.29 0 0 NA 702808 TCGA-AB-2987 AML37 9 19266716 19266716 A G SNP DENND4C NM_017925.4 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-14066 NULL 0.935 - - - no_errors tier3 813 42 4.91 821 358 30.36 3 0 0 702808 TCGA-AB-2987 AML37 9 19645973 19645973 G T SNP SLC24A2 NM_020344.1 human genbank 54_36p -1 provisional intronic c.931-33676 e2-33676 0.001 - - - no_errors tier3 1865 109 5.52 1528 723 32.12 0 0 NA 702808 TCGA-AB-2987 AML37 9 32264021 32264021 G A SNP ENSG00000210615 ENST00000387880 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19535 NULL 0 - - - pseudogene tier3 1039 82 7.31 1144 443 27.91 0 0 NA 702808 TCGA-AB-2987 AML37 9 74870603 74870603 C T SNP ENSG00000220631 ENST00000407176 human ensembl 54_36p 1 known 3_prime_flanking_region c.*9339 NULL 0 - - - no_coding_region:pseudogene tier3 1383 105 7.05 1153 496 30.04 0 0 NA 702808 TCGA-AB-2987 AML37 9 77543528 77543528 A C SNP ENSG00000217149 ENST00000402108 human ensembl 54_36p -1 known 5_prime_flanking_region c.-14220 NULL 0 - - - no_coding_region:pseudogene tier3 1365 85 5.86 1139 544 32.32 0 0 NA 702808 TCGA-AB-2987 AML37 9 88351103 88351103 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 702808 TCGA-AB-2987 AML37 9 101344872 101344872 G T SNP - - - - - - - - - - - - - - - tier3 1369 83 5.72 1139 529 31.68 0 0 NA 702808 TCGA-AB-2987 AML37 9 111809599 111809599 G A SNP PALM2-AKAP2 NM_007203.3 human genbank 54_36p 1 validated intronic c.497-8456 e7-8456 0.385 - - - no_errors tier3 935 66 6.59 837 366 30.37 0 0 NA 702808 TCGA-AB-2987 AML37 10 8840339 8840339 G A SNP LOC100133979 XR_037040.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-45526 NULL 0 - - - pseudogene tier3 1459 95 6.11 1247 570 31.35 0 0 NA 702808 TCGA-AB-2987 AML37 10 49917087 49917087 C T SNP C10orf72 NM_001031746.3 human genbank 54_36p -1 validated intronic c.837+7947 e7+7947 0 - - - no_errors tier3 1132 81 6.65 761 384 33.42 0 0 NA 702808 TCGA-AB-2987 AML37 10 53984677 53984677 G A SNP - - - - - - - - - - - - - - - tier3 1474 108 6.83 1179 493 29.49 0 0 NA 702808 TCGA-AB-2987 AML37 10 57074412 57074412 G A SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known 5_prime_flanking_region c.-980384 NULL 0.01 - - - no_errors tier3 753 37 4.68 632 239 27.38 0 0 NA 702808 TCGA-AB-2987 AML37 10 60803937 60803937 C G SNP FAM13C NM_198215.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11711 NULL 0.003 - - - no_errors tier3 1206 79 6.13 990 449 31.18 0 0 NA 702808 TCGA-AB-2987 AML37 10 63738557 63738557 A G SNP RTKN2 NM_145307.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-40182 NULL 0.009 - - - no_errors tier3 780 54 6.47 766 332 30.21 0 0 NA 702808 TCGA-AB-2987 AML37 10 64733024 64733024 G C SNP JMJD1C NM_032776.2 human genbank 54_36p -1 validated intronic c.334-38494 e3-38494 0.005 - - - no_errors tier3 1121 74 6.18 777 373 32.35 4 0 0 702808 TCGA-AB-2987 AML37 10 66565076 66565076 T C SNP ENSG00000219154 ENST00000401862 human ensembl 54_36p -1 known 3_prime_flanking_region c.*34126 NULL 0.011 - - - no_coding_region:pseudogene tier3 311 48 13.37 537 296 35.53 0 0 NA 702808 TCGA-AB-2987 AML37 10 83891703 83891703 G A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.824-216772 e2-216772 0.001 - - - no_errors tier3 826 52 5.92 818 359 30.48 0 0 NA 702808 TCGA-AB-2987 AML37 10 84802504 84802504 C T SNP ENSG00000200774 ENST00000363904 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*15194 NULL 0 - - - no_errors tier3 882 54 5.77 922 409 30.71 0 0 NA 702808 TCGA-AB-2987 AML37 10 87864469 87864469 G A SNP GRID1 NM_017551.2 human genbank 54_36p -1 reviewed intronic c.726+24087 e4+24087 0 - - - no_errors tier3 1896 154 7.51 1528 720 31.99 0 0 NA 702808 TCGA-AB-2987 AML37 10 94316650 94316650 C T SNP IDE NM_004969.2 human genbank 54_36p -1 validated intronic c.98+7009 e1+7009 0.002 - - - no_errors tier3 1666 132 7.34 1332 614 31.54 2 1 33.33 702808 TCGA-AB-2987 AML37 10 125099407 125099407 G A SNP - - - - - - - - - - - - - - - tier3 683 34 4.74 501 245 32.8 0 0 NA 702808 TCGA-AB-2987 AML37 10 125503972 125503972 C T SNP CPXM2 NM_198148.2 human genbank 54_36p -1 validated intronic c.2017+197 e13+197 0.008 - - - no_errors tier3 842 51 5.7 692 324 31.76 0 0 NA 702808 TCGA-AB-2987 AML37 10 129744414 129744414 T A SNP PTPRE NM_006504.4 human genbank 54_36p 1 reviewed missense c.458 p.L153Q 0.997 "HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 1466 107 6.8 1104 553 33.29 105 114 52.05 702808 TCGA-AB-2987 AML37 10 132691484 132691484 G A SNP - - - - - - - - - - - - - - - tier3 859 56 6.1 605 297 32.75 0 0 NA 702808 TCGA-AB-2987 AML37 10 134253598 134253598 C T SNP INPP5A NM_005539.3 human genbank 54_36p 1 reviewed intronic c.76-17811 e2-17811 0.001 - - - no_errors tier3 1031 85 7.6 768 288 27.2 0 0 0 702808 TCGA-AB-2987 AML37 10 134580837 134580837 G A SNP ENSG00000203774 ENST00000368578 human ensembl 54_36p 1 known 5_prime_flanking_region c.-57248 NULL 0 - - - no_errors tier3 170 9 5 128 65 33.68 0 0 NA 702808 TCGA-AB-2987 AML37 11 21263664 21263664 G A SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1549+56088 e14+56088 0 - - - no_errors tier3 1298 100 7.15 1438 675 31.93 0 0 NA 702808 TCGA-AB-2987 AML37 11 24235667 24235667 A G SNP - - - - - - - - - - - - - - - tier3 494 59 10.61 696 281 28.76 0 0 NA 702808 TCGA-AB-2987 AML37 11 25423582 25423582 T C SNP - - - - - - - - - - - - - - - tier3 494 53 9.69 624 285 31.35 0 0 NA 702808 TCGA-AB-2987 AML37 11 27889422 27889422 G T SNP ENSG00000176668 ENST00000314102 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20266 NULL 0.002 - - - no_coding_region:pseudogene tier3 1375 108 7.28 1297 574 30.65 0 0 NA 702808 TCGA-AB-2987 AML37 11 28616769 28616769 A G SNP - - - - - - - - - - - - - - - tier3 1560 155 9.04 1343 660 32.93 0 0 NA 702808 TCGA-AB-2987 AML37 11 32477457 32477457 C T SNP - - - - - - - - - - - - - - - tier3 813 62 7.07 591 248 29.49 0 0 NA 702808 TCGA-AB-2987 AML37 11 35101417 35101417 C T SNP CD44 NM_000610.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-16010 NULL 0 - - - no_errors tier3 1551 122 7.28 1073 429 28.54 0 0 NA 702808 TCGA-AB-2987 AML37 11 42063322 42063322 C T SNP - - - - - - - - - - - - - - - tier3 1331 89 6.25 941 404 29.97 0 0 NA 702808 TCGA-AB-2987 AML37 11 48514352 48514352 T G SNP ENSG00000213607 ENST00000395232 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-43212 NULL 0.06 - - - no_coding_region:pseudogene tier3 484 31 6.02 685 349 33.75 0 0 NA 702808 TCGA-AB-2987 AML37 11 51387577 51387577 C T SNP OR4C46 NM_001004703.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*14790 NULL 0.001 - - - no_errors tier3 815 62 7.05 814 341 29.4 0 0 NA 702808 TCGA-AB-2987 AML37 11 66261350 66261350 G A SNP SPTBN2 NM_006946.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16063 NULL 0.042 - - - no_errors tier3 1047 71 6.35 684 272 28.42 0 0 NA 702808 TCGA-AB-2987 AML37 11 67939401 67939401 C T SNP LRP5 NM_002335.2 human genbank 54_36p 1 validated intronic c.2828-971 e13-971 0 - - - no_errors tier3 783 58 6.87 570 257 31 0 0 NA 702808 TCGA-AB-2987 AML37 11 69248013 69248013 C T SNP FGF19 NM_005117.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20188 NULL 0.001 - - - no_errors tier3 728 46 5.94 498 229 31.5 0 0 NA 702808 TCGA-AB-2987 AML37 11 80057513 80057513 C A SNP - - - - - - - - - - - - - - - tier3 242 16 6.2 411 188 31.39 0 0 NA 702808 TCGA-AB-2987 AML37 11 81629738 81629738 C T SNP - - - - - - - - - - - - - - - tier3 869 60 6.44 998 439 30.53 0 0 NA 702808 TCGA-AB-2987 AML37 11 86713099 86713099 A G SNP TMEM135 NM_022918.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*3076 NULL 0 - - - no_errors tier3 936 71 7.04 1064 503 32.08 0 1 100 702808 TCGA-AB-2987 AML37 11 105934471 105934471 C T SNP - - - - - - - - - - - - - - - tier3 272 16 5.56 431 181 29.48 0 0 NA 702808 TCGA-AB-2987 AML37 11 115780720 115780720 G A SNP - - - - - - - - - - - - - - - tier3 1560 102 6.13 1070 532 33.17 0 0 NA 702808 TCGA-AB-2987 AML37 11 117101176 117101176 C T SNP DSCAML1 NM_020693.2 human genbank 54_36p -1 provisional intronic c.691+51540 e3+51540 0 - - - no_errors tier3 551 66 10.65 310 220 41.51 0 0 NA 702808 TCGA-AB-2987 AML37 11 127971025 127971025 C T SNP ETS1 ENST00000392668 human ensembl 54_36p -1 known 5_prime_flanking_region c.-22790 NULL 0.002 - - - no_errors tier3 1171 57 4.63 825 402 32.71 0 0 NA 702808 TCGA-AB-2987 AML37 11 132988949 132988949 G A SNP - - - - - - - - - - - - - - - tier3 427 23 5.11 584 272 31.74 0 0 NA 702808 TCGA-AB-2987 AML37 11 133396335 133396335 C T SNP JAM3 NM_032801.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47719 NULL 0.001 - - - no_errors tier3 1251 96 7.12 685 287 29.44 0 0 NA 702808 TCGA-AB-2987 AML37 11 133442968 133442968 T C SNP JAM3 NM_032801.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1086 NULL 0.005 - - - no_errors tier3 798 67 7.75 768 356 31.62 0 0 NA 702808 TCGA-AB-2987 AML37 12 688635 688635 A G SNP WNK1 NM_018979.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44358 NULL 0 - - - no_errors tier3 268 43 13.78 425 256 37.54 0 0 NA 702808 TCGA-AB-2987 AML37 12 797433 797434 - T INS WNK1 NM_018979.2 human genbank 54_36p 1 validated intronic c.932+4192_932+4191 e2+4192 0.032:0.037 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 702808 TCGA-AB-2987 AML37 12 13934995 13934995 G A SNP GRIN2B NM_000834.3 human genbank 54_36p -1 reviewed intronic c.1-24568 e1-24568 0 - - - no_errors tier3 1280 82 6.02 1135 495 30.37 0 0 NA 702808 TCGA-AB-2987 AML37 12 13979480 13979480 T A SNP GRIN2B NM_000834.3 human genbank 54_36p -1 reviewed intronic c.1+44649 e0+44649 0.001 - - - no_errors tier3 1775 118 6.23 1397 692 33.13 0 0 NA 702808 TCGA-AB-2987 AML37 12 17863073 17863073 T A SNP - - - - - - - - - - - - - - - tier3 1050 40 3.67 934 445 32.27 0 0 NA 702808 TCGA-AB-2987 AML37 12 20687538 20687538 C T SNP PDE3A NM_000921.3 human genbank 54_36p 1 validated intronic c.2252-3153 e11-3153 0.001 - - - no_errors tier3 1838 150 7.54 1580 718 31.2 0 0 NA 702808 TCGA-AB-2987 AML37 12 25289548 25289548 C T SNP KRAS NM_033360.3 human genbank 54_36p -1 reviewed missense c.38 p.G13D 1 "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 962 54 5.29 1012 459 31.14 9 10 52.63 702808 TCGA-AB-2987 AML37 12 27966262 27966262 T C SNP PTHLH NM_198965.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*36497 NULL 0 - - - no_errors tier3 1115 75 6.29 938 478 33.73 0 0 NA 702808 TCGA-AB-2987 AML37 12 30906820 30906820 C T SNP ENSG00000203501 ENST00000366316 human ensembl 54_36p 1 known 3_prime_flanking_region c.*41618 NULL 0.001 - - - no_coding_region:pseudogene tier3 1671 116 6.48 1402 710 33.47 0 0 NA 702808 TCGA-AB-2987 AML37 12 66531298 66531298 G A SNP - - - - - - - - - - - - - - - tier3 992 75 7.02 894 422 32.07 0 0 NA 702808 TCGA-AB-2987 AML37 12 78316341 78316341 G C SNP SYT1 NM_005639.1 human genbank 54_36p 1 validated intronic c.928+44811 e6+44811 0 - - - no_errors tier3 1008 63 5.86 772 397 33.82 0 0 NA 702808 TCGA-AB-2987 AML37 12 80792874 80792874 T G SNP - - - - - - - - - - - - - - - tier3 824 44 5.06 860 417 32.65 0 0 NA 702808 TCGA-AB-2987 AML37 12 87677693 87677693 C G SNP - - - - - - - - - - - - - - - tier3 772 60 7.19 803 347 30.12 0 0 NA 702808 TCGA-AB-2987 AML37 12 96034957 96034957 G A SNP - - - - - - - - - - - - - - - tier3 2813 171 5.72 2175 962 30.59 0 0 NA 702808 TCGA-AB-2987 AML37 12 96231234 96231234 C G SNP - - - - - - - - - - - - - - - tier3 1706 120 6.56 1229 516 29.55 0 0 NA 702808 TCGA-AB-2987 AML37 12 105781811 105781811 G A SNP RIC8B NM_018157.2 human genbank 54_36p 1 validated intronic c.1451+3491 e8+3491 0.007 - - - no_errors tier3 1118 61 5.17 1088 414 27.56 0 2 100 702808 TCGA-AB-2987 AML37 12 120428628 120428628 G A SNP FBXL10 NM_032590.1 human genbank 54_36p -1 reviewed intronic c.1647+3125 e11+3125 0 - - - no_errors tier3 567 48 7.78 225 91 28.71 2 1 33.33 702808 TCGA-AB-2987 AML37 13 26229436 26229436 A G SNP GPR12 NM_005288.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*1524 NULL 0 - - - no_errors tier3 727 69 8.67 637 291 31.36 0 0 NA 702808 TCGA-AB-2987 AML37 13 47022188 47022188 G A SNP - - - - - - - - - - - - - - - tier3 975 65 6.24 971 511 34.48 0 0 NA 702808 TCGA-AB-2987 AML37 13 50256214 50256214 G C SNP DLEU7 NM_198989.2 human genbank 54_36p -1 provisional intronic c.459+59111 e1+59111 0.008 - - - no_errors tier3 1036 57 5.22 887 403 31.14 0 2 100 702808 TCGA-AB-2987 AML37 13 52639208 52639208 C T SNP ENSG00000218221 ENST00000401786 human ensembl 54_36p 1 known 5_prime_flanking_region c.-32909 NULL 0 - - - no_coding_region:pseudogene tier3 1029 74 6.68 705 308 30.37 0 0 NA 702808 TCGA-AB-2987 AML37 13 62410034 62410034 G A SNP - - - - - - - - - - - - - - - tier3 294 16 5.16 480 183 27.56 0 0 NA 702808 TCGA-AB-2987 AML37 13 62792272 62792272 C T SNP - - - - - - - - - - - - - - - tier3 617 33 5.06 664 265 28.49 0 0 NA 702808 TCGA-AB-2987 AML37 13 73905047 73905047 T C SNP LOC647283 XM_934682.2 human genbank 54_36p 1 model intronic c.97-1594 e2-1594 0 - - - no_errors tier3 879 65 6.89 948 349 26.89 0 0 NA 702808 TCGA-AB-2987 AML37 13 80435952 80435952 T C SNP - - - - - - - - - - - - - - - tier3 1089 43 3.8 793 368 31.62 0 0 NA 702808 TCGA-AB-2987 AML37 13 92331629 92331629 G A SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*14936 NULL 0 - - - no_errors tier3 1555 112 6.71 1285 637 33.09 0 0 NA 702808 TCGA-AB-2987 AML37 13 96638695 96638695 T G SNP MBNL2 NM_144778.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-87796 NULL 0 - - - no_errors tier3 2003 145 6.74 1483 648 30.38 0 0 NA 702808 TCGA-AB-2987 AML37 13 102414133 102414133 C T SNP - - - - - - - - - - - - - - - tier3 1401 93 6.21 1384 603 30.29 0 0 NA 702808 TCGA-AB-2987 AML37 13 109180132 109180132 T G SNP IRS2 NM_003749.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*26520 NULL 0 - - - no_errors tier3 566 41 6.75 385 158 29.04 17 16 48.48 702808 TCGA-AB-2987 AML37 13 111678940 111678940 G A SNP - - - - - - - - - - - - - - - tier3 342 20 5.52 301 152 33.48 0 0 NA 702808 TCGA-AB-2987 AML37 13 111733393 111733393 G A SNP SOX1 NM_005986.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36581 NULL 0 - - - no_errors tier3 1834 126 6.42 1452 573 28.28 0 0 NA 702808 TCGA-AB-2987 AML37 14 26820471 26820471 G A SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*40603 NULL 0.024 - - - no_errors tier3 971 66 6.35 982 439 30.85 0 0 NA 702808 TCGA-AB-2987 AML37 14 43933380 43933380 G T SNP - - - - - - - - - - - - - - - tier3 777 47 5.7 823 356 30.12 0 0 NA 702808 TCGA-AB-2987 AML37 14 47516655 47516655 A T SNP - - - - - - - - - - - - - - - tier3 478 38 7.35 574 234 28.92 0 0 NA 702808 TCGA-AB-2987 AML37 14 53624173 53624173 G A SNP - - - - - - - - - - - - - - - tier3 522 54 9.36 531 289 35.24 0 0 NA 702808 TCGA-AB-2987 AML37 14 60167957 60167957 G C SNP SIX1 NM_005982.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*14797 NULL 0.039 - - - no_errors tier3 831 55 6.2 722 331 31.4 0 0 NA 702808 TCGA-AB-2987 AML37 14 78341298 78341298 G A SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.1129+1379 e4+1379 0 - - - no_errors tier3 1250 104 7.63 1349 701 34.08 0 0 NA 702808 TCGA-AB-2987 AML37 14 83874128 83874128 C G SNP - - - - - - - - - - - - - - - tier3 1479 98 6.2 1630 707 30.19 0 0 NA 702808 TCGA-AB-2987 AML37 14 84647813 84647813 G T SNP - - - - - - - - - - - - - - - tier3 1666 105 5.93 1392 676 32.69 0 0 NA 702808 TCGA-AB-2987 AML37 14 92989250 92989250 C T SNP KIAA1409 NM_020818.3 human genbank 54_36p 1 validated intronic c.1-14520 e1-14520 0.005 - - - no_errors tier3 1024 68 6.22 823 356 30.12 0 0 NA 702808 TCGA-AB-2987 AML37 14 101373029 101373029 T C SNP PPP2R5C NM_002719.2 human genbank 54_36p 1 reviewed intronic c.95-19747 e2-19747 0.001 - - - no_errors tier3 1176 90 7.1 945 397 29.54 11 5 31.25 702808 TCGA-AB-2987 AML37 15 20671352 20671352 A T SNP NIPA1 NM_144599.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33500 NULL 0.058 - - - no_errors tier3 832 82 8.95 731 337 31.52 0 3 100 702808 TCGA-AB-2987 AML37 15 21404293 21404293 C T SNP MKRN3 NM_005664.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*40747 NULL 0.003 - - - no_errors tier3 1079 76 6.56 929 430 31.62 0 0 NA 702808 TCGA-AB-2987 AML37 15 22905602 22905602 C T SNP ENSG00000212428 ENST00000391126 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-49859 NULL 0.018 - - - no_errors tier3 1158 89 7.12 1341 635 32.02 5 0 0 702808 TCGA-AB-2987 AML37 15 23007337 23007337 G A SNP SNORD115-23 NR_003315.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-699 NULL 0 - - - no_errors tier3 285 9 3.06 136 79 36.74 0 0 NA 702808 TCGA-AB-2987 AML37 15 27064971 27064971 A G SNP APBA2 NM_005503.1 human genbank 54_36p 1 reviewed intronic c.1-10277 e1-10277 0.114 - - - no_errors tier3 940 47 4.76 717 372 34.16 1 0 0 702808 TCGA-AB-2987 AML37 15 62092724 62092724 T A SNP DAPK2 NM_014326.3 human genbank 54_36p -1 reviewed intronic c.92+26698 e1+26698 0.733 - - - no_errors tier3 743 59 7.35 518 230 30.71 0 0 NA 702808 TCGA-AB-2987 AML37 15 63389178 63389178 G T SNP PARP16 NM_017851.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-23361 NULL 0 - - - no_errors tier3 906 51 5.33 565 233 29.2 1 0 0 702808 TCGA-AB-2987 AML37 15 75008154 75008154 C T SNP RCN2 NM_002902.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3084 NULL 0 - - - no_errors tier3 1135 90 7.35 685 296 30.11 0 0 NA 702808 TCGA-AB-2987 AML37 15 79946933 79946933 C T SNP - - - - - - - - - - - - - - - tier3 4581 299 6.1 3425 1576 31.43 0 0 NA 702808 TCGA-AB-2987 AML37 15 95268340 95268340 C T SNP - - - - - - - - - - - - - - - tier3 1332 79 5.58 1021 458 30.9 0 0 NA 702808 TCGA-AB-2987 AML37 16 6582882 6582882 A G SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-61723 e1-61723 0.001 - - - no_errors tier3 886 57 6.03 811 357 30.54 0 0 NA 702808 TCGA-AB-2987 AML37 16 29258287 29258287 C T SNP RUNDC2B ENST00000398878 human ensembl 54_36p 1 known intronic c.1+10841 e0+10841 0.01 - - - no_errors tier3 1137 65 5.4 784 358 31.24 0 0 0 702808 TCGA-AB-2987 AML37 16 47653854 47653854 A T SNP - - - - - - - - - - - - - - - tier3 1498 91 5.71 1411 535 27.45 0 0 NA 702808 TCGA-AB-2987 AML37 16 51399667 51399667 G A SNP - - - - - - - - - - - - - - - tier3 920 46 4.76 712 313 30.54 0 0 NA 702808 TCGA-AB-2987 AML37 17 9677487 9677487 G A SNP GLP2R NM_004246.1 human genbank 54_36p 1 reviewed intronic c.190-362 e2-362 0 - - - no_errors tier3 1311 81 5.82 1072 484 31.07 0 0 NA 702808 TCGA-AB-2987 AML37 17 10437743 10437743 C A SNP LOC100134147 XM_001716952.1 human genbank 54_36p -1 model intronic c.820+114 e3+114 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1199 58 4.61 853 372 30.37 0 0 NA 702808 TCGA-AB-2987 AML37 17 17315005 17315005 C A SNP MED9 NM_018019.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6076 NULL 0.001 - - - no_errors tier3 653 46 6.58 301 148 32.96 0 0 NA 702808 TCGA-AB-2987 AML37 17 26192115 26192115 T A SNP ATAD5 NM_024857.3 human genbank 54_36p 1 provisional intronic c.2241+190 e4+190 0 - - - no_errors tier3 742 61 7.6 626 279 30.79 0 0 0 702808 TCGA-AB-2987 AML37 17 49431149 49431149 G A SNP - - - - - - - - - - - - - - - tier3 1737 112 6.05 1380 706 33.76 0 0 NA 702808 TCGA-AB-2987 AML37 17 49879550 49879550 C A SNP - - - - - - - - - - - - - - - tier3 1054 83 7.29 857 375 30.44 0 0 NA 702808 TCGA-AB-2987 AML37 17 56568344 56568344 A G SNP BCAS3 NM_001099432.1 human genbank 54_36p 1 validated intronic c.2470+51637 e22+51637 0.003 - - - no_errors tier3 1007 86 7.87 990 441 30.82 12 3 20 702808 TCGA-AB-2987 AML37 17 61404130 61404130 G A SNP CCDC46 NM_145036.2 human genbank 54_36p -1 validated intronic c.1737-15952 e17-15952 0 - - - no_errors tier3 1270 97 7.1 982 447 31.26 0 0 0 702808 TCGA-AB-2987 AML37 17 65784774 65784774 T G SNP - - - - - - - - - - - - - - - tier3 2139 144 6.3 1596 694 30.28 0 0 NA 702808 TCGA-AB-2987 AML37 17 66273977 66273977 T C SNP - - - - - - - - - - - - - - - tier3 413 26 5.92 486 233 32.41 0 0 NA 702808 TCGA-AB-2987 AML37 17 66992020 66992020 A C SNP LOC124685 XR_040247.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24503 NULL 0 - - - no_errors tier3 1026 49 4.55 853 402 32.01 0 0 NA 702808 TCGA-AB-2987 AML37 17 68088609 68088609 G T SNP - - - - - - - - - - - - - - - tier3 1088 79 6.77 793 344 30.26 0 0 NA 702808 TCGA-AB-2987 AML37 17 74942520 74942520 C T SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1+47611 e0+47611 0.001 - - - no_errors tier3 364 35 8.77 288 134 31.68 0 0 NA 702808 TCGA-AB-2987 AML37 17 75344288 75344288 C T SNP CBX2 NM_005189.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22342 NULL 0 - - - no_errors tier3 488 33 6.32 273 101 27.01 0 0 NA 702808 TCGA-AB-2987 AML37 18 25365760 25365760 C T SNP ENSG00000221731 ENST00000408804 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48374 NULL 0 - - - no_errors tier3 1610 81 4.78 1290 540 29.49 0 0 NA 702808 TCGA-AB-2987 AML37 18 28766552 28766552 G T SNP C18orf34 NM_001105528.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*5421 NULL 0 - - - no_errors tier3 920 59 6.03 945 370 28.14 0 0 NA 702808 TCGA-AB-2987 AML37 18 35490800 35490800 T A SNP ENSG00000212354 ENST00000391052 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*21682 NULL 0 - - - no_errors tier3 214 9 4.02 325 112 25.4 0 0 NA 702808 TCGA-AB-2987 AML37 18 37549062 37549062 C T SNP - - - - - - - - - - - - - - - tier3 2419 169 6.53 1906 812 29.85 0 0 NA 702808 TCGA-AB-2987 AML37 18 40811702 40811702 G A SNP SETBP1 NM_015559.1 human genbank 54_36p 1 validated intronic c.3838+24399 e3+24399 0 - - - no_errors tier3 2079 149 6.69 1408 625 30.74 0 0 0 702808 TCGA-AB-2987 AML37 18 63142877 63142877 G A SNP - - - - - - - - - - - - - - - tier3 434 39 8.25 536 248 31.63 0 0 NA 702808 TCGA-AB-2987 AML37 18 63405786 63405786 G A SNP - - - - - - - - - - - - - - - tier3 559 37 6.2 626 294 31.96 0 0 NA 702808 TCGA-AB-2987 AML37 18 73802113 73802113 C T SNP - - - - - - - - - - - - - - - tier3 879 78 8.13 593 284 32.38 0 0 NA 702808 TCGA-AB-2987 AML37 19 9201699 9201699 G A SNP OR7E24 NM_001079935.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-21021 NULL 0.007 - - - no_errors tier3 755 36 4.55 657 301 31.39 0 0 NA 702808 TCGA-AB-2987 AML37 19 36846708 36846708 C T SNP - - - - - - - - - - - - - - - tier3 1383 96 6.49 1271 570 30.83 0 0 NA 702808 TCGA-AB-2987 AML37 19 51661309 51661309 T C SNP PNMAL2 ENST00000377652 human ensembl 54_36p 1 known 5_prime_flanking_region c.-28421 NULL 0.003 - - - no_errors tier3 920 50 5.15 681 297 30.34 0 0 NA 702808 TCGA-AB-2987 AML37 20 7102767 7102767 G A SNP - - - - - - - - - - - - - - - tier3 748 63 7.77 880 446 33.61 0 0 NA 702808 TCGA-AB-2987 AML37 20 11836794 11836794 G A SNP BTBD3 NM_181443.2 human genbank 54_36p 1 validated intronic c.1-10188 e1-10188 0 - - - no_errors tier3 1122 73 6.1 752 355 32.04 0 0 NA 702808 TCGA-AB-2987 AML37 20 30924896 30924896 G A SNP EFCAB8 ENST00000400522 human ensembl 54_36p 1 known intronic c.209-2497 e3-2497 0.001 - - - no_stop_codon tier3 1208 82 6.35 844 421 33.23 0 2 100 702808 TCGA-AB-2987 AML37 20 31010474 31010474 C T SNP BPIL1 NM_025227.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49568 NULL 0.003 - - - no_errors tier3 1265 96 7.04 853 380 30.77 0 0 NA 702808 TCGA-AB-2987 AML37 20 33732681 33732681 G C SNP NFS1 NM_021100.3 human genbank 54_36p -1 reviewed intronic c.656-474 e7-474 0.001 - - - no_errors tier3 416 42 9.17 541 334 38.17 0 0 0 702808 TCGA-AB-2987 AML37 20 46098010 46098010 C T SNP LOC100130372 XM_001722388.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-28677 NULL 0 - - - no_errors tier3 264 18 6.36 287 119 29.17 3 0 0 702808 TCGA-AB-2987 AML37 20 48692658 48692658 C T SNP C20orf175 ENST00000327979 human ensembl 54_36p -1 known intronic c.1-11858 e1-11858 0.006 - - - no_errors tier3 661 51 7.14 359 160 30.71 0 0 NA 702808 TCGA-AB-2987 AML37 20 49087740 49087740 G A SNP KCNG1 NM_002237.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27458 NULL 0 - - - no_errors tier3 664 60 8.29 645 270 29.44 0 0 NA 702808 TCGA-AB-2987 AML37 20 50670921 50670921 C T SNP ENSG00000210771 ENST00000388036 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19099 NULL 0.001 - - - pseudogene tier3 1111 94 7.79 681 316 31.63 0 0 NA 702808 TCGA-AB-2987 AML37 20 51229501 51229501 G T SNP TSHZ2 NM_173485.4 human genbank 54_36p 1 validated intronic c.41-73944 e2-73944 0 - - - no_errors tier3 2274 167 6.84 2030 948 31.8 0 0 0 702808 TCGA-AB-2987 AML37 21 18920456 18920456 A G SNP - - - - - - - - - - - - - - - tier3 866 61 6.58 755 321 29.81 0 0 NA 702808 TCGA-AB-2987 AML37 21 23132566 23132566 A G SNP ENSG00000219889 ENST00000401698 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44208 NULL 0 - - - no_coding_region:pseudogene tier3 644 45 6.52 632 251 28.36 0 0 NA 702808 TCGA-AB-2987 AML37 21 30791864 30791864 C A SNP KRTAP19-3 NM_181609.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5718 NULL 0 - - - no_errors tier3 1171 55 4.48 880 386 30.47 0 0 NA 702808 TCGA-AB-2987 AML37 21 44856866 44856866 G A SNP KRTAP10-8 NM_198695.1 human genbank 54_36p 1 provisional missense c.421 p.A141T 0.041 NULL HMMPfam_Keratin_B2 - no_errors tier1 1919 119 5.82 1206 578 31.97 NA 702808 TCGA-AB-2987 AML37 22 17350548 17350548 A G SNP DGCR5 NR_002733.1 human genbank 54_36p 1 provisional intronic c.NULL NULL 0.012 - - - no_errors tier3 616 48 7.23 368 158 29.98 0 0 NA 702808 TCGA-AB-2987 AML37 22 32744280 32744280 C T SNP - - - - - - - - - - - - - - - tier3 812 91 10.08 768 340 30.63 0 0 NA 224143 TCGA-AB-2988 AML21 X 4275259 4275259 G A SNP LOC100131265 XR_037341.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-15490 NULL 0.005 - - - pseudogene tier3 463 4 0.86 553 372 40.17 NA NA NA 224143 TCGA-AB-2988 AML21 X 11368654 11368654 C T SNP ARHGAP6 NM_013427.2 human genbank 54_36p -1 reviewed intronic c.589-185906 e2-185906 0.002 - - - no_errors tier3 664 12 1.78 499 442 46.92 NA NA NA 224143 TCGA-AB-2988 AML21 X 12063713 12063713 G A SNP FRMPD4 NM_014728.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3299 NULL 0.993 - - - no_errors tier2 571 11 1.89 347 288 45.35 NA NA NA 224143 TCGA-AB-2988 AML21 X 12540752 12540752 T A SNP FRMPD4 NM_014728.2 human genbank 54_36p 1 validated intronic c.320-2067 e4-2067 0 - - - no_errors tier3 340 7 2.02 384 260 40.37 NA NA NA 224143 TCGA-AB-2988 AML21 X 22510281 22510281 A G SNP ENSG00000216582 ENST00000402756 human ensembl 54_36p -1 known 3_prime_flanking_region c.*34501 NULL 0.143 - - - no_coding_region:pseudogene tier3 404 9 2.18 449 386 46.23 NA NA NA 224143 TCGA-AB-2988 AML21 X 25559784 25559784 T A SNP ENSG00000217775 ENST00000403311 human ensembl 54_36p -1 known 5_prime_flanking_region c.-39938 NULL 0 - - - no_coding_region:pseudogene tier3 1241 34 2.67 683 599 46.69 NA NA NA 224143 TCGA-AB-2988 AML21 X 29017046 29017046 C T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.83-193930 e2-193930 0.393 - - - no_errors tier3 608 6 0.97 623 459 42.38 NA NA NA 224143 TCGA-AB-2988 AML21 X 32057008 32057008 A C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6438+87946 e44+87946 0.671 - - - no_errors tier2 1270 22 1.7 1009 729 41.94 NA NA NA 224143 TCGA-AB-2988 AML21 X 34989414 34989414 A G SNP ENSG00000222864 ENST00000410932 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4918 NULL 0.058 - - - no_errors tier3 487 10 2.01 470 361 43.44 NA NA NA 224143 TCGA-AB-2988 AML21 X 35011884 35011884 G T SNP ENSG00000222864 ENST00000410932 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27388 NULL 0.001 - - - no_errors tier3 514 2 0.39 679 406 37.42 NA NA NA 224143 TCGA-AB-2988 AML21 X 35697443 35697443 C T SNP MAGEB16 NM_001099921.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-32792 NULL 0.08 - - - no_errors tier3 434 4 0.91 447 367 45.09 NA NA NA 224143 TCGA-AB-2988 AML21 X 43611643 43611643 A C SNP MAOB NM_000898.4 human genbank 54_36p -1 reviewed intronic c.46+14801 e1+14801 0.003 - - - no_errors tier3 695 8 1.14 484 380 43.93 NA NA NA 224143 TCGA-AB-2988 AML21 X 55838284 55838284 A G SNP RRAGB NM_016656.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*36783 NULL 0 - - - no_errors tier3 1376 33 2.34 1321 1031 43.84 NA NA NA 224143 TCGA-AB-2988 AML21 X 62058801 62058801 T G SNP ENSG00000219933 ENST00000401584 human ensembl 54_36p -1 known 5_prime_flanking_region c.-37764 NULL 0 - - - no_coding_region:pseudogene tier3 517 10 1.88 449 396 46.53 NA NA NA 224143 TCGA-AB-2988 AML21 X 68607438 68607438 T - DEL FAM155B NM_015686.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-34413 NULL 0.114 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 X 72548904 72548904 T C SNP CDX4 NM_005193.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-34911 NULL 0.003 - - - no_errors tier3 1286 42 3.16 1000 801 44.45 NA NA NA 224143 TCGA-AB-2988 AML21 X 85003437 85003437 C T SNP CHM NM_000390.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*2854 NULL 0.006 - - - no_errors tier3 244 5 2.01 395 276 41.13 NA NA NA 224143 TCGA-AB-2988 AML21 X 85438909 85438909 A G SNP DACH2 NM_053281.1 human genbank 54_36p 1 reviewed intronic c.489-79574 e2-79574 0.158 - - - no_errors tier3 617 9 1.44 357 348 49.36 NA NA NA 224143 TCGA-AB-2988 AML21 X 87267346 87267346 C T SNP ENSG00000217397 ENST00000405579 human ensembl 54_36p -1 known 5_prime_flanking_region c.-28464 NULL 0.002 - - - no_coding_region:pseudogene tier2 820 14 1.68 711 493 40.95 NA NA NA 224143 TCGA-AB-2988 AML21 X 88290239 88290239 A C SNP - - - - - - - - - - - - - - - tier2 980 34 3.35 835 588 41.29 NA NA NA 224143 TCGA-AB-2988 AML21 X 89748505 89748505 A G SNP ENSG00000207515 ENST00000384784 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9510 NULL 0.117 - - - no_errors tier3 426 9 2.07 303 246 44.81 NA NA NA 224143 TCGA-AB-2988 AML21 X 94080158 94080158 T C SNP ENSG00000221665 ENST00000408738 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44910 NULL 0 - - - no_errors tier2 533 14 2.56 517 351 40.44 NA NA NA 224143 TCGA-AB-2988 AML21 X 96951948 96951948 C G SNP ERVWE2 ENST00000404461 human ensembl 54_36p 1 known 5_prime_flanking_region c.-36969 NULL 0 - - - no_coding_region:pseudogene tier3 665 25 3.62 537 422 43.91 NA NA NA 224143 TCGA-AB-2988 AML21 X 97626614 97626614 T A SNP - - - - - - - - - - - - - - - tier3 526 9 1.68 552 405 42.19 NA NA NA 224143 TCGA-AB-2988 AML21 X 105867073 105867073 T A SNP RNF128 NM_194463.3 human genbank 54_36p 1 reviewed intronic c.484+9790 e1+9790 0.003 - - - no_errors tier3 341 9 2.57 188 202 51.79 NA NA NA 224143 TCGA-AB-2988 AML21 X 108166390 108166390 G A SNP LOC100132394 XM_001713809.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-17743 NULL 0.037 - - - no_errors tier3 969 22 2.22 681 531 43.81 NA NA NA 224143 TCGA-AB-2988 AML21 X 110466324 110466324 C T SNP DCX NM_000555.2 human genbank 54_36p -1 reviewed intronic c.949-3287 e4-3287 0.065 - - - no_errors tier3 999 20 1.96 832 683 45.05 NA NA NA 224143 TCGA-AB-2988 AML21 X 112995732 112995732 T A SNP - - - - - - - - - - - - - - - tier3 476 6 1.24 548 423 43.56 NA NA NA 224143 TCGA-AB-2988 AML21 X 115409685 115409685 G A SNP ENSG00000207033 ENST00000384306 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*36350 NULL 0.552 - - - no_errors tier2 201 12 5.63 245 201 45.07 NA NA NA 224143 TCGA-AB-2988 AML21 X 119888650 119888650 C T SNP ENSG00000217987 ENST00000404865 human ensembl 54_36p -1 known 5_prime_flanking_region c.-961 NULL 0.026 - - - no_coding_region:pseudogene tier2 373 10 2.61 260 247 48.72 NA NA NA 224143 TCGA-AB-2988 AML21 X 122502382 122502382 G A SNP LOC100133154 XM_001714925.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-26262 NULL 0.026 - - - no_errors tier3 781 14 1.76 504 432 46.15 NA NA NA 224143 TCGA-AB-2988 AML21 X 123438448 123438448 T G SNP ODZ1 NM_014253.2 human genbank 54_36p -1 provisional intronic c.3928+4815 e21+4815 0.08 - - - no_errors tier3 403 14 3.36 438 314 41.76 NA NA NA 224143 TCGA-AB-2988 AML21 X 125860983 125860983 A T SNP - - - - - - - - - - - - - - - tier2 917 8 0.86 996 604 37.75 NA NA NA 224143 TCGA-AB-2988 AML21 X 126667177 126667177 C T SNP ENSG00000216888 ENST00000405690 human ensembl 54_36p -1 known 3_prime_flanking_region c.*23219 NULL 0.002 - - - no_coding_region:pseudogene tier3 205 4 1.91 298 237 44.3 NA NA NA 224143 TCGA-AB-2988 AML21 X 128929813 128929813 A T SNP BCORL1 NM_021946.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37076 NULL 0 - - - no_errors tier3 461 23 4.75 216 157 42.09 NA NA NA 224143 TCGA-AB-2988 AML21 X 132672302 132672302 C T SNP GPC3 NM_004484.2 human genbank 54_36p -1 reviewed intronic c.1033-10580 e4-10580 0.008 - - - no_errors tier3 761 18 2.31 686 576 45.64 NA NA NA 224143 TCGA-AB-2988 AML21 X 132886255 132886255 C T SNP GPC3 NM_004484.2 human genbank 54_36p -1 reviewed intronic c.337+28488 e2+28488 1 - - - no_errors tier2 812 31 3.68 736 606 45.09 NA NA NA 224143 TCGA-AB-2988 AML21 X 133628339 133628339 G A SNP PLAC1 NM_021796.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-99961 NULL 0.205 - - - no_errors tier3 888 12 1.33 571 508 46.99 NA NA NA 224143 TCGA-AB-2988 AML21 X 142642999 142642999 C A SNP SPANXN2 NM_001009615.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-11571 NULL 0.001 - - - no_errors tier3 902 18 1.96 459 349 43.14 NA NA NA 224143 TCGA-AB-2988 AML21 X 145020961 145020961 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 X 149904513 149904513 C T SNP HMGB3 NM_005342.2 human genbank 54_36p 1 validated intronic c.1-213 e1-213 0.433 - - - no_errors tier2 271 6 2.17 202 136 40 NA NA NA 224143 TCGA-AB-2988 AML21 X 152363002 152363002 G A SNP LOC389904 XM_001716796.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-29292 NULL 0 - - - no_errors tier3 178 3 1.66 134 122 47.66 NA NA NA 224143 TCGA-AB-2988 AML21 X 152412956 152412956 G A SNP UCHL5IP ENST00000370210 human ensembl 54_36p -1 known intronic c.1+1070 e0+1070 0.002 - - - no_errors tier2 74 3 3.9 44 34 43.59 NA NA NA 224143 TCGA-AB-2988 AML21 X 153211088 153211088 C T SNP TKTL1 NM_012253.1 human genbank 54_36p 1 validated silent c.1647 p.A549 0.915 "HMMPfam_Transketolase_C,superfamily_TK C-terminal domain-like" "HMMPfam_Transketolase_N,HMMPfam_Transket_pyr,PatternScan_TRANSKETOLASE_2,HMMPfam_Transketolase_C,superfamily_TK C-terminal domain-like,superfamily_Thiamin diphosphate-binding fold (THDP-binding)" - no_errors tier1 602 17 2.75 308 215 41.11 NA NA NA 224143 TCGA-AB-2988 AML21 X 153758581 153758581 T A SNP F8 NM_000132.3 human genbank 54_36p -1 reviewed intronic c.6430-13885 e23-13885 0.132 - - - no_errors tier3 572 19 3.21 538 348 39.23 NA NA NA 224143 TCGA-AB-2988 AML21 1 2122565 2122565 C T SNP SKI NM_003036.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27501 NULL 0.001 - - - no_errors tier2 129 9 6.52 65 51 43.97 NA NA NA 224143 TCGA-AB-2988 AML21 1 19636303 19636303 G C SNP CAPZB NM_004930.2 human genbank 54_36p -1 reviewed intronic c.4-17472 e2-17472 0 - - - no_errors tier3 526 13 2.41 326 237 42.02 NA NA NA 224143 TCGA-AB-2988 AML21 1 24785348 24785348 C T SNP C1orf130 NM_001010980.3 human genbank 54_36p 1 provisional intronic c.1-9154 e1-9154 0.037 - - - no_errors tier3 432 15 3.36 261 183 41.22 NA NA NA 224143 TCGA-AB-2988 AML21 1 29695625 29695625 G A SNP ENSG00000219178 ENST00000404255 human ensembl 54_36p -1 known intronic c.NULL NULL 0.002 - - - no_coding_region:pseudogene tier3 373 5 1.32 291 217 42.72 NA NA NA 224143 TCGA-AB-2988 AML21 1 30545295 30545295 C G SNP - - - - - - - - - - - - - - - tier3 383 19 4.73 238 167 41.23 NA NA NA 224143 TCGA-AB-2988 AML21 1 30573019 30573019 G C SNP LOC100134154 XM_001726211.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*39513 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 855 19 2.17 515 407 44.14 NA NA NA 224143 TCGA-AB-2988 AML21 1 30714565 30714565 G A SNP - - - - - - - - - - - - - - - tier3 631 9 1.41 442 283 39.03 NA NA NA 224143 TCGA-AB-2988 AML21 1 31864779 31864779 A G SNP HCRTR1 NM_001525.2 human genbank 54_36p 1 reviewed intronic c.1088-199 e7-199 0.017 - - - no_errors tier2 343 6 1.72 245 188 43.42 NA NA NA 224143 TCGA-AB-2988 AML21 1 37942808 37942808 A G SNP CDCA8 NM_018101.2 human genbank 54_36p 1 validated intronic c.585-892 e8-892 0 - - - no_errors tier2 773 6 0.77 373 266 41.56 NA NA NA 224143 TCGA-AB-2988 AML21 1 42372763 42372763 C T SNP GUCA2B NM_007102.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-18946 NULL 0.098 - - - no_errors tier2 611 12 1.93 511 406 44.27 NA NA NA 224143 TCGA-AB-2988 AML21 1 42401777 42401777 A G SNP GUCA2A NM_033553.2 human genbank 54_36p -1 validated missense c.167 p.F56S 0 "HMMPfam_Guanylin,superfamily_Proguanylin" "HMMPfam_Guanylin,superfamily_Proguanylin,PatternScan_2FE2S_FER_1" - no_errors tier1 246 3 1.2 150 109 42.08 NA NA NA 224143 TCGA-AB-2988 AML21 1 51795451 51795451 C T SNP EPS15 NM_001981.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37960 NULL 0.025 - - - no_errors tier3 802 16 1.96 786 612 43.78 NA NA NA 224143 TCGA-AB-2988 AML21 1 76595114 76595114 G A SNP ST6GALNAC3 NM_152996.1 human genbank 54_36p 1 provisional intronic c.213+42842 e2+42842 0.053 - - - no_errors tier3 1277 29 2.22 860 651 43.06 NA NA NA 224143 TCGA-AB-2988 AML21 1 76786917 76786917 G A SNP ST6GALNAC3 NM_152996.1 human genbank 54_36p 1 provisional intronic c.624-78808 e4-78808 0.003 - - - no_errors tier3 885 23 2.53 867 684 44.1 NA NA NA 224143 TCGA-AB-2988 AML21 1 77549456 77549456 C T SNP AK5 NM_174858.2 human genbank 54_36p 1 reviewed intronic c.699+13236 e5+13236 0.001 - - - no_errors tier3 676 13 1.89 546 448 45.03 NA NA NA 224143 TCGA-AB-2988 AML21 1 79107571 79107571 G A SNP ELTD1 NM_022159.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*21856 NULL 0 - - - no_errors tier3 318 10 3.05 605 453 42.78 NA NA NA 224143 TCGA-AB-2988 AML21 1 81864556 81864556 A G SNP LPHN2 ENST00000370725 human ensembl 54_36p 1 known intronic c.1+45303 e0+45303 0.073 - - - no_errors tier3 745 15 1.97 457 442 49.17 NA NA NA 224143 TCGA-AB-2988 AML21 1 86984529 86984529 A G SNP SH3GLB1 NM_016009.3 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*3023 NULL 0 - - - no_errors tier3 805 22 2.66 864 607 41.24 NA NA NA 224143 TCGA-AB-2988 AML21 1 90094378 90094378 T G SNP LRRC8D NM_018103.1 human genbank 54_36p 1 validated intronic c.1+12449 e0+12449 0.003 - - - no_errors tier3 697 23 3.19 617 353 36.35 NA NA NA 224143 TCGA-AB-2988 AML21 1 90425139 90425139 A T SNP - - - - - - - - - - - - - - - tier2 867 35 3.88 804 595 42.53 NA NA NA 224143 TCGA-AB-2988 AML21 1 92311733 92311733 G A SNP BTBD8 NM_183242.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-6984 NULL 0.059 - - - no_errors tier2 478 19 3.82 252 175 40.89 NA NA NA 224143 TCGA-AB-2988 AML21 1 95105052 95105052 A G SNP SLC44A3 NM_152369.1 human genbank 54_36p 1 validated intronic c.1252-423 e10-423 0.002 - - - no_errors tier3 259 5 1.89 296 242 44.98 NA NA NA 224143 TCGA-AB-2988 AML21 1 95881287 95881287 A G SNP - - - - - - - - - - - - - - - tier3 492 7 1.4 584 412 41.32 NA NA NA 224143 TCGA-AB-2988 AML21 1 96166599 96166599 G A SNP ENSG00000221798 ENST00000408871 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41829 NULL 0.001 - - - no_errors tier3 320 11 3.32 437 301 40.79 NA NA NA 224143 TCGA-AB-2988 AML21 1 104429796 104429796 A G SNP LOC100129138 XR_036957.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*8564 NULL 0.766 - - - no_errors tier3 293 5 1.68 283 211 42.71 NA NA NA 224143 TCGA-AB-2988 AML21 1 107811511 107811511 G A SNP NTNG1 NM_014917.1 human genbank 54_36p 1 provisional intronic c.1088-13245 e5-13245 0 - - - no_errors tier3 1002 32 3.09 748 556 42.64 NA NA NA 224143 TCGA-AB-2988 AML21 1 114521481 114521481 C T SNP SYT6 NM_205848.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-37465 NULL 0 - - - no_errors tier3 729 23 3.06 810 677 45.53 NA NA NA 224143 TCGA-AB-2988 AML21 1 150298131 150298131 G A SNP S100A11 NM_005620.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22116 NULL 0.082 - - - no_errors tier3 786 17 2.11 774 580 42.8 NA NA NA 224143 TCGA-AB-2988 AML21 1 153006718 153006718 C T SNP KCNN3 NM_002249.4 human genbank 54_36p -1 reviewed intronic c.1448+4357 e3+4357 0 - - - no_errors tier2 349 9 2.51 209 212 50.36 NA NA NA 224143 TCGA-AB-2988 AML21 1 154933630 154933630 C T SNP NES NM_006617.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-19950 NULL 0.003 - - - no_errors tier3 239 7 2.83 125 109 46.58 NA NA NA 224143 TCGA-AB-2988 AML21 1 155864078 155864078 C T SNP FCRL4 NM_031282.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-29720 NULL 0.017 - - - no_errors tier3 528 11 2.02 538 401 42.57 NA NA NA 224143 TCGA-AB-2988 AML21 1 168801405 168801405 C T SNP LOC100129153 XM_001726250.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-48021 NULL 1 - - - no_errors tier2 915 29 3.07 630 602 48.86 NA NA NA 224143 TCGA-AB-2988 AML21 1 173996398 173996398 A G SNP TNR NM_003285.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-353925 NULL 0 - - - no_errors tier3 1145 17 1.46 646 485 42.88 NA NA NA 224143 TCGA-AB-2988 AML21 1 183008491 183008491 A T SNP EDEM3 NM_025191.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-18217 NULL 0 - - - no_errors tier3 862 37 4.11 544 408 42.86 NA NA NA 224143 TCGA-AB-2988 AML21 1 184081684 184081684 C A SNP HMCN1 NM_031935.2 human genbank 54_36p 1 reviewed intronic c.269-97 e2-97 0 - - - no_errors tier3 853 23 2.63 1038 767 42.47 NA NA NA 224143 TCGA-AB-2988 AML21 1 188785313 188785313 A T SNP - - - - - - - - - - - - - - - tier3 1019 20 1.92 755 510 40.32 NA NA NA 224143 TCGA-AB-2988 AML21 1 189125129 189125129 T C SNP - - - - - - - - - - - - - - - tier3 206 11 5.07 259 200 43.57 NA NA NA 224143 TCGA-AB-2988 AML21 1 193448307 193448307 A G SNP - - - - - - - - - - - - - - - tier3 366 13 3.43 388 379 49.41 NA NA NA 224143 TCGA-AB-2988 AML21 1 195505915 195505915 C - DEL CRB1 NM_201253.1 human genbank 54_36p 1 reviewed intronic c.70+1680 e1+1680 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 1 199712757 199712757 T C SNP PHLDA3 NM_012396.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-8220 NULL 0.998 - - - no_errors tier3 245 8 3.16 154 161 51.11 NA NA NA 224143 TCGA-AB-2988 AML21 1 211982110 211982110 A G SNP - - - - - - - - - - - - - - - tier3 508 27 5.05 510 450 46.88 NA NA NA 224143 TCGA-AB-2988 AML21 1 214444706 214444706 A G SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.3316+2532 e15+2532 0.999 - - - no_errors tier2 350 10 2.75 403 327 44.67 NA NA NA 224143 TCGA-AB-2988 AML21 1 214738755 214738755 A G SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*8149 NULL 0 - - - no_errors tier3 762 28 3.54 652 574 46.82 NA NA NA 224143 TCGA-AB-2988 AML21 1 215309577 215309577 G A SNP ESRRG NM_206594.1 human genbank 54_36p -1 validated intronic c.1+19895 e0+19895 0 - - - no_errors tier3 412 13 3.05 495 345 41.07 NA NA NA 224143 TCGA-AB-2988 AML21 1 218466704 218466704 T C SNP RAB3GAP2 NM_012414.3 human genbank 54_36p -1 validated intronic c.180+6060 e2+6060 0.006 - - - no_errors tier2 328 4 1.2 387 291 42.92 NA NA NA 224143 TCGA-AB-2988 AML21 1 226364237 226364237 G A SNP GJC2 NM_020435.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47846 NULL 0.425 - - - no_errors tier2 298 5 1.65 172 134 43.79 NA NA NA 224143 TCGA-AB-2988 AML21 1 227537093 227537094 - A INS C1orf96 NM_145257.3 human genbank 54_36p -1 validated intronic c.367+7375_367+7374 e1+7375 0.010:0.012 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 1 227783377 227783377 G A SNP ABCB10 NM_012089.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22355 NULL 0.008 - - - no_errors tier3 561 13 2.26 330 255 43.59 NA NA NA 224143 TCGA-AB-2988 AML21 1 227820523 227820523 A G SNP TAF5L NM_014409.1 human genbank 54_36p -1 reviewed intronic c.1-3668 e1-3668 0.017 - - - no_errors tier3 503 6 1.18 329 253 43.47 NA NA NA 224143 TCGA-AB-2988 AML21 1 235136487 235136487 A T SNP LOC440737 XM_496446.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40023 NULL 0 - - - pseudogene tier3 980 25 2.48 723 517 41.59 NA NA NA 224143 TCGA-AB-2988 AML21 1 235432642 235432642 C A SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.49-67778 e2-67778 0 - - - no_errors tier3 438 19 4.16 427 294 40.78 NA NA NA 224143 TCGA-AB-2988 AML21 1 238634329 238634329 G A SNP FMN2 NM_020066.4 human genbank 54_36p 1 validated intronic c.5339+11844 e15+11844 1 - - - no_errors tier2 447 4 0.88 411 307 42.76 NA NA NA 224143 TCGA-AB-2988 AML21 2 7638132 7638132 G A SNP ENSG00000221255 ENST00000408328 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*3586 NULL 0.013 - - - no_errors tier3 754 18 2.33 691 538 43.78 NA NA NA 224143 TCGA-AB-2988 AML21 2 14627767 14627767 T A SNP - - - - - - - - - - - - - - - tier3 578 15 2.53 565 417 42.46 NA NA NA 224143 TCGA-AB-2988 AML21 2 15140320 15140320 C G SNP - - - - - - - - - - - - - - - tier3 493 11 2.18 369 261 41.43 NA NA NA 224143 TCGA-AB-2988 AML21 2 17679827 17679827 C A SNP VSNL1 NM_003385.4 human genbank 54_36p 1 reviewed intronic c.163-14331 e2-14331 0.998 - - - no_errors tier2 927 20 2.11 616 526 46.02 NA NA NA 224143 TCGA-AB-2988 AML21 2 21947952 21947952 C G SNP LOC100133704 XM_001715784.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*18466 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 418 9 2.11 486 333 40.66 NA NA NA 224143 TCGA-AB-2988 AML21 2 23040553 23040553 G A SNP - - - - - - - - - - - - - - - tier3 405 5 1.22 426 349 45.03 NA NA NA 224143 TCGA-AB-2988 AML21 2 23457579 23457579 G A SNP KLHL29 XM_001717454.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-1624 NULL 0.003 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 190 5 2.56 184 143 43.73 NA NA NA 224143 TCGA-AB-2988 AML21 2 25310665 25310665 A C SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed missense c.2726 p.F909C 1 superfamily_S-adenosyl-L-methionine-dependent methyltransferases "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 703 21 2.9 329 274 45.44 NA NA NA 224143 TCGA-AB-2988 AML21 2 26655629 26655629 G A SNP C2orf70 NM_001105519.1 human genbank 54_36p 1 predicted intronic c.462-37 e4-37 0.001 - - - no_errors tier3 413 14 3.28 256 201 43.98 NA NA NA 224143 TCGA-AB-2988 AML21 2 33676275 33676275 C A SNP FAM98A NM_015475.3 human genbank 54_36p -1 validated intronic c.53+1465 e1+1465 0.001 - - - no_errors tier2 437 11 2.46 300 248 45.26 NA NA NA 224143 TCGA-AB-2988 AML21 2 35791214 35791214 A C SNP ENSG00000220706 ENST00000404819 human ensembl 54_36p -1 known 3_prime_flanking_region c.*12115 NULL 0.004 - - - no_coding_region:pseudogene tier2 316 3 0.94 291 160 35.4 NA NA NA 224143 TCGA-AB-2988 AML21 2 40639037 40639037 G A SNP SLC8A1 ENST00000405269 human ensembl 54_36p -1 known intronic c.1+52537 e0+52537 0.13 - - - no_errors tier3 611 10 1.61 438 339 43.63 NA NA NA 224143 TCGA-AB-2988 AML21 2 53078116 53078116 G A SNP - - - - - - - - - - - - - - - tier2 1006 22 2.14 762 611 44.47 NA NA NA 224143 TCGA-AB-2988 AML21 2 66928421 66928421 A G SNP - - - - - - - - - - - - - - - tier3 522 7 1.32 477 324 40.45 NA NA NA 224143 TCGA-AB-2988 AML21 2 70528574 70528574 G A SNP TGFA NM_003236.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*2925 NULL 0 - - - no_errors tier3 558 12 2.11 583 482 45.26 NA NA NA 224143 TCGA-AB-2988 AML21 2 76586337 76586337 G C SNP - - - - - - - - - - - - - - - tier3 416 10 2.35 501 397 44.16 NA NA NA 224143 TCGA-AB-2988 AML21 2 80066421 80066421 A C SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1059+75987 e6+75987 0.007 - - - no_errors tier2 663 12 1.78 548 385 41.22 NA NA NA 224143 TCGA-AB-2988 AML21 2 80923310 80923310 G C SNP - - - - - - - - - - - - - - - tier3 507 13 2.5 425 311 42.26 NA NA NA 224143 TCGA-AB-2988 AML21 2 80971639 80971639 C A SNP - - - - - - - - - - - - - - - tier3 415 11 2.58 484 389 44.51 NA NA NA 224143 TCGA-AB-2988 AML21 2 84468860 84468860 C A SNP LOC729749 XM_001133991.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-47893 NULL 0.001 - - - no_errors tier3 907 11 1.2 703 508 41.91 NA NA NA 224143 TCGA-AB-2988 AML21 2 84569872 84569872 G A SNP SUCLG1 NM_003849.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-29968 NULL 0.039 - - - no_errors tier2 706 7 0.98 558 415 42.61 NA NA NA 224143 TCGA-AB-2988 AML21 2 89090542 89090542 C G SNP IGKC ENST00000390246 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43170 NULL 0 - - - no_stop_codon:bad_bp_length_for_coding_region tier2 143 3 2.05 148 108 42.19 NA NA NA 224143 TCGA-AB-2988 AML21 2 95163715 95163715 C T SNP MRPS5 NM_031902.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12452 NULL 0 - - - no_errors tier3 890 22 2.41 440 332 42.95 NA NA NA 224143 TCGA-AB-2988 AML21 2 107444622 107444622 G A SNP - - - - - - - - - - - - - - - tier3 775 21 2.64 601 406 40.32 NA NA NA 224143 TCGA-AB-2988 AML21 2 114563907 114563907 G T SNP - - - - - - - - - - - - - - - tier3 814 31 3.67 851 681 44.42 NA NA NA 224143 TCGA-AB-2988 AML21 2 114737933 114737933 G A SNP ENSG00000208615 ENST00000385880 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17198 NULL 0 - - - pseudogene tier3 880 23 2.55 718 580 44.68 NA NA NA 224143 TCGA-AB-2988 AML21 2 115778621 115778621 G A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.61-4664 e2-4664 0.002 - - - no_errors tier3 359 16 4.27 459 356 43.68 NA NA NA 224143 TCGA-AB-2988 AML21 2 116933773 116933773 G T SNP - - - - - - - - - - - - - - - tier2 558 19 3.29 485 400 45.2 NA NA NA 224143 TCGA-AB-2988 AML21 2 117828620 117828620 G A SNP - - - - - - - - - - - - - - - tier2 882 19 2.11 954 810 45.89 NA NA NA 224143 TCGA-AB-2988 AML21 2 118332548 118332548 T C SNP uc010flc.1 ENST00000389240 human ensembl 54_36p 1 known 5_prime_flanking_region c.-962 NULL 0.001 - - - no_coding_region:pseudogene tier3 409 9 2.15 418 309 42.45 NA NA NA 224143 TCGA-AB-2988 AML21 2 125363943 125363943 G A SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.3434-12986 e22-12986 0.002 - - - no_errors tier3 578 12 2.03 705 492 41.1 NA NA NA 224143 TCGA-AB-2988 AML21 2 126371379 126371379 T C SNP - - - - - - - - - - - - - - - tier2 288 7 2.37 373 287 43.48 NA NA NA 224143 TCGA-AB-2988 AML21 2 128789036 128789036 G C SNP HS6ST1 NM_004807.2 human genbank 54_36p -1 reviewed intronic c.527+3045 e1+3045 0.003 - - - no_errors tier2 192 4 2.04 89 77 46.39 NA NA NA 224143 TCGA-AB-2988 AML21 2 136871669 136871669 G A SNP - - - - - - - - - - - - - - - tier3 678 17 2.44 650 507 43.78 NA NA NA 224143 TCGA-AB-2988 AML21 2 137654805 137654805 A G SNP THSD7B NM_001080427.1 human genbank 54_36p 1 provisional intronic c.1630+9827 e6+9827 0.001 - - - no_errors tier3 537 12 2.19 719 546 43.16 NA NA NA 224143 TCGA-AB-2988 AML21 2 138895131 138895131 C T SNP LOC100129375 XR_039335.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-7562 NULL 0.002 - - - pseudogene tier3 237 4 1.66 326 195 37.43 NA NA NA 224143 TCGA-AB-2988 AML21 2 146814851 146814851 T A SNP - - - - - - - - - - - - - - - tier3 778 24 2.99 755 581 43.49 NA NA NA 224143 TCGA-AB-2988 AML21 2 150789846 150789846 C T SNP - - - - - - - - - - - - - - - tier3 461 16 3.31 413 496 54.09 NA NA NA 224143 TCGA-AB-2988 AML21 2 154016425 154016425 G T SNP ENSG00000200377 ENST00000363507 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4782 NULL 0.265 - - - no_errors tier3 511 6 1.16 369 311 45.74 NA NA NA 224143 TCGA-AB-2988 AML21 2 161990410 161990410 G A SNP LOC100130897 XM_001715939.1 human genbank 54_36p -1 model intronic c.250+1433 e1+1433 1 - - - no_errors tier2 137 5 3.52 186 143 43.47 NA NA NA 224143 TCGA-AB-2988 AML21 2 163187081 163187081 G C SNP KCNH7 NM_033272.2 human genbank 54_36p -1 reviewed intronic c.308-85245 e3-85245 0 - - - no_errors tier3 657 15 2.23 756 536 41.42 NA NA NA 224143 TCGA-AB-2988 AML21 2 163187783 163187783 C T SNP KCNH7 NM_033272.2 human genbank 54_36p -1 reviewed intronic c.308-85947 e3-85947 0.005 - - - no_errors tier3 263 5 1.87 359 271 43.02 NA NA NA 224143 TCGA-AB-2988 AML21 2 166583370 166583370 T C SNP SCN1A NM_006920.4 human genbank 54_36p -1 validated intronic c.3397-2887 e17-2887 0.074 - - - no_errors tier3 266 6 2.21 325 250 43.48 NA NA NA 224143 TCGA-AB-2988 AML21 2 168092020 168092020 G A SNP LOC643496 XR_041928.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 491 7 1.4 528 405 43.36 NA NA NA 224143 TCGA-AB-2988 AML21 2 185689432 185689432 G A SNP - - - - - - - - - - - - - - - tier3 403 9 2.18 274 209 43.18 NA NA NA 224143 TCGA-AB-2988 AML21 2 189350905 189350905 A - DEL DIRC1 NM_052952.2 human genbank 54_36p -1 validated intronic c.1+11930 e0+11930 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 2 190059353 190059353 T C SNP WDR75 NM_032168.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*10965 NULL 0.168 - - - no_errors tier2 374 9 2.35 345 273 44.17 NA NA NA 224143 TCGA-AB-2988 AML21 2 197412424 197412424 A C SNP PGAP1 NM_024989.3 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1779 NULL 0.001 - - - no_errors tier3 462 9 1.91 470 384 44.96 NA NA NA 224143 TCGA-AB-2988 AML21 2 198215046 198215046 C T SNP RFTN2 NM_144629.2 human genbank 54_36p -1 validated intronic c.438+2081 e3+2081 0 - - - no_errors tier3 253 10 3.8 221 161 42.15 NA NA NA 224143 TCGA-AB-2988 AML21 2 208662730 208662730 G A SNP ENSG00000208110 ENST00000385375 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15600 NULL 0.003 - - - pseudogene tier3 279 6 2.11 314 214 40.53 NA NA NA 224143 TCGA-AB-2988 AML21 2 209727648 209727648 T C SNP LOC402116 XR_017081.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24089 NULL 0.002 - - - pseudogene tier2 315 4 1.25 215 173 44.59 NA NA NA 224143 TCGA-AB-2988 AML21 2 213129074 213129074 C T SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-17575 NULL 0.096 - - - no_errors tier3 380 6 1.55 243 224 47.97 NA NA NA 224143 TCGA-AB-2988 AML21 2 214803572 214803572 C G SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1720+81337 e15+81337 0.081 - - - no_errors tier3 514 15 2.84 550 455 45.27 NA NA NA 224143 TCGA-AB-2988 AML21 2 216655643 216655643 A G SNP TMEM169 NM_138390.1 human genbank 54_36p 1 validated intronic c.1+700 e0+700 0.002 - - - no_errors tier3 353 4 1.12 179 127 41.5 NA NA NA 224143 TCGA-AB-2988 AML21 2 217626453 217626453 G A SNP - - - - - - - - - - - - - - - tier2 874 18 2.02 604 476 44.07 NA NA NA 224143 TCGA-AB-2988 AML21 2 217966634 217966634 C T SNP - - - - - - - - - - - - - - - tier3 584 10 1.68 531 357 40.2 NA NA NA 224143 TCGA-AB-2988 AML21 2 218290760 218290760 G C SNP LOC100128899 XR_039503.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*42755 NULL 1 - - - pseudogene tier3 721 54 6.96 443 367 45.31 NA NA NA 224143 TCGA-AB-2988 AML21 2 218869996 218869996 G A SNP PNKD NM_015488.1 human genbank 54_36p 1 validated intronic c.236+25480 e2+25480 0.048 - - - no_errors tier3 862 17 1.93 362 265 42.26 NA NA NA 224143 TCGA-AB-2988 AML21 2 220085208 220085208 T C SNP ACCN4 NM_018674.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2102 NULL 0.011 - - - no_errors tier3 156 0 0 112 77 40.74 NA NA NA 224143 TCGA-AB-2988 AML21 2 220897477 220897477 G A SNP - - - - - - - - - - - - - - - tier3 1123 41 3.52 964 861 47.13 NA NA NA 224143 TCGA-AB-2988 AML21 2 229749641 229749641 C T SNP PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.124-20717 e2-20717 0 - - - no_errors tier3 764 17 2.17 752 556 42.44 NA NA NA 224143 TCGA-AB-2988 AML21 2 234551885 234551885 T C SNP TRPM8 NM_024080.4 human genbank 54_36p 1 validated intronic c.2356-1686 e17-1686 0 - - - no_errors tier2 281 6 2.09 246 152 38.19 NA NA NA 224143 TCGA-AB-2988 AML21 2 237157176 237157176 G A SNP LOC100128709 XM_001714208.1 human genbank 54_36p -1 model intronic c.225+41 e2+41 0 - - - no_errors tier3 694 34 4.67 389 309 44.27 NA NA NA 224143 TCGA-AB-2988 AML21 3 1814486 1814486 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 3 9170393 9170393 G C SNP SRGAP3 NM_014850.1 human genbank 54_36p -1 validated intronic c.68-28792 e2-28792 0 - - - no_errors tier3 1356 30 2.16 805 552 40.65 NA NA NA 224143 TCGA-AB-2988 AML21 3 10994700 10994700 C T SNP SLC6A1 NM_003042.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-39198 NULL 0 - - - no_errors tier3 522 11 2.06 260 234 47.27 NA NA NA 224143 TCGA-AB-2988 AML21 3 11030794 11030794 C G SNP SLC6A1 NM_003042.3 human genbank 54_36p 1 validated intronic c.1-1564 e1-1564 0.007 - - - no_errors tier3 355 8 2.2 237 165 41.04 NA NA NA 224143 TCGA-AB-2988 AML21 3 13605938 13605938 T A SNP FBLN2 ENST00000295761 human ensembl 54_36p 1 known intronic c.1303+17776 e2+17776 0.005 - - - no_errors tier3 405 9 2.16 224 169 42.89 NA NA NA 224143 TCGA-AB-2988 AML21 3 15559781 15559781 C G SNP COLQ NM_005677.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-21645 NULL 0 - - - no_errors tier3 1378 43 3.03 997 815 44.98 NA NA NA 224143 TCGA-AB-2988 AML21 3 19603961 19603961 C G SNP - - - - - - - - - - - - - - - tier3 606 15 2.41 623 473 43.16 NA NA NA 224143 TCGA-AB-2988 AML21 3 20997435 20997435 G A SNP LOC729684 XR_039360.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24675 NULL 0.057 - - - pseudogene tier3 305 2 0.65 456 258 36.13 NA NA NA 224143 TCGA-AB-2988 AML21 3 26853905 26853905 C T SNP - - - - - - - - - - - - - - - tier3 723 13 1.76 620 419 40.33 NA NA NA 224143 TCGA-AB-2988 AML21 3 27175136 27175136 C T SNP NEK10 ENST00000396636 human ensembl 54_36p -1 known intronic c.1201+3820 e11+3820 0.005 - - - no_errors tier3 556 19 3.3 723 611 45.73 NA NA NA 224143 TCGA-AB-2988 AML21 3 35713348 35713348 C T SNP ARPP-21 NM_016300.1 human genbank 54_36p 1 validated intronic c.686+5847 e7+5847 0 - - - no_errors tier3 308 7 2.22 449 361 44.51 NA NA NA 224143 TCGA-AB-2988 AML21 3 48978750 48978750 T C SNP ARIH2 NM_006321.2 human genbank 54_36p 1 provisional intronic c.388-812 e4-812 0.016 - - - no_errors tier3 296 8 2.63 207 149 41.85 NA NA NA 224143 TCGA-AB-2988 AML21 3 64985327 64985327 C T SNP - - - - - - - - - - - - - - - tier3 662 13 1.93 703 571 44.82 NA NA NA 224143 TCGA-AB-2988 AML21 3 65129885 65129885 G A SNP - - - - - - - - - - - - - - - tier3 714 12 1.64 667 517 43.37 NA NA NA 224143 TCGA-AB-2988 AML21 3 67701244 67701244 G A SNP SUCLG2 NM_003848.2 human genbank 54_36p -1 validated intronic c.227-38944 e3-38944 0.014 - - - no_errors tier3 653 9 1.36 633 479 43.08 NA NA NA 224143 TCGA-AB-2988 AML21 3 68532734 68532734 C T SNP FAM19A1 NM_213609.2 human genbank 54_36p 1 reviewed intronic c.119-16386 e2-16386 0.001 - - - no_errors tier3 336 13 3.72 399 285 41.67 NA NA NA 224143 TCGA-AB-2988 AML21 3 75299938 75299938 G A SNP ENSG00000222549 ENST00000410617 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14659 NULL 0.006 - - - no_errors tier3 1155 108 8.55 1865 479 20.43 NA NA NA 224143 TCGA-AB-2988 AML21 3 78270023 78270023 T - DEL ENSG00000222574 ENST00000410642 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23516 NULL 0.031 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 3 83103974 83103974 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 3 84574897 84574897 C A SNP - - - - - - - - - - - - - - - tier3 285 10 3.39 303 219 41.87 NA NA NA 224143 TCGA-AB-2988 AML21 3 85039230 85039230 G T SNP - - - - - - - - - - - - - - - tier3 397 9 2.22 260 221 45.85 NA NA NA 224143 TCGA-AB-2988 AML21 3 85246786 85246786 G A SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+155277 e1+155277 0 - - - no_errors tier2 648 17 2.56 544 396 42.08 NA NA NA 224143 TCGA-AB-2988 AML21 3 85296873 85296873 A T SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+205364 e1+205364 0.001 - - - no_errors tier3 628 15 2.33 513 386 42.94 NA NA NA 224143 TCGA-AB-2988 AML21 3 87000130 87000130 G A SNP - - - - - - - - - - - - - - - tier3 632 14 2.17 629 533 45.87 NA NA NA 224143 TCGA-AB-2988 AML21 3 90233659 90233659 C T SNP - - - - - - - - - - - - - - - tier2 309 7 2.22 312 242 43.68 NA NA NA 224143 TCGA-AB-2988 AML21 3 90281993 90281993 A - DEL ENSG00000222490 ENST00000410558 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-34481 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 3 97650514 97650514 G A SNP ENSG00000216136 ENST00000401317 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15570 NULL 0 - - - no_errors tier3 319 4 1.24 320 270 45.76 NA NA NA 224143 TCGA-AB-2988 AML21 3 101120383 101120383 A - DEL FILIP1L NM_182909.1 human genbank 54_36p -1 validated intronic c.605+5381 e3+5381 0.904 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 3 105295863 105295863 A G SNP ENSG00000214405 ENST00000341355 human ensembl 54_36p 1 known 3_prime_flanking_region c.*30288 NULL 0.963 - - - no_start_codon tier3 405 7 1.7 505 410 44.81 NA NA NA 224143 TCGA-AB-2988 AML21 3 109701637 109701637 T G SNP MYH15 NM_014981.1 human genbank 54_36p -1 validated intronic c.556+18 e5+18 0.974 - - - no_errors tier2 682 21 2.97 588 432 42.31 NA NA NA 224143 TCGA-AB-2988 AML21 3 118105272 118105272 C T SNP ENSG00000196797 ENST00000356047 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-39373 NULL 0 - - - no_coding_region:pseudogene tier3 168 3 1.75 224 180 44.55 NA NA NA 224143 TCGA-AB-2988 AML21 3 118547434 118547434 A G SNP - - - - - - - - - - - - - - - tier3 911 7 0.76 671 373 35.73 NA NA NA 224143 TCGA-AB-2988 AML21 3 118547435 118547435 T A SNP - - - - - - - - - - - - - - - tier3 913 7 0.76 675 374 35.65 NA NA NA 224143 TCGA-AB-2988 AML21 3 118618248 118618248 C T SNP - - - - - - - - - - - - - - - tier3 590 9 1.5 492 422 46.12 NA NA NA 224143 TCGA-AB-2988 AML21 3 118788116 118788116 C A SNP ENSG00000206889 ENST00000384162 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*42268 NULL 0.073 - - - no_errors tier3 446 12 2.62 428 308 41.85 NA NA NA 224143 TCGA-AB-2988 AML21 3 120198445 120198445 T C SNP IGSF11 NM_001015887.1 human genbank 54_36p -1 validated intronic c.52+37623 e1+37623 0.005 - - - no_errors tier3 1124 32 2.77 871 627 41.83 NA NA NA 224143 TCGA-AB-2988 AML21 3 120953912 120953912 A G SNP C3orf15 NM_033364.3 human genbank 54_36p 1 validated intronic c.2304+1277 e17+1277 0.02 - - - no_errors tier3 464 6 1.28 412 279 40.38 NA NA NA 224143 TCGA-AB-2988 AML21 3 126758650 126758650 G A SNP OSBPL11 NM_022776.4 human genbank 54_36p -1 reviewed intronic c.1155+3263 e8+3263 0.006 - - - no_errors tier3 444 3 0.67 420 287 40.59 NA NA NA 224143 TCGA-AB-2988 AML21 3 127909977 127909977 G A SNP CHCHD6 NM_032343.1 human genbank 54_36p 1 provisional intronic c.87+4045 e1+4045 0.002 - - - no_errors tier3 880 11 1.23 484 391 44.69 NA NA NA 224143 TCGA-AB-2988 AML21 3 128376077 128376077 G A SNP C3orf56 ENST00000398112 human ensembl 54_36p 1 known 5_prime_flanking_region c.-22142 NULL 0.002 - - - no_errors tier3 738 18 2.37 391 287 40.88 NA NA NA 224143 TCGA-AB-2988 AML21 3 133058875 133058875 G A SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.180+47923 e1+47923 0 - - - no_errors tier3 672 9 1.32 637 473 42.57 NA NA NA 224143 TCGA-AB-2988 AML21 3 136839813 136839813 T C SNP - - - - - - - - - - - - - - - tier3 859 9 1.04 582 443 43.22 NA NA NA 224143 TCGA-AB-2988 AML21 3 138431144 138431144 T C SNP - - - - - - - - - - - - - - - tier3 1186 35 2.86 1028 863 45.64 NA NA NA 224143 TCGA-AB-2988 AML21 3 140359479 140359479 T C SNP - - - - - - - - - - - - - - - tier3 486 6 1.22 426 370 46.48 NA NA NA 224143 TCGA-AB-2988 AML21 3 147588784 147588784 C T SNP PLSCR2 NM_020359.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*53485 NULL 0.031 - - - no_errors tier3 523 9 1.69 464 344 42.52 NA NA NA 224143 TCGA-AB-2988 AML21 3 159088708 159088708 G A SNP ENSG00000208653 ENST00000385918 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*42298 NULL 0.196 - - - pseudogene tier3 447 17 3.66 460 380 45.13 NA NA NA 224143 TCGA-AB-2988 AML21 3 159792229 159792229 A - DEL MLF1 NM_022443.1 human genbank 54_36p 1 validated intronic c.48-688 e2-688 0.013 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 3 160144189 160144189 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 3 160849493 160849493 G C SNP SCHIP1 NM_014575.2 human genbank 54_36p 1 provisional intronic c.64-115433 e2-115433 0.066 - - - no_errors tier3 640 23 3.47 775 642 45.18 NA NA NA 224143 TCGA-AB-2988 AML21 3 164933003 164933003 T A SNP - - - - - - - - - - - - - - - tier3 192 3 1.54 267 207 43.67 NA NA NA 224143 TCGA-AB-2988 AML21 3 165809979 165809979 C A SNP - - - - - - - - - - - - - - - tier3 294 3 1.01 311 263 45.82 NA NA NA 224143 TCGA-AB-2988 AML21 3 167193472 167193472 G A SNP - - - - - - - - - - - - - - - tier3 342 7 2.01 356 300 45.66 NA NA NA 224143 TCGA-AB-2988 AML21 3 172760087 172760087 C T SNP PLD1 NM_002662.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*43475 NULL 0 - - - no_errors tier3 892 10 1.11 865 646 42.75 NA NA NA 224143 TCGA-AB-2988 AML21 3 176843340 176843340 T G SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated intronic c.1896+15472 e11+15472 0.002 - - - no_errors tier3 454 4 0.87 496 285 36.49 NA NA NA 224143 TCGA-AB-2988 AML21 3 190344237 190344237 A G SNP TPRG1 NM_198485.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-63631 NULL 0 - - - no_errors tier3 502 13 2.52 448 394 46.79 NA NA NA 224143 TCGA-AB-2988 AML21 3 190908897 190908897 G T SNP TP63 NM_003722.1 human genbank 54_36p 1 reviewed intronic c.63-29326 e2-29326 0 - - - no_errors tier3 295 5 1.66 333 198 37.29 NA NA NA 224143 TCGA-AB-2988 AML21 3 192359524 192359524 T C SNP - - - - - - - - - - - - - - - tier3 752 22 2.84 628 524 45.49 NA NA NA 224143 TCGA-AB-2988 AML21 3 195105131 195105131 G A SNP - - - - - - - - - - - - - - - tier3 432 9 2.04 449 338 42.95 NA NA NA 224143 TCGA-AB-2988 AML21 4 1580078 1580078 G C SNP FAM53A NM_001013622.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*32758 NULL 0 - - - no_errors tier3 122 2 1.61 56 55 49.55 NA NA NA 224143 TCGA-AB-2988 AML21 4 7395708 7395708 G A SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.31-53208 e2-53208 0 - - - no_errors tier3 633 21 3.21 412 355 46.28 NA NA NA 224143 TCGA-AB-2988 AML21 4 10721610 10721610 G A SNP - - - - - - - - - - - - - - - tier3 748 10 1.32 773 667 46.32 NA NA NA 224143 TCGA-AB-2988 AML21 4 14719735 14719735 A - DEL LOC100129903 XM_001721453.1 human genbank 54_36p -1 model intronic c.1-91132 e1-91132 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 4 16600274 16600274 T C SNP LOC729006 XM_001129047.2 human genbank 54_36p -1 model intronic c.251-15982 e4-15982 1 - - - no_errors tier2 456 11 2.36 726 523 41.84 NA NA NA 224143 TCGA-AB-2988 AML21 4 20292328 20292328 G A SNP PACRGL NM_145048.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22875 NULL 0.356 - - - no_errors tier3 564 20 3.42 563 444 44.09 NA NA NA 224143 TCGA-AB-2988 AML21 4 20340152 20340152 A T SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*651 NULL 0.038 - - - no_errors tier3 161 5 3.01 238 233 49.47 NA NA NA 224143 TCGA-AB-2988 AML21 4 23668788 23668788 C T SNP - - - - - - - - - - - - - - - tier3 725 24 3.2 597 467 43.85 NA NA NA 224143 TCGA-AB-2988 AML21 4 24633443 24633443 C A SNP LGI2 NM_018176.3 human genbank 54_36p -1 validated intronic c.413+2097 e4+2097 0 - - - no_errors tier2 1132 35 3 530 475 47.26 NA NA NA 224143 TCGA-AB-2988 AML21 4 27832211 27832211 C T SNP - - - - - - - - - - - - - - - tier3 362 5 1.36 355 232 39.52 NA NA NA 224143 TCGA-AB-2988 AML21 4 28855649 28855649 G A SNP - - - - - - - - - - - - - - - tier3 180 3 1.64 246 125 33.69 NA NA NA 224143 TCGA-AB-2988 AML21 4 29332181 29332181 G A SNP ENSG00000212045 ENST00000390756 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-28735 NULL 0.001 - - - no_errors tier3 483 12 2.42 501 358 41.68 NA NA NA 224143 TCGA-AB-2988 AML21 4 30470734 30470734 A T SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3034-60139 e3-60139 0.011 - - - no_errors tier3 312 4 1.27 416 333 44.46 NA NA NA 224143 TCGA-AB-2988 AML21 4 31065449 31065449 T C SNP - - - - - - - - - - - - - - - tier3 616 8 1.28 460 377 45.04 NA NA NA 224143 TCGA-AB-2988 AML21 4 37214232 37214232 G A SNP C4orf19 NM_001104629.1 human genbank 54_36p 1 validated intronic c.1-21812 e1-21812 0.002 - - - no_errors tier3 814 12 1.45 713 509 41.65 NA NA NA 224143 TCGA-AB-2988 AML21 4 38213524 38213524 G A SNP ENSG00000211560 ENST00000390134 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*27373 NULL 0.002 - - - no_errors tier3 619 13 2.06 598 461 43.53 NA NA NA 224143 TCGA-AB-2988 AML21 4 43912602 43912602 A G SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated intronic c.962-40578 e2-40578 0.006 - - - no_errors tier3 437 18 3.96 433 322 42.65 NA NA NA 224143 TCGA-AB-2988 AML21 4 45800687 45800687 G A SNP GABRG1 NM_173536.3 human genbank 54_36p -1 reviewed intronic c.105-6564 e2-6564 0.001 - - - no_errors tier3 594 16 2.62 672 441 39.62 NA NA NA 224143 TCGA-AB-2988 AML21 4 56722986 56722986 C A SNP KIAA1211 NM_020722.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-136167 NULL 0.001 - - - no_errors tier3 376 16 4.08 344 288 45.57 NA NA NA 224143 TCGA-AB-2988 AML21 4 57235050 57235050 C T SNP HOPX NM_032495.1 human genbank 54_36p -1 reviewed intronic c.1+7128 e0+7128 0.014 - - - no_errors tier2 422 10 2.31 275 228 45.33 NA NA NA 224143 TCGA-AB-2988 AML21 4 57894519 57894519 G A SNP - - - - - - - - - - - - - - - tier3 606 8 1.3 608 455 42.76 NA NA NA 224143 TCGA-AB-2988 AML21 4 61940487 61940487 G T SNP ENSG00000205682 ENST00000381217 human ensembl 54_36p -1 known 3_prime_flanking_region c.*35195 NULL 0.021 - - - no_errors tier3 213 0 0 165 86 34.26 NA NA NA 224143 TCGA-AB-2988 AML21 4 65592501 65592501 G A SNP - - - - - - - - - - - - - - - tier3 280 5 1.75 927 122 11.62 NA NA NA 224143 TCGA-AB-2988 AML21 4 71760008 71760008 A T SNP RUFY3 NM_001037442.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-47147 NULL 0 - - - no_errors tier3 515 12 2.27 404 339 45.63 NA NA NA 224143 TCGA-AB-2988 AML21 4 76246678 76246678 G T SNP - - - - - - - - - - - - - - - tier3 681 19 2.71 760 583 43.38 NA NA NA 224143 TCGA-AB-2988 AML21 4 80770284 80770284 C T SNP - - - - - - - - - - - - - - - tier2 611 16 2.55 708 557 44 NA NA NA 224143 TCGA-AB-2988 AML21 4 81621943 81621943 C T SNP C4orf22 NM_152770.1 human genbank 54_36p 1 predicted intronic c.243-101328 e3-101328 0.002 - - - no_errors tier3 399 7 1.72 296 220 42.64 NA NA NA 224143 TCGA-AB-2988 AML21 4 86150490 86150490 G A SNP WDFY3 NM_014991.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-149722 NULL 0.01 - - - no_errors tier3 331 7 2.07 492 334 40.44 NA NA NA 224143 TCGA-AB-2988 AML21 4 86715698 86715698 C G SNP ARHGAP24 NM_001025616.2 human genbank 54_36p 1 validated intronic c.180+4800 e1+4800 0.001 - - - no_errors tier3 465 20 4.12 449 401 47.18 NA NA NA 224143 TCGA-AB-2988 AML21 4 107894888 107894888 T A SNP - - - - - - - - - - - - - - - tier3 222 4 1.77 301 243 44.67 NA NA NA 224143 TCGA-AB-2988 AML21 4 113310635 113310636 - T INS C4orf32 NM_152400.2 human genbank 54_36p 1 validated intronic c.154-16663_154-16662 e2-16662 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 4 114003649 114003649 A C SNP ENSG00000188258 ENST00000341244 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*35440 NULL 0.893 - - - no_coding_region:pseudogene tier3 302 5 1.63 384 324 45.76 NA NA NA 224143 TCGA-AB-2988 AML21 4 117818009 117818009 C T SNP - - - - - - - - - - - - - - - tier3 267 6 2.2 334 200 37.45 NA NA NA 224143 TCGA-AB-2988 AML21 4 120185549 120185549 A G SNP SYNPO2 NM_133477.1 human genbank 54_36p 1 validated intronic c.3253-12455 e5-12455 0.001 - - - no_errors tier3 453 14 2.99 379 337 47.07 NA NA NA 224143 TCGA-AB-2988 AML21 4 125644497 125644497 C T SNP - - - - - - - - - - - - - - - tier3 978 13 1.31 644 527 45 NA NA NA 224143 TCGA-AB-2988 AML21 4 127515600 127515600 A T SNP - - - - - - - - - - - - - - - tier3 1087 24 2.16 901 670 42.62 NA NA NA 224143 TCGA-AB-2988 AML21 4 127927136 127927137 GA - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 4 134376729 134376730 - A INS PCDH10 NM_032961.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45964 NULL 0.002:0.002 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 4 147190438 147190438 G A SNP - - - - - - - - - - - - - - - tier3 1033 94 8.34 1466 323 18.03 NA NA NA 224143 TCGA-AB-2988 AML21 4 149813895 149813895 T C SNP - - - - - - - - - - - - - - - tier3 570 10 1.72 488 475 49.27 NA NA NA 224143 TCGA-AB-2988 AML21 4 150095820 150095820 T C SNP - - - - - - - - - - - - - - - tier3 276 11 3.83 435 332 43.23 NA NA NA 224143 TCGA-AB-2988 AML21 4 154226791 154226791 A G SNP - - - - - - - - - - - - - - - tier3 500 19 3.66 459 335 42.19 NA NA NA 224143 TCGA-AB-2988 AML21 4 154765273 154765273 C T SNP KIAA0922 NM_015196.1 human genbank 54_36p 1 validated intronic c.3602-1476 e25-1476 0 - - - no_errors tier3 635 7 1.09 566 448 44.18 NA NA NA 224143 TCGA-AB-2988 AML21 4 156992521 156992521 G - DEL ACCN5 NM_017419.2 human genbank 54_36p -1 reviewed intronic c.711+272 e4+272 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 4 157193653 157193653 T C SNP - - - - - - - - - - - - - - - tier3 486 11 2.21 531 374 41.33 NA NA NA 224143 TCGA-AB-2988 AML21 4 160740154 160740154 A G SNP - - - - - - - - - - - - - - - tier3 619 12 1.9 648 562 46.45 NA NA NA 224143 TCGA-AB-2988 AML21 4 164129548 164129548 A C SNP - - - - - - - - - - - - - - - tier3 454 16 3.4 458 345 42.96 NA NA NA 224143 TCGA-AB-2988 AML21 4 170491496 170491496 C T SNP - - - - - - - - - - - - - - - tier2 532 7 1.3 534 396 42.58 NA NA NA 224143 TCGA-AB-2988 AML21 4 171496902 171496902 C T SNP - - - - - - - - - - - - - - - tier3 773 22 2.77 839 586 41.12 NA NA NA 224143 TCGA-AB-2988 AML21 4 178885554 178885554 G A SNP LOC285501 NM_001085490.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-233444 NULL 0 - - - no_errors tier2 710 7 0.98 971 579 37.33 NA NA NA 224143 TCGA-AB-2988 AML21 4 179010800 179010800 T - DEL LOC285501 NM_001085490.1 human genbank 54_36p 1 predicted intronic c.1-108105 e1-108105 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 4 187499274 187499274 A G SNP ENSG00000213332 ENST00000393502 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-11527 NULL 0.001 - - - no_coding_region:pseudogene tier3 539 9 1.64 519 412 44.21 NA NA NA 224143 TCGA-AB-2988 AML21 4 188809167 188809167 C T SNP ENSG00000203364 ENST00000366188 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15586 NULL 0.001 - - - no_coding_region:pseudogene tier3 340 9 2.58 335 295 46.75 NA NA NA 224143 TCGA-AB-2988 AML21 5 5825786 5825786 C T SNP - - - - - - - - - - - - - - - tier2 1486 31 2.04 887 744 45.59 NA NA NA 224143 TCGA-AB-2988 AML21 5 7136720 7136720 G A SNP ENSG00000212258 ENST00000390956 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36271 NULL 0.002 - - - no_errors tier3 986 38 3.71 723 584 44.68 NA NA NA 224143 TCGA-AB-2988 AML21 5 7864067 7864067 G A SNP ADCY2 NM_020546.2 human genbank 54_36p 1 reviewed intronic c.2884-5912 e23-5912 0.001 - - - no_errors tier3 310 7 2.21 273 240 46.78 NA NA NA 224143 TCGA-AB-2988 AML21 5 8437560 8437560 G T SNP - - - - - - - - - - - - - - - tier3 379 8 2.07 375 265 41.28 NA NA NA 224143 TCGA-AB-2988 AML21 5 9030106 9030106 A G SNP - - - - - - - - - - - - - - - tier3 866 15 1.7 946 626 39.8 NA NA NA 224143 TCGA-AB-2988 AML21 5 13611805 13611805 C T SNP - - - - - - - - - - - - - - - tier3 370 5 1.33 294 209 41.55 NA NA NA 224143 TCGA-AB-2988 AML21 5 15557079 15557079 C T SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.37+3257 e1+3257 0 - - - no_errors tier2 375 7 1.83 309 201 39.41 NA NA NA 224143 TCGA-AB-2988 AML21 5 15662659 15662659 G C SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.38-6433 e2-6433 0.024 - - - no_errors tier3 758 12 1.56 745 506 40.45 NA NA NA 224143 TCGA-AB-2988 AML21 5 16315793 16315793 C T SNP - - - - - - - - - - - - - - - tier3 942 15 1.57 646 535 45.22 NA NA NA 224143 TCGA-AB-2988 AML21 5 20824890 20824890 T G SNP - - - - - - - - - - - - - - - tier2 202 1 0.49 182 116 38.93 NA NA NA 224143 TCGA-AB-2988 AML21 5 22339675 22339675 G A SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-91166 e1-91166 0 - - - no_errors tier3 613 7 1.13 457 353 43.58 NA NA NA 224143 TCGA-AB-2988 AML21 5 25518148 25518148 C A SNP - - - - - - - - - - - - - - - tier3 288 5 1.71 361 235 39.43 NA NA NA 224143 TCGA-AB-2988 AML21 5 26861110 26861110 T C SNP - - - - - - - - - - - - - - - tier3 122 4 3.17 184 129 41.08 NA NA NA 224143 TCGA-AB-2988 AML21 5 30889361 30889361 C T SNP - - - - - - - - - - - - - - - tier3 634 10 1.55 570 460 44.66 NA NA NA 224143 TCGA-AB-2988 AML21 5 31191861 31191861 C A SNP LOC100128783 XM_001717030.1 human genbank 54_36p 1 model intronic c.77-37714 e2-37714 0.013 - - - no_errors tier2 701 19 2.64 667 582 46.56 NA NA NA 224143 TCGA-AB-2988 AML21 5 34010622 34010622 C T SNP SLC45A2 NM_016180.2 human genbank 54_36p -1 reviewed intronic c.562+7476 e2+7476 0.114 - - - no_errors tier3 388 14 3.48 385 300 43.73 NA NA NA 224143 TCGA-AB-2988 AML21 5 35502063 35502063 G A SNP ENSG00000201368 ENST00000364498 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36928 NULL 0.001 - - - no_errors tier3 311 9 2.81 430 332 43.51 NA NA NA 224143 TCGA-AB-2988 AML21 5 43572661 43572662 - A INS PAIP1 NM_006451.4 human genbank 54_36p -1 reviewed intronic c.972+16_972+15 e6+16 0.000:0.007 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 5 52204144 52204144 C - DEL ITGA1 NM_181501.1 human genbank 54_36p 1 reviewed intronic c.624+6736 e6+6736 0.003 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 5 58376204 58376204 A G SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.809-5649 e6-5649 1 - - - no_errors tier3 220 6 2.65 205 102 33.22 NA NA NA 224143 TCGA-AB-2988 AML21 5 58670749 58670749 G T SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.456-123198 e2-123198 0.003 - - - no_errors tier3 792 27 3.3 665 546 45.09 NA NA NA 224143 TCGA-AB-2988 AML21 5 75183000 75183000 C T SNP ENSG00000214913 ENST00000399235 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18833 NULL 0.003 - - - no_coding_region:pseudogene tier3 729 9 1.22 544 360 39.82 NA NA NA 224143 TCGA-AB-2988 AML21 5 78757596 78757596 T C SNP HOMER1 NM_004272.3 human genbank 54_36p -1 validated intronic c.527+12993 e5+12993 0.001 - - - no_errors tier2 755 17 2.2 432 331 43.27 NA NA NA 224143 TCGA-AB-2988 AML21 5 84621446 84621446 A T SNP - - - - - - - - - - - - - - - tier3 383 6 1.54 406 314 43.61 NA NA NA 224143 TCGA-AB-2988 AML21 5 85277237 85277237 T C SNP - - - - - - - - - - - - - - - tier3 163 4 2.4 215 164 43.27 NA NA NA 224143 TCGA-AB-2988 AML21 5 93837584 93837584 G A SNP uc003kko.1 ENST00000312498 human ensembl 54_36p -1 known intronic c.72+988 e1+988 0 - - - no_start_codon tier3 317 7 2.16 393 267 40.45 NA NA NA 224143 TCGA-AB-2988 AML21 5 95385905 95385905 C T SNP LOC441097 XM_499010.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24501 NULL 0.001 - - - no_errors tier3 254 3 1.16 249 187 42.89 NA NA NA 224143 TCGA-AB-2988 AML21 5 101989610 101989610 G C SNP - - - - - - - - - - - - - - - tier3 621 12 1.9 730 553 43 NA NA NA 224143 TCGA-AB-2988 AML21 5 105880560 105880560 C A SNP ENSG00000209177 ENST00000386442 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36490 NULL 0.001 - - - pseudogene tier3 345 9 2.54 434 355 44.99 NA NA NA 224143 TCGA-AB-2988 AML21 5 110721765 110721765 G A SNP CAMK4 NM_001744.3 human genbank 54_36p 1 reviewed intronic c.240+14066 e2+14066 0.07 - - - no_errors tier3 968 25 2.52 787 557 41.44 NA NA NA 224143 TCGA-AB-2988 AML21 5 123766468 123766468 T A SNP - - - - - - - - - - - - - - - tier3 634 16 2.46 488 399 44.93 NA NA NA 224143 TCGA-AB-2988 AML21 5 124696688 124696688 G T SNP ENSG00000222107 ENST00000410175 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17728 NULL 0.017 - - - no_errors tier3 550 18 3.17 761 594 43.84 NA NA NA 224143 TCGA-AB-2988 AML21 5 125380516 125380516 C T SNP - - - - - - - - - - - - - - - tier3 340 8 2.3 319 217 40.26 NA NA NA 224143 TCGA-AB-2988 AML21 5 126798610 126798610 T - DEL MEGF10 NM_032446.2 human genbank 54_36p 1 validated intronic c.1975+198 e14+198 0.002 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 5 127644390 127644390 G A SNP FBN2 NM_001999.3 human genbank 54_36p -1 reviewed intronic c.7013-482 e56-482 0.002 - - - no_errors tier3 627 8 1.26 712 546 43.4 NA NA NA 224143 TCGA-AB-2988 AML21 5 140320477 140320477 T C SNP PCDHAC1 NM_018898.3 human genbank 54_36p 1 reviewed intronic c.2434-18241 e2-18241 0.814 - - - no_errors tier3 104 1 0.95 182 133 42.22 NA NA NA 224143 TCGA-AB-2988 AML21 5 140659556 140659556 A T SNP PCDHGA2 NM_018915.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-39167 NULL 0.32 - - - no_errors tier3 491 5 1.01 289 246 45.98 NA NA NA 224143 TCGA-AB-2988 AML21 5 150239727 150239727 G T SNP ZNF300 NM_052860.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*15452 NULL 0 - - - no_errors tier3 759 16 2.06 566 451 44.35 NA NA NA 224143 TCGA-AB-2988 AML21 5 151620840 151620840 A G SNP - - - - - - - - - - - - - - - tier3 528 11 2.03 556 453 44.85 NA NA NA 224143 TCGA-AB-2988 AML21 5 160479232 160479232 T G SNP - - - - - - - - - - - - - - - tier3 527 13 2.41 493 404 45.04 NA NA NA 224143 TCGA-AB-2988 AML21 5 160932434 160932434 G A SNP GABRB2 NM_021911.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-26207 NULL 0 - - - no_errors tier3 252 4 1.56 274 181 39.78 NA NA NA 224143 TCGA-AB-2988 AML21 5 162646601 162646601 C T SNP - - - - - - - - - - - - - - - tier3 575 17 2.87 578 395 40.6 NA NA NA 224143 TCGA-AB-2988 AML21 5 166735878 166735878 C T SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.502+822 e2+822 0.929 - - - no_errors tier2 482 7 1.43 539 353 39.57 NA NA NA 224143 TCGA-AB-2988 AML21 5 170770152 170770153 - CATG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 5 174708483 174708483 C T SNP - - - - - - - - - - - - - - - tier3 1106 27 2.38 813 603 42.58 NA NA NA 224143 TCGA-AB-2988 AML21 6 2863017 2863017 C T SNP SERPINB9 NM_004155.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-17173 NULL 0.003 - - - no_errors tier3 411 7 1.67 336 271 44.65 NA NA NA 224143 TCGA-AB-2988 AML21 6 5878383 5878383 A T SNP ENSG00000222735 ENST00000410803 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14307 NULL 1 - - - no_errors tier3 633 6 0.94 619 501 44.65 NA NA NA 224143 TCGA-AB-2988 AML21 6 6222038 6222038 G A SNP F13A1 NM_000129.3 human genbank 54_36p -1 reviewed intronic c.320-9997 e3-9997 0 - - - no_errors tier3 488 3 0.61 499 280 35.94 NA NA NA 224143 TCGA-AB-2988 AML21 6 8332283 8332283 G A SNP SLC35B3 NM_015948.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*26498 NULL 0 - - - no_errors tier3 631 24 3.66 731 655 47.26 NA NA NA 224143 TCGA-AB-2988 AML21 6 9842939 9842939 G A SNP OFCC1 ENST00000336327 human ensembl 54_36p -1 known intronic c.690-26748 e8-26748 0.001 - - - no_start_codon:no_stop_codon tier3 577 10 1.7 522 452 46.41 NA NA NA 224143 TCGA-AB-2988 AML21 6 11202675 11202675 T G SNP HERV-FRD NM_207582.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*9238 NULL 0 - - - no_errors tier2 220 2 0.9 231 66 22.22 NA NA NA 224143 TCGA-AB-2988 AML21 6 18759587 18759587 A G SNP - - - - - - - - - - - - - - - tier3 992 38 3.69 996 749 42.87 NA NA NA 224143 TCGA-AB-2988 AML21 6 22509522 22509522 C A SNP - - - - - - - - - - - - - - - tier3 843 23 2.66 820 647 44.1 NA NA NA 224143 TCGA-AB-2988 AML21 6 24740256 24740256 G A SNP KIAA0319 NM_014809.3 human genbank 54_36p -1 validated intronic c.1+13687 e0+13687 0 - - - no_errors tier3 281 6 2.09 272 190 41.04 NA NA NA 224143 TCGA-AB-2988 AML21 6 25958309 25958309 G A SNP SLC17A3 NM_001098486.1 human genbank 54_36p -1 validated missense c.1069 p.L357F 1 "HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter" "HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter" - no_errors tier1 810 29 3.45 762 619 44.82 NA NA NA 224143 TCGA-AB-2988 AML21 6 40902452 40902452 C T SNP - - - - - - - - - - - - - - - tier3 489 5 1.01 415 322 43.69 NA NA NA 224143 TCGA-AB-2988 AML21 6 50677137 50677137 C T SNP - - - - - - - - - - - - - - - tier3 621 10 1.58 687 504 42.32 NA NA NA 224143 TCGA-AB-2988 AML21 6 51674246 51674246 A G SNP PKHD1 NM_138694.3 human genbank 54_36p -1 reviewed intronic c.10157-41520 e60-41520 0.001 - - - no_errors tier2 611 22 3.48 652 561 46.25 NA NA NA 224143 TCGA-AB-2988 AML21 6 52141657 52141657 C T SNP IL17A NM_002190.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17532 NULL 0.005 - - - no_errors tier3 980 19 1.9 879 623 41.45 NA NA NA 224143 TCGA-AB-2988 AML21 6 55433515 55433515 G T SNP HMGCLL1 NM_019036.1 human genbank 54_36p -1 validated intronic c.886-21199 e9-21199 0.002 - - - no_errors tier3 417 9 2.11 625 473 43.08 NA NA NA 224143 TCGA-AB-2988 AML21 6 69228090 69228090 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 6 69813061 69813061 T C SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.2108-1737 e12-1737 0 - - - no_errors tier3 449 13 2.81 621 484 43.8 NA NA NA 224143 TCGA-AB-2988 AML21 6 70156254 70156254 A G SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*750 NULL 1 - - - no_errors tier2 225 3 1.32 248 240 49.18 NA NA NA 224143 TCGA-AB-2988 AML21 6 75053812 75053812 G A SNP ENSG00000217178 ENST00000404728 human ensembl 54_36p 1 known 3_prime_flanking_region c.*4716 NULL 0.001 - - - no_coding_region:pseudogene tier2 571 21 3.55 506 401 44.21 NA NA NA 224143 TCGA-AB-2988 AML21 6 76900424 76900424 A C SNP ENSG00000222652 ENST00000410720 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41047 NULL 0.005 - - - no_errors tier2 1000 18 1.77 735 645 46.74 NA NA NA 224143 TCGA-AB-2988 AML21 6 90550833 90550833 A G SNP MDN1 NM_014611.1 human genbank 54_36p -1 provisional intronic c.1449+619 e9+619 0.081 - - - no_errors tier3 576 14 2.37 529 374 41.42 NA NA NA 224143 TCGA-AB-2988 AML21 6 93628855 93628855 A G SNP ENSG00000219387 ENST00000406040 human ensembl 54_36p -1 known 3_prime_flanking_region c.*25378 NULL 0.051 - - - no_coding_region:pseudogene tier3 422 9 2.09 444 262 37.11 NA NA NA 224143 TCGA-AB-2988 AML21 6 93724685 93724685 A G SNP - - - - - - - - - - - - - - - tier3 361 8 2.17 353 262 42.6 NA NA NA 224143 TCGA-AB-2988 AML21 6 97679900 97679900 T G SNP KLHL32 NM_052904.3 human genbank 54_36p 1 validated intronic c.1355-2101 e7-2101 0 - - - no_errors tier3 416 8 1.89 499 370 42.58 NA NA NA 224143 TCGA-AB-2988 AML21 6 97679902 97679902 A C SNP KLHL32 NM_052904.3 human genbank 54_36p 1 validated intronic c.1355-2099 e7-2099 0.001 - - - no_errors tier3 415 8 1.89 495 374 43.04 NA NA NA 224143 TCGA-AB-2988 AML21 6 99228719 99228719 C T SNP - - - - - - - - - - - - - - - tier3 484 14 2.81 560 377 40.23 NA NA NA 224143 TCGA-AB-2988 AML21 6 100999673 100999673 C T SNP SIM1 NM_005068.2 human genbank 54_36p -1 reviewed intronic c.998+2192 e8+2192 0.988 - - - no_errors tier2 476 5 1.04 229 192 45.5 NA NA NA 224143 TCGA-AB-2988 AML21 6 103319863 103319863 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 6 109428967 109428967 T C SNP SESN1 NM_014454.1 human genbank 54_36p -1 provisional intronic c.546+217 e3+217 0 - - - no_errors tier3 306 3 0.97 264 197 42.64 NA NA NA 224143 TCGA-AB-2988 AML21 6 112046250 112046250 G A SNP TRAF3IP2 NM_147200.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-17140 NULL 0.007 - - - no_errors tier3 1156 20 1.7 669 496 42.58 NA NA NA 224143 TCGA-AB-2988 AML21 6 113507758 113507758 A G SNP - - - - - - - - - - - - - - - tier3 345 8 2.27 429 384 47.17 NA NA NA 224143 TCGA-AB-2988 AML21 6 116379352 116379352 A T SNP FRK NM_002031.2 human genbank 54_36p -1 reviewed intronic c.958+4956 e5+4956 0.027 - - - no_errors tier3 182 5 2.67 139 116 45.49 NA NA NA 224143 TCGA-AB-2988 AML21 6 117127069 117127069 G A SNP KPNA5 NM_002269.2 human genbank 54_36p 1 reviewed intronic c.435+415 e5+415 0 - - - no_errors tier3 212 1 0.47 273 184 40.26 NA NA NA 224143 TCGA-AB-2988 AML21 6 118342032 118342032 G T SNP SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated intronic c.173+6277 e1+6277 0 - - - no_errors tier3 30 0 0 39 43 52.44 NA NA NA 224143 TCGA-AB-2988 AML21 6 123483961 123483961 G A SNP - - - - - - - - - - - - - - - tier3 372 3 0.8 370 223 37.54 NA NA NA 224143 TCGA-AB-2988 AML21 6 138547929 138547929 G A SNP KIAA1244 NM_020340.3 human genbank 54_36p 1 validated intronic c.137+14386 e2+14386 0.023 - - - no_errors tier2 737 14 1.86 414 361 46.52 NA NA NA 224143 TCGA-AB-2988 AML21 6 140054051 140054051 G A SNP ENSG00000205695 ENST00000381279 human ensembl 54_36p 1 known 3_prime_flanking_region c.*29714 NULL 0.014 - - - no_coding_region:pseudogene tier3 358 6 1.65 299 219 42.28 NA NA NA 224143 TCGA-AB-2988 AML21 6 142094979 142094979 A G SNP - - - - - - - - - - - - - - - tier2 169 4 2.31 172 135 43.97 NA NA NA 224143 TCGA-AB-2988 AML21 6 145705050 145705050 A T SNP ENSG00000221796 ENST00000408869 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6537 NULL 0 - - - no_errors tier3 251 6 2.33 241 180 42.76 NA NA NA 224143 TCGA-AB-2988 AML21 6 148568221 148568221 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 6 154546399 154546399 G A SNP IPCEF1 NM_015553.1 human genbank 54_36p -1 validated intronic c.908-15459 e9-15459 0.004 - - - no_errors tier3 588 13 2.16 636 467 42.34 NA NA NA 224143 TCGA-AB-2988 AML21 6 158742634 158742634 T C SNP TULP4 NM_020245.1 human genbank 54_36p 1 validated intronic c.253-11451 e2-11451 0.003 - - - no_errors tier3 356 25 6.53 523 209 28.44 NA NA NA 224143 TCGA-AB-2988 AML21 7 6681136 6681136 T A SNP - - - - - - - - - - - - - - - tier3 558 11 1.93 328 248 43.06 NA NA NA 224143 TCGA-AB-2988 AML21 7 7109517 7109517 C T SNP - - - - - - - - - - - - - - - tier3 402 17 4.06 345 239 40.92 NA NA NA 224143 TCGA-AB-2988 AML21 7 8724031 8724031 G A SNP - - - - - - - - - - - - - - - tier3 132 2 1.49 191 74 27.82 NA NA NA 224143 TCGA-AB-2988 AML21 7 11819482 11819482 A G SNP THSD7A NM_015204.1 human genbank 54_36p -1 validated intronic c.190+18426 e1+18426 0.002 - - - no_errors tier3 315 4 1.25 389 272 41.15 NA NA NA 224143 TCGA-AB-2988 AML21 7 22389275 22389275 G A SNP - - - - - - - - - - - - - - - tier3 508 12 2.31 400 304 43.18 NA NA NA 224143 TCGA-AB-2988 AML21 7 23431936 23431936 G C SNP - - - - - - - - - - - - - - - tier3 246 11 4.28 161 119 42.5 NA NA NA 224143 TCGA-AB-2988 AML21 7 27436446 27436447 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 7 33447556 33447556 A G SNP - - - - - - - - - - - - - - - tier3 443 7 1.56 407 318 43.86 NA NA NA 224143 TCGA-AB-2988 AML21 7 40240205 40240205 G T SNP - - - - - - - - - - - - - - - tier3 315 20 5.97 345 248 41.75 NA NA NA 224143 TCGA-AB-2988 AML21 7 41207398 41207398 T C SNP - - - - - - - - - - - - - - - tier3 463 18 3.74 358 335 48.34 NA NA NA 224143 TCGA-AB-2988 AML21 7 42114584 42114584 C T SNP - - - - - - - - - - - - - - - tier3 722 9 1.23 581 458 44.04 NA NA NA 224143 TCGA-AB-2988 AML21 7 46563249 46563249 C A SNP - - - - - - - - - - - - - - - tier3 681 14 2.01 520 367 41.33 NA NA NA 224143 TCGA-AB-2988 AML21 7 46768318 46768318 C T SNP - - - - - - - - - - - - - - - tier2 835 19 2.22 684 518 43.09 NA NA NA 224143 TCGA-AB-2988 AML21 7 52002898 52002898 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 7 52261280 52261280 C T SNP - - - - - - - - - - - - - - - tier2 556 8 1.42 491 348 41.48 NA NA NA 224143 TCGA-AB-2988 AML21 7 54623877 54623877 C T SNP - - - - - - - - - - - - - - - tier3 810 20 2.4 616 557 47.49 NA NA NA 224143 TCGA-AB-2988 AML21 7 56309966 56309966 T G SNP - - - - - - - - - - - - - - - tier3 169 6 3.43 121 125 50.81 NA NA NA 224143 TCGA-AB-2988 AML21 7 57886921 57886921 C A SNP - - - - - - - - - - - - - - - tier3 301 9 2.9 232 166 41.71 NA NA NA 224143 TCGA-AB-2988 AML21 7 96253410 96253410 C A SNP - - - - - - - - - - - - - - - tier2 588 12 2 524 422 44.61 NA NA NA 224143 TCGA-AB-2988 AML21 7 101893698 101893698 C A SNP LRWD1 NM_152892.1 human genbank 54_36p 1 provisional missense c.408 p.N136K 0.923 superfamily_SSF52058 "HMMPfam_LRR_1,HMMSmart_WD40,HMMSmart_LRR_TYP,superfamily_WD40_like,PatternScan_WD_REPEATS_1,HMMPfam_WD40,superfamily_SSF52058" - no_errors tier1 194 2 1.02 110 95 46.34 NA NA NA 224143 TCGA-AB-2988 AML21 7 108090193 108090193 G T SNP - - - - - - - - - - - - - - - tier3 694 16 2.25 492 401 44.85 NA NA NA 224143 TCGA-AB-2988 AML21 7 109410189 109410189 T A SNP EIF3IP1 NR_003024.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-22683 NULL 0.009 - - - pseudogene tier3 670 13 1.9 474 318 40.15 NA NA NA 224143 TCGA-AB-2988 AML21 7 109582797 109582797 A G SNP - - - - - - - - - - - - - - - tier3 1045 15 1.42 1086 328 23.18 NA NA NA 224143 TCGA-AB-2988 AML21 7 111280040 111280040 C T SNP DOCK4 NM_014705.3 human genbank 54_36p -1 reviewed intronic c.2474-5622 e24-5622 0.433 - - - no_errors tier3 468 11 2.3 370 286 43.6 NA NA NA 224143 TCGA-AB-2988 AML21 7 123618595 123618595 G T SNP - - - - - - - - - - - - - - - tier3 558 7 1.24 563 407 41.92 NA NA NA 224143 TCGA-AB-2988 AML21 7 123785218 123785218 G C SNP - - - - - - - - - - - - - - - tier3 296 9 2.95 344 279 44.78 NA NA NA 224143 TCGA-AB-2988 AML21 7 130365028 130365028 G C SNP ENSG00000199627 ENST00000362757 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*25157 NULL 0 - - - no_errors tier3 554 21 3.65 391 324 45.31 NA NA NA 224143 TCGA-AB-2988 AML21 7 131513466 131513466 C A SNP PLXNA4 NM_020911.1 human genbank 54_36p -1 validated intronic c.3874+1520 e19+1520 0 - - - no_errors tier3 1202 27 2.2 414 346 45.47 NA NA NA 224143 TCGA-AB-2988 AML21 7 139511313 139511313 C T SNP JHDM1D NM_030647.1 human genbank 54_36p -1 provisional intronic c.194+11700 e1+11700 0.005 - - - no_errors tier3 534 12 2.2 412 281 40.43 NA NA NA 224143 TCGA-AB-2988 AML21 7 140590516 140590516 C T SNP LOC100129514 XM_001716072.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*31529 NULL 0 - - - no_errors tier2 641 19 2.88 603 508 45.72 NA NA NA 224143 TCGA-AB-2988 AML21 7 144073777 144073777 C T SNP TPK1 NM_022445.1 human genbank 54_36p -1 reviewed intronic c.115+20129 e2+20129 0 - - - no_errors tier3 593 15 2.47 625 458 42.29 NA NA NA 224143 TCGA-AB-2988 AML21 7 152960080 152960080 G A SNP - - - - - - - - - - - - - - - tier2 572 26 4.35 446 330 42.47 NA NA NA 224143 TCGA-AB-2988 AML21 7 155582876 155582876 C T SNP LOC393076 XR_016902.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-6998 NULL 0.001 - - - no_errors tier3 634 17 2.61 230 185 44.47 NA NA NA 224143 TCGA-AB-2988 AML21 7 156020901 156020901 A C SNP - - - - - - - - - - - - - - - tier3 580 14 2.36 480 308 39.09 NA NA NA 224143 TCGA-AB-2988 AML21 7 158811724 158811724 C T SNP - - - - - - - - - - - - - - - tier3 679 17 2.44 413 385 48.25 NA NA NA 224143 TCGA-AB-2988 AML21 8 3984235 3984235 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.416-107206 e4-107206 0.002 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 377 7 1.82 404 278 40.76 NA NA NA 224143 TCGA-AB-2988 AML21 8 5914325 5914325 G A SNP - - - - - - - - - - - - - - - tier3 1113 26 2.28 583 431 42.46 NA NA NA 224143 TCGA-AB-2988 AML21 8 9175651 9175651 G T SNP ENSG00000207415 ENST00000384684 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*6741 NULL 0 - - - no_errors tier2 570 11 1.89 523 402 43.46 NA NA NA 224143 TCGA-AB-2988 AML21 8 13681075 13681075 C T SNP - - - - - - - - - - - - - - - tier3 373 20 5.09 546 508 48.15 NA NA NA 224143 TCGA-AB-2988 AML21 8 21469827 21469827 G A SNP ENSG00000210349 ENST00000387614 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-30425 NULL 0.007 - - - pseudogene tier3 888 20 2.2 676 456 40.28 NA NA NA 224143 TCGA-AB-2988 AML21 8 26635824 26635824 A - DEL ADRA1A NM_033303.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*26200 NULL 0.115 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 8 28835951 28835951 A T SNP HMBOX1 NM_024567.1 human genbank 54_36p 1 validated intronic c.1+30725 e0+30725 0.017 - - - no_errors tier2 403 6 1.47 313 194 38.26 NA NA NA 224143 TCGA-AB-2988 AML21 8 28970371 28970371 G A SNP ENSG00000200719 ENST00000363849 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-8331 NULL 0.001 - - - no_errors tier3 411 9 2.14 268 191 41.61 NA NA NA 224143 TCGA-AB-2988 AML21 8 33274820 33274820 T A SNP ENSG00000210599 ENST00000387864 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41104 NULL 0.122 - - - pseudogene tier3 177 1 0.56 188 146 43.71 NA NA NA 224143 TCGA-AB-2988 AML21 8 35568274 35568274 A T SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.452-4340 e4-4340 0.002 - - - no_errors tier3 623 13 2.04 674 462 40.67 NA NA NA 224143 TCGA-AB-2988 AML21 8 36290285 36290285 C T SNP ENSG00000206871 ENST00000384144 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3537 NULL 0 - - - no_errors tier3 420 9 2.1 275 195 41.49 NA NA NA 224143 TCGA-AB-2988 AML21 8 57304985 57304985 A G SNP PLAG1 NM_002655.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-61603 NULL 0.006 - - - no_errors tier3 858 17 1.94 569 440 43.56 NA NA NA 224143 TCGA-AB-2988 AML21 8 59857390 59857390 T C SNP TOX NM_014729.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*25470 NULL 0.036 - - - no_errors tier3 886 16 1.77 601 461 43.41 NA NA NA 224143 TCGA-AB-2988 AML21 8 62686159 62686159 C T SNP ASPH NM_004318.3 human genbank 54_36p -1 validated intronic c.976+7932 e14+7932 0 - - - no_errors tier2 674 14 2.03 717 499 41.04 NA NA NA 224143 TCGA-AB-2988 AML21 8 64868022 64868022 T C SNP - - - - - - - - - - - - - - - tier3 378 7 1.82 484 432 47.11 NA NA NA 224143 TCGA-AB-2988 AML21 8 64881664 64881664 A G SNP - - - - - - - - - - - - - - - tier3 606 6 0.98 568 402 41.44 NA NA NA 224143 TCGA-AB-2988 AML21 8 71490161 71490161 C A SNP NCOA2 NM_006540.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-198627 NULL 0.014 - - - no_errors tier3 821 28 3.3 427 355 45.4 NA NA NA 224143 TCGA-AB-2988 AML21 8 73838484 73838484 C T SNP KCNB2 NM_004770.2 human genbank 54_36p 1 reviewed intronic c.580-172240 e2-172240 0.002 - - - no_errors tier3 444 15 3.27 533 436 44.9 NA NA NA 224143 TCGA-AB-2988 AML21 8 73973346 73973346 T A SNP KCNB2 NM_004770.2 human genbank 54_36p 1 reviewed intronic c.580-37378 e2-37378 0.507 - - - no_errors tier3 846 28 3.2 633 506 44.35 NA NA NA 224143 TCGA-AB-2988 AML21 8 82908629 82908629 C - DEL SNX16 NM_022133.3 human genbank 54_36p -1 reviewed intronic c.376-4323 e2-4323 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 8 86941367 86941367 G A SNP REXO1L6P XM_376784.4 human genbank 54_36p -1 model 5_prime_flanking_region c.-43108 NULL 0.002 - - - pseudogene tier3 592 13 2.15 656 451 40.74 NA NA NA 224143 TCGA-AB-2988 AML21 8 98544916 98544916 G A SNP - - - - - - - - - - - - - - - tier2 412 10 2.37 360 287 44.36 NA NA NA 224143 TCGA-AB-2988 AML21 8 104621505 104621505 C G SNP RIMS2 NM_001100117.1 human genbank 54_36p 1 validated intronic c.176+39039 e1+39039 0.013 - - - no_errors tier3 878 30 3.3 963 685 41.52 NA NA NA 224143 TCGA-AB-2988 AML21 8 105257811 105257811 C T SNP RIMS2 NM_001100117.1 human genbank 54_36p 1 validated intronic c.3335-68509 e20-68509 0.004 - - - no_errors tier3 983 30 2.96 800 601 42.87 NA NA NA 224143 TCGA-AB-2988 AML21 8 105877999 105877999 C A SNP - - - - - - - - - - - - - - - tier3 458 18 3.76 442 326 42.34 NA NA NA 224143 TCGA-AB-2988 AML21 8 106064985 106064985 G A SNP - - - - - - - - - - - - - - - tier2 583 8 1.35 667 502 42.94 NA NA NA 224143 TCGA-AB-2988 AML21 8 108034293 108034293 C A SNP - - - - - - - - - - - - - - - tier3 880 22 2.44 742 684 47.93 NA NA NA 224143 TCGA-AB-2988 AML21 8 108110247 108110247 C A SNP - - - - - - - - - - - - - - - tier3 515 10 1.9 464 424 47.75 NA NA NA 224143 TCGA-AB-2988 AML21 8 110811745 110811746 - C INS GOLSYN NM_001099744.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-85681 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 8 112628153 112628153 A G SNP - - - - - - - - - - - - - - - tier3 138 6 4.17 205 176 46.19 NA NA NA 224143 TCGA-AB-2988 AML21 8 113399858 113399858 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.7360+384 e47+384 0 - - - no_errors tier3 387 8 2.03 479 347 41.96 NA NA NA 224143 TCGA-AB-2988 AML21 8 118340269 118340269 C T SNP - - - - - - - - - - - - - - - tier2 741 17 2.24 630 575 47.68 NA NA NA 224143 TCGA-AB-2988 AML21 8 118499236 118499236 C T SNP - - - - - - - - - - - - - - - tier3 449 15 3.23 360 298 45.22 NA NA NA 224143 TCGA-AB-2988 AML21 8 120738873 120738873 C T SNP ENPP2 NM_006209.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-18672 NULL 0 - - - no_errors tier3 570 11 1.89 583 309 34.64 NA NA NA 224143 TCGA-AB-2988 AML21 8 123494142 123494142 T C SNP - - - - - - - - - - - - - - - tier3 459 7 1.5 638 512 44.52 NA NA NA 224143 TCGA-AB-2988 AML21 8 127731281 127731281 G A SNP ENSG00000212451 ENST00000391149 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21668 NULL 0 - - - no_errors tier3 447 6 1.32 517 363 41.16 NA NA NA 224143 TCGA-AB-2988 AML21 8 132514205 132514205 G A SNP - - - - - - - - - - - - - - - tier3 292 4 1.35 281 166 37.14 NA NA NA 224143 TCGA-AB-2988 AML21 8 135402860 135402860 C A SNP - - - - - - - - - - - - - - - tier2 1026 27 2.56 1053 788 42.8 NA NA NA 224143 TCGA-AB-2988 AML21 8 135465008 135465008 G A SNP - - - - - - - - - - - - - - - tier3 593 13 2.15 506 404 44.4 NA NA NA 224143 TCGA-AB-2988 AML21 8 136415668 136415668 C T SNP - - - - - - - - - - - - - - - tier3 597 11 1.81 455 371 44.92 NA NA NA 224143 TCGA-AB-2988 AML21 8 143230803 143230803 G A SNP - - - - - - - - - - - - - - - tier3 509 15 2.86 206 158 43.41 NA NA NA 224143 TCGA-AB-2988 AML21 8 144397323 144397323 G A SNP GLI4 NM_138465.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25619 NULL 0.985 - - - no_errors tier3 76 3 3.8 40 18 31.03 NA NA NA 224143 TCGA-AB-2988 AML21 9 2480874 2480874 G A SNP - - - - - - - - - - - - - - - tier3 330 8 2.37 354 282 44.34 NA NA NA 224143 TCGA-AB-2988 AML21 9 2988658 2988658 C T SNP - - - - - - - - - - - - - - - tier3 519 10 1.88 668 467 41.07 NA NA NA 224143 TCGA-AB-2988 AML21 9 3058680 3058680 T C SNP - - - - - - - - - - - - - - - tier3 466 18 3.72 411 275 40.09 NA NA NA 224143 TCGA-AB-2988 AML21 9 14021550 14021550 C T SNP LOC138864 XR_016343.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37381 NULL 0.946 - - - no_errors tier3 487 8 1.62 287 230 44.4 NA NA NA 224143 TCGA-AB-2988 AML21 9 17981959 17981959 A C SNP - - - - - - - - - - - - - - - tier3 413 9 2.13 402 325 44.7 NA NA NA 224143 TCGA-AB-2988 AML21 9 22660182 22660182 G A SNP - - - - - - - - - - - - - - - tier3 617 11 1.75 820 574 41.18 NA NA NA 224143 TCGA-AB-2988 AML21 9 24247302 24247302 T C SNP - - - - - - - - - - - - - - - tier3 504 14 2.7 515 445 46.35 NA NA NA 224143 TCGA-AB-2988 AML21 9 26568487 26568487 G A SNP - - - - - - - - - - - - - - - tier2 508 4 0.78 427 295 40.86 NA NA NA 224143 TCGA-AB-2988 AML21 9 27600708 27600708 C T SNP ENSG00000217362 ENST00000402391 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-27600708 NULL 0 - - - no_coding_region:pseudogene tier3 182 4 2.15 157 94 37.45 NA NA NA 224143 TCGA-AB-2988 AML21 9 29030903 29030903 A G SNP - - - - - - - - - - - - - - - tier3 287 5 1.71 522 356 40.55 NA NA NA 224143 TCGA-AB-2988 AML21 9 30454772 30454772 C A SNP - - - - - - - - - - - - - - - tier3 368 5 1.34 352 306 46.5 NA NA NA 224143 TCGA-AB-2988 AML21 9 31631543 31631543 T G SNP ENSG00000217739 ENST00000402171 human ensembl 54_36p -1 known 3_prime_flanking_region c.*3035 NULL 0.002 - - - no_coding_region:pseudogene tier3 790 5 0.63 755 470 38.34 NA NA NA 224143 TCGA-AB-2988 AML21 9 35858722 35858722 G C SNP C9orf128 NM_001012446.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42564 NULL 0.006 - - - no_errors tier3 389 7 1.77 406 308 43.08 NA NA NA 224143 TCGA-AB-2988 AML21 9 38723656 38723656 G T SNP - - - - - - - - - - - - - - - tier3 419 8 1.87 297 177 37.34 NA NA NA 224143 TCGA-AB-2988 AML21 9 38762032 38762032 T C SNP - - - - - - - - - - - - - - - tier3 451 7 1.53 224 188 45.63 NA NA NA 224143 TCGA-AB-2988 AML21 9 69130484 69130484 A T SNP ENSG00000222887 ENST00000410955 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18823 NULL 0.011 - - - no_errors tier3 125 1 0.79 328 87 20.96 NA NA NA 224143 TCGA-AB-2988 AML21 9 77461301 77461301 T G SNP ENSG00000211133 ENST00000388398 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20342 NULL 0.006 - - - pseudogene tier3 464 8 1.69 563 470 45.5 NA NA NA 224143 TCGA-AB-2988 AML21 9 82566628 82566628 G A SNP ENSG00000221581 ENST00000408654 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27564 NULL 0.314 - - - no_errors tier3 471 5 1.05 491 329 40.12 NA NA NA 224143 TCGA-AB-2988 AML21 9 83072994 83072994 G C SNP - - - - - - - - - - - - - - - tier3 761 23 2.93 711 550 43.62 NA NA NA 224143 TCGA-AB-2988 AML21 9 83950591 83950591 C T SNP ENSG00000217167 ENST00000403378 human ensembl 54_36p 1 known 3_prime_flanking_region c.*14229 NULL 0.003 - - - no_coding_region:pseudogene tier2 463 12 2.52 297 263 46.96 NA NA NA 224143 TCGA-AB-2988 AML21 9 87089187 87089187 G T SNP - - - - - - - - - - - - - - - tier3 210 3 1.4 91 99 52.11 NA NA NA 224143 TCGA-AB-2988 AML21 9 91899422 91899422 C T SNP ENSG00000219080 ENST00000405139 human ensembl 54_36p -1 known 5_prime_flanking_region c.-14801 NULL 0 - - - no_coding_region:pseudogene tier3 880 19 2.11 526 401 43.26 NA NA NA 224143 TCGA-AB-2988 AML21 9 94462864 94462864 C T SNP IPPK NM_022755.4 human genbank 54_36p -1 validated intronic c.82-2080 e2-2080 0.001 - - - no_errors tier3 146 4 2.67 126 69 35.38 NA NA NA 224143 TCGA-AB-2988 AML21 9 94618193 94618193 C T SNP ANKRD19 ENST00000375504 human ensembl 54_36p 1 known intronic c.495+2043 e3+2043 0.022 - - - no_errors tier2 90 2 2.17 87 78 47.27 NA NA NA 224143 TCGA-AB-2988 AML21 9 103164661 103164661 G A SNP BAAT NM_001701.1 human genbank 54_36p -1 reviewed missense c.1127 p.T376M 0 "HMMPfam_BAAT_C,superfamily_SSF53474" "HMMPfam_Bile_Hydr_Trans,HMMPfam_BAAT_C,superfamily_SSF53474" - no_errors tier1 757 20 2.57 641 600 48.35 NA NA NA 224143 TCGA-AB-2988 AML21 9 107852164 107852164 G A SNP - - - - - - - - - - - - - - - tier3 554 11 1.94 457 401 46.74 NA NA NA 224143 TCGA-AB-2988 AML21 9 112094676 112094676 C T SNP TXN NM_003329.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-36140 NULL 0.003 - - - no_errors tier3 449 6 1.32 287 217 43.06 NA NA NA 224143 TCGA-AB-2988 AML21 9 113948058 113948058 T C SNP SUSD1 NM_022486.3 human genbank 54_36p -1 validated intronic c.374-2334 e4-2334 0 - - - no_errors tier3 860 23 2.6 405 316 43.83 NA NA NA 224143 TCGA-AB-2988 AML21 9 115940632 115940632 T A SNP COL27A1 NM_032888.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-17420 NULL 0 - - - no_errors tier3 572 13 2.21 268 190 41.39 NA NA NA 224143 TCGA-AB-2988 AML21 9 119981397 119981397 G A SNP - - - - - - - - - - - - - - - tier3 454 8 1.73 440 328 42.71 NA NA NA 224143 TCGA-AB-2988 AML21 9 125476714 125476714 G A SNP DENND1A NM_020946.1 human genbank 54_36p -1 validated intronic c.372+2106 e6+2106 0 - - - no_errors tier3 741 18 2.37 660 493 42.72 NA NA NA 224143 TCGA-AB-2988 AML21 9 126919139 126919139 A G SNP C9orf126 NM_173690.1 human genbank 54_36p -1 validated intronic c.98+25594 e2+25594 0.002 - - - no_errors tier3 524 9 1.69 271 229 45.8 NA NA NA 224143 TCGA-AB-2988 AML21 9 129001440 129001440 A T SNP RALGPS1 NM_014636.1 human genbank 54_36p 1 provisional intronic c.1247+274 e13+274 0.007 - - - no_errors tier2 392 8 2 226 181 44.36 NA NA NA 224143 TCGA-AB-2988 AML21 9 131543121 131543121 C T SNP PTGES NM_004878.4 human genbank 54_36p -1 reviewed intronic c.210-1161 e3-1161 0.001 - - - no_errors tier3 137 4 2.84 50 46 47.92 NA NA NA 224143 TCGA-AB-2988 AML21 9 131946907 131946907 C T SNP FREQ NM_014286.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27857 NULL 0.006 - - - no_errors tier3 323 8 2.41 202 145 41.79 NA NA NA 224143 TCGA-AB-2988 AML21 9 133441027 133441027 C G SNP UCK1 NM_031432.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44645 NULL 0.002 - - - no_errors tier3 301 9 2.9 211 116 35.47 NA NA NA 224143 TCGA-AB-2988 AML21 9 138136401 138136402 - A INS NACC2 NM_144653.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-54213 NULL 0.005:0.003 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 10 4440047 4440047 C T SNP LOC728544 XM_001127725.1 human genbank 54_36p 1 model intronic c.110-600 e3-600 0.998 - - - no_errors tier3 550 10 1.79 710 565 44.31 NA NA NA 224143 TCGA-AB-2988 AML21 10 4859992 4859992 C T SNP AKR1CL2 NM_001040177.1 human genbank 54_36p 1 provisional intronic c.39+1437 e1+1437 0.005 - - - no_errors tier3 384 15 3.76 249 179 41.72 NA NA NA 224143 TCGA-AB-2988 AML21 10 23912132 23912132 A T SNP - - - - - - - - - - - - - - - tier3 436 8 1.8 605 508 45.64 NA NA NA 224143 TCGA-AB-2988 AML21 10 27946305 27946305 C G SNP - - - - - - - - - - - - - - - tier3 620 19 2.97 494 437 46.94 NA NA NA 224143 TCGA-AB-2988 AML21 10 29820683 29820683 G T SNP SVIL NM_021738.3 human genbank 54_36p -1 reviewed intronic c.4020-729 e19-729 0 - - - no_errors tier3 313 5 1.57 210 168 44.44 NA NA NA 224143 TCGA-AB-2988 AML21 10 36256452 36256452 G A SNP - - - - - - - - - - - - - - - tier3 646 15 2.27 563 449 44.24 NA NA NA 224143 TCGA-AB-2988 AML21 10 48202514 48202514 C G SNP - - - - - - - - - - - - - - - tier3 640 13 1.99 357 272 43.24 NA NA NA 224143 TCGA-AB-2988 AML21 10 49249034 49249034 T C SNP MAPK8 ENST00000374189 human ensembl 54_36p 1 known intronic c.1-30627 e1-30627 0.01 - - - no_errors tier3 746 25 3.23 870 680 43.87 NA NA NA 224143 TCGA-AB-2988 AML21 10 54863524 54863524 G A SNP ENSG00000209957 ENST00000387222 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24430 NULL 0 - - - pseudogene tier3 272 8 2.86 348 221 38.84 NA NA NA 224143 TCGA-AB-2988 AML21 10 56584561 56584561 T A SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+11781 e0+11781 0.001 - - - no_errors tier3 585 11 1.85 481 368 43.24 NA NA NA 224143 TCGA-AB-2988 AML21 10 57022485 57022485 T G SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+34906 e0+34906 0.009 - - - no_errors tier3 231 7 2.94 257 169 39.67 NA NA NA 224143 TCGA-AB-2988 AML21 10 57563663 57563663 C T SNP - - - - - - - - - - - - - - - tier3 905 12 1.31 549 376 40.65 NA NA NA 224143 TCGA-AB-2988 AML21 10 70937736 70937736 C A SNP TSPAN15 NM_012339.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*996 NULL 0 - - - no_errors tier2 630 12 1.87 373 339 47.48 NA NA NA 224143 TCGA-AB-2988 AML21 10 71118850 71118850 G A SNP - - - - - - - - - - - - - - - tier3 578 14 2.36 493 412 45.52 NA NA NA 224143 TCGA-AB-2988 AML21 10 72593442 72593442 G A SNP UNC5B NM_170744.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49307 NULL 0.013 - - - no_errors tier3 543 4 0.73 507 461 47.62 NA NA NA 224143 TCGA-AB-2988 AML21 10 102537840 102537840 C T SNP PAX2 NM_003990.3 human genbank 54_36p 1 reviewed intronic c.685+1082 e6+1082 1 - - - no_errors tier2 731 10 1.35 505 399 43.99 NA NA NA 224143 TCGA-AB-2988 AML21 10 107143239 107143239 G A SNP - - - - - - - - - - - - - - - tier3 846 29 3.31 613 410 40.04 NA NA NA 224143 TCGA-AB-2988 AML21 10 107408713 107408713 A C SNP ENSG00000213260 ENST00000393174 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-27357 NULL 0.048 - - - no_coding_region:pseudogene tier2 559 24 4.12 597 501 45.59 NA NA NA 224143 TCGA-AB-2988 AML21 10 110008252 110008252 T C SNP ENSG00000217870 ENST00000401516 human ensembl 54_36p 1 known 5_prime_flanking_region c.-37595 NULL 0 - - - no_coding_region:pseudogene tier3 432 8 1.82 545 395 41.93 NA NA NA 224143 TCGA-AB-2988 AML21 10 111277845 111277845 C T SNP ENSG00000218906 ENST00000404325 human ensembl 54_36p 1 known 5_prime_flanking_region c.-22 NULL 0.005 - - - no_coding_region:pseudogene tier3 662 18 2.65 524 452 46.22 NA NA NA 224143 TCGA-AB-2988 AML21 10 111489433 111489433 C T SNP - - - - - - - - - - - - - - - tier3 476 9 1.86 548 407 42.62 NA NA NA 224143 TCGA-AB-2988 AML21 10 117747450 117747450 C A SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*53170 NULL 0.002 - - - no_errors tier3 997 32 3.11 825 637 43.57 NA NA NA 224143 TCGA-AB-2988 AML21 10 118557589 118557589 G A SNP DKFZp781N1041 XM_370577.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-41479 NULL 0.001 - - - no_errors tier3 440 12 2.65 365 303 45.36 NA NA NA 224143 TCGA-AB-2988 AML21 10 119999630 119999630 A G SNP C10orf84 ENST00000369172 human ensembl 54_36p -1 known intronic c.702-21700 e8-21700 0 - - - no_errors tier3 698 18 2.51 576 441 43.32 NA NA NA 224143 TCGA-AB-2988 AML21 10 124856564 124856564 A C SNP BUB3 NM_004725.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47860 NULL 1 - - - no_errors tier2 496 8 1.59 498 393 44.11 NA NA NA 224143 TCGA-AB-2988 AML21 10 124856566 124856566 A T SNP BUB3 NM_004725.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47858 NULL 1 - - - no_errors tier2 499 8 1.57 496 396 44.39 NA NA NA 224143 TCGA-AB-2988 AML21 10 128793585 128793585 A G SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.2383-900 e24-900 0 - - - no_errors tier3 1377 23 1.64 822 607 42.45 NA NA NA 224143 TCGA-AB-2988 AML21 10 132570430 132570430 G A SNP - - - - - - - - - - - - - - - tier3 489 15 2.97 410 330 44.59 NA NA NA 224143 TCGA-AB-2988 AML21 11 1226345 1226345 C A SNP MUC5B NM_002458.1 human genbank 54_36p 1 validated missense c.11668 p.P3890T 0 NULL "HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_VWD,HMMSmart_SM00216,superfamily_Serine proterase inhibitors,HMMSmart_SM00041,PatternScan_CTCK_1,HMMPfam_Cys_knot,HMMSmart_SM00215,superfamily_PMP inhibitors,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 4 1 20 8 12 60 NA NA NA 224143 TCGA-AB-2988 AML21 11 1228728 1228728 C T SNP MUC5B NM_002458.1 human genbank 54_36p 1 validated missense c.14051 p.T4684I 0.023 NULL "HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_VWD,HMMSmart_SM00216,superfamily_Serine proterase inhibitors,HMMSmart_SM00041,PatternScan_CTCK_1,HMMPfam_Cys_knot,HMMSmart_SM00215,superfamily_PMP inhibitors,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 3 0 1 100 NA NA NA 224143 TCGA-AB-2988 AML21 11 2959849 2959849 A T SNP NAP1L4 NM_005969.3 human genbank 54_36p -1 reviewed intronic c.1-2806 e1-2806 0.001 - - - no_errors tier3 668 11 1.62 393 277 41.34 NA NA NA 224143 TCGA-AB-2988 AML21 11 11565166 11565166 A G SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated intronic c.235+34316 e1+34316 0 - - - no_errors tier3 640 13 1.99 535 371 40.95 NA NA NA 224143 TCGA-AB-2988 AML21 11 12679342 12679342 T - DEL TEAD1 NM_021961.4 human genbank 54_36p 1 validated intronic c.1+25658 e0+25658 0.008 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 11 19138761 19138761 T G SNP ZDHHC13 NM_019028.1 human genbank 54_36p 1 validated intronic c.1108+1598 e10+1598 0.022 - - - no_errors tier3 151 6 3.82 186 128 40.76 NA NA NA 224143 TCGA-AB-2988 AML21 11 23708861 23708861 G T SNP - - - - - - - - - - - - - - - tier2 456 1 0.22 319 227 41.5 NA NA NA 224143 TCGA-AB-2988 AML21 11 27691694 27691694 G A SNP BDNF NM_170731.1 human genbank 54_36p -1 reviewed intronic c.3+7841 e1+7841 0.005 - - - no_errors tier2 441 9 2 260 205 44.09 NA NA NA 224143 TCGA-AB-2988 AML21 11 28635965 28635965 G C SNP - - - - - - - - - - - - - - - tier2 560 8 1.41 642 461 41.8 NA NA NA 224143 TCGA-AB-2988 AML21 11 30575498 30575498 G A SNP MPPED2 NM_001584.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-17002 NULL 0.984 - - - no_errors tier3 507 4 0.78 438 324 42.52 NA NA NA 224143 TCGA-AB-2988 AML21 11 32953679 32953679 G T SNP QSER1 NM_001076786.1 human genbank 54_36p 1 provisional intronic c.5067+214 e10+214 0.001 - - - no_errors tier2 386 10 2.52 488 368 42.99 NA NA NA 224143 TCGA-AB-2988 AML21 11 38285828 38285828 C T SNP - - - - - - - - - - - - - - - tier3 428 7 1.61 262 198 43.04 NA NA NA 224143 TCGA-AB-2988 AML21 11 43205620 43205620 A - DEL LOC399881 XR_040375.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*34010 NULL 0.001 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 11 51246143 51246143 G A SNP OR4A5 NM_001005272.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*21881 NULL 0 - - - no_errors tier3 260 7 2.62 383 335 46.66 NA NA NA 224143 TCGA-AB-2988 AML21 11 56268473 56268473 A G SNP OR9G4 NM_001005284.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-610 NULL 0.001 - - - no_errors tier3 837 13 1.53 624 458 42.33 NA NA NA 224143 TCGA-AB-2988 AML21 11 70797961 70797961 G A SNP ENSG00000172900 ENST00000331301 human ensembl 54_36p -1 known intronic c.1-1485 e1-1485 0 - - - no_errors tier3 259 3 1.15 150 112 42.75 NA NA NA 224143 TCGA-AB-2988 AML21 11 79380178 79380178 G A SNP - - - - - - - - - - - - - - - tier3 469 8 1.68 539 407 43.02 NA NA NA 224143 TCGA-AB-2988 AML21 11 79963608 79963608 A G SNP ENSG00000200146 ENST00000363276 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46850 NULL 0.071 - - - no_errors tier3 365 8 2.14 306 246 44.57 NA NA NA 224143 TCGA-AB-2988 AML21 11 88111615 88111615 C T SNP GRM5 NM_000842.2 human genbank 54_36p -1 reviewed intronic c.912-85396 e3-85396 0 - - - no_errors tier3 666 14 2.06 706 628 47.04 NA NA NA 224143 TCGA-AB-2988 AML21 11 88822822 88822822 A G SNP NOX4 NM_016931.1 human genbank 54_36p -1 reviewed intronic c.265-482 e4-482 0 - - - no_errors tier3 617 9 1.44 780 574 42.39 NA NA NA 224143 TCGA-AB-2988 AML21 11 92649984 92649984 T C SNP - - - - - - - - - - - - - - - tier3 263 5 1.87 287 176 38.01 NA NA NA 224143 TCGA-AB-2988 AML21 11 93441691 93441691 A G SNP HEPHL1 NM_001098672.1 human genbank 54_36p 1 validated intronic c.1063+1127 e5+1127 0.004 - - - no_errors tier3 582 18 3 477 367 43.48 NA NA NA 224143 TCGA-AB-2988 AML21 11 96751468 96751468 C T SNP - - - - - - - - - - - - - - - tier3 542 2 0.37 597 343 36.49 NA NA NA 224143 TCGA-AB-2988 AML21 11 98631545 98631545 C T SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-69742 e1-69742 0.01 - - - no_errors tier3 244 0 0 257 188 42.25 NA NA NA 224143 TCGA-AB-2988 AML21 11 103714353 103714353 C T SNP - - - - - - - - - - - - - - - tier3 332 4 1.19 477 371 43.75 NA NA NA 224143 TCGA-AB-2988 AML21 11 105051895 105051895 C T SNP GRIA4 NM_000829.3 human genbank 54_36p 1 reviewed intronic c.247+63524 e2+63524 0 - - - no_errors tier3 342 2 0.58 367 301 45.06 NA NA NA 224143 TCGA-AB-2988 AML21 11 110473623 110473623 T C SNP - - - - - - - - - - - - - - - tier3 824 18 2.14 626 518 45.12 NA NA NA 224143 TCGA-AB-2988 AML21 11 113479732 113479732 A G SNP ZBTB16 NM_001018011.1 human genbank 54_36p 1 reviewed intronic c.1268+39232 e1+39232 0 - - - no_errors tier3 903 18 1.95 506 450 47.07 NA NA NA 224143 TCGA-AB-2988 AML21 11 120523821 120523821 A G SNP TECTA NM_005422.2 human genbank 54_36p 1 reviewed intronic c.4105+1786 e11+1786 0 - - - no_errors tier3 527 7 1.31 202 171 45.72 NA NA NA 224143 TCGA-AB-2988 AML21 11 125889413 125889413 G A SNP KIRREL3 NM_032531.2 human genbank 54_36p -1 provisional intronic c.433+7007 e4+7007 0.703 - - - no_errors tier3 736 18 2.38 379 304 44.51 NA NA NA 224143 TCGA-AB-2988 AML21 11 127426437 127426437 C T SNP - - - - - - - - - - - - - - - tier3 1137 26 2.24 949 771 44.77 NA NA NA 224143 TCGA-AB-2988 AML21 11 130164274 130164274 G A SNP - - - - - - - - - - - - - - - tier3 603 10 1.63 416 315 43.03 NA NA NA 224143 TCGA-AB-2988 AML21 11 131477589 131477589 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.168-43797 e3-43797 0 - - - no_errors tier3 801 22 2.67 520 399 43.37 NA NA NA 224143 TCGA-AB-2988 AML21 11 131872039 131872039 C T SNP OPCML NM_002545.1 human genbank 54_36p -1 reviewed intronic c.526+32126 e3+32126 0 - - - no_errors tier3 769 18 2.29 717 592 45.23 NA NA NA 224143 TCGA-AB-2988 AML21 12 2392253 2392253 G A SNP CACNA1C NM_000719.6 human genbank 54_36p 1 reviewed intronic c.478-36150 e4-36150 0 - - - no_errors tier3 520 8 1.51 259 203 43.94 NA NA NA 224143 TCGA-AB-2988 AML21 12 3173024 3173024 G A SNP TSPAN9 NM_006675.3 human genbank 54_36p 1 reviewed intronic c.1-7580 e1-7580 0.399 - - - no_errors tier3 2087 44 2.06 951 600 38.66 NA NA NA 224143 TCGA-AB-2988 AML21 12 13377801 13377801 T C SNP C12orf36 NM_182558.1 human genbank 54_36p -1 predicted 3_prime_flanking_region c.*39604 NULL 0.064 - - - no_errors tier3 845 37 4.2 869 724 45.45 NA NA NA 224143 TCGA-AB-2988 AML21 12 17177337 17177337 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 12 18179730 18179730 A - DEL RERGL NM_024730.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-46246 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 12 19049752 19049752 G A SNP - - - - - - - - - - - - - - - tier3 303 6 1.94 267 200 42.83 NA NA NA 224143 TCGA-AB-2988 AML21 12 22961151 22961151 G A SNP - - - - - - - - - - - - - - - tier2 368 8 2.13 469 360 43.43 NA NA NA 224143 TCGA-AB-2988 AML21 12 23708370 23708370 C T SNP SOX5 NM_006940.4 human genbank 54_36p -1 reviewed intronic c.931+1275 e7+1275 0.001 - - - no_errors tier3 310 1 0.32 355 237 40.03 NA NA NA 224143 TCGA-AB-2988 AML21 12 24209134 24209134 A G SNP SOX5 NM_152989.4 human genbank 54_36p -1 reviewed intronic c.1+112283 e0+112283 0.001 - - - no_errors tier3 148 5 3.27 260 160 38.1 NA NA NA 224143 TCGA-AB-2988 AML21 12 33326894 33326894 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 12 42913488 42913488 A G SNP TMEM117 NM_032256.1 human genbank 54_36p 1 provisional intronic c.608+22051 e4+22051 0.654 - - - no_errors tier3 357 8 2.19 517 389 42.94 NA NA NA 224143 TCGA-AB-2988 AML21 12 51435802 51435802 G A SNP ENSG00000181735 ENST00000314555 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7652 NULL 0.054 - - - no_coding_region:pseudogene tier3 616 14 2.22 518 420 44.78 NA NA NA 224143 TCGA-AB-2988 AML21 12 61635513 61635513 T - DEL PPM1H NM_020700.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20730 NULL 0.039 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 12 69837513 69837513 C A SNP TSPAN8 NM_004616.2 human genbank 54_36p -1 reviewed intronic c.60+153 e1+153 1 - - - no_errors tier3 312 7 2.19 244 183 42.86 NA NA NA 224143 TCGA-AB-2988 AML21 12 70852484 70852484 T A SNP - - - - - - - - - - - - - - - tier3 413 10 2.36 451 359 44.27 NA NA NA 224143 TCGA-AB-2988 AML21 12 85559657 85559657 G A SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+85460 e0+85460 0.004 - - - no_errors tier3 441 5 1.12 508 338 39.91 NA NA NA 224143 TCGA-AB-2988 AML21 12 86488073 86488073 C T SNP - - - - - - - - - - - - - - - tier3 237 1 0.42 236 208 46.85 NA NA NA 224143 TCGA-AB-2988 AML21 12 87839587 87839587 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 12 90101419 90101419 T C SNP DCN NM_001920.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4959 NULL 0 - - - no_errors tier3 348 10 2.79 373 299 44.49 NA NA NA 224143 TCGA-AB-2988 AML21 12 91191736 91191736 C T SNP - - - - - - - - - - - - - - - tier3 1105 26 2.29 802 628 43.85 NA NA NA 224143 TCGA-AB-2988 AML21 12 111054352 111054353 - T INS TRAFD1 NM_006700.1 human genbank 54_36p 1 validated intronic c.47+1596_47+1595 e1+1596 0.179:0.175 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 12 115352260 115352260 A T SNP - - - - - - - - - - - - - - - tier2 942 24 2.48 601 506 45.71 NA NA NA 224143 TCGA-AB-2988 AML21 12 116124784 116124784 G A SNP NOS1 ENST00000397607 human ensembl 54_36p -1 known intronic c.4290-4272 e28-4272 0 - - - no_stop_codon tier3 1015 23 2.21 425 310 42.18 NA NA NA 224143 TCGA-AB-2988 AML21 12 118231133 118231133 G A SNP CCDC60 NM_178499.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26232 NULL 0.002 - - - no_errors tier3 761 9 1.17 428 291 40.42 NA NA NA 224143 TCGA-AB-2988 AML21 12 119292914 119292914 C G SNP MSI1 NM_002442.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-1637 NULL 0.001 - - - no_errors tier3 78 5 6.02 40 44 51.76 NA NA NA 224143 TCGA-AB-2988 AML21 12 119754256 119754256 A C SNP SPPL3 NM_139015.3 human genbank 54_36p -1 validated intronic c.24-21184 e2-21184 0.001 - - - no_errors tier3 266 4 1.48 144 90 38.46 NA NA NA 224143 TCGA-AB-2988 AML21 12 122873755 122873755 G A SNP DNAH10 ENST00000409039 human ensembl 54_36p 1 known intronic c.3825+2497 e23+2497 0 - - - no_errors tier3 561 27 4.59 438 412 48.3 NA NA NA 224143 TCGA-AB-2988 AML21 12 127718414 127718414 T C SNP TMEM132C ENST00000315208 human ensembl 54_36p 1 known intronic c.154-1501 e2-1501 0.004 - - - no_errors tier3 1162 16 1.36 533 456 46.01 NA NA NA 224143 TCGA-AB-2988 AML21 12 127850202 127850202 G T SNP SLC15A4 NM_145648.3 human genbank 54_36p -1 validated intronic c.1415-287 e7-287 0 - - - no_errors tier2 216 5 2.26 210 157 42.78 NA NA NA 224143 TCGA-AB-2988 AML21 12 128534459 128534459 A G SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1115+47098 e3+47098 0.005 - - - no_errors tier3 507 20 3.8 361 290 44.55 NA NA NA 224143 TCGA-AB-2988 AML21 12 130146289 130146289 C T SNP GPR133 NM_198827.3 human genbank 54_36p 1 validated intronic c.1672-9040 e16-9040 0 - - - no_errors tier3 349 5 1.41 172 142 45.22 NA NA NA 224143 TCGA-AB-2988 AML21 12 131086997 131086997 C T SNP EP400 NM_015409.3 human genbank 54_36p 1 validated intronic c.5949-1183 e30-1183 0.983 - - - no_errors tier3 178 3 1.66 90 62 40.79 NA NA NA 224143 TCGA-AB-2988 AML21 13 22650586 22650586 G C SNP SGCG NM_000231.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25248 NULL 0.138 - - - no_errors tier3 611 20 3.17 108 567 84 NA NA NA 224143 TCGA-AB-2988 AML21 13 23809893 23809893 G A SNP C1QTNF9 NM_178540.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*15987 NULL 0.001 - - - no_errors tier3 161 7 4.17 34 194 85.09 NA NA NA 224143 TCGA-AB-2988 AML21 13 27506214 27506215 - TTACCAAACTCTAAATTTTCTCTTGGAAACTCCCAT INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins in_frame_ins 0.779:0.796 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 13 37496695 37496695 C T SNP ENSG00000217350 ENST00000403854 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29838 NULL 0.001 - - - no_coding_region:pseudogene tier3 454 8 1.73 109 509 82.36 NA NA NA 224143 TCGA-AB-2988 AML21 13 49896694 49896694 C T SNP - - - - - - - - - - - - - - - tier3 565 13 2.25 111 760 87.26 NA NA NA 224143 TCGA-AB-2988 AML21 13 52534200 52534200 A T SNP OLFM4 NM_006418.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*11293 NULL 0 - - - no_errors tier3 437 11 2.46 76 545 87.48 NA NA NA 224143 TCGA-AB-2988 AML21 13 52903072 52903072 G T SNP - - - - - - - - - - - - - - - tier3 352 7 1.95 51 320 86.25 NA NA NA 224143 TCGA-AB-2988 AML21 13 56174121 56174121 G T SNP - - - - - - - - - - - - - - - tier3 349 6 1.69 111 520 82.41 NA NA NA 224143 TCGA-AB-2988 AML21 13 60227569 60227569 G A SNP ENSG00000206854 ENST00000384127 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-34126 NULL 0.001 - - - no_errors tier3 633 29 4.38 220 1248 84.96 NA NA NA 224143 TCGA-AB-2988 AML21 13 65633509 65633509 C T SNP - - - - - - - - - - - - - - - tier3 286 5 1.72 119 507 80.99 NA NA NA 224143 TCGA-AB-2988 AML21 13 77114864 77114864 T C SNP SCEL NM_144777.2 human genbank 54_36p 1 reviewed missense c.1970 p.L657S 1 "HMMSmart_SM00132,PatternScan_LIM_DOMAIN_1" "HMMSmart_SM00132,PatternScan_LIM_DOMAIN_1" - no_errors tier1 467 17 3.51 72 449 86.18 NA NA NA 224143 TCGA-AB-2988 AML21 13 80947186 80947186 C T SNP - - - - - - - - - - - - - - - tier3 507 19 3.61 126 701 84.76 NA NA NA 224143 TCGA-AB-2988 AML21 13 81974499 81974499 A C SNP - - - - - - - - - - - - - - - tier3 650 14 2.11 155 755 82.88 NA NA NA 224143 TCGA-AB-2988 AML21 13 82184581 82184581 T G SNP - - - - - - - - - - - - - - - tier3 531 11 2.03 151 832 84.64 NA NA NA 224143 TCGA-AB-2988 AML21 13 87216328 87216328 G A SNP - - - - - - - - - - - - - - - tier3 436 9 2.02 139 791 84.78 NA NA NA 224143 TCGA-AB-2988 AML21 13 92632784 92632784 C G SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-44927 NULL 0.062 - - - no_errors tier3 531 19 3.45 131 769 85.35 NA NA NA 224143 TCGA-AB-2988 AML21 13 94256150 94256150 A T SNP ENSG00000216894 ENST00000403940 human ensembl 54_36p -1 known 5_prime_flanking_region c.-44880 NULL 0.082 - - - no_coding_region:pseudogene tier3 481 19 3.8 1198 280 18.94 NA NA NA 224143 TCGA-AB-2988 AML21 13 95694255 95694255 A G SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+152431 e1+152431 0.289 - - - no_errors tier2 475 16 3.26 132 880 86.96 NA NA NA 224143 TCGA-AB-2988 AML21 13 99365906 99365906 T A SNP ENSG00000210405 ENST00000387670 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16233 NULL 0.002 - - - pseudogene tier3 530 18 3.28 60 431 87.6 NA NA NA 224143 TCGA-AB-2988 AML21 13 109780266 109780266 C T SNP COL4A2 NM_001846.2 human genbank 54_36p 1 reviewed intronic c.99+21795 e2+21795 0.001 - - - no_errors tier2 385 18 4.47 57 347 85.89 NA NA NA 224143 TCGA-AB-2988 AML21 13 112552790 112552790 A C SNP ATP11A NM_032189.2 human genbank 54_36p 1 reviewed intronic c.1810-562 e18-562 0.01 - - - no_errors tier3 203 6 2.87 27 148 84.57 NA NA NA 224143 TCGA-AB-2988 AML21 13 112943373 112943373 A C SNP CUL4A NM_001008895.1 human genbank 54_36p 1 validated intronic c.1035+1507 e10+1507 0 - - - no_errors tier3 425 17 3.84 81 360 81.63 NA NA NA 224143 TCGA-AB-2988 AML21 14 20231582 20231582 G A SNP ANG NM_001097577.2 human genbank 54_36p 1 reviewed missense c.19 p.V7I 0.001 NULL "HMMPfam_RnaseA,HMMSmart_SM00092,PatternScan_RNASE_PANCREATIC,superfamily_RNase A-like" - no_errors tier1 551 5 0.9 346 314 47.43 NA NA NA 224143 TCGA-AB-2988 AML21 14 27081282 27081282 G A SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model intronic c.201+114207 e2+114207 0.001 - - - no_errors tier3 409 18 4.22 408 292 41.71 NA NA NA 224143 TCGA-AB-2988 AML21 14 40152245 40152245 G A SNP - - - - - - - - - - - - - - - tier3 534 9 1.66 314 247 44.03 NA NA NA 224143 TCGA-AB-2988 AML21 14 40795007 40795007 A G SNP - - - - - - - - - - - - - - - tier3 490 18 3.54 521 440 45.79 NA NA NA 224143 TCGA-AB-2988 AML21 14 41196730 41196730 C T SNP LRFN5 NM_152447.3 human genbank 54_36p 1 validated intronic c.1+49215 e0+49215 0 - - - no_errors tier2 490 17 3.35 402 327 44.79 NA NA NA 224143 TCGA-AB-2988 AML21 14 44187345 44187345 C T SNP - - - - - - - - - - - - - - - tier3 268 1 0.37 336 240 41.67 NA NA NA 224143 TCGA-AB-2988 AML21 14 49661102 49661103 - A INS SOS2 NM_006939.2 human genbank 54_36p -1 validated intronic c.3380-4251_3380-4250 e22-4250 0.003:0.002 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 14 50302072 50302072 A G SNP NIN NM_020921.3 human genbank 54_36p -1 reviewed intronic c.1635+703 e12+703 0.006 - - - no_errors tier3 204 9 4.23 189 151 44.41 NA NA NA 224143 TCGA-AB-2988 AML21 14 51175006 51175006 G A SNP FRMD6 NM_001042481.1 human genbank 54_36p 1 validated intronic c.1-51153 e1-51153 0.094 - - - no_errors tier3 955 14 1.44 597 444 42.61 NA NA NA 224143 TCGA-AB-2988 AML21 14 54739903 54739903 T C SNP DLGAP5 NM_014750.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-14253 NULL 0.018 - - - no_errors tier3 404 6 1.46 307 231 42.94 NA NA NA 224143 TCGA-AB-2988 AML21 14 62374316 62374316 C T SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed intronic c.1569+11808 e8+11808 0 - - - no_errors tier3 397 9 2.22 501 321 39 NA NA NA 224143 TCGA-AB-2988 AML21 14 62744471 62744471 T C SNP RHOJ NM_020663.3 human genbank 54_36p 1 provisional intronic c.178+2953 e1+2953 0 - - - no_errors tier2 607 9 1.46 589 461 43.86 NA NA NA 224143 TCGA-AB-2988 AML21 14 71567077 71567077 C A SNP RGS6 NM_004296.4 human genbank 54_36p 1 validated intronic c.84+65732 e1+65732 0.003 - - - no_errors tier3 641 20 3.03 812 637 43.9 NA NA NA 224143 TCGA-AB-2988 AML21 14 72008283 72008283 A G SNP RGS6 NM_004296.4 human genbank 54_36p 1 validated intronic c.537-1050 e8-1050 0 - - - no_errors tier3 557 12 2.11 431 294 40.55 NA NA NA 224143 TCGA-AB-2988 AML21 14 84079440 84079440 C A SNP - - - - - - - - - - - - - - - tier3 247 2 0.8 424 237 35.85 NA NA NA 224143 TCGA-AB-2988 AML21 14 84435411 84435411 G A SNP - - - - - - - - - - - - - - - tier3 324 7 2.11 410 327 44.37 NA NA NA 224143 TCGA-AB-2988 AML21 14 89408207 89408207 A T SNP C14orf143 NM_145231.2 human genbank 54_36p -1 validated intronic c.410+59431 e5+59431 0.041 - - - no_errors tier3 398 9 2.21 286 277 49.11 NA NA NA 224143 TCGA-AB-2988 AML21 14 98041851 98041851 T A SNP - - - - - - - - - - - - - - - tier3 441 11 2.43 449 343 43.31 NA NA NA 224143 TCGA-AB-2988 AML21 14 98070511 98070511 C T SNP - - - - - - - - - - - - - - - tier3 690 6 0.86 545 427 43.93 NA NA NA 224143 TCGA-AB-2988 AML21 14 98729481 98729481 C T SNP BCL11B NM_138576.1 human genbank 54_36p -1 reviewed intronic c.641-17196 e4-17196 1 - - - no_errors tier2 1267 20 1.55 665 519 43.83 NA NA NA 224143 TCGA-AB-2988 AML21 14 103973721 103973721 G A SNP ENSG00000222761 ENST00000410829 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35291 NULL 0.047 - - - no_errors tier3 105 6 5.41 59 43 42.16 NA NA NA 224143 TCGA-AB-2988 AML21 14 104156590 104156590 C T SNP TMEM179 NM_207379.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-14467 NULL 0.001 - - - no_errors tier3 476 8 1.65 187 151 44.67 NA NA NA 224143 TCGA-AB-2988 AML21 14 104906783 104906783 C T SNP PACS2 NM_001100913.1 human genbank 54_36p 1 validated intronic c.742-440 e8-440 0.006 - - - no_errors tier2 89 5 5.32 47 44 48.35 NA NA NA 224143 TCGA-AB-2988 AML21 15 21588008 21588008 C A SNP ENSG00000206616 ENST00000383889 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14225 NULL 0.002 - - - no_errors tier2 288 5 1.71 214 207 49.17 NA NA NA 224143 TCGA-AB-2988 AML21 15 22198858 22198858 T C SNP - - - - - - - - - - - - - - - tier3 388 10 2.5 323 324 50 NA NA NA 224143 TCGA-AB-2988 AML21 15 22753692 22753692 G A SNP SNRPN NM_003097.3 human genbank 54_36p 1 reviewed intronic c.1+2390 e0+2390 0.001 - - - no_errors tier3 392 8 2 206 171 45.36 NA NA NA 224143 TCGA-AB-2988 AML21 15 27540218 27540218 T C SNP - - - - - - - - - - - - - - - tier3 296 9 2.94 225 185 45.12 NA NA NA 224143 TCGA-AB-2988 AML21 15 38986492 38986492 C A SNP DLL4 NM_019074.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-22667 NULL 1 - - - no_errors tier2 122 2 1.61 66 43 39.45 NA NA NA 224143 TCGA-AB-2988 AML21 15 39955685 39955685 G A SNP SPTBN5 NM_016642.2 human genbank 54_36p -1 validated silent c.4041 p.N1347 0.001 "HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_Spectrin repeat" "PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Spectrin,superfamily_Calponin-homology domain CH-domain,HMMSmart_SM00150,superfamily_Spectrin repeat,superfamily_PH domain-like" - no_errors tier1 194 7 3.48 105 102 49.28 NA NA NA 224143 TCGA-AB-2988 AML21 15 44015630 44015630 T C SNP - - - - - - - - - - - - - - - tier3 745 24 3.12 464 386 45.41 NA NA NA 224143 TCGA-AB-2988 AML21 15 44920975 44920975 T C SNP ENSG00000214983 ENST00000399372 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13525 NULL 0.006 - - - no_coding_region:pseudogene tier3 465 12 2.52 465 359 43.57 NA NA NA 224143 TCGA-AB-2988 AML21 15 46106109 46106109 C T SNP - - - - - - - - - - - - - - - tier3 781 11 1.39 747 515 40.81 NA NA NA 224143 TCGA-AB-2988 AML21 15 46959849 46959849 T A SNP SHC4 NM_203349.3 human genbank 54_36p -1 validated intronic c.840+3888 e4+3888 0.037 - - - no_errors tier2 708 10 1.39 564 511 47.49 NA NA NA 224143 TCGA-AB-2988 AML21 15 48083718 48083718 A C SNP ATP8B4 NM_024837.2 human genbank 54_36p -1 validated intronic c.436-2006 e7-2006 0 - - - no_errors tier2 621 7 1.11 608 435 41.67 NA NA NA 224143 TCGA-AB-2988 AML21 15 56187476 56187476 T A SNP ALDH1A2 NM_003888.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42336 NULL 0.168 - - - no_errors tier3 571 14 2.39 419 325 43.68 NA NA NA 224143 TCGA-AB-2988 AML21 15 57469646 57469646 G T SNP MYO1E NM_004998.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-17655 NULL 0 - - - no_errors tier3 515 17 3.2 405 331 44.91 NA NA NA 224143 TCGA-AB-2988 AML21 15 59588846 59588846 T A SNP - - - - - - - - - - - - - - - tier3 914 18 1.93 632 485 43.42 NA NA NA 224143 TCGA-AB-2988 AML21 15 60685259 60685259 A G SNP TLN2 NM_015059.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-41543 NULL 0 - - - no_errors tier3 922 12 1.28 797 574 41.87 NA NA NA 224143 TCGA-AB-2988 AML21 15 64882613 64882613 G A SNP LOC390597 XR_017154.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-5185 NULL 0.058 - - - pseudogene tier3 383 7 1.79 189 160 45.85 NA NA NA 224143 TCGA-AB-2988 AML21 15 67223696 67223696 G T SNP GLCE NM_015554.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-111504 NULL 0.008 - - - no_errors tier2 444 10 2.2 281 256 47.67 NA NA NA 224143 TCGA-AB-2988 AML21 15 68031324 68031324 T C SNP - - - - - - - - - - - - - - - tier3 666 7 1.04 435 402 47.97 NA NA NA 224143 TCGA-AB-2988 AML21 15 75176107 75176107 G A SNP TSPAN3 NM_005724.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25756 NULL 0 - - - no_errors tier3 454 13 2.78 285 248 46.53 NA NA NA 224143 TCGA-AB-2988 AML21 15 83209626 83209626 C T SNP ALPK3 NM_020778.4 human genbank 54_36p 1 validated intronic c.5329+726 e12+726 0.005 - - - no_errors tier3 326 8 2.4 230 213 48.08 NA NA NA 224143 TCGA-AB-2988 AML21 15 84306442 84306442 G C SNP - - - - - - - - - - - - - - - tier3 524 10 1.87 469 417 46.96 NA NA NA 224143 TCGA-AB-2988 AML21 15 84461880 84461880 C T SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26077 NULL 0.001 - - - no_errors tier3 723 12 1.63 776 537 40.9 NA NA NA 224143 TCGA-AB-2988 AML21 15 84699516 84699516 C T SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.2237-42085 e16-42085 0 - - - no_errors tier3 821 18 2.15 1150 806 41.19 NA NA NA 224143 TCGA-AB-2988 AML21 15 85255102 85255102 C A SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.3084-77120 e22-77120 0 - - - no_errors tier3 1092 22 1.97 659 488 42.55 NA NA NA 224143 TCGA-AB-2988 AML21 15 86598512 86598512 G A SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed intronic c.248+1629 e1+1629 0.001 - - - no_errors tier3 175 5 2.78 126 99 44 NA NA NA 224143 TCGA-AB-2988 AML21 15 89979291 89979291 G T SNP - - - - - - - - - - - - - - - tier3 708 2 0.28 1204 147 10.87 NA NA NA 224143 TCGA-AB-2988 AML21 15 93991950 93991950 C T SNP - - - - - - - - - - - - - - - tier3 247 8 3.14 181 128 41.29 NA NA NA 224143 TCGA-AB-2988 AML21 15 94127723 94127723 G A SNP ENSG00000208900 ENST00000386165 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1155 NULL 0.289 - - - pseudogene tier3 632 7 1.1 731 421 36.55 NA NA NA 224143 TCGA-AB-2988 AML21 16 5894328 5894328 C T SNP - - - - - - - - - - - - - - - tier2 557 8 1.42 315 260 45.14 NA NA NA 224143 TCGA-AB-2988 AML21 16 6462971 6462971 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+155912 e0+155912 0.002 - - - no_errors tier3 506 17 3.25 353 268 43.09 NA NA NA 224143 TCGA-AB-2988 AML21 16 27335488 27335488 T C SNP IL21R NM_181078.2 human genbank 54_36p 1 reviewed intronic c.1-13390 e1-13390 0.95 - - - no_errors tier2 442 11 2.43 370 288 43.77 NA NA NA 224143 TCGA-AB-2988 AML21 16 27833664 27833664 G C SNP GSG1L NM_001109763.1 human genbank 54_36p -1 validated intronic c.398-30204 e3-30204 0.002 - - - no_errors tier3 780 13 1.64 434 314 41.87 NA NA NA 224143 TCGA-AB-2988 AML21 16 28954005 28954006 - A INS LOC730153 XM_001717676.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-2651 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 16 48075899 48075900 - T INS ZNF423 NM_015069.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*6788 NULL 0.305:0.087 - - - no_errors tier2 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 16 49770925 49770925 G C SNP SALL1 NM_002968.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-28272 NULL 0 - - - no_errors tier3 341 9 2.57 329 280 45.9 NA NA NA 224143 TCGA-AB-2988 AML21 16 52992669 52992669 T A SNP - - - - - - - - - - - - - - - tier2 664 17 2.49 414 337 44.81 NA NA NA 224143 TCGA-AB-2988 AML21 16 53596103 53596103 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 16 58504517 58504517 T C SNP - - - - - - - - - - - - - - - tier3 285 8 2.73 380 254 40.06 NA NA NA 224143 TCGA-AB-2988 AML21 16 60386650 60386650 C A SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.1278-5763 e7-5763 0 - - - no_errors tier3 302 3 0.98 241 254 51.31 NA NA NA 224143 TCGA-AB-2988 AML21 16 64033720 64033720 A C SNP LOC283867 NM_001101346.1 human genbank 54_36p -1 inferred intronic c.1-78508 e1-78508 0.016 - - - no_errors tier2 407 9 2.16 266 224 45.71 NA NA NA 224143 TCGA-AB-2988 AML21 16 70573608 70573608 G A SNP PKD1L3 ENST00000335106 human ensembl 54_36p -1 known silent c.994 p.L332 0.72 NULL "HMMPfam_GPS,HMMSmart_SM00303,HMMPfam_PLAT,HMMSmart_SM00308,HMMPfam_Ion_trans,superfamily_Lipase/lipooxygenase domain (PLAT/LH2 domain),superfamily_C-type lectin-like" - no_errors tier1 599 14 2.28 323 309 48.74 NA NA NA 224143 TCGA-AB-2988 AML21 16 78766240 78766240 G A SNP LOC729847 XM_001131495.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*43356 NULL 0 - - - no_errors tier3 421 6 1.4 445 236 34.65 NA NA NA 224143 TCGA-AB-2988 AML21 16 81504431 81504431 T G SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.157+54852 e2+54852 0 - - - no_errors tier3 422 7 1.63 363 307 45.75 NA NA NA 224143 TCGA-AB-2988 AML21 16 81535924 81535924 C A SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.157+86345 e2+86345 0.001 - - - no_errors tier2 585 13 2.17 594 380 38.93 NA NA NA 224143 TCGA-AB-2988 AML21 16 82089182 82089182 G T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.960+11421 e7+11421 0.002 - - - no_errors tier3 1011 13 1.27 658 463 41.3 NA NA NA 224143 TCGA-AB-2988 AML21 16 82306524 82306524 G A SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.1539-32690 e11-32690 0 - - - no_errors tier3 639 19 2.89 381 329 46.34 NA NA NA 224143 TCGA-AB-2988 AML21 16 83426940 83426940 G A SNP CRISPLD2 NM_031476.3 human genbank 54_36p 1 validated intronic c.1-2589 e1-2589 0.005 - - - no_errors tier3 497 10 1.97 294 297 50.25 NA NA NA 224143 TCGA-AB-2988 AML21 16 84803634 84803634 C A SNP - - - - - - - - - - - - - - - tier3 1083 12 1.1 654 485 42.58 NA NA NA 224143 TCGA-AB-2988 AML21 16 85096551 85096551 G A SNP LOC283904 XM_001719681.1 human genbank 54_36p -1 model intronic c.268+3211 e2+3211 0.001 - - - no_errors tier2 91 3 3.12 111 85 43.37 NA NA NA 224143 TCGA-AB-2988 AML21 16 85897799 85897799 G A SNP uc002fju.2 ENST00000253461 human ensembl 54_36p -1 known intronic c.331-787 e4-787 0 - - - no_errors tier3 535 9 1.65 325 246 43.08 NA NA NA 224143 TCGA-AB-2988 AML21 16 86211221 86211221 G A SNP JPH3 NM_020655.2 human genbank 54_36p 1 reviewed intronic c.382+16586 e1+16586 0.183 - - - no_errors tier3 274 5 1.79 145 113 43.8 NA NA NA 224143 TCGA-AB-2988 AML21 16 87259566 87259566 C G SNP MVD NM_002461.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2577 NULL 0 - - - no_errors tier3 122 3 2.4 50 37 42.53 NA NA NA 224143 TCGA-AB-2988 AML21 17 4038544 4038544 T C SNP ANKFY1 NM_016376.3 human genbank 54_36p -1 validated intronic c.1470+882 e11+882 0 - - - no_errors tier3 254 9 3.42 159 172 51.96 NA NA NA 224143 TCGA-AB-2988 AML21 17 12171897 12171897 T A SNP - - - - - - - - - - - - - - - tier3 201 5 2.43 319 275 46.3 NA NA NA 224143 TCGA-AB-2988 AML21 17 12679630 12679630 G A SNP RICH2 NM_014859.4 human genbank 54_36p 1 validated intronic c.53+45697 e1+45697 0.03 - - - no_errors tier3 584 12 2.01 491 375 43.3 NA NA NA 224143 TCGA-AB-2988 AML21 17 12907370 12907370 C G SNP ELAC2 NM_018127.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-45381 NULL 0.04 - - - no_errors tier2 154 0 0 133 96 41.92 NA NA NA 224143 TCGA-AB-2988 AML21 17 12908435 12908435 G A SNP ELAC2 NM_018127.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-46446 NULL 0.029 - - - no_errors tier2 401 10 2.43 274 208 42.98 NA NA NA 224143 TCGA-AB-2988 AML21 17 14842130 14842130 C T SNP LOC441781 XR_017517.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-49890 NULL 0 - - - pseudogene tier2 903 23 2.45 527 387 41.84 NA NA NA 224143 TCGA-AB-2988 AML21 17 23223381 23223381 A G SNP LOC201229 NM_001076680.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*7245 NULL 0.011 - - - no_errors tier3 581 18 3.01 396 358 47.35 NA NA NA 224143 TCGA-AB-2988 AML21 17 23344812 23344812 C T SNP NLK NM_016231.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49215 NULL 0.002 - - - no_errors tier3 622 12 1.89 427 324 43.14 NA NA NA 224143 TCGA-AB-2988 AML21 17 32350114 32350114 G C SNP AATF NM_012138.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30425 NULL 0.001 - - - no_errors tier3 611 9 1.45 386 255 39.78 NA NA NA 224143 TCGA-AB-2988 AML21 17 32375476 32375476 C T SNP AATF NM_012138.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-5063 NULL 1 - - - no_errors tier2 102 3 2.86 109 73 40.11 NA NA NA 224143 TCGA-AB-2988 AML21 17 36817833 36817833 C T SNP ENSG00000220834 ENST00000404551 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-36817833 NULL 0.828 - - - no_coding_region:pseudogene tier3 445 12 2.63 308 230 42.75 NA NA NA 224143 TCGA-AB-2988 AML21 17 45454284 45454284 C G SNP ITGA3 NM_005501.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34519 NULL 0.004 - - - no_errors tier3 464 19 3.93 249 243 49.29 NA NA NA 224143 TCGA-AB-2988 AML21 17 49833173 49833173 C T SNP - - - - - - - - - - - - - - - tier3 693 16 2.25 650 564 46.38 NA NA NA 224143 TCGA-AB-2988 AML21 17 56879464 56879464 G T SNP TBX4 NM_018488.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-9170 NULL 0.005 - - - no_errors tier3 341 11 3.12 175 141 44.62 NA NA NA 224143 TCGA-AB-2988 AML21 17 64682512 64682512 T C SNP ABCA10 NM_080282.3 human genbank 54_36p -1 reviewed missense c.2879 p.K960R 0.597 NULL "HMMPfam_ABC_tran,HMMSmart_SM00382,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 461 7 1.5 363 305 45.66 NA NA NA 224143 TCGA-AB-2988 AML21 17 66091658 66091658 C G SNP - - - - - - - - - - - - - - - tier3 202 4 1.94 173 112 39.3 NA NA NA 224143 TCGA-AB-2988 AML21 17 68111955 68111955 G A SNP SLC39A11 NM_139177.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*43363 NULL 0.004 - - - no_errors tier2 820 18 2.15 356 284 44.31 NA NA NA 224143 TCGA-AB-2988 AML21 17 74767200 74767200 G A SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1-23718 e1-23718 0.004 - - - no_errors tier3 437 8 1.79 207 134 39.3 NA NA NA 224143 TCGA-AB-2988 AML21 18 1043425 1043425 C T SNP - - - - - - - - - - - - - - - tier3 651 12 1.8 733 576 44 NA NA NA 224143 TCGA-AB-2988 AML21 18 3197837 3197837 G A SNP MYOM1 NM_003803.3 human genbank 54_36p -1 reviewed intronic c.290+7095 e1+7095 0.004 - - - no_errors tier3 608 5 0.82 421 263 38.45 NA NA NA 224143 TCGA-AB-2988 AML21 18 4119198 4119198 C G SNP - - - - - - - - - - - - - - - tier3 448 15 3.24 590 567 49.01 NA NA NA 224143 TCGA-AB-2988 AML21 18 4234855 4234855 C T SNP LOC284215 XM_001127273.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-19984 NULL 0 - - - no_errors tier3 527 8 1.5 628 466 42.6 NA NA NA 224143 TCGA-AB-2988 AML21 18 8440987 8440987 C T SNP ENSG00000222891 ENST00000410959 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20842 NULL 0.001 - - - no_errors tier3 555 7 1.24 344 294 46.01 NA NA NA 224143 TCGA-AB-2988 AML21 18 14465764 14465764 G A SNP LOC100132255 XM_001723581.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*26429 NULL 0 - - - no_errors tier2 81 4 4.71 78 65 45.45 NA NA NA 224143 TCGA-AB-2988 AML21 18 24350716 24350716 T C SNP - - - - - - - - - - - - - - - tier3 717 13 1.78 702 607 46.37 NA NA NA 224143 TCGA-AB-2988 AML21 18 24977125 24977125 A G SNP - - - - - - - - - - - - - - - tier3 409 13 3.08 384 310 44.67 NA NA NA 224143 TCGA-AB-2988 AML21 18 26581459 26581459 C A SNP - - - - - - - - - - - - - - - tier3 502 7 1.38 494 388 43.99 NA NA NA 224143 TCGA-AB-2988 AML21 18 27023441 27023441 G A SNP DSC1 NM_024421.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-26886 NULL 0 - - - no_errors tier3 507 20 3.8 604 526 46.55 NA NA NA 224143 TCGA-AB-2988 AML21 18 29493321 29493321 T A SNP ASXL3 NM_030632.1 human genbank 54_36p 1 validated intronic c.356-2257 e5-2257 0 - - - no_errors tier3 546 14 2.5 769 637 45.31 NA NA NA 224143 TCGA-AB-2988 AML21 18 31019227 31019227 G A SNP MAPRE2 NM_014268.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*44896 NULL 0.003 - - - no_errors tier2 794 13 1.61 716 507 41.42 NA NA NA 224143 TCGA-AB-2988 AML21 18 34320554 34320554 C A SNP - - - - - - - - - - - - - - - tier3 1063 24 2.21 935 719 43.47 NA NA NA 224143 TCGA-AB-2988 AML21 18 37128724 37128724 A G SNP - - - - - - - - - - - - - - - tier3 493 15 2.95 528 392 42.56 NA NA NA 224143 TCGA-AB-2988 AML21 18 37539270 37539270 G A SNP - - - - - - - - - - - - - - - tier3 548 10 1.79 403 301 42.76 NA NA NA 224143 TCGA-AB-2988 AML21 18 39230448 39230448 T A SNP - - - - - - - - - - - - - - - tier3 898 23 2.49 1020 845 45.28 NA NA NA 224143 TCGA-AB-2988 AML21 18 39290900 39290900 A C SNP - - - - - - - - - - - - - - - tier3 496 18 3.5 498 345 40.93 NA NA NA 224143 TCGA-AB-2988 AML21 18 40650283 40650283 A G SNP SETBP1 NM_015559.1 human genbank 54_36p 1 validated intronic c.325-52910 e2-52910 0.936 - - - no_errors tier3 1114 20 1.76 595 482 44.75 NA NA NA 224143 TCGA-AB-2988 AML21 18 41246375 41246375 C T SNP - - - - - - - - - - - - - - - tier2 480 19 3.81 400 342 46.09 NA NA NA 224143 TCGA-AB-2988 AML21 18 43981757 43981757 G A SNP ENSG00000206944 ENST00000384217 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31498 NULL 0 - - - no_errors tier3 487 10 2.01 268 197 42.27 NA NA NA 224143 TCGA-AB-2988 AML21 18 45738065 45738065 A C SNP MYO5B NM_001080467.1 human genbank 54_36p -1 provisional intronic c.1546-3262 e13-3262 0.002 - - - no_errors tier3 1481 41 2.69 1787 371 17.18 NA NA NA 224143 TCGA-AB-2988 AML21 18 46505645 46505645 G A SNP MAPK4 NM_002747.3 human genbank 54_36p 1 reviewed intronic c.854-685 e4-685 0.013 - - - no_errors tier3 430 10 2.27 265 169 38.94 NA NA NA 224143 TCGA-AB-2988 AML21 18 53753641 53753641 C T SNP - - - - - - - - - - - - - - - tier3 784 19 2.35 629 490 43.71 NA NA NA 224143 TCGA-AB-2988 AML21 18 56955614 56955614 T C SNP - - - - - - - - - - - - - - - tier3 554 6 1.07 698 570 44.92 NA NA NA 224143 TCGA-AB-2988 AML21 18 58176726 58176726 A G SNP TNFRSF11A NM_003839.2 human genbank 54_36p 1 reviewed intronic c.521+172 e5+172 0 - - - no_errors tier3 297 5 1.66 200 178 46.97 NA NA NA 224143 TCGA-AB-2988 AML21 18 64906566 64906566 A T SNP CCDC102B NM_001093729.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*34212 NULL 0.006 - - - no_errors tier3 400 9 2.2 441 361 45.01 NA NA NA 224143 TCGA-AB-2988 AML21 18 70319475 70319475 G A SNP CNDP2 NM_018235.1 human genbank 54_36p 1 provisional intronic c.61-69 e2-69 0 - - - no_errors tier3 496 14 2.75 308 206 40.08 NA NA NA 224143 TCGA-AB-2988 AML21 18 71522343 71522343 C T SNP - - - - - - - - - - - - - - - tier2 667 14 2.05 451 340 42.98 NA NA NA 224143 TCGA-AB-2988 AML21 18 74572236 74572236 G A SNP - - - - - - - - - - - - - - - tier2 280 9 3.11 154 144 48.32 NA NA NA 224143 TCGA-AB-2988 AML21 18 74587182 74587182 G A SNP - - - - - - - - - - - - - - - tier3 384 8 2.04 243 222 47.74 NA NA NA 224143 TCGA-AB-2988 AML21 19 10661529 10661529 G A SNP ILF3 NM_012218.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*541 NULL 0.116 - - - no_errors tier2 233 1 0.43 163 151 48.09 NA NA NA 224143 TCGA-AB-2988 AML21 19 14873318 14873318 C T SNP OR7C2 NM_012377.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-39983 NULL 0 - - - no_errors tier3 253 6 2.32 345 229 39.9 NA NA NA 224143 TCGA-AB-2988 AML21 19 36950798 36950798 T C SNP ENSG00000201894 ENST00000365024 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19096 NULL 0.001 - - - no_errors tier3 770 17 2.16 581 420 41.96 NA NA NA 224143 TCGA-AB-2988 AML21 19 37150756 37150756 T C SNP ENSG00000221504 ENST00000408577 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41322 NULL 0.001 - - - no_errors tier3 734 17 2.26 578 479 45.32 NA NA NA 224143 TCGA-AB-2988 AML21 19 55475196 55475196 C G SNP MYH14 NM_001077186.1 human genbank 54_36p 1 reviewed missense c.4024 p.L1342V 1 HMMPfam_Myosin_tail_1 "HMMPfam_IQ,HMMSmart_SM00015,HMMPfam_Myosin_head,HMMSmart_SM00242,HMMPfam_Myosin_tail_1,HMMPfam_Myosin_N,superfamily_Prefoldin,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 896 31 3.34 317 293 47.95 NA NA NA 224143 TCGA-AB-2988 AML21 19 57272101 57272101 A G SNP ZNF841 ENST00000389534 human ensembl 54_36p -1 known intronic c.1+7751 e0+7751 0.998 - - - no_errors tier2 473 7 1.46 366 302 45.21 NA NA NA 224143 TCGA-AB-2988 AML21 19 61463323 61463323 C T SNP ZSCAN5A ENST00000254165 human ensembl 54_36p -1 known intronic c.1-35094 e1-35094 0 - - - no_errors tier3 692 13 1.84 566 401 41.43 NA NA NA 224143 TCGA-AB-2988 AML21 20 1752886 1752886 C T SNP - - - - - - - - - - - - - - - tier3 613 10 1.61 311 221 41.54 NA NA NA 224143 TCGA-AB-2988 AML21 20 3754830 3754830 G A SNP CENPB NM_001810.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-39700 NULL 0.134 - - - no_errors tier3 347 8 2.22 252 187 42.12 NA NA NA 224143 TCGA-AB-2988 AML21 20 5843305 5843305 A C SNP CHGB NM_001819.2 human genbank 54_36p 1 reviewed intronic c.50-1667 e2-1667 0.013 - - - no_errors tier3 357 8 2.19 262 236 47.39 NA NA NA 224143 TCGA-AB-2988 AML21 20 22199329 22199329 T G SNP ST13P ENST00000402944 human ensembl 54_36p -1 known 3_prime_flanking_region c.*1418 NULL 0 - - - no_coding_region:pseudogene tier3 525 16 2.95 412 408 49.76 NA NA NA 224143 TCGA-AB-2988 AML21 20 22261034 22261034 C T SNP - - - - - - - - - - - - - - - tier3 942 15 1.57 519 387 42.67 NA NA NA 224143 TCGA-AB-2988 AML21 20 23866199 23866199 T G SNP LOC651452 XR_038038.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-49873 NULL 0.001 - - - pseudogene tier2 1016 32 3.05 758 607 44.44 NA NA NA 224143 TCGA-AB-2988 AML21 20 40285507 40285507 G T SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.2399+12776 e16+12776 0 - - - no_errors tier3 734 10 1.34 662 464 41.21 NA NA NA 224143 TCGA-AB-2988 AML21 20 40387389 40387389 G A SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.1866-9339 e12-9339 0 - - - no_errors tier3 584 11 1.85 488 328 40.15 NA NA NA 224143 TCGA-AB-2988 AML21 20 45760225 45760225 G A SNP SULF2 NM_018837.2 human genbank 54_36p -1 validated intronic c.567+4445 e3+4445 0 - - - no_errors tier3 333 5 1.48 163 143 46.73 NA NA NA 224143 TCGA-AB-2988 AML21 20 50293211 50293211 A G SNP - - - - - - - - - - - - - - - tier2 387 10 2.52 371 314 45.71 NA NA NA 224143 TCGA-AB-2988 AML21 20 53405037 53405037 G C SNP - - - - - - - - - - - - - - - tier3 728 12 1.62 688 560 44.87 NA NA NA 224143 TCGA-AB-2988 AML21 20 53939909 53939909 G A SNP - - - - - - - - - - - - - - - tier3 1219 43 3.4 969 749 43.6 NA NA NA 224143 TCGA-AB-2988 AML21 20 54953158 54953158 G A SNP - - - - - - - - - - - - - - - tier2 386 4 1.03 216 143 39.72 NA NA NA 224143 TCGA-AB-2988 AML21 20 59752224 59752224 C T SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed missense c.380 p.P127L 0 superfamily_Cadherin "HMMPfam_Cadherin_C,HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_pro,superfamily_Cadherin" - no_errors tier1 289 6 2.03 131 121 48.02 NA NA NA 224143 TCGA-AB-2988 AML21 20 61479252 61479252 C T SNP CHRNA4 NM_000744.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-16291 NULL 0.007 - - - no_errors tier3 63 2 3.08 17 18 51.43 NA NA NA 224143 TCGA-AB-2988 AML21 21 19658607 19658607 C T SNP ENSG00000212609 ENST00000391307 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*19107 NULL 0.007 - - - no_errors tier3 409 6 1.45 402 218 35.16 NA NA NA 224143 TCGA-AB-2988 AML21 21 29478913 29478914 - A INS ENSG00000215533 ENST00000400527 human ensembl 54_36p 1 known 5_prime_flanking_region c.-9435 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 21 32435634 32435634 G A SNP ENSG00000211541 ENST00000390207 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49032 NULL 0 - - - no_errors tier3 696 15 2.11 580 508 46.69 NA NA NA 224143 TCGA-AB-2988 AML21 21 40925819 40925819 G A SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.508+60787 e3+60787 0 - - - no_errors tier3 988 23 2.27 703 520 42.48 NA NA NA 224143 TCGA-AB-2988 AML21 21 45209544 45209544 C T SNP C21orf70 NM_058190.2 human genbank 54_36p 1 predicted intronic c.353-1833 e4-1833 0 - - - no_errors tier3 173 3 1.7 101 73 41.95 NA NA NA 224143 TCGA-AB-2988 AML21 21 45840550 45840550 G A SNP PCBP3 ENST00000400314 human ensembl 54_36p 1 known 5_prime_flanking_region c.-300086 NULL 0.035 - - - no_errors tier3 295 4 1.34 114 85 42.71 NA NA NA 224143 TCGA-AB-2988 AML21 22 14537982 14537982 G T SNP LOC400879 XR_041650.1 human genbank 54_36p -1 model rna NULL NULL 0 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 224143 TCGA-AB-2988 AML21 22 17551313 17551313 C T SNP CLTCL1 ENST00000263200 human ensembl 54_36p -1 known intronic c.4606-189 e31-189 0.008 - - - no_errors tier3 137 6 4.2 118 113 48.92 NA NA NA 224143 TCGA-AB-2988 AML21 22 28215618 28215618 T A SNP NEFH NM_021076.3 human genbank 54_36p 1 reviewed silent c.1989 p.P663 0.041 NULL "HMMPfam_DUF1388,HMMPfam_Filament,PatternScan_IF" - no_errors tier1 375 1 0.26 528 121 18.33 NA NA NA 224143 TCGA-AB-2988 AML21 22 32854294 32854294 A G SNP - - - - - - - - - - - - - - - tier2 1025 25 2.38 808 576 41.62 NA NA NA 224143 TCGA-AB-2988 AML21 22 35293572 35293572 G A SNP CACNG2 NM_006078.2 human genbank 54_36p -1 reviewed intronic c.296-1086 e3-1086 0.019 - - - no_errors tier3 230 6 2.54 120 115 48.94 NA NA NA 224143 TCGA-AB-2988 AML21 22 36342568 36342568 A G SNP GGA1 NM_013365.1 human genbank 54_36p 1 reviewed intronic c.129-307 e3-307 0 - - - no_errors tier3 233 10 4.12 121 76 38.58 NA NA NA 224143 TCGA-AB-2988 AML21 22 42971892 42971892 C A SNP KIAA1644 NM_001099294.1 human genbank 54_36p -1 predicted 3_prime_untranslated_region c.*5006 NULL 0.001 - - - no_errors tier3 323 5 1.52 235 183 43.78 NA NA NA 224143 TCGA-AB-2988 AML21 22 44309402 44309402 C T SNP FBLN1 NM_006486.2 human genbank 54_36p 1 reviewed intronic c.785-342 e8-342 0.145 - - - no_errors tier3 483 15 3.01 251 205 44.96 NA NA NA 224143 TCGA-AB-2988 AML21 22 46181823 46181823 C T SNP - - - - - - - - - - - - - - - tier3 351 5 1.4 144 121 45.66 NA NA NA 224143 TCGA-AB-2988 AML21 22 47621527 47621527 T C SNP ENSG00000205632 ENST00000380981 human ensembl 54_36p 1 known 5_prime_flanking_region c.-55078 NULL 0.003 - - - no_errors tier3 303 5 1.62 153 112 42.26 NA NA NA 224143 TCGA-AB-2988 AML21 22 47707375 47707375 C T SNP LOC100128946 XM_001725064.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*30336 NULL 0 - - - no_errors tier3 893 22 2.4 550 401 42.12 NA NA NA 224143 TCGA-AB-2988 AML21 22 48425654 48425654 C G SNP C22orf34 ENST00000405854 human ensembl 54_36p -1 known intronic c.1+10622 e0+10622 0.001 - - - no_errors tier3 255 11 4.14 88 30 25 NA NA NA 753374 TCGA-AB-2989 AML38 Y 3529468 3529468 C T SNP TGIF2LY NM_139214.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*21625 NULL 0.037 - - - no_errors tier3 105 3 2.78 31 272 89.77 NA NA NA 753374 TCGA-AB-2989 AML38 Y 4748643 4748643 T G SNP ENSG00000217045 ENST00000404516 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17754 NULL 0.828 - - - no_coding_region:pseudogene tier3 106 3 2.75 214 303 58.61 NA NA NA 753374 TCGA-AB-2989 AML38 Y 14846750 14846750 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 X 26172570 26172570 T C SNP MAGEB6 NM_173523.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*49462 NULL 0 - - - no_errors tier3 144 2 1.37 91 541 85.47 NA NA NA 753374 TCGA-AB-2989 AML38 X 47999499 47999499 G T SNP SSX1 ENST00000403001 human ensembl 54_36p 1 known intronic c.203-11167 e3-11167 0.003 - - - no_errors tier3 456 4 0.87 92 790 89.57 NA NA NA 753374 TCGA-AB-2989 AML38 X 78929776 78929776 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 X 85302265 85302265 C T SNP LOC100130211 XM_001717632.1 human genbank 54_36p -1 model missense c.736 p.G246S 1 "HMMPfam_GTP_EFTU_D3,superfamily_EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain" "HMMPfam_GTP_EFTU,HMMPfam_GTP_EFTU_D3,HMMPfam_GTP_EFTU_D2,superfamily_Translation proteins,superfamily_EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain,superfamily_P-loop containing nucleoside triphosphate hydrolases" - pseudogene tier1 306 10 3.16 105 709 87.1 NA NA NA 753374 TCGA-AB-2989 AML38 X 93208401 93208401 G T SNP - - - - - - - - - - - - - - - tier3 262 8 2.96 165 791 82.74 NA NA NA 753374 TCGA-AB-2989 AML38 X 141699926 141699926 T C SNP - - - - - - - - - - - - - - - tier3 128 2 1.54 253 402 61.28 NA NA NA 753374 TCGA-AB-2989 AML38 X 147830171 147830171 A C SNP AFF2 NM_002025.2 human genbank 54_36p 1 validated intronic c.1398-12639 e10-12639 0.908 - - - no_errors tier3 286 12 4.03 116 618 84.08 NA NA NA 753374 TCGA-AB-2989 AML38 X 153040103 153040103 T C SNP MECP2 NM_004992.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29242 NULL 0.007 - - - no_errors tier3 226 3 1.31 39 309 88.79 NA NA NA 753374 TCGA-AB-2989 AML38 1 18546835 18546835 C T SNP IGSF21 NM_032880.2 human genbank 54_36p 1 provisional intronic c.424+12744 e4+12744 0.057 - - - no_errors tier3 271 6 2.16 278 227 44.77 NA NA NA 753374 TCGA-AB-2989 AML38 1 21671037 21671037 C T SNP NBPF3 NM_032264.2 human genbank 54_36p 1 validated intronic c.661+174 e4+174 0.002 - - - no_errors tier3 424 8 1.85 426 453 51.54 NA NA NA 753374 TCGA-AB-2989 AML38 1 30503459 30503459 C A SNP ENSG00000217351 ENST00000404941 human ensembl 54_36p 1 known 3_prime_flanking_region c.*31410 NULL 0 - - - no_coding_region:pseudogene tier3 616 11 1.75 424 275 39.34 NA NA NA 753374 TCGA-AB-2989 AML38 1 44054031 44054031 T G SNP ST3GAL3 NM_174963.2 human genbank 54_36p 1 reviewed intronic c.254+839 e3+839 0 - - - no_errors tier3 1123 18 1.58 1784 1342 42.86 NA NA NA 753374 TCGA-AB-2989 AML38 1 49331314 49331314 C T SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.378-47255 e5-47255 0.697 - - - no_errors tier3 373 1 0.27 745 608 44.9 NA NA NA 753374 TCGA-AB-2989 AML38 1 57251884 57251885 - T INS DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.1444+1259_1444+1258 e11+1259 0.006:0.024 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 1 62659634 62659634 A C SNP USP1 NM_001017415.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-18493 NULL 0.025 - - - no_errors tier3 219 2 0.9 375 315 45.59 NA NA NA 753374 TCGA-AB-2989 AML38 1 75028536 75028536 A T SNP TYW3 NM_138467.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*26151 NULL 0.001 - - - no_errors tier3 615 7 1.13 1134 836 42.42 NA NA NA 753374 TCGA-AB-2989 AML38 1 80220010 80220010 C A SNP - - - - - - - - - - - - - - - tier3 789 14 1.74 1211 959 44.17 NA NA NA 753374 TCGA-AB-2989 AML38 1 91306496 91306496 A C SNP ZNF644 NM_201269.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-85998 NULL 0 - - - no_errors tier3 447 6 1.32 702 552 43.98 NA NA NA 753374 TCGA-AB-2989 AML38 1 99876038 99876038 G A SNP PALMD NM_017734.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-8424 NULL 0.004 - - - no_errors tier3 563 17 2.93 1110 897 44.6 NA NA NA 753374 TCGA-AB-2989 AML38 1 100800433 100800433 G C SNP CDC14A NM_003672.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*44009 NULL 0 - - - no_errors tier3 114 1 0.87 387 298 43.44 NA NA NA 753374 TCGA-AB-2989 AML38 1 114672511 114672511 T A SNP - - - - - - - - - - - - - - - tier3 337 5 1.46 608 489 44.58 NA NA NA 753374 TCGA-AB-2989 AML38 1 148118513 148118514 - T INS HIST2H2BE ENST00000327774 human ensembl 54_36p -1 known intronic c.381+5910_5909 e1+5910 0.014:0.002 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 1 154302405 154302405 C A SNP RAB25 NM_020387.2 human genbank 54_36p 1 provisional missense c.123 p.S41R 0.993 "HMMSmart_RAB,HMMPfam_Ras,superfamily_SSF52540" "HMMSmart_RAB,HMMPfam_Ras,superfamily_SSF52540" - no_errors tier1 718 13 1.78 245 179 42.22 NA NA NA 753374 TCGA-AB-2989 AML38 1 169299882 169299882 G A SNP FMO3 NM_001002294.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28542 NULL 0.001 - - - no_errors tier3 411 10 2.38 983 731 42.62 NA NA NA 753374 TCGA-AB-2989 AML38 1 175060007 175060007 C T SNP PAPPA2 NM_020318.2 human genbank 54_36p 1 validated intronic c.5203-15925 e21-15925 0.175 - - - no_errors tier3 872 12 1.36 851 583 40.54 NA NA NA 753374 TCGA-AB-2989 AML38 1 185513612 185513612 A G SNP - - - - - - - - - - - - - - - tier3 709 12 1.66 1445 1063 42.33 NA NA NA 753374 TCGA-AB-2989 AML38 1 187950407 187950407 G T SNP - - - - - - - - - - - - - - - tier3 140 1 0.71 527 165 23.84 NA NA NA 753374 TCGA-AB-2989 AML38 1 189026177 189026177 A G SNP ENSG00000219198 ENST00000404999 human ensembl 54_36p 1 known 5_prime_flanking_region c.-7100 NULL 0 - - - no_coding_region:pseudogene tier3 38 0 0 168 139 45.28 NA NA NA 753374 TCGA-AB-2989 AML38 1 201308434 201308435 TT - DEL PPFIA4 NM_015053.1 human genbank 54_36p 1 validated intronic c.1875+923_1875+922 e15+923 0.005:0.003 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 1 205936817 205936817 A G SNP CR1L NM_175710.1 human genbank 54_36p 1 validated intronic c.863-654 e6-654 0.016 - - - no_errors tier3 506 3 0.59 665 340 33.8 NA NA NA 753374 TCGA-AB-2989 AML38 1 206031113 206031113 T C SNP CD46 NM_172359.3 human genbank 54_36p 1 reviewed intronic c.1128-2374 e13-2374 0 - - - no_errors tier3 235 1 0.42 585 441 42.73 NA NA NA 753374 TCGA-AB-2989 AML38 1 211063504 211063504 G A SNP NSL1 NM_015471.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31776 NULL 0.012 - - - no_errors tier3 249 11 4.23 411 359 46.56 NA NA NA 753374 TCGA-AB-2989 AML38 1 241070500 241070501 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 1 245829544 245829544 G - DEL OR2G3 NM_001001914.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-5967 NULL 0.014 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 2 1266223 1266223 C T SNP SNTG2 ENST00000308624 human ensembl 54_36p 1 known intronic c.1284+12299 e14+12299 0.003 - - - no_errors tier3 1452 24 1.62 1128 877 43.61 NA NA NA 753374 TCGA-AB-2989 AML38 2 1610073 1610073 G C SNP LOC100133877 XM_001722039.1 human genbank 54_36p -1 model intronic c.291-50015 e3-50015 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 497 10 1.97 499 350 41.08 NA NA NA 753374 TCGA-AB-2989 AML38 2 2982070 2982070 G A SNP - - - - - - - - - - - - - - - tier3 446 4 0.89 782 572 42.15 NA NA NA 753374 TCGA-AB-2989 AML38 2 5808192 5808192 C T SNP SOX11 NM_003108.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*56562 NULL 0 - - - no_errors tier3 331 6 1.78 463 409 46.74 NA NA NA 753374 TCGA-AB-2989 AML38 2 10279874 10279874 G A SNP C2orf48 NM_182626.1 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*11700 NULL 0.002 - - - no_errors tier3 715 11 1.51 366 394 51.71 NA NA NA 753374 TCGA-AB-2989 AML38 2 14322625 14322625 G T SNP ENSG00000210748 ENST00000388013 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9572 NULL 0 - - - pseudogene tier3 905 11 1.2 1152 439 27.59 NA NA NA 753374 TCGA-AB-2989 AML38 2 18459818 18459818 A G SNP - - - - - - - - - - - - - - - tier3 275 7 2.48 686 541 44.06 NA NA NA 753374 TCGA-AB-2989 AML38 2 18784246 18784246 T G SNP - - - - - - - - - - - - - - - tier3 795 12 1.49 1002 822 45.04 NA NA NA 753374 TCGA-AB-2989 AML38 2 35273242 35273242 A C SNP ENSG00000217899 ENST00000407648 human ensembl 54_36p -1 known 3_prime_flanking_region c.*24705 NULL 0 - - - no_coding_region:pseudogene tier3 142 2 1.39 392 337 46.1 NA NA NA 753374 TCGA-AB-2989 AML38 2 50654069 50654069 C G SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.1321-20402 e8-20402 0 - - - no_errors tier3 290 7 2.35 706 564 44.41 NA NA NA 753374 TCGA-AB-2989 AML38 2 51911126 51911126 G A SNP - - - - - - - - - - - - - - - tier3 459 8 1.71 843 626 42.61 NA NA NA 753374 TCGA-AB-2989 AML38 2 52155467 52155467 C A SNP ZNF863P ENST00000407098 human ensembl 54_36p 1 known intronic c.NULL NULL 0.004 - - - no_coding_region:pseudogene tier3 504 14 2.7 984 635 39.22 NA NA NA 753374 TCGA-AB-2989 AML38 2 59701254 59701254 A G SNP ENSG00000200101 ENST00000363231 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-27006 NULL 0 - - - no_errors tier3 347 2 0.57 936 466 33.21 NA NA NA 753374 TCGA-AB-2989 AML38 2 67349090 67349090 G A SNP - - - - - - - - - - - - - - - tier3 241 8 3.21 567 431 43.14 NA NA NA 753374 TCGA-AB-2989 AML38 2 86858156 86858156 T C SNP LOC729854 XM_001134103.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-47607 NULL 0.002 - - - no_errors tier3 461 9 1.91 595 440 42.39 NA NA NA 753374 TCGA-AB-2989 AML38 2 100823384 100823384 C T SNP NPAS2 NM_002518.3 human genbank 54_36p 1 reviewed intronic c.1+20076 e0+20076 0.001 - - - no_errors tier3 289 1 0.34 415 352 45.89 NA NA NA 753374 TCGA-AB-2989 AML38 2 103527284 103527285 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 2 103667496 103667496 C G SNP - - - - - - - - - - - - - - - tier3 284 1 0.35 580 427 42.32 NA NA NA 753374 TCGA-AB-2989 AML38 2 121243330 121243330 G C SNP GLI2 NM_005270.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28037 NULL 0.001 - - - no_errors tier3 409 6 1.45 308 199 39.17 NA NA NA 753374 TCGA-AB-2989 AML38 2 123297842 123297842 C T SNP - - - - - - - - - - - - - - - tier3 854 8 0.93 1448 1098 43.09 NA NA NA 753374 TCGA-AB-2989 AML38 2 125117495 125117495 A C SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.1874-4310 e13-4310 0 - - - no_errors tier3 307 5 1.6 711 498 41.12 NA NA NA 753374 TCGA-AB-2989 AML38 2 125443555 125443555 G A SNP ENSG00000206726 ENST00000383999 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19711 NULL 0 - - - no_errors tier3 140 2 1.41 293 201 40.61 NA NA NA 753374 TCGA-AB-2989 AML38 2 128026031 128026031 C T SNP MYO7B NM_001080527.1 human genbank 54_36p 1 provisional intronic c.1-7714 e1-7714 0 - - - no_errors tier3 910 17 1.83 766 475 38.15 NA NA NA 753374 TCGA-AB-2989 AML38 2 133422616 133422616 G T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.579+15147 e6+15147 0.001 - - - no_errors tier3 639 15 2.29 1254 861 40.63 NA NA NA 753374 TCGA-AB-2989 AML38 2 148086395 148086395 C A SNP - - - - - - - - - - - - - - - tier3 236 3 1.26 513 404 44.01 NA NA NA 753374 TCGA-AB-2989 AML38 2 159825801 159825801 C T SNP WDSUB1 NM_152528.1 human genbank 54_36p -1 validated intronic c.771-1201 e5-1201 0 - - - no_errors tier3 112 8 6.67 389 227 36.85 NA NA NA 753374 TCGA-AB-2989 AML38 2 164204453 164204453 T C SNP FIGN NM_018086.2 human genbank 54_36p -1 validated intronic c.26-27891 e2-27891 0 - - - no_errors tier3 119 3 2.46 339 303 47.12 NA NA NA 753374 TCGA-AB-2989 AML38 2 180240053 180240053 A G SNP ZNF385B NM_152520.1 human genbank 54_36p -1 validated intronic c.253+102422 e1+102422 0.057 - - - no_errors tier3 93 1 1.06 263 217 45.21 NA NA NA 753374 TCGA-AB-2989 AML38 2 182487117 182487117 A G SNP SSFA2 NM_006751.1 human genbank 54_36p 1 validated intronic c.1575+212 e10+212 0 - - - no_errors tier3 109 6 5.22 362 283 43.88 NA NA NA 753374 TCGA-AB-2989 AML38 2 191385274 191385274 C A SNP - - - - - - - - - - - - - - - tier3 1459 26 1.75 1699 1290 43.13 NA NA NA 753374 TCGA-AB-2989 AML38 2 194247003 194247003 G T SNP - - - - - - - - - - - - - - - tier3 190 0 0 370 174 31.93 NA NA NA 753374 TCGA-AB-2989 AML38 2 199588696 199588696 C T SNP - - - - - - - - - - - - - - - tier3 345 2 0.58 611 504 45.2 NA NA NA 753374 TCGA-AB-2989 AML38 2 206679769 206679769 T A SNP INO80D NM_017759.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-43784 NULL 0.002 - - - no_errors tier3 366 6 1.61 353 212 37.46 NA NA NA 753374 TCGA-AB-2989 AML38 2 211799533 211799533 T C SNP - - - - - - - - - - - - - - - tier3 182 4 2.15 534 464 46.45 NA NA NA 753374 TCGA-AB-2989 AML38 2 213899833 213899833 A T SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.536+9508 e5+9508 0 - - - no_errors tier3 81 1 1.22 293 208 41.52 NA NA NA 753374 TCGA-AB-2989 AML38 2 217688776 217688776 C A SNP - - - - - - - - - - - - - - - tier3 976 17 1.71 902 693 43.45 NA NA NA 753374 TCGA-AB-2989 AML38 2 219517759 219517760 - A INS CDK5R2 NM_003936.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15028 NULL 0.099:0.122 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 2 234541591 234541591 C T SNP TRPM8 NM_024080.4 human genbank 54_36p 1 validated intronic c.2025+1453 e14+1453 0.003 - - - no_errors tier3 371 7 1.85 295 219 42.28 NA NA NA 753374 TCGA-AB-2989 AML38 3 1249160 1249160 A C SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.358+4483 e3+4483 0.001 - - - no_errors tier3 211 4 1.86 450 324 41.86 NA NA NA 753374 TCGA-AB-2989 AML38 3 4926792 4926792 T C SNP LOC100128500 XM_001719603.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-24342 NULL 0.001 - - - no_errors tier3 196 3 1.5 453 319 41.32 NA NA NA 753374 TCGA-AB-2989 AML38 3 29029722 29029722 A G SNP - - - - - - - - - - - - - - - tier3 429 8 1.83 669 588 46.78 NA NA NA 753374 TCGA-AB-2989 AML38 3 37919963 37919963 G C SNP CTDSPL NM_001008392.1 human genbank 54_36p 1 validated intronic c.79+41190 e1+41190 0.002 - - - no_errors tier3 595 0 0 902 643 41.51 NA NA NA 753374 TCGA-AB-2989 AML38 3 39447410 39447410 G C SNP MOBP NM_182935.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-71155 NULL 0.002 - - - no_errors tier3 407 4 0.97 473 303 39.05 NA NA NA 753374 TCGA-AB-2989 AML38 3 54376672 54376672 G T SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.322-19110 e4-19110 0.012 - - - no_errors tier3 597 10 1.64 869 777 47.09 NA NA NA 753374 TCGA-AB-2989 AML38 3 55341604 55341604 A - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 3 65391533 65391533 C T SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed missense c.1427 p.R476Q 1 "HMMPfam_PDZ,superfamily_PDZ domain-like" "HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_Guanylate_kin,HMMSmart_SM00072,PatternScan_GUANYLATE_KINASE_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 743 12 1.59 1076 843 43.88 NA NA NA 753374 TCGA-AB-2989 AML38 3 76153337 76153337 G A SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.109+83894 e1+83894 0.001 - - - no_stop_codon:overly_large_intron tier3 600 10 1.64 1039 794 43.29 NA NA NA 753374 TCGA-AB-2989 AML38 3 77915635 77915635 T C SNP ENSG00000206891 ENST00000384164 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*27947 NULL 0.002 - - - no_errors tier3 210 11 4.98 339 233 40.73 NA NA NA 753374 TCGA-AB-2989 AML38 3 79771098 79771098 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49347 NULL 0 - - - no_errors tier3 321 5 1.53 875 641 42.25 NA NA NA 753374 TCGA-AB-2989 AML38 3 80059124 80059125 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 3 81368964 81368964 C G SNP - - - - - - - - - - - - - - - tier3 298 3 1 608 486 44.42 NA NA NA 753374 TCGA-AB-2989 AML38 3 85330308 85330308 T - DEL CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+238799 e1+238799 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 3 96483439 96483439 A G SNP - - - - - - - - - - - - - - - tier3 120 1 0.83 666 204 23.45 NA NA NA 753374 TCGA-AB-2989 AML38 3 96917195 96917195 C T SNP - - - - - - - - - - - - - - - tier3 268 3 1.11 625 493 44.06 NA NA NA 753374 TCGA-AB-2989 AML38 3 104220931 104220931 G A SNP - - - - - - - - - - - - - - - tier3 378 10 2.58 959 829 46.36 NA NA NA 753374 TCGA-AB-2989 AML38 3 104491251 104491251 C T SNP ENSG00000198957 ENST00000362039 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48480 NULL 0 - - - no_coding_region:pseudogene tier3 132 2 1.48 371 264 41.51 NA NA NA 753374 TCGA-AB-2989 AML38 3 106831585 106831585 G A SNP CBLB NM_170662.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*28919 NULL 0.044 - - - no_errors tier3 288 8 2.69 737 528 41.67 NA NA NA 753374 TCGA-AB-2989 AML38 3 109290161 109290161 A - DEL CD47 NM_001777.1 human genbank 54_36p -1 reviewed intronic c.46+2239 e1+2239 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 3 111785149 111785149 C A SNP ENSG00000221206 ENST00000408279 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31647 NULL 0.001 - - - no_errors tier3 738 9 1.2 986 834 45.82 NA NA NA 753374 TCGA-AB-2989 AML38 3 111977447 111977447 G A SNP ENSG00000201426 ENST00000364556 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48789 NULL 0 - - - no_errors tier3 97 2 2.02 396 280 41.36 NA NA NA 753374 TCGA-AB-2989 AML38 3 117821774 117821774 G A SNP ENSG00000209192 ENST00000386457 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-37407 NULL 0 - - - pseudogene tier3 1172 45 3.7 1687 1291 43.26 NA NA NA 753374 TCGA-AB-2989 AML38 3 121536174 121536174 C T SNP LRRC58 NM_001099678.1 human genbank 54_36p -1 validated intronic c.907+225 e3+225 0.002 - - - no_errors tier3 125 4 3.1 365 255 41.13 NA NA NA 753374 TCGA-AB-2989 AML38 3 136990365 136990365 T A SNP - - - - - - - - - - - - - - - tier3 699 5 0.71 875 603 40.69 NA NA NA 753374 TCGA-AB-2989 AML38 3 137109823 137109823 C T SNP - - - - - - - - - - - - - - - tier3 815 14 1.69 774 616 44.25 NA NA NA 753374 TCGA-AB-2989 AML38 3 138467283 138467283 G T SNP - - - - - - - - - - - - - - - tier3 729 2 0.27 1218 386 24.06 NA NA NA 753374 TCGA-AB-2989 AML38 3 141415678 141415678 A - DEL CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.232+38073 e2+38073 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 3 148990563 148990563 G A SNP - - - - - - - - - - - - - - - tier3 480 11 2.24 834 700 45.57 NA NA NA 753374 TCGA-AB-2989 AML38 3 155589434 155589434 T C SNP GPR149 NM_001038705.1 human genbank 54_36p -1 provisional intronic c.1623+32088 e3+32088 0.013 - - - no_errors tier3 560 10 1.75 888 653 42.21 NA NA NA 753374 TCGA-AB-2989 AML38 3 158263964 158263964 G A SNP LEKR1 NM_001004316.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*17731 NULL 0 - - - no_errors tier3 479 6 1.23 892 269 23.15 NA NA NA 753374 TCGA-AB-2989 AML38 3 161138515 161138515 A G SNP SCHIP1 NM_014575.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*41258 NULL 0 - - - no_errors tier3 683 6 0.87 910 619 40.48 NA NA NA 753374 TCGA-AB-2989 AML38 3 167609054 167609054 G A SNP - - - - - - - - - - - - - - - tier3 395 8 1.99 547 420 43.43 NA NA NA 753374 TCGA-AB-2989 AML38 3 168103357 168103357 A G SNP - - - - - - - - - - - - - - - tier3 83 2 2.35 367 207 36.06 NA NA NA 753374 TCGA-AB-2989 AML38 3 194562568 194562568 G A SNP ATP13A5 NM_198505.2 human genbank 54_36p -1 provisional intronic c.536+296 e5+296 0 - - - no_errors tier3 443 5 1.12 1101 313 22.12 NA NA NA 753374 TCGA-AB-2989 AML38 4 7164647 7164647 C T SNP GRPEL1 NM_025196.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-43987 NULL 0.002 - - - no_errors tier3 384 8 2.04 185 160 46.24 NA NA NA 753374 TCGA-AB-2989 AML38 4 13629992 13629992 G A SNP LOC391636 XR_016698.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*41066 NULL 0.001 - - - pseudogene tier3 697 10 1.41 1018 675 39.8 NA NA NA 753374 TCGA-AB-2989 AML38 4 20163937 20163937 A G SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.2562-589 e26-589 0 - - - no_errors tier3 549 8 1.43 1043 728 41.01 NA NA NA 753374 TCGA-AB-2989 AML38 4 26085231 26085231 G C SNP CCKAR NM_000730.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*7127 NULL 0 - - - no_errors tier3 645 8 1.23 910 682 42.76 NA NA NA 753374 TCGA-AB-2989 AML38 4 36901487 36901487 C T SNP ENSG00000215243 ENST00000389006 human ensembl 54_36p 1 known 5_prime_flanking_region c.-132956 NULL 0 - - - no_start_codon:no_stop_codon tier3 381 3 0.78 478 271 36.13 NA NA NA 753374 TCGA-AB-2989 AML38 4 39895228 39895228 C T SNP RHOH NM_004310.3 human genbank 54_36p 1 validated intronic c.1+19913 e0+19913 0.003 - - - no_errors tier3 244 1 0.41 477 374 43.85 NA NA NA 753374 TCGA-AB-2989 AML38 4 42553358 42553358 G A SNP GRXCR1 NM_001080476.1 human genbank 54_36p 1 inferred 5_prime_flanking_region c.-36683 NULL 0 - - - no_errors tier3 431 8 1.82 929 626 40.21 NA NA NA 753374 TCGA-AB-2989 AML38 4 44072885 44072885 C T SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated intronic c.961+71452 e1+71452 0.011 - - - no_errors tier3 931 6 0.64 1524 1183 43.69 NA NA NA 753374 TCGA-AB-2989 AML38 4 54563861 54563861 G A SNP uc010igo.1 ENST00000334328 human ensembl 54_36p -1 known 5_prime_flanking_region c.-15943 NULL 0.003 - - - no_errors tier3 168 1 0.59 642 386 37.48 NA NA NA 753374 TCGA-AB-2989 AML38 4 58158541 58158541 C T SNP - - - - - - - - - - - - - - - tier3 223 4 1.76 653 477 42.18 NA NA NA 753374 TCGA-AB-2989 AML38 4 58402535 58402535 T C SNP - - - - - - - - - - - - - - - tier3 460 4 0.86 799 626 43.9 NA NA NA 753374 TCGA-AB-2989 AML38 4 60391538 60391538 T C SNP ENSG00000201676 ENST00000364806 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*9949 NULL 0.01 - - - no_errors tier3 108 1 0.92 357 235 39.7 NA NA NA 753374 TCGA-AB-2989 AML38 4 64601932 64601932 T C SNP - - - - - - - - - - - - - - - tier3 164 1 0.61 323 260 44.6 NA NA NA 753374 TCGA-AB-2989 AML38 4 91721515 91721515 G T SNP KIAA1680 NM_207491.1 human genbank 54_36p 1 validated intronic c.1725-46684 e5-46684 0 - - - no_errors tier3 106 5 4.5 410 284 40.92 NA NA NA 753374 TCGA-AB-2989 AML38 4 92172452 92172452 T G SNP - - - - - - - - - - - - - - - tier3 250 5 1.96 510 397 43.72 NA NA NA 753374 TCGA-AB-2989 AML38 4 125874823 125874823 A G SNP ANKRD50 NM_020337.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23707 NULL 0 - - - no_errors tier3 212 1 0.47 423 319 42.99 NA NA NA 753374 TCGA-AB-2989 AML38 4 125937252 125937252 G A SNP - - - - - - - - - - - - - - - tier3 78 2 2.5 314 274 46.36 NA NA NA 753374 TCGA-AB-2989 AML38 4 131124026 131124026 G A SNP - - - - - - - - - - - - - - - tier3 252 2 0.79 522 428 44.96 NA NA NA 753374 TCGA-AB-2989 AML38 4 133158541 133158541 A G SNP LOC646187 XR_016991.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-40176 NULL 0.002 - - - no_errors tier3 123 1 0.81 451 378 45.6 NA NA NA 753374 TCGA-AB-2989 AML38 4 146459095 146459095 C T SNP - - - - - - - - - - - - - - - tier2 754 11 1.44 898 788 46.68 NA NA NA 753374 TCGA-AB-2989 AML38 4 152561666 152561666 C T SNP FAM160A1 ENST00000340515 human ensembl 54_36p 1 known intronic c.1+11599 e0+11599 0 - - - no_stop_codon tier3 298 6 1.97 760 222 22.61 NA NA NA 753374 TCGA-AB-2989 AML38 4 158971525 158971525 A G SNP - - - - - - - - - - - - - - - tier3 436 26 5.63 888 653 42.32 NA NA NA 753374 TCGA-AB-2989 AML38 4 165859433 165859433 C A SNP LOC653794 XM_001718785.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-9199 NULL 0.13 - - - no_errors tier3 165 3 1.78 296 218 42.33 NA NA NA 753374 TCGA-AB-2989 AML38 4 168010508 168010508 G T SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated intronic c.598+36348 e6+36348 0.017 - - - no_errors tier3 313 2 0.63 538 349 39.35 NA NA NA 753374 TCGA-AB-2989 AML38 4 168276796 168276796 G T SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated intronic c.190-35824 e2-35824 0.001 - - - no_errors tier3 351 6 1.68 524 524 49.95 NA NA NA 753374 TCGA-AB-2989 AML38 4 185123963 185123963 G A SNP STOX2 NM_020225.1 human genbank 54_36p 1 provisional intronic c.167-35509 e2-35509 0.001 - - - no_errors tier3 310 2 0.64 416 261 38.55 NA NA NA 753374 TCGA-AB-2989 AML38 4 187250902 187250902 G A SNP TLR3 NM_003265.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*7881 NULL 0 - - - no_errors tier3 1152 34 2.86 821 606 42.38 NA NA NA 753374 TCGA-AB-2989 AML38 4 188644505 188644505 A C SNP - - - - - - - - - - - - - - - tier3 223 5 2.19 473 471 49.84 NA NA NA 753374 TCGA-AB-2989 AML38 5 4632767 4632767 C T SNP - - - - - - - - - - - - - - - tier3 597 25 4 857 702 44.94 NA NA NA 753374 TCGA-AB-2989 AML38 5 6822753 6822753 G T SNP POLS NM_006999.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*14695 NULL 0.046 - - - no_errors tier3 74 3 3.9 53 56 51.38 NA NA NA 753374 TCGA-AB-2989 AML38 5 13566116 13566116 T C SNP - - - - - - - - - - - - - - - tier3 1057 9 0.84 1388 1030 42.54 NA NA NA 753374 TCGA-AB-2989 AML38 5 15201184 15201184 C T SNP ENSG00000202269 ENST00000365399 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-37155 NULL 0 - - - no_errors tier3 293 3 1.01 466 358 43.39 NA NA NA 753374 TCGA-AB-2989 AML38 5 15745750 15745750 G A SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.127+76569 e2+76569 0 - - - no_errors tier3 523 9 1.69 739 529 41.69 NA NA NA 753374 TCGA-AB-2989 AML38 5 29347665 29347665 T A SNP - - - - - - - - - - - - - - - tier3 198 4 1.98 385 273 41.49 NA NA NA 753374 TCGA-AB-2989 AML38 5 50899665 50899665 G A SNP - - - - - - - - - - - - - - - tier3 179 5 2.72 519 423 44.86 NA NA NA 753374 TCGA-AB-2989 AML38 5 51374343 51374343 A G SNP - - - - - - - - - - - - - - - tier3 223 7 3.04 611 510 45.45 NA NA NA 753374 TCGA-AB-2989 AML38 5 56578691 56578692 - A INS GPBP1 NM_022913.1 human genbank 54_36p 1 validated frame_shift_ins c.696_697 p.V233fs 1.000:1.000 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 5 58434538 58434538 A G SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.809-63983 e6-63983 0 - - - no_errors tier3 474 7 1.46 778 628 44.6 NA NA NA 753374 TCGA-AB-2989 AML38 5 59136946 59136946 T A SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.455+87806 e1+87806 0.014 - - - no_errors tier3 335 7 2.04 1194 383 24.29 NA NA NA 753374 TCGA-AB-2989 AML38 5 71675657 71675657 G A SNP PTCD2 NM_024754.3 human genbank 54_36p 1 validated intronic c.828+1038 e8+1038 0.001 - - - no_errors tier3 395 2 0.5 493 369 42.81 NA NA NA 753374 TCGA-AB-2989 AML38 5 72323589 72323589 G A SNP FCHO2 NM_138782.1 human genbank 54_36p 1 provisional intronic c.495+1142 e5+1142 0.001 - - - no_errors tier3 75 0 0 161 120 42.7 NA NA NA 753374 TCGA-AB-2989 AML38 5 83544418 83544418 G A SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.226+17011 e3+17011 0 - - - no_errors tier3 545 10 1.8 729 509 41.11 NA NA NA 753374 TCGA-AB-2989 AML38 5 85563085 85563085 G A SNP - - - - - - - - - - - - - - - tier3 202 8 3.81 523 388 42.59 NA NA NA 753374 TCGA-AB-2989 AML38 5 90494586 90494586 A C SNP GPR98 NM_032119.3 human genbank 54_36p 1 reviewed intronic c.18803-769 e90-769 0 - - - no_errors tier3 888 10 1.11 1749 703 28.65 NA NA NA 753374 TCGA-AB-2989 AML38 5 110343338 110343338 C A SNP - - - - - - - - - - - - - - - tier3 449 8 1.75 691 491 41.54 NA NA NA 753374 TCGA-AB-2989 AML38 5 121167063 121167063 G A SNP FTMT NM_177478.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-48495 NULL 0.001 - - - no_errors tier3 361 6 1.63 1011 694 40.7 NA NA NA 753374 TCGA-AB-2989 AML38 5 123574181 123574181 G - DEL ENSG00000214750 ENST00000398908 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*10315 NULL 0.001 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 5 148377020 148377020 C T SNP SH3TC2 NM_024577.3 human genbank 54_36p -1 reviewed intronic c.3054-4530 e13-4530 0.004 - - - no_errors tier3 495 9 1.79 737 528 41.71 NA NA NA 753374 TCGA-AB-2989 AML38 5 153068551 153068551 G A SNP GRIA1 NM_000827.3 human genbank 54_36p 1 reviewed intronic c.1823+2731 e11+2731 0 - - - no_errors tier3 543 13 2.33 754 614 44.88 NA NA NA 753374 TCGA-AB-2989 AML38 5 170770152 170770153 - TCAG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 5 179748941 179748941 C T SNP GFPT2 NM_005110.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-36118 NULL 0 - - - no_errors tier3 177 7 3.8 174 111 38.95 NA NA NA 753374 TCGA-AB-2989 AML38 6 318610 318610 G A SNP LOC730077 XM_001132307.2 human genbank 54_36p 1 model intronic c.173+70422 e1+70422 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 387 3 0.77 1556 598 27.74 NA NA NA 753374 TCGA-AB-2989 AML38 6 33219134 33219134 C T SNP COL11A2P ENST00000401545 human ensembl 54_36p -1 known 5_prime_flanking_region c.-36049 NULL 0.504 - - - no_coding_region:pseudogene tier3 655 18 2.66 566 393 40.81 NA NA NA 753374 TCGA-AB-2989 AML38 6 49848501 49848501 A C SNP CRISP3 NM_006061.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-35433 NULL 0.002 - - - no_errors tier3 210 0 0 411 367 47.17 NA NA NA 753374 TCGA-AB-2989 AML38 6 62433321 62433321 T G SNP LOC727798 XM_001125736.1 human genbank 54_36p -1 model intronic c.1-4093 e1-4093 0.015 - - - no_errors tier3 212 1 0.47 583 388 39.96 NA NA NA 753374 TCGA-AB-2989 AML38 6 62781699 62781699 C - DEL KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.336+34043 e3+34043 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 6 73192082 73192082 C T SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*24945 NULL 0 - - - no_errors tier3 975 15 1.51 1189 915 43.41 NA NA NA 753374 TCGA-AB-2989 AML38 6 82329010 82329010 A G SNP LOC100131508 XM_001720073.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-9754 NULL 0 - - - no_errors tier3 150 3 1.96 554 530 48.85 NA NA NA 753374 TCGA-AB-2989 AML38 6 85009956 85009956 C T SNP KIAA1009 NM_014895.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-17126 NULL 0 - - - no_errors tier3 60 0 0 185 130 41.27 NA NA NA 753374 TCGA-AB-2989 AML38 6 90551105 90551105 T A SNP MDN1 NM_014611.1 human genbank 54_36p -1 provisional intronic c.1449+347 e9+347 0.001 - - - no_errors tier3 280 7 2.44 637 494 43.68 NA NA NA 753374 TCGA-AB-2989 AML38 6 95942945 95942945 G A SNP - - - - - - - - - - - - - - - tier3 699 21 2.92 1210 910 42.92 NA NA NA 753374 TCGA-AB-2989 AML38 6 98435060 98435060 T A SNP - - - - - - - - - - - - - - - tier3 274 3 1.08 731 617 45.77 NA NA NA 753374 TCGA-AB-2989 AML38 6 102144460 102144460 A G SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.116-32057 e2-32057 0.047 - - - no_errors tier3 278 2 0.71 676 514 43.16 NA NA NA 753374 TCGA-AB-2989 AML38 6 122401030 122401030 C T SNP - - - - - - - - - - - - - - - tier3 426 9 2.07 840 400 32.23 NA NA NA 753374 TCGA-AB-2989 AML38 6 125729269 125729269 T C SNP - - - - - - - - - - - - - - - tier3 1098 14 1.26 1105 943 45.91 NA NA NA 753374 TCGA-AB-2989 AML38 6 132408968 132408968 G A SNP LOC100131774 XM_001717693.1 human genbank 54_36p 1 model intronic c.788-31073 e3-31073 0.884 - - - no_errors tier2 350 8 2.23 843 687 44.9 NA NA NA 753374 TCGA-AB-2989 AML38 6 153169923 153169924 - A INS VIP NM_003381.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*49954 NULL 0.022:0.019 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 6 158970560 158970560 G A SNP TMEM181 NM_020823.1 human genbank 54_36p 1 validated intronic c.1604-190 e15-190 0 - - - no_errors tier3 440 7 1.56 423 362 46.06 NA NA NA 753374 TCGA-AB-2989 AML38 6 170225127 170225127 A G SNP - - - - - - - - - - - - - - - tier3 70 2 2.78 30 28 47.46 NA NA NA 753374 TCGA-AB-2989 AML38 7 14029553 14029553 G A SNP ETV1 ENST00000405358 human ensembl 54_36p -1 known 5_prime_flanking_region c.-34637 NULL 0 - - - no_errors tier3 664 11 1.63 1012 759 42.86 NA NA NA 753374 TCGA-AB-2989 AML38 7 20356779 20356779 G C SNP ITGB8 NM_002214.2 human genbank 54_36p 1 reviewed intronic c.128-13006 e2-13006 0 - - - no_errors tier3 787 11 1.38 1436 1218 45.86 NA NA NA 753374 TCGA-AB-2989 AML38 7 24082004 24082004 C A SNP - - - - - - - - - - - - - - - tier3 151 4 2.58 459 311 40.34 NA NA NA 753374 TCGA-AB-2989 AML38 7 28298390 28298390 C T SNP CREB5 NM_182899.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-202683 NULL 0 - - - no_errors tier3 767 7 0.9 1419 311 17.96 NA NA NA 753374 TCGA-AB-2989 AML38 7 28753129 28753129 C A SNP CREB5 NM_182898.1 human genbank 54_36p 1 reviewed intronic c.702+22655 e7+22655 0 - - - no_errors tier3 133 2 1.48 334 246 42.27 NA NA NA 753374 TCGA-AB-2989 AML38 7 46611430 46611430 G T SNP - - - - - - - - - - - - - - - tier3 731 4 0.54 1901 610 24.27 NA NA NA 753374 TCGA-AB-2989 AML38 7 76705488 76705488 G A SNP CCDC146 NM_020879.2 human genbank 54_36p 1 validated intronic c.239+1206 e2+1206 0.001 - - - no_errors tier3 726 16 2.15 746 588 43.98 NA NA NA 753374 TCGA-AB-2989 AML38 7 78708406 78708406 G A SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.301+211866 e1+211866 0 - - - no_errors tier3 346 6 1.7 640 504 44.06 NA NA NA 753374 TCGA-AB-2989 AML38 7 86700748 86700748 A T SNP C7orf23 NM_024315.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-13993 NULL 0.036 - - - no_errors tier3 313 3 0.95 664 496 42.69 NA NA NA 753374 TCGA-AB-2989 AML38 7 89674213 89674213 A C SNP STEAP2 NM_001040665.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-18120 NULL 0.018 - - - no_errors tier3 209 7 3.24 305 262 46.21 NA NA NA 753374 TCGA-AB-2989 AML38 7 94987089 94987090 - T INS ASB4 NM_016116.1 human genbank 54_36p 1 reviewed intronic c.488-7972_488-7971 e3-7971 0.001:0.005 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 7 95055034 95055034 G A SNP PDK4 NM_002612.3 human genbank 54_36p -1 reviewed missense c.811 p.P271S 0.859 "HMMPfam_HATPase_c,HMMSmart_SM00387,superfamily_ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase" "HMMPfam_HATPase_c,HMMSmart_SM00387,superfamily_ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase,HMMPfam_BCDHK_Adom3,superfamily_alpha-ketoacid dehydrogenase kinase N-terminal domain" - no_errors tier1 384 15 3.76 571 425 42.63 NA NA NA 753374 TCGA-AB-2989 AML38 7 101044623 101044623 C T SNP MYL10 NM_138403.4 human genbank 54_36p -1 validated intronic c.534-913 e7-913 0.001 - - - no_errors tier3 461 10 2.12 223 211 48.28 NA NA NA 753374 TCGA-AB-2989 AML38 7 105035885 105035885 A G SNP ATXN7L1 ENST00000297416 human ensembl 54_36p -1 known intronic c.2557-312 e13-312 0 - - - no_start_codon tier3 490 9 1.8 456 364 44.23 NA NA NA 753374 TCGA-AB-2989 AML38 7 107786143 107786143 T - DEL NRCAM NM_001037132.1 human genbank 54_36p -1 reviewed intronic c.1+40973 e0+40973 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 7 117423516 117423516 C T SNP - - - - - - - - - - - - - - - tier3 899 18 1.96 1315 888 40.24 NA NA NA 753374 TCGA-AB-2989 AML38 7 119280515 119280515 T A SNP - - - - - - - - - - - - - - - tier3 421 2 0.47 1006 759 42.95 NA NA NA 753374 TCGA-AB-2989 AML38 7 120216906 120216906 T C SNP TSPAN12 NM_012338.3 human genbank 54_36p -1 reviewed intronic c.613-719 e7-719 0 - - - no_errors tier3 375 4 1.06 1308 1031 44.04 NA NA NA 753374 TCGA-AB-2989 AML38 7 120310564 120310564 A G SNP TSPAN12 NM_012338.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-26511 NULL 0.011 - - - no_errors tier3 230 9 3.77 355 294 45.23 NA NA NA 753374 TCGA-AB-2989 AML38 7 121939386 121939386 A - DEL CADPS2 NM_017954.2 human genbank 54_36p -1 validated intronic c.1542+1153 e9+1153 0.01 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 7 123883530 123883530 A G SNP LOC136157 NM_001085395.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20131 NULL 0.212 - - - no_errors tier3 353 9 2.48 778 559 41.81 NA NA NA 753374 TCGA-AB-2989 AML38 7 126382520 126382520 C - DEL GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.728-50547 e3-50547 0.286 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 7 142589843 142589843 T C SNP TAS2R39 NM_176881.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-791 NULL 0.001 - - - no_errors tier3 199 0 0 625 319 33.79 NA NA NA 753374 TCGA-AB-2989 AML38 8 4392502 4392502 A C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.302+89770 e2+89770 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 382 4 1.04 971 277 22.18 NA NA NA 753374 TCGA-AB-2989 AML38 8 5007229 5007229 A C SNP ENSG00000206661 ENST00000383934 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33887 NULL 0.003 - - - no_errors tier3 534 3 0.56 1371 350 20.33 NA NA NA 753374 TCGA-AB-2989 AML38 8 13799844 13799844 C T SNP - - - - - - - - - - - - - - - tier3 153 3 1.92 430 272 38.75 NA NA NA 753374 TCGA-AB-2989 AML38 8 33869332 33869332 C T SNP ENSG00000184844 ENST00000402289 human ensembl 54_36p -1 known 3_prime_flanking_region c.*77289 NULL 0.003 - - - no_errors tier3 208 0 0 938 693 42.44 NA NA NA 753374 TCGA-AB-2989 AML38 8 34303228 34303228 A G SNP RPL10AP3 ENST00000399893 human ensembl 54_36p -1 known 5_prime_flanking_region c.-2526 NULL 0.004 - - - no_stop_codon tier3 148 2 1.33 697 187 21.15 NA NA NA 753374 TCGA-AB-2989 AML38 8 36597872 36597872 C T SNP - - - - - - - - - - - - - - - tier3 565 6 1.05 796 498 38.49 NA NA NA 753374 TCGA-AB-2989 AML38 8 41701472 41701472 G A SNP ANK1 NM_020476.3 human genbank 54_36p -1 reviewed intronic c.613-243 e7-243 0 - - - no_errors tier3 361 7 1.9 426 324 43.14 NA NA NA 753374 TCGA-AB-2989 AML38 8 51117265 51117265 C T SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1+129921 e0+129921 0 - - - no_errors tier3 209 1 0.47 517 324 38.43 NA NA NA 753374 TCGA-AB-2989 AML38 8 56934975 56934975 C G SNP LYN NM_002350.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-81998 NULL 0 - - - no_errors tier3 316 4 1.25 501 331 39.74 NA NA NA 753374 TCGA-AB-2989 AML38 8 75479549 75479549 G A SNP GDAP1 NM_018972.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*40392 NULL 0.006 - - - no_errors tier3 778 3 0.38 1516 378 19.85 NA NA NA 753374 TCGA-AB-2989 AML38 8 81074076 81074076 G T SNP MRPS28 NM_014018.2 human genbank 54_36p -1 reviewed intronic c.395+3713 e2+3713 0.003 - - - no_errors tier3 370 4 1.07 677 502 42.47 NA NA NA 753374 TCGA-AB-2989 AML38 8 88080771 88080771 C A SNP CNBD1 NM_173538.2 human genbank 54_36p 1 provisional intronic c.431+59673 e4+59673 0.001 - - - no_errors tier3 524 2 0.38 1152 755 39.55 NA NA NA 753374 TCGA-AB-2989 AML38 8 89960423 89960423 A C SNP - - - - - - - - - - - - - - - tier3 79 0 0 387 271 41.19 NA NA NA 753374 TCGA-AB-2989 AML38 8 91612867 91612867 A C SNP ENSG00000199354 ENST00000362484 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*20227 NULL 0.042 - - - no_errors tier3 216 2 0.92 487 364 42.72 NA NA NA 753374 TCGA-AB-2989 AML38 8 97045310 97045310 C A SNP - - - - - - - - - - - - - - - tier3 796 13 1.6 894 685 43.38 NA NA NA 753374 TCGA-AB-2989 AML38 8 114918622 114918622 G A SNP - - - - - - - - - - - - - - - tier3 126 1 0.79 495 113 18.59 NA NA NA 753374 TCGA-AB-2989 AML38 8 140092286 140092286 G A SNP - - - - - - - - - - - - - - - tier3 168 4 2.33 487 405 45.25 NA NA NA 753374 TCGA-AB-2989 AML38 8 142962314 142962314 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 9 3004192 3004192 A T SNP - - - - - - - - - - - - - - - tier3 642 9 1.38 1054 907 46.25 NA NA NA 753374 TCGA-AB-2989 AML38 9 18434846 18434846 C T SNP ADAMTSL1 NM_001040272.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29385 NULL 0.002 - - - no_errors tier3 581 7 1.19 990 718 42.01 NA NA NA 753374 TCGA-AB-2989 AML38 9 20230285 20230285 G T SNP - - - - - - - - - - - - - - - tier3 743 11 1.46 1138 799 41.19 NA NA NA 753374 TCGA-AB-2989 AML38 9 21713627 21713627 C G SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 3_prime_flanking_region c.*26679 NULL 0.103 - - - no_coding_region:pseudogene tier3 311 1 0.32 805 138 14.63 NA NA NA 753374 TCGA-AB-2989 AML38 9 21713694 21713694 C T SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 3_prime_flanking_region c.*26746 NULL 0 - - - no_coding_region:pseudogene tier3 396 1 0.25 933 169 15.32 NA NA NA 753374 TCGA-AB-2989 AML38 9 21714107 21714107 C G SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 3_prime_flanking_region c.*27159 NULL 0.002 - - - no_coding_region:pseudogene tier3 125 0 0 515 101 16.4 NA NA NA 753374 TCGA-AB-2989 AML38 9 21715812 21715812 C A SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 3_prime_flanking_region c.*28864 NULL 0.009 - - - no_coding_region:pseudogene tier3 360 2 0.55 1074 203 15.88 NA NA NA 753374 TCGA-AB-2989 AML38 9 21716327 21716327 C G SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 3_prime_flanking_region c.*29379 NULL 0.004 - - - no_coding_region:pseudogene tier3 328 4 1.2 964 191 16.51 NA NA NA 753374 TCGA-AB-2989 AML38 9 22076280 22076280 T C SNP CDKN2BAS NR_003529.3 human genbank 54_36p 1 validated intronic c.NULL NULL 0.542 - - - no_errors tier3 336 8 2.33 646 838 56.36 NA NA NA 753374 TCGA-AB-2989 AML38 9 24924147 24924147 T C SNP ENSG00000223088 ENST00000411156 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*28414 NULL 0.036 - - - no_errors tier3 433 3 0.69 729 662 47.52 NA NA NA 753374 TCGA-AB-2989 AML38 9 26105851 26105851 A G SNP ENSG00000196478 ENST00000359978 human ensembl 54_36p 1 known intronic c.303-276 e4-276 0.929 - - - no_errors tier3 855 22 2.51 1142 847 42.56 NA NA NA 753374 TCGA-AB-2989 AML38 9 28344641 28344641 C T SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1+18193 e0+18193 0 - - - no_errors tier3 383 8 2.05 848 687 44.64 NA NA NA 753374 TCGA-AB-2989 AML38 9 29083878 29083878 C A SNP - - - - - - - - - - - - - - - tier3 101 0 0 326 180 35.57 NA NA NA 753374 TCGA-AB-2989 AML38 9 70607101 70607101 C T SNP PIP5K1B NM_003558.2 human genbank 54_36p 1 validated intronic c.1-16096 e1-16096 0 - - - no_errors tier3 596 10 1.65 1115 795 41.58 NA NA NA 753374 TCGA-AB-2989 AML38 9 71188305 71188305 C T SNP C9orf61 NM_004816.1 human genbank 54_36p 1 validated intronic c.495-61 e6-61 0 - - - no_errors tier3 709 19 2.61 756 561 42.53 NA NA NA 753374 TCGA-AB-2989 AML38 9 95045942 95045942 G T SNP WNK2 NM_006648.3 human genbank 54_36p 1 reviewed intronic c.1543-3704 e7-3704 0.003 - - - no_errors tier3 737 7 0.94 651 362 35.56 NA NA NA 753374 TCGA-AB-2989 AML38 9 107362539 107362539 G A SNP FKTN NM_001079802.1 human genbank 54_36p 1 reviewed intronic c.1+2272 e0+2272 0.008 - - - no_errors tier3 525 5 0.94 816 664 44.83 NA NA NA 753374 TCGA-AB-2989 AML38 9 113460177 113460177 T - DEL DNAJC25-GNG10 NM_004125.2 human genbank 54_36p 1 validated intronic c.337-8739 e2-8739 0.005 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 9 137750607 137750607 G A SNP KCNT1 NM_020822.1 human genbank 54_36p 1 provisional intronic c.254+4220 e2+4220 0.001 - - - no_errors tier3 126 2 1.56 106 72 40.45 NA NA NA 753374 TCGA-AB-2989 AML38 10 25363996 25363997 - A INS C10orf63 NM_145010.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-19125 NULL 0.322:0.315 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 10 25909398 25909398 G A SNP GPR158 NM_020752.2 human genbank 54_36p 1 validated intronic c.1753+7576 e7+7576 0.018 - - - no_errors tier3 291 1 0.34 689 493 41.64 NA NA NA 753374 TCGA-AB-2989 AML38 10 32302113 32302113 C T SNP ARHGAP12 NM_018287.5 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-64324 NULL 0.015 - - - no_errors tier3 550 4 0.72 528 269 33.58 NA NA NA 753374 TCGA-AB-2989 AML38 10 37717163 37717163 A - DEL LOC646360 XM_933553.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*45896 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 10 44980907 44980907 A C SNP ENSG00000219268 ENST00000403872 human ensembl 54_36p 1 known intronic c.NULL NULL 0.015 - - - no_coding_region:pseudogene tier3 108 0 0 486 167 25.57 NA NA NA 753374 TCGA-AB-2989 AML38 10 45309838 45309838 T C SNP MARCH8 NM_001002265.1 human genbank 54_36p -1 validated intronic c.103-4967 e2-4967 0.007 - - - no_errors tier3 497 7 1.39 682 474 40.9 NA NA NA 753374 TCGA-AB-2989 AML38 10 52061945 52061945 C T SNP SGMS1 NM_147156.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-288065 NULL 0.994 - - - no_errors tier3 186 5 2.62 262 192 42.29 NA NA NA 753374 TCGA-AB-2989 AML38 10 55618801 55618801 A G SNP PCDH15 NM_033056.1 human genbank 54_36p -1 reviewed intronic c.1306-3767 e11-3767 0 - - - no_errors tier3 174 6 3.33 505 406 44.52 NA NA NA 753374 TCGA-AB-2989 AML38 10 57368734 57368734 T A SNP - - - - - - - - - - - - - - - tier3 121 4 3.2 298 220 42.31 NA NA NA 753374 TCGA-AB-2989 AML38 10 58083198 58083198 T G SNP - - - - - - - - - - - - - - - tier3 191 3 1.55 507 447 46.81 NA NA NA 753374 TCGA-AB-2989 AML38 10 58713780 58713780 C T SNP - - - - - - - - - - - - - - - tier3 74 0 0 267 142 34.72 NA NA NA 753374 TCGA-AB-2989 AML38 10 68105039 68105039 T C SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1282-53491 e9-53491 0 - - - no_errors tier3 225 7 3.02 386 258 39.94 NA NA NA 753374 TCGA-AB-2989 AML38 10 79247187 79247187 G A SNP DLG5 NM_004747.3 human genbank 54_36p -1 reviewed intronic c.3785-327 e19-327 0.001 - - - no_errors tier3 276 4 1.42 298 265 46.74 NA NA NA 753374 TCGA-AB-2989 AML38 10 84537027 84537027 T G SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.1027+48641 e3+48641 0 - - - no_errors tier3 697 3 0.43 1728 556 24.33 NA NA NA 753374 TCGA-AB-2989 AML38 10 89500366 89500366 C T SNP PAPSS2 NM_001015880.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*4659 NULL 0.115 - - - no_errors tier3 103 2 1.9 386 279 41.95 NA NA NA 753374 TCGA-AB-2989 AML38 10 93343302 93343302 C T SNP PPP1R3C NM_005398.4 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*36362 NULL 0 - - - no_errors tier3 922 18 1.91 1013 813 44.52 NA NA NA 753374 TCGA-AB-2989 AML38 10 98082398 98082398 G C SNP DNTT NM_004088.1 human genbank 54_36p 1 reviewed intronic c.1359+55 e9+55 0 - - - no_errors tier3 494 2 0.4 650 422 39.22 NA NA NA 753374 TCGA-AB-2989 AML38 10 108347259 108347259 C T SNP SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed intronic c.3166-61 e24-61 0 - - - no_errors tier3 447 6 1.32 636 465 42.2 NA NA NA 753374 TCGA-AB-2989 AML38 10 112639536 112639536 T G SNP PDCD4 NM_014456.3 human genbank 54_36p 1 reviewed intronic c.875+158 e6+158 0.001 - - - no_errors tier3 294 5 1.67 578 417 41.91 NA NA NA 753374 TCGA-AB-2989 AML38 10 115855877 115855877 A T SNP ENSG00000216620 ENST00000405664 human ensembl 54_36p 1 known 5_prime_flanking_region c.-11019 NULL 0.021 - - - no_coding_region:pseudogene tier3 304 10 3.18 745 522 41.2 NA NA NA 753374 TCGA-AB-2989 AML38 10 117680282 117680282 T C SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.4019-13877 e29-13877 0.006 - - - no_errors tier2 499 8 1.57 833 715 46.19 NA NA NA 753374 TCGA-AB-2989 AML38 10 118282211 118282211 G A SNP PNLIP NM_000936.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13384 NULL 0.003 - - - no_errors tier3 1272 20 1.55 1356 1087 44.44 NA NA NA 753374 TCGA-AB-2989 AML38 10 118706055 118706055 T C SNP KIAA1598 NM_018330.1 human genbank 54_36p -1 validated intronic c.268-2344 e5-2344 0.007 - - - no_errors tier3 195 4 2.01 569 402 41.36 NA NA NA 753374 TCGA-AB-2989 AML38 10 126224370 126224370 G A SNP LHPP NM_022126.2 human genbank 54_36p 1 provisional intronic c.716+28540 e6+28540 0.001 - - - no_errors tier3 183 1 0.54 289 136 31.85 NA NA NA 753374 TCGA-AB-2989 AML38 11 21495406 21495406 C - DEL NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1646-17090 e16-17090 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 11 24550597 24550597 C A SNP LUZP2 NM_001009909.2 human genbank 54_36p 1 validated intronic c.62+75170 e1+75170 0.044 - - - no_errors tier3 470 12 2.49 1247 959 43.45 NA NA NA 753374 TCGA-AB-2989 AML38 11 25783183 25783183 T A SNP - - - - - - - - - - - - - - - tier3 447 8 1.76 790 697 46.81 NA NA NA 753374 TCGA-AB-2989 AML38 11 31055759 31055759 G A SNP uc001msu.1 ENST00000342355 human ensembl 54_36p -1 known intronic c.1155+229 e10+229 0 - - - no_errors tier3 169 2 1.17 497 344 40.9 NA NA NA 753374 TCGA-AB-2989 AML38 11 32374422 32374423 AT - DEL WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_del c.1206_1205 p.Y402fs 1.000:1.000 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 11 44411490 44411490 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 11 78706816 78706816 G A SNP - - - - - - - - - - - - - - - tier3 543 12 2.16 455 1032 69.35 NA NA NA 753374 TCGA-AB-2989 AML38 11 79752297 79752297 C T SNP - - - - - - - - - - - - - - - tier3 663 5 0.75 658 1441 68.65 NA NA NA 753374 TCGA-AB-2989 AML38 11 98836457 98836457 T - DEL CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-95629 e1-95629 0.014 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 11 100646055 100646055 C T SNP - - - - - - - - - - - - - - - tier3 303 9 2.88 388 902 69.87 NA NA NA 753374 TCGA-AB-2989 AML38 11 118654090 118654090 A G SNP CBL NM_005188.2 human genbank 54_36p 1 reviewed missense c.1100 p.Q367R 1 superfamily_SSF57850 "HMMPfam_UBA,HMMSmart_RING,HMMPfam_Cbl_N,superfamily_Adaptor_Cbl_N,HMMPfam_Cbl_N2,HMMPfam_Cbl_N3,HMMSmart_UBA,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,superfamily_SSF47473,superfamily_SSF55550,superfamily_SSF57850" - no_errors tier1 138 2 1.43 86 208 70.75 NA NA NA 753374 TCGA-AB-2989 AML38 11 123776916 123776916 G T SNP OR8B3 NM_001005467.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-4459 NULL 0 - - - no_errors tier3 459 16 3.37 896 204 18.55 NA NA NA 753374 TCGA-AB-2989 AML38 11 130707093 130707093 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-38819 NULL 0.036 - - - no_errors tier3 494 13 2.56 518 1095 67.84 NA NA NA 753374 TCGA-AB-2989 AML38 11 131633298 131633298 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.526+46047 e4+46047 0 - - - no_errors tier3 488 9 1.81 703 159 18.4 NA NA NA 753374 TCGA-AB-2989 AML38 12 8609499 8609499 G A SNP CLEC4E NM_014358.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24839 NULL 0 - - - no_errors tier3 394 12 2.95 667 570 46 NA NA NA 753374 TCGA-AB-2989 AML38 12 11763127 11763127 G A SNP ETV6 NM_001987.4 human genbank 54_36p 1 reviewed intronic c.34-33524 e2-33524 0.667 - - - no_errors tier3 714 24 3.25 940 635 40.24 NA NA NA 753374 TCGA-AB-2989 AML38 12 12603251 12603251 C T SNP DUSP16 NM_030640.1 human genbank 54_36p -1 validated intronic c.1+3067 e0+3067 0 - - - no_errors tier3 380 3 0.78 541 216 28.53 NA NA NA 753374 TCGA-AB-2989 AML38 12 17721750 17721750 C T SNP ENSG00000206662 ENST00000383935 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33385 NULL 0.005 - - - no_errors tier3 235 4 1.67 548 592 51.75 NA NA NA 753374 TCGA-AB-2989 AML38 12 18086511 18086511 G A SNP RERGL NM_024730.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*38881 NULL 0 - - - no_errors tier3 455 5 1.09 654 619 48.55 NA NA NA 753374 TCGA-AB-2989 AML38 12 32184137 32184137 G A SNP BICD1 NM_001714.1 human genbank 54_36p 1 reviewed intronic c.213+32392 e1+32392 0.113 - - - no_errors tier3 775 12 1.52 1010 737 42.11 NA NA NA 753374 TCGA-AB-2989 AML38 12 54234808 54234808 C T SNP OR2AP1 ENST00000321688 human ensembl 54_36p 1 known 5_prime_flanking_region c.-19658 NULL 0 - - - no_errors tier3 623 10 1.57 891 780 46.65 NA NA NA 753374 TCGA-AB-2989 AML38 12 70845269 70845269 G A SNP - - - - - - - - - - - - - - - tier3 754 14 1.82 997 742 42.64 NA NA NA 753374 TCGA-AB-2989 AML38 12 71857908 71857908 G A SNP - - - - - - - - - - - - - - - tier3 345 3 0.86 791 712 47.31 NA NA NA 753374 TCGA-AB-2989 AML38 12 83983463 83983463 G A SNP LRRIQ1 NM_001079910.1 human genbank 54_36p 1 validated intronic c.2544+140 e8+140 0.001 - - - no_errors tier3 394 5 1.25 1101 758 40.77 NA NA NA 753374 TCGA-AB-2989 AML38 12 87674534 87674534 A G SNP - - - - - - - - - - - - - - - tier3 767 19 2.42 1282 1108 46.32 NA NA NA 753374 TCGA-AB-2989 AML38 12 107314699 107314699 C T SNP - - - - - - - - - - - - - - - tier3 665 12 1.77 883 643 42 NA NA NA 753374 TCGA-AB-2989 AML38 12 107556460 107556461 - G INS SELPLG NM_003006.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14248 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 12 107934832 107934832 C T SNP USP30 NM_032663.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40062 NULL 0 - - - no_errors tier3 382 4 1.04 907 246 21.28 NA NA NA 753374 TCGA-AB-2989 AML38 12 115891006 115891007 - A INS FBXW8 NM_153348.1 human genbank 54_36p 1 reviewed intronic c.835+3964_835+3963 e5+3964 0.009:0.002 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 12 126028811 126028811 T C SNP - - - - - - - - - - - - - - - tier3 650 6 0.91 1250 362 22.43 NA NA NA 753374 TCGA-AB-2989 AML38 13 24401008 24401008 G A SNP CENPJ NM_018451.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15845 NULL 0.008 - - - no_errors tier3 327 6 1.8 669 427 38.96 NA NA NA 753374 TCGA-AB-2989 AML38 13 26532342 26532342 A C SNP LOC100129306 XM_001719801.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-42367 NULL 0.113 - - - pseudogene tier3 316 8 2.47 195 177 47.58 NA NA NA 753374 TCGA-AB-2989 AML38 13 27949934 27949934 C T SNP FLT1 NM_002019.3 human genbank 54_36p -1 validated intronic c.65-10180 e2-10180 0 - - - no_errors tier3 1050 23 2.14 1063 835 43.99 NA NA NA 753374 TCGA-AB-2989 AML38 13 40371706 40371706 T A SNP SUGT1L1 NR_003365.1 human genbank 54_36p -1 provisional intronic c.NULL NULL 0.967 - - - pseudogene tier3 99 1 1 193 146 43.07 NA NA NA 753374 TCGA-AB-2989 AML38 13 42386563 42386564 - A INS EPSTI1 NM_001002264.1 human genbank 54_36p -1 validated intronic c.774+3113_774+3112 e9+3113 0.035:0.066 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 13 46604191 46604191 C T SNP - - - - - - - - - - - - - - - tier3 249 7 2.72 654 307 31.95 NA NA NA 753374 TCGA-AB-2989 AML38 13 46957133 46957133 G C SNP ENSG00000222527 ENST00000410595 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-25763 NULL 0.001 - - - no_errors tier3 724 17 2.29 1340 1093 44.85 NA NA NA 753374 TCGA-AB-2989 AML38 13 54040216 54040216 A - DEL LOC100128485 XM_001717043.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*45280 NULL 0.056 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 13 54288784 54288784 T A SNP - - - - - - - - - - - - - - - tier3 374 11 2.85 653 315 32.47 NA NA NA 753374 TCGA-AB-2989 AML38 13 57970355 57970355 G T SNP LOC341689 XR_017487.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 99 0 0 215 163 43.12 NA NA NA 753374 TCGA-AB-2989 AML38 13 61969306 61969306 C A SNP - - - - - - - - - - - - - - - tier3 239 1 0.42 815 395 32.64 NA NA NA 753374 TCGA-AB-2989 AML38 13 63279690 63279690 A G SNP ENSG00000216484 ENST00000402308 human ensembl 54_36p 1 known 5_prime_flanking_region c.-29477 NULL 0.001 - - - no_coding_region:pseudogene tier3 283 10 3.41 626 536 46.13 NA NA NA 753374 TCGA-AB-2989 AML38 13 65658544 65658544 A G SNP - - - - - - - - - - - - - - - tier3 348 6 1.69 632 466 42.4 NA NA NA 753374 TCGA-AB-2989 AML38 13 65931165 65931165 C T SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed intronic c.3341-154004 e4-154004 0.015 - - - no_errors tier3 130 0 0 436 304 40.86 NA NA NA 753374 TCGA-AB-2989 AML38 13 68674599 68674599 G A SNP - - - - - - - - - - - - - - - tier3 344 6 1.71 682 517 43.08 NA NA NA 753374 TCGA-AB-2989 AML38 13 68893640 68893640 G T SNP ENSG00000219601 ENST00000403252 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12772 NULL 0.033 - - - no_coding_region:pseudogene tier3 213 3 1.39 614 404 39.61 NA NA NA 753374 TCGA-AB-2989 AML38 13 77875331 77875331 T G SNP ENSG00000200686 ENST00000363816 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-47867 NULL 0.001 - - - no_errors tier3 369 12 3.15 579 423 42.17 NA NA NA 753374 TCGA-AB-2989 AML38 13 90127369 90127369 T C SNP - - - - - - - - - - - - - - - tier3 522 4 0.76 1082 756 41.09 NA NA NA 753374 TCGA-AB-2989 AML38 13 97776917 97776917 G A SNP FARP1 NM_005766.2 human genbank 54_36p 1 reviewed intronic c.172-17100 e2-17100 0 - - - no_errors tier3 403 12 2.89 595 478 44.47 NA NA NA 753374 TCGA-AB-2989 AML38 14 25341881 25341881 C A SNP ENSG00000212270 ENST00000390968 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*3813 NULL 0.002 - - - no_errors tier3 132 0 0 310 137 29.46 NA NA NA 753374 TCGA-AB-2989 AML38 14 26046557 26046557 A C SNP NOVA1 NM_002515.2 human genbank 54_36p -1 reviewed intronic c.281-27368 e3-27368 0.142 - - - no_errors tier3 69 3 4.17 255 234 47.85 NA NA NA 753374 TCGA-AB-2989 AML38 14 42621434 42621434 G T SNP - - - - - - - - - - - - - - - tier3 171 4 2.29 488 343 41.28 NA NA NA 753374 TCGA-AB-2989 AML38 14 43821211 43821211 G A SNP - - - - - - - - - - - - - - - tier3 256 8 3.03 743 399 34.94 NA NA NA 753374 TCGA-AB-2989 AML38 14 44184564 44184564 G A SNP - - - - - - - - - - - - - - - tier3 169 3 1.74 511 406 44.18 NA NA NA 753374 TCGA-AB-2989 AML38 14 44375029 44375029 C T SNP - - - - - - - - - - - - - - - tier3 158 7 4.24 230 201 46.31 NA NA NA 753374 TCGA-AB-2989 AML38 14 45996899 45996899 A C SNP - - - - - - - - - - - - - - - tier3 48 2 4 142 138 49.29 NA NA NA 753374 TCGA-AB-2989 AML38 14 80061225 80061225 T C SNP C14orf145 NM_152446.3 human genbank 54_36p -1 validated intronic c.3072+1741 e21+1741 0.996 - - - no_errors tier3 318 5 1.55 652 482 42.47 NA NA NA 753374 TCGA-AB-2989 AML38 14 81807121 81807121 G A SNP - - - - - - - - - - - - - - - tier3 358 4 1.1 631 465 42.39 NA NA NA 753374 TCGA-AB-2989 AML38 14 82356828 82356828 C T SNP LOC730105 XM_001132445.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22888 NULL 0 - - - no_errors tier3 224 4 1.75 426 384 47.41 NA NA NA 753374 TCGA-AB-2989 AML38 15 24553556 24553556 G A SNP GABRB3 NM_000814.4 human genbank 54_36p -1 reviewed intronic c.240+15086 e3+15086 0 - - - no_errors tier3 972 18 1.81 1027 760 42.46 NA NA NA 753374 TCGA-AB-2989 AML38 15 24850733 24850733 C T SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.203-3914 e3-3914 0 - - - no_errors tier3 632 12 1.86 629 553 46.75 NA NA NA 753374 TCGA-AB-2989 AML38 15 25446355 25446355 G A SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known silent c.1047 p.T349 0.011 "HMMPfam_Neur_chan_memb,superfamily_Neu_channel_TM" "HMMPfam_Neur_chan_memb,superfamily_Neu_channel_TM,HMMPfam_Neur_chan_LBD,superfamily_Neur_chan_LBD,PatternScan_NEUROTR_ION_CHANNEL" - no_errors tier1 892 29 3.14 989 833 45.69 NA NA NA 753374 TCGA-AB-2989 AML38 15 45375617 45375617 G A SNP ENSG00000222343 ENST00000410411 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23216 NULL 0 - - - no_errors tier3 436 4 0.91 619 462 42.74 NA NA NA 753374 TCGA-AB-2989 AML38 15 47519762 47519762 A G SNP FGF7 NM_002009.3 human genbank 54_36p 1 reviewed intronic c.286+15690 e1+15690 0.003 - - - no_errors tier3 847 21 2.42 1505 1239 45.07 NA NA NA 753374 TCGA-AB-2989 AML38 15 47872120 47872120 G A SNP LOC645453 XR_017437.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-1393 NULL 0 - - - pseudogene tier3 102 1 0.97 315 257 44.85 NA NA NA 753374 TCGA-AB-2989 AML38 15 57868372 57868372 C T SNP LOC100130107 XM_001719310.1 human genbank 54_36p -1 model intronic c.1+4663 e0+4663 0 - - - no_errors tier3 92 3 3.16 215 154 41.73 NA NA NA 753374 TCGA-AB-2989 AML38 15 66095357 66095357 C T SNP PIAS1 NM_016166.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-38362 NULL 0 - - - no_errors tier3 746 24 3.12 710 577 44.73 NA NA NA 753374 TCGA-AB-2989 AML38 15 84149135 84149135 G C SNP KLHL25 NM_022480.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35090 NULL 0.002 - - - no_errors tier3 439 7 1.57 318 214 40.23 NA NA NA 753374 TCGA-AB-2989 AML38 15 84569320 84569320 C A SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.388+134 e4+134 0.001 - - - no_errors tier3 252 5 1.95 577 107 15.57 NA NA NA 753374 TCGA-AB-2989 AML38 15 92986588 92986588 C A SNP - - - - - - - - - - - - - - - tier3 471 1 0.21 1493 391 20.75 NA NA NA 753374 TCGA-AB-2989 AML38 15 96771687 96771687 G A SNP FAM169B NM_182562.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*28696 NULL 0.003 - - - no_errors tier3 633 15 2.31 580 384 39.79 NA NA NA 753374 TCGA-AB-2989 AML38 15 97989918 97989919 - AC INS MEF2A NM_005587.1 human genbank 54_36p 1 validated intronic c.1-788_787 e1-787 0.015:0.017 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 16 20835982 20835982 A G SNP LYRM1 NM_020424.1 human genbank 54_36p 1 validated intronic c.159+1445 e1+1445 0 - - - no_errors tier3 464 13 2.73 715 539 42.98 NA NA NA 753374 TCGA-AB-2989 AML38 16 27000355 27000355 G A SNP - - - - - - - - - - - - - - - tier3 714 17 2.33 380 257 40.35 NA NA NA 753374 TCGA-AB-2989 AML38 16 31206717 31206717 G T SNP ITGAM NM_000632.3 human genbank 54_36p 1 reviewed intronic c.1357-9619 e13-9619 0.029 - - - no_errors tier3 910 13 1.41 874 659 42.96 NA NA NA 753374 TCGA-AB-2989 AML38 16 45750526 45750526 T - DEL ITFG1 NM_030790.3 human genbank 54_36p -1 provisional intronic c.1662-124 e17-124 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 16 50047150 50047150 A G SNP - - - - - - - - - - - - - - - tier3 378 5 1.31 808 392 32.64 NA NA NA 753374 TCGA-AB-2989 AML38 16 60135706 60135706 G A SNP - - - - - - - - - - - - - - - tier3 1201 15 1.23 1326 1038 43.82 NA NA NA 753374 TCGA-AB-2989 AML38 16 60358365 60358365 C T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.1414+22386 e7+22386 0 - - - no_errors tier3 1084 10 0.91 1388 1136 44.97 NA NA NA 753374 TCGA-AB-2989 AML38 16 64708554 64708554 C T SNP - - - - - - - - - - - - - - - tier3 543 7 1.27 604 611 50.21 NA NA NA 753374 TCGA-AB-2989 AML38 16 72840858 72840858 A T SNP PSMD7 NM_002811.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47456 NULL 0.172 - - - no_errors tier3 504 4 0.79 715 524 42.29 NA NA NA 753374 TCGA-AB-2989 AML38 16 74967200 74967200 C T SNP CNTNAP4 NM_138994.3 human genbank 54_36p 1 validated intronic c.315+20291 e3+20291 0.002 - - - no_errors tier3 613 2 0.32 1097 243 18.09 NA NA NA 753374 TCGA-AB-2989 AML38 16 75749362 75749362 G T SNP MON1B NM_014940.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-33522 NULL 0.001 - - - no_errors tier3 672 15 2.18 734 527 41.76 NA NA NA 753374 TCGA-AB-2989 AML38 16 77130925 77130925 C T SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1056+106775 e8+106775 0.761 - - - no_errors tier3 519 11 2.07 629 400 38.87 NA NA NA 753374 TCGA-AB-2989 AML38 16 78201073 78201073 C T SNP MAF NM_005360.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9773 NULL 0.041 - - - no_errors tier3 1081 17 1.55 814 612 42.89 NA NA NA 753374 TCGA-AB-2989 AML38 16 84777106 84777106 G T SNP - - - - - - - - - - - - - - - tier3 1016 27 2.59 968 864 47.16 NA NA NA 753374 TCGA-AB-2989 AML38 16 87401458 87401458 G T SNP CDT1 NM_030928.3 human genbank 54_36p 1 validated intronic c.1477+67 e9+67 0.002 - - - no_errors tier3 81 0 0 89 48 35.04 NA NA NA 753374 TCGA-AB-2989 AML38 17 10447576 10447576 C T SNP LOC100134147 XM_001716952.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-5935 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 462 13 2.74 548 523 48.79 NA NA NA 753374 TCGA-AB-2989 AML38 17 12127017 12127017 C A SNP - - - - - - - - - - - - - - - tier3 988 12 1.2 1691 1264 42.72 NA NA NA 753374 TCGA-AB-2989 AML38 17 27887977 27887977 G A SNP MYO1D NM_015194.1 human genbank 54_36p -1 provisional intronic c.2865-41931 e22-41931 0.035 - - - no_errors tier3 443 20 4.32 570 432 43.03 NA NA NA 753374 TCGA-AB-2989 AML38 17 45423898 45423898 G T SNP DLX3 NM_005220.2 human genbank 54_36p -1 reviewed missense c.846 p.N282K 1 NULL "HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like,PatternScan_HOMEOBOX_1" - no_errors tier1 585 12 2.01 206 146 41.36 NA NA NA 753374 TCGA-AB-2989 AML38 17 53774806 53774806 C T SNP BZRAP1 NM_004758.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14526 NULL 0.644 - - - no_errors tier3 385 8 2.04 330 244 42.36 NA NA NA 753374 TCGA-AB-2989 AML38 17 60993062 60993062 G C SNP AXIN2 NM_004655.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7862 NULL 0 - - - no_errors tier3 561 4 0.71 264 186 41.15 NA NA NA 753374 TCGA-AB-2989 AML38 17 68242551 68242551 C T SNP SLC39A11 NM_139177.2 human genbank 54_36p -1 provisional intronic c.671+1833 e6+1833 0 - - - no_errors tier3 515 8 1.53 492 388 44.09 NA NA NA 753374 TCGA-AB-2989 AML38 18 34526101 34526101 G A SNP - - - - - - - - - - - - - - - tier3 923 7 0.75 1672 670 28.58 NA NA NA 753374 TCGA-AB-2989 AML38 18 38762086 38762086 C T SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional intronic c.235-4360 e4-4360 0.003 - - - no_errors tier3 417 1 0.24 1086 451 29.29 NA NA NA 753374 TCGA-AB-2989 AML38 18 42457502 42457502 T C SNP LOXHD1 ENST00000398722 human ensembl 54_36p -1 known 5_prime_flanking_region c.-22025 NULL 0 - - - no_errors tier3 1391 26 1.83 875 734 45.34 NA NA NA 753374 TCGA-AB-2989 AML38 18 44041128 44041128 G A SNP C18orf12 XR_040899.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*7922 NULL 0.001 - - - no_errors tier3 920 9 0.97 1148 905 44.08 NA NA NA 753374 TCGA-AB-2989 AML38 18 66881407 66881407 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 753374 TCGA-AB-2989 AML38 19 9215601 9215601 G A SNP OR7E24 NM_001079935.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-7119 NULL 0 - - - no_errors tier3 453 8 1.74 270 181 39.87 NA NA NA 753374 TCGA-AB-2989 AML38 19 13441052 13441052 C T SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known intronic c.295-14027 e2-14027 0.001 - - - no_errors tier3 1769 23 1.28 1179 949 44.57 NA NA NA 753374 TCGA-AB-2989 AML38 19 14898755 14898755 C G SNP OR7C2 NM_012377.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-14546 NULL 0 - - - no_errors tier3 360 8 2.17 583 401 40.71 NA NA NA 753374 TCGA-AB-2989 AML38 19 22496086 22496086 C T SNP ZNF729 ENST00000357491 human ensembl 54_36p 1 known intronic c.2644+49602 e5+49602 0.855 - - - no_stop_codon tier3 187 3 1.56 160 138 46.31 NA NA NA 753374 TCGA-AB-2989 AML38 19 34474446 34474446 C T SNP - - - - - - - - - - - - - - - tier3 490 10 2 697 275 28.23 NA NA NA 753374 TCGA-AB-2989 AML38 19 44641493 44641493 G C SNP SUPT5H NM_003169.2 human genbank 54_36p 1 validated missense c.398 p.R133P 1 NULL "HMMPfam_Supt5,HMMPfam_KOW,HMMSmart_SM00739,HMMSmart_SM00738,superfamily_Translation proteins SH3-like domain" - no_errors tier1 1241 45 3.5 783 521 39.83 NA NA NA 753374 TCGA-AB-2989 AML38 19 46478923 46478923 C T SNP HNRNPUL1 NM_007040.3 human genbank 54_36p 1 reviewed missense c.902 p.S301F 1 "HMMPfam_SPRY,HMMSmart_SM00449" "HMMPfam_SAP,HMMSmart_SM00513,HMMPfam_SPRY,HMMSmart_SM00449,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_SAP domain" - no_errors tier1 516 6 1.15 537 430 44.42 NA NA NA 753374 TCGA-AB-2989 AML38 19 50929346 50929346 C A SNP SNRPD2 NM_004597.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42360 NULL 0 - - - no_errors tier3 307 2 0.65 354 109 23.54 NA NA NA 753374 TCGA-AB-2989 AML38 20 9730637 9730637 G T SNP PAK7 NM_020341.3 human genbank 54_36p -1 reviewed intronic c.1-17483 e1-17483 0 - - - no_errors tier3 535 5 0.93 1329 1012 43.23 NA NA NA 753374 TCGA-AB-2989 AML38 20 12396977 12396977 C A SNP - - - - - - - - - - - - - - - tier3 1402 9 0.64 2485 575 18.77 NA NA NA 753374 TCGA-AB-2989 AML38 20 24694763 24694763 G C SNP - - - - - - - - - - - - - - - tier3 240 5 2.04 322 277 46.24 NA NA NA 753374 TCGA-AB-2989 AML38 20 31286625 31286625 G A SNP C20orf114 NM_033197.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-50916 NULL 0.001 - - - no_errors tier3 635 16 2.46 625 460 42.4 NA NA NA 753374 TCGA-AB-2989 AML38 20 31380877 31380877 C T SNP ENSG00000216386 ENST00000404644 human ensembl 54_36p 1 known intronic c.NULL NULL 0.055 - - - no_coding_region:pseudogene tier3 62 0 0 149 88 36.82 NA NA NA 753374 TCGA-AB-2989 AML38 20 33144232 33144232 G A SNP TRPC4AP NM_015638.2 human genbank 54_36p -1 validated missense c.14 p.P5L 0.997 NULL NULL - no_errors tier1 129 1 0.76 77 63 43.75 NA NA NA 753374 TCGA-AB-2989 AML38 20 36626042 36626042 G A SNP KIAA1219 NM_020336.2 human genbank 54_36p 1 validated intronic c.3697+1288 e23+1288 0.003 - - - no_errors tier3 1073 23 2.1 1733 1288 42.59 NA NA NA 753374 TCGA-AB-2989 AML38 20 38030818 38030818 G T SNP HSPEP1 ENST00000404611 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35523 NULL 0.195 - - - no_coding_region:pseudogene tier3 374 10 2.6 701 525 42.75 NA NA NA 753374 TCGA-AB-2989 AML38 20 47500499 47500499 G A SNP KCNB1 NM_004975.2 human genbank 54_36p -1 reviewed intronic c.567+31359 e1+31359 0.003 - - - no_errors tier3 529 16 2.93 473 379 44.48 NA NA NA 753374 TCGA-AB-2989 AML38 20 52318662 52318662 C A SNP PFDN4 NM_002623.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*49566 NULL 0.905 - - - no_errors tier3 650 6 0.91 938 700 42.74 NA NA NA 753374 TCGA-AB-2989 AML38 20 55013444 55013444 G T SNP - - - - - - - - - - - - - - - tier3 595 12 1.98 664 535 44.58 NA NA NA 753374 TCGA-AB-2989 AML38 21 13586530 13586530 C G SNP LOC100129305 XM_001714760.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-22104 NULL 0.003 - - - no_errors tier3 304 1 0.33 783 409 34.23 NA NA NA 753374 TCGA-AB-2989 AML38 21 21031005 21031005 T C SNP - - - - - - - - - - - - - - - tier3 319 4 1.24 697 545 43.81 NA NA NA 753374 TCGA-AB-2989 AML38 21 21651819 21651819 T A SNP NCAM2 NM_004540.2 human genbank 54_36p 1 reviewed intronic c.1045-16235 e9-16235 0.001 - - - no_errors tier3 52 1 1.89 390 205 34.45 NA NA NA 753374 TCGA-AB-2989 AML38 21 44834582 44834582 C T SNP C21orf29 NM_144991.2 human genbank 54_36p -1 provisional intronic c.83-22265 e2-22265 0.002 - - - no_errors tier3 635 13 2.01 543 393 41.68 NA NA NA 753374 TCGA-AB-2989 AML38 22 42712211 42712211 C T SNP SAMM50 NM_015380.4 human genbank 54_36p 1 validated intronic c.1075+998 e12+998 0.002 - - - no_errors tier3 138 3 2.13 203 191 48.48 NA NA NA 753374 TCGA-AB-2989 AML38 22 42902675 42902675 G C SNP PARVG NM_022141.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7868 NULL 0.028 - - - no_errors tier3 313 5 1.57 226 165 42.09 NA NA NA 753374 TCGA-AB-2989 AML38 22 42972672 42972672 C A SNP KIAA1644 NM_001099294.1 human genbank 54_36p -1 predicted 3_prime_untranslated_region c.*4226 NULL 0.059 - - - no_errors tier3 171 1 0.58 294 262 46.95 NA NA NA 753374 TCGA-AB-2989 AML38 22 48177568 48177568 G C SNP - - - - - - - - - - - - - - - tier3 835 17 2 852 584 40.64 NA NA NA 548327 TCGA-AB-2990 AML34 X 765191 765191 C T SNP LOC728188 XM_001126103.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-34450 NULL 0.024 - - - no_start_codon:pseudogene:no_stop_codon tier2 967 85 8.08 892 638 41.7 0 0 NA 548327 TCGA-AB-2990 AML34 1 5393221 5393221 G A SNP LOC645466 XR_039534.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-42905 NULL 0.001 - - - pseudogene tier3 508 59 10.41 603 471 43.77 0 0 NA 548327 TCGA-AB-2990 AML34 1 20626293 20626293 G A SNP LOC729715 XM_001131116.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*13509 NULL 0 - - - no_errors tier3 1372 190 12.15 1475 1083 42.24 0 0 NA 548327 TCGA-AB-2990 AML34 1 36650834 36650834 C T SNP STK40 NM_032017.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-51314 NULL 0.001 - - - no_errors tier3 1205 150 11.02 799 611 43.18 0 0 NA 548327 TCGA-AB-2990 AML34 1 63867599 63867599 T A SNP PGM1 NM_002633.2 human genbank 54_36p 1 provisional intronic c.247-85 e2-85 0.001 - - - no_errors tier3 434 50 10.33 464 278 37.37 0 0 0 548327 TCGA-AB-2990 AML34 1 80763837 80763837 C T SNP ENSG00000217175 ENST00000402172 human ensembl 54_36p 1 known 3_prime_flanking_region c.*29331 NULL 0.001 - - - no_coding_region:pseudogene tier3 719 66 8.4 769 525 40.45 0 0 NA 548327 TCGA-AB-2990 AML34 1 85131809 85131809 T G SNP LPAR3 NM_012152.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27418 NULL 0 - - - no_errors tier2 457 44 8.76 564 377 40.02 0 0 NA 548327 TCGA-AB-2990 AML34 1 118017196 118017196 A C SNP ENSG00000213262 ENST00000393177 human ensembl 54_36p -1 known 5_prime_flanking_region c.-31395 NULL 0.011 - - - no_coding_region:pseudogene tier3 702 70 9.06 809 548 40.32 0 0 NA 548327 TCGA-AB-2990 AML34 1 165428591 165428591 G A SNP POU2F1 NM_002697.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-139748 NULL 0.001 - - - no_errors tier3 778 66 7.82 732 483 39.75 0 0 NA 548327 TCGA-AB-2990 AML34 1 173629089 173629089 T C SNP TNR NM_003285.2 human genbank 54_36p -1 validated intronic c.1356+450 e4+450 0 - - - no_errors tier3 690 83 10.72 864 568 39.66 0 0 NA 548327 TCGA-AB-2990 AML34 1 176055044 176055044 C A SNP - - - - - - - - - - - - - - - tier2 692 69 9.07 748 568 43.16 0 0 NA 548327 TCGA-AB-2990 AML34 1 210481765 210481765 C T SNP LOC643143 XM_931358.1 human genbank 54_36p -1 model intronic c.1-2824 e1-2824 0.001 - - - no_errors tier3 440 49 10.02 553 363 39.63 0 0 NA 548327 TCGA-AB-2990 AML34 1 238830341 238830341 C A SNP GREM2 NM_022469.3 human genbank 54_36p -1 reviewed intronic c.1+11466 e0+11466 0.003 - - - no_errors tier3 1216 160 11.63 1000 916 47.78 0 0 NA 548327 TCGA-AB-2990 AML34 1 245238187 245238187 C T SNP ZNF695 NM_020394.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-354 NULL 0.07 - - - no_errors tier2 613 39 5.98 1070 380 26.19 1 0 0 548327 TCGA-AB-2990 AML34 2 3158138 3158138 G A SNP LOC100132738 XM_001714359.1 human genbank 54_36p 1 model intronic c.581+384 e5+384 0.003 - - - no_errors tier3 234 21 8.24 330 241 42.13 0 0 NA 548327 TCGA-AB-2990 AML34 2 8708786 8708786 C T SNP ID2 NM_002166.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30961 NULL 0.001 - - - no_errors tier3 337 47 12.24 380 251 39.72 0 0 NA 548327 TCGA-AB-2990 AML34 2 39103418 39103418 C T SNP SOS1 NM_005633.3 human genbank 54_36p -1 reviewed missense c.1655 p.R552K 1 NULL "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_RasGEF_N,HMMSmart_SM00229,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_RasGEF,HMMSmart_SM00147,HMMPfam_Histone,superfamily_Ras GEF,superfamily_Histone-fold,PatternScan_RASGEF,superfamily_PH domain-like" - no_errors tier1 436 31 6.64 630 438 41.01 16 9 36 548327 TCGA-AB-2990 AML34 2 57215834 57215834 C T SNP - - - - - - - - - - - - - - - tier2 215 9 4.02 450 124 21.6 0 0 NA 548327 TCGA-AB-2990 AML34 2 79777553 79777553 C A SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.102+45261 e1+45261 0.003 - - - no_errors tier3 361 27 6.96 501 282 36.02 0 0 NA 548327 TCGA-AB-2990 AML34 2 97997171 97997171 C A SNP TMEM131 NM_015348.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-18614 NULL 0.136 - - - no_errors tier3 370 37 9.09 508 401 44.07 0 0 NA 548327 TCGA-AB-2990 AML34 2 120565690 120565690 G A SNP EPB41L5 NM_020909.2 human genbank 54_36p 1 provisional missense c.1133 p.R378Q 0.995 HMMPfam_FA "HMMPfam_FA,HMMPfam_FERM_N,HMMPfam_FERM_C,PatternScan_FERM_1,PatternScan_FERM_2,HMMPfam_FERM_M,superfamily_Second domain of FERM,HMMSmart_SM00295,superfamily_PH domain-like,superfamily_Ubiquitin-like" - no_errors tier1 443 45 9.22 921 494 34.91 2 3 60 548327 TCGA-AB-2990 AML34 2 166005950 166005950 C A SNP CSRNP3 ENST00000409664 human ensembl 54_36p 1 known 5_prime_flanking_region c.-153872 NULL 0.001 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 91 3 3.16 162 35 17.77 0 0 NA 548327 TCGA-AB-2990 AML34 2 183899917 183899917 G A SNP - - - - - - - - - - - - - - - tier3 404 36 8.18 466 265 36.2 1 0 0 548327 TCGA-AB-2990 AML34 2 208821358 208821358 G C SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132G 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 441 50 10.18 580 405 41.12 35 36 50.7 548327 TCGA-AB-2990 AML34 2 212897380 212897380 C T SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.83-199507 e2-199507 0.001 - - - no_errors tier3 399 54 11.92 457 270 37.14 0 0 NA 548327 TCGA-AB-2990 AML34 2 231480476 231480476 G A SNP GPR55 NM_005683.3 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*2486 NULL 0 - - - no_errors tier3 809 85 9.49 767 533 40.72 0 2 100 548327 TCGA-AB-2990 AML34 2 241533418 241533418 C T SNP LOC728763 XR_037106.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.001 - - - pseudogene tier3 279 35 11.11 274 206 42.83 0 0 NA 548327 TCGA-AB-2990 AML34 3 31051703 31051703 G T SNP - - - - - - - - - - - - - - - tier3 568 60 9.54 674 500 42.52 0 0 NA 548327 TCGA-AB-2990 AML34 3 86197523 86197523 C T SNP CADM2 NM_153184.2 human genbank 54_36p 1 validated missense c.1148 p.T383M 1 NULL "HMMSmart_4.1m,HMMSmart_IGc2,HMMSmart_IG,HMMPfam_V-set,HMMPfam_ig,HMMPfam_C2-set_2,superfamily_SSF48726" - no_errors tier1 433 35 7.46 428 303 41.45 1 0 548327 TCGA-AB-2990 AML34 3 107970043 107970043 C T SNP - - - - - - - - - - - - - - - tier3 476 22 4.42 677 333 32.91 0 0 NA 548327 TCGA-AB-2990 AML34 3 154506355 154506355 A G SNP - - - - - - - - - - - - - - - tier3 450 46 9.27 529 384 42.06 0 0 NA 548327 TCGA-AB-2990 AML34 3 155473909 155473909 A C SNP DHX36 NM_020865.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*2745 NULL 0.002 - - - no_errors tier3 272 20 6.85 594 431 42.05 14 9 39.13 548327 TCGA-AB-2990 AML34 3 166233759 166233759 C T SNP SI NM_001041.2 human genbank 54_36p -1 validated intronic c.2565+118 e22+118 0 - - - no_errors tier3 85 2 2.3 151 107 41.47 0 0 NA 548327 TCGA-AB-2990 AML34 3 183792756 183792756 G A SNP - - - - - - - - - - - - - - - tier3 414 29 6.55 693 476 40.72 0 0 NA 548327 TCGA-AB-2990 AML34 3 194330816 194330816 T C SNP ENSG00000220985 ENST00000408058 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33229 NULL 0.006 - - - no_errors tier3 1228 101 7.59 1010 726 41.75 0 0 NA 548327 TCGA-AB-2990 AML34 4 31779598 31779598 G A SNP LOC100130644 XM_001717608.1 human genbank 54_36p -1 model intronic c.1219-3767 e8-3767 0.002 - - - pseudogene:no_stop_codon tier3 450 32 6.63 514 307 37.39 0 0 NA 548327 TCGA-AB-2990 AML34 4 75948435 75948435 G A SNP BTC NM_001729.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-9876 NULL 0.001 - - - no_errors tier3 647 78 10.76 782 645 45.2 0 0 NA 548327 TCGA-AB-2990 AML34 4 77361003 77361003 T G SNP FAM47E ENST00000339906 human ensembl 54_36p 1 known intronic c.81+3138 e1+3138 0.003 - - - no_errors tier3 463 43 8.5 536 370 40.84 0 0 NA 548327 TCGA-AB-2990 AML34 4 122535948 122535948 A G SNP QRFPR NM_198179.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14696 NULL 0.004 - - - no_errors tier3 494 42 7.82 928 710 43.35 0 0 NA 548327 TCGA-AB-2990 AML34 4 131671240 131671240 G A SNP ENSG00000199896 ENST00000363026 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-23860 NULL 0.001 - - - no_errors tier3 534 66 11 727 569 43.9 0 0 NA 548327 TCGA-AB-2990 AML34 4 132395811 132395811 G A SNP ENSG00000206782 ENST00000384055 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18036 NULL 0 - - - no_errors tier2 423 39 8.44 381 255 40.09 0 0 NA 548327 TCGA-AB-2990 AML34 4 138914511 138914511 A G SNP - - - - - - - - - - - - - - - tier3 587 52 8.14 759 453 37.38 0 0 NA 548327 TCGA-AB-2990 AML34 4 166820778 166820778 C A SNP - - - - - - - - - - - - - - - tier3 499 51 9.24 611 374 37.97 0 0 NA 548327 TCGA-AB-2990 AML34 4 175245183 175245183 C T SNP - - - - - - - - - - - - - - - tier2 659 70 9.6 781 559 41.69 0 0 NA 548327 TCGA-AB-2990 AML34 5 36687279 36687279 G A SNP SLC1A3 NM_004172.4 human genbank 54_36p 1 validated intronic c.320-19609 e3-19609 0 - - - no_errors tier3 229 26 10.2 288 209 42.05 5 7 58.33 548327 TCGA-AB-2990 AML34 5 38691991 38691991 C T SNP - - - - - - - - - - - - - - - tier3 208 22 9.57 248 179 41.92 0 0 NA 548327 TCGA-AB-2990 AML34 5 45258679 45258679 C T SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*39101 NULL 0.001 - - - no_errors tier2 482 45 8.52 637 465 42.2 0 0 NA 548327 TCGA-AB-2990 AML34 5 67515751 67515751 T C SNP PIK3R1 NM_181523.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-42509 NULL 0.001 - - - no_errors tier2 531 80 13.09 607 452 42.64 0 0 NA 548327 TCGA-AB-2990 AML34 5 109400700 109400700 C T SNP - - - - - - - - - - - - - - - tier3 967 91 8.6 1135 673 37.22 0 0 NA 548327 TCGA-AB-2990 AML34 5 113003489 113003489 G A SNP YTHDC2 NM_022828.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*46510 NULL 0.061 - - - no_errors tier3 269 28 9.43 396 276 41.07 0 0 NA 548327 TCGA-AB-2990 AML34 5 113767963 113767963 T C SNP KCNN2 NM_021614.2 human genbank 54_36p 1 reviewed intronic c.583-71 e3-71 0.035 - - - no_errors tier3 896 84 8.57 1032 738 41.65 0 0 NA 548327 TCGA-AB-2990 AML34 5 155230106 155230106 G A SNP ENSG00000200275 ENST00000363405 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24964 NULL 0 - - - no_errors tier3 288 49 14.54 407 323 44.25 0 0 NA 548327 TCGA-AB-2990 AML34 5 155698275 155698275 G A SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.4-5802 e2-5802 0.01 - - - no_errors tier3 631 45 6.66 785 576 42.32 0 0 NA 548327 TCGA-AB-2990 AML34 5 166610754 166610754 A - DEL ODZ2 ENST00000388903 human ensembl 54_36p 1 known 5_prime_flanking_region c.-33667 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 548327 TCGA-AB-2990 AML34 5 169986333 169986333 C T SNP KCNIP1 NM_001034837.1 human genbank 54_36p 1 reviewed intronic c.62-86103 e2-86103 0 - - - no_errors tier3 636 93 12.7 391 317 44.77 0 0 NA 548327 TCGA-AB-2990 AML34 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 548327 TCGA-AB-2990 AML34 5 175243356 175243356 G A SNP CPLX2 NM_001008220.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*3702 NULL 0.001 - - - no_errors tier3 956 94 8.95 1012 729 41.87 0 0 NA 548327 TCGA-AB-2990 AML34 6 4413646 4413646 T C SNP LOC100134205 XM_001716692.1 human genbank 54_36p -1 model intronic c.225+6238 e2+6238 0.003 - - - no_start_codon:pseudogene:no_stop_codon tier3 477 49 9.32 579 424 42.23 0 0 NA 548327 TCGA-AB-2990 AML34 6 19633765 19633765 G T SNP - - - - - - - - - - - - - - - tier2 580 35 5.69 733 373 33.73 0 0 NA 548327 TCGA-AB-2990 AML34 6 100606850 100606850 G A SNP LOC728012 XR_040015.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.177 - - - no_errors tier3 433 28 6.07 709 498 41.26 0 0 NA 548327 TCGA-AB-2990 AML34 6 102541334 102541334 A C SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.2086-48575 e14-48575 0 - - - no_errors tier3 495 37 6.95 705 420 37.33 0 0 NA 548327 TCGA-AB-2990 AML34 6 143074681 143074681 G A SNP HIVEP2 NM_006734.3 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*41256 NULL 0 - - - no_errors tier3 782 97 11.02 860 730 45.91 0 0 NA 548327 TCGA-AB-2990 AML34 6 162938751 162938751 C A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.7+129933 e1+129933 0.005 - - - no_errors tier3 349 29 7.67 335 258 43.43 1 0 0 548327 TCGA-AB-2990 AML34 7 9274356 9274356 T C SNP - - - - - - - - - - - - - - - tier3 350 28 7.41 413 286 40.92 0 0 NA 548327 TCGA-AB-2990 AML34 7 50325178 50325178 T A SNP LOC100132224 XM_001714418.1 human genbank 54_36p 1 model intronic c.1-4011 e1-4011 0 - - - no_errors tier2 332 35 9.49 383 255 39.72 1 1 50 548327 TCGA-AB-2990 AML34 7 62148303 62148303 G A SNP LOC100128613 XM_001715200.1 human genbank 54_36p -1 model intronic c.123+3866 e1+3866 0 - - - no_errors tier3 332 56 14.43 377 324 46.15 0 0 NA 548327 TCGA-AB-2990 AML34 7 146625253 146625253 C T SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.1349-2913 e9-2913 0.005 - - - no_errors tier3 646 51 7.32 782 498 38.88 0 0 NA 548327 TCGA-AB-2990 AML34 8 20120612 20120612 C G SNP ATP6V1B2 NM_001693.3 human genbank 54_36p 1 reviewed intronic c.1396+539 e13+539 0.001 - - - no_errors tier3 721 69 8.72 861 629 42.21 3 4 57.14 548327 TCGA-AB-2990 AML34 8 25015045 25015045 A T SNP - - - - - - - - - - - - - - - tier3 392 36 8.39 496 349 41.25 0 0 NA 548327 TCGA-AB-2990 AML34 8 25277946 25277946 G C SNP DOCK5 NM_024940.6 human genbank 54_36p 1 validated intronic c.3045-113 e30-113 0 - - - no_errors tier3 396 41 9.36 660 483 42.26 2 4 66.67 548327 TCGA-AB-2990 AML34 8 27208141 27208141 A G SNP TRIM35 NM_171982.3 human genbank 54_36p -1 validated intronic c.532-397 e3-397 0.001 - - - no_errors tier3 316 27 7.87 533 194 26.65 0 0 0 548327 TCGA-AB-2990 AML34 8 89972026 89972026 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 548327 TCGA-AB-2990 AML34 8 98901942 98901942 A T SNP LAPTM4B NM_018407.4 human genbank 54_36p 1 validated intronic c.780+1300 e5+1300 0 - - - no_errors tier3 433 44 9.22 513 343 40.07 0 0 0 548327 TCGA-AB-2990 AML34 8 113792750 113792750 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1973-21295 e14-21295 0 - - - no_errors tier3 806 78 8.82 919 752 44.98 0 0 NA 548327 TCGA-AB-2990 AML34 9 11695192 11695192 T C SNP - - - - - - - - - - - - - - - tier3 259 18 6.5 384 256 40 0 0 NA 548327 TCGA-AB-2990 AML34 9 22782825 22782825 C T SNP LOC646609 XR_037907.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*44549 NULL 0.039 - - - pseudogene tier3 1041 113 9.37 846 625 39.16 0 0 NA 548327 TCGA-AB-2990 AML34 9 94941845 94941845 G A SNP WNK2 NM_006648.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45188 NULL 0.008 - - - no_errors tier3 156 21 11.86 234 148 38.74 1 0 0 548327 TCGA-AB-2990 AML34 9 108731052 108731052 C T SNP ZNF462 NM_021224.4 human genbank 54_36p 1 validated missense c.5038 p.R1680C 1 "PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers,superfamily_beta-sandwich domain of Sec23/24" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers,superfamily_beta-sandwich domain of Sec23/24" - no_errors tier1 567 61 9.71 582 367 38.63 NA 548327 TCGA-AB-2990 AML34 9 110639353 110639353 C T SNP ACTL7A NM_006687.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25071 NULL 0.027 - - - no_errors tier3 363 14 3.7 676 177 20.73 0 0 NA 548327 TCGA-AB-2990 AML34 9 119243905 119243905 G T SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-26868 NULL 0 - - - no_errors tier3 718 70 8.88 636 424 40 0 0 NA 548327 TCGA-AB-2990 AML34 9 121025804 121025804 A C SNP DBC1 NM_014618.2 human genbank 54_36p -1 validated intronic c.686-9550 e5-9550 0 - - - no_errors tier3 1015 108 9.61 1122 896 44.38 0 0 NA 548327 TCGA-AB-2990 AML34 9 137406848 137406848 G A SNP LOC100131900 XM_001719692.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*21159 NULL 0 - - - no_errors tier2 114 13 10.24 148 102 40.8 0 0 NA 548327 TCGA-AB-2990 AML34 10 70887882 70887882 C T SNP TSPAN15 NM_012339.3 human genbank 54_36p 1 reviewed intronic c.96+6430 e1+6430 0 - - - no_errors tier3 398 56 12.33 431 313 42.01 0 0 NA 548327 TCGA-AB-2990 AML34 10 72519135 72519135 C T SNP - - - - - - - - - - - - - - - tier3 758 57 6.99 601 478 44.26 0 0 NA 548327 TCGA-AB-2990 AML34 10 84259214 84259214 T C SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.953+150610 e2+150610 0.008 - - - no_errors tier3 838 88 9.5 955 675 41.39 0 0 NA 548327 TCGA-AB-2990 AML34 10 113896998 113896998 C T SNP GPAM NM_020918.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*6300 NULL 0.006 - - - no_errors tier3 356 40 10.08 539 359 39.98 1 0 0 548327 TCGA-AB-2990 AML34 10 119283343 119283343 G A SNP EMX2OS NR_002791.2 human genbank 54_36p -1 provisional intronic c.NULL NULL 0.001 - - - no_errors tier3 203 34 14.29 341 248 42.11 0 0 NA 548327 TCGA-AB-2990 AML34 10 128141569 128141569 T C SNP C10orf90 NM_001004298.2 human genbank 54_36p -1 validated intronic c.1535-1425 e5-1425 0.005 - - - no_errors tier3 138 16 10.39 232 141 37.8 0 0 NA 548327 TCGA-AB-2990 AML34 10 133313004 133313004 G A SNP - - - - - - - - - - - - - - - tier2 200 21 9.5 129 89 40.83 0 0 NA 548327 TCGA-AB-2990 AML34 11 8018110 8018110 T G SNP TUB NM_003320.4 human genbank 54_36p 1 reviewed intronic c.203+295 e2+295 0.001 - - - no_errors tier3 1036 116 10.07 1211 987 44.84 0 0 NA 548327 TCGA-AB-2990 AML34 11 12072279 12072279 C T SNP MICAL2 NM_014632.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-68000 NULL 0 - - - no_errors tier3 934 108 10.32 722 504 40.91 0 0 NA 548327 TCGA-AB-2990 AML34 11 49873907 49873907 G A SNP LOC387770 XR_017307.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-7827 NULL 0 - - - pseudogene tier2 235 31 11.65 295 185 38.54 0 0 NA 548327 TCGA-AB-2990 AML34 11 128820989 128820989 C T SNP BARX2 NM_003658.4 human genbank 54_36p 1 reviewed intronic c.573+2965 e3+2965 0.246 - - - no_errors tier3 539 57 9.55 654 516 44.03 0 0 NA 548327 TCGA-AB-2990 AML34 11 132891814 132891814 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+15555 e1+15555 0 - - - no_errors tier3 454 57 11 320 231 41.32 0 0 NA 548327 TCGA-AB-2990 AML34 12 10440989 10440989 G A SNP KLRK1 NM_007360.2 human genbank 54_36p -1 reviewed intronic c.1-5232 e1-5232 0.001 - - - no_errors tier3 472 56 10.61 554 358 39.25 0 0 NA 548327 TCGA-AB-2990 AML34 12 16453928 16453928 C T SNP ENSG00000215923 ENST00000401104 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-396 NULL 0.012 - - - no_errors tier3 833 54 6.09 766 541 41.36 0 0 NA 548327 TCGA-AB-2990 AML34 12 23095666 23095666 C A SNP - - - - - - - - - - - - - - - tier3 144 16 10 249 138 35.66 0 0 NA 548327 TCGA-AB-2990 AML34 12 28261078 28261078 T C SNP LOC729291 XR_041493.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.014 - - - no_errors tier2 411 22 5.08 719 434 37.64 0 2 100 548327 TCGA-AB-2990 AML34 12 43204015 43204015 G A SNP NELL2 NM_006159.1 human genbank 54_36p -1 reviewed intronic c.1805-481 e17-481 0 - - - no_errors tier3 684 60 8.06 650 437 40.17 0 0 NA 548327 TCGA-AB-2990 AML34 12 77159009 77159009 C A SNP NAV3 NM_014903.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*30581 NULL 0 - - - no_errors tier3 225 47 10.44 423 369 44.03 0 0 NA 548327 TCGA-AB-2990 AML34 12 86674077 86674077 C T SNP ENSG00000205071 ENST00000378575 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*26949 NULL 0.108 - - - no_coding_region:pseudogene tier3 668 54 7.48 801 469 36.93 0 0 NA 548327 TCGA-AB-2990 AML34 12 126340748 126340748 G A SNP - - - - - - - - - - - - - - - tier3 692 56 7.47 762 477 38.47 0 0 NA 548327 TCGA-AB-2990 AML34 13 61817939 61817939 T C SNP LOC100133193 XR_039110.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*17409 NULL 0.001 - - - pseudogene tier3 293 36 10.94 289 269 48.04 0 0 NA 548327 TCGA-AB-2990 AML34 13 100262099 100262099 C T SNP - - - - - - - - - - - - - - - tier2 571 55 8.76 588 436 42.5 0 0 NA 548327 TCGA-AB-2990 AML34 14 101084357 101084357 G A SNP DIO3 NM_001362.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13308 NULL 0.01 - - - pseudogene tier3 303 41 11.85 296 241 44.3 0 0 NA 548327 TCGA-AB-2990 AML34 14 104124263 104124263 G A SNP C14orf180 NM_001008404.1 human genbank 54_36p 1 predicted intronic c.111+340 e1+340 0.005 - - - no_errors tier3 319 39 10.89 358 246 40.66 0 0 NA 548327 TCGA-AB-2990 AML34 14 105516246 105516246 G A SNP ENSG00000217399 ENST00000402682 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-105516246 NULL 1 - - - no_coding_region:pseudogene tier2 345 24 6.5 365 255 40.8 0 0 0 548327 TCGA-AB-2990 AML34 15 22990586 22990586 C T SNP SNORD115-14 NR_003306.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-575 NULL 0 - - - no_errors tier3 72 5 6.49 62 48 43.64 0 0 NA 548327 TCGA-AB-2990 AML34 15 25047599 25047599 G A SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.271-107103 e4-107103 0 - - - no_errors tier3 302 37 10.91 404 279 40.85 0 0 NA 548327 TCGA-AB-2990 AML34 15 33808696 33808696 G A SNP - - - - - - - - - - - - - - - tier2 643 64 9.04 684 470 40.73 0 0 NA 548327 TCGA-AB-2990 AML34 15 43629505 43629505 C T SNP C15orf21 ENST00000313559 human ensembl 54_36p 1 known intronic c.20+2848 e1+2848 0.021 - - - no_errors tier3 474 49 9.37 543 329 37.73 0 0 NA 548327 TCGA-AB-2990 AML34 15 67921036 67921036 C T SNP - - - - - - - - - - - - - - - tier3 691 74 9.67 650 454 41.12 0 0 NA 548327 TCGA-AB-2990 AML34 15 84296668 84296668 T C SNP - - - - - - - - - - - - - - - tier2 827 67 7.49 869 602 40.9 0 0 NA 548327 TCGA-AB-2990 AML34 16 22598549 22598549 C T SNP - - - - - - - - - - - - - - - tier3 1001 60 5.66 1571 500 24.12 0 0 NA 548327 TCGA-AB-2990 AML34 16 62907760 62907760 C T SNP - - - - - - - - - - - - - - - tier3 748 90 10.74 986 742 42.94 0 0 NA 548327 TCGA-AB-2990 AML34 16 64253972 64253972 G A SNP - - - - - - - - - - - - - - - tier2 350 33 8.62 419 225 34.94 0 0 NA 548327 TCGA-AB-2990 AML34 16 69201086 69201086 T C SNP IL34 NM_152456.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-37266 NULL 0.001 - - - no_errors tier3 421 28 6.24 321 238 42.5 0 0 NA 548327 TCGA-AB-2990 AML34 16 69574456 69574456 T C SNP HYDIN NM_032821.2 human genbank 54_36p -1 validated intronic c.4330-1484 e28-1484 0.069 - - - no_errors tier3 179 13 6.7 574 170 22.85 0 0 NA 548327 TCGA-AB-2990 AML34 16 69977001 69977001 C T SNP CALB2 NM_007088.3 human genbank 54_36p 1 reviewed missense c.554 p.T185M 0.999 NULL "HMMSmart_EFh,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_SSF47473" - no_errors tier1 1079 108 9.1 909 629 40.82 NA 548327 TCGA-AB-2990 AML34 16 78317780 78317780 C T SNP LOC440389 XM_498648.1 human genbank 54_36p -1 model intronic c.249-4761 e5-4761 0.001 - - - no_errors tier3 288 24 7.69 289 173 37.45 0 0 NA 548327 TCGA-AB-2990 AML34 17 5515430 5515430 G A SNP - - - - - - - - - - - - - - - tier3 182 28 13.33 220 184 45.54 0 0 NA 548327 TCGA-AB-2990 AML34 17 67983335 67983335 G A SNP - - - - - - - - - - - - - - - tier3 237 34 12.55 308 159 34.05 0 0 NA 548327 TCGA-AB-2990 AML34 18 7162110 7162110 C T SNP - - - - - - - - - - - - - - - tier3 557 32 5.43 900 244 21.33 0 0 NA 548327 TCGA-AB-2990 AML34 18 16963269 16963269 C G SNP ROCK1 NM_005406.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-18400 NULL 0 - - - no_errors tier2 438 37 7.79 422 248 36.96 0 0 NA 548327 TCGA-AB-2990 AML34 18 30319576 30319576 C T SNP DTNA NM_032975.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-270363 NULL 0 - - - no_errors tier3 727 46 5.94 791 519 39.62 0 0 NA 548327 TCGA-AB-2990 AML34 18 67658899 67658899 C T SNP - - - - - - - - - - - - - - - tier3 261 20 7.12 368 251 40.55 0 0 NA 548327 TCGA-AB-2990 AML34 19 4137441 4137441 C T SNP ANKRD24 NM_133475.1 human genbank 54_36p 1 provisional nonsense c.19 p.R7* 0.921 NULL "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat" - no_errors tier1 447 58 11.49 364 257 41.38 NA 548327 TCGA-AB-2990 AML34 19 8087756 8087756 G A SNP FBN3 NM_032447.3 human genbank 54_36p -1 reviewed intronic c.3587-73 e28-73 0.011 - - - no_errors tier3 743 77 9.34 936 743 43.96 0 0 NA 548327 TCGA-AB-2990 AML34 20 10087694 10087694 A T SNP LOC100131208 XM_001725409.1 human genbank 54_36p -1 model intronic c.22+37772 e1+37772 0.005 - - - no_errors tier3 427 41 8.76 578 350 37.63 0 0 NA 548327 TCGA-AB-2990 AML34 20 15828970 15828970 C A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.775+14514 e10+14514 0.14 - - - no_errors tier3 392 50 11.31 436 365 45.51 0 0 NA 548327 TCGA-AB-2990 AML34 20 24364186 24364186 T C SNP C20orf39 NM_024893.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-107548 NULL 0 - - - no_errors tier3 540 58 9.68 357 278 43.78 0 0 NA 548327 TCGA-AB-2990 AML34 20 37333168 37333168 G A SNP ENSG00000211534 ENST00000390200 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-429 NULL 1 - - - no_errors tier2 688 85 11 759 537 41.21 0 0 NA 548327 TCGA-AB-2990 AML34 20 58695747 58695747 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 548327 TCGA-AB-2990 AML34 20 60333829 60333829 C T SNP LAMA5 NM_005560.3 human genbank 54_36p -1 reviewed missense c.5467 p.A1823T 0.013 HMMPfam_Laminin_B "HMMPfam_Laminin_B,PatternScan_TNFR_NGFR_1,HMMSmart_SM00282,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMSmart_SM00181,HMMPfam_Laminin_N,HMMSmart_SM00136,superfamily_Galactose-binding domain-like,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_I,HMMPfam_Laminin_II,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMSmart_SM00281,superfamily_EGF/Laminin" - no_errors tier1 66 6 8.22 56 41 41.84 4 1 20 548327 TCGA-AB-2990 AML34 21 9963441 9963441 C T SNP TPTE NM_199261.2 human genbank 54_36p -1 validated intronic c.795+338 e11+338 0.303 - - - no_errors tier3 677 29 4.11 1065 307 22.38 0 0 NA 548327 TCGA-AB-2990 AML34 21 35640378 35640378 G A SNP - - - - - - - - - - - - - - - tier3 867 66 7.07 1073 759 41.43 0 0 NA 548327 TCGA-AB-2990 AML34 21 37126347 37126347 A G SNP HLCS NM_000411.4 human genbank 54_36p -1 validated intronic c.1451+64683 e4+64683 0 - - - no_errors tier3 534 93 14.69 531 453 46.04 1 0 0 548327 TCGA-AB-2990 AML34 21 43545785 43545785 G A SNP C21orf136 XM_001722584.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*27221 NULL 0 - - - no_errors tier3 162 20 10.93 128 88 40.74 1 0 0 501944 TCGA-AB-2991 AML50 X 4565194 4565194 G A SNP - - - - - - - - - - - - - - - tier3 634 0 0 620 158 20.31 0 0 NA 501944 TCGA-AB-2991 AML50 X 9245626 9245626 T C SNP - - - - - - - - - - - - - - - tier3 1638 2 0.12 634 381 37.5 0 0 NA 501944 TCGA-AB-2991 AML50 X 13844619 13844619 C G SNP GPM6B NM_001001994.1 human genbank 54_36p -1 validated intronic c.4+21928 e1+21928 0.01 - - - no_errors tier3 1168 0 0 454 289 38.84 0 1 100 501944 TCGA-AB-2991 AML50 X 23432415 23432415 A G SNP ENSG00000210537 ENST00000387802 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*2834 NULL 0.004 - - - pseudogene tier3 1717 2 0.12 668 488 42.21 0 0 NA 501944 TCGA-AB-2991 AML50 X 25307310 25307310 G T SNP - - - - - - - - - - - - - - - tier3 1543 1 0.06 881 329 27.17 0 0 NA 501944 TCGA-AB-2991 AML50 X 26525044 26525044 C A SNP VENTXP1 NR_001559.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*35954 NULL 0.004 - - - pseudogene tier3 1554 0 0 879 612 40.99 0 0 NA 501944 TCGA-AB-2991 AML50 X 26592991 26592991 T A SNP LOC646346 XR_017105.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-17614 NULL 0.003 - - - pseudogene tier3 969 0 0 733 391 34.79 0 0 NA 501944 TCGA-AB-2991 AML50 X 28371629 28371629 T A SNP - - - - - - - - - - - - - - - tier3 1465 0 0 1300 387 22.94 0 0 NA 501944 TCGA-AB-2991 AML50 X 29177199 29177199 G T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.83-33777 e2-33777 0 - - - no_errors tier3 432 0 0 279 169 37.72 0 0 NA 501944 TCGA-AB-2991 AML50 X 29653712 29653712 G A SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.778+57170 e5+57170 0 - - - no_errors tier3 1511 0 0 783 552 41.32 0 0 NA 501944 TCGA-AB-2991 AML50 X 30165642 30165642 G A SNP MAGEB1 NM_002363.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-12890 NULL 0.001 - - - no_errors tier3 769 1 0.13 390 220 36.07 0 0 NA 501944 TCGA-AB-2991 AML50 X 31242737 31242737 A G SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.9224+8899 e62+8899 0.003 - - - no_errors tier3 1126 1 0.09 536 362 40.27 0 0 NA 501944 TCGA-AB-2991 AML50 X 31969841 31969841 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6439-73289 e45-73289 0.054 - - - no_errors tier3 1498 6 0.4 1252 674 34.99 0 0 NA 501944 TCGA-AB-2991 AML50 X 33860018 33860018 G C SNP - - - - - - - - - - - - - - - tier3 1127 2 0.18 1093 559 33.82 0 0 NA 501944 TCGA-AB-2991 AML50 X 34807989 34807989 C T SNP - - - - - - - - - - - - - - - tier3 1010 1 0.1 548 385 41.26 0 0 NA 501944 TCGA-AB-2991 AML50 X 37963465 37963465 G C SNP SRPX NM_006307.3 human genbank 54_36p -1 provisional intronic c.97+1428 e1+1428 0.017 - - - no_errors tier3 1218 0 0 303 242 44.4 0 0 0 501944 TCGA-AB-2991 AML50 X 43613507 43613507 C T SNP MAOB NM_000898.4 human genbank 54_36p -1 reviewed intronic c.46+12937 e1+12937 0 - - - no_errors tier3 1402 1 0.07 590 330 35.87 0 0 NA 501944 TCGA-AB-2991 AML50 X 45097069 45097069 G A SNP ENSG00000219063 ENST00000407377 human ensembl 54_36p -1 known 3_prime_flanking_region c.*28647 NULL 0.003 - - - no_coding_region:pseudogene tier2 1492 1 0.07 829 548 39.74 0 0 NA 501944 TCGA-AB-2991 AML50 X 45460738 45460738 C T SNP LOC392452 XR_016360.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-14530 NULL 0 - - - pseudogene tier3 1600 4 0.25 679 434 38.96 0 0 NA 501944 TCGA-AB-2991 AML50 X 46272207 46272207 G A SNP ZNF674 NM_001039891.1 human genbank 54_36p -1 provisional intronic c.253+507 e3+507 0.001 - - - no_errors tier2 964 0 0 810 373 31.5 2 0 0 501944 TCGA-AB-2991 AML50 X 49643227 49643227 G A SNP CLCN5 ENST00000376088 human ensembl 54_36p 1 known intronic c.1-50438 e1-50438 0.027 - - - no_errors tier3 1602 3 0.19 1452 799 35.48 0 0 NA 501944 TCGA-AB-2991 AML50 X 67907685 67907685 G T SNP ENSG00000216820 ENST00000407198 human ensembl 54_36p 1 known 5_prime_flanking_region c.-205 NULL 0.043 - - - no_coding_region:pseudogene tier3 833 2 0.24 419 315 42.86 0 0 NA 501944 TCGA-AB-2991 AML50 X 83976607 83976607 G A SNP RPS6KA6 NM_014496.2 human genbank 54_36p -1 provisional intronic c.1+49806 e0+49806 0.035 - - - no_errors tier3 555 0 0 408 132 24.44 0 0 NA 501944 TCGA-AB-2991 AML50 X 87828117 87828117 C A SNP - - - - - - - - - - - - - - - tier3 260 0 0 351 115 24.68 0 0 NA 501944 TCGA-AB-2991 AML50 X 87828135 87828135 A T SNP - - - - - - - - - - - - - - - tier3 269 0 0 383 122 24.16 0 0 NA 501944 TCGA-AB-2991 AML50 X 90951522 90951522 A C SNP PCDH11X NM_032967.1 human genbank 54_36p 1 reviewed intronic c.1-606 e1-606 0.009 - - - no_errors tier3 1289 0 0 1096 354 24.4 0 0 NA 501944 TCGA-AB-2991 AML50 X 91256444 91256444 C T SNP PCDH11X NM_032968.1 human genbank 54_36p 1 reviewed intronic c.3034-86586 e3-86586 0.001 - - - no_errors tier3 1162 2 0.17 1020 719 41.25 0 0 NA 501944 TCGA-AB-2991 AML50 X 94999402 94999402 A G SNP - - - - - - - - - - - - - - - tier3 1722 2 0.12 1184 768 39.32 0 0 NA 501944 TCGA-AB-2991 AML50 X 96121077 96121077 C T SNP DIAPH2 NM_006729.4 human genbank 54_36p 1 reviewed intronic c.2050+14215 e17+14215 0 - - - no_errors tier3 666 0 0 563 411 42.15 0 6 100 501944 TCGA-AB-2991 AML50 X 104782477 104782477 C T SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.773-65539 e6-65539 0.007 - - - no_errors tier3 1912 0 0 1518 277 15.41 0 0 NA 501944 TCGA-AB-2991 AML50 X 106501543 106501543 T C SNP KRT18P49 XR_016590.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-48629 NULL 0 - - - pseudogene tier2 1665 0 0 814 542 39.97 0 0 NA 501944 TCGA-AB-2991 AML50 X 110451482 110451482 G T SNP DCX NM_000555.2 human genbank 54_36p -1 reviewed intronic c.1175-8862 e6-8862 0 - - - no_errors tier3 1101 1 0.09 592 350 37.12 0 0 NA 501944 TCGA-AB-2991 AML50 X 111702386 111702386 G A SNP - - - - - - - - - - - - - - - tier3 655 3 0.46 559 407 42.13 0 0 NA 501944 TCGA-AB-2991 AML50 X 119397779 119397779 T A SNP ATP1B4 NM_012069.1 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*262 NULL 0.606 - - - no_errors tier2 762 0 0 557 375 40.24 0 0 NA 501944 TCGA-AB-2991 AML50 X 120437459 120437459 G T SNP - - - - - - - - - - - - - - - tier3 556 0 0 365 178 32.78 0 0 NA 501944 TCGA-AB-2991 AML50 X 125252306 125252306 G A SNP - - - - - - - - - - - - - - - tier3 1208 1 0.08 909 339 27.16 0 0 NA 501944 TCGA-AB-2991 AML50 X 125899541 125899541 C T SNP - - - - - - - - - - - - - - - tier2 1505 1 0.07 1243 714 36.48 0 0 NA 501944 TCGA-AB-2991 AML50 X 139395135 139395135 C A SNP ENSG00000219242 ENST00000403063 human ensembl 54_36p -1 known 5_prime_flanking_region c.-14030 NULL 0.001 - - - no_coding_region:pseudogene tier3 1299 2 0.15 522 373 41.63 0 0 NA 501944 TCGA-AB-2991 AML50 X 145442619 145442619 T G SNP ENSG00000220179 ENST00000405443 human ensembl 54_36p 1 known 5_prime_flanking_region c.-319 NULL 0 - - - no_coding_region:pseudogene tier3 676 1 0.15 554 330 37.33 0 0 NA 501944 TCGA-AB-2991 AML50 X 150070962 150070962 C - DEL GPR50 NM_004224.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-24890 NULL 0.005 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 X 153633243 153633243 G A SNP GAB3 NM_001081573.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-749 NULL 0.003 - - - no_errors tier2 978 1 0.1 429 290 40.33 0 0 NA 501944 TCGA-AB-2991 AML50 1 15534764 15534764 A C SNP FHAD1 ENST00000358897 human ensembl 54_36p 1 known intronic c.1-3800 e1-3800 0 - - - no_errors tier3 1755 1 0.06 781 447 36.37 0 0 NA 501944 TCGA-AB-2991 AML50 1 19139809 19139809 C T SNP IFFO2 ENST00000355609 human ensembl 54_36p -1 known intronic c.182+14940 e1+14940 0 - - - no_start_codon tier3 505 0 0 189 138 42.2 8 10 55.56 501944 TCGA-AB-2991 AML50 1 22531849 22531849 G A SNP LOC343384 XM_291544.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-9438 NULL 0 - - - no_errors tier3 1106 2 0.18 467 186 28.44 0 0 NA 501944 TCGA-AB-2991 AML50 1 22857011 22857011 C T SNP C1QB NM_000491.3 human genbank 54_36p 1 reviewed intronic c.1-1509 e1-1509 0.002 - - - no_errors tier3 1497 4 0.27 668 406 37.8 0 0 0 501944 TCGA-AB-2991 AML50 1 35679474 35679474 C A SNP KIAA0319L NM_024874.3 human genbank 54_36p -1 reviewed intronic c.2871-148 e19-148 0.011 - - - no_errors tier3 1010 23 2.22 431 207 32.45 4 6 60 501944 TCGA-AB-2991 AML50 1 43764755 43764756 - T INS PTPRF NM_002840.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-18579 NULL 0.000:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 1 46987591 46987591 C T SNP CYP4B1 NM_001099772.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49750 NULL 0.007 - - - no_errors tier3 1685 3 0.18 955 571 37.39 0 0 NA 501944 TCGA-AB-2991 AML50 1 62407644 62407644 G A SNP L1TD1 NM_019079.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37245 NULL 0 - - - no_errors tier3 778 1 0.13 351 242 40.67 0 0 NA 501944 TCGA-AB-2991 AML50 1 66416496 66416496 A G SNP PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.282-69235 e3-69235 0.012 - - - no_errors tier3 444 0 0 687 406 37.15 0 0 NA 501944 TCGA-AB-2991 AML50 1 69050689 69050689 G A SNP - - - - - - - - - - - - - - - tier3 658 1 0.15 300 173 36.58 0 0 NA 501944 TCGA-AB-2991 AML50 1 87663549 87663549 G C SNP ENSG00000199318 ENST00000362448 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*27987 NULL 0 - - - no_errors tier3 849 0 0 467 206 30.56 0 0 NA 501944 TCGA-AB-2991 AML50 1 100969425 100969425 G A SNP VCAM1 NM_001078.2 human genbank 54_36p 1 reviewed missense c.1288 p.V430M 0.987 "HMMPfam_C2-set,superfamily_Immunoglobulin" "HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_C2-set,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 1112 0 597 258 30.18 8 0 501944 TCGA-AB-2991 AML50 1 104356075 104356075 C G SNP LOC100129138 XR_036957.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.003 - - - no_errors tier2 1037 1 0.1 1459 670 31.44 0 0 NA 501944 TCGA-AB-2991 AML50 1 107253322 107253322 A T SNP - - - - - - - - - - - - - - - tier2 738 0 0 534 315 37.1 0 0 NA 501944 TCGA-AB-2991 AML50 1 112773999 112773999 G A SNP CTTNBP2NL NM_018704.2 human genbank 54_36p 1 validated intronic c.99+13590 e1+13590 0.137 - - - no_errors tier3 1554 1 0.06 1098 591 34.99 0 0 NA 501944 TCGA-AB-2991 AML50 1 118335873 118335873 C A SNP SPAG17 NM_206996.2 human genbank 54_36p -1 validated intronic c.5362-199 e37-199 0.001 - - - no_errors tier3 764 0 0 510 261 33.85 0 0 NA 501944 TCGA-AB-2991 AML50 1 165427437 165427437 A G SNP POU2F1 NM_002697.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-140902 NULL 0.307 - - - no_errors tier3 790 0 0 412 272 39.77 0 0 NA 501944 TCGA-AB-2991 AML50 1 185788756 185788756 G A SNP ENSG00000203918 ENST00000370430 human ensembl 54_36p -1 known 5_prime_flanking_region c.-16702 NULL 0.387 - - - no_coding_region:pseudogene tier3 682 0 0 389 205 34.51 0 0 NA 501944 TCGA-AB-2991 AML50 1 187984897 187984897 C A SNP - - - - - - - - - - - - - - - tier3 728 0 0 702 401 36.36 0 0 NA 501944 TCGA-AB-2991 AML50 1 188083951 188083951 T C SNP - - - - - - - - - - - - - - - tier3 1047 1 0.1 743 468 38.61 0 0 NA 501944 TCGA-AB-2991 AML50 1 207813435 207813435 G A SNP CAMK1G NM_020439.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-21517 NULL 0.007 - - - no_errors tier3 2374 2 0.08 931 555 37.35 0 0 NA 501944 TCGA-AB-2991 AML50 1 214871197 214871197 C A SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.589+19741 e3+19741 0 - - - no_errors tier3 1168 0 0 721 141 16.36 0 0 NA 501944 TCGA-AB-2991 AML50 1 218862354 218862354 T A SNP MARK1 NM_018650.3 human genbank 54_36p 1 validated intronic c.909+3634 e9+3634 0.002 - - - no_errors tier3 941 0 0 709 429 37.7 0 0 NA 501944 TCGA-AB-2991 AML50 1 223593731 223593731 A C SNP ENSG00000185842 ENST00000327794 human ensembl 54_36p 1 known intronic c.1718+1224 e12+1224 0.286 - - - no_errors tier3 630 3 0.47 530 348 39.59 0 0 0 501944 TCGA-AB-2991 AML50 1 226979072 226979072 G A SNP RHOU NM_021205.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*32962 NULL 0.841 - - - no_errors tier2 1395 0 0 638 392 37.98 0 0 NA 501944 TCGA-AB-2991 AML50 1 233639358 233639358 A G SNP TBCE NM_001079515.1 human genbank 54_36p 1 reviewed intronic c.186-5013 e3-5013 0 - - - no_errors tier3 444 0 0 158 136 46.26 0 3 100 501944 TCGA-AB-2991 AML50 1 242352787 242352787 G T SNP ENSG00000208068 ENST00000385333 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*18652 NULL 0 - - - pseudogene tier3 807 0 0 580 360 38.3 0 0 NA 501944 TCGA-AB-2991 AML50 1 246858146 246858146 G A SNP OR2T11 NM_001001964.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-1094 NULL 0 - - - no_errors tier3 1837 1 0.05 702 522 42.65 0 0 NA 501944 TCGA-AB-2991 AML50 2 4123758 4123758 C T SNP - - - - - - - - - - - - - - - tier3 2305 7 0.3 1449 982 40.38 0 0 NA 501944 TCGA-AB-2991 AML50 2 8807811 8807811 G A SNP KIDINS220 NM_020738.2 human genbank 54_36p -1 validated missense c.3296 p.P1099L 0.282 NULL "HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,superfamily_SAM/Pointed domain,HMMPfam_KAP_NTPase" - no_errors tier1 608 0 296 190 39.09 19 17 47.22 501944 TCGA-AB-2991 AML50 2 20454995 20454995 G C SNP PUM2 ENST00000403432 human ensembl 54_36p -1 known 5_prime_flanking_region c.-64393 NULL 0.132 - - - no_errors tier2 869 0 0 385 267 40.83 0 0 NA 501944 TCGA-AB-2991 AML50 2 40232568 40232568 G A SNP SLC8A1 NM_021097.1 human genbank 54_36p -1 validated intronic c.2269+8841 e8+8841 0 - - - no_errors tier3 640 1 0.16 371 176 32.18 0 0 NA 501944 TCGA-AB-2991 AML50 2 41910550 41910550 T A SNP LDHAL3 XM_001726960.1 human genbank 54_36p 1 model intronic c.1062+9155 e2+9155 0.007 - - - pseudogene tier3 1305 0 0 1072 625 36.83 0 0 NA 501944 TCGA-AB-2991 AML50 2 51169604 51169604 C G SNP LOC730100 XR_041273.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.005 - - - no_errors tier3 1498 0 0 893 538 37.54 0 0 NA 501944 TCGA-AB-2991 AML50 2 56435553 56435553 C T SNP CCDC85A NM_001080433.1 human genbank 54_36p 1 provisional intronic c.1317+11959 e3+11959 0 - - - no_errors tier3 1199 1 0.08 669 404 37.62 0 0 NA 501944 TCGA-AB-2991 AML50 2 58377515 58377515 A T SNP ENSG00000187684 ENST00000340221 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44351 NULL 0 - - - no_coding_region:pseudogene tier3 375 0 0 466 246 34.55 0 0 NA 501944 TCGA-AB-2991 AML50 2 63103525 63103525 A G SNP EHBP1 NM_015252.1 human genbank 54_36p 1 validated intronic c.3317-14649 e21-14649 0.007 - - - no_errors tier3 762 1 0.13 348 240 40.82 0 1 100 501944 TCGA-AB-2991 AML50 2 65832326 65832326 A C SNP KRT18P33 XR_017456.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*15338 NULL 0.001 - - - pseudogene tier3 1706 1 0.06 986 677 40.71 0 0 NA 501944 TCGA-AB-2991 AML50 2 67597742 67597742 A G SNP - - - - - - - - - - - - - - - tier3 860 1 0.12 519 229 30.61 0 0 NA 501944 TCGA-AB-2991 AML50 2 79384989 79384989 T A SNP LOC100132577 XM_001726289.1 human genbank 54_36p 1 model intronic c.1-8354 e1-8354 0 - - - no_errors tier3 713 1 0.14 536 355 39.84 0 0 NA 501944 TCGA-AB-2991 AML50 2 79428515 79428515 A G SNP CTNNA2 ENST00000409536 human ensembl 54_36p 1 known intronic c.1-25950 e1-25950 0.001 - - - no_errors tier3 1394 1 0.07 900 479 34.74 0 0 NA 501944 TCGA-AB-2991 AML50 2 104256877 104256877 C T SNP - - - - - - - - - - - - - - - tier3 1075 0 0 796 573 41.73 0 0 NA 501944 TCGA-AB-2991 AML50 2 116719887 116719887 G A SNP - - - - - - - - - - - - - - - tier3 1510 2 0.13 1023 579 36.12 0 0 NA 501944 TCGA-AB-2991 AML50 2 117107247 117107247 C G SNP - - - - - - - - - - - - - - - tier3 1311 0 0 819 525 38.98 0 0 NA 501944 TCGA-AB-2991 AML50 2 121852457 121852457 T C SNP CLASP1 NM_015282.1 human genbank 54_36p -1 validated intronic c.3492-762 e33-762 0 - - - no_errors tier3 891 0 0 428 244 36.26 0 6 100 501944 TCGA-AB-2991 AML50 2 126483150 126483150 G A SNP - - - - - - - - - - - - - - - tier3 710 0 0 808 287 26.21 0 0 NA 501944 TCGA-AB-2991 AML50 2 129978471 129978471 A G SNP - - - - - - - - - - - - - - - tier3 1432 1 0.07 1266 279 18.03 0 0 NA 501944 TCGA-AB-2991 AML50 2 133631952 133631952 C T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.208-27799 e4-27799 0.002 - - - no_errors tier3 769 1 0.13 640 364 36.22 0 0 NA 501944 TCGA-AB-2991 AML50 2 134130695 134130695 G A SNP - - - - - - - - - - - - - - - tier3 1081 1 0.09 935 438 31.9 0 0 NA 501944 TCGA-AB-2991 AML50 2 140676382 140676382 A T SNP ENSG00000208282 ENST00000385547 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18093 NULL 0.898 - - - pseudogene tier2 649 0 0 511 220 30.05 0 0 NA 501944 TCGA-AB-2991 AML50 2 141184117 141184117 A G SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.6023+5895 e37+5895 0.001 - - - no_errors tier3 1174 0 0 847 439 34.14 0 0 NA 501944 TCGA-AB-2991 AML50 2 143217232 143217232 A C SNP - - - - - - - - - - - - - - - tier3 1345 5 0.37 792 505 38.94 0 0 NA 501944 TCGA-AB-2991 AML50 2 144322915 144322915 C T SNP ENSG00000200287 ENST00000363417 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48383 NULL 0.005 - - - no_errors tier3 676 1 0.15 646 321 33.2 0 0 NA 501944 TCGA-AB-2991 AML50 2 150649048 150649048 C T SNP - - - - - - - - - - - - - - - tier3 515 0 0 389 256 39.69 0 0 NA 501944 TCGA-AB-2991 AML50 2 156015415 156015415 C T SNP - - - - - - - - - - - - - - - tier3 1797 0 0 1276 446 25.9 0 0 NA 501944 TCGA-AB-2991 AML50 2 156512289 156512289 C T SNP - - - - - - - - - - - - - - - tier2 1043 4 0.38 508 287 36.1 0 0 NA 501944 TCGA-AB-2991 AML50 2 163418959 163418959 C A SNP KCNH7 NM_033272.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15685 NULL 0.002 - - - no_errors tier3 937 0 0 751 359 32.34 0 0 NA 501944 TCGA-AB-2991 AML50 2 164630455 164630455 G T SNP - - - - - - - - - - - - - - - tier2 649 0 0 662 235 26.2 0 0 NA 501944 TCGA-AB-2991 AML50 2 165679355 165679355 T C SNP SCN3A NM_006922.1 human genbank 54_36p -1 reviewed intronic c.3515-629 e18-629 0 - - - no_errors tier3 1364 1 0.07 1093 710 39.36 0 0 0 501944 TCGA-AB-2991 AML50 2 171593532 171593532 C T SNP TLK1 NM_012290.1 human genbank 54_36p -1 validated intronic c.1170-371 e12-371 0 - - - no_errors tier3 507 0 0 364 221 37.78 1 0 0 501944 TCGA-AB-2991 AML50 2 172556761 172556761 G A SNP HAT1 NM_003642.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*249 NULL 0.826 - - - no_errors tier2 717 0 0 460 299 39.39 4 1 20 501944 TCGA-AB-2991 AML50 2 173325573 173325573 C T SNP RAPGEF4 NM_007023.1 human genbank 54_36p 1 validated intronic c.65+16551 e1+16551 0.636 - - - no_errors tier3 558 0 0 312 185 37.15 0 1 100 501944 TCGA-AB-2991 AML50 2 173502020 173502020 C T SNP RAPGEF4 NM_007023.1 human genbank 54_36p 1 validated intronic c.537+6746 e6+6746 0 - - - no_errors tier3 1885 5 0.26 831 550 39.83 1 0 0 501944 TCGA-AB-2991 AML50 2 178494059 178494059 A G SNP PDE11A NM_016953.1 human genbank 54_36p -1 reviewed intronic c.1072-15899 e3-15899 0.025 - - - no_errors tier3 813 0 0 476 171 26.39 0 0 NA 501944 TCGA-AB-2991 AML50 2 178592266 178592266 G A SNP PDE11A NM_016953.1 human genbank 54_36p -1 reviewed intronic c.913-4833 e2-4833 0.06 - - - no_errors tier3 1057 2 0.19 1011 334 24.83 0 0 NA 501944 TCGA-AB-2991 AML50 2 183436880 183436880 C T SNP FRZB NM_001463.2 human genbank 54_36p -1 validated intronic c.478+2168 e1+2168 0.001 - - - no_errors tier3 913 0 0 520 237 31.27 0 0 NA 501944 TCGA-AB-2991 AML50 2 198629677 198629677 G A SNP PLCL1 NM_006226.1 human genbank 54_36p 1 provisional intronic c.1-27050 e1-27050 0.963 - - - no_errors tier3 1026 1 0.1 775 438 36.11 0 0 NA 501944 TCGA-AB-2991 AML50 2 206387387 206387387 T C SNP NRP2 NM_201266.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*19360 NULL 0.001 - - - no_errors tier3 1261 1 0.08 612 389 38.82 0 0 NA 501944 TCGA-AB-2991 AML50 2 212212111 212212111 A G SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.1947-8547 e17-8547 0.01 - - - no_errors tier3 238 0 0 231 121 34.38 0 0 NA 501944 TCGA-AB-2991 AML50 2 217858851 217858851 C T SNP - - - - - - - - - - - - - - - tier3 899 0 0 603 353 36.92 0 0 NA 501944 TCGA-AB-2991 AML50 2 221411646 221411646 C A SNP - - - - - - - - - - - - - - - tier3 477 0 0 397 141 26.21 0 0 NA 501944 TCGA-AB-2991 AML50 2 226703920 226703920 T C SNP - - - - - - - - - - - - - - - tier3 766 1 0.13 743 458 38.13 0 0 NA 501944 TCGA-AB-2991 AML50 2 226889797 226889797 G T SNP - - - - - - - - - - - - - - - tier3 550 1 0.18 470 266 36.14 0 0 NA 501944 TCGA-AB-2991 AML50 3 1115003 1115003 C T SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.1+5190 e0+5190 0.001 - - - no_errors tier3 1498 0 0 1179 214 15.35 0 0 NA 501944 TCGA-AB-2991 AML50 3 1493561 1493561 T C SNP - - - - - - - - - - - - - - - tier3 1020 4 0.39 712 434 37.84 0 0 NA 501944 TCGA-AB-2991 AML50 3 2694888 2694888 A - DEL CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.56-58011 e2-58011 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 3 3696775 3696775 C T SNP ENSG00000223036 ENST00000411104 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33513 NULL 0.001 - - - no_errors tier3 394 2 0.51 435 126 22.42 0 0 NA 501944 TCGA-AB-2991 AML50 3 8531818 8531818 G A SNP LMCD1 NM_014583.2 human genbank 54_36p 1 reviewed intronic c.42+13152 e1+13152 0.014 - - - no_errors tier3 825 0 0 275 169 38.06 0 0 NA 501944 TCGA-AB-2991 AML50 3 17708490 17708490 T C SNP TBC1D5 NM_014744.1 human genbank 54_36p -1 validated intronic c.1+47349 e0+47349 0 - - - no_errors tier3 1424 0 0 768 451 37 0 0 0 501944 TCGA-AB-2991 AML50 3 31564378 31564378 T A SNP STT3B NM_178862.1 human genbank 54_36p 1 provisional intronic c.314+14570 e1+14570 0.037 - - - no_errors tier2 1227 0 0 637 417 39.49 1 0 0 501944 TCGA-AB-2991 AML50 3 32780258 32780258 A C SNP CNOT10 NM_015442.1 human genbank 54_36p 1 provisional intronic c.1841-693 e16-693 0 - - - no_errors tier3 365 0 0 196 118 37.46 4 5 55.56 501944 TCGA-AB-2991 AML50 3 38553866 38553866 C T SNP EXOG ENST00000358249 human ensembl 54_36p 1 known intronic c.271-4396 e5-4396 0.002 - - - no_errors tier3 778 2 0.26 235 238 50.32 3 0 0 501944 TCGA-AB-2991 AML50 3 40314326 40314326 G A SNP EIF1B NM_005875.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-12111 NULL 0.066 - - - no_errors tier3 562 0 0 346 179 34.1 0 0 NA 501944 TCGA-AB-2991 AML50 3 40676797 40676797 G C SNP LOC729505 XM_001130480.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*38764 NULL 0.158 - - - no_errors tier3 1139 1 0.09 570 363 38.87 0 0 NA 501944 TCGA-AB-2991 AML50 3 40725926 40725926 A G SNP LOC729505 XM_001130480.2 human genbank 54_36p -1 model intronic c.117+1012 e1+1012 0.002 - - - no_errors tier3 1813 2 0.11 931 596 39.01 0 0 NA 501944 TCGA-AB-2991 AML50 3 65213278 65213278 T C SNP - - - - - - - - - - - - - - - tier3 944 0 0 768 243 24.04 0 0 NA 501944 TCGA-AB-2991 AML50 3 66990189 66990189 T A SNP - - - - - - - - - - - - - - - tier2 832 0 0 662 417 38.65 0 0 NA 501944 TCGA-AB-2991 AML50 3 70351759 70351759 A G SNP LOC100128160 XM_001714107.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-4592 NULL 0.059 - - - no_errors tier2 1395 1 0.07 701 492 41.24 0 0 NA 501944 TCGA-AB-2991 AML50 3 73778206 73778206 G A SNP PDZRN3 NM_015009.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-21540 NULL 0.003 - - - no_errors tier3 1214 0 0 535 367 40.69 0 0 NA 501944 TCGA-AB-2991 AML50 3 80186325 80186325 G A SNP - - - - - - - - - - - - - - - tier3 273 1 0.36 215 103 32.39 0 0 NA 501944 TCGA-AB-2991 AML50 3 82208492 82208492 A G SNP - - - - - - - - - - - - - - - tier3 599 1 0.17 557 305 35.34 0 0 NA 501944 TCGA-AB-2991 AML50 3 83460586 83460586 G A SNP - - - - - - - - - - - - - - - tier3 1189 0 0 588 219 27.14 0 0 NA 501944 TCGA-AB-2991 AML50 3 84391630 84391630 G A SNP ENSG00000221380 ENST00000408453 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*30323 NULL 0 - - - no_errors tier3 169 0 0 255 160 38.55 0 0 NA 501944 TCGA-AB-2991 AML50 3 86552465 86552465 G T SNP - - - - - - - - - - - - - - - tier3 774 0 0 531 261 32.95 0 0 NA 501944 TCGA-AB-2991 AML50 3 96925780 96925780 G A SNP - - - - - - - - - - - - - - - tier3 524 2 0.38 495 247 33.29 0 0 NA 501944 TCGA-AB-2991 AML50 3 105891081 105891081 T C SNP - - - - - - - - - - - - - - - tier3 1146 2 0.17 600 331 35.48 0 0 NA 501944 TCGA-AB-2991 AML50 3 107489630 107489630 C G SNP - - - - - - - - - - - - - - - tier3 859 0 0 665 430 39.27 0 0 NA 501944 TCGA-AB-2991 AML50 3 113068119 113068119 C T SNP PLCXD2 ENST00000273356 human ensembl 54_36p 1 known intronic c.68-17482 e2-17482 0 - - - no_errors tier2 1903 5 0.26 497 375 43 1 0 0 501944 TCGA-AB-2991 AML50 3 116908108 116908108 G T SNP GAP43 NM_002045.1 human genbank 54_36p 1 reviewed intronic c.629-14223 e3-14223 0.002 - - - no_errors tier3 1234 0 0 744 369 33.15 0 0 NA 501944 TCGA-AB-2991 AML50 3 118738767 118738767 C A SNP ENSG00000206889 ENST00000384162 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6975 NULL 0.002 - - - no_errors tier3 610 0 0 462 134 22.45 0 0 NA 501944 TCGA-AB-2991 AML50 3 140907082 140907082 A T SNP NMNAT3 NM_178177.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-126497 NULL 0.007 - - - no_errors tier3 2571 2 0.08 979 638 39.43 0 0 NA 501944 TCGA-AB-2991 AML50 3 143119232 143119232 C T SNP ATP1B3 NM_001679.2 human genbank 54_36p 1 reviewed intronic c.582+1680 e5+1680 0.012 - - - no_errors tier3 1058 4 0.38 387 247 38.96 13 4 23.53 501944 TCGA-AB-2991 AML50 3 146386979 146386979 C T SNP - - - - - - - - - - - - - - - tier3 407 1 0.24 594 260 30.44 0 0 NA 501944 TCGA-AB-2991 AML50 3 148895177 148895177 C T SNP - - - - - - - - - - - - - - - tier3 578 0 0 437 143 24.61 0 0 NA 501944 TCGA-AB-2991 AML50 3 154006631 154006631 T C SNP P2RY1 NM_002563.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29631 NULL 0.003 - - - no_errors tier3 636 1 0.16 643 216 25.15 0 0 NA 501944 TCGA-AB-2991 AML50 3 155344221 155344221 G A SNP uc003ezv.1 ENST00000356448 human ensembl 54_36p 1 known intronic c.1270-5647 e4-5647 0 - - - no_errors tier3 663 0 0 469 262 35.84 0 0 0 501944 TCGA-AB-2991 AML50 3 164293564 164293564 A G SNP - - - - - - - - - - - - - - - tier3 1072 2 0.19 714 481 40.25 0 0 NA 501944 TCGA-AB-2991 AML50 3 166343020 166343020 A C SNP ENSG00000200052 ENST00000363182 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19715 NULL 0 - - - no_errors tier3 761 0 0 776 281 26.56 0 0 NA 501944 TCGA-AB-2991 AML50 3 193364823 193364823 A C SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed intronic c.613+6118 e4+6118 0.011 - - - no_errors tier3 588 0 0 252 112 30.77 0 0 NA 501944 TCGA-AB-2991 AML50 3 197439460 197439460 C T SNP OSTalpha NM_152672.5 human genbank 54_36p 1 validated missense c.440 p.T147M 0.998 NULL NULL - no_errors tier1 882 3 0.34 261 187 41.74 1 1 50 501944 TCGA-AB-2991 AML50 4 13121775 13121775 G A SNP RAB28 NM_001017979.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-26903 NULL 0.004 - - - no_errors tier3 671 0 0 443 236 34.76 0 0 NA 501944 TCGA-AB-2991 AML50 4 19338426 19338426 C A SNP - - - - - - - - - - - - - - - tier3 1299 1 0.08 902 418 31.64 0 0 NA 501944 TCGA-AB-2991 AML50 4 21663358 21663358 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 4 29749636 29749636 C A SNP - - - - - - - - - - - - - - - tier2 1113 0 0 521 361 40.93 0 0 NA 501944 TCGA-AB-2991 AML50 4 30352549 30352549 T C SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3033+17233 e2+17233 0 - - - no_errors tier3 590 1 0.17 304 123 28.81 0 0 NA 501944 TCGA-AB-2991 AML50 4 31366768 31366768 A C SNP - - - - - - - - - - - - - - - tier2 1518 0 0 840 648 43.55 0 0 NA 501944 TCGA-AB-2991 AML50 4 32318534 32318534 C A SNP - - - - - - - - - - - - - - - tier2 2345 3 0.13 1736 340 16.37 0 0 NA 501944 TCGA-AB-2991 AML50 4 32564992 32564992 T G SNP - - - - - - - - - - - - - - - tier3 470 0 0 593 144 19.54 0 0 NA 501944 TCGA-AB-2991 AML50 4 37299500 37299500 G A SNP RELL1 NM_001085399.1 human genbank 54_36p -1 validated intronic c.816+9902 e6+9902 0 - - - no_errors tier3 265 1 0.38 196 94 32.41 2 3 60 501944 TCGA-AB-2991 AML50 4 43058045 43058045 C A SNP LOC441013 XR_016299.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*48726 NULL 0 - - - pseudogene tier3 1001 1 0.1 629 347 35.52 0 0 NA 501944 TCGA-AB-2991 AML50 4 58102345 58102345 A C SNP ENSG00000210638 ENST00000387903 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49049 NULL 0.994 - - - pseudogene tier2 718 0 0 696 425 37.85 0 0 NA 501944 TCGA-AB-2991 AML50 4 60928310 60928310 G A SNP - - - - - - - - - - - - - - - tier3 1258 2 0.16 773 509 39.67 0 0 NA 501944 TCGA-AB-2991 AML50 4 64539625 64539625 A T SNP - - - - - - - - - - - - - - - tier3 702 0 0 423 265 38.52 0 0 NA 501944 TCGA-AB-2991 AML50 4 73871966 73871966 C T SNP - - - - - - - - - - - - - - - tier3 1818 5 0.27 886 361 28.95 0 0 NA 501944 TCGA-AB-2991 AML50 4 74975553 74975553 C A SNP CXCL1 NM_001511.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*20436 NULL 0.001 - - - no_errors tier3 310 0 0 259 161 38.33 0 0 NA 501944 TCGA-AB-2991 AML50 4 85255515 85255515 C T SNP - - - - - - - - - - - - - - - tier3 2633 3 0.11 1387 832 37.49 0 0 NA 501944 TCGA-AB-2991 AML50 4 96666873 96666874 - A INS UNC5C NM_003728.2 human genbank 54_36p -1 reviewed intronic c.124+22034_124+22033 e1+22034 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 4 106746801 106746801 G A SNP FLJ20184 NM_017700.1 human genbank 54_36p 1 predicted intronic c.385-7189 e3-7189 0.002 - - - no_errors tier3 747 0 0 417 255 37.95 0 0 NA 501944 TCGA-AB-2991 AML50 4 125223803 125223803 T A SNP ENSG00000213466 ENST00000394336 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*20211 NULL 0.008 - - - no_coding_region:pseudogene tier3 728 0 0 916 562 38 0 0 NA 501944 TCGA-AB-2991 AML50 4 127446717 127446717 C G SNP - - - - - - - - - - - - - - - tier3 1189 1 0.08 616 329 34.81 0 0 NA 501944 TCGA-AB-2991 AML50 4 129494842 129494842 G A SNP - - - - - - - - - - - - - - - tier3 1028 2 0.19 535 358 40.09 0 0 NA 501944 TCGA-AB-2991 AML50 4 132309910 132309910 C T SNP - - - - - - - - - - - - - - - tier3 525 0 0 779 127 14.02 0 0 NA 501944 TCGA-AB-2991 AML50 4 135237227 135237227 T A SNP - - - - - - - - - - - - - - - tier3 279 0 0 216 175 44.76 0 0 NA 501944 TCGA-AB-2991 AML50 4 135558392 135558392 C T SNP - - - - - - - - - - - - - - - tier3 772 1 0.13 652 356 35.28 0 0 NA 501944 TCGA-AB-2991 AML50 4 143288747 143288747 A G SNP INPP4B NM_001101669.1 human genbank 54_36p -1 reviewed intronic c.1564-2148 e15-2148 0 - - - no_errors tier3 1227 1 0.08 833 534 39.04 0 0 0 501944 TCGA-AB-2991 AML50 4 144116933 144116933 G A SNP LOC729675 XM_001130993.1 human genbank 54_36p -1 model intronic c.570-36085 e3-36085 0.005 - - - no_errors tier2 1027 2 0.19 494 379 43.41 0 0 NA 501944 TCGA-AB-2991 AML50 4 150080741 150080741 G A SNP - - - - - - - - - - - - - - - tier3 1860 1 0.05 1581 300 15.95 0 0 NA 501944 TCGA-AB-2991 AML50 4 151028325 151028325 T - DEL ENSG00000202331 ENST00000365461 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19845 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 4 151044965 151044965 G A SNP ENSG00000202331 ENST00000365461 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-3205 NULL 0.008 - - - no_errors tier3 1100 0 0 1160 224 16.16 0 0 NA 501944 TCGA-AB-2991 AML50 4 155638482 155638482 T C SNP DCHS2 ENST00000339452 human ensembl 54_36p -1 known 5_prime_flanking_region c.-6525 NULL 0 - - - no_errors tier3 1070 0 0 485 306 38.64 0 0 NA 501944 TCGA-AB-2991 AML50 4 161636679 161636679 G A SNP - - - - - - - - - - - - - - - tier3 591 0 0 253 134 34.63 0 0 NA 501944 TCGA-AB-2991 AML50 4 163708107 163708108 TA - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 4 164040700 164040700 A G SNP - - - - - - - - - - - - - - - tier2 969 0 0 447 505 53.05 0 0 NA 501944 TCGA-AB-2991 AML50 4 165338360 165338360 A G SNP ANP32C NM_012403.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-47 NULL 0.942 - - - no_errors tier2 996 1 0.1 317 219 40.78 0 0 NA 501944 TCGA-AB-2991 AML50 4 169819574 169819574 T A SNP PALLD NM_016081.3 human genbank 54_36p 1 validated intronic c.909-6342 e2-6342 0.038 - - - no_errors tier3 346 1 0.29 210 135 39.13 0 0 NA 501944 TCGA-AB-2991 AML50 4 173277053 173277053 A G SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.139-110329 e2-110329 0.82 - - - no_errors tier3 999 3 0.3 729 414 36.22 0 0 NA 501944 TCGA-AB-2991 AML50 4 187411364 187411364 C G SNP KLKB1 NM_000892.3 human genbank 54_36p 1 reviewed intronic c.1313+1031 e10+1031 0.001 - - - no_errors tier3 202 2 0.98 296 152 33.93 0 0 NA 501944 TCGA-AB-2991 AML50 4 187825172 187825172 T C SNP FAT1 NM_005245.3 human genbank 54_36p -1 reviewed intronic c.3266-3411 e2-3411 0.002 - - - no_errors tier3 864 1 0.12 612 364 37.26 0 0 NA 501944 TCGA-AB-2991 AML50 4 188106115 188106115 G C SNP - - - - - - - - - - - - - - - tier3 755 1 0.13 441 277 38.53 0 0 NA 501944 TCGA-AB-2991 AML50 4 189800982 189800982 C T SNP - - - - - - - - - - - - - - - tier3 885 1 0.11 393 242 38.05 0 0 NA 501944 TCGA-AB-2991 AML50 5 4725361 4725361 T A SNP - - - - - - - - - - - - - - - tier3 976 1 0.1 558 320 36.41 0 0 NA 501944 TCGA-AB-2991 AML50 5 8160943 8160943 G T SNP - - - - - - - - - - - - - - - tier3 944 0 0 730 318 30.34 0 0 NA 501944 TCGA-AB-2991 AML50 5 8545290 8545290 G A SNP LOC729506 XM_001130481.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-33742 NULL 0.003 - - - no_errors tier3 1040 2 0.19 485 315 39.38 0 0 NA 501944 TCGA-AB-2991 AML50 5 8741301 8741302 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 5 18641695 18641695 C A SNP - - - - - - - - - - - - - - - tier3 571 1 0.17 572 294 33.91 0 0 NA 501944 TCGA-AB-2991 AML50 5 19299941 19299941 T A SNP - - - - - - - - - - - - - - - tier3 817 1 0.12 786 157 16.65 0 0 NA 501944 TCGA-AB-2991 AML50 5 24482209 24482209 A G SNP CDH10 NM_006727.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*41320 NULL 0.192 - - - no_errors tier3 2142 5 0.23 1170 581 33.18 0 0 NA 501944 TCGA-AB-2991 AML50 5 24708302 24708302 A G SNP CDH10 NM_006727.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-78946 NULL 0 - - - no_errors tier3 273 0 0 315 169 34.92 0 0 NA 501944 TCGA-AB-2991 AML50 5 25063591 25063591 T C SNP - - - - - - - - - - - - - - - tier2 1554 2 0.13 968 501 34.1 0 0 NA 501944 TCGA-AB-2991 AML50 5 31363879 31363879 C T SNP CDH6 NM_004932.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*4707 NULL 0.003 - - - no_errors tier3 1220 1 0.08 613 290 32.12 0 0 NA 501944 TCGA-AB-2991 AML50 5 39746682 39746682 C T SNP LOC285634 XR_017261.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*7915 NULL 0.004 - - - pseudogene tier3 1345 2 0.15 758 506 40 0 0 NA 501944 TCGA-AB-2991 AML50 5 55772529 55772529 C T SNP - - - - - - - - - - - - - - - tier2 1505 0 0 741 420 36.14 0 0 NA 501944 TCGA-AB-2991 AML50 5 71257466 71257466 G C SNP - - - - - - - - - - - - - - - tier3 627 1 0.16 258 180 40.82 0 0 NA 501944 TCGA-AB-2991 AML50 5 72621424 72621424 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 5 74207109 74207109 A G SNP FAM169A NM_015566.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-33852 NULL 0.003 - - - no_errors tier3 767 0 0 299 104 25.81 0 0 NA 501944 TCGA-AB-2991 AML50 5 83475950 83475950 A G SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.356-7022 e5-7022 0 - - - no_errors tier3 1424 0 0 882 492 35.81 0 0 0 501944 TCGA-AB-2991 AML50 5 89024070 89024070 A G SNP - - - - - - - - - - - - - - - tier2 507 0 0 788 315 28.56 0 0 NA 501944 TCGA-AB-2991 AML50 5 91016342 91016342 C A SNP - - - - - - - - - - - - - - - tier2 1286 0 0 1249 115 8.42 0 0 NA 501944 TCGA-AB-2991 AML50 5 97236459 97236459 G C SNP - - - - - - - - - - - - - - - tier3 449 1 0.22 558 311 35.71 0 0 NA 501944 TCGA-AB-2991 AML50 5 100177308 100177308 A C SNP ST8SIA4 NM_005668.4 human genbank 54_36p -1 reviewed intronic c.798-1576 e5-1576 0.013 - - - no_errors tier3 789 1 0.13 502 366 42.17 5 4 44.44 501944 TCGA-AB-2991 AML50 5 101993409 101993409 G A SNP - - - - - - - - - - - - - - - tier3 540 1 0.18 543 253 31.78 0 0 NA 501944 TCGA-AB-2991 AML50 5 103188617 103188617 C G SNP - - - - - - - - - - - - - - - tier3 815 0 0 422 207 32.86 0 0 NA 501944 TCGA-AB-2991 AML50 5 108603667 108603667 C G SNP - - - - - - - - - - - - - - - tier3 1161 0 0 691 362 34.35 0 0 NA 501944 TCGA-AB-2991 AML50 5 113114190 113114190 A G SNP - - - - - - - - - - - - - - - tier3 459 0 0 236 155 39.64 0 0 NA 501944 TCGA-AB-2991 AML50 5 113292218 113292218 A G SNP - - - - - - - - - - - - - - - tier3 772 1 0.13 463 238 33.95 0 0 NA 501944 TCGA-AB-2991 AML50 5 114083649 114083649 T C SNP - - - - - - - - - - - - - - - tier3 332 0 0 322 132 29.07 0 0 NA 501944 TCGA-AB-2991 AML50 5 115548917 115548917 A G SNP COMMD10 NM_016144.2 human genbank 54_36p 1 provisional intronic c.510+51143 e5+51143 0.043 - - - no_errors tier3 2421 2 0.08 1353 786 36.69 3 1 25 501944 TCGA-AB-2991 AML50 5 116453238 116453238 G A SNP - - - - - - - - - - - - - - - tier3 1236 2 0.16 568 367 39.25 0 0 NA 501944 TCGA-AB-2991 AML50 5 117541796 117541796 C T SNP - - - - - - - - - - - - - - - tier3 2631 5 0.19 916 726 44.21 1 4 80 501944 TCGA-AB-2991 AML50 5 125382577 125382577 T C SNP - - - - - - - - - - - - - - - tier3 878 2 0.23 662 327 33.06 0 0 NA 501944 TCGA-AB-2991 AML50 5 132633819 132633819 G C SNP FSTL4 NM_015082.1 human genbank 54_36p -1 validated intronic c.728-20652 e6-20652 0.926 - - - no_errors tier2 1010 1 0.1 532 361 40.43 0 0 NA 501944 TCGA-AB-2991 AML50 5 151918843 151918843 A T SNP - - - - - - - - - - - - - - - tier3 870 0 0 513 310 37.67 0 0 NA 501944 TCGA-AB-2991 AML50 5 152932047 152932047 G T SNP GRIA1 NM_000827.3 human genbank 54_36p 1 reviewed intronic c.221-74634 e3-74634 0 - - - no_errors tier3 1323 5 0.38 799 440 35.51 0 0 NA 501944 TCGA-AB-2991 AML50 5 160370412 160370412 C T SNP - - - - - - - - - - - - - - - tier2 1491 12 0.8 593 381 39.08 0 0 NA 501944 TCGA-AB-2991 AML50 5 174573952 174573952 A T SNP - - - - - - - - - - - - - - - tier3 1613 3 0.19 1248 429 25.57 0 0 NA 501944 TCGA-AB-2991 AML50 5 177310899 177310899 C T SNP LOC100128340 XM_001721455.1 human genbank 54_36p 1 model missense c.103 p.P35S 0 NULL NULL - no_errors tier1 221 0 100 63 38.65 1 0 501944 TCGA-AB-2991 AML50 5 177924722 177924722 T C SNP COL23A1 NM_173465.3 human genbank 54_36p -1 validated intronic c.295-4367 e2-4367 0 - - - no_errors tier3 785 3 0.38 179 99 35.61 2 2 50 501944 TCGA-AB-2991 AML50 6 3857927 3857927 A T SNP LOC728344 XR_015265.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-30829 NULL 0 - - - pseudogene tier3 946 3 0.32 333 217 39.45 0 0 NA 501944 TCGA-AB-2991 AML50 6 10678989 10678989 C G SNP GCNT2 NM_145649.2 human genbank 54_36p 1 reviewed intronic c.925+40934 e1+40934 0.005 - - - no_errors tier3 690 0 0 350 225 39.06 0 0 NA 501944 TCGA-AB-2991 AML50 6 12500745 12500746 - A INS ENSG00000223321 ENST00000411389 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13957 NULL 0.000:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 6 25921648 25921648 C T SNP SLC17A1 NM_005074.3 human genbank 54_36p -1 validated intronic c.617-228 e6-228 0 - - - no_errors tier3 1632 3 0.18 850 493 36.71 0 0 NA 501944 TCGA-AB-2991 AML50 6 35894584 35894584 C A SNP LHFPL5 NM_182548.3 human genbank 54_36p 1 reviewed intronic c.650-608 e3-608 0.002 - - - no_errors tier3 903 1 0.11 405 265 39.43 0 0 NA 501944 TCGA-AB-2991 AML50 6 42422939 42422939 C T SNP TRERF1 NM_033502.2 human genbank 54_36p -1 reviewed intronic c.1+15774 e0+15774 0.005 - - - no_errors tier3 826 0 0 442 312 41.38 13 10 43.48 501944 TCGA-AB-2991 AML50 6 45165971 45165971 T C SNP SUPT3H NM_181356.2 human genbank 54_36p -1 provisional intronic c.219+15666 e3+15666 0.005 - - - no_errors tier3 434 1 0.23 437 253 36.67 0 0 0 501944 TCGA-AB-2991 AML50 6 46663444 46663444 C A SNP CYP39A1 NM_016593.3 human genbank 54_36p -1 reviewed intronic c.1161+286 e9+286 0.002 - - - no_errors tier3 794 1 0.13 916 294 24.3 0 0 NA 501944 TCGA-AB-2991 AML50 6 48098865 48098865 G A SNP C6orf138 NM_001013732.2 human genbank 54_36p -1 validated intronic c.376-14056 e2-14056 0 - - - no_errors tier3 676 2 0.29 730 240 24.72 0 0 NA 501944 TCGA-AB-2991 AML50 6 49036611 49036611 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 6 54772670 54772670 G A SNP FAM83B NM_001010872.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-70334 NULL 0.001 - - - no_errors tier3 421 0 0 433 300 40.93 0 0 NA 501944 TCGA-AB-2991 AML50 6 57360323 57360323 C G SNP PRIM2 ENST00000389488 human ensembl 54_36p 1 known intronic c.693+5398 e6+5398 0.001 - - - no_errors tier3 1312 0 0 1698 349 17.03 1 0 0 501944 TCGA-AB-2991 AML50 6 57487256 57487256 A G SNP PRIM2 ENST00000389488 human ensembl 54_36p 1 known intronic c.761+6942 e7+6942 0.022 - - - no_errors tier3 1132 0 0 1355 149 9.91 0 0 0 501944 TCGA-AB-2991 AML50 6 67571324 67571324 A G SNP - - - - - - - - - - - - - - - tier3 244 0 0 300 180 37.5 0 0 NA 501944 TCGA-AB-2991 AML50 6 85436874 85436874 T G SNP ENSG00000219604 ENST00000405071 human ensembl 54_36p -1 known 3_prime_flanking_region c.*18855 NULL 0.01 - - - no_coding_region:pseudogene tier3 1055 2 0.19 655 420 39.03 0 1 100 501944 TCGA-AB-2991 AML50 6 86710756 86710756 C T SNP ENSG00000202103 ENST00000365233 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*48702 NULL 0.021 - - - no_errors tier3 581 0 0 410 214 34.29 0 0 NA 501944 TCGA-AB-2991 AML50 6 92462752 92462752 T C SNP ENSG00000222902 ENST00000410970 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-43296 NULL 0.012 - - - no_errors tier3 1485 3 0.2 843 422 33.36 0 0 NA 501944 TCGA-AB-2991 AML50 6 93461429 93461429 A G SNP - - - - - - - - - - - - - - - tier3 582 0 0 354 238 40.2 0 0 NA 501944 TCGA-AB-2991 AML50 6 94719613 94719613 G T SNP - - - - - - - - - - - - - - - tier3 1042 0 0 779 240 23.53 0 0 NA 501944 TCGA-AB-2991 AML50 6 95125296 95125296 G T SNP ENSG00000220370 ENST00000404458 human ensembl 54_36p 1 known 3_prime_flanking_region c.*13895 NULL 0 - - - no_coding_region:pseudogene tier3 361 0 0 562 121 17.72 0 0 NA 501944 TCGA-AB-2991 AML50 6 95978620 95978620 C G SNP - - - - - - - - - - - - - - - tier3 974 0 0 595 350 37.04 0 0 NA 501944 TCGA-AB-2991 AML50 6 99870579 99870579 G A SNP C6orf168 NM_032511.2 human genbank 54_36p -1 validated intronic c.823+7462 e4+7462 0.015 - - - no_errors tier3 1972 2 0.1 1026 638 38.3 0 0 NA 501944 TCGA-AB-2991 AML50 6 104568050 104568050 G A SNP ENSG00000214428 ENST00000398310 human ensembl 54_36p -1 known 3_prime_flanking_region c.*12058 NULL 0 - - - no_coding_region:pseudogene tier3 1664 0 0 790 551 41.09 0 0 NA 501944 TCGA-AB-2991 AML50 6 114309132 114309132 C T SNP ENSG00000175967 ENST00000314481 human ensembl 54_36p 1 known 5_prime_flanking_region c.-23165 NULL 0 - - - no_errors tier3 930 1 0.11 464 255 35.47 0 0 NA 501944 TCGA-AB-2991 AML50 6 115217079 115217079 T G SNP - - - - - - - - - - - - - - - tier3 1088 2 0.18 635 404 38.88 0 0 NA 501944 TCGA-AB-2991 AML50 6 126897752 126897752 C T SNP - - - - - - - - - - - - - - - tier3 1092 1 0.09 450 298 39.84 0 0 NA 501944 TCGA-AB-2991 AML50 6 127428643 127428643 G C SNP - - - - - - - - - - - - - - - tier3 2282 5 0.22 1071 703 39.61 0 0 NA 501944 TCGA-AB-2991 AML50 6 133949177 133949178 AA - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 6 144828414 144828414 G A SNP UTRN NM_007124.2 human genbank 54_36p 1 reviewed intronic c.3066+2719 e22+2719 0 - - - no_errors tier2 555 1 0.18 270 156 36.62 1 0 0 501944 TCGA-AB-2991 AML50 6 149542111 149542111 G A SNP - - - - - - - - - - - - - - - tier3 1572 1 0.06 803 515 39.04 0 0 NA 501944 TCGA-AB-2991 AML50 6 154179748 154179748 G A SNP - - - - - - - - - - - - - - - tier3 1362 2 0.15 973 486 33.31 0 0 NA 501944 TCGA-AB-2991 AML50 6 160398558 160398558 G A SNP IGF2R NM_000876.2 human genbank 54_36p 1 reviewed intronic c.2797-487 e21-487 0.001 - - - no_errors tier2 1073 0 0 741 138 15.7 0 0 0 501944 TCGA-AB-2991 AML50 6 160703189 160703190 - G INS SLC22A3 NM_021977.2 human genbank 54_36p 1 reviewed intronic c.429+13319_429+13318 e1+13319 0.002:0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 6 166310512 166310512 C A SNP ENSG00000176424 ENST00000322838 human ensembl 54_36p 1 known 5_prime_flanking_region c.-11092 NULL 0 - - - no_errors tier3 1154 0 0 694 331 32.29 0 0 NA 501944 TCGA-AB-2991 AML50 7 2138025 2138025 G A SNP MAD1L1 NM_001013836.1 human genbank 54_36p -1 reviewed intronic c.1073+17288 e9+17288 0 - - - no_errors tier3 558 1 0.18 154 119 43.27 1 1 50 501944 TCGA-AB-2991 AML50 7 14860922 14860922 C T SNP DGKB ENST00000403951 human ensembl 54_36p -1 known intronic c.1-13425 e1-13425 0.001 - - - no_errors tier3 726 0 0 456 149 24.63 0 0 NA 501944 TCGA-AB-2991 AML50 7 16015642 16015642 T C SNP - - - - - - - - - - - - - - - tier3 721 0 0 527 340 39.17 0 0 NA 501944 TCGA-AB-2991 AML50 7 18715891 18715891 C T SNP HDAC9 NM_178425.1 human genbank 54_36p 1 reviewed intronic c.1732-17837 e12-17837 0.01 - - - no_errors tier3 1511 0 0 909 556 37.85 0 0 NA 501944 TCGA-AB-2991 AML50 7 20414124 20414124 A G SNP ITGB8 NM_002214.2 human genbank 54_36p 1 reviewed intronic c.2024-1639 e13-1639 0 - - - no_errors tier2 794 0 0 425 309 42.04 0 0 NA 501944 TCGA-AB-2991 AML50 7 20637021 20637021 C T SNP ABCB5 ENST00000404938 human ensembl 54_36p 1 known intronic c.260-1186 e4-1186 0.071 - - - no_errors tier3 1108 2 0.18 790 489 38.2 0 0 NA 501944 TCGA-AB-2991 AML50 7 43168805 43168805 T C SNP HECW1 NM_015052.3 human genbank 54_36p 1 validated intronic c.1+48290 e0+48290 0 - - - no_errors tier3 744 2 0.27 478 317 39.87 0 0 NA 501944 TCGA-AB-2991 AML50 7 43770892 43770892 C T SNP BLVRA NM_000712.3 human genbank 54_36p 1 validated intronic c.1+6034 e0+6034 0.039 - - - no_errors tier3 516 1 0.19 297 222 42.77 0 0 0 501944 TCGA-AB-2991 AML50 7 44991233 44991233 T G SNP C7orf40 NR_003697.1 human genbank 54_36p -1 provisional intronic c.NULL NULL 0.001 - - - no_errors tier3 417 0 0 98 46 31.94 28 17 37.78 501944 TCGA-AB-2991 AML50 7 52170006 52170006 A T SNP - - - - - - - - - - - - - - - tier2 295 0 0 284 182 39.06 0 0 NA 501944 TCGA-AB-2991 AML50 7 52208491 52208491 C T SNP - - - - - - - - - - - - - - - tier3 569 0 0 391 196 33.39 0 0 NA 501944 TCGA-AB-2991 AML50 7 52534577 52534577 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 7 57231612 57231612 C G SNP ZNF479 NM_033273.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-27639 NULL 0.379 - - - no_errors tier2 774 1 0.13 537 252 31.9 0 0 NA 501944 TCGA-AB-2991 AML50 7 77510428 77510428 G C SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.3707-23199 e22-23199 0.018 - - - no_errors tier3 1040 0 0 815 493 37.66 0 0 NA 501944 TCGA-AB-2991 AML50 7 88273169 88273169 G A SNP ZNF804B NM_181646.2 human genbank 54_36p 1 provisional intronic c.108+45835 e1+45835 0 - - - no_errors tier3 2202 2 0.09 1155 645 35.83 0 0 NA 501944 TCGA-AB-2991 AML50 7 120888768 120888768 G T SNP - - - - - - - - - - - - - - - tier2 568 1 0.18 463 302 39.48 0 0 NA 501944 TCGA-AB-2991 AML50 7 121325248 121325248 G A SNP PTPRZ1 NM_002851.2 human genbank 54_36p 1 reviewed intronic c.58+24401 e1+24401 0 - - - no_errors tier3 428 0 0 275 156 36.19 0 0 NA 501944 TCGA-AB-2991 AML50 7 123345198 123345198 T - DEL SPAM1 NM_003117.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35663 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 7 124804373 124804373 A T SNP - - - - - - - - - - - - - - - tier2 840 0 0 869 322 27.04 0 0 NA 501944 TCGA-AB-2991 AML50 7 126035431 126035431 C T SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.1494+1221 e7+1221 0 - - - no_errors tier3 790 0 0 500 363 41.97 0 0 NA 501944 TCGA-AB-2991 AML50 7 128239200 128239200 G A SNP CCDC136 NM_022742.3 human genbank 54_36p 1 validated silent c.2139 p.R713 0.972 superfamily_Spectrin repeat "superfamily_Prefoldin,superfamily_Spectrin repeat" - no_errors tier1 1272 0 409 310 43.06 1 100 501944 TCGA-AB-2991 AML50 7 147127010 147127010 C T SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2099-104580 e14-104580 0 - - - no_errors tier3 725 1 0.14 288 198 40.74 0 0 NA 501944 TCGA-AB-2991 AML50 7 154022549 154022549 C - DEL DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.628-37915 e6-37915 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 7 154237073 154237073 G A SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.1666+7318 e16+7318 0.001 - - - no_errors tier3 1200 0 0 440 254 36.6 0 0 NA 501944 TCGA-AB-2991 AML50 7 154313236 154313236 C T SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.2451+1063 e25+1063 0 - - - no_errors tier3 329 0 0 112 79 41.36 0 0 NA 501944 TCGA-AB-2991 AML50 8 2206057 2206057 C T SNP - - - - - - - - - - - - - - - tier2 1906 5 0.26 1190 250 17.35 0 0 NA 501944 TCGA-AB-2991 AML50 8 3230587 3230587 G C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.2786+1836 e19+1836 0.007 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 294 1 0.34 405 275 40.44 0 0 NA 501944 TCGA-AB-2991 AML50 8 3635854 3635854 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.819-36882 e6-36882 0.006 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 2127 1 0.05 897 634 41.38 0 0 NA 501944 TCGA-AB-2991 AML50 8 4742505 4742505 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+96757 e1+96757 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1017 2 0.2 948 454 32.38 0 0 NA 501944 TCGA-AB-2991 AML50 8 14997910 14997910 G C SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.39+141555 e1+141555 0.073 - - - no_errors tier3 1076 0 0 669 366 35.36 0 0 NA 501944 TCGA-AB-2991 AML50 8 15418773 15418773 C T SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23538 NULL 0 - - - no_errors tier3 379 0 0 525 82 13.51 0 0 NA 501944 TCGA-AB-2991 AML50 8 31571038 31571038 G A SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46005 NULL 0.867 - - - overly_large_intron tier3 1563 0 0 1012 716 41.41 0 0 NA 501944 TCGA-AB-2991 AML50 8 33985568 33985568 G A SNP ENSG00000184844 ENST00000402289 human ensembl 54_36p -1 known 5_prime_flanking_region c.-38630 NULL 0.001 - - - no_errors tier2 511 0 0 438 204 31.78 0 0 NA 501944 TCGA-AB-2991 AML50 8 51442129 51442129 C T SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1-27196 e1-27196 0.001 - - - no_errors tier3 1058 2 0.19 404 242 37.46 0 0 NA 501944 TCGA-AB-2991 AML50 8 56523932 56523932 C T SNP XKR4 NM_052898.1 human genbank 54_36p 1 provisional intronic c.1007-74462 e3-74462 0 - - - no_errors tier3 447 0 0 423 212 33.28 0 0 NA 501944 TCGA-AB-2991 AML50 8 64719431 64719431 C T SNP ENSG00000211148 ENST00000388413 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-34720 NULL 0.001 - - - pseudogene tier3 947 0 0 666 421 38.73 0 0 NA 501944 TCGA-AB-2991 AML50 8 66769223 66769223 G A SNP MTFR1 NM_014637.1 human genbank 54_36p 1 reviewed intronic c.281+675 e3+675 0.001 - - - no_errors tier3 346 0 0 357 56 13.56 3 0 0 501944 TCGA-AB-2991 AML50 8 68853169 68853169 C A SNP CPA6 NM_020361.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-32251 NULL 0.006 - - - no_errors tier3 1985 2 0.1 651 398 37.9 0 0 NA 501944 TCGA-AB-2991 AML50 8 76807478 76807478 T C SNP - - - - - - - - - - - - - - - tier3 415 0 0 383 230 37.46 0 0 NA 501944 TCGA-AB-2991 AML50 8 80770293 80770293 C T SNP STMN2 NM_007029.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*30629 NULL 0 - - - no_errors tier2 2720 6 0.22 1742 611 25.96 0 0 NA 501944 TCGA-AB-2991 AML50 8 86706888 86706888 C T SNP REXO1L1 NM_172239.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*54063 NULL 0.027 - - - no_errors tier3 918 1 0.11 534 381 41.64 0 0 NA 501944 TCGA-AB-2991 AML50 8 119032341 119032341 A T SNP EXT1 NM_000127.2 human genbank 54_36p -1 reviewed intronic c.963-113720 e2-113720 0.892 - - - no_errors tier3 908 4 0.44 583 344 37.11 0 0 NA 501944 TCGA-AB-2991 AML50 8 138300787 138300787 G A SNP - - - - - - - - - - - - - - - tier3 1470 2 0.14 1079 385 26.3 0 0 NA 501944 TCGA-AB-2991 AML50 8 140772524 140772524 G A SNP KCNK9 NM_016601.2 human genbank 54_36p -1 reviewed intronic c.283+11611 e1+11611 0 - - - no_errors tier3 870 1 0.11 175 89 33.71 0 0 NA 501944 TCGA-AB-2991 AML50 8 145953631 145953631 A G SNP ZNF251 NM_138367.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2713 NULL 0.025 - - - no_errors tier3 1984 3 0.15 475 252 34.66 0 3 100 501944 TCGA-AB-2991 AML50 9 9065402 9065402 C T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-56667 e1-56667 0 - - - no_errors tier3 712 1 0.14 601 213 26.17 0 0 NA 501944 TCGA-AB-2991 AML50 9 9833327 9833328 - A INS PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-76477_76478 e1-76476 0.965:0.948 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 9 12963085 12963085 T G SNP ENSG00000214121 ENST00000397589 human ensembl 54_36p -1 novel 5_prime_untranslated_region c.-12963085 NULL 1 - - - no_coding_region:pseudogene tier2 1346 2 0.15 522 332 38.88 36 1 2.7 501944 TCGA-AB-2991 AML50 9 13201435 13201435 G A SNP MPDZ NM_003829.3 human genbank 54_36p -1 validated intronic c.1291-5337 e10-5337 0 - - - no_errors tier3 780 1 0.13 696 316 31.19 0 0 NA 501944 TCGA-AB-2991 AML50 9 17860164 17860164 C A SNP - - - - - - - - - - - - - - - tier3 1209 0 0 879 278 24.03 0 0 NA 501944 TCGA-AB-2991 AML50 9 23825282 23825282 T A SNP ELAVL2 NM_004432.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-73050 NULL 0.465 - - - no_errors tier3 287 1 0.35 299 117 28.12 0 0 NA 501944 TCGA-AB-2991 AML50 9 71224606 71224606 G C SNP APBA1 NM_001163.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*11457 NULL 0.001 - - - no_errors tier3 1089 0 0 664 417 38.58 0 0 NA 501944 TCGA-AB-2991 AML50 9 71250271 71250271 A G SNP APBA1 NM_001163.3 human genbank 54_36p -1 reviewed intronic c.2181+4049 e9+4049 0.945 - - - no_errors tier2 1827 1 0.05 693 496 41.72 0 0 0 501944 TCGA-AB-2991 AML50 9 72183268 72183268 G A SNP KLF9 NM_001206.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*9244 NULL 0.001 - - - no_errors tier2 2321 2 0.09 1755 1049 37.4 0 0 NA 501944 TCGA-AB-2991 AML50 9 72708421 72708421 T G SNP TRPM3 NM_001007471.1 human genbank 54_36p -1 reviewed intronic c.178-39174 e2-39174 0.003 - - - no_errors tier3 438 1 0.23 580 339 36.89 0 0 NA 501944 TCGA-AB-2991 AML50 9 75421043 75421043 G A SNP ENSG00000219821 ENST00000402152 human ensembl 54_36p 1 known 5_prime_flanking_region c.-32521 NULL 0 - - - no_coding_region:pseudogene tier3 2352 1 0.04 1225 829 40.36 0 0 NA 501944 TCGA-AB-2991 AML50 9 82639071 82639071 G A SNP - - - - - - - - - - - - - - - tier3 878 2 0.23 689 362 34.41 0 0 NA 501944 TCGA-AB-2991 AML50 9 89013465 89013465 C A SNP LOC100132348 XM_001723287.1 human genbank 54_36p -1 model intronic c.1-10609 e1-10609 0.726 - - - no_errors tier3 972 1 0.1 833 456 35.38 0 0 NA 501944 TCGA-AB-2991 AML50 9 120953825 120953825 C T SNP DBC1 NM_014618.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*15358 NULL 0 - - - no_errors tier3 1934 3 0.15 763 480 38.62 0 0 NA 501944 TCGA-AB-2991 AML50 9 125183266 125183266 C T SNP DENND1A NM_020946.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*266 NULL 0.439 - - - no_errors tier2 179 0 0 127 35 21.6 27 11 28.95 501944 TCGA-AB-2991 AML50 9 137671130 137671130 C T SNP GLT6D1 NM_182974.2 human genbank 54_36p -1 provisional 5_prime_untranslated_region c.-276 NULL 0 - - - no_errors tier3 1459 2 0.14 452 223 32.99 0 0 NA 501944 TCGA-AB-2991 AML50 9 139831845 139831845 C T SNP EHMT1 NM_024757.1 human genbank 54_36p 1 reviewed intronic c.3368+47 e22+47 0.001 - - - no_errors tier3 377 0 0 207 100 32.57 3 3 50 501944 TCGA-AB-2991 AML50 10 4133120 4133120 C T SNP - - - - - - - - - - - - - - - tier3 596 2 0.33 505 320 38.79 0 0 NA 501944 TCGA-AB-2991 AML50 10 13504167 13504167 A C SNP BEND7 NM_152751.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*17011 NULL 0.089 - - - no_errors tier3 1615 3 0.19 670 437 39.48 0 0 NA 501944 TCGA-AB-2991 AML50 10 19187147 19187147 G A SNP - - - - - - - - - - - - - - - tier2 461 0 0 261 134 33.92 0 0 NA 501944 TCGA-AB-2991 AML50 10 21130767 21130767 G T SNP NEBL NM_006393.2 human genbank 54_36p -1 validated intronic c.2761+6678 e26+6678 0 - - - no_errors tier3 1615 0 0 888 375 29.69 0 0 NA 501944 TCGA-AB-2991 AML50 10 31590361 31590361 C T SNP ENSG00000209675 ENST00000386940 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*1738 NULL 0.196 - - - pseudogene tier3 904 1 0.11 572 326 36.26 0 0 NA 501944 TCGA-AB-2991 AML50 10 36641234 36641234 G T SNP - - - - - - - - - - - - - - - tier3 626 1 0.16 559 370 39.83 0 0 NA 501944 TCGA-AB-2991 AML50 10 42216108 42216108 T - DEL uc001izw.1 ENST00000355576 human ensembl 54_36p -1 known 5_prime_flanking_region c.-32609 NULL 0 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 10 45018622 45018622 C T SNP ENSG00000207071 ENST00000384343 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14272 NULL 0 - - - no_errors tier3 325 0 0 160 114 41.61 0 0 NA 501944 TCGA-AB-2991 AML50 10 49976081 49976081 G T SNP C10orf72 NM_001031746.3 human genbank 54_36p -1 validated intronic c.457+9564 e2+9564 0 - - - no_errors tier3 1516 0 0 532 159 23.01 0 0 NA 501944 TCGA-AB-2991 AML50 10 51492420 51492420 T - DEL ENSG00000219365 ENST00000407799 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-51492420 NULL 0.985 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 10 57763201 57763201 G A SNP ZWINT NM_007057.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*24984 NULL 0.018 - - - no_errors tier3 358 2 0.56 374 190 33.69 0 0 NA 501944 TCGA-AB-2991 AML50 10 60942389 60942389 C A SNP ENSG00000219119 ENST00000402893 human ensembl 54_36p -1 known 3_prime_flanking_region c.*38779 NULL 0.007 - - - no_coding_region:pseudogene tier3 1272 1 0.08 1035 297 22.3 0 0 NA 501944 TCGA-AB-2991 AML50 10 67835139 67835139 G A SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1532-26023 e11-26023 0 - - - no_errors tier3 349 0 0 463 163 26 0 0 NA 501944 TCGA-AB-2991 AML50 10 78913798 78913798 G A SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.379-80011 e2-80011 0.006 - - - no_errors tier3 857 1 0.12 369 199 35.04 0 0 NA 501944 TCGA-AB-2991 AML50 10 79614925 79614925 G A SNP - - - - - - - - - - - - - - - tier2 881 3 0.34 326 246 43.01 0 0 NA 501944 TCGA-AB-2991 AML50 10 82658511 82658511 G A SNP ENSG00000220859 ENST00000403693 human ensembl 54_36p -1 known 3_prime_flanking_region c.*31890 NULL 0 - - - no_coding_region:pseudogene tier3 994 1 0.1 509 257 33.51 0 0 NA 501944 TCGA-AB-2991 AML50 10 82798067 82798067 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 10 90997157 90997157 A C SNP LIPA NM_000235.2 human genbank 54_36p -1 reviewed intronic c.111+118 e1+118 0.012 - - - no_errors tier3 855 0 0 361 207 36.44 0 0 0 501944 TCGA-AB-2991 AML50 10 97843053 97843053 T C SNP LOC728558 XM_001130313.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-3139 NULL 0 - - - no_errors tier3 1783 2 0.11 679 417 37.94 0 0 NA 501944 TCGA-AB-2991 AML50 10 106624451 106624451 G C SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.695+31844 e2+31844 0.001 - - - no_errors tier2 1792 1 0.06 1119 803 41.76 0 0 NA 501944 TCGA-AB-2991 AML50 10 114839358 114839358 T C SNP TCF7L2 NM_030756.3 human genbank 54_36p 1 validated intronic c.483+49483 e4+49483 0.001 - - - no_errors tier3 1006 0 0 352 257 42.06 3 1 25 501944 TCGA-AB-2991 AML50 10 119173547 119173547 C T SNP PDZD8 NM_173791.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-48819 NULL 0 - - - no_errors tier3 910 2 0.22 484 342 41.4 0 0 NA 501944 TCGA-AB-2991 AML50 10 119367584 119367584 C T SNP - - - - - - - - - - - - - - - tier3 1663 1 0.06 884 512 36.65 0 0 NA 501944 TCGA-AB-2991 AML50 10 125346892 125346892 C T SNP - - - - - - - - - - - - - - - tier3 342 0 0 241 173 41.79 0 0 NA 501944 TCGA-AB-2991 AML50 10 130870623 130870623 A G SNP - - - - - - - - - - - - - - - tier3 770 0 0 494 322 39.46 0 0 NA 501944 TCGA-AB-2991 AML50 11 2559514 2559514 C T SNP - - - - - - - - - - - - - - - tier3 164 0 0 91 57 38.51 0 0 0 501944 TCGA-AB-2991 AML50 11 18085115 18085115 C T SNP - - - - - - - - - - - - - - - tier3 527 0 0 339 187 35.55 0 0 NA 501944 TCGA-AB-2991 AML50 11 20611566 20611566 G A SNP - - - - - - - - - - - - - - - tier3 1229 2 0.16 498 335 40.17 0 0 NA 501944 TCGA-AB-2991 AML50 11 41073817 41073817 T A SNP - - - - - - - - - - - - - - - tier3 485 0 0 412 237 36.46 0 0 NA 501944 TCGA-AB-2991 AML50 11 79993242 79993242 G A SNP - - - - - - - - - - - - - - - tier3 1911 2 0.1 1653 290 14.93 0 0 NA 501944 TCGA-AB-2991 AML50 11 89957588 89957588 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 11 91833149 91833149 C T SNP - - - - - - - - - - - - - - - tier2 1138 2 0.18 671 447 39.95 0 0 NA 501944 TCGA-AB-2991 AML50 11 92187300 92187300 G A SNP - - - - - - - - - - - - - - - tier3 577 1 0.17 545 186 25.44 0 0 NA 501944 TCGA-AB-2991 AML50 11 99839282 99839282 C T SNP - - - - - - - - - - - - - - - tier2 682 2 0.29 606 493 44.82 0 0 NA 501944 TCGA-AB-2991 AML50 11 99952114 99952114 C G SNP - - - - - - - - - - - - - - - tier2 833 0 0 765 252 24.78 0 0 NA 501944 TCGA-AB-2991 AML50 11 101047854 101047854 G T SNP - - - - - - - - - - - - - - - tier3 1813 0 0 1165 684 36.93 0 0 NA 501944 TCGA-AB-2991 AML50 11 110884032 110884032 G A SNP BTG4 NM_017589.2 human genbank 54_36p -1 reviewed intronic c.1+4084 e0+4084 0.001 - - - no_errors tier2 1003 1 0.1 460 286 38.34 0 0 NA 501944 TCGA-AB-2991 AML50 11 121519750 121519750 G A SNP BLID NM_001001786.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27910 NULL 0.002 - - - no_errors tier2 1113 1 0.09 722 534 42.48 0 0 0 501944 TCGA-AB-2991 AML50 11 128109615 128109615 T G SNP FLI1 NM_002017.3 human genbank 54_36p 1 validated intronic c.19-23605 e2-23605 0 - - - no_errors tier3 1247 1 0.08 544 274 33.5 7 4 36.36 501944 TCGA-AB-2991 AML50 11 130025462 130025462 C T SNP C11orf44 XR_039978.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-22601 NULL 0.001 - - - no_errors tier3 611 2 0.33 293 153 34.23 0 0 NA 501944 TCGA-AB-2991 AML50 11 134119307 134119307 C T SNP LOC729305 XM_001133309.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*8193 NULL 0.005 - - - no_errors tier2 1167 0 0 461 248 34.98 0 0 NA 501944 TCGA-AB-2991 AML50 12 13640454 13640454 C A SNP GRIN2B NM_000834.3 human genbank 54_36p -1 reviewed intronic c.2010+12350 e8+12350 0.844 - - - no_errors tier3 2622 3 0.11 1106 752 40.47 0 0 NA 501944 TCGA-AB-2991 AML50 12 14981969 14981969 T A SNP ERP27 NM_152321.2 human genbank 54_36p -1 validated intronic c.195+184 e2+184 0.006 - - - no_errors tier3 1158 0 0 717 243 25.31 6 0 0 501944 TCGA-AB-2991 AML50 12 25023484 25023484 T C SNP BCAT1 NM_005504.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-30351 NULL 0 - - - no_errors tier3 1255 3 0.24 718 415 36.5 0 0 NA 501944 TCGA-AB-2991 AML50 12 27716550 27716550 A G SNP PPFIBP1 NM_003622.2 human genbank 54_36p 1 reviewed intronic c.1263-77 e13-77 0 - - - no_errors tier2 532 2 0.37 539 291 35.02 0 0 0 501944 TCGA-AB-2991 AML50 12 30977199 30977199 A G SNP TSPAN11 NM_001080509.2 human genbank 54_36p 1 validated intronic c.1+5993 e0+5993 0.004 - - - no_errors tier3 843 3 0.35 262 196 42.79 0 0 NA 501944 TCGA-AB-2991 AML50 12 44540986 44540986 C T SNP ARID2 NM_152641.2 human genbank 54_36p 1 validated nonsense c.4909 p.Q1637* 1 PatternScan_ZINC_FINGER_C2H2_1 "HMMPfam_ARID,HMMSmart_SM00501,superfamily_ARID-like,PatternScan_ZINC_FINGER_C2H2_1,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 767 1 0.13 623 220 26.04 16 3 15.79 501944 TCGA-AB-2991 AML50 12 56762845 56762845 G A SNP - - - - - - - - - - - - - - - tier2 701 4 0.57 554 319 36.54 0 0 NA 501944 TCGA-AB-2991 AML50 12 57299921 57299921 T G SNP - - - - - - - - - - - - - - - tier2 2266 1 0.04 881 744 45.73 0 0 NA 501944 TCGA-AB-2991 AML50 12 77108690 77108690 C T SNP NAV3 NM_014903.4 human genbank 54_36p 1 validated intronic c.6225+560 e33+560 0.001 - - - no_errors tier3 1535 2 0.13 943 653 40.84 0 0 0 501944 TCGA-AB-2991 AML50 12 78091239 78091239 A C SNP SYT1 ENST00000261205 human ensembl 54_36p 1 known intronic c.1-44175 e1-44175 0 - - - no_errors tier3 1622 2 0.12 1110 400 26.47 0 0 NA 501944 TCGA-AB-2991 AML50 12 78091240 78091240 G T SNP SYT1 ENST00000261205 human ensembl 54_36p 1 known intronic c.1-44174 e1-44174 0 - - - no_errors tier3 1613 2 0.12 1106 401 26.61 0 0 NA 501944 TCGA-AB-2991 AML50 12 87671693 87671693 G A SNP - - - - - - - - - - - - - - - tier2 1853 6 0.32 1101 543 33.03 0 0 NA 501944 TCGA-AB-2991 AML50 12 97398781 97398781 G A SNP LOC121456 XR_016411.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - no_errors tier3 768 0 0 408 214 34.41 0 1 100 501944 TCGA-AB-2991 AML50 12 108851429 108851429 T G SNP GLTP NM_016433.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-48867 NULL 0 - - - no_errors tier3 519 0 0 302 183 37.73 1 2 66.67 501944 TCGA-AB-2991 AML50 12 113025068 113025068 A G SNP - - - - - - - - - - - - - - - tier3 790 1 0.13 329 200 37.81 0 0 NA 501944 TCGA-AB-2991 AML50 12 114038277 114038277 C T SNP - - - - - - - - - - - - - - - tier3 2059 0 0 726 505 41.02 0 0 NA 501944 TCGA-AB-2991 AML50 12 118260236 118260236 G A SNP CCDC60 NM_178499.3 human genbank 54_36p 1 validated intronic c.90+2782 e1+2782 0.004 - - - no_errors tier3 1762 3 0.17 698 448 39.06 0 0 NA 501944 TCGA-AB-2991 AML50 12 118403217 118403217 C T SNP LOC100132232 XM_001716552.1 human genbank 54_36p -1 model missense c.88 p.D30N 0.075 NULL NULL - no_errors tier1 1226 3 0.24 350 219 38.49 NA 501944 TCGA-AB-2991 AML50 12 118475159 118475159 T A SNP ENSG00000222647 ENST00000410715 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-27821 NULL 0 - - - no_errors tier3 2006 6 0.3 1025 631 38.08 0 0 NA 501944 TCGA-AB-2991 AML50 12 123485475 123485475 C T SNP NCOR2 NM_006312.1 human genbank 54_36p -1 validated intronic c.882+2954 e8+2954 0.001 - - - no_errors tier3 382 1 0.26 93 65 41.14 4 2 33.33 501944 TCGA-AB-2991 AML50 12 128381890 128381890 T C SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1299+6242 e4+6242 0.001 - - - no_errors tier3 1105 4 0.36 477 358 42.87 0 0 NA 501944 TCGA-AB-2991 AML50 12 129179058 129179058 C G SNP FZD10 NM_007197.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34383 NULL 0.001 - - - no_errors tier3 464 0 0 121 98 44.75 0 0 NA 501944 TCGA-AB-2991 AML50 13 18776975 18776975 T C SNP ENSG00000215349 ENST00000400109 human ensembl 54_36p -1 novel 5_prime_untranslated_region c.-18776975 NULL 0.865 - - - no_coding_region:pseudogene tier3 694 0 0 512 179 25.9 28 0 0 501944 TCGA-AB-2991 AML50 13 26093262 26093262 A G SNP WASF3 NM_006646.5 human genbank 54_36p 1 reviewed intronic c.1+8067 e0+8067 0.001 - - - no_errors tier3 909 4 0.44 628 421 40.1 0 0 NA 501944 TCGA-AB-2991 AML50 13 29597135 29597135 G A SNP - - - - - - - - - - - - - - - tier3 1108 2 0.18 337 223 39.82 0 0 NA 501944 TCGA-AB-2991 AML50 13 30354941 30354941 C T SNP LOC440132 XM_001129572.2 human genbank 54_36p 1 model intronic c.313+145 e3+145 0.637 - - - no_errors tier3 1116 3 0.27 587 250 29.87 0 0 NA 501944 TCGA-AB-2991 AML50 13 30959146 30959146 C T SNP - - - - - - - - - - - - - - - tier3 1091 2 0.18 740 467 38.56 0 0 NA 501944 TCGA-AB-2991 AML50 13 48700060 48700060 G A SNP CDADC1 NM_030911.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-20115 NULL 0.001 - - - no_errors tier2 790 1 0.13 261 167 39.02 0 0 NA 501944 TCGA-AB-2991 AML50 13 54318980 54318980 G T SNP - - - - - - - - - - - - - - - tier3 157 0 0 171 110 39.15 0 0 NA 501944 TCGA-AB-2991 AML50 13 60500527 60500527 C G SNP - - - - - - - - - - - - - - - tier3 3386 0 0 1692 787 31.73 0 0 NA 501944 TCGA-AB-2991 AML50 13 64092265 64092265 C T SNP - - - - - - - - - - - - - - - tier3 761 0 0 496 473 48.81 0 0 NA 501944 TCGA-AB-2991 AML50 13 68199621 68199621 G A SNP ENSG00000209895 ENST00000387160 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33409 NULL 0 - - - pseudogene tier3 936 2 0.21 585 380 39.38 0 0 NA 501944 TCGA-AB-2991 AML50 13 76628271 76628271 G A SNP MYCBP2 NM_015057.3 human genbank 54_36p -1 validated missense c.6724 p.R2242C 1 superfamily_E set domains "HMMPfam_RCC1,PatternScan_RCC1_2,HMMSmart_SM00184,superfamily_Galactose-binding domain-like,superfamily_RCC1/BLIP-II,HMMPfam_PHR,superfamily_E set domains,superfamily_RING/U-box" - no_errors tier1 1751 6 0.34 951 306 24.31 27 13 32.5 501944 TCGA-AB-2991 AML50 13 86997982 86997982 C T SNP - - - - - - - - - - - - - - - tier3 585 0 0 422 183 30.25 0 0 NA 501944 TCGA-AB-2991 AML50 13 91551947 91551947 T A SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1402-43137 e7-43137 0.577 - - - no_errors tier2 773 2 0.26 470 259 35.53 1 0 0 501944 TCGA-AB-2991 AML50 13 91709377 91709377 C T SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1561+114134 e7+114134 0 - - - no_errors tier3 1175 0 0 1013 608 37.48 0 0 NA 501944 TCGA-AB-2991 AML50 13 92678994 92678994 T A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.160+1124 e1+1124 0.976 - - - no_errors tier3 841 5 0.59 291 163 35.9 0 0 0 501944 TCGA-AB-2991 AML50 13 95904312 95904312 C T SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+362488 e1+362488 0 - - - no_errors tier3 259 2 0.77 255 110 30.14 0 0 NA 501944 TCGA-AB-2991 AML50 13 95904906 95904906 T A SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+363082 e1+363082 0.001 - - - no_errors tier3 484 0 0 497 156 23.85 0 0 NA 501944 TCGA-AB-2991 AML50 13 97712922 97712922 A C SNP FARP1 NM_005766.2 human genbank 54_36p 1 reviewed intronic c.171+49254 e1+49254 0.004 - - - no_errors tier3 1059 0 0 579 388 40.12 0 0 NA 501944 TCGA-AB-2991 AML50 13 100816252 100816253 - A INS NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.644+10799_644+10798 e5+10799 0.005:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 13 102725575 102725575 C T SNP LOC728183 XM_001128627.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*1813 NULL 0 - - - no_errors tier3 979 0 0 514 364 41.41 0 0 NA 501944 TCGA-AB-2991 AML50 13 103961388 103961388 A T SNP - - - - - - - - - - - - - - - tier3 1680 2 0.12 1212 413 25.38 0 0 NA 501944 TCGA-AB-2991 AML50 13 104148308 104148308 G A SNP - - - - - - - - - - - - - - - tier3 1492 3 0.2 1054 341 24.44 0 0 NA 501944 TCGA-AB-2991 AML50 13 109684278 109684278 G A SNP COL4A1 NM_001845.4 human genbank 54_36p -1 reviewed intronic c.144+8745 e2+8745 0.006 - - - no_errors tier3 800 0 0 397 150 27.42 0 0 0 501944 TCGA-AB-2991 AML50 14 26000504 26000504 A G SNP NOVA1 NM_002515.2 human genbank 54_36p -1 reviewed intronic c.519+10862 e4+10862 0.063 - - - no_errors tier3 848 2 0.24 507 303 37.41 0 0 NA 501944 TCGA-AB-2991 AML50 14 27556447 27556447 A T SNP ENSG00000223164 ENST00000411232 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*27286 NULL 0.004 - - - no_errors tier3 1124 2 0.18 515 384 42.71 0 0 NA 501944 TCGA-AB-2991 AML50 14 32746845 32746845 C T SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.51-7294 e2-7294 1 - - - no_errors tier2 851 2 0.23 240 208 46.43 0 0 NA 501944 TCGA-AB-2991 AML50 14 36162404 36162404 C G SNP PAX9 NM_006194.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38642 NULL 0 - - - no_errors tier2 1383 2 0.14 532 351 39.75 0 0 NA 501944 TCGA-AB-2991 AML50 14 47051713 47051713 G A SNP MDGA2 ENST00000399232 human ensembl 54_36p -1 known intronic c.73+161757 e1+161757 0.012 - - - no_errors tier3 1684 5 0.3 1169 408 25.87 0 0 NA 501944 TCGA-AB-2991 AML50 14 53624180 53624180 C T SNP - - - - - - - - - - - - - - - tier3 619 0 0 375 225 37.5 0 0 NA 501944 TCGA-AB-2991 AML50 14 54624212 54624212 G A SNP LGALS3 NM_002306.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49633 NULL 0.003 - - - no_errors tier3 641 0 0 315 211 40.11 0 0 NA 501944 TCGA-AB-2991 AML50 14 56220098 56220098 G A SNP C14orf101 NM_017799.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*36130 NULL 0.994 - - - no_errors tier2 1159 1 0.09 635 327 33.99 1 0 0 501944 TCGA-AB-2991 AML50 14 61867397 61867397 C T SNP - - - - - - - - - - - - - - - tier3 1228 1 0.08 1038 568 35.3 0 0 NA 501944 TCGA-AB-2991 AML50 14 63598643 63598643 T C SNP SYNE2 NM_182914.4 human genbank 54_36p 1 validated intronic c.10068-579 e49-579 0.037 - - - no_errors tier3 70 0 0 144 80 35.71 1 0 0 501944 TCGA-AB-2991 AML50 14 64614500 64614500 C T SNP MAX NM_002382.3 human genbank 54_36p -1 reviewed missense c.179 p.R60Q 1 "HMMPfam_HLH,HMMSmart_SM00353,superfamily_HLH helix-loop-helix DNA-binding domain" "HMMPfam_HLH,HMMSmart_SM00353,superfamily_HLH helix-loop-helix DNA-binding domain" - no_errors tier1 536 2 0.37 252 32 11.27 339 79 18.76 501944 TCGA-AB-2991 AML50 14 83353278 83353278 A T SNP - - - - - - - - - - - - - - - tier3 785 0 0 524 382 42.16 0 0 NA 501944 TCGA-AB-2991 AML50 14 88410827 88410827 T C SNP TTC8 NM_144596.2 human genbank 54_36p 1 reviewed intronic c.1348-296 e14-296 0.001 - - - no_errors tier3 769 0 0 994 296 22.95 0 0 0 501944 TCGA-AB-2991 AML50 14 100403156 100403156 G A SNP SNORD112 NR_003080.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-30854 NULL 0.003 - - - no_errors tier3 528 0 0 217 134 38.18 0 5 100 501944 TCGA-AB-2991 AML50 15 19428279 19428279 T A SNP LOC727899 XM_001125912.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-23609 NULL 0.993 - - - no_errors tier2 363 0 0 231 127 35.47 0 0 NA 501944 TCGA-AB-2991 AML50 15 21238802 21238802 C T SNP FLJ36144 XR_040633.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.017 - - - no_errors tier2 239 0 0 167 58 25.78 0 0 NA 501944 TCGA-AB-2991 AML50 15 23780926 23780926 G T SNP LOC100128714 XM_001723960.1 human genbank 54_36p 1 model intronic c.184-30648 e2-30648 0 - - - no_errors tier3 1601 0 0 697 474 40.48 0 0 NA 501944 TCGA-AB-2991 AML50 15 25050773 25050773 C T SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.271-103929 e4-103929 0.001 - - - no_errors tier3 797 0 0 460 150 24.59 0 0 NA 501944 TCGA-AB-2991 AML50 15 29079069 29079069 T C SNP MTMR10 NM_017762.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-8068 NULL 0 - - - no_errors tier2 904 0 0 639 355 35.68 0 0 NA 501944 TCGA-AB-2991 AML50 15 30195351 30195351 C T SNP CHRNA7 NM_000746.3 human genbank 54_36p 1 reviewed intronic c.350+3959 e4+3959 0 - - - no_errors tier3 595 1 0.17 289 164 36.2 0 0 NA 501944 TCGA-AB-2991 AML50 15 31371072 31371072 T A SNP LOC440268 XR_041884.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.131 - - - no_errors tier3 315 1 0.32 225 89 28.25 0 0 NA 501944 TCGA-AB-2991 AML50 15 35119676 35119676 G T SNP MEIS2 NM_170675.2 human genbank 54_36p -1 reviewed intronic c.755-3224 e8-3224 0 - - - no_errors tier3 1340 4 0.3 743 467 38.6 0 0 NA 501944 TCGA-AB-2991 AML50 15 35411671 35411671 C G SNP - - - - - - - - - - - - - - - tier3 1180 4 0.34 964 375 27.99 0 0 NA 501944 TCGA-AB-2991 AML50 15 39068990 39068990 C A SNP INO80 NM_017553.1 human genbank 54_36p -1 validated intronic c.3571-1526 e29-1526 0.001 - - - no_errors tier3 1409 2 0.14 487 307 38.66 1 8 88.89 501944 TCGA-AB-2991 AML50 15 43416761 43416761 C T SNP LOC645263 XM_928304.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-15885 NULL 0.941 - - - no_errors tier3 713 1 0.14 238 195 45.03 0 0 NA 501944 TCGA-AB-2991 AML50 15 47124173 47124173 A C SNP SECISBP2L NM_014701.2 human genbank 54_36p -1 provisional intronic c.24+1592 e1+1592 0.141 - - - no_errors tier3 231 0 0 154 77 33.33 2 0 0 501944 TCGA-AB-2991 AML50 15 49143353 49143353 C T SNP TNFAIP8L3 NM_207381.2 human genbank 54_36p -1 provisional intronic c.317-5421 e3-5421 0.003 - - - no_errors tier3 796 1 0.13 517 311 37.47 1 0 0 501944 TCGA-AB-2991 AML50 15 51474025 51474025 A G SNP - - - - - - - - - - - - - - - tier3 1961 4 0.2 956 529 35.62 0 0 NA 501944 TCGA-AB-2991 AML50 15 52645839 52645839 T G SNP UNC13C NM_001080534.1 human genbank 54_36p 1 provisional intronic c.5959-1451 e29-1451 0.002 - - - no_errors tier3 569 0 0 726 278 27.69 0 0 NA 501944 TCGA-AB-2991 AML50 15 54566143 54566143 C A SNP MNS1 NM_018365.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-21681 NULL 0.001 - - - no_errors tier3 577 1 0.17 370 164 30.71 0 0 NA 501944 TCGA-AB-2991 AML50 15 63121313 63121313 C T SNP MTFMT NM_139242.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14928 NULL 0.002 - - - no_errors tier3 405 0 0 161 76 32.07 7 1 12.5 501944 TCGA-AB-2991 AML50 15 69244831 69244831 G A SNP THSD4 NM_024817.2 human genbank 54_36p 1 provisional intronic c.99+10506 e2+10506 0.023 - - - no_errors tier3 977 0 0 457 249 35.27 64 0 0 501944 TCGA-AB-2991 AML50 15 91646273 91646273 C T SNP ENSG00000212063 ENST00000390774 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15717 NULL 0 - - - no_errors tier3 667 0 0 450 230 33.82 0 0 NA 501944 TCGA-AB-2991 AML50 16 7042795 7042795 T C SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.27+695 e1+695 0 - - - no_errors tier3 717 2 0.28 505 260 33.94 0 0 NA 501944 TCGA-AB-2991 AML50 16 7829547 7829547 C T SNP - - - - - - - - - - - - - - - tier3 1297 1 0.08 620 413 39.98 0 0 NA 501944 TCGA-AB-2991 AML50 16 19889635 19889635 C T SNP - - - - - - - - - - - - - - - tier3 758 0 0 448 344 43.43 0 0 NA 501944 TCGA-AB-2991 AML50 16 22617600 22617600 G C SNP - - - - - - - - - - - - - - - tier2 1188 0 0 924 151 14.05 0 0 NA 501944 TCGA-AB-2991 AML50 16 23077121 23077121 T C SNP USP31 NM_020718.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9029 NULL 0.219 - - - no_errors tier3 1727 1 0.06 445 149 25.04 0 0 NA 501944 TCGA-AB-2991 AML50 16 27760488 27760488 A G SNP GSG1L NM_001109763.1 human genbank 54_36p -1 validated intronic c.662+3284 e4+3284 0.001 - - - no_errors tier3 972 1 0.1 334 270 44.7 0 0 0 501944 TCGA-AB-2991 AML50 16 28196201 28196201 C T SNP SBK1 NM_001024401.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-40013 NULL 0.343 - - - no_errors tier3 578 0 0 110 63 36.21 0 0 NA 501944 TCGA-AB-2991 AML50 16 34129722 34129723 - T INS CCNYL3 XM_925865.1 human genbank 54_36p 1 model intronic c.691-2314_691-2313 e5-2313 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 16 47436962 47436962 G A SNP - - - - - - - - - - - - - - - tier2 1170 0 0 522 321 38.08 0 0 NA 501944 TCGA-AB-2991 AML50 16 52589216 52589216 G A SNP FTO NM_001080432.1 human genbank 54_36p 1 provisional intronic c.1364+63694 e8+63694 0.01 - - - no_errors tier3 532 0 0 368 216 36.99 1 0 0 501944 TCGA-AB-2991 AML50 16 58093137 58093137 C T SNP ENSG00000200062 ENST00000363192 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38394 NULL 0 - - - no_errors tier3 1215 3 0.25 714 339 32.19 0 0 NA 501944 TCGA-AB-2991 AML50 16 62373628 62373628 A T SNP - - - - - - - - - - - - - - - tier3 656 0 0 522 179 25.53 0 0 NA 501944 TCGA-AB-2991 AML50 16 63925634 63925634 C A SNP LOC283867 NM_001101346.1 human genbank 54_36p -1 inferred intronic c.126+20013 e3+20013 0 - - - no_errors tier3 1073 2 0.19 508 324 38.94 0 0 NA 501944 TCGA-AB-2991 AML50 16 72334460 72334460 G C SNP - - - - - - - - - - - - - - - tier2 692 0 0 563 321 36.27 0 0 NA 501944 TCGA-AB-2991 AML50 16 72567122 72567122 G T SNP LOC441506 XR_017565.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-33941 NULL 0.002 - - - pseudogene tier2 1022 0 0 591 362 37.95 0 0 NA 501944 TCGA-AB-2991 AML50 17 11928419 11928419 C T SNP MAP2K4 NM_003010.2 human genbank 54_36p 1 reviewed intronic c.393+2847 e3+2847 0.002 - - - no_errors tier3 860 0 0 925 343 27.03 1 0 0 501944 TCGA-AB-2991 AML50 17 12057403 12057403 T C SNP - - - - - - - - - - - - - - - tier2 1430 1 0.07 399 218 35.22 0 0 NA 501944 TCGA-AB-2991 AML50 17 13919344 13919344 G A SNP COX10 NM_001303.3 human genbank 54_36p 1 reviewed intronic c.177+846 e2+846 0.007 - - - no_errors tier3 703 0 0 469 295 38.61 0 0 0 501944 TCGA-AB-2991 AML50 17 14469117 14469117 A T SNP - - - - - - - - - - - - - - - tier3 1401 0 0 856 459 34.9 0 0 NA 501944 TCGA-AB-2991 AML50 17 14505337 14505337 C G SNP LOC388339 XM_371019.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*43781 NULL 0.296 - - - pseudogene tier3 2227 0 0 1620 328 16.83 0 0 NA 501944 TCGA-AB-2991 AML50 17 14801770 14801770 G A SNP LOC441781 XR_017517.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-9530 NULL 0.03 - - - pseudogene tier3 1306 3 0.23 696 489 41.27 0 0 NA 501944 TCGA-AB-2991 AML50 17 29196486 29196486 G A SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.555+310624 e1+310624 0 - - - overly_large_intron tier3 1264 1 0.08 534 259 32.62 0 0 NA 501944 TCGA-AB-2991 AML50 17 44157110 44157110 T C SNP LOC100132903 XM_001726558.1 human genbank 54_36p 1 model 3_prime_untranslated_region c.*66 NULL 0.061 - - - no_errors tier2 681 2 0.29 231 167 41.96 0 0 NA 501944 TCGA-AB-2991 AML50 17 70273822 70273822 C G SNP SLC9A3R1 NM_004252.3 human genbank 54_36p 1 validated intronic c.758-848 e4-848 0.006 - - - no_errors tier3 713 1 0.14 234 157 40.15 7 13 59.09 501944 TCGA-AB-2991 AML50 18 6016943 6016943 G T SNP L3MBTL4 NM_173464.3 human genbank 54_36p -1 validated intronic c.1471+19784 e15+19784 0.001 - - - no_errors tier3 1120 4 0.36 1417 648 31.38 0 0 NA 501944 TCGA-AB-2991 AML50 18 6028024 6028024 C T SNP L3MBTL4 NM_173464.3 human genbank 54_36p -1 validated intronic c.1471+8703 e15+8703 0.001 - - - no_errors tier3 2059 4 0.19 1376 885 39.11 0 0 NA 501944 TCGA-AB-2991 AML50 18 38907016 38907016 C T SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional intronic c.104-39186 e2-39186 0 - - - no_errors tier3 862 0 0 584 370 38.78 0 0 NA 501944 TCGA-AB-2991 AML50 18 42129017 42129017 A G SNP RNF165 NM_152470.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-39219 NULL 0.001 - - - no_errors tier3 923 2 0.22 478 305 38.95 0 1 100 501944 TCGA-AB-2991 AML50 18 48980366 48980366 G T SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.1574-5218 e10-5218 0 - - - no_errors tier3 712 3 0.42 437 225 33.94 0 0 NA 501944 TCGA-AB-2991 AML50 18 48980369 48980369 A C SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.1574-5215 e10-5215 0.016 - - - no_errors tier3 716 3 0.42 433 229 34.59 0 0 NA 501944 TCGA-AB-2991 AML50 18 48997912 48997912 C T SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.1911+1947 e12+1947 0.014 - - - no_errors tier3 606 1 0.16 446 139 23.76 0 0 NA 501944 TCGA-AB-2991 AML50 18 60402826 60402826 C A SNP - - - - - - - - - - - - - - - tier3 521 0 0 416 143 25.58 0 0 NA 501944 TCGA-AB-2991 AML50 18 61335115 61335115 G A SNP ENSG00000210497 ENST00000387762 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41299 NULL 0.004 - - - pseudogene tier3 1185 0 0 739 411 35.74 0 0 NA 501944 TCGA-AB-2991 AML50 18 62860540 62860540 G A SNP - - - - - - - - - - - - - - - tier3 380 0 0 434 213 32.92 0 0 NA 501944 TCGA-AB-2991 AML50 18 63650122 63650122 T A SNP - - - - - - - - - - - - - - - tier2 1267 0 0 919 556 37.69 0 0 NA 501944 TCGA-AB-2991 AML50 19 11495314 11495314 C T SNP ENSG00000213303 ENST00000393374 human ensembl 54_36p 1 novel 3_prime_untranslated_region c.*11495314 NULL 1 - - - no_coding_region:pseudogene tier2 364 2 0.55 85 71 45.51 12 6 33.33 501944 TCGA-AB-2991 AML50 19 12084966 12084966 G A SNP ZNF788 ENST00000339302 human ensembl 54_36p 1 known missense c.1604 p.R535H 0.989 superfamily_SSF57667 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 637 0 313 113 26.53 3 2 40 501944 TCGA-AB-2991 AML50 19 23848505 23848505 T C SNP LOC730087 XM_001726951.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-35725 NULL 0.031 - - - no_errors tier3 450 2 0.44 146 101 40.56 0 0 0 501944 TCGA-AB-2991 AML50 19 32974835 32974835 T C SNP LOC100131141 XR_036861.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-1808 NULL 0 - - - pseudogene tier2 537 0 0 457 255 35.71 1 0 0 501944 TCGA-AB-2991 AML50 19 34116424 34116424 C T SNP ENSG00000209828 ENST00000387093 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*2573 NULL 0.003 - - - pseudogene tier3 1602 0 0 675 373 35.42 1 0 0 501944 TCGA-AB-2991 AML50 19 59348746 59348746 C T SNP CNOT3 ENST00000358389 human ensembl 54_36p 1 known missense c.1511 p.T504I 0 NULL HMMPfam_Not3 - no_errors tier1 451 2 0.44 162 51 23.94 1 100 501944 TCGA-AB-2991 AML50 20 846759 846759 A T SNP ANGPT4 NM_015985.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-1902 NULL 0 - - - no_errors tier3 2210 7 0.32 730 492 40.23 0 0 NA 501944 TCGA-AB-2991 AML50 20 4220745 4220745 G C SNP ADRA1D NM_000678.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43141 NULL 0.218 - - - no_errors tier3 668 0 0 591 370 38.22 0 0 NA 501944 TCGA-AB-2991 AML50 20 8298932 8298932 T - DEL PLCB1 NM_015192.2 human genbank 54_36p 1 reviewed intronic c.178-1097 e3-1097 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 20 10662354 10662354 C T SNP - - - - - - - - - - - - - - - tier3 1058 3 0.28 550 360 39.56 0 2 100 501944 TCGA-AB-2991 AML50 20 11203870 11203870 G A SNP - - - - - - - - - - - - - - - tier2 1455 1 0.07 869 513 37.07 0 0 NA 501944 TCGA-AB-2991 AML50 20 42994250 42994250 G A SNP PABPC1L ENST00000372822 human ensembl 54_36p 1 known 5_prime_untranslated_region c.-885 NULL 0 - - - no_errors tier3 1164 0 0 468 290 38.26 16 17 51.52 501944 TCGA-AB-2991 AML50 20 53339582 53339582 G C SNP - - - - - - - - - - - - - - - tier3 1672 1 0.06 900 619 40.7 0 0 NA 501944 TCGA-AB-2991 AML50 20 54078444 54078444 C T SNP - - - - - - - - - - - - - - - tier3 1075 1 0.09 724 475 39.62 0 0 NA 501944 TCGA-AB-2991 AML50 20 58064490 58064490 C T SNP C20orf197 NM_173644.1 human genbank 54_36p 1 predicted intronic c.1+32 e0+32 0 - - - no_errors tier3 840 0 0 375 270 41.73 0 0 0 501944 TCGA-AB-2991 AML50 21 30113909 30113909 C T SNP GRIK1 NM_000830.3 human genbank 54_36p -1 reviewed intronic c.118+119663 e1+119663 0.009 - - - no_errors tier3 1191 1 0.08 622 357 36.43 0 0 NA 501944 TCGA-AB-2991 AML50 21 30515532 30515532 A G SNP CLDN8 NM_199328.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5418 NULL 0 - - - no_errors tier3 578 0 0 488 143 22.66 0 0 NA 501944 TCGA-AB-2991 AML50 21 30613984 30613984 C T SNP KRTAP26-1 NM_203405.1 human genbank 54_36p -1 validated missense c.241 p.G81S 0 HMMPfam_PMG HMMPfam_PMG - no_errors tier1 1542 0 556 352 38.77 NA 501944 TCGA-AB-2991 AML50 21 38998499 38998500 - T INS ERG NM_004449.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-129005 NULL 0.066:0.078 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 501944 TCGA-AB-2991 AML50 22 27035974 27035974 A G SNP TTC28 ENST00000397906 human ensembl 54_36p -1 known intronic c.382-3343 e3-3343 0.012 - - - no_errors tier3 1069 0 0 962 340 26.11 0 0 0 501944 TCGA-AB-2991 AML50 22 36392296 36392296 C A SNP PDXP NM_020315.4 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*472 NULL 0 - - - no_errors tier3 528 0 0 167 95 36.26 29 19 39.58 501944 TCGA-AB-2991 AML50 22 47618173 47618173 G A SNP ENSG00000205632 ENST00000380981 human ensembl 54_36p 1 known 5_prime_flanking_region c.-58432 NULL 0 - - - no_errors tier3 712 1 0.14 256 170 39.91 0 0 NA 327733 TCGA-AB-2992 AML08 X 11584926 11584926 G A SNP ARHGAP6 NM_013427.2 human genbank 54_36p -1 reviewed intronic c.588+7356 e1+7356 0.001 - - - no_errors tier3 794 17 2.09 267 114 29.84 0 0 NA 327733 TCGA-AB-2992 AML08 X 20229732 20229732 A G SNP RPS6KA3 NM_004586.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-35061 NULL 0.006 - - - no_errors tier3 512 16 3.02 533 278 34.28 0 0 NA 327733 TCGA-AB-2992 AML08 X 23711246 23711246 C T SNP SAT1 NM_002970.1 human genbank 54_36p 1 provisional 5_prime_untranslated_region c.-144 NULL 0 - - - no_errors tier2 684 6 0.87 244 165 40.34 307 4 1.29 327733 TCGA-AB-2992 AML08 X 25717189 25717189 C G SNP - - - - - - - - - - - - - - - tier3 528 8 1.49 511 205 28.63 0 0 NA 327733 TCGA-AB-2992 AML08 X 28018027 28018027 G C SNP - - - - - - - - - - - - - - - tier3 1130 14 1.22 1536 632 29.12 0 0 NA 327733 TCGA-AB-2992 AML08 X 28206808 28206808 C T SNP - - - - - - - - - - - - - - - tier3 886 8 0.89 875 417 32.25 0 0 NA 327733 TCGA-AB-2992 AML08 X 28907766 28907766 G T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.82+190303 e1+190303 0.008 - - - no_errors tier3 2026 19 0.93 1867 809 30.22 0 0 NA 327733 TCGA-AB-2992 AML08 X 41444465 41444465 C T SNP CASK NM_003688.2 human genbank 54_36p -1 validated intronic c.430-28738 e6-28738 0.324 - - - no_errors tier3 448 7 1.54 306 142 31.7 2 0 0 327733 TCGA-AB-2992 AML08 X 45093062 45093062 C A SNP ENSG00000219063 ENST00000407377 human ensembl 54_36p -1 known 3_prime_flanking_region c.*32654 NULL 0.052 - - - no_coding_region:pseudogene tier3 1975 21 1.05 1578 777 32.98 0 0 NA 327733 TCGA-AB-2992 AML08 X 46736510 46736510 C A SNP PHF16 NM_001077445.1 human genbank 54_36p 1 reviewed intronic c.127-5956 e3-5956 0 - - - no_errors tier3 697 7 0.99 690 298 30.16 1 0 0 327733 TCGA-AB-2992 AML08 X 56685358 56685358 G C SNP - - - - - - - - - - - - - - - tier3 533 9 1.66 282 120 29.85 0 0 NA 327733 TCGA-AB-2992 AML08 X 57033999 57033999 G T SNP SPIN3 NM_001010862.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*3330 NULL 0.991 - - - no_errors tier3 664 6 0.9 532 156 22.67 1 0 0 327733 TCGA-AB-2992 AML08 X 74746947 74746948 - A INS ENSG00000217374 ENST00000405568 human ensembl 54_36p 1 known 3_prime_flanking_region c.*24881 NULL 0.187:0.193 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 X 104645625 104645625 G T SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.772+30590 e5+30590 0.001 - - - no_errors tier3 1414 9 0.63 866 357 29.19 0 0 NA 327733 TCGA-AB-2992 AML08 X 106490851 106490851 G A SNP ENSG00000215007 ENST00000399417 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-8123 NULL 0.001 - - - no_coding_region:pseudogene tier3 1137 21 1.81 630 325 33.96 0 0 NA 327733 TCGA-AB-2992 AML08 X 107572539 107572539 G A SNP COL4A5 NM_033380.3 human genbank 54_36p 1 reviewed intronic c.81+2447 e1+2447 0.002 - - - no_errors tier2 708 18 2.48 870 365 29.55 0 0 0 327733 TCGA-AB-2992 AML08 X 107754013 107754013 G T SNP COL4A5 NM_033380.3 human genbank 54_36p 1 reviewed intronic c.2918-109 e34-109 0 - - - no_errors tier3 724 7 0.96 758 343 31.15 0 0 0 327733 TCGA-AB-2992 AML08 X 111945310 111945310 A T SNP AMOT NM_133265.1 human genbank 54_36p -1 reviewed missense c.97 p.S33T 0.996 NULL NULL - no_errors tier1 1815 15 0.82 926 477 33.97 1 0 327733 TCGA-AB-2992 AML08 X 130386505 130386505 C T SNP OR1AA1P ENST00000407136 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*130386505 NULL 0.409 - - - no_coding_region:pseudogene tier2 1823 27 1.46 2243 1014 31.12 0 0 NA 327733 TCGA-AB-2992 AML08 X 134940681 134940681 G C SNP SLC9A6 NM_001042537.1 human genbank 54_36p 1 validated intronic c.1647+694 e13+694 0.003 - - - no_errors tier3 1031 15 1.43 951 410 30.12 1 0 0 327733 TCGA-AB-2992 AML08 X 134958208 134958208 C G SNP ENSG00000219930 ENST00000403369 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29460 NULL 0.002 - - - no_coding_region:pseudogene tier2 853 24 2.73 555 322 36.72 0 0 NA 327733 TCGA-AB-2992 AML08 X 137795242 137795242 A G SNP FGF13 ENST00000370603 human ensembl 54_36p -1 known intronic c.68-27735 e2-27735 0.003 - - - no_errors tier3 2149 42 1.92 854 405 32.17 0 0 NA 327733 TCGA-AB-2992 AML08 X 139740784 139740784 C T SNP CDR1 NM_004065.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-46587 NULL 0.004 - - - no_errors tier3 710 5 0.7 540 222 29.1 0 0 NA 327733 TCGA-AB-2992 AML08 X 145302527 145302527 C G SNP ENSG00000201594 ENST00000364724 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14139 NULL 0.97 - - - no_errors tier3 773 17 2.15 803 365 31.25 0 0 NA 327733 TCGA-AB-2992 AML08 X 149471007 149471007 T A SNP MTM1 NM_000252.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40728 NULL 0 - - - no_errors tier3 914 8 0.87 348 115 24.84 0 0 NA 327733 TCGA-AB-2992 AML08 1 2937174 2937174 G A SNP ENSG00000177133 ENST00000321399 human ensembl 54_36p -1 known intronic c.447+30345 e1+30345 0 - - - no_errors tier3 276 4 1.43 199 111 35.81 0 0 NA 327733 TCGA-AB-2992 AML08 1 4006653 4006653 C G SNP - - - - - - - - - - - - - - - tier3 1025 21 2.01 416 201 32.58 0 0 NA 327733 TCGA-AB-2992 AML08 1 14096506 14096506 G T SNP C1orf196 ENST00000401953 human ensembl 54_36p 1 known intronic c.121+3668 e1+3668 0.006 - - - no_stop_codon tier3 1830 43 2.3 306 155 33.62 1 0 0 327733 TCGA-AB-2992 AML08 1 18237415 18237415 C T SNP - - - - - - - - - - - - - - - tier3 1914 38 1.94 949 474 33.31 0 0 NA 327733 TCGA-AB-2992 AML08 1 21676682 21676682 G A SNP NBPF3 NM_032264.2 human genbank 54_36p 1 validated intronic c.993-542 e8-542 0 - - - no_errors tier3 842 7 0.82 442 145 24.66 0 0 0 327733 TCGA-AB-2992 AML08 1 51548269 51548269 A T SNP TTC39A NM_001080494.2 human genbank 54_36p -1 validated intronic c.427-684 e6-684 0.021 - - - no_errors tier3 1819 27 1.46 563 278 33.06 0 0 NA 327733 TCGA-AB-2992 AML08 1 56629947 56629947 C T SNP - - - - - - - - - - - - - - - tier3 2684 37 1.36 943 444 31.99 0 0 NA 327733 TCGA-AB-2992 AML08 1 58829874 58829874 T C SNP TACSTD2 NM_002353.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14458 NULL 0 - - - no_errors tier3 2178 45 2.02 735 317 30.13 7 0 0 327733 TCGA-AB-2992 AML08 1 81269796 81269796 G A SNP ENSG00000220876 ENST00000404408 human ensembl 54_36p 1 known 5_prime_flanking_region c.-49267 NULL 0 - - - no_coding_region:pseudogene tier3 252 8 3.08 84 36 30 0 0 NA 327733 TCGA-AB-2992 AML08 1 102636641 102636641 T A SNP - - - - - - - - - - - - - - - tier3 630 2 0.32 713 87 10.88 0 0 NA 327733 TCGA-AB-2992 AML08 1 103037905 103037906 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 1 105844639 105844640 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 1 106162350 106162350 C G SNP - - - - - - - - - - - - - - - tier3 3792 53 1.37 917 392 29.92 0 0 NA 327733 TCGA-AB-2992 AML08 1 161695249 161695249 G A SNP ENSG00000218131 ENST00000401780 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35671 NULL 1 - - - no_coding_region:pseudogene tier2 2066 35 1.67 934 450 32.49 0 0 NA 327733 TCGA-AB-2992 AML08 1 187528675 187528675 T A SNP - - - - - - - - - - - - - - - tier3 693 10 1.42 583 254 30.35 0 0 NA 327733 TCGA-AB-2992 AML08 1 204661467 204661467 G A SNP SRGAP2 ENST00000367123 human ensembl 54_36p 1 known intronic c.1+219 e0+219 0 - - - no_stop_codon tier3 875 17 1.91 789 342 30.24 7 0 0 327733 TCGA-AB-2992 AML08 1 209968722 209968722 A G SNP LPGAT1 NM_014873.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*21142 NULL 0.036 - - - no_errors tier3 615 9 1.44 244 163 40.05 1 0 0 327733 TCGA-AB-2992 AML08 1 212284207 212284207 A G SNP PROX1 NM_002763.3 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*8407 NULL 0.002 - - - no_errors tier2 781 7 0.89 493 214 30.27 0 0 NA 327733 TCGA-AB-2992 AML08 1 232529286 232529286 T C SNP C1orf31 NM_001012985.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-46802 NULL 0.001 - - - no_errors tier2 1800 18 0.99 1274 628 33.02 0 0 NA 327733 TCGA-AB-2992 AML08 2 2787616 2787616 C T SNP - - - - - - - - - - - - - - - tier3 1411 38 2.62 646 253 28.14 0 0 NA 327733 TCGA-AB-2992 AML08 2 66178748 66178748 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 2 88157833 88157833 A G SNP SMYD1 NM_198274.2 human genbank 54_36p 1 provisional intronic c.138-7117 e2-7117 0 - - - no_errors tier3 1460 23 1.55 614 315 33.91 0 0 NA 327733 TCGA-AB-2992 AML08 2 116043637 116043637 G T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.441+43619 e5+43619 0 - - - no_errors tier3 666 8 1.19 512 217 29.77 0 0 NA 327733 TCGA-AB-2992 AML08 2 120034525 120034525 C T SNP PCDP1 NM_001029996.2 human genbank 54_36p 1 provisional intronic c.1+453 e0+453 0.004 - - - no_errors tier3 519 10 1.88 391 195 32.88 0 0 NA 327733 TCGA-AB-2992 AML08 2 130115571 130115571 G A SNP - - - - - - - - - - - - - - - tier3 1083 11 1.01 820 394 32.45 0 0 NA 327733 TCGA-AB-2992 AML08 2 136612959 136612959 C T SNP CXCR4 NM_001008540.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22980 NULL 0.002 - - - no_errors tier3 612 14 2.24 316 149 32.04 0 0 NA 327733 TCGA-AB-2992 AML08 2 145712683 145712683 C T SNP - - - - - - - - - - - - - - - tier3 907 15 1.63 616 332 35.02 0 0 NA 327733 TCGA-AB-2992 AML08 2 145827694 145827694 A T SNP ENSG00000214064 ENST00000397427 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*15593 NULL 0 - - - no_coding_region:pseudogene tier3 428 7 1.61 314 119 27.48 0 0 NA 327733 TCGA-AB-2992 AML08 2 149526670 149526670 C A SNP KIF5C ENST00000397413 human ensembl 54_36p 1 known intronic c.273-61 e4-61 0.002 - - - no_errors tier3 1082 2 0.18 602 57 8.65 0 0 NA 327733 TCGA-AB-2992 AML08 2 157197783 157197783 G C SNP GPD2 NM_000408.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*50107 NULL 0.005 - - - no_errors tier3 562 7 1.23 351 163 31.53 0 0 NA 327733 TCGA-AB-2992 AML08 2 157366726 157366726 G C SNP - - - - - - - - - - - - - - - tier3 948 18 1.86 707 357 33.52 0 0 NA 327733 TCGA-AB-2992 AML08 2 194760558 194760558 G A SNP - - - - - - - - - - - - - - - tier3 443 6 1.34 202 107 34.63 0 0 NA 327733 TCGA-AB-2992 AML08 2 203684703 203684703 A G SNP NBEAL1 NM_001099273.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-24086 NULL 0.009 - - - no_errors tier3 252 6 2.33 302 176 36.82 1 0 0 327733 TCGA-AB-2992 AML08 2 205993154 205993154 A G SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated intronic c.2555+19062 e18+19062 0 - - - no_errors tier3 1305 9 0.68 775 389 33.39 0 0 NA 327733 TCGA-AB-2992 AML08 2 208702733 208702733 T G SNP CRYGC NM_020989.3 human genbank 54_36p -1 reviewed intronic c.9+20 e1+20 0.001 - - - no_errors tier3 810 10 1.22 494 180 26.71 0 0 NA 327733 TCGA-AB-2992 AML08 2 208821358 208821358 G A SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132C 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 1083 14 1.28 429 197 31.47 49 56 53.33 327733 TCGA-AB-2992 AML08 2 223604358 223604358 T C SNP KCNE4 NM_080671.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21435 NULL 0.049 - - - no_errors tier3 1249 3 0.24 733 109 12.93 0 0 NA 327733 TCGA-AB-2992 AML08 2 228032998 228032998 A T SNP AGFG1 NM_004504.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-12384 NULL 0 - - - no_errors tier3 531 5 0.93 235 99 29.64 0 0 NA 327733 TCGA-AB-2992 AML08 2 229430563 229430563 T C SNP - - - - - - - - - - - - - - - tier3 1223 50 3.92 1435 747 34.23 0 0 NA 327733 TCGA-AB-2992 AML08 2 234380113 234380113 C T SNP LOC339766 XM_291007.1 human genbank 54_36p 1 model intronic c.2152-695 e20-695 0.007 - - - no_errors tier3 712 9 1.25 345 128 27.06 0 0 NA 327733 TCGA-AB-2992 AML08 2 236852295 236852295 T C SNP LOC100128572 XM_001714193.1 human genbank 54_36p 1 model intronic c.546+1461 e3+1461 0.002 - - - no_errors tier3 1013 10 0.98 803 382 32.24 0 0 NA 327733 TCGA-AB-2992 AML08 2 236852319 236852319 A T SNP LOC100128572 XM_001714193.1 human genbank 54_36p 1 model intronic c.546+1485 e3+1485 0.001 - - - no_errors tier3 1003 11 1.08 759 364 32.36 0 0 NA 327733 TCGA-AB-2992 AML08 3 10850430 10850430 G A SNP SLC6A11 NM_014229.1 human genbank 54_36p 1 provisional intronic c.623+10353 e4+10353 0.003 - - - no_errors tier3 864 9 1.03 478 238 33.19 0 0 NA 327733 TCGA-AB-2992 AML08 3 17370605 17370605 T C SNP TBC1D5 NM_014744.1 human genbank 54_36p -1 validated intronic c.995+17966 e11+17966 0.002 - - - no_errors tier3 945 23 2.38 623 295 32.14 2 0 0 327733 TCGA-AB-2992 AML08 3 43564871 43564871 T C SNP ANO10 NM_018075.3 human genbank 54_36p -1 validated intronic c.1797+1345 e10+1345 0.742 - - - no_errors tier3 1487 32 2.11 1195 520 30.32 2 0 0 327733 TCGA-AB-2992 AML08 3 56005825 56005825 T A SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2062-4507 e10-4507 0.007 - - - no_errors tier3 888 13 1.44 643 286 30.79 0 0 NA 327733 TCGA-AB-2992 AML08 3 64310288 64310288 G A SNP - - - - - - - - - - - - - - - tier3 653 7 1.06 800 377 32.03 0 0 NA 327733 TCGA-AB-2992 AML08 3 64473604 64473604 T C SNP ADAMTS9 NM_182920.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*9283 NULL 0 - - - no_errors tier3 1336 13 0.96 1010 468 31.66 0 0 NA 327733 TCGA-AB-2992 AML08 3 71234567 71234567 G A SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.282+9810 e2+9810 0.075 - - - no_errors tier3 1639 15 0.91 1071 486 31.19 16 2 11.11 327733 TCGA-AB-2992 AML08 3 72433392 72433392 A G SNP ENSG00000212070 ENST00000390781 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-39123 NULL 0.014 - - - no_errors tier3 618 6 0.96 411 193 31.9 0 0 NA 327733 TCGA-AB-2992 AML08 3 88995644 88995644 T A SNP - - - - - - - - - - - - - - - tier3 1209 15 1.22 734 375 33.81 0 0 NA 327733 TCGA-AB-2992 AML08 3 89959637 89959637 G T SNP - - - - - - - - - - - - - - - tier3 410 7 1.68 382 157 29.07 0 0 NA 327733 TCGA-AB-2992 AML08 3 107205365 107205365 A G SNP - - - - - - - - - - - - - - - tier3 600 16 2.6 481 192 28.53 0 0 NA 327733 TCGA-AB-2992 AML08 3 111501462 111501462 T G SNP - - - - - - - - - - - - - - - tier2 613 7 1.13 414 133 24.31 0 0 NA 327733 TCGA-AB-2992 AML08 3 113263987 113263987 G A SNP TMPRSS7 NM_001042575.2 human genbank 54_36p 1 validated intronic c.634+527 e5+527 0.003 - - - no_errors tier3 927 23 2.42 984 494 33.42 0 0 NA 327733 TCGA-AB-2992 AML08 3 115700850 115700850 T C SNP ZBTB20 NM_015642.3 human genbank 54_36p -1 provisional intronic c.1+1039 e0+1039 0.067 - - - no_errors tier2 1296 17 1.29 701 327 31.81 0 0 0 327733 TCGA-AB-2992 AML08 3 117387020 117387020 C G SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.156-98927 e2-98927 0.003 - - - no_errors tier3 2766 18 0.65 1268 514 28.84 0 0 NA 327733 TCGA-AB-2992 AML08 3 118131033 118131033 C T SNP ENSG00000196797 ENST00000356047 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13612 NULL 0.002 - - - no_coding_region:pseudogene tier3 740 7 0.94 901 463 33.92 0 0 NA 327733 TCGA-AB-2992 AML08 3 122330343 122330343 A T SNP STXBP5L NM_014980.2 human genbank 54_36p 1 validated intronic c.669+7102 e6+7102 0 - - - no_errors tier3 479 4 0.83 464 203 30.39 0 0 NA 327733 TCGA-AB-2992 AML08 3 134483358 134483358 C T SNP TMEM108 NM_023943.1 human genbank 54_36p 1 validated intronic c.40+52473 e1+52473 0 - - - no_errors tier3 986 17 1.69 902 328 26.62 0 0 0 327733 TCGA-AB-2992 AML08 3 140743882 140743882 C T SNP RBP1 NM_002899.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2818 NULL 0.004 - - - no_errors tier3 707 15 2.07 259 117 31.03 0 0 NA 327733 TCGA-AB-2992 AML08 3 155678364 155678364 C T SNP GPR149 NM_001038705.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-48266 NULL 0.024 - - - no_errors tier3 1006 24 2.33 593 273 31.52 0 0 NA 327733 TCGA-AB-2992 AML08 3 165436186 165436186 G A SNP - - - - - - - - - - - - - - - tier3 694 7 1 569 264 31.69 0 0 NA 327733 TCGA-AB-2992 AML08 3 187581448 187581448 C T SNP DGKG NM_001346.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-60506 NULL 0.013 - - - no_errors tier3 1140 15 1.3 645 290 31.02 0 0 NA 327733 TCGA-AB-2992 AML08 3 195422309 195422309 A G SNP - - - - - - - - - - - - - - - tier3 1423 33 2.27 691 367 34.66 0 0 NA 327733 TCGA-AB-2992 AML08 3 195989393 195989393 C T SNP - - - - - - - - - - - - - - - tier3 1054 9 0.85 950 498 34.06 0 0 NA 327733 TCGA-AB-2992 AML08 4 3813051 3813051 C T SNP - - - - - - - - - - - - - - - tier3 1427 17 1.17 410 276 40.23 0 0 NA 327733 TCGA-AB-2992 AML08 4 11931781 11931781 C T SNP ENSG00000212282 ENST00000390980 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*8369 NULL 0.002 - - - no_errors tier3 765 8 1.03 510 223 30.34 0 0 NA 327733 TCGA-AB-2992 AML08 4 27151032 27151033 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 4 28154927 28154927 G T SNP - - - - - - - - - - - - - - - tier3 836 11 1.3 492 188 27.61 0 0 NA 327733 TCGA-AB-2992 AML08 4 31893240 31893240 G A SNP LOC100130644 XM_001717608.1 human genbank 54_36p -1 model intronic c.333+5855 e2+5855 0 - - - pseudogene:no_stop_codon tier2 464 7 1.49 394 208 34.55 0 0 NA 327733 TCGA-AB-2992 AML08 4 34152180 34152180 A G SNP - - - - - - - - - - - - - - - tier3 1445 22 1.5 668 333 33.23 0 0 NA 327733 TCGA-AB-2992 AML08 4 39135654 39135654 T C SNP RPL9 NM_000661.4 human genbank 54_36p -1 reviewed missense c.205 p.T69A 1 "HMMPfam_Ribosomal_L6,superfamily_Ribosomal protein L6" "PatternScan_RIBOSOMAL_L6_2,HMMPfam_Ribosomal_L6,superfamily_Ribosomal protein L6" - no_errors tier1 487 17 3.36 205 89 30.27 18 13 41.94 327733 TCGA-AB-2992 AML08 4 44213784 44213784 C T SNP - - - - - - - - - - - - - - - tier3 452 6 1.31 505 194 27.75 0 0 NA 327733 TCGA-AB-2992 AML08 4 58003173 58003173 C T SNP - - - - - - - - - - - - - - - tier2 1610 17 1.04 834 361 30.21 0 0 NA 327733 TCGA-AB-2992 AML08 4 65782625 65782625 A G SNP - - - - - - - - - - - - - - - tier3 708 10 1.39 555 255 31.48 0 0 NA 327733 TCGA-AB-2992 AML08 4 67675008 67675008 T C SNP - - - - - - - - - - - - - - - tier3 967 18 1.83 802 320 28.47 0 0 NA 327733 TCGA-AB-2992 AML08 4 70425914 70425914 C T SNP UGT2B4 NM_021139.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-29746 NULL 0 - - - no_errors tier2 415 3 0.72 376 176 31.88 0 0 NA 327733 TCGA-AB-2992 AML08 4 88594905 88594905 G A SNP NUDT9 NM_024047.3 human genbank 54_36p 1 validated intronic c.874+274 e7+274 0.001 - - - no_errors tier3 275 3 1.08 322 136 29.57 0 0 0 327733 TCGA-AB-2992 AML08 4 91185493 91185493 C T SNP - - - - - - - - - - - - - - - tier3 646 11 1.67 424 202 32.27 0 0 NA 327733 TCGA-AB-2992 AML08 4 95689259 95689259 A G SNP PDLIM5 NM_006457.2 human genbank 54_36p 1 reviewed intronic c.249-24266 e3-24266 0.001 - - - no_errors tier3 495 6 1.2 405 192 32.16 2 0 0 327733 TCGA-AB-2992 AML08 4 96190254 96190254 G A SNP BMPR1B NM_001203.2 human genbank 54_36p 1 reviewed intronic c.1+53946 e0+53946 0.545 - - - no_errors tier3 1213 28 2.26 697 295 29.74 0 0 NA 327733 TCGA-AB-2992 AML08 4 102095820 102095820 G A SNP - - - - - - - - - - - - - - - tier3 789 7 0.88 1067 497 31.78 0 0 NA 327733 TCGA-AB-2992 AML08 4 102615419 102615419 G A SNP - - - - - - - - - - - - - - - tier3 1595 39 2.39 1557 706 31.2 0 0 NA 327733 TCGA-AB-2992 AML08 4 106727285 106727285 T G SNP FLJ20184 NM_017700.1 human genbank 54_36p 1 predicted intronic c.197-2569 e2-2569 0.001 - - - no_errors tier3 969 27 2.71 709 276 27.96 0 0 NA 327733 TCGA-AB-2992 AML08 4 112850913 112850913 T C SNP - - - - - - - - - - - - - - - tier3 561 8 1.41 577 286 33.14 0 0 NA 327733 TCGA-AB-2992 AML08 4 121148531 121148531 A G SNP - - - - - - - - - - - - - - - tier3 347 3 0.86 313 112 26.35 0 0 NA 327733 TCGA-AB-2992 AML08 4 121627531 121627531 G T SNP - - - - - - - - - - - - - - - tier3 812 11 1.34 677 274 28.78 0 0 NA 327733 TCGA-AB-2992 AML08 4 144623720 144623720 C A SNP SMARCA5 NM_003601.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30808 NULL 0.025 - - - no_errors tier3 966 10 1.02 1089 356 24.64 0 0 NA 327733 TCGA-AB-2992 AML08 4 162236591 162236591 T A SNP - - - - - - - - - - - - - - - tier3 143 5 3.38 311 146 31.95 0 0 NA 327733 TCGA-AB-2992 AML08 4 162236602 162236602 A C SNP - - - - - - - - - - - - - - - tier3 122 4 3.17 285 150 34.48 0 0 NA 327733 TCGA-AB-2992 AML08 4 171087565 171087565 C T SNP - - - - - - - - - - - - - - - tier2 789 34 4.13 632 338 34.85 0 0 NA 327733 TCGA-AB-2992 AML08 5 4470270 4470270 G A SNP - - - - - - - - - - - - - - - tier3 792 16 1.98 551 242 30.52 0 0 NA 327733 TCGA-AB-2992 AML08 5 4725109 4725109 G A SNP - - - - - - - - - - - - - - - tier3 417 17 3.92 348 162 31.76 0 0 NA 327733 TCGA-AB-2992 AML08 5 5313158 5313158 C T SNP ADAMTS16 NM_139056.2 human genbank 54_36p 1 reviewed intronic c.2663-2612 e18-2612 0.004 - - - no_errors tier3 648 9 1.37 593 269 31.21 0 0 NA 327733 TCGA-AB-2992 AML08 5 6582119 6582119 C G SNP uc003jdp.2 ENST00000399816 human ensembl 54_36p 1 known 3_prime_flanking_region c.*37657 NULL 0.075 - - - no_start_codon tier3 2077 32 1.52 936 392 29.52 0 0 NA 327733 TCGA-AB-2992 AML08 5 22155769 22155769 G T SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-41041 e1-41041 0.472 - - - no_errors tier3 591 6 1.01 503 213 29.75 0 0 NA 327733 TCGA-AB-2992 AML08 5 28130366 28130366 G A SNP - - - - - - - - - - - - - - - tier3 169 1 0.59 143 72 33.49 0 0 NA 327733 TCGA-AB-2992 AML08 5 52832837 52832837 C T SNP FST NM_013409.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*15217 NULL 0.009 - - - no_errors tier3 1953 37 1.86 1363 641 31.97 0 0 NA 327733 TCGA-AB-2992 AML08 5 67715660 67715660 G C SNP - - - - - - - - - - - - - - - tier3 1085 27 2.43 692 329 32.22 0 0 NA 327733 TCGA-AB-2992 AML08 5 74985751 74985751 G T SNP LOC728780 XM_001128459.2 human genbank 54_36p 1 model intronic c.1335+930 e9+930 0.002 - - - no_errors tier3 1643 10 0.6 1025 520 33.64 0 0 NA 327733 TCGA-AB-2992 AML08 5 90928019 90928019 G A SNP - - - - - - - - - - - - - - - tier3 1004 9 0.89 921 356 27.88 0 0 NA 327733 TCGA-AB-2992 AML08 5 92336588 92336588 G A SNP LOC391810 XM_001723772.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-5762 NULL 0.001 - - - pseudogene tier3 687 12 1.71 807 250 23.54 0 0 NA 327733 TCGA-AB-2992 AML08 5 100399714 100399714 A G SNP ENSG00000203447 ENST00000366265 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29706 NULL 0.022 - - - no_coding_region:pseudogene tier3 517 17 3.18 638 334 34.36 0 0 NA 327733 TCGA-AB-2992 AML08 5 101262507 101262507 C T SNP - - - - - - - - - - - - - - - tier3 414 3 0.72 358 142 28.34 0 0 NA 327733 TCGA-AB-2992 AML08 5 105355078 105355078 T A SNP - - - - - - - - - - - - - - - tier3 561 5 0.88 779 396 33.67 0 0 NA 327733 TCGA-AB-2992 AML08 5 105355090 105355090 C A SNP - - - - - - - - - - - - - - - tier3 546 4 0.73 777 388 33.28 0 0 NA 327733 TCGA-AB-2992 AML08 5 119977176 119977176 G T SNP PRR16 NM_016644.1 human genbank 54_36p 1 provisional intronic c.91-72372 e2-72372 0 - - - no_errors tier3 201 4 1.95 292 172 37.07 0 0 NA 327733 TCGA-AB-2992 AML08 5 136352532 136352532 T C SNP SPOCK1 NM_004598.3 human genbank 54_36p -1 reviewed intronic c.707-301 e7-301 0 - - - no_errors tier2 499 1 0.2 478 196 29.08 0 0 NA 327733 TCGA-AB-2992 AML08 5 157766407 157766407 C T SNP - - - - - - - - - - - - - - - tier3 1716 20 1.15 1779 843 32.14 0 0 NA 327733 TCGA-AB-2992 AML08 5 161139525 161139525 A T SNP GLRXL ENST00000309178 human ensembl 54_36p -1 known 5_prime_flanking_region c.-28173 NULL 0.006 - - - no_errors tier3 445 11 2.41 493 217 30.56 0 0 NA 327733 TCGA-AB-2992 AML08 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 327733 TCGA-AB-2992 AML08 6 15384052 15384052 G A SNP JARID2 NM_004973.2 human genbank 54_36p 1 reviewed intronic c.45+29258 e1+29258 0.646 - - - no_errors tier3 602 7 1.15 466 225 32.56 31 2 6.06 327733 TCGA-AB-2992 AML08 6 20033197 20033197 G A SNP LOC100130822 XR_038409.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-39542 NULL 0.001 - - - pseudogene tier3 878 20 2.23 490 197 28.68 0 0 NA 327733 TCGA-AB-2992 AML08 6 27829014 27829014 G A SNP LOC100131289 XM_001722683.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-8511 NULL 0.01 - - - no_errors tier3 861 6 0.69 494 181 26.81 0 0 NA 327733 TCGA-AB-2992 AML08 6 50627646 50627646 C T SNP - - - - - - - - - - - - - - - tier3 1070 19 1.74 685 332 32.65 0 0 NA 327733 TCGA-AB-2992 AML08 6 50794692 50794692 A C SNP TFAP2D NM_172238.3 human genbank 54_36p 1 validated intronic c.538-70 e3-70 0.008 - - - no_errors tier3 1183 9 0.75 327 175 34.86 0 0 NA 327733 TCGA-AB-2992 AML08 6 62882941 62882941 G T SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.219+62108 e2+62108 0.008 - - - no_errors tier3 412 3 0.72 379 149 28.22 0 0 NA 327733 TCGA-AB-2992 AML08 6 64260367 64260367 T C SNP ENSG00000218048 ENST00000402043 human ensembl 54_36p 1 known 3_prime_flanking_region c.*48923 NULL 0.072 - - - no_coding_region:pseudogene tier3 749 7 0.93 483 267 35.6 0 0 NA 327733 TCGA-AB-2992 AML08 6 70842369 70842369 C T SNP COL19A1 NM_001858.4 human genbank 54_36p 1 reviewed intronic c.1224+7280 e14+7280 0 - - - no_errors tier3 1003 16 1.57 732 308 29.59 0 0 NA 327733 TCGA-AB-2992 AML08 6 72023748 72023748 C T SNP OGFRL1 NM_024576.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-31613 NULL 0.076 - - - no_errors tier2 1060 18 1.67 464 223 32.46 0 0 NA 327733 TCGA-AB-2992 AML08 6 74421559 74421559 C T SNP SLC17A5 NM_012434.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-1229 NULL 0.003 - - - no_errors tier2 360 3 0.83 248 88 26.19 0 0 NA 327733 TCGA-AB-2992 AML08 6 74830523 74830523 A G SNP - - - - - - - - - - - - - - - tier3 770 7 0.9 683 340 33.24 0 0 NA 327733 TCGA-AB-2992 AML08 6 76251243 76251243 C T SNP FILIP1 NM_015687.2 human genbank 54_36p -1 validated intronic c.1+8607 e0+8607 0 - - - no_errors tier3 1802 14 0.77 930 447 32.46 0 0 NA 327733 TCGA-AB-2992 AML08 6 78524900 78524900 C T SNP ENSG00000214481 ENST00000398401 human ensembl 54_36p 1 known intronic c.256-2683 e3-2683 0.002 - - - no_stop_codon tier3 1436 38 2.58 1267 566 30.88 0 0 NA 327733 TCGA-AB-2992 AML08 6 104822051 104822051 G A SNP - - - - - - - - - - - - - - - tier3 233 2 0.85 222 88 28.39 0 0 NA 327733 TCGA-AB-2992 AML08 6 118998466 118998466 T C SNP C6orf204 NM_001042475.1 human genbank 54_36p -1 validated intronic c.233-4294 e3-4294 0.111 - - - no_errors tier3 696 10 1.42 754 345 31.39 2 0 0 327733 TCGA-AB-2992 AML08 6 119667266 119667266 T C SNP MAN1A1 NM_005907.2 human genbank 54_36p -1 reviewed intronic c.701-2299 e3-2299 0.243 - - - no_errors tier3 174 3 1.69 207 102 33.01 0 0 0 327733 TCGA-AB-2992 AML08 6 130994203 130994203 T C SNP - - - - - - - - - - - - - - - tier3 235 2 0.84 254 121 32.27 0 0 NA 327733 TCGA-AB-2992 AML08 6 138957094 138957094 C G SNP NHSL1 ENST00000342260 human ensembl 54_36p -1 known 5_prime_flanking_region c.-22353 NULL 0 - - - no_errors tier3 625 5 0.79 461 192 29.36 0 0 NA 327733 TCGA-AB-2992 AML08 6 164162124 164162124 T C SNP ENSG00000222470 ENST00000410538 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19459 NULL 0.108 - - - no_errors tier3 600 12 1.96 301 178 37.08 0 0 NA 327733 TCGA-AB-2992 AML08 6 166808983 166808983 G A SNP RPS6KA2 NM_001006932.1 human genbank 54_36p -1 reviewed intronic c.932-5600 e12-5600 0 - - - no_errors tier3 630 20 3.05 275 133 31.97 0 0 0 327733 TCGA-AB-2992 AML08 6 168252899 168252899 C T SNP FRMD1 NM_024919.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-30276 NULL 0 - - - no_errors tier3 1020 14 1.35 306 195 38.92 0 0 NA 327733 TCGA-AB-2992 AML08 6 168383068 168383068 C T SNP ENSG00000214211 ENST00000397819 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*47368 NULL 0.004 - - - no_coding_region:pseudogene tier3 381 5 1.29 261 188 41.87 0 0 NA 327733 TCGA-AB-2992 AML08 7 20859896 20859896 A T SNP ENSG00000210258 ENST00000387523 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-34680 NULL 0.004 - - - pseudogene tier2 65 0 0 66 30 31.25 0 0 NA 327733 TCGA-AB-2992 AML08 7 30767172 30767172 C T SNP C7orf67 NM_032222.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-10463 NULL 0 - - - no_errors tier3 1440 9 0.62 430 239 35.72 0 0 NA 327733 TCGA-AB-2992 AML08 7 36069244 36069244 G A SNP PP13004 XM_001724805.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-16124 NULL 0 - - - no_errors tier3 710 19 2.6 526 255 32.65 0 0 NA 327733 TCGA-AB-2992 AML08 7 55195295 55195295 C T SNP EGFR NM_005228.3 human genbank 54_36p 1 reviewed intronic c.1299-31 e12-31 0.006 - - - no_errors tier3 501 3 0.59 361 150 29.3 0 0 NA 327733 TCGA-AB-2992 AML08 7 55226725 55226725 C T SNP EGFR NM_005228.3 human genbank 54_36p 1 reviewed intronic c.2470-181 e21-181 0.005 - - - no_errors tier3 953 9 0.93 611 260 29.85 0 0 NA 327733 TCGA-AB-2992 AML08 7 83162580 83162580 G T SNP SEMA3E NM_012431.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-46786 NULL 0.001 - - - no_errors tier3 717 9 1.24 685 357 34.26 0 0 NA 327733 TCGA-AB-2992 AML08 7 83855657 83855657 G A SNP - - - - - - - - - - - - - - - tier3 487 13 2.6 372 182 32.85 0 0 NA 327733 TCGA-AB-2992 AML08 7 88243593 88243593 A T SNP ZNF804B NM_181646.2 human genbank 54_36p 1 provisional intronic c.108+16259 e1+16259 0.002 - - - no_errors tier3 1184 17 1.41 849 274 24.38 0 0 NA 327733 TCGA-AB-2992 AML08 7 100492733 100492733 A G SNP TRIM56 NM_030961.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-24581 NULL 0.001 - - - no_errors tier3 2800 61 2.13 885 416 31.95 0 0 NA 327733 TCGA-AB-2992 AML08 7 106734426 106734426 T C SNP COG5 NM_006348.2 human genbank 54_36p -1 validated intronic c.1202-8399 e12-8399 0.016 - - - no_errors tier3 1242 11 0.88 762 313 29.09 4 2 33.33 327733 TCGA-AB-2992 AML08 7 109695862 109695862 C T SNP - - - - - - - - - - - - - - - tier3 1427 20 1.38 1001 478 32.3 0 0 NA 327733 TCGA-AB-2992 AML08 7 113901720 113901720 G T SNP FOXP2 NM_148898.2 human genbank 54_36p 1 reviewed intronic c.168+47750 e1+47750 0.002 - - - no_errors tier3 896 2 0.22 748 81 9.77 0 0 NA 327733 TCGA-AB-2992 AML08 7 124313252 124313252 T C SNP POT1 NM_015450.1 human genbank 54_36p -1 reviewed intronic c.124+6304 e2+6304 0.002 - - - no_errors tier3 189 2 1.04 409 199 32.73 0 0 0 327733 TCGA-AB-2992 AML08 7 130011862 130011862 C T SNP TSGA13 NM_052933.2 human genbank 54_36p -1 provisional intronic c.387+2671 e4+2671 0 - - - no_errors tier3 1109 16 1.42 358 171 32.33 0 0 NA 327733 TCGA-AB-2992 AML08 7 152921718 152921718 A C SNP - - - - - - - - - - - - - - - tier3 368 9 2.38 351 165 31.91 0 0 NA 327733 TCGA-AB-2992 AML08 7 153054151 153054151 G A SNP FLJ16734 XR_040945.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-38161 NULL 0 - - - no_errors tier3 511 9 1.73 475 212 30.81 0 0 NA 327733 TCGA-AB-2992 AML08 8 3170980 3170980 G C SNP LOC100133607 XM_001713683.1 human genbank 54_36p 1 model 3_prime_untranslated_region c.*2371 NULL 0.003 - - - no_start_codon:pseudogene tier2 851 18 2.07 697 400 36.46 0 0 NA 327733 TCGA-AB-2992 AML08 8 9812481 9812481 G A SNP MIRN124-1 ENST00000385275 human ensembl 54_36p -1 known 5_prime_flanking_region c.-14089 NULL 0 - - - no_errors tier3 1048 18 1.69 411 197 32.35 0 0 NA 327733 TCGA-AB-2992 AML08 8 34712682 34712682 G A SNP - - - - - - - - - - - - - - - tier3 558 2 0.36 493 203 29.17 0 0 NA 327733 TCGA-AB-2992 AML08 8 35006121 35006121 C A SNP - - - - - - - - - - - - - - - tier3 649 10 1.52 596 234 28.16 0 0 NA 327733 TCGA-AB-2992 AML08 8 36074043 36074043 A T SNP - - - - - - - - - - - - - - - tier3 1911 16 0.83 1127 529 31.93 0 0 NA 327733 TCGA-AB-2992 AML08 8 40835340 40835340 G T SNP ZMAT4 NM_024645.1 human genbank 54_36p -1 validated intronic c.1-32984 e1-32984 0 - - - no_errors tier3 2174 45 2.03 1420 682 32.45 0 0 NA 327733 TCGA-AB-2992 AML08 8 48072905 48072905 C T SNP ENSG00000222099 ENST00000410167 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*25916 NULL 0.006 - - - no_errors tier3 689 16 2.27 663 339 33.83 0 0 NA 327733 TCGA-AB-2992 AML08 8 49342668 49342668 G A SNP ENSG00000210964 ENST00000388229 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*40375 NULL 0.092 - - - pseudogene tier3 463 13 2.73 285 142 33.26 0 0 NA 327733 TCGA-AB-2992 AML08 8 82671313 82671313 A C SNP ENSG00000173078 ENST00000311489 human ensembl 54_36p -1 known 3_prime_flanking_region c.*30367 NULL 0 - - - no_stop_codon tier3 1043 9 0.86 539 230 29.91 0 0 NA 327733 TCGA-AB-2992 AML08 8 90683714 90683714 G A SNP - - - - - - - - - - - - - - - tier3 756 13 1.69 673 260 27.87 1 0 0 327733 TCGA-AB-2992 AML08 8 99671612 99671612 T C SNP STK3 NM_006281.2 human genbank 54_36p -1 validated intronic c.822+5824 e7+5824 0 - - - no_errors tier3 531 18 3.27 709 370 34.26 1 2 66.67 327733 TCGA-AB-2992 AML08 8 114726416 114726416 T G SNP - - - - - - - - - - - - - - - tier3 558 6 1.06 421 188 30.87 0 0 NA 327733 TCGA-AB-2992 AML08 8 116335356 116335356 C A SNP - - - - - - - - - - - - - - - tier2 1399 12 0.85 1094 524 32.39 0 0 NA 327733 TCGA-AB-2992 AML08 8 127467234 127467234 G C SNP - - - - - - - - - - - - - - - tier3 1284 22 1.68 958 526 35.4 0 0 NA 327733 TCGA-AB-2992 AML08 8 142568221 142568221 C T SNP FLJ43860 NM_207414.2 human genbank 54_36p -1 validated intronic c.698-336 e6-336 0 - - - pseudogene tier3 159 4 2.45 91 27 22.88 0 0 NA 327733 TCGA-AB-2992 AML08 9 10738915 10738915 G A SNP ENSG00000219748 ENST00000401476 human ensembl 54_36p 1 known 5_prime_flanking_region c.-28442 NULL 0 - - - no_coding_region:pseudogene tier3 802 6 0.74 454 221 32.74 0 0 NA 327733 TCGA-AB-2992 AML08 9 21667991 21667991 T C SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 5_prime_flanking_region c.-17184 NULL 0.009 - - - no_coding_region:pseudogene tier3 538 6 1.1 496 272 35.37 0 0 NA 327733 TCGA-AB-2992 AML08 9 22800620 22800620 G T SNP - - - - - - - - - - - - - - - tier2 909 12 1.3 722 313 30.24 0 0 NA 327733 TCGA-AB-2992 AML08 9 30040353 30040353 G A SNP - - - - - - - - - - - - - - - tier3 667 5 0.74 558 269 32.53 0 0 NA 327733 TCGA-AB-2992 AML08 9 38326083 38326083 C T SNP - - - - - - - - - - - - - - - tier3 1498 24 1.58 606 296 32.74 0 0 NA 327733 TCGA-AB-2992 AML08 9 82127935 82127935 A G SNP ENSG00000218777 ENST00000404193 human ensembl 54_36p -1 known 3_prime_flanking_region c.*33829 NULL 0.003 - - - no_coding_region:pseudogene tier2 1588 43 2.64 926 423 31.36 0 0 NA 327733 TCGA-AB-2992 AML08 9 86997741 86997741 G A SNP ENSG00000218863 ENST00000402586 human ensembl 54_36p 1 known 3_prime_flanking_region c.*33056 NULL 0.013 - - - no_coding_region:pseudogene tier3 1255 8 0.63 905 480 34.66 0 0 NA 327733 TCGA-AB-2992 AML08 9 93627808 93627808 T A SNP ROR2 NM_004560.2 human genbank 54_36p -1 reviewed intronic c.98-49887 e2-49887 0.057 - - - no_errors tier3 1004 14 1.37 485 253 34.28 1 0 0 327733 TCGA-AB-2992 AML08 9 108464419 108464419 G A SNP LOC644620 XM_001718226.1 human genbank 54_36p 1 model intronic c.89-10552 e2-10552 0 - - - no_errors tier3 1840 31 1.66 1191 535 31 0 0 NA 327733 TCGA-AB-2992 AML08 9 117461071 117461072 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 9 117610402 117610402 C A SNP - - - - - - - - - - - - - - - tier2 946 13 1.36 703 359 33.8 0 0 NA 327733 TCGA-AB-2992 AML08 9 118699373 118699373 G A SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.1890-33540 e11-33540 0.001 - - - no_errors tier3 4298 68 1.56 1520 701 31.56 0 0 NA 327733 TCGA-AB-2992 AML08 9 135531487 135531487 C T SNP SARDH NM_007101.1 human genbank 54_36p -1 reviewed intronic c.2164-4847 e17-4847 0.013 - - - no_errors tier2 456 13 2.77 187 111 37.25 0 0 0 327733 TCGA-AB-2992 AML08 10 9071093 9071093 G A SNP - - - - - - - - - - - - - - - tier3 421 7 1.63 319 160 33.4 0 0 NA 327733 TCGA-AB-2992 AML08 10 17697139 17697139 G A SNP PTPLA NM_014241.3 human genbank 54_36p -1 reviewed intronic c.257+1949 e1+1949 0.004 - - - no_errors tier3 1171 20 1.68 186 78 29.55 0 0 0 327733 TCGA-AB-2992 AML08 10 21488228 21488228 C T SNP NEBL NM_213569.2 human genbank 54_36p -1 validated intronic c.164+13090 e2+13090 0 - - - no_errors tier3 987 3 0.3 469 67 12.48 0 0 NA 327733 TCGA-AB-2992 AML08 10 21546959 21546959 C T SNP ENSG00000218822 ENST00000402780 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*21546959 NULL 1 - - - no_coding_region:pseudogene tier2 1227 17 1.37 740 348 31.96 0 0 NA 327733 TCGA-AB-2992 AML08 10 24217016 24217016 C T SNP KIAA1217 NM_001098500.1 human genbank 54_36p 1 validated intronic c.1-119144 e1-119144 0.101 - - - no_errors tier3 505 9 1.75 784 347 30.68 0 0 NA 327733 TCGA-AB-2992 AML08 10 29656863 29656863 G A SNP LYZL1 NM_032517.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*16869 NULL 0.002 - - - no_errors tier3 1464 28 1.88 1129 483 29.94 0 0 NA 327733 TCGA-AB-2992 AML08 10 42475841 42475841 T A SNP LOC728064 XR_015196.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - no_errors tier3 897 16 1.75 797 363 31.27 0 0 NA 327733 TCGA-AB-2992 AML08 10 47168808 47168808 G C SNP ANTXRL ENST00000354871 human ensembl 54_36p 1 known intronic c.1411-2033 e17-2033 0.005 - - - no_errors tier2 1177 25 2.08 475 253 34.75 0 0 0 327733 TCGA-AB-2992 AML08 10 57469976 57469976 G T SNP - - - - - - - - - - - - - - - tier3 284 2 0.7 393 151 27.76 0 0 NA 327733 TCGA-AB-2992 AML08 10 57962239 57962239 C T SNP - - - - - - - - - - - - - - - tier3 1595 18 1.12 970 508 34.37 0 0 NA 327733 TCGA-AB-2992 AML08 10 58535716 58535716 A G SNP - - - - - - - - - - - - - - - tier3 1485 23 1.53 754 397 34.49 0 0 NA 327733 TCGA-AB-2992 AML08 10 65287697 65287697 C T SNP ENSG00000213609 ENST00000395235 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*44513 NULL 0.028 - - - no_coding_region:pseudogene tier3 482 2 0.41 538 219 28.93 0 0 NA 327733 TCGA-AB-2992 AML08 10 79962500 79962500 A C SNP LOC100132987 XM_001716093.1 human genbank 54_36p 1 model intronic c.150+3923 e2+3923 0 - - - no_errors tier3 1477 12 0.81 890 448 33.48 0 0 NA 327733 TCGA-AB-2992 AML08 10 82479901 82479901 T C SNP ENSG00000220228 ENST00000404154 human ensembl 54_36p -1 known 5_prime_flanking_region c.-13097 NULL 0.011 - - - no_coding_region:pseudogene tier3 783 4 0.51 736 389 34.58 0 0 NA 327733 TCGA-AB-2992 AML08 10 85935901 85935901 C T SNP PCDH21 NM_033100.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8596 NULL 0 - - - no_errors tier3 4348 63 1.43 498 287 36.38 0 0 NA 327733 TCGA-AB-2992 AML08 10 86267937 86267937 G A SNP KIAA1128 NM_018999.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*4658 NULL 0.071 - - - no_errors tier3 801 5 0.62 614 243 28.35 5 2 28.57 327733 TCGA-AB-2992 AML08 10 91339165 91339165 G A SNP PANK1 NM_148977.2 human genbank 54_36p -1 reviewed intronic c.1612-651 e6-651 0.001 - - - no_errors tier3 1419 40 2.74 778 320 29.14 1 0 0 327733 TCGA-AB-2992 AML08 10 103275622 103275622 A G SNP BTRC NM_033637.3 human genbank 54_36p 1 reviewed intronic c.557-138 e6-138 0.997 - - - no_errors tier2 838 0 0 454 64 12.36 3 0 0 327733 TCGA-AB-2992 AML08 10 103920796 103920796 G A SNP PPRC1 NM_015062.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*21020 NULL 0.003 - - - no_errors tier3 675 9 1.32 494 183 27.03 0 0 NA 327733 TCGA-AB-2992 AML08 10 106600556 106600556 C T SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.695+7949 e2+7949 0.014 - - - no_errors tier3 1413 24 1.67 1153 542 31.98 0 0 NA 327733 TCGA-AB-2992 AML08 10 106819322 106819322 G A SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.1029-20201 e6-20201 0.001 - - - no_errors tier3 1237 25 1.98 1168 490 29.55 0 0 NA 327733 TCGA-AB-2992 AML08 10 113021160 113021160 G C SNP - - - - - - - - - - - - - - - tier3 900 11 1.21 411 204 33.17 0 0 NA 327733 TCGA-AB-2992 AML08 10 119701481 119701481 A T SNP - - - - - - - - - - - - - - - tier3 698 17 2.38 482 208 30.1 0 0 NA 327733 TCGA-AB-2992 AML08 10 127011417 127011417 A G SNP - - - - - - - - - - - - - - - tier2 533 1 0.19 542 249 31.48 0 0 NA 327733 TCGA-AB-2992 AML08 10 133145342 133145342 T C SNP - - - - - - - - - - - - - - - tier3 584 13 2.18 689 331 32.45 0 0 NA 327733 TCGA-AB-2992 AML08 11 27070557 27070557 C - DEL BBOX1 NM_003986.2 human genbank 54_36p 1 reviewed intronic c.335-734 e3-734 0.08 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 11 35011047 35011047 G T SNP PDHX NM_003477.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*37752 NULL 0.002 - - - no_errors tier3 1775 36 1.99 1382 623 31.04 0 0 NA 327733 TCGA-AB-2992 AML08 11 40996597 40996597 C A SNP - - - - - - - - - - - - - - - tier3 1662 34 2 1126 499 30.67 0 0 NA 327733 TCGA-AB-2992 AML08 11 42453325 42453325 G T SNP - - - - - - - - - - - - - - - tier3 1036 12 1.15 739 367 33.12 0 0 NA 327733 TCGA-AB-2992 AML08 11 42896820 42896820 G T SNP - - - - - - - - - - - - - - - tier3 653 12 1.8 231 88 27.5 0 0 NA 327733 TCGA-AB-2992 AML08 11 63004804 63004804 T C SNP HRASLS5 NM_054108.2 human genbank 54_36p -1 provisional intronic c.375+8115 e3+8115 0.01 - - - no_errors tier3 1391 17 1.21 559 291 34.2 0 0 NA 327733 TCGA-AB-2992 AML08 11 69873641 69873641 T C SNP PPFIA1 NM_003626.2 human genbank 54_36p 1 reviewed intronic c.2163+1467 e15+1467 0.076 - - - no_errors tier3 542 8 1.45 337 211 38.5 11 2 15.38 327733 TCGA-AB-2992 AML08 11 81572152 81572152 C T SNP - - - - - - - - - - - - - - - tier3 1584 39 2.4 322 162 33.4 0 0 NA 327733 TCGA-AB-2992 AML08 11 92296943 92296943 G A SNP MTNR1B NM_005959.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45597 NULL 0 - - - no_errors tier2 1360 23 1.66 589 223 27.46 0 0 NA 327733 TCGA-AB-2992 AML08 11 98843882 98843882 C T SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-88204 e1-88204 0.276 - - - no_errors tier3 260 3 1.14 571 245 30.02 0 0 NA 327733 TCGA-AB-2992 AML08 11 98920798 98920798 G A SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-11288 e1-11288 0.008 - - - no_errors tier3 691 7 1 552 308 35.77 0 0 NA 327733 TCGA-AB-2992 AML08 11 99010906 99010906 T G SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.55+78696 e1+78696 0 - - - no_errors tier3 542 6 1.09 583 267 31.34 0 0 NA 327733 TCGA-AB-2992 AML08 11 111050482 111050482 G T SNP SIK2 NM_015191.1 human genbank 54_36p 1 validated intronic c.317-13453 e4-13453 0.067 - - - no_errors tier2 617 8 1.28 725 293 28.78 2 4 66.67 327733 TCGA-AB-2992 AML08 11 112412802 112412802 G T SNP NCAM1 NM_181351.5 human genbank 54_36p 1 validated intronic c.53+75206 e1+75206 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1405 29 2.02 1300 645 33.13 0 0 0 327733 TCGA-AB-2992 AML08 11 121465207 121465207 G A SNP BLID NM_001001786.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*26307 NULL 0.01 - - - no_errors tier3 2131 26 1.2 1767 829 31.93 1 0 0 327733 TCGA-AB-2992 AML08 11 122337580 122337580 C T SNP ENSG00000211401 ENST00000388666 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41934 NULL 0 - - - pseudogene tier2 1246 12 0.95 659 281 29.86 0 0 NA 327733 TCGA-AB-2992 AML08 12 1055619 1055619 C T SNP ERC1 NM_178040.2 human genbank 54_36p 1 reviewed intronic c.670-6972 e2-6972 0.004 - - - no_errors tier2 220 3 1.35 147 63 30 1 0 0 327733 TCGA-AB-2992 AML08 12 17831141 17831141 C T SNP - - - - - - - - - - - - - - - tier3 2521 20 0.79 1279 609 32.26 0 0 NA 327733 TCGA-AB-2992 AML08 12 22934873 22934873 C T SNP - - - - - - - - - - - - - - - tier3 856 12 1.38 826 329 28.48 0 0 NA 327733 TCGA-AB-2992 AML08 12 24178108 24178108 T A SNP SOX5 NM_152989.4 human genbank 54_36p -1 reviewed intronic c.1+143309 e0+143309 0.718 - - - no_errors tier2 1663 14 0.83 1097 490 30.86 0 0 NA 327733 TCGA-AB-2992 AML08 12 25023099 25023099 C T SNP BCAT1 NM_005504.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29966 NULL 0.122 - - - no_errors tier3 1033 26 2.45 902 400 30.7 0 0 NA 327733 TCGA-AB-2992 AML08 12 38656545 38656545 C T SNP SLC2A13 NM_052885.3 human genbank 54_36p -1 validated intronic c.869-25111 e4-25111 0.001 - - - no_errors tier3 476 0 0 443 208 31.95 0 0 0 327733 TCGA-AB-2992 AML08 12 42124242 42124242 C T SNP ADAMTS20 NM_025003.3 human genbank 54_36p -1 validated intronic c.2198-289 e16-289 0.001 - - - no_errors tier3 312 8 2.5 257 163 38.81 0 0 NA 327733 TCGA-AB-2992 AML08 12 85622933 85622933 C A SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+22184 e0+22184 0.009 - - - no_errors tier2 891 8 0.89 561 268 32.29 0 0 NA 327733 TCGA-AB-2992 AML08 12 90498699 90498699 C T SNP - - - - - - - - - - - - - - - tier3 185 2 1.06 244 93 27.6 0 0 NA 327733 TCGA-AB-2992 AML08 12 93450563 93450563 A G SNP LOC283398 XM_208658.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-13578 NULL 0 - - - no_errors tier3 2224 33 1.46 693 370 34.81 0 0 NA 327733 TCGA-AB-2992 AML08 12 104407904 104407904 T C SNP - - - - - - - - - - - - - - - tier3 1336 8 0.6 1183 594 33.41 0 0 NA 327733 TCGA-AB-2992 AML08 12 108433363 108433363 T G SNP UBE3B NM_130466.2 human genbank 54_36p 1 reviewed intronic c.1857-29 e16-29 0 - - - no_errors tier3 1278 12 0.93 856 439 33.9 0 0 0 327733 TCGA-AB-2992 AML08 12 114108293 114108293 C A SNP - - - - - - - - - - - - - - - tier2 2785 35 1.24 1782 869 32.78 0 0 NA 327733 TCGA-AB-2992 AML08 12 115217185 115217185 G A SNP MED13L NM_015335.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-17866 NULL 0.051 - - - no_errors tier3 743 12 1.59 230 93 28.79 0 0 NA 327733 TCGA-AB-2992 AML08 12 116263523 116263523 C A SNP NOS1 NM_000620.2 human genbank 54_36p -1 validated intronic c.1-9846 e1-9846 0 - - - no_errors tier3 1592 30 1.85 383 189 33.04 0 0 NA 327733 TCGA-AB-2992 AML08 12 126360323 126360323 A G SNP - - - - - - - - - - - - - - - tier3 1040 12 1.14 604 265 30.49 0 0 NA 327733 TCGA-AB-2992 AML08 12 126787218 126787218 G A SNP - - - - - - - - - - - - - - - tier3 924 18 1.91 500 242 32.61 0 0 NA 327733 TCGA-AB-2992 AML08 13 35346313 35346313 C T SNP DCLK1 NM_004734.3 human genbank 54_36p -1 validated intronic c.824-2836 e4-2836 0 - - - no_errors tier2 482 6 1.22 360 138 27.71 0 0 NA 327733 TCGA-AB-2992 AML08 13 40134781 40134781 T G SNP FOXO1 NM_002015.3 human genbank 54_36p -1 reviewed intronic c.630+2939 e1+2939 0.002 - - - no_errors tier2 361 6 1.63 140 72 33.96 4 2 33.33 327733 TCGA-AB-2992 AML08 13 45764894 45764894 A G SNP C13orf18 NM_025113.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*50627 NULL 0 - - - no_errors tier3 1274 26 2 1002 483 32.5 0 0 NA 327733 TCGA-AB-2992 AML08 13 52948257 52948257 G T SNP - - - - - - - - - - - - - - - tier3 345 3 0.86 445 157 26.08 0 0 NA 327733 TCGA-AB-2992 AML08 13 55550461 55550462 - T INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 13 61355826 61355826 A G SNP - - - - - - - - - - - - - - - tier3 159 2 1.24 182 81 30.8 0 0 NA 327733 TCGA-AB-2992 AML08 13 82096803 82096803 G T SNP - - - - - - - - - - - - - - - tier3 460 4 0.86 730 212 22.51 0 0 NA 327733 TCGA-AB-2992 AML08 13 84657522 84657522 A T SNP - - - - - - - - - - - - - - - tier3 182 3 1.62 113 64 36.16 0 0 NA 327733 TCGA-AB-2992 AML08 13 101068378 101068378 A G SNP ITGBL1 NM_004791.1 human genbank 54_36p 1 provisional intronic c.1015+19728 e7+19728 0.012 - - - no_errors tier3 622 8 1.27 652 305 31.84 0 0 NA 327733 TCGA-AB-2992 AML08 13 101222655 101222655 C T SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.424-45494 e4-45494 0.001 - - - no_errors tier3 786 7 0.88 1020 426 29.46 0 0 NA 327733 TCGA-AB-2992 AML08 13 104479032 104479033 TT - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 13 106687738 106687738 T C SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.916-26634 e2-26634 0 - - - no_errors tier3 380 3 0.78 399 198 33.17 0 0 NA 327733 TCGA-AB-2992 AML08 14 19888609 19888609 A T SNP PARP2 NM_005484.1 human genbank 54_36p 1 reviewed nonsense c.448 p.R150* 1 "HMMPfam_WGR,HMMSmart_SM00773" "HMMPfam_PARP_reg,superfamily_Domain of poly(ADP-ribose) polymerase,PatternScan_CPSASE_2,HMMPfam_WGR,HMMSmart_SM00773,HMMPfam_PARP,PatternScan_CASPASE_HIS,superfamily_ADP-ribosylation" - no_errors tier1 1825 33 1.78 675 336 33.14 23 1 4.17 327733 TCGA-AB-2992 AML08 14 31842279 31842279 A T SNP AKAP6 NM_004274.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-130172 NULL 0.022 - - - no_errors tier3 867 22 2.47 714 366 33.86 0 0 NA 327733 TCGA-AB-2992 AML08 14 38653960 38653960 C T SNP SIP1 NM_003616.1 human genbank 54_36p 1 validated intronic c.255+92 e2+92 0.001 - - - no_errors tier3 541 6 1.09 198 87 30.53 1 0 0 327733 TCGA-AB-2992 AML08 14 40649411 40649411 A T SNP - - - - - - - - - - - - - - - tier2 548 6 1.08 459 155 25.24 1 0 0 327733 TCGA-AB-2992 AML08 14 45908850 45908850 C A SNP - - - - - - - - - - - - - - - tier3 754 3 0.4 799 371 31.71 0 0 NA 327733 TCGA-AB-2992 AML08 14 46635498 46635498 T C SNP MDGA2 NM_182830.1 human genbank 54_36p -1 validated intronic c.301+309 e2+309 0.001 - - - no_errors tier3 316 2 0.63 526 245 31.78 0 0 NA 327733 TCGA-AB-2992 AML08 14 65023644 65023644 A G SNP FUT8 NM_178154.3 human genbank 54_36p 1 reviewed intronic c.1+31455 e0+31455 0.014 - - - no_errors tier3 679 7 1.02 438 235 34.92 3 0 0 327733 TCGA-AB-2992 AML08 14 66700365 66700365 C T SNP GPHN NM_020806.1 human genbank 54_36p 1 reviewed intronic c.1911-1267 e20-1267 0 - - - no_errors tier2 687 5 0.72 796 453 36.27 0 0 0 327733 TCGA-AB-2992 AML08 14 73928985 73928985 C T SNP ENSG00000177776 ENST00000315233 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13926 NULL 0.001 - - - no_coding_region:pseudogene tier3 1402 18 1.27 434 171 28.22 0 0 NA 327733 TCGA-AB-2992 AML08 14 79338231 79338231 T C SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2806-2977 e14-2977 0 - - - no_errors tier3 1305 11 0.84 650 281 30.18 0 0 NA 327733 TCGA-AB-2992 AML08 14 84738406 84738406 A G SNP ENSG00000222836 ENST00000410904 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13109 NULL 0 - - - no_errors tier3 1133 27 2.33 703 294 29.46 0 0 NA 327733 TCGA-AB-2992 AML08 14 89125712 89125712 T A SNP FOXN3 NM_001085471.1 human genbank 54_36p -1 reviewed intronic c.1+29413 e0+29413 0.023 - - - no_errors tier3 1078 11 1.01 431 222 33.94 4 0 0 327733 TCGA-AB-2992 AML08 15 29209554 29209554 A G SNP TRPM1 NM_002420.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-53138 NULL 0.005 - - - no_errors tier3 739 12 1.6 661 346 34.33 0 0 NA 327733 TCGA-AB-2992 AML08 15 42170453 42170453 C G SNP FRMD5 NM_032892.3 human genbank 54_36p -1 validated intronic c.102+103990 e1+103990 0.963 - - - no_errors tier2 1639 17 1.03 1272 643 33.54 0 0 NA 327733 TCGA-AB-2992 AML08 15 51583122 51583122 C A SNP WDR72 NM_182758.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*14066 NULL 0 - - - no_errors tier3 2163 36 1.64 1467 659 30.98 0 0 NA 327733 TCGA-AB-2992 AML08 15 59904821 59904821 G T SNP VPS13C NM_020821.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*29127 NULL 0.002 - - - no_errors tier3 993 14 1.39 435 238 35.36 0 0 NA 327733 TCGA-AB-2992 AML08 15 64186679 64186679 C T SNP MEGF11 NM_032445.2 human genbank 54_36p -1 validated intronic c.77-12793 e2-12793 0.001 - - - no_errors tier3 1302 28 2.11 590 303 33.85 1 0 0 327733 TCGA-AB-2992 AML08 15 72306941 72306941 C A SNP STRA6 NM_022369.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25280 NULL 0.089 - - - no_errors tier3 933 28 2.91 437 207 32.14 0 0 NA 327733 TCGA-AB-2992 AML08 15 84591961 84591961 G T SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated silent c.444 p.L148 0.993 superfamily_ARM repeat "HMMPfam_Peptidase_M14,superfamily_ARM repeat,superfamily_Zn-dependent exopeptidases" - no_errors tier1 1386 29 2.05 659 287 30.27 NA 327733 TCGA-AB-2992 AML08 15 85028463 85028463 A T SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.3083+9792 e21+9792 0 - - - no_errors tier3 543 9 1.63 453 194 29.98 0 0 NA 327733 TCGA-AB-2992 AML08 15 90885900 90885900 G A SNP C15orf32 NM_153040.2 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*41266 NULL 0.004 - - - no_errors tier3 1122 18 1.57 646 338 34.25 0 0 NA 327733 TCGA-AB-2992 AML08 15 98045240 98045240 C T SNP MEF2A NM_005587.1 human genbank 54_36p 1 validated intronic c.677-2729 e6-2729 0.001 - - - no_errors tier3 1490 24 1.58 885 472 34.73 4 0 0 327733 TCGA-AB-2992 AML08 15 98641107 98641107 C T SNP ADAMTS17 NM_139057.2 human genbank 54_36p -1 reviewed intronic c.617-1978 e4-1978 0.051 - - - no_errors tier3 763 14 1.8 497 245 33.02 0 0 NA 327733 TCGA-AB-2992 AML08 16 61309312 61309312 A G SNP - - - - - - - - - - - - - - - tier3 972 14 1.42 167 66 28.33 0 0 NA 327733 TCGA-AB-2992 AML08 16 62360726 62360726 G A SNP - - - - - - - - - - - - - - - tier3 1187 21 1.74 821 367 30.89 0 0 NA 327733 TCGA-AB-2992 AML08 16 63699738 63699738 A G SNP CDH11 NM_001797.2 human genbank 54_36p -1 reviewed intronic c.1+13546 e0+13546 0.883 - - - no_errors tier3 1017 9 0.88 359 187 34.25 0 0 0 327733 TCGA-AB-2992 AML08 16 66020178 66020178 T A SNP ZDHHC1 NM_013304.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20999 NULL 0.001 - - - no_errors tier2 859 20 2.27 160 76 31.93 2 0 0 327733 TCGA-AB-2992 AML08 16 69202257 69202257 G A SNP IL34 NM_152456.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-36095 NULL 0 - - - no_errors tier2 1545 19 1.21 441 237 34.96 0 0 NA 327733 TCGA-AB-2992 AML08 16 75060797 75060797 G T SNP CNTNAP4 NM_138994.3 human genbank 54_36p 1 validated intronic c.1436+1876 e9+1876 0.005 - - - no_errors tier3 886 13 1.45 556 268 32.48 0 0 NA 327733 TCGA-AB-2992 AML08 16 80162833 80162833 C T SNP CMIP NM_198390.2 human genbank 54_36p 1 validated intronic c.199-35840 e2-35840 0.09 - - - no_errors tier3 1587 23 1.43 1209 444 26.86 7 15 68.18 327733 TCGA-AB-2992 AML08 16 84988071 84988071 C T SNP - - - - - - - - - - - - - - - tier2 1762 30 1.67 740 370 33.33 0 0 NA 327733 TCGA-AB-2992 AML08 16 88639429 88639429 G A SNP uc002fql.2 ENST00000409768 human ensembl 54_36p -1 known intronic c.1-897 e1-897 0 - - - no_errors tier3 206 3 1.44 82 35 29.91 0 0 NA 327733 TCGA-AB-2992 AML08 17 671303 671303 G A SNP NXN NM_022463.3 human genbank 54_36p -1 validated intronic c.713+1044 e4+1044 0.001 - - - no_errors tier3 1463 12 0.81 485 210 30.22 0 0 NA 327733 TCGA-AB-2992 AML08 17 11805811 11805811 G A SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed intronic c.12844-98 e68-98 0 - - - no_errors tier3 835 8 0.95 967 449 31.71 0 0 NA 327733 TCGA-AB-2992 AML08 17 43799484 43799484 T C SNP SKAP1 NM_003726.1 human genbank 54_36p -1 reviewed intronic c.153-3309 e3-3309 0.019 - - - no_errors tier3 982 9 0.91 592 286 32.54 1 0 0 327733 TCGA-AB-2992 AML08 17 52483492 52483492 C - DEL AKAP1 NM_003488.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-54333 NULL 0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 17 74851273 74851273 C T SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1-35772 e1-35772 0 - - - no_errors tier3 2470 55 2.18 1664 866 34.22 0 0 NA 327733 TCGA-AB-2992 AML08 18 4152824 4152824 G A SNP - - - - - - - - - - - - - - - tier2 1144 10 0.87 974 488 33.38 0 0 NA 327733 TCGA-AB-2992 AML08 18 48294430 48294430 T - DEL DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.91+173184 e1+173184 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 327733 TCGA-AB-2992 AML08 18 48947419 48947419 C A SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.1418+9539 e8+9539 0 - - - no_errors tier3 437 4 0.91 383 138 26.39 0 0 NA 327733 TCGA-AB-2992 AML08 18 50250416 50250416 A G SNP - - - - - - - - - - - - - - - tier3 951 13 1.35 471 280 37.28 0 0 NA 327733 TCGA-AB-2992 AML08 18 57279341 57279341 G C SNP CDH20 NM_031891.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29426 NULL 0.019 - - - no_errors tier3 352 1 0.28 359 134 27.18 0 0 NA 327733 TCGA-AB-2992 AML08 18 59103633 59103633 G A SNP BCL2 NM_000633.2 human genbank 54_36p -1 reviewed intronic c.585+32662 e1+32662 0 - - - no_errors tier3 883 21 2.32 453 243 34.91 20 1 4.76 327733 TCGA-AB-2992 AML08 18 59709885 59709885 A G SNP SERPINB2 NM_002575.1 human genbank 54_36p 1 validated intronic c.168+59 e1+59 0 - - - no_errors tier3 943 6 0.63 836 406 32.69 3 0 0 327733 TCGA-AB-2992 AML08 19 3695040 3695040 G T SNP TJP3 NM_014428.1 human genbank 54_36p 1 provisional splice_region c.2038+8 e14+8 0 - - - no_errors tier3 546 6 1.09 115 57 33.14 0 0 NA 327733 TCGA-AB-2992 AML08 19 4305113 4305113 C T SNP MPND NM_032868.3 human genbank 54_36p 1 provisional missense c.736 p.R246C 1 NULL "HMMPfam_Mov34,superfamily_JAB1/MPN domain" - no_errors tier1 1609 35 2.13 157 103 39.62 26 2 7.14 327733 TCGA-AB-2992 AML08 19 11729853 11729853 C T SNP ZNF441 NM_152355.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21988 NULL 0.224 - - - no_errors tier3 485 5 1.02 130 66 33.67 0 0 NA 327733 TCGA-AB-2992 AML08 19 22532885 22532885 C T SNP LOC440518 XR_041921.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.492 - - - no_errors tier3 488 7 1.41 623 280 30.94 0 0 0 327733 TCGA-AB-2992 AML08 19 33834355 33834355 A G SNP - - - - - - - - - - - - - - - tier3 1123 22 1.92 932 427 31.42 0 0 NA 327733 TCGA-AB-2992 AML08 19 56172720 56172720 G A SNP KLK7 NM_005046.2 human genbank 54_36p -1 reviewed nonsense c.646 p.Q216* 0.616 "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases" "HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER" - no_errors tier1 224 8 3.45 118 73 38.22 NA 327733 TCGA-AB-2992 AML08 20 9638357 9638357 A G SNP PAK7 NM_020341.3 human genbank 54_36p -1 reviewed intronic c.1+1577 e0+1577 0.002 - - - no_errors tier2 1001 11 1.09 556 296 34.74 0 0 NA 327733 TCGA-AB-2992 AML08 20 19610539 19610539 A G SNP SLC24A3 NM_020689.3 human genbank 54_36p 1 validated missense c.805 p.T269A 0.998 NULL HMMPfam_Na_Ca_ex - no_errors tier1 2254 18 0.79 398 196 33 3 1 25 327733 TCGA-AB-2992 AML08 20 20309663 20309663 G T SNP LOC100131342 XM_001725765.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16011 NULL 0 - - - no_errors tier3 487 8 1.62 255 97 27.56 1 0 0 327733 TCGA-AB-2992 AML08 20 41237198 41237198 T G SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.88+14502 e1+14502 0 - - - no_errors tier3 853 16 1.84 467 176 27.29 0 0 NA 327733 TCGA-AB-2992 AML08 20 53973454 53973454 G T SNP CBLN4 NM_080617.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*33566 NULL 0.053 - - - no_errors tier3 862 8 0.92 904 409 31.15 0 0 NA 327733 TCGA-AB-2992 AML08 20 56107971 56107971 C T SNP ENSG00000221385 ENST00000408458 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*31902 NULL 0.002 - - - no_errors tier3 1522 15 0.98 874 356 28.92 0 0 NA 327733 TCGA-AB-2992 AML08 20 57298257 57298257 G A SNP EDN3 NM_000114.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11006 NULL 0.001 - - - no_errors tier3 1067 11 1.02 345 156 31.14 0 0 NA 327733 TCGA-AB-2992 AML08 20 58308979 58308979 G A SNP LOC100131710 XM_001716744.1 human genbank 54_36p 1 model intronic c.122-12784 e3-12784 0 - - - no_errors tier3 1873 30 1.58 1418 703 33.13 3 0 0 327733 TCGA-AB-2992 AML08 20 62100760 62100760 G C SNP PRPF6 NM_012469.3 human genbank 54_36p 1 reviewed intronic c.772-82 e7-82 0.022 - - - no_errors tier3 815 10 1.21 323 138 29.93 4 1 20 327733 TCGA-AB-2992 AML08 21 29921855 29921855 T C SNP GRIK1 NM_000830.3 human genbank 54_36p -1 reviewed intronic c.1098+15162 e7+15162 0 - - - no_errors tier3 803 7 0.86 478 241 33.52 0 0 0 327733 TCGA-AB-2992 AML08 22 19691825 19691825 C A SNP P2RX6 NM_005446.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-7639 NULL 0 - - - no_errors tier3 1152 15 1.29 188 114 37.75 0 1 100 327733 TCGA-AB-2992 AML08 22 39048080 39048080 G A SNP TNRC6B NM_015088.1 human genbank 54_36p 1 validated intronic c.4785-724 e21-724 0 - - - no_errors tier3 2245 26 1.14 1243 577 31.67 11 0 0 327733 TCGA-AB-2992 AML08 22 47765933 47765933 C T SNP - - - - - - - - - - - - - - - tier3 2989 58 1.9 1032 411 28.36 0 0 NA 933124 TCGA-AB-2993 AML01 X 4565458 4565458 T C SNP - - - - - - - - - - - - - - - tier3 1731 267 13.36 470 355 42.77 0 0 NA 933124 TCGA-AB-2993 AML01 X 5661876 5661876 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 X 6154028 6154028 A G SNP NLGN4X NM_020742.2 human genbank 54_36p -1 reviewed intronic c.1+1702 e0+1702 0.994 - - - no_errors tier2 421 63 12.99 94 75 44.38 0 0 NA 933124 TCGA-AB-2993 AML01 X 6272915 6272915 G T SNP ENSG00000217694 ENST00000405313 human ensembl 54_36p -1 known 3_prime_flanking_region c.*36600 NULL 0.032 - - - no_coding_region:pseudogene tier3 1810 250 12.12 626 424 40.38 0 0 NA 933124 TCGA-AB-2993 AML01 X 6998334 6998334 A G SNP HDHD1A NM_012080.1 human genbank 54_36p -1 validated intronic c.468+6927 e3+6927 0.004 - - - no_errors tier3 4235 3 0.07 3126 1 0.03 5 0 0 933124 TCGA-AB-2993 AML01 X 12373168 12373168 C G SNP FRMPD4 NM_014728.2 human genbank 54_36p 1 validated intronic c.42-53552 e2-53552 0 - - - no_errors tier2 1899 289 13.2 957 895 48.12 0 0 NA 933124 TCGA-AB-2993 AML01 X 12406196 12406196 G T SNP FRMPD4 NM_014728.2 human genbank 54_36p 1 validated intronic c.42-20524 e2-20524 0 - - - no_errors tier3 780 162 17.18 650 629 49.1 0 0 NA 933124 TCGA-AB-2993 AML01 X 14461078 14461078 T - DEL GLRA2 NM_002063.1 human genbank 54_36p 1 validated intronic c.202+663 e2+663 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 X 19646812 19646812 C T SNP SH3KBP1 NM_031892.2 human genbank 54_36p -1 validated intronic c.287-11789 e4-11789 0 - - - no_errors tier2 1926 388 16.66 1157 967 45.23 5 0 0 933124 TCGA-AB-2993 AML01 X 34224266 34224266 A G SNP - - - - - - - - - - - - - - - tier3 2185 388 15.07 482 431 47.16 0 0 NA 933124 TCGA-AB-2993 AML01 X 42622444 42622444 A C SNP - - - - - - - - - - - - - - - tier2 1516 269 15.04 289 290 50 0 0 NA 933124 TCGA-AB-2993 AML01 X 46583110 46583110 C T SNP RP2 NM_006915.2 human genbank 54_36p 1 reviewed intronic c.102+1529 e1+1529 0.003 - - - no_errors tier3 750 121 13.86 342 162 32.08 8 0 0 933124 TCGA-AB-2993 AML01 X 67382982 67382982 G T SNP OPHN1 NM_002547.2 human genbank 54_36p -1 reviewed intronic c.385-11827 e5-11827 0.01 - - - no_errors tier3 1429 229 13.81 612 500 44.72 0 0 0 933124 TCGA-AB-2993 AML01 X 81473655 81473655 A T SNP - - - - - - - - - - - - - - - tier3 864 118 12.02 328 260 44.07 0 0 NA 933124 TCGA-AB-2993 AML01 X 94805832 94805832 A G SNP ENSG00000220889 ENST00000405817 human ensembl 54_36p -1 known 3_prime_flanking_region c.*14943 NULL 0.003 - - - no_coding_region:pseudogene tier3 1668 274 14.09 586 591 50.04 0 0 NA 933124 TCGA-AB-2993 AML01 X 98819620 98819620 G A SNP ENSG00000215070 ENST00000399535 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*41389 NULL 0 - - - no_coding_region:pseudogene tier3 3100 494 13.74 1097 876 44.09 0 0 NA 933124 TCGA-AB-2993 AML01 X 100063990 100063990 C T SNP XKRX NM_212559.1 human genbank 54_36p -1 provisional intronic c.643+448 e2+448 0.089 - - - no_errors tier3 1592 210 11.63 351 329 48.31 0 0 NA 933124 TCGA-AB-2993 AML01 X 100781299 100781299 C A SNP ARMCX6 NM_001009584.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23033 NULL 0 - - - no_errors tier3 2231 378 14.48 1898 1428 42.88 1 0 0 933124 TCGA-AB-2993 AML01 X 103782883 103782883 A G SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.1-7349 e1-7349 0.002 - - - no_errors tier3 1765 275 13.46 405 355 46.71 0 0 NA 933124 TCGA-AB-2993 AML01 X 104572042 104572042 G T SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.698-42919 e5-42919 0.067 - - - no_errors tier3 2744 1 0.04 1710 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 X 114186799 114186799 C G SNP IL13RA2 NM_000640.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-28711 NULL 0.974 - - - no_errors tier3 3029 0 0 1683 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 X 121017574 121017574 A T SNP ENSG00000219462 ENST00000404341 human ensembl 54_36p -1 known 5_prime_flanking_region c.-44428 NULL 0.116 - - - no_coding_region:pseudogene tier3 2553 0 0 1196 2 0.17 0 0 NA 933124 TCGA-AB-2993 AML01 X 121382719 121382719 T A SNP - - - - - - - - - - - - - - - tier3 808 107 11.69 205 175 45.81 0 0 NA 933124 TCGA-AB-2993 AML01 X 127355500 127355500 T C SNP ENSG00000218487 ENST00000406346 human ensembl 54_36p 1 known 5_prime_flanking_region c.-47088 NULL 0.135 - - - no_coding_region:pseudogene tier3 1294 1 0.08 466 1 0.21 0 0 NA 933124 TCGA-AB-2993 AML01 X 127868848 127868848 C T SNP - - - - - - - - - - - - - - - tier3 4659 4 0.09 2290 2 0.09 0 0 NA 933124 TCGA-AB-2993 AML01 X 128453096 128453096 C A SNP SMARCA1 NM_003069.3 human genbank 54_36p -1 reviewed intronic c.1815+503 e14+503 0.006 - - - no_errors tier3 1471 200 11.97 333 196 36.98 0 0 0 933124 TCGA-AB-2993 AML01 X 130043768 130043768 A G SNP FLJ30058 NM_144967.3 human genbank 54_36p 1 validated intronic c.253+195 e1+195 0.127 - - - no_errors tier2 1277 188 12.82 393 383 49.36 0 0 NA 933124 TCGA-AB-2993 AML01 X 130987641 130987642 - A INS MST4 NM_016542.1 human genbank 54_36p 1 reviewed intronic c.42+2273_42+2272 e1+2273 0.000:0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 X 135056937 135056937 C G SNP FHL1 NM_001449.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-59321 NULL 0.629 - - - no_errors tier2 126 12 8.7 93 34 26.56 0 0 NA 933124 TCGA-AB-2993 AML01 X 147623123 147623123 C A SNP AFF2 NM_002025.2 human genbank 54_36p 1 validated intronic c.1041+71142 e3+71142 0.468 - - - no_errors tier2 1998 0 0 2532 3 0.12 2 0 0 933124 TCGA-AB-2993 AML01 X 147623124 147623124 C G SNP AFF2 NM_002025.2 human genbank 54_36p 1 validated intronic c.1041+71143 e3+71143 0.472 - - - no_errors tier2 2014 0 0 2572 1 0.04 2 0 0 933124 TCGA-AB-2993 AML01 1 2554021 2554021 C T SNP MMEL1 NM_033467.2 human genbank 54_36p -1 reviewed intronic c.1+144 e0+144 0.025 - - - no_errors tier3 264 47 15.06 94 64 40.51 0 0 NA 933124 TCGA-AB-2993 AML01 1 11965332 11965332 A G SNP MFN2 NM_014874.1 human genbank 54_36p 1 reviewed intronic c.1+574 e0+574 0 - - - no_errors tier3 1039 177 14.52 251 147 36.84 2 4 66.67 933124 TCGA-AB-2993 AML01 1 18952534 18952534 T C SNP PAX7 NM_002584.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*17414 NULL 0 - - - no_errors tier3 941 172 15.44 564 541 48.92 0 0 NA 933124 TCGA-AB-2993 AML01 1 20382629 20382629 G A SNP UBXN10 NM_152376.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-7013 NULL 0 - - - no_errors tier3 1019 182 15.15 264 266 50 0 0 NA 933124 TCGA-AB-2993 AML01 1 28395117 28395117 G A SNP ATPIF1 NM_016311.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40165 NULL 0.002 - - - no_errors tier3 3021 1 0.03 2505 1 0.04 1 0 0 933124 TCGA-AB-2993 AML01 1 30729775 30729775 G A SNP - - - - - - - - - - - - - - - tier3 659 149 18.42 258 216 45.38 0 0 NA 933124 TCGA-AB-2993 AML01 1 37094213 37094213 G A SNP GRIK3 NM_000831.3 human genbank 54_36p -1 reviewed intronic c.1105-2303 e8-2303 0 - - - no_errors tier2 834 155 15.67 472 346 42.09 0 0 NA 933124 TCGA-AB-2993 AML01 1 37145319 37145319 G C SNP GRIK3 NM_000831.3 human genbank 54_36p -1 reviewed intronic c.116-16035 e2-16035 0.002 - - - no_errors tier3 1517 273 15.23 540 509 48.43 0 0 NA 933124 TCGA-AB-2993 AML01 1 55348624 55348624 C T SNP USP24 NM_015306.1 human genbank 54_36p -1 validated intronic c.4029-117 e36-117 0 - - - no_errors tier3 1831 0 0 580 0 0 10 0 0 933124 TCGA-AB-2993 AML01 1 77738410 77738410 C A SNP AK5 NM_174858.2 human genbank 54_36p 1 reviewed intronic c.1147+13785 e10+13785 0 - - - no_errors tier3 1390 237 14.56 594 480 44.61 0 1 100 933124 TCGA-AB-2993 AML01 1 79857474 79857474 G A SNP - - - - - - - - - - - - - - - tier3 1383 191 12.12 392 251 38.98 0 0 NA 933124 TCGA-AB-2993 AML01 1 80466160 80466160 T G SNP - - - - - - - - - - - - - - - tier3 1738 1 0.06 1333 1 0.07 0 0 NA 933124 TCGA-AB-2993 AML01 1 93826068 93826068 T C SNP BCAR3 NM_003567.2 human genbank 54_36p -1 reviewed intronic c.929+1054 e4+1054 0 - - - no_errors tier2 1471 225 13.24 563 457 44.76 0 0 NA 933124 TCGA-AB-2993 AML01 1 96795533 96795533 G A SNP ENSG00000211377 ENST00000388642 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-25823 NULL 0 - - - pseudogene tier3 1834 323 14.95 838 751 47.2 0 0 NA 933124 TCGA-AB-2993 AML01 1 104112500 104112500 C A SNP AMY1C NM_001008219.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*9697 NULL 0.001 - - - no_errors tier3 864 0 0 143 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 1 106633528 106633528 G A SNP - - - - - - - - - - - - - - - tier3 849 128 13.1 108 82 42.93 0 0 NA 933124 TCGA-AB-2993 AML01 1 110367526 110367526 G A SNP AHCYL1 NM_006621.4 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*1701 NULL 0.967 - - - no_errors tier2 1114 173 13.43 435 348 44.27 39 64 62.14 933124 TCGA-AB-2993 AML01 1 113854727 113854727 G C SNP MAGI3 NM_152900.1 human genbank 54_36p 1 validated intronic c.317-38933 e2-38933 0.072 - - - no_errors tier3 1584 336 17.49 596 492 45.18 0 0 NA 933124 TCGA-AB-2993 AML01 1 115611558 115611558 T C SNP NGF NM_002506.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*18656 NULL 0 - - - no_errors tier3 1795 323 15.23 935 835 47.1 0 0 NA 933124 TCGA-AB-2993 AML01 1 166955879 166955879 A G SNP DPT NM_001937.3 human genbank 54_36p -1 reviewed intronic c.306-5671 e2-5671 0.529 - - - no_errors tier3 1783 259 12.68 827 675 44.88 0 0 NA 933124 TCGA-AB-2993 AML01 1 169734487 169734487 A T SNP BAT2D1 ENST00000392080 human ensembl 54_36p 1 known intronic c.1+12989 e0+12989 0.001 - - - no_errors tier3 1106 235 17.46 847 665 43.95 9 5 35.71 933124 TCGA-AB-2993 AML01 1 173369482 173369482 C T SNP TNN NM_022093.1 human genbank 54_36p 1 validated intronic c.3331-2122 e15-2122 0.001 - - - no_errors tier3 3928 758 16.16 1226 1037 45.78 4 0 0 933124 TCGA-AB-2993 AML01 1 175059712 175059712 C T SNP PAPPA2 NM_020318.2 human genbank 54_36p 1 validated intronic c.5203-16220 e21-16220 0.002 - - - no_errors tier3 2768 534 16.13 767 828 51.81 0 0 NA 933124 TCGA-AB-2993 AML01 1 186605739 186605739 C A SNP - - - - - - - - - - - - - - - tier3 1121 1 0.09 623 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 1 188411987 188411987 C A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional intronic c.962-15344 e6-15344 0.014 - - - no_errors tier2 1143 196 14.62 989 710 41.64 0 0 NA 933124 TCGA-AB-2993 AML01 1 209326699 209326699 G A SNP KCNH1 NM_172362.3 human genbank 54_36p -1 reviewed intronic c.439+3828 e4+3828 0.009 - - - no_errors tier3 2359 378 13.81 1213 973 44.45 0 0 NA 933124 TCGA-AB-2993 AML01 1 217678391 217678391 G C SNP LOC728510 XM_001127601.1 human genbank 54_36p -1 model intronic c.145-1253 e2-1253 0 - - - no_errors tier3 1727 284 14.11 426 349 44.97 0 0 NA 933124 TCGA-AB-2993 AML01 1 220067708 220067708 A G SNP ENSG00000200033 ENST00000363163 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9591 NULL 0.057 - - - no_errors tier3 3648 552 13.11 1081 980 47.37 0 0 NA 933124 TCGA-AB-2993 AML01 1 221714803 221714803 C T SNP - - - - - - - - - - - - - - - tier3 710 103 12.65 109 101 48.1 0 0 NA 933124 TCGA-AB-2993 AML01 1 232382467 232382467 C A SNP SLC35F3 NM_173508.2 human genbank 54_36p 1 provisional intronic c.284-51319 e3-51319 0 - - - no_errors tier3 1340 241 15.22 552 500 47.39 0 0 NA 933124 TCGA-AB-2993 AML01 1 240735204 240735204 A C SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.1+18809 e0+18809 0.128 - - - no_errors tier3 1115 215 16.17 205 161 43.99 0 0 NA 933124 TCGA-AB-2993 AML01 1 243693578 243693578 G A SNP KIF26B NM_018012.3 human genbank 54_36p 1 provisional intronic c.1166+43908 e4+43908 0.002 - - - no_errors tier3 2303 371 13.83 636 500 43.78 0 0 NA 933124 TCGA-AB-2993 AML01 2 4358173 4358173 G A SNP - - - - - - - - - - - - - - - tier3 1964 0 0 1235 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 2 6078059 6078059 G A SNP ENSG00000212983 ENST00000391666 human ensembl 54_36p 1 known 3_prime_flanking_region c.*48072 NULL 0.003 - - - no_errors tier3 2193 420 16.07 743 623 45.41 0 0 NA 933124 TCGA-AB-2993 AML01 2 14285436 14285436 T G SNP ENSG00000210748 ENST00000388013 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46761 NULL 1 - - - pseudogene tier2 3152 3 0.09 832 1 0.12 0 0 NA 933124 TCGA-AB-2993 AML01 2 19867750 19867750 C A SNP CISD1B ENST00000272235 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21741 NULL 0 - - - no_coding_region:pseudogene tier3 1913 402 17.31 719 735 50.34 0 0 NA 933124 TCGA-AB-2993 AML01 2 25317018 25317018 A - DEL DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed frame_shift_del c.2168 p.L723fs 0.999 "HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases" "HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT" - no_errors tier1 NA NA NA NA NA NA NA 933124 TCGA-AB-2993 AML01 2 29610259 29610259 G T SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.953-1773 e4-1773 0.001 - - - no_errors tier3 2155 313 12.66 1196 992 45.17 0 0 NA 933124 TCGA-AB-2993 AML01 2 45371720 45371720 G C SNP ENSG00000205054 ENST00000378479 human ensembl 54_36p -1 known 5_prime_flanking_region c.-100095 NULL 0 - - - no_errors tier3 1002 153 13.25 385 371 48.88 0 0 NA 933124 TCGA-AB-2993 AML01 2 59364713 59364713 G C SNP LOC730134 XM_001132580.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-34163 NULL 0 - - - no_errors tier3 2290 361 13.58 633 629 49.57 0 0 NA 933124 TCGA-AB-2993 AML01 2 66437367 66437367 T C SNP LOC729348 XR_015959.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-26575 NULL 0.001 - - - no_errors tier3 1690 83 4.67 1357 276 16.89 0 0 NA 933124 TCGA-AB-2993 AML01 2 77520173 77520173 A T SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+78779 e2+78779 0 - - - no_errors tier3 405 64 13.65 62 51 45.13 0 0 NA 933124 TCGA-AB-2993 AML01 2 80340878 80340878 C A SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1060-132969 e7-132969 0.003 - - - no_errors tier3 1447 205 12.39 652 359 35.47 0 0 NA 933124 TCGA-AB-2993 AML01 2 106766704 106766704 G A SNP ST6GAL2 NM_032528.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*22862 NULL 0.009 - - - no_errors tier3 2921 2 0.07 2179 2 0.09 0 0 NA 933124 TCGA-AB-2993 AML01 2 109230419 109230420 - A INS SH3RF3 NM_001099289.1 human genbank 54_36p 1 provisional intronic c.574-100143_574-100142 e2-100142 0.005:0.005 - - - no_stop_codon tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 2 109400331 109400331 G A SNP SH3RF3 NM_001099289.1 human genbank 54_36p 1 provisional intronic c.1300-2096 e5-2096 0 - - - no_stop_codon tier3 517 88 14.55 219 184 45.66 1 2 66.67 933124 TCGA-AB-2993 AML01 2 119250670 119250670 G A SNP - - - - - - - - - - - - - - - tier3 1839 3 0.16 1073 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 2 129918104 129918104 T C SNP ENSG00000208427 ENST00000385692 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*16538 NULL 0.008 - - - pseudogene tier3 830 118 12.09 225 245 50.41 0 0 NA 933124 TCGA-AB-2993 AML01 2 134580402 134580402 G T SNP MGAT5 ENST00000409645 human ensembl 54_36p 1 known 5_prime_flanking_region c.-148043 NULL 0.006 - - - no_errors tier3 1401 231 14.11 264 219 45.34 0 0 NA 933124 TCGA-AB-2993 AML01 2 139934206 139934206 G A SNP - - - - - - - - - - - - - - - tier3 1529 221 12.63 886 692 43.8 0 0 NA 933124 TCGA-AB-2993 AML01 2 143692014 143692015 - G INS ARHGAP15 NM_018460.3 human genbank 54_36p 1 validated intronic c.296+1530_296+1529 e3+1530 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 2 146514310 146514310 G T SNP - - - - - - - - - - - - - - - tier2 1159 200 14.71 387 295 43.13 0 0 NA 933124 TCGA-AB-2993 AML01 2 149054310 149054310 C T SNP - - - - - - - - - - - - - - - tier3 1201 234 16.3 503 401 43.83 0 0 NA 933124 TCGA-AB-2993 AML01 2 155081458 155081458 C T SNP - - - - - - - - - - - - - - - tier3 2135 1 0.05 2889 4 0.14 0 0 NA 933124 TCGA-AB-2993 AML01 2 163976195 163976195 G C SNP - - - - - - - - - - - - - - - tier3 944 116 10.92 56 33 36.67 0 0 NA 933124 TCGA-AB-2993 AML01 2 179184790 179184790 C T SNP TTN ENST00000375038 human ensembl 54_36p -1 known missense c.38437 p.E12813K 1 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_WD40 repeat-like,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_PPAK,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Protein kinase-like (PK-like),superfamily_WD40 repeat-like,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,HMMPfam_Pkinase,PatternScan_FGGY_KINASES_1,PatternScan_PEROXIDASE_1,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" - no_errors tier1 1975 391 16.52 817 657 44.54 49 52 51.49 933124 TCGA-AB-2993 AML01 2 184127103 184127103 C A SNP - - - - - - - - - - - - - - - tier3 1682 0 0 507 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 2 191883652 191883652 C T SNP MYO1B NM_012223.1 human genbank 54_36p 1 validated intronic c.251+14455 e2+14455 0.856 - - - no_errors tier2 1554 200 11.38 573 454 44.16 0 0 0 933124 TCGA-AB-2993 AML01 2 194259132 194259132 T C SNP - - - - - - - - - - - - - - - tier3 706 107 13.16 87 128 59.53 0 0 NA 933124 TCGA-AB-2993 AML01 2 195658613 195658613 C T SNP - - - - - - - - - - - - - - - tier3 1863 304 14.02 662 476 41.75 0 0 NA 933124 TCGA-AB-2993 AML01 2 212856235 212856235 C G SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.83-158362 e2-158362 0 - - - no_errors tier3 2012 1 0.05 1254 1 0.08 0 0 NA 933124 TCGA-AB-2993 AML01 2 214133301 214133301 T A SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1070+70242 e10+70242 0 - - - no_errors tier3 665 121 15.37 191 161 45.61 0 0 NA 933124 TCGA-AB-2993 AML01 2 236377937 236377937 C T SNP AGAP1 NM_001037131.1 human genbank 54_36p 1 validated intronic c.958-2685 e9-2685 0.003 - - - no_errors tier3 1316 168 11.31 514 381 42.33 0 0 0 933124 TCGA-AB-2993 AML01 3 1799169 1799169 A T SNP - - - - - - - - - - - - - - - tier3 2000 0 0 1479 1 0.07 0 0 NA 933124 TCGA-AB-2993 AML01 3 20956204 20956204 C T SNP - - - - - - - - - - - - - - - tier2 1678 2 0.12 2033 2 0.1 1 0 0 933124 TCGA-AB-2993 AML01 3 37458956 37458956 C - DEL ITGA9 NM_002207.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-9914 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 3 41545224 41545224 G A SNP ULK4 NM_017886.2 human genbank 54_36p -1 validated intronic c.3226+37296 e31+37296 0.002 - - - no_errors tier3 1819 1 0.05 1851 1 0.05 1 0 0 933124 TCGA-AB-2993 AML01 3 48273720 48273720 A G SNP ZNF589 NM_016089.2 human genbank 54_36p 1 validated intronic c.97-3587 e3-3587 0.107 - - - no_errors tier3 1062 149 12.28 60 92 60.53 0 1 100 933124 TCGA-AB-2993 AML01 3 49181344 49181344 T C SNP CCDC36 ENST00000296449 human ensembl 54_36p 1 known intronic c.1-29974 e1-29974 0.014 - - - no_errors tier3 787 132 14.29 287 232 44.62 0 0 NA 933124 TCGA-AB-2993 AML01 3 55314225 55314225 C A SNP - - - - - - - - - - - - - - - tier3 1782 260 12.72 415 340 44.91 0 0 NA 933124 TCGA-AB-2993 AML01 3 56748325 56748325 C T SNP ARHGEF3 NM_019555.1 human genbank 54_36p -1 reviewed intronic c.871-1902 e8-1902 0.008 - - - no_errors tier3 1570 242 13.36 398 306 43.16 1 0 0 933124 TCGA-AB-2993 AML01 3 71728586 71728586 A G SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-398364 NULL 0 - - - no_errors tier3 1759 342 16.22 538 408 42.86 2 2 50 933124 TCGA-AB-2993 AML01 3 72575849 72575850 - T INS RYBP NM_012234.4 human genbank 54_36p -1 validated intronic c.126+2487_126+2486 e1+2487 0.000:0.000 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 3 81965563 81965563 T C SNP - - - - - - - - - - - - - - - tier2 947 135 12.48 161 144 46.91 0 0 NA 933124 TCGA-AB-2993 AML01 3 82029867 82029867 C G SNP - - - - - - - - - - - - - - - tier2 1579 205 11.47 555 389 41.16 0 0 NA 933124 TCGA-AB-2993 AML01 3 86727730 86727730 C T SNP - - - - - - - - - - - - - - - tier3 1337 205 13.29 532 444 45.45 0 0 NA 933124 TCGA-AB-2993 AML01 3 116130136 116130136 A G SNP ZBTB20 NM_015642.3 human genbank 54_36p -1 provisional intronic c.1-28257 e1-28257 0.001 - - - no_errors tier2 1320 258 16.34 516 561 52.04 1 2 66.67 933124 TCGA-AB-2993 AML01 3 120886135 120886135 T A SNP POPDC2 NM_022135.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24175 NULL 0 - - - no_errors tier3 1745 250 12.53 416 368 46.94 0 0 NA 933124 TCGA-AB-2993 AML01 3 129781481 129781481 C T SNP C3orf27 NM_007354.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-6219 NULL 0.001 - - - no_errors tier3 2911 467 13.76 685 591 46.21 0 1 100 933124 TCGA-AB-2993 AML01 3 148129000 148129000 G T SNP - - - - - - - - - - - - - - - tier2 1257 203 13.82 821 514 38.13 0 0 NA 933124 TCGA-AB-2993 AML01 3 170082969 170082969 C T SNP - - - - - - - - - - - - - - - tier3 856 129 13.1 507 418 45.04 0 0 NA 933124 TCGA-AB-2993 AML01 3 179282914 179282914 G A SNP - - - - - - - - - - - - - - - tier3 1415 223 13.61 623 509 44.89 0 0 NA 933124 TCGA-AB-2993 AML01 3 199128760 199128760 A G SNP IQCG NM_032263.1 human genbank 54_36p -1 validated intronic c.727-3450 e6-3450 0.009 - - - no_errors tier3 1604 338 17.38 233 327 58.29 0 0 0 933124 TCGA-AB-2993 AML01 4 5197668 5197668 C T SNP STK32B NM_018401.1 human genbank 54_36p 1 provisional intronic c.108+5080 e2+5080 0.029 - - - no_errors tier3 1805 245 11.93 1041 862 45.23 0 0 0 933124 TCGA-AB-2993 AML01 4 7444454 7444454 C T SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.31-4462 e2-4462 0.011 - - - no_errors tier2 1053 146 12.16 729 699 48.71 0 0 NA 933124 TCGA-AB-2993 AML01 4 19220182 19220182 C A SNP - - - - - - - - - - - - - - - tier2 1399 196 12.28 251 233 47.94 0 0 NA 933124 TCGA-AB-2993 AML01 4 23737618 23737618 C T SNP - - - - - - - - - - - - - - - tier3 2152 408 15.93 1287 1067 45.27 0 0 NA 933124 TCGA-AB-2993 AML01 4 28354616 28354616 C T SNP ENSG00000210070 ENST00000387335 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*32461 NULL 0.001 - - - pseudogene tier3 1452 224 13.36 257 198 43.42 0 0 NA 933124 TCGA-AB-2993 AML01 4 29467513 29467513 A G SNP - - - - - - - - - - - - - - - tier3 1628 249 13.27 633 575 47.44 0 0 NA 933124 TCGA-AB-2993 AML01 4 39379194 39379195 - G INS UBE2K NM_005339.1 human genbank 54_36p 1 reviewed intronic c.63+2789_63+2788 e1+2789 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 4 46808012 46808012 C T SNP GABRB1 NM_000812.3 human genbank 54_36p 1 reviewed intronic c.241-50011 e4-50011 0.001 - - - no_errors tier3 1231 180 12.76 264 203 43.19 0 0 NA 933124 TCGA-AB-2993 AML01 4 46955181 46955181 C T SNP GABRB1 NM_000812.3 human genbank 54_36p 1 reviewed intronic c.462-61720 e5-61720 0.001 - - - no_errors tier3 2301 2 0.09 552 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 4 48048728 48048728 A T SNP SLAIN2 NM_020846.1 human genbank 54_36p 1 validated intronic c.389+9826 e1+9826 0.135 - - - no_errors tier3 1105 187 14.46 202 148 42.29 2 3 60 933124 TCGA-AB-2993 AML01 4 68587383 68587383 G A SNP LOC339970 XR_038239.1 human genbank 54_36p 1 model rna NULL NULL 0.001 - - - pseudogene tier1 874 114 11.53 498 438 46.74 1 100 933124 TCGA-AB-2993 AML01 4 85060750 85060750 G T SNP - - - - - - - - - - - - - - - tier2 1559 226 12.63 517 554 51.44 0 0 NA 933124 TCGA-AB-2993 AML01 4 91456184 91456184 T C SNP KIAA1680 NM_207491.1 human genbank 54_36p 1 validated intronic c.1509+2963 e2+2963 0.003 - - - no_errors tier3 842 169 16.7 316 315 49.76 0 2 100 933124 TCGA-AB-2993 AML01 4 97290438 97290438 G A SNP ENSG00000201744 ENST00000364874 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*2033 NULL 0.064 - - - no_errors tier2 1794 261 12.68 331 302 47.56 0 0 NA 933124 TCGA-AB-2993 AML01 4 116138267 116138267 C G SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.979-20388 e2-20388 0 - - - no_errors tier3 778 116 12.98 398 273 40.62 0 0 NA 933124 TCGA-AB-2993 AML01 4 118103083 118103083 G A SNP - - - - - - - - - - - - - - - tier3 1600 202 11.21 519 382 42.26 0 0 NA 933124 TCGA-AB-2993 AML01 4 123486087 123486087 G A SNP KIAA1109 NM_015312.2 human genbank 54_36p 1 validated intronic c.12733+921 e72+921 0.013 - - - no_errors tier3 1058 171 13.9 422 271 38.99 2 3 60 933124 TCGA-AB-2993 AML01 4 124091534 124091534 T C SNP SPATA5 NM_145207.2 human genbank 54_36p 1 validated intronic c.1714+3441 e9+3441 0.002 - - - no_errors tier3 1660 307 15.6 1283 1092 45.94 0 0 0 933124 TCGA-AB-2993 AML01 4 149316450 149316450 A T SNP NR3C2 NM_000901.3 human genbank 54_36p -1 validated intronic c.2014+18897 e3+18897 0 - - - no_errors tier3 501 3 0.59 93 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 4 150025553 150025553 A G SNP - - - - - - - - - - - - - - - tier3 300 1 0.33 68 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 4 154576734 154576734 A - DEL KIAA0922 NM_015196.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-120846 NULL 0.029 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 4 158256256 158256256 C T SNP GLRB NM_000824.3 human genbank 54_36p 1 validated intronic c.123-4902 e2-4902 0 - - - no_errors tier3 1653 0 0 594 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 4 163130129 163130132 ACTA - DEL FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.160+44095_160+44092 e2+44095 0.001:0.002:0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 4 178634377 178634377 C A SNP AGA NM_000027.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33854 NULL 0.001 - - - no_errors tier2 1140 184 13.9 299 277 48.09 1 2 66.67 933124 TCGA-AB-2993 AML01 4 189384083 189384083 G C SNP - - - - - - - - - - - - - - - tier2 1465 238 13.98 389 256 39.69 0 0 NA 933124 TCGA-AB-2993 AML01 4 189695139 189695139 G C SNP - - - - - - - - - - - - - - - tier3 2579 0 0 2461 3 0.12 0 0 NA 933124 TCGA-AB-2993 AML01 4 190940937 190940937 C T SNP - - - - - - - - - - - - - - - tier3 2353 549 18.89 419 370 46.89 1 0 0 933124 TCGA-AB-2993 AML01 5 2384507 2384507 C T SNP - - - - - - - - - - - - - - - tier3 906 195 17.71 648 501 43.53 0 0 NA 933124 TCGA-AB-2993 AML01 5 7094623 7094623 G A SNP ENSG00000212258 ENST00000390956 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-5717 NULL 0 - - - no_errors tier3 1397 276 16.48 294 384 56.3 0 0 NA 933124 TCGA-AB-2993 AML01 5 15286895 15286895 G A SNP - - - - - - - - - - - - - - - tier2 856 175 16.97 658 558 45.81 0 0 NA 933124 TCGA-AB-2993 AML01 5 15823239 15823239 G T SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.127+154058 e2+154058 0 - - - no_errors tier3 2501 0 0 1440 3 0.21 0 0 NA 933124 TCGA-AB-2993 AML01 5 19515547 19515547 G A SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed intronic c.1882+3620 e10+3620 0.007 - - - no_errors tier3 1216 175 12.53 658 576 46.41 0 0 NA 933124 TCGA-AB-2993 AML01 5 22531555 22531555 G A SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1+9581 e0+9581 0 - - - no_errors tier3 2249 335 12.95 322 242 42.91 0 0 NA 933124 TCGA-AB-2993 AML01 5 23096117 23096117 G A SNP - - - - - - - - - - - - - - - tier2 1750 4 0.23 1459 21 1.42 0 0 NA 933124 TCGA-AB-2993 AML01 5 29358302 29358302 G C SNP - - - - - - - - - - - - - - - tier2 896 132 12.84 342 285 45.31 0 0 NA 933124 TCGA-AB-2993 AML01 5 29515287 29515287 A C SNP - - - - - - - - - - - - - - - tier2 1717 1 0.06 1422 1 0.07 0 0 NA 933124 TCGA-AB-2993 AML01 5 39934482 39934482 C T SNP LOC100134241 XM_001717424.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*462 NULL 0.046 - - - no_start_codon:pseudogene:no_stop_codon tier3 1855 285 13.31 575 466 44.68 0 0 NA 933124 TCGA-AB-2993 AML01 5 40462054 40462054 C G SNP - - - - - - - - - - - - - - - tier3 1288 180 12.25 660 514 43.67 0 0 NA 933124 TCGA-AB-2993 AML01 5 55184111 55184111 T G SNP IL31RA NM_139017.4 human genbank 54_36p 1 validated intronic c.63+893 e1+893 0.003 - - - no_errors tier2 1276 223 14.88 290 255 46.79 0 0 NA 933124 TCGA-AB-2993 AML01 5 58140630 58140630 A C SNP RAB3C NM_138453.2 human genbank 54_36p 1 provisional intronic c.372-15992 e4-15992 0 - - - no_errors tier2 2382 356 13 962 860 47.12 0 0 NA 933124 TCGA-AB-2993 AML01 5 72638602 72638602 G A SNP - - - - - - - - - - - - - - - tier3 2704 421 13.45 741 538 41.97 0 0 NA 933124 TCGA-AB-2993 AML01 5 73517294 73517294 G A SNP ENSG00000210914 ENST00000388179 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-10056 NULL 0.006 - - - pseudogene tier3 1767 325 15.51 608 584 48.71 0 0 NA 933124 TCGA-AB-2993 AML01 5 79267485 79267485 C T SNP MTX3 NM_001010891.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*47778 NULL 0.003 - - - no_errors tier3 1264 227 15.19 554 384 40.89 0 0 NA 933124 TCGA-AB-2993 AML01 5 79306739 79306739 G C SNP MTX3 NM_001010891.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*8524 NULL 0.004 - - - no_errors tier3 1528 246 13.86 666 525 44.01 0 0 NA 933124 TCGA-AB-2993 AML01 5 97053721 97053721 A G SNP ENSG00000211332 ENST00000388597 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*14790 NULL 0.001 - - - pseudogene tier3 1597 307 16.09 619 682 51.59 0 0 NA 933124 TCGA-AB-2993 AML01 5 104466311 104466311 C A SNP RAB9P1 NR_000039.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*2613 NULL 0.001 - - - pseudogene tier2 1823 1 0.05 1138 1 0.09 0 0 NA 933124 TCGA-AB-2993 AML01 5 107125647 107125647 T G SNP ENSG00000223057 ENST00000411125 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26981 NULL 0.178 - - - no_errors tier3 1716 238 12.17 322 331 50.61 0 0 NA 933124 TCGA-AB-2993 AML01 5 113840798 113840798 G T SNP KCNN2 NM_021614.2 human genbank 54_36p 1 reviewed intronic c.1254+4038 e5+4038 0.027 - - - no_errors tier3 1017 0 0 553 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 5 118292794 118292794 T C SNP DTWD2 NM_173666.2 human genbank 54_36p -1 validated intronic c.405-471 e4-471 0.032 - - - no_errors tier3 1539 257 14.3 1076 900 45.48 0 0 0 933124 TCGA-AB-2993 AML01 5 122482597 122482597 A G SNP PRDM6 ENST00000407847 human ensembl 54_36p 1 known intronic c.900+19042 e2+19042 0.006 - - - no_errors tier3 2472 471 15.98 470 576 54.96 0 0 NA 933124 TCGA-AB-2993 AML01 5 137966197 137966197 C T SNP HSPA9 NM_004134.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-27291 NULL 0.935 - - - no_errors tier2 1928 328 14.53 654 494 42.99 0 0 NA 933124 TCGA-AB-2993 AML01 5 143131070 143131070 G A SNP HMHB1 NM_021182.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40956 NULL 0.599 - - - no_errors tier3 2095 319 13.21 685 496 41.89 0 0 NA 933124 TCGA-AB-2993 AML01 5 159736606 159736606 T C SNP PTTG1 NM_004219.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45292 NULL 0.042 - - - no_errors tier2 1565 301 16.11 548 486 46.96 0 0 NA 933124 TCGA-AB-2993 AML01 5 168256047 168256047 C T SNP SLIT3 NM_003062.2 human genbank 54_36p -1 validated intronic c.414-13128 e5-13128 0.001 - - - no_errors tier3 3179 545 14.63 966 923 48.78 0 0 NA 933124 TCGA-AB-2993 AML01 5 169060195 169060196 - TAGTTTT INS DOCK2 NM_004946.2 human genbank 54_36p 1 validated intronic c.1258+474_1258+473 e13+474 0.170:0.161 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 5 170079783 170079783 G A SNP KCNIP1 NM_001034837.1 human genbank 54_36p 1 reviewed intronic c.220-120 e4-120 0 - - - no_errors tier2 966 173 15.19 464 387 45.32 0 0 NA 933124 TCGA-AB-2993 AML01 5 170770152 170770153 - CATG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 933124 TCGA-AB-2993 AML01 5 175948939 175948939 C T SNP PCDH24 NM_017675.3 human genbank 54_36p 1 reviewed missense c.3011 p.P1004L 0.982 "HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin" "HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,superfamily_Cadherin" - no_errors tier1 1178 131 9.98 207 130 38.58 NA 933124 TCGA-AB-2993 AML01 5 177727421 177727421 G A SNP COL23A1 NM_173465.3 human genbank 54_36p -1 validated intronic c.362-60895 e3-60895 0 - - - no_errors tier3 653 102 13.51 302 252 45.41 0 0 NA 933124 TCGA-AB-2993 AML01 5 178842439 178842439 C T SNP ENSG00000202120 ENST00000365250 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9207 NULL 0.139 - - - no_errors tier3 1358 218 13.82 518 479 48 0 0 NA 933124 TCGA-AB-2993 AML01 5 179961228 179961228 G A SNP FLT4 NM_182925.4 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*1570 NULL 0 - - - no_errors tier2 982 0 0 686 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 6 843274 843274 G A SNP LOC730031 XM_001132155.2 human genbank 54_36p 1 model intronic c.106-8663 e2-8663 0 - - - no_start_codon:pseudogene:no_stop_codon tier2 1794 281 13.54 760 638 45.6 0 0 NA 933124 TCGA-AB-2993 AML01 6 5956298 5956298 G T SNP NRN1 NM_016588.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4317 NULL 0.002 - - - no_errors tier3 987 155 13.57 121 65 34.95 0 0 NA 933124 TCGA-AB-2993 AML01 6 9855937 9855937 C T SNP OFCC1 ENST00000336327 human ensembl 54_36p -1 known intronic c.689+21213 e7+21213 0.989 - - - no_start_codon:no_stop_codon tier3 1644 0 0 712 1 0.14 0 0 NA 933124 TCGA-AB-2993 AML01 6 10707923 10707923 C A SNP GCNT2 NM_145649.2 human genbank 54_36p 1 reviewed intronic c.926-21647 e2-21647 0.013 - - - no_errors tier3 1193 246 17.08 458 489 51.42 0 0 NA 933124 TCGA-AB-2993 AML01 6 23872497 23872497 C T SNP - - - - - - - - - - - - - - - tier3 1539 234 13.18 904 743 44.87 0 0 NA 933124 TCGA-AB-2993 AML01 6 38352606 38352606 A C SNP BTBD9 NM_001099272.1 human genbank 54_36p -1 validated intronic c.1454+11420 e7+11420 0.081 - - - no_errors tier3 1962 0 0 469 0 0 1 0 0 933124 TCGA-AB-2993 AML01 6 41353299 41353299 C T SNP TREM1 NM_018643.2 human genbank 54_36p -1 provisional intronic c.600-1353 e4-1353 0 - - - no_errors tier3 2142 362 14.45 708 620 46.51 1 1 50 933124 TCGA-AB-2993 AML01 6 46669798 46669798 T C SNP CYP39A1 NM_016593.3 human genbank 54_36p -1 reviewed intronic c.1065+1885 e8+1885 0.069 - - - no_errors tier3 1555 260 14.29 656 625 48.79 0 0 NA 933124 TCGA-AB-2993 AML01 6 49771279 49771279 A G SNP CRISP2 NM_003296.1 human genbank 54_36p -1 validated intronic c.604+229 e6+229 0 - - - no_errors tier3 649 111 14.61 245 185 42.92 0 0 NA 933124 TCGA-AB-2993 AML01 6 66736510 66736510 A G SNP - - - - - - - - - - - - - - - tier3 1022 180 14.94 235 217 47.8 0 0 NA 933124 TCGA-AB-2993 AML01 6 68551603 68551603 T C SNP - - - - - - - - - - - - - - - tier3 1814 337 15.67 513 451 46.74 0 0 NA 933124 TCGA-AB-2993 AML01 6 70987814 70987814 G A SNP COL9A1 NM_001851.4 human genbank 54_36p -1 reviewed intronic c.2582-4309 e38-4309 0.004 - - - no_errors tier3 1206 188 13.49 228 248 51.99 0 0 NA 933124 TCGA-AB-2993 AML01 6 82180779 82180779 C T SNP - - - - - - - - - - - - - - - tier2 884 122 12.13 207 118 36.2 0 0 NA 933124 TCGA-AB-2993 AML01 6 89027696 89027696 A T SNP ENSG00000220131 ENST00000404250 human ensembl 54_36p 1 known 5_prime_flanking_region c.-3900 NULL 0.005 - - - no_coding_region:pseudogene tier3 931 172 15.59 319 238 42.58 0 0 NA 933124 TCGA-AB-2993 AML01 6 96112105 96112105 A C SNP MANEA NM_024641.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28932 NULL 0.115 - - - no_errors tier3 1872 0 0 653 2 0.31 5 0 0 933124 TCGA-AB-2993 AML01 6 96207554 96207554 A G SNP ENSG00000219549 ENST00000401718 human ensembl 54_36p -1 known 5_prime_flanking_region c.-20028 NULL 0.002 - - - no_coding_region:pseudogene tier3 1179 195 14.17 296 266 47.16 0 0 NA 933124 TCGA-AB-2993 AML01 6 114999438 114999438 T G SNP - - - - - - - - - - - - - - - tier3 749 125 14.27 46 39 45.88 0 0 NA 933124 TCGA-AB-2993 AML01 6 115214023 115214023 C A SNP - - - - - - - - - - - - - - - tier3 894 0 0 204 1 0.49 0 0 NA 933124 TCGA-AB-2993 AML01 6 116187978 116187978 C A SNP ENSG00000217019 ENST00000401765 human ensembl 54_36p -1 known 3_prime_flanking_region c.*17112 NULL 0.001 - - - no_coding_region:pseudogene tier3 2636 372 12.36 990 734 42.5 0 0 NA 933124 TCGA-AB-2993 AML01 6 122642113 122642113 A G SNP - - - - - - - - - - - - - - - tier3 644 93 12.6 112 108 48.87 0 0 NA 933124 TCGA-AB-2993 AML01 6 126994888 126994888 G A SNP LOC728666 XR_015645.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-11427 NULL 0.907 - - - no_errors tier2 2146 373 14.78 697 722 50.77 0 0 NA 933124 TCGA-AB-2993 AML01 6 133770285 133770285 G A SNP EYA4 NM_004100.4 human genbank 54_36p 1 reviewed intronic c.83+25013 e2+25013 0 - - - no_errors tier2 1092 2 0.18 1235 2 0.16 0 0 NA 933124 TCGA-AB-2993 AML01 6 135641514 135641514 G T SNP AHI1 NM_017651.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*6962 NULL 0.051 - - - no_errors tier3 2196 353 13.84 627 439 41.07 0 0 NA 933124 TCGA-AB-2993 AML01 7 4190422 4190422 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.5098+5678 e35+5678 0 - - - no_errors tier3 867 97 10.05 305 253 45.18 0 0 NA 933124 TCGA-AB-2993 AML01 7 15006915 15006915 C T SNP ENSG00000218558 ENST00000405671 human ensembl 54_36p -1 known 5_prime_flanking_region c.-14691 NULL 0.001 - - - no_coding_region:pseudogene tier3 1895 270 12.46 731 701 48.82 0 0 NA 933124 TCGA-AB-2993 AML01 7 20452265 20452265 A G SNP ITGB8 NM_002214.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*36120 NULL 0.002 - - - no_errors tier3 1805 322 15.13 631 495 43.81 0 0 NA 933124 TCGA-AB-2993 AML01 7 27727645 27727645 T C SNP TAX1BP1 NM_006024.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27024 NULL 0.042 - - - no_errors tier3 1725 302 14.77 828 685 44.83 2 0 0 933124 TCGA-AB-2993 AML01 7 57276498 57276498 G A SNP LOC642006 XM_001719189.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-24852 NULL 0 - - - pseudogene tier3 999 149 12.96 289 293 50.34 0 0 NA 933124 TCGA-AB-2993 AML01 7 70054236 70054236 G T SNP - - - - - - - - - - - - - - - tier3 1040 199 16.05 680 539 44.04 0 0 NA 933124 TCGA-AB-2993 AML01 7 70789795 70789795 C G SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.1500+9568 e9+9568 0 - - - no_errors tier2 1578 228 12.62 308 211 40.58 0 0 NA 933124 TCGA-AB-2993 AML01 7 72038393 72038393 A G SNP POM121 NM_172020.1 human genbank 54_36p 1 reviewed intronic c.309-21 e4-21 0 - - - no_errors tier3 1027 149 12.66 158 136 46.26 4 4 50 933124 TCGA-AB-2993 AML01 7 77935249 77935249 C G SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.1045+21765 e6+21765 0 - - - no_errors tier2 1025 166 13.93 157 143 47.67 0 0 NA 933124 TCGA-AB-2993 AML01 7 82670696 82670696 C T SNP PCLO NM_033026.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-40852 NULL 0 - - - no_errors tier3 681 99 12.66 305 221 42.02 0 0 NA 933124 TCGA-AB-2993 AML01 7 83413239 83413239 T C SNP ENSG00000222994 ENST00000411062 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26284 NULL 0.001 - - - no_errors tier3 1796 289 13.85 621 436 41.25 0 0 NA 933124 TCGA-AB-2993 AML01 7 85571815 85571815 C T SNP - - - - - - - - - - - - - - - tier3 571 99 14.71 56 38 40.43 0 0 NA 933124 TCGA-AB-2993 AML01 7 85741672 85741672 A C SNP - - - - - - - - - - - - - - - tier3 1656 285 14.68 207 221 51.64 0 0 NA 933124 TCGA-AB-2993 AML01 7 115412686 115412698 TATTTACTGTGCT GGGA DEL TFEC NM_012252.1 human genbank 54_36p -1 validated intronic c.1-895_907 e1-883 0.584:0.859:0.981:0.997:1.000:1.000:0.997:0.948:0.877:0.868:0.845:0.743:0.490 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 7 118814318 118814318 C T SNP - - - - - - - - - - - - - - - tier3 1477 243 14.12 594 431 41.93 0 0 NA 933124 TCGA-AB-2993 AML01 7 120710150 120710150 T A SNP C7orf58 NM_024913.1 human genbank 54_36p 1 validated intronic c.2868+11430 e21+11430 0.749 - - - no_errors tier2 1811 306 14.41 904 759 45.59 0 0 NA 933124 TCGA-AB-2993 AML01 7 121412639 121412640 - T INS PTPRZ1 NM_002851.2 human genbank 54_36p 1 reviewed intronic c.928+1232_928+1231 e8+1232 0.000:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 7 121880780 121880780 C T SNP CADPS2 NM_017954.2 human genbank 54_36p -1 validated intronic c.2187-2015 e15-2015 0 - - - no_errors tier3 1528 255 14.28 469 352 42.87 0 0 NA 933124 TCGA-AB-2993 AML01 7 129716211 129716211 C A SNP CPA2 NM_001869.2 human genbank 54_36p 1 reviewed intronic c.1067-425 e11-425 0.01 - - - no_errors tier3 2214 463 17.28 1863 1538 45.16 0 0 NA 933124 TCGA-AB-2993 AML01 7 131136495 131136495 A G SNP ENSG00000172400 ENST00000305171 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-47175 NULL 0 - - - no_coding_region:pseudogene tier3 1652 314 15.96 745 705 48.55 0 0 NA 933124 TCGA-AB-2993 AML01 7 135717417 135717417 C T SNP - - - - - - - - - - - - - - - tier3 1010 156 13.38 358 242 39.93 0 0 NA 933124 TCGA-AB-2993 AML01 7 137113192 137113192 G A SNP DGKI NM_004717.2 human genbank 54_36p -1 reviewed intronic c.401+68556 e1+68556 0.003 - - - no_errors tier3 1700 311 15.46 941 706 42.74 0 0 NA 933124 TCGA-AB-2993 AML01 7 137769879 137769879 G A SNP TRIM24 NM_015905.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25955 NULL 0 - - - no_errors tier3 3095 482 13.46 629 444 41.34 0 0 NA 933124 TCGA-AB-2993 AML01 7 141689176 141689176 A C SNP uc003vxy.2 ENST00000390359 human ensembl 54_36p 1 known 5_prime_flanking_region c.-31793 NULL 0.003 - - - no_stop_codon:bad_bp_length_for_coding_region tier2 2706 0 0 1936 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 8 2568547 2568547 G T SNP - - - - - - - - - - - - - - - tier3 840 0 0 165 2 1.18 0 0 NA 933124 TCGA-AB-2993 AML01 8 8974206 8974206 G A SNP ENSG00000210052 ENST00000387317 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20656 NULL 0 - - - pseudogene tier3 1965 331 14.41 708 595 45.56 0 1 100 933124 TCGA-AB-2993 AML01 8 15661762 15661762 G A SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed intronic c.1047+2027 e10+2027 0 - - - no_errors tier3 1394 264 15.89 980 837 45.96 0 0 NA 933124 TCGA-AB-2993 AML01 8 18043420 18043420 C T SNP - - - - - - - - - - - - - - - tier3 2323 354 13.19 1230 970 44.03 0 0 NA 933124 TCGA-AB-2993 AML01 8 19445887 19445887 G A SNP CSGALNACT1 NM_018371.1 human genbank 54_36p -1 validated intronic c.1-37966 e1-37966 0 - - - no_errors tier3 1216 132 9.75 456 364 44.12 0 0 NA 933124 TCGA-AB-2993 AML01 8 31261001 31261001 G A SNP - - - - - - - - - - - - - - - tier3 1502 1 0.07 251 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 8 34327019 34327019 A T SNP RPL10AP3 ENST00000399893 human ensembl 54_36p -1 known 5_prime_flanking_region c.-26317 NULL 0.009 - - - no_stop_codon tier3 899 144 13.81 417 343 45.07 0 0 NA 933124 TCGA-AB-2993 AML01 8 35523488 35523488 G A SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated intronic c.88+1893 e1+1893 0.113 - - - no_errors tier3 1808 349 16.17 839 924 52.12 0 0 NA 933124 TCGA-AB-2993 AML01 8 36819114 36819114 G T SNP KCNU1 NM_001031836.2 human genbank 54_36p 1 validated intronic c.1703+1435 e16+1435 0.002 - - - no_errors tier3 1781 0 0 1316 2 0.15 0 0 NA 933124 TCGA-AB-2993 AML01 8 37405787 37405787 C A SNP LOC100128034 XM_001717929.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*46584 NULL 0.001 - - - no_errors tier3 2606 520 16.62 1166 1055 47.46 0 0 NA 933124 TCGA-AB-2993 AML01 8 56090350 56090350 G A SNP - - - - - - - - - - - - - - - tier3 1404 235 14.34 910 765 45.56 0 0 NA 933124 TCGA-AB-2993 AML01 8 69432926 69432926 C T SNP C8orf34 ENST00000349492 human ensembl 54_36p 1 known intronic c.327+26798 e1+26798 0 - - - no_errors tier2 2091 315 13.09 623 464 42.65 0 0 NA 933124 TCGA-AB-2993 AML01 8 70394475 70394475 G A SNP - - - - - - - - - - - - - - - tier3 878 139 13.65 288 270 48.13 0 0 NA 933124 TCGA-AB-2993 AML01 8 77071599 77071599 G T SNP - - - - - - - - - - - - - - - tier2 1041 201 16.18 475 432 47.58 0 0 NA 933124 TCGA-AB-2993 AML01 8 77811962 77811962 T C SNP ZFHX4 NM_024721.3 human genbank 54_36p 1 validated intronic c.3015+29124 e2+29124 0.003 - - - no_errors tier3 2234 363 13.96 820 657 44.24 0 0 NA 933124 TCGA-AB-2993 AML01 8 88484802 88484802 C T SNP CNBD1 NM_173538.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*20831 NULL 0.001 - - - no_errors tier3 1524 234 13.28 756 722 48.75 0 0 NA 933124 TCGA-AB-2993 AML01 8 115843335 115843335 G A SNP - - - - - - - - - - - - - - - tier3 1327 215 13.93 577 555 48.98 0 0 NA 933124 TCGA-AB-2993 AML01 8 118550836 118550836 T G SNP - - - - - - - - - - - - - - - tier2 1923 328 14.56 667 606 47.6 0 0 NA 933124 TCGA-AB-2993 AML01 8 129786127 129786127 T C SNP - - - - - - - - - - - - - - - tier3 1210 183 13.1 399 315 43.99 1 0 0 933124 TCGA-AB-2993 AML01 9 2471880 2471880 G A SNP - - - - - - - - - - - - - - - tier3 1141 197 14.71 586 363 38.01 0 0 NA 933124 TCGA-AB-2993 AML01 9 5297444 5297444 T C SNP RLN2 NM_134441.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2864 NULL 0 - - - no_errors tier3 2776 547 16.45 835 636 43.12 0 0 NA 933124 TCGA-AB-2993 AML01 9 17997460 17997460 G A SNP - - - - - - - - - - - - - - - tier3 1832 325 15.05 979 936 48.83 0 0 NA 933124 TCGA-AB-2993 AML01 9 24541903 24541903 G C SNP LOC100129669 XM_001718121.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-5899 NULL 0 - - - no_errors tier3 955 158 14.2 290 225 43.69 0 0 NA 933124 TCGA-AB-2993 AML01 9 26544775 26544775 G A SNP - - - - - - - - - - - - - - - tier3 1758 298 14.48 799 729 47.52 0 0 NA 933124 TCGA-AB-2993 AML01 9 27488503 27488503 G A SNP MOBKL2B NM_024761.3 human genbank 54_36p -1 reviewed intronic c.1+31050 e0+31050 0.029 - - - no_errors tier3 1118 216 16.18 540 555 50.59 0 0 0 933124 TCGA-AB-2993 AML01 9 38030097 38030097 G A SNP SHB NM_003028.2 human genbank 54_36p -1 validated intronic c.718-23969 e2-23969 0.005 - - - no_errors tier3 817 142 14.78 347 310 46.83 1 0 0 933124 TCGA-AB-2993 AML01 9 75985332 75985332 C A SNP - - - - - - - - - - - - - - - tier3 2123 0 0 1007 2 0.2 0 0 NA 933124 TCGA-AB-2993 AML01 9 79005857 79005857 G C SNP VPS13A NM_033305.1 human genbank 54_36p 1 reviewed intronic c.145-244 e3-244 0 - - - no_errors tier3 589 87 12.87 47 46 49.46 0 0 0 933124 TCGA-AB-2993 AML01 9 82308637 82308637 C A SNP - - - - - - - - - - - - - - - tier2 1723 0 0 1307 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 9 83692876 83692876 G A SNP uc004amh.1 ENST00000341875 human ensembl 54_36p 1 known 5_prime_flanking_region c.-40373 NULL 0.001 - - - no_errors tier3 1902 325 14.56 1182 1078 47.51 0 0 NA 933124 TCGA-AB-2993 AML01 9 86898540 86898540 G A SNP - - - - - - - - - - - - - - - tier3 3772 684 15.33 4021 3413 45.82 0 0 NA 933124 TCGA-AB-2993 AML01 9 97963721 97963722 - A INS LOC100128771 XR_037860.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*13642 NULL 0.001:0.002 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 9 104622553 104622553 G T SNP - - - - - - - - - - - - - - - tier2 1515 299 16.46 656 585 47.1 0 0 NA 933124 TCGA-AB-2993 AML01 9 112769906 112769906 A G SNP LPAR1 NM_001401.3 human genbank 54_36p -1 reviewed intronic c.45+4268 e1+4268 0.011 - - - no_errors tier3 1597 0 0 1614 1 0.06 1 0 0 933124 TCGA-AB-2993 AML01 10 3561926 3561926 G A SNP - - - - - - - - - - - - - - - tier3 1048 171 14.02 692 655 48.41 0 0 NA 933124 TCGA-AB-2993 AML01 10 22510615 22510615 G C SNP ENSG00000218957 ENST00000404370 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44018 NULL 0.011 - - - no_coding_region:pseudogene tier3 1013 0 0 648 1 0.15 0 0 NA 933124 TCGA-AB-2993 AML01 10 23382721 23382721 C A SNP MSRB2 NM_012228.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-41823 NULL 0 - - - no_errors tier3 1170 0 0 579 1 0.17 0 0 NA 933124 TCGA-AB-2993 AML01 10 52232296 52232296 T C SNP A1CF NM_138932.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*4199 NULL 0.022 - - - no_errors tier3 819 0 0 160 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 10 60433140 60433140 A C SNP - - - - - - - - - - - - - - - tier3 2544 459 15.28 709 856 54.63 0 0 NA 933124 TCGA-AB-2993 AML01 10 95087690 95087690 T C SNP MYOF NM_013451.3 human genbank 54_36p -1 reviewed intronic c.4339-30 e40-30 0 - - - no_errors tier3 4192 823 16.4 898 756 45.54 0 0 NA 933124 TCGA-AB-2993 AML01 10 105228735 105228735 C T SNP CALHM3 ENST00000369783 human ensembl 54_36p -1 known silent c.45 p.S15 0.104 NULL NULL - no_errors tier1 1381 283 16.99 321 268 45.42 NA 933124 TCGA-AB-2993 AML01 10 112346166 112346166 G T SNP SMC3 NM_005445.3 human genbank 54_36p 1 reviewed missense c.1984 p.G662C 1 "HMMPfam_SMC_N,superfamily_Smc hinge domain,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain" - no_errors tier1 604 99 14.08 162 201 55.22 38 44 53.66 933124 TCGA-AB-2993 AML01 10 114348204 114348204 C T SNP VTI1A NM_145206.2 human genbank 54_36p 1 validated intronic c.427+60125 e5+60125 1 - - - no_errors tier2 1079 159 12.84 426 331 43.73 4 6 60 933124 TCGA-AB-2993 AML01 10 123947341 123947341 G A SNP TACC2 NM_206862.2 human genbank 54_36p 1 reviewed intronic c.5971+2660 e7+2660 0 - - - no_errors tier3 701 155 17.8 167 191 52.76 0 0 NA 933124 TCGA-AB-2993 AML01 10 132153077 132153077 G A SNP ENSG00000222997 ENST00000411065 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-40283 NULL 0 - - - no_errors tier3 1793 299 14.28 766 647 45.76 0 0 NA 933124 TCGA-AB-2993 AML01 10 134734535 134734535 C T SNP GPR123 ENST00000368577 human ensembl 54_36p 1 known missense c.113 p.T38I 0 NULL "HMMPfam_7tm_2,PatternScan_G_PROTEIN_RECEP_F2_2" - no_errors tier1 175 41 18.98 82 63 43.45 NA 933124 TCGA-AB-2993 AML01 10 134866164 134866164 C T SNP KNDC1 NM_152643.6 human genbank 54_36p 1 validated intronic c.3387+772 e17+772 0 - - - no_errors tier2 152 25 14.04 90 56 38.1 0 0 NA 933124 TCGA-AB-2993 AML01 11 6320063 6320063 A G SNP SMPD1 NM_000543.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48342 NULL 0.002 - - - no_errors tier3 2132 431 16.82 1236 1074 46.39 0 0 NA 933124 TCGA-AB-2993 AML01 11 11459230 11459230 G C SNP GALNTL4 NM_198516.2 human genbank 54_36p -1 validated intronic c.236-32171 e2-32171 0.046 - - - no_errors tier3 1520 223 12.79 771 694 47.21 0 0 NA 933124 TCGA-AB-2993 AML01 11 22017700 22017700 C G SNP - - - - - - - - - - - - - - - tier3 1617 277 14.63 934 786 45.62 0 0 NA 933124 TCGA-AB-2993 AML01 11 23560993 23560993 A G SNP - - - - - - - - - - - - - - - tier3 413 70 14.49 75 67 47.18 0 0 NA 933124 TCGA-AB-2993 AML01 11 26651719 26651719 C A SNP SLC5A12 NM_178498.3 human genbank 54_36p -1 validated intronic c.1580-67 e14-67 0 - - - no_errors tier3 1212 2 0.16 577 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 11 28542151 28542151 T - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 11 31783643 31783643 G A SNP PAX6 NM_001604.3 human genbank 54_36p -1 reviewed intronic c.10+883 e1+883 0 - - - no_errors tier2 1140 186 14.01 273 169 38.15 0 0 NA 933124 TCGA-AB-2993 AML01 11 32116909 32116909 A G SNP ENSG00000209623 ENST00000386888 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26086 NULL 0.002 - - - pseudogene tier3 1156 233 16.76 360 338 48.15 0 0 NA 933124 TCGA-AB-2993 AML01 11 38973823 38973823 T A SNP - - - - - - - - - - - - - - - tier3 1154 149 11.44 333 263 44.13 0 0 NA 933124 TCGA-AB-2993 AML01 11 44255438 44255438 C T SNP ALX4 NM_021926.2 human genbank 54_36p -1 validated intronic c.467-1654 e2-1654 0 - - - no_errors tier3 1889 316 14.29 794 650 44.89 1 0 0 933124 TCGA-AB-2993 AML01 11 57189638 57189638 G A SNP ZDHHC5 NM_015457.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7501 NULL 0.001 - - - no_errors tier3 1681 220 11.56 329 207 38.62 0 0 NA 933124 TCGA-AB-2993 AML01 11 57364966 57364967 - AGTCCC INS CTNND1 NM_001085458.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*24610 NULL 0.056:0.055 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 11 59102497 59102497 G A SNP OSBP NM_002556.2 human genbank 54_36p -1 reviewed intronic c.1879-118 e12-118 0 - - - no_errors tier3 1285 207 13.87 451 360 44.33 9 5 35.71 933124 TCGA-AB-2993 AML01 11 59667167 59667167 C T SNP MS4A6A NM_152852.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*29040 NULL 0.152 - - - no_errors tier3 1325 263 16.55 682 516 43.04 0 0 NA 933124 TCGA-AB-2993 AML01 11 61152920 61152920 C T SNP RPLP0P2 NR_002775.2 human genbank 54_36p 1 inferred rna NULL NULL 0 - - - pseudogene tier1 923 136 12.83 313 200 38.99 NA 933124 TCGA-AB-2993 AML01 11 68094328 68094328 T A SNP SAPS3 NM_018312.3 human genbank 54_36p 1 validated intronic c.1125+387 e8+387 0 - - - no_errors tier2 940 197 17.33 170 144 45.71 1 2 66.67 933124 TCGA-AB-2993 AML01 11 76183866 76183866 G A SNP TSKU NM_015516.3 human genbank 54_36p 1 validated intronic c.1-435 e1-435 0 - - - no_errors tier3 877 171 16.29 260 259 49.81 0 0 NA 933124 TCGA-AB-2993 AML01 11 82054955 82054955 T A SNP - - - - - - - - - - - - - - - tier2 2078 2 0.1 1570 5 0.32 0 0 NA 933124 TCGA-AB-2993 AML01 11 87112863 87112863 G A SNP - - - - - - - - - - - - - - - tier2 2728 359 11.62 980 827 45.62 0 0 NA 933124 TCGA-AB-2993 AML01 11 89708905 89708905 C T SNP ENSG00000223101 ENST00000411169 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*11205 NULL 0.02 - - - no_errors tier3 1272 1 0.08 898 1 0.11 0 0 NA 933124 TCGA-AB-2993 AML01 11 91088924 91088924 G A SNP - - - - - - - - - - - - - - - tier3 1104 159 12.59 428 368 46.17 0 0 NA 933124 TCGA-AB-2993 AML01 11 95419621 95419621 C T SNP MAML2 NM_032427.1 human genbank 54_36p -1 validated intronic c.2139+45083 e2+45083 0 - - - no_errors tier3 2605 480 15.52 1112 971 46.55 0 0 0 933124 TCGA-AB-2993 AML01 11 106067082 106067082 T G SNP GUCY1A2 NM_000855.1 human genbank 54_36p -1 validated intronic c.1992-3390 e8-3390 0.001 - - - no_errors tier3 1612 271 14.37 383 366 48.8 0 0 NA 933124 TCGA-AB-2993 AML01 11 117101343 117101343 A G SNP DSCAML1 NM_020693.2 human genbank 54_36p -1 provisional intronic c.691+51373 e3+51373 0 - - - no_errors tier3 986 152 13.23 446 347 43.76 0 0 NA 933124 TCGA-AB-2993 AML01 12 3464622 3464622 G A SNP PRMT8 NM_019854.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-6431 NULL 0 - - - no_errors tier3 2113 3 0.14 865 3 0.34 0 0 NA 933124 TCGA-AB-2993 AML01 12 6182996 6182996 G A SNP CD9 NM_001769.2 human genbank 54_36p 1 reviewed intronic c.66+3004 e1+3004 0 - - - no_errors tier3 1569 292 15.66 313 307 49.44 0 0 0 933124 TCGA-AB-2993 AML01 12 25930534 25930534 A T SNP - - - - - - - - - - - - - - - tier3 980 140 12.48 343 210 37.91 0 0 NA 933124 TCGA-AB-2993 AML01 12 42178672 42178672 T A SNP ADAMTS20 NM_025003.3 human genbank 54_36p -1 validated intronic c.867+3550 e4+3550 0 - - - no_errors tier3 1276 300 19 672 661 49.4 0 0 NA 933124 TCGA-AB-2993 AML01 12 43022207 43022207 G A SNP TMEM117 NM_032256.1 human genbank 54_36p 1 provisional intronic c.769-34438 e6-34438 0 - - - no_errors tier3 2342 0 0 1613 3 0.19 0 0 NA 933124 TCGA-AB-2993 AML01 12 45210907 45210907 A G SNP - - - - - - - - - - - - - - - tier3 581 98 14.33 665 498 42.75 0 0 0 933124 TCGA-AB-2993 AML01 12 59994312 59994312 G A SNP - - - - - - - - - - - - - - - tier3 1138 198 14.81 177 135 43.27 0 0 NA 933124 TCGA-AB-2993 AML01 12 72136658 72136658 G A SNP - - - - - - - - - - - - - - - tier3 256 0 0 39 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 12 74517961 74517961 G A SNP - - - - - - - - - - - - - - - tier3 1260 227 15.27 684 628 47.79 0 0 NA 933124 TCGA-AB-2993 AML01 12 86035630 86035630 G A SNP - - - - - - - - - - - - - - - tier3 1136 191 14.38 461 385 45.35 0 0 NA 933124 TCGA-AB-2993 AML01 12 90320127 90320127 A C SNP - - - - - - - - - - - - - - - tier3 907 165 15.38 185 134 42.01 0 0 NA 933124 TCGA-AB-2993 AML01 12 91063778 91063778 C - DEL BTG1 NM_001731.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-336 NULL 0.983 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 12 103237000 103237000 C T SNP TXNRD1 ENST00000354940 human ensembl 54_36p 1 known intronic c.423+37 e4+37 0.01 - - - no_errors tier3 864 41 4.53 100 7 6.48 1 0 0 933124 TCGA-AB-2993 AML01 12 124839422 124839422 C T SNP - - - - - - - - - - - - - - - tier3 1016 152 13.01 371 277 42.48 0 0 NA 933124 TCGA-AB-2993 AML01 12 129593530 129593530 G A SNP RIMBP2 NM_015347.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-64019 NULL 0.003 - - - no_errors tier3 4393 3 0.07 2776 7 0.25 0 0 NA 933124 TCGA-AB-2993 AML01 12 131934150 131934150 T C SNP CHFR NM_018223.1 human genbank 54_36p -1 provisional intronic c.1561-361 e14-361 0 - - - no_errors tier3 700 155 18.13 247 218 46.78 2 2 50 933124 TCGA-AB-2993 AML01 13 18776146 18776146 T A SNP ENSG00000218022 ENST00000407333 human ensembl 54_36p -1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 759 103 11.95 70 49 40.83 0 0 0 933124 TCGA-AB-2993 AML01 13 27506273 27506274 - GAAATCAACGTAGAAGTACTCATTATCTGA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1783_1782 p.594in_frame_insSDNEYFYVDF 1.000:1.000 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 933124 TCGA-AB-2993 AML01 13 27818040 27818040 A T SNP FLT1 NM_002019.3 human genbank 54_36p -1 validated intronic c.2249-352 e16-352 0.921 - - - no_errors tier2 1441 237 14.06 94 70 42.42 0 0 NA 933124 TCGA-AB-2993 AML01 13 30128153 30128153 A G SNP USPL1 NM_005800.4 human genbank 54_36p 1 validated intronic c.1397-1458 e8-1458 0.001 - - - no_errors tier3 1727 296 14.62 246 179 42.02 11 5 31.25 933124 TCGA-AB-2993 AML01 13 39618436 39618436 C T SNP - - - - - - - - - - - - - - - tier3 3920 172 4.2 2105 362 14.63 0 0 NA 933124 TCGA-AB-2993 AML01 13 42312208 42312208 T - DEL EPSTI1 NM_001002264.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*48178 NULL 0.103 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 13 47286737 47286737 G A SNP ENSG00000217434 ENST00000404873 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47516 NULL 0.001 - - - no_coding_region:pseudogene tier3 1069 207 16.21 296 237 44.13 0 0 NA 933124 TCGA-AB-2993 AML01 13 56924160 56924160 A G SNP - - - - - - - - - - - - - - - tier3 1215 213 14.92 340 324 48.8 0 0 NA 933124 TCGA-AB-2993 AML01 13 57495350 57495350 T C SNP ENSG00000202422 ENST00000365552 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*31751 NULL 0.994 - - - no_errors tier2 1385 211 13.2 601 570 48.55 0 0 NA 933124 TCGA-AB-2993 AML01 13 88456565 88456565 A T SNP ENSG00000216681 ENST00000403339 human ensembl 54_36p -1 known 5_prime_flanking_region c.-27525 NULL 0.011 - - - no_coding_region:pseudogene tier3 1237 216 14.87 371 322 46.46 0 0 NA 933124 TCGA-AB-2993 AML01 13 93097763 93097763 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.319+102088 e2+102088 0.001 - - - no_errors tier3 1410 234 14.22 677 497 42.23 0 0 NA 933124 TCGA-AB-2993 AML01 13 95632247 95632247 G C SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+90423 e1+90423 0.001 - - - no_errors tier3 1497 236 13.58 615 485 44.01 0 0 NA 933124 TCGA-AB-2993 AML01 13 98176393 98176393 C T SNP SLC15A1 NM_005073.3 human genbank 54_36p -1 validated nonsense c.230 p.W77* 1 "superfamily_MFS general substrate transporter,PatternScan_PTR2_1" "HMMPfam_PTR2,superfamily_MFS general substrate transporter,PatternScan_PTR2_1,PatternScan_PTR2_2" - no_errors tier1 1664 268 13.86 872 760 46.45 NA 933124 TCGA-AB-2993 AML01 13 98745388 98745388 G A SNP GPR183 NM_004951.4 human genbank 54_36p -1 reviewed missense c.1013 p.A338V 1 superfamily_SSF81321 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 1494 327 17.96 680 659 49.03 27 45 62.5 933124 TCGA-AB-2993 AML01 13 103448163 103448163 C T SNP - - - - - - - - - - - - - - - tier3 1044 128 10.91 176 119 40.2 0 0 NA 933124 TCGA-AB-2993 AML01 14 20830373 20830373 A T SNP RPGRIP1 NM_020366.3 human genbank 54_36p 1 reviewed intronic c.86-2303 e2-2303 0.011 - - - no_errors tier3 1209 3 0.25 111 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 14 22588266 22588266 G T SNP CDH24 NM_022478.3 human genbank 54_36p -1 validated nonsense c.1770 p.Y590* 0.998 "HMMPfam_Cadherin,superfamily_Cadherin-like" "HMMPfam_Cadherin_C,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" - no_errors tier1 327 49 13.03 113 72 38.71 3 2 40 933124 TCGA-AB-2993 AML01 14 22676367 22676367 C T SNP SLC7A8 NM_012244.2 human genbank 54_36p -1 validated intronic c.1016+603 e7+603 0 - - - no_errors tier3 844 134 13.67 342 324 48.65 0 0 NA 933124 TCGA-AB-2993 AML01 14 27252020 27252020 C G SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-39805 NULL 0.09 - - - no_errors tier3 1292 232 15.21 388 275 41.42 0 0 NA 933124 TCGA-AB-2993 AML01 14 38298621 38298621 G A SNP - - - - - - - - - - - - - - - tier3 2787 441 13.65 1568 1377 46.68 0 1 100 933124 TCGA-AB-2993 AML01 14 39339654 39339654 G A SNP - - - - - - - - - - - - - - - tier3 1847 325 14.95 1118 929 45.27 2 0 0 933124 TCGA-AB-2993 AML01 14 42844279 42844279 G A SNP - - - - - - - - - - - - - - - tier3 1074 181 14.41 311 278 47.04 0 0 NA 933124 TCGA-AB-2993 AML01 14 43499979 43499979 G T SNP - - - - - - - - - - - - - - - tier3 1781 0 0 624 1 0.16 0 0 NA 933124 TCGA-AB-2993 AML01 14 55340735 55340735 G A SNP ENSG00000177350 ENST00000313768 human ensembl 54_36p 1 known 3_prime_flanking_region c.*37517 NULL 0.027 - - - no_errors tier3 996 184 15.51 476 439 47.61 0 0 NA 933124 TCGA-AB-2993 AML01 14 77567488 77567488 A G SNP - - - - - - - - - - - - - - - tier3 4557 732 13.83 1429 1229 46.19 0 0 NA 933124 TCGA-AB-2993 AML01 14 81290411 81290411 G A SNP - - - - - - - - - - - - - - - tier3 1177 187 13.69 241 173 41.29 0 0 NA 933124 TCGA-AB-2993 AML01 14 84831262 84831262 C T SNP ENSG00000210442 ENST00000387707 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23160 NULL 0 - - - pseudogene tier3 1209 180 12.95 524 466 47.07 0 0 NA 933124 TCGA-AB-2993 AML01 14 85096059 85096059 C T SNP FLRT2 NM_013231.4 human genbank 54_36p 1 reviewed intronic c.1+29428 e0+29428 0.158 - - - no_errors tier3 1960 326 14.25 567 457 44.5 0 0 NA 933124 TCGA-AB-2993 AML01 15 22778840 22778840 A G SNP SNORD108 NR_001292.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-4325 NULL 0.002 - - - no_errors tier3 1783 286 13.81 530 488 47.89 4 0 0 933124 TCGA-AB-2993 AML01 15 36730078 36730078 G A SNP C15orf53 NM_207444.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46023 NULL 0.002 - - - no_errors tier3 1778 370 17.19 1043 1040 49.78 0 0 NA 933124 TCGA-AB-2993 AML01 15 40183833 40183833 G A SNP PLA2G4D NM_178034.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9884 NULL 0.03 - - - no_errors tier2 1300 203 13.47 727 532 42.09 0 0 NA 933124 TCGA-AB-2993 AML01 15 43120553 43120553 A G SNP SORD NM_003104.4 human genbank 54_36p 1 validated intronic c.100+622 e2+622 0.003 - - - no_errors tier3 677 104 13.3 295 207 41.15 1 1 50 933124 TCGA-AB-2993 AML01 15 43165312 43165312 C A SNP DUOX1 NM_017434.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46145 NULL 0.2 - - - no_errors tier3 908 123 11.92 41 30 41.67 0 0 NA 933124 TCGA-AB-2993 AML01 15 57669751 57669751 C T SNP GCNT3 NM_004751.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27979 NULL 0 - - - no_errors tier3 1969 369 15.77 704 641 47.55 0 0 NA 933124 TCGA-AB-2993 AML01 15 76806819 76806819 G A SNP LOC646934 XR_042348.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.936 - - - pseudogene tier2 703 0 0 512 1 0.19 0 0 NA 933124 TCGA-AB-2993 AML01 15 89035342 89035342 T A SNP BLM NM_000057.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-56285 NULL 0.001 - - - no_errors tier3 1879 295 13.57 387 356 47.91 0 2 100 933124 TCGA-AB-2993 AML01 15 91592526 91592527 - A INS UNQ9370 XR_041834.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*41554 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 15 96792215 96792215 G C SNP FAM169B NM_182562.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*8168 NULL 0 - - - no_errors tier3 1405 219 13.47 591 444 42.65 0 0 NA 933124 TCGA-AB-2993 AML01 16 3082843 3082843 G A SNP ZSCAN10 NM_032805.1 human genbank 54_36p -1 provisional 5_prime_untranslated_region c.-69 NULL 0.006 - - - no_errors tier3 643 100 13.4 183 137 42.55 0 0 NA 933124 TCGA-AB-2993 AML01 16 3631558 3631558 G A SNP DNASE1 NM_005223.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13818 NULL 0.048 - - - no_errors tier2 623 109 14.87 220 221 50.11 1 1 50 933124 TCGA-AB-2993 AML01 16 5746405 5746405 G A SNP ENSG00000221257 ENST00000408330 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*4284 NULL 0 - - - no_errors tier3 2394 28 1.15 1475 72 4.65 0 0 NA 933124 TCGA-AB-2993 AML01 16 11762063 11762063 G A SNP ZC3H7A NM_014153.2 human genbank 54_36p -1 provisional intronic c.2319+700 e18+700 0 - - - no_errors tier3 2035 372 15.45 965 781 44.65 9 9 50 933124 TCGA-AB-2993 AML01 16 15030292 15030292 G A SNP PDXDC1 NM_015027.2 human genbank 54_36p 1 validated missense c.1261 p.E421K 0.936 superfamily_PLP-dependent transferases "HMMPfam_Pyridoxal_deC,superfamily_PLP-dependent transferases" - no_errors tier1 1102 122 9.94 809 354 30.36 44 16 26.23 933124 TCGA-AB-2993 AML01 16 48870823 48870823 A C SNP ADCY7 ENST00000394697 human ensembl 54_36p 1 known intronic c.1-8501 e1-8501 0.04 - - - no_errors tier3 1055 202 16.01 244 207 45.9 0 0 0 933124 TCGA-AB-2993 AML01 16 57198624 57198634 ATATGGATAGT CCCC DEL CNOT1 NM_016284.3 human genbank 54_36p -1 validated intronic c.1-7718_7728 e1-7708 0.003:0.001:0.001:0.000:0.000:0.000:0.001:0.000:0.000:0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 16 59519213 59519213 C A SNP ENSG00000180019 ENST00000321498 human ensembl 54_36p -1 novel intronic c.NULL NULL 0.003 - - - no_coding_region:pseudogene tier2 1183 0 0 1090 2 0.18 0 0 NA 933124 TCGA-AB-2993 AML01 16 61156674 61156674 T C SNP - - - - - - - - - - - - - - - tier2 1396 280 16.71 352 282 44.41 0 0 NA 933124 TCGA-AB-2993 AML01 16 61360685 61360685 C T SNP - - - - - - - - - - - - - - - tier3 2623 497 15.9 817 605 42.52 0 0 NA 933124 TCGA-AB-2993 AML01 16 62264218 62264218 C A SNP - - - - - - - - - - - - - - - tier3 1050 209 16.59 193 173 47.01 0 0 NA 933124 TCGA-AB-2993 AML01 16 69454209 69454209 A G SNP HYDIN NM_032821.2 human genbank 54_36p -1 validated intronic c.11566+280 e67+280 0.001 - - - no_errors tier3 2279 198 7.99 1231 361 22.65 0 0 NA 933124 TCGA-AB-2993 AML01 16 72303308 72303308 C T SNP - - - - - - - - - - - - - - - tier3 1873 333 15.08 1080 874 44.5 0 0 NA 933124 TCGA-AB-2993 AML01 16 79743791 79743791 A G SNP PKD1L2 ENST00000299598 human ensembl 54_36p -1 known intronic c.4407-772 e27-772 0.463 - - - no_errors tier3 1482 244 14.12 351 286 44.69 0 0 NA 933124 TCGA-AB-2993 AML01 16 80180538 80180538 A G SNP CMIP NM_198390.2 human genbank 54_36p 1 validated intronic c.199-18135 e2-18135 0.033 - - - no_errors tier3 2041 333 14 939 712 43 3 1 25 933124 TCGA-AB-2993 AML01 16 84039293 84039293 C T SNP - - - - - - - - - - - - - - - tier3 465 0 0 215 0 0 1 0 0 933124 TCGA-AB-2993 AML01 17 9018278 9018278 C T SNP NTN1 NM_004822.2 human genbank 54_36p 1 reviewed intronic c.1208-5571 e3-5571 0.006 - - - no_errors tier3 1348 194 12.56 441 361 44.79 0 0 NA 933124 TCGA-AB-2993 AML01 17 12510562 12510562 G A SNP MYOCD NM_153604.1 human genbank 54_36p 1 provisional intronic c.55+277 e1+277 0.065 - - - no_errors tier3 1372 196 12.5 252 248 49.4 0 0 NA 933124 TCGA-AB-2993 AML01 17 22057902 22057902 G T SNP - - - - - - - - - - - - - - - tier2 1091 0 0 308 0 0 0 0 NA 933124 TCGA-AB-2993 AML01 17 22336285 22336285 G T SNP - - - - - - - - - - - - - - - tier3 908 129 12.42 497 324 39.23 0 0 NA 933124 TCGA-AB-2993 AML01 17 34068941 34068942 - T INS MLLT6 NM_005937.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46471 NULL 0.002:0.002 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 17 35085722 35085722 C A SNP PERLD1 NM_033419.3 human genbank 54_36p -1 validated intronic c.433-1264 e4-1264 0 - - - no_errors tier3 2301 437 15.93 999 830 45.28 2 1 33.33 933124 TCGA-AB-2993 AML01 17 35479804 35479804 C T SNP THRA NM_003250.4 human genbank 54_36p 1 reviewed intronic c.1-4167 e1-4167 0.979 - - - no_errors tier3 1372 209 13.07 139 134 48.03 2 2 50 933124 TCGA-AB-2993 AML01 17 40722465 40722465 A G SNP MAP3K14 ENST00000344686 human ensembl 54_36p -1 known intronic c.257-11 e2-11 0.001 - - - no_errors tier3 2553 387 13.16 602 531 46.78 1 4 80 933124 TCGA-AB-2993 AML01 17 43068885 43068885 G T SNP LOC728896 XM_001719193.1 human genbank 54_36p -1 model missense c.138 p.F46L 0.078 NULL NULL - no_errors tier1 1446 260 15.23 535 481 47.2 2 0 933124 TCGA-AB-2993 AML01 17 45162654 45162654 G T SNP FAM117A NM_030802.3 human genbank 54_36p -1 validated intronic c.366+2258 e2+2258 0.686 - - - no_errors tier2 1834 349 15.97 795 668 45.47 5 4 44.44 933124 TCGA-AB-2993 AML01 17 53018928 53018928 C T SNP MSI2 NM_138962.2 human genbank 54_36p 1 reviewed intronic c.455-10300 e8-10300 0 - - - no_errors tier3 1344 175 11.48 363 275 43.04 8 5 38.46 933124 TCGA-AB-2993 AML01 17 73280214 73280214 C T SNP - - - - - - - - - - - - - - - tier3 1245 206 14.19 437 349 44.4 0 0 NA 933124 TCGA-AB-2993 AML01 18 7332101 7332101 T C SNP ENSG00000212626 ENST00000391324 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40950 NULL 0.001 - - - no_errors tier3 1660 286 14.68 617 625 50.32 0 0 NA 933124 TCGA-AB-2993 AML01 18 13846987 13846987 C T SNP ENSG00000211528 ENST00000390194 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33002 NULL 0.001 - - - no_errors tier3 1399 0 0 482 2 0.41 0 0 NA 933124 TCGA-AB-2993 AML01 18 25078580 25078580 T G SNP ENSG00000212085 ENST00000390796 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*48090 NULL 0.001 - - - no_errors tier3 1308 99 7.04 787 236 23.02 0 0 NA 933124 TCGA-AB-2993 AML01 18 27511211 27511211 A C SNP B4GALT6 NM_004775.3 human genbank 54_36p -1 reviewed intronic c.115+7062 e1+7062 0.021 - - - no_errors tier3 1032 188 15.41 107 81 43.09 6 2 25 933124 TCGA-AB-2993 AML01 18 30238019 30238019 C T SNP - - - - - - - - - - - - - - - tier3 1172 241 17.06 672 631 48.35 0 0 NA 933124 TCGA-AB-2993 AML01 18 36377895 36377895 G A SNP - - - - - - - - - - - - - - - tier3 1360 214 13.6 474 374 44.05 0 0 NA 933124 TCGA-AB-2993 AML01 18 43806086 43806086 G A SNP ZBTB7C NM_001039360.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*3543 NULL 0.041 - - - no_errors tier3 732 135 15.57 140 104 42.62 0 0 NA 933124 TCGA-AB-2993 AML01 18 70969390 70969390 C T SNP C18orf33 XM_001714254.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22194 NULL 0 - - - no_errors tier3 1403 253 15.23 530 368 40.84 0 0 NA 933124 TCGA-AB-2993 AML01 18 73710705 73710705 T C SNP - - - - - - - - - - - - - - - tier3 2777 487 14.91 1557 1268 44.84 0 0 NA 933124 TCGA-AB-2993 AML01 19 7615495 7615495 C T SNP STXBP2 NM_006949.1 human genbank 54_36p 1 validated splice_region c.1108-5 e14-5 0.115 - - - no_errors tier2 1129 222 16.36 656 635 49.07 5 7 50 933124 TCGA-AB-2993 AML01 19 14631846 14631846 T C SNP EMR3 NM_032571.3 human genbank 54_36p -1 reviewed intronic c.356-1484 e5-1484 0.714 - - - no_errors tier2 1503 238 13.66 148 126 45.82 0 0 0 933124 TCGA-AB-2993 AML01 19 18478169 18478169 T G SNP ELL NM_006532.2 human genbank 54_36p -1 validated intronic c.135+15562 e1+15562 0.002 - - - no_errors tier3 1044 114 9.84 508 384 42.76 1 1 50 933124 TCGA-AB-2993 AML01 19 33657718 33657718 C T SNP - - - - - - - - - - - - - - - tier3 2929 435 12.93 1059 1043 49.53 0 0 NA 933124 TCGA-AB-2993 AML01 20 30031568 30031568 G A SNP XKR7 NM_001011718.1 human genbank 54_36p 1 provisional intronic c.584+11345 e1+11345 0.997 - - - no_errors tier3 543 75 12.14 154 97 38.49 0 0 NA 933124 TCGA-AB-2993 AML01 20 36495690 36495690 T C SNP ENSG00000196756 ENST00000360896 human ensembl 54_36p -1 known intronic c.174+871 e2+871 0.17 - - - no_start_codon tier3 524 72 12.06 153 143 48.31 3 9 69.23 933124 TCGA-AB-2993 AML01 20 36667333 36667333 G T SNP C20orf95 XM_293123.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-18105 NULL 0.002 - - - no_errors tier3 1919 411 17.64 1352 1324 49.38 0 0 NA 933124 TCGA-AB-2993 AML01 20 39017156 39017156 C T SNP LOC100128988 XM_001721091.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-25731 NULL 0.001 - - - no_errors tier3 2011 362 15.24 562 446 44.16 0 0 NA 933124 TCGA-AB-2993 AML01 20 40164254 40164254 G A SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed missense c.3695 p.P1232L 1 "HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II" "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMSmart_SM00404,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,PatternScan_TYR_PHOSPHATASE_1,superfamily_Immunoglobulin,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 1491 314 17.39 791 711 47.27 NA 933124 TCGA-AB-2993 AML01 20 43469052 43469052 G C SNP LOC100128997 XM_001721816.1 human genbank 54_36p -1 model 5_prime_untranslated_region c.-626 NULL 0.002 - - - no_errors tier2 397 0 0 221 0 0 0 0 0 933124 TCGA-AB-2993 AML01 21 23804253 23804253 G A SNP - - - - - - - - - - - - - - - tier3 1519 228 13.03 354 281 44.18 0 0 NA 933124 TCGA-AB-2993 AML01 21 40246036 40246036 T C SNP PCP4 NM_006198.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*23130 NULL 0.246 - - - no_errors tier2 853 157 15.54 832 676 44.77 0 0 NA 933124 TCGA-AB-2993 AML01 21 40336315 40336315 A G SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated silent c.5539 p.L1847 1 NULL "HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 495 85 14.63 784 745 48.69 NA 933124 TCGA-AB-2993 AML01 21 45379918 45379918 G A SNP ADARB1 NM_015833.1 human genbank 54_36p 1 reviewed intronic c.1+7002 e0+7002 0.006 - - - no_errors tier3 991 172 14.79 419 372 46.97 1 0 0 933124 TCGA-AB-2993 AML01 21 45384952 45384953 - GTA INS ADARB1 NM_015833.1 human genbank 54_36p 1 reviewed intronic c.1+12036_12037 e0+12036 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 933124 TCGA-AB-2993 AML01 22 15941647 15941647 C T SNP IL17RA NM_014339.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-4335 NULL 0.01 - - - no_errors tier3 1301 207 13.66 444 369 45.33 0 0 NA 933124 TCGA-AB-2993 AML01 22 24837011 24837011 G A SNP - - - - - - - - - - - - - - - tier3 2452 408 14.24 1405 1007 41.66 0 0 NA 933124 TCGA-AB-2993 AML01 22 26431410 26431410 C A SNP MN1 NM_002430.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*45493 NULL 0.003 - - - no_errors tier3 3471 689 16.55 1538 1240 44.59 0 0 NA 933124 TCGA-AB-2993 AML01 22 47444827 47444827 G A SNP FAM19A5 ENST00000402357 human ensembl 54_36p 1 known intronic c.262+15833 e2+15833 0 - - - no_errors tier3 1034 209 16.81 521 463 46.96 0 0 NA 709968 TCGA-AB-2994 AML09 X 2149342 2149342 A G SNP DHRSX NM_145177.2 human genbank 54_36p -1 validated intronic c.805-72 e7-72 0.041 - - - no_errors tier3 540 7 1.28 342 131 27.7 7 6 46.15 709968 TCGA-AB-2994 AML09 X 7739945 7739945 G A SNP VCX NM_013452.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-31300 NULL 0 - - - no_errors tier3 361 9 2.43 260 230 46.84 0 0 NA 709968 TCGA-AB-2994 AML09 X 65635563 65635563 C T SNP ENSG00000217558 ENST00000403381 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*65635563 NULL 1 - - - no_coding_region:pseudogene tier2 325 10 2.99 209 530 71.72 0 0 NA 709968 TCGA-AB-2994 AML09 X 71340236 71340236 A G SNP ERCC6L NM_017669.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*1353 NULL 0.011 - - - no_errors tier3 820 36 4.2 549 1211 68.81 1 3 75 709968 TCGA-AB-2994 AML09 1 9321497 9321497 A G SNP SPSB1 NM_025106.3 human genbank 54_36p 1 validated intronic c.1-16892 e1-16892 0 - - - no_errors tier3 807 20 2.41 606 168 21.71 1 0 0 709968 TCGA-AB-2994 AML09 1 19716100 19716100 C G SNP CAPZB NM_004930.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31581 NULL 0.001 - - - no_errors tier3 1413 29 2.01 694 372 34.86 0 0 NA 709968 TCGA-AB-2994 AML09 1 33692230 33692231 - A INS ZSCAN20 NM_145238.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25247 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 709968 TCGA-AB-2994 AML09 1 37195298 37195298 G A SNP GRIK3 NM_000831.3 human genbank 54_36p -1 reviewed intronic c.116-66014 e2-66014 0.007 - - - no_errors tier3 2722 33 1.2 1423 805 36.13 0 0 NA 709968 TCGA-AB-2994 AML09 1 64475512 64475512 C T SNP UBE2U NM_152489.1 human genbank 54_36p 1 provisional intronic c.596-4411 e8-4411 0.054 - - - no_errors tier3 592 5 0.84 850 452 34.72 0 0 NA 709968 TCGA-AB-2994 AML09 1 75755880 75755880 C G SNP SLC44A5 NM_152697.1 human genbank 54_36p -1 validated intronic c.13+23828 e1+23828 0.038 - - - no_errors tier2 1390 25 1.77 1341 790 37.07 0 0 NA 709968 TCGA-AB-2994 AML09 1 80908495 80908495 C T SNP - - - - - - - - - - - - - - - tier3 908 11 1.2 1278 363 22.12 0 0 NA 709968 TCGA-AB-2994 AML09 1 82908708 82908708 A G SNP - - - - - - - - - - - - - - - tier3 1343 39 2.82 1483 842 36.2 0 0 NA 709968 TCGA-AB-2994 AML09 1 92385369 92385369 T A SNP BTBD8 NM_183242.3 human genbank 54_36p 1 validated silent c.975 p.I325 1 NULL "HMMSmart_SM00225,superfamily_POZ domain,HMMPfam_BTB" - no_errors tier1 608 9 1.46 895 505 36.07 2 1 33.33 709968 TCGA-AB-2994 AML09 1 97208709 97208709 G A SNP - - - - - - - - - - - - - - - tier2 794 13 1.61 982 523 34.7 0 0 NA 709968 TCGA-AB-2994 AML09 1 101492601 101492601 G A SNP LOC100131646 XM_001719599.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-15573 NULL 0.002 - - - no_errors tier2 440 11 2.43 612 329 34.96 0 0 NA 709968 TCGA-AB-2994 AML09 1 114319879 114319879 A G SNP HIPK1 NM_198268.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*2222 NULL 0.821 - - - no_errors tier3 1091 11 1 989 562 36.16 73 66 47.48 709968 TCGA-AB-2994 AML09 1 155712256 155712256 T C SNP FCRL5 NM_031281.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*39833 NULL 0.199 - - - no_errors tier3 776 11 1.4 730 416 36.27 0 0 NA 709968 TCGA-AB-2994 AML09 1 160944846 160944846 C T SNP DDR2 NM_001014796.1 human genbank 54_36p 1 reviewed intronic c.1+3301 e0+3301 0.06 - - - no_errors tier3 1949 32 1.61 1278 362 22.03 0 0 NA 709968 TCGA-AB-2994 AML09 1 167830362 167830362 C T SNP SELP NM_003005.3 human genbank 54_36p -1 reviewed intronic c.2287+192 e13+192 0.001 - - - no_errors tier3 509 11 2.12 784 352 30.96 0 0 0 709968 TCGA-AB-2994 AML09 1 178417868 178417868 G T SNP QSOX1 NM_002826.2 human genbank 54_36p 1 reviewed intronic c.607-64 e6-64 0 - - - no_errors tier3 2076 25 1.19 860 553 39.11 3 6 66.67 709968 TCGA-AB-2994 AML09 1 206349793 206349793 G A SNP PLXNA2 NM_025179.3 human genbank 54_36p -1 reviewed intronic c.1507-6578 e4-6578 0 - - - no_errors tier3 1867 36 1.89 1042 559 34.92 0 1 100 709968 TCGA-AB-2994 AML09 1 207012790 207012790 G A SNP - - - - - - - - - - - - - - - tier3 1775 17 0.95 2044 1165 36.27 0 0 NA 709968 TCGA-AB-2994 AML09 1 211557294 211557294 A G SNP RPS6KC1 NM_012424.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*44694 NULL 0 - - - no_errors tier3 663 37 5.28 351 447 55.94 0 1 100 709968 TCGA-AB-2994 AML09 1 222549891 222549891 T C SNP NVL NM_002533.2 human genbank 54_36p -1 validated intronic c.1180+935 e11+935 0.102 - - - no_errors tier3 1409 16 1.12 1179 427 26.57 1 0 0 709968 TCGA-AB-2994 AML09 1 225813215 225813215 C T SNP ZNF678 NM_178549.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-92101 NULL 0 - - - no_errors tier3 910 30 3.19 921 458 33.16 0 0 NA 709968 TCGA-AB-2994 AML09 2 19099 19099 G T SNP LOC728944 XM_001128859.2 human genbank 54_36p -1 model splice_region c.1614+8 e5+8 0.012 - - - no_start_codon:pseudogene:no_stop_codon tier3 1341 29 2.12 1133 410 26.54 0 0 NA 709968 TCGA-AB-2994 AML09 2 421800 421800 G A SNP - - - - - - - - - - - - - - - tier3 605 5 0.82 755 242 24.27 0 0 NA 709968 TCGA-AB-2994 AML09 2 2154657 2154657 T A SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.1+994 e0+994 0.715 - - - no_errors tier2 1119 24 2.1 875 476 35.21 0 0 NA 709968 TCGA-AB-2994 AML09 2 14885000 14885000 G T SNP - - - - - - - - - - - - - - - tier3 1469 23 1.54 1442 825 36.34 0 0 NA 709968 TCGA-AB-2994 AML09 2 47426613 47426613 T C SNP EPCAM ENST00000405271 human ensembl 54_36p 1 known intronic c.1+747 e0+747 0.001 - - - no_errors tier3 1016 27 2.59 702 376 34.88 0 0 NA 709968 TCGA-AB-2994 AML09 2 55007989 55007989 C G SNP EML6 XM_001725001.2 human genbank 54_36p 1 model intronic c.3676-965 e26-965 0.001 - - - no_errors tier3 654 13 1.95 467 227 32.71 0 0 NA 709968 TCGA-AB-2994 AML09 2 64440075 64440075 C T SNP LOC130773 XM_065899.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-11698 NULL 0.006 - - - pseudogene tier3 801 15 1.83 583 320 35.44 0 0 NA 709968 TCGA-AB-2994 AML09 2 66150824 66150824 G A SNP ENSG00000221524 ENST00000408597 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*28796 NULL 0.146 - - - no_errors tier3 2378 57 2.34 1540 694 31.07 0 0 NA 709968 TCGA-AB-2994 AML09 2 75690828 75690828 C T SNP MRPL19 NM_014763.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36614 NULL 0 - - - no_errors tier2 831 20 2.35 676 357 34.53 0 0 NA 709968 TCGA-AB-2994 AML09 2 98762970 98762970 T C SNP MGAT4A NM_012214.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-53743 NULL 0.001 - - - no_errors tier3 645 6 0.92 568 329 36.68 0 0 NA 709968 TCGA-AB-2994 AML09 2 112710625 112710625 G A SNP ZC3H8 NM_032494.2 human genbank 54_36p -1 validated silent c.489 p.S163 0 NULL "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" - no_errors tier1 1187 34 2.78 1246 642 33.99 5 6 54.55 709968 TCGA-AB-2994 AML09 2 122302708 122302708 C T SNP LOC646179 XR_040904.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*32306 NULL 0.001 - - - no_errors tier3 1373 11 0.79 1305 354 21.34 0 0 NA 709968 TCGA-AB-2994 AML09 2 132999292 132999292 C T SNP GPR39 NM_001508.2 human genbank 54_36p 1 validated intronic c.856+107351 e1+107351 0.001 - - - no_errors tier3 1250 8 0.64 1070 547 33.79 0 0 NA 709968 TCGA-AB-2994 AML09 2 168142964 168142964 C T SNP LOC643496 XR_041928.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*19875 NULL 0 - - - no_errors tier3 1226 44 3.46 1046 633 37.7 0 0 NA 709968 TCGA-AB-2994 AML09 2 169917047 169917047 G A SNP LRP2 NM_004525.2 human genbank 54_36p -1 validated intronic c.79+10030 e1+10030 0.004 - - - no_errors tier2 1637 10 0.61 2075 668 24.32 0 0 NA 709968 TCGA-AB-2994 AML09 2 206568094 206568094 T C SNP INO80D NM_017759.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*9243 NULL 0.983 - - - no_errors tier2 748 7 0.93 820 453 35.59 29 24 45.28 709968 TCGA-AB-2994 AML09 3 14385016 14385016 C A SNP SLC6A6 NM_003043.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-75131 NULL 0 - - - no_errors tier3 2731 40 1.44 1166 714 37.98 0 0 NA 709968 TCGA-AB-2994 AML09 3 18470717 18470717 C T SNP LOC100132345 XM_001716679.1 human genbank 54_36p 1 model intronic c.274+8779 e2+8779 0.002 - - - no_errors tier3 696 17 2.38 438 239 35.2 2 5 71.43 709968 TCGA-AB-2994 AML09 3 36642048 36642048 A G SNP - - - - - - - - - - - - - - - tier3 1388 17 1.21 1434 841 36.97 0 0 NA 709968 TCGA-AB-2994 AML09 3 36748557 36748557 G A SNP DCLK3 NM_033403.1 human genbank 54_36p -1 validated intronic c.1452+5146 e1+5146 0.003 - - - no_errors tier2 1970 34 1.7 1901 966 33.69 0 0 NA 709968 TCGA-AB-2994 AML09 3 68564508 68564508 C T SNP FAM19A1 NM_213609.2 human genbank 54_36p 1 reviewed intronic c.259+15248 e2+15248 0.004 - - - no_errors tier2 1924 37 1.89 1439 800 35.71 0 0 NA 709968 TCGA-AB-2994 AML09 3 117930258 117930258 A T SNP - - - - - - - - - - - - - - - tier3 1711 26 1.5 1706 507 22.91 0 0 NA 709968 TCGA-AB-2994 AML09 3 140998899 140998899 C T SNP - - - - - - - - - - - - - - - tier3 2492 76 2.96 2040 1112 35.25 0 0 NA 709968 TCGA-AB-2994 AML09 3 141415097 141415097 C G SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.232+37492 e2+37492 0.002 - - - no_errors tier2 2047 24 1.16 1654 944 36.32 0 0 NA 709968 TCGA-AB-2994 AML09 3 151241702 151241702 C G SNP ENSG00000216176 ENST00000401357 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*49757 NULL 0.004 - - - no_errors tier3 878 10 1.12 1177 715 37.77 0 0 NA 709968 TCGA-AB-2994 AML09 3 162586382 162586382 C G SNP C3orf57 NM_001040100.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-39577 NULL 0 - - - no_errors tier3 749 6 0.79 974 561 36.55 0 0 NA 709968 TCGA-AB-2994 AML09 3 169141155 169141155 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 709968 TCGA-AB-2994 AML09 4 1358069 1358069 C A SNP KIAA1530 NM_020894.2 human genbank 54_36p 1 validated intronic c.1289-1083 e8-1083 0.038 - - - no_errors tier3 117 2 1.68 101 88 46.56 3 0 0 709968 TCGA-AB-2994 AML09 4 6010214 6010214 G A SNP FLJ46481 NM_207405.1 human genbank 54_36p -1 predicted 3_prime_untranslated_region c.*1789 NULL 0 - - - no_errors tier2 1084 30 2.69 655 362 35.56 0 0 NA 709968 TCGA-AB-2994 AML09 4 9926768 9926768 G A SNP - - - - - - - - - - - - - - - tier3 729 2 0.27 561 277 33.02 0 0 NA 709968 TCGA-AB-2994 AML09 4 11225517 11225517 T C SNP - - - - - - - - - - - - - - - tier3 1374 21 1.51 1174 717 37.92 0 0 NA 709968 TCGA-AB-2994 AML09 4 18402045 18402045 T A SNP - - - - - - - - - - - - - - - tier3 1147 24 2.05 1149 593 34.02 0 0 NA 709968 TCGA-AB-2994 AML09 4 19174678 19174678 G A SNP - - - - - - - - - - - - - - - tier3 1139 8 0.69 1209 655 34.9 0 0 NA 709968 TCGA-AB-2994 AML09 4 27933461 27933461 C T SNP - - - - - - - - - - - - - - - tier3 616 11 1.75 885 472 34.78 0 0 NA 709968 TCGA-AB-2994 AML09 4 30494192 30494192 T C SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3034-36681 e3-36681 0.002 - - - no_errors tier3 1422 22 1.52 1174 433 26.94 0 0 NA 709968 TCGA-AB-2994 AML09 4 55087415 55087415 T C SNP - - - - - - - - - - - - - - - tier2 1680 30 1.75 1853 894 32.54 0 0 NA 709968 TCGA-AB-2994 AML09 4 64905204 64905204 A T SNP SRD5A2L2 NM_001010874.4 human genbank 54_36p -1 validated intronic c.286+18281 e2+18281 0.016 - - - no_errors tier3 246 0 0 547 297 35.19 0 0 NA 709968 TCGA-AB-2994 AML09 4 71445135 71445135 G A SNP AMBN NM_016519.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47530 NULL 0 - - - no_errors tier2 1120 11 0.97 1508 771 33.83 0 0 NA 709968 TCGA-AB-2994 AML09 4 76113392 76113392 G A SNP DKFZP564O0823 NM_015393.2 human genbank 54_36p 1 validated intronic c.43+35788 e1+35788 0 - - - no_errors tier3 998 23 2.25 1114 597 34.89 0 0 NA 709968 TCGA-AB-2994 AML09 4 81442449 81442449 T - DEL C4orf22 NM_152770.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-33498 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 709968 TCGA-AB-2994 AML09 4 85654249 85654249 C T SNP NKX6-1 NM_006168.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-15844 NULL 0.029 - - - no_errors tier2 1521 32 2.06 1462 765 34.34 0 0 NA 709968 TCGA-AB-2994 AML09 4 101039393 101039393 T C SNP MAPKSP1 NM_021970.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-5250 NULL 0.343 - - - no_errors tier3 486 13 2.61 412 221 34.91 9 11 55 709968 TCGA-AB-2994 AML09 4 105168042 105168042 G A SNP - - - - - - - - - - - - - - - tier3 1211 21 1.7 1149 568 33.06 0 0 NA 709968 TCGA-AB-2994 AML09 4 127063975 127063975 G C SNP - - - - - - - - - - - - - - - tier3 809 10 1.22 937 453 32.57 0 0 NA 709968 TCGA-AB-2994 AML09 4 133925778 133925778 G A SNP - - - - - - - - - - - - - - - tier3 647 5 0.77 817 444 35.21 0 0 NA 709968 TCGA-AB-2994 AML09 4 138066825 138066825 A T SNP LOC729578 XM_001130691.2 human genbank 54_36p -1 model intronic c.110-9995 e3-9995 0.001 - - - no_errors tier2 490 6 1.21 653 203 23.71 0 0 NA 709968 TCGA-AB-2994 AML09 4 142982747 142982747 C T SNP - - - - - - - - - - - - - - - tier3 813 7 0.85 1162 594 33.81 0 0 NA 709968 TCGA-AB-2994 AML09 4 146086236 146086236 A T SNP ANAPC10 NM_014885.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*49739 NULL 0.017 - - - no_errors tier3 2627 34 1.28 2310 1319 36.33 1 1 50 709968 TCGA-AB-2994 AML09 4 154974350 154974350 G A SNP SFRP2 NM_003013.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-44913 NULL 0 - - - no_errors tier3 1725 56 3.14 2161 1179 35.28 0 0 NA 709968 TCGA-AB-2994 AML09 4 155324451 155324451 G A SNP - - - - - - - - - - - - - - - tier3 1020 14 1.35 892 277 23.7 0 0 NA 709968 TCGA-AB-2994 AML09 4 161164281 161164281 C T SNP - - - - - - - - - - - - - - - tier2 1996 30 1.48 2460 1381 35.95 0 0 NA 709968 TCGA-AB-2994 AML09 4 186699950 186699950 C A SNP PDLIM3 NM_014476.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-6368 NULL 0 - - - no_errors tier3 2685 21 0.78 1373 739 34.92 0 0 NA 709968 TCGA-AB-2994 AML09 5 6945292 6945292 C T SNP ENSG00000200243 ENST00000363373 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43717 NULL 0.002 - - - no_errors tier3 1126 14 1.23 750 406 35.12 0 0 NA 709968 TCGA-AB-2994 AML09 5 8300276 8300276 G T SNP - - - - - - - - - - - - - - - tier3 990 16 1.59 755 427 36.13 0 0 NA 709968 TCGA-AB-2994 AML09 5 17440780 17440780 C T SNP ENSG00000201715 ENST00000364845 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41719 NULL 0.004 - - - no_errors tier3 1348 15 1.1 932 449 32.51 0 0 NA 709968 TCGA-AB-2994 AML09 5 26722536 26722536 T A SNP LOC100131678 XM_001722351.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*25247 NULL 0.004 - - - no_errors tier3 642 5 0.77 657 398 37.73 0 0 NA 709968 TCGA-AB-2994 AML09 5 31499037 31499037 G A SNP RNASEN NM_013235.1 human genbank 54_36p -1 validated intronic c.2574+1063 e17+1063 0 - - - no_errors tier3 1307 19 1.43 1325 718 35.14 2 0 0 709968 TCGA-AB-2994 AML09 5 38411137 38411137 C T SNP EGFLAM NM_152403.2 human genbank 54_36p 1 validated intronic c.712+4816 e6+4816 0.017 - - - no_errors tier3 1256 20 1.57 1151 629 35.34 0 0 NA 709968 TCGA-AB-2994 AML09 5 41253661 41253661 T C SNP C6 ENST00000263413 human ensembl 54_36p -1 known intronic c.1-14552 e1-14552 0.002 - - - no_errors tier3 627 13 2.03 895 516 36.54 0 0 NA 709968 TCGA-AB-2994 AML09 5 77108261 77108261 C A SNP TBCA NM_004607.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-424 NULL 0.007 - - - no_errors tier2 912 21 2.25 886 493 35.7 0 0 NA 709968 TCGA-AB-2994 AML09 5 92299536 92299536 C T SNP LOC391810 XM_001723772.1 human genbank 54_36p -1 model intronic c.277-7392 e3-7392 0.002 - - - pseudogene tier3 701 6 0.85 1137 521 31.4 0 0 NA 709968 TCGA-AB-2994 AML09 5 122574760 122574760 C T SNP ENSG00000213655 ENST00000395448 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24908 NULL 0 - - - no_coding_region:pseudogene tier3 610 2 0.33 590 289 32.84 0 0 NA 709968 TCGA-AB-2994 AML09 5 125781864 125781864 G A SNP GRAMD3 NM_023927.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-5334 NULL 0.001 - - - no_errors tier3 1199 17 1.4 1084 633 36.85 0 0 NA 709968 TCGA-AB-2994 AML09 5 127784564 127784564 C T SNP FBN2 NM_001999.3 human genbank 54_36p -1 reviewed intronic c.953-12173 e8-12173 0.001 - - - no_errors tier2 616 8 1.28 1041 610 36.92 0 0 0 709968 TCGA-AB-2994 AML09 5 134963893 134963893 A G SNP CXCL14 NM_004887.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-21490 NULL 0.002 - - - no_errors tier3 1584 41 2.52 1287 625 32.6 0 0 NA 709968 TCGA-AB-2994 AML09 5 140352282 140352282 G T SNP PCDHAC2 NM_018899.4 human genbank 54_36p 1 reviewed intronic c.2713+9950 e3+9950 0 - - - no_errors tier3 2078 7 0.34 1280 711 35.69 0 0 NA 709968 TCGA-AB-2994 AML09 5 167621693 167621693 G T SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known missense c.7622 p.G2541V 1 NULL "HMMPfam_NHL,HMMPfam_EGF,HMMSmart_SM00181,HMMPfam_RHS_repeat,superfamily_Carboxypeptidase regulatory domain,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Ten_N,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_NHL repeat,superfamily_EGF/Laminin" - no_errors tier1 1844 54 2.84 969 553 36.29 NA 709968 TCGA-AB-2994 AML09 6 12893812 12893812 G C SNP PHACTR1 NM_030948.1 human genbank 54_36p 1 validated intronic c.250+35804 e2+35804 0.002 - - - no_errors tier3 1066 15 1.39 1249 675 35.05 0 0 NA 709968 TCGA-AB-2994 AML09 6 16001045 16001045 T C SNP LOC441131 XR_016719.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-41947 NULL 0.009 - - - pseudogene tier3 1517 26 1.69 1152 732 38.81 0 0 NA 709968 TCGA-AB-2994 AML09 6 18211756 18211756 A T SNP TPMT NM_000367.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*27122 NULL 0.003 - - - no_errors tier3 875 20 2.23 952 486 33.75 0 0 NA 709968 TCGA-AB-2994 AML09 6 20104854 20104854 G A SNP ENSG00000177246 ENST00000320470 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46105 NULL 0 - - - no_coding_region:pseudogene tier3 1493 9 0.6 1546 461 22.97 0 0 NA 709968 TCGA-AB-2994 AML09 6 26482365 26482365 G A SNP BTN3A2 NM_007047.3 human genbank 54_36p 1 reviewed intronic c.965-169 e7-169 0.004 - - - no_errors tier3 913 22 2.35 665 323 32.66 2 0 0 709968 TCGA-AB-2994 AML09 6 33907684 33907684 T G SNP MLN NM_002418.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-30766 NULL 0 - - - no_errors tier3 156 8 4.88 348 121 25.8 0 0 NA 709968 TCGA-AB-2994 AML09 6 39807623 39807623 T A SNP KIF6 NM_145027.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-6559 NULL 0.87 - - - no_errors tier3 2664 36 1.33 2849 1719 37.61 0 0 NA 709968 TCGA-AB-2994 AML09 6 54097557 54097557 G A SNP C6orf142 NM_138569.2 human genbank 54_36p 1 validated missense c.547 p.D183N 0.239 NULL NULL - no_errors tier1 1236 13 1.04 1051 553 34.48 NA 709968 TCGA-AB-2994 AML09 6 64147212 64147212 C T SNP ENSG00000218617 ENST00000406684 human ensembl 54_36p 1 known 5_prime_flanking_region c.-12874 NULL 0.003 - - - no_coding_region:pseudogene tier3 1312 19 1.43 1056 549 34.18 0 0 NA 709968 TCGA-AB-2994 AML09 6 70061918 70061918 T C SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.2815-29567 e19-29567 0 - - - no_errors tier3 1245 12 0.95 898 466 34.16 0 0 NA 709968 TCGA-AB-2994 AML09 6 99240687 99240687 G A SNP - - - - - - - - - - - - - - - tier3 2233 28 1.24 2501 1212 32.63 0 0 NA 709968 TCGA-AB-2994 AML09 6 99746826 99746826 C A SNP ENSG00000168768 ENST00000305402 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*16716 NULL 0.057 - - - no_coding_region:pseudogene tier3 1185 16 1.33 975 538 35.56 0 0 NA 709968 TCGA-AB-2994 AML09 6 99840752 99840752 G T SNP C6orf168 NM_032511.2 human genbank 54_36p -1 validated intronic c.941-4702 e6-4702 0.003 - - - no_errors tier2 3340 37 1.1 2776 1272 31.42 0 0 NA 709968 TCGA-AB-2994 AML09 6 112439245 112439245 C G SNP WISP3 NM_198239.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-42955 NULL 0 - - - no_errors tier2 1967 16 0.81 1920 1036 35.04 0 0 NA 709968 TCGA-AB-2994 AML09 6 128811258 128811258 G A SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.101-50732 e2-50732 0 - - - no_errors tier3 1204 15 1.23 1423 724 33.72 0 0 NA 709968 TCGA-AB-2994 AML09 6 147078102 147078102 C G SNP C6orf103 ENST00000326929 human ensembl 54_36p 1 known intronic c.1708-109 e14-109 0 - - - no_errors tier3 173 4 2.26 369 108 22.55 0 0 NA 709968 TCGA-AB-2994 AML09 6 163581549 163581549 G T SNP PACRG NM_152410.1 human genbank 54_36p 1 reviewed intronic c.614-72252 e5-72252 0 - - - no_errors tier2 839 6 0.71 943 433 31.45 0 0 NA 709968 TCGA-AB-2994 AML09 6 166536612 166536612 G A SNP T NM_003181.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-35543 NULL 0 - - - no_errors tier3 828 16 1.9 675 389 36.53 0 0 NA 709968 TCGA-AB-2994 AML09 7 2601193 2601193 C T SNP IQCE NM_152558.1 human genbank 54_36p 1 validated intronic c.1440+57 e16+57 0 - - - no_errors tier3 1310 10 0.76 961 574 37.35 1 2 66.67 709968 TCGA-AB-2994 AML09 7 4041681 4041681 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.2603-13825 e18-13825 0 - - - no_errors tier3 1160 17 1.44 1319 732 35.67 0 0 NA 709968 TCGA-AB-2994 AML09 7 15501168 15501168 G C SNP TMEM195 NM_001004320.1 human genbank 54_36p -1 provisional intronic c.409+49754 e3+49754 0 - - - no_errors tier3 1009 6 0.59 1326 659 33.15 0 0 NA 709968 TCGA-AB-2994 AML09 7 24921256 24921256 A G SNP OSBPL3 NM_015550.2 human genbank 54_36p -1 reviewed intronic c.1-22491 e1-22491 0 - - - no_errors tier3 1679 38 2.21 1491 867 36.72 0 0 0 709968 TCGA-AB-2994 AML09 7 31034986 31034986 A T SNP ADCYAP1R1 NM_001118.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34420 NULL 0.938 - - - no_errors tier3 930 13 1.38 380 206 34.97 0 0 NA 709968 TCGA-AB-2994 AML09 7 42248874 42248874 G A SNP GLI3 NM_000168.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-19497 NULL 0 - - - no_errors tier2 464 7 1.48 429 224 34.3 0 0 NA 709968 TCGA-AB-2994 AML09 7 46151335 46151335 G T SNP - - - - - - - - - - - - - - - tier3 1266 16 1.25 1056 545 34.04 0 0 NA 709968 TCGA-AB-2994 AML09 7 50212336 50212336 T A SNP LOC100130988 XM_001713888.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*43025 NULL 0.191 - - - no_errors tier3 1981 40 1.98 1236 690 35.81 0 0 NA 709968 TCGA-AB-2994 AML09 7 50891091 50891091 A G SNP - - - - - - - - - - - - - - - tier3 2324 32 1.36 1588 838 34.51 0 0 NA 709968 TCGA-AB-2994 AML09 7 52285664 52285664 T C SNP ENSG00000210739 ENST00000388004 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*18971 NULL 0.002 - - - pseudogene tier3 669 15 2.19 750 362 32.52 0 0 NA 709968 TCGA-AB-2994 AML09 7 55306372 55306372 G T SNP - - - - - - - - - - - - - - - tier2 921 25 2.64 928 472 33.71 0 0 NA 709968 TCGA-AB-2994 AML09 7 70252371 70252371 G T SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.238+16409 e1+16409 0.001 - - - no_errors tier3 1129 12 1.05 1034 544 34.45 0 0 NA 709968 TCGA-AB-2994 AML09 7 75352663 75352663 C T SNP RHBDD2 NM_001040456.1 human genbank 54_36p 1 validated intronic c.737+1561 e3+1561 0 - - - no_errors tier2 854 18 2.06 337 176 34.24 2 9 81.82 709968 TCGA-AB-2994 AML09 7 78500294 78500294 G T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.302-25836 e2-25836 0.003 - - - no_errors tier2 583 6 1.02 984 292 22.88 0 0 NA 709968 TCGA-AB-2994 AML09 7 82669219 82669219 C T SNP PCLO NM_033026.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-39375 NULL 0.001 - - - no_errors tier3 407 6 1.45 803 223 21.67 0 0 NA 709968 TCGA-AB-2994 AML09 7 84142852 84142852 C T SNP - - - - - - - - - - - - - - - tier3 529 21 3.82 770 207 21.19 0 0 NA 709968 TCGA-AB-2994 AML09 7 85577296 85577296 C T SNP - - - - - - - - - - - - - - - tier3 780 3 0.38 636 314 33.05 0 0 NA 709968 TCGA-AB-2994 AML09 7 100183007 100183007 G C SNP ZAN ENST00000349350 human ensembl 54_36p 1 known intronic c.932-102 e8-102 0 - - - no_errors tier2 1646 26 1.55 452 227 33.38 0 0 NA 709968 TCGA-AB-2994 AML09 7 100554388 100554388 G A SNP AP1S1 NM_001283.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30128 NULL 0 - - - no_errors tier2 2144 39 1.78 917 598 39.45 0 1 100 709968 TCGA-AB-2994 AML09 7 108585742 108585742 G A SNP - - - - - - - - - - - - - - - tier3 904 7 0.77 839 431 33.94 0 0 NA 709968 TCGA-AB-2994 AML09 7 118907881 118907881 A G SNP - - - - - - - - - - - - - - - tier3 1034 12 1.15 907 602 39.87 0 0 NA 709968 TCGA-AB-2994 AML09 7 119950467 119950467 C T SNP KCND2 NM_012281.2 human genbank 54_36p 1 reviewed intronic c.1116-209726 e2-209726 0 - - - no_errors tier2 568 8 1.39 1066 507 32.21 0 0 NA 709968 TCGA-AB-2994 AML09 7 143430502 143430502 C T SNP OR2A2 NM_001005480.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7107 NULL 0 - - - no_errors tier3 665 1 0.15 738 365 33.06 0 0 NA 709968 TCGA-AB-2994 AML09 7 145735063 145735063 T C SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.97+290065 e1+290065 0 - - - no_errors tier3 1050 16 1.5 938 522 35.7 0 0 NA 709968 TCGA-AB-2994 AML09 7 146747871 146747871 G T SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.1670+24066 e10+24066 0 - - - no_errors tier2 1093 14 1.26 1556 876 36.02 0 0 NA 709968 TCGA-AB-2994 AML09 7 156025291 156025291 C T SNP - - - - - - - - - - - - - - - tier3 631 10 1.56 407 195 32.39 0 0 NA 709968 TCGA-AB-2994 AML09 7 158016548 158016548 G C SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.113-41310 e2-41310 0.008 - - - no_errors tier3 2009 38 1.86 1165 598 33.9 0 0 NA 709968 TCGA-AB-2994 AML09 8 3707250 3707250 C A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.819-108278 e6-108278 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 914 16 1.72 1265 724 36.4 0 0 NA 709968 TCGA-AB-2994 AML09 8 4059846 4059846 G C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.416-182817 e4-182817 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1443 16 1.1 1166 678 36.73 0 0 NA 709968 TCGA-AB-2994 AML09 8 14396517 14396517 G C SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.234+60095 e2+60095 0.012 - - - no_errors tier3 544 12 2.16 555 236 29.84 0 0 NA 709968 TCGA-AB-2994 AML09 8 24867916 24867916 A G SNP NEFL ENST00000221169 human ensembl 54_36p -1 known intronic c.1045-180 e2-180 0 - - - no_errors tier3 983 8 0.81 811 395 32.75 0 0 NA 709968 TCGA-AB-2994 AML09 8 25861666 25861666 G A SNP EBF2 NM_022659.2 human genbank 54_36p -1 validated intronic c.552-39678 e7-39678 0.004 - - - no_errors tier2 1024 18 1.73 745 424 36.21 0 0 NA 709968 TCGA-AB-2994 AML09 8 50423958 50423958 T C SNP ENSG00000199640 ENST00000362770 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*18300 NULL 0.003 - - - no_errors tier3 709 12 1.66 990 566 36.38 0 0 NA 709968 TCGA-AB-2994 AML09 8 50825108 50825108 G A SNP C8orf62 XR_016569.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-8674 NULL 0 - - - pseudogene tier3 807 9 1.1 1077 566 34.45 0 0 NA 709968 TCGA-AB-2994 AML09 8 62562315 62562315 G A SNP RLBP1L1 NM_173519.2 human genbank 54_36p 1 validated intronic c.978-12253 e5-12253 0.002 - - - no_errors tier3 1011 13 1.27 683 330 32.54 0 0 NA 709968 TCGA-AB-2994 AML09 8 85981692 85981692 C A SNP RALYL NM_001100391.1 human genbank 54_36p 1 validated intronic c.898-13992 e9-13992 0.033 - - - no_errors tier3 1345 8 0.59 1086 581 34.77 0 0 NA 709968 TCGA-AB-2994 AML09 8 95680287 95680287 G A SNP KIAA1429 NM_015496.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-45436 NULL 0.022 - - - no_errors tier3 1516 26 1.69 704 393 35.79 0 0 NA 709968 TCGA-AB-2994 AML09 8 109423618 109423618 A C SNP LOC100128549 XM_001724332.1 human genbank 54_36p -1 model intronic c.200-32750 e3-32750 0 - - - no_errors tier3 1243 20 1.58 992 443 30.85 0 0 NA 709968 TCGA-AB-2994 AML09 8 125718426 125718426 G T SNP MTSS1 NM_014751.4 human genbank 54_36p -1 validated intronic c.209-45769 e4-45769 0.002 - - - no_errors tier3 845 8 0.94 924 376 28.92 1 0 0 709968 TCGA-AB-2994 AML09 8 127168808 127168808 A C SNP - - - - - - - - - - - - - - - tier2 1635 34 2.04 1193 614 33.96 0 0 NA 709968 TCGA-AB-2994 AML09 8 135992117 135992117 G C SNP - - - - - - - - - - - - - - - tier2 1356 14 1.02 1002 553 35.56 0 0 NA 709968 TCGA-AB-2994 AML09 8 145743702 145743702 G C SNP KIAA1688 NM_025251.1 human genbank 54_36p -1 validated missense c.1576 p.Q526E 0.411 NULL "HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_MyTH4,HMMSmart_SM00139,HMMPfam_WW,HMMSmart_SM00456,superfamily_WW domain,superfamily_GTPase activation domain GAP" - no_errors tier1 176 4 2.22 149 59 28.37 NA 709968 TCGA-AB-2994 AML09 8 145974246 145974246 G A SNP ZNF34 NM_030580.3 human genbank 54_36p -1 validated silent c.204 p.Y68 0.09 "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352)" "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 777 18 2.26 565 320 36.16 3 3 50 709968 TCGA-AB-2994 AML09 9 8595502 8595502 G A SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.352+27815 e3+27815 0.009 - - - no_errors tier3 741 8 1.07 946 313 24.86 0 0 NA 709968 TCGA-AB-2994 AML09 9 24240372 24240372 G C SNP - - - - - - - - - - - - - - - tier3 1411 18 1.26 1631 829 33.7 0 0 NA 709968 TCGA-AB-2994 AML09 9 94857417 94857417 T A SNP C9orf89 NM_032310.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-41032 NULL 0.005 - - - no_errors tier3 758 19 2.44 607 328 34.97 0 0 NA 709968 TCGA-AB-2994 AML09 9 122020827 122020827 G A SNP MIRN147 ENST00000385079 human ensembl 54_36p -1 known 3_prime_flanking_region c.*26251 NULL 0 - - - no_errors tier3 1588 44 2.7 2035 1129 35.63 0 0 NA 709968 TCGA-AB-2994 AML09 9 131778685 131778685 G A SNP FNBP1 NM_015033.2 human genbank 54_36p -1 reviewed intronic c.345+1880 e4+1880 0.04 - - - no_errors tier3 1267 20 1.55 1054 642 37.81 5 8 61.54 709968 TCGA-AB-2994 AML09 9 139478661 139478661 G A SNP PNPLA7 NM_001098537.1 human genbank 54_36p -1 validated silent c.3108 p.A1036 0.336 "HMMPfam_Patatin,superfamily_FabD/lysophospholipase-like" "HMMPfam_cNMP_binding,HMMSmart_SM00100,HMMPfam_Patatin,superfamily_FabD/lysophospholipase-like,superfamily_cAMP-binding domain-like" - no_errors tier1 316 3 0.94 139 82 36.94 8 4 33.33 709968 TCGA-AB-2994 AML09 10 24832308 24832308 C T SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated intronic c.2001+1828 e9+1828 0.003 - - - no_errors tier2 1375 36 2.55 1247 628 33.49 1 0 0 709968 TCGA-AB-2994 AML09 10 59818835 59818835 G A SNP TFAM NM_003201.1 human genbank 54_36p 1 provisional intronic c.441+250 e4+250 0.008 - - - no_errors tier3 1082 24 2.17 1139 564 33.12 1 1 50 709968 TCGA-AB-2994 AML09 10 72937014 72937014 G A SNP CDH23 NM_022124.4 human genbank 54_36p 1 reviewed intronic c.146-2831 e3-2831 0.003 - - - no_errors tier3 1313 27 2.01 914 465 33.7 0 0 NA 709968 TCGA-AB-2994 AML09 10 76449455 76449455 A C SNP MYST4 NM_012330.2 human genbank 54_36p 1 validated intronic c.2630-891 e12-891 0.842 - - - no_errors tier3 1143 25 2.14 891 456 33.83 1 2 66.67 709968 TCGA-AB-2994 AML09 10 83377921 83377921 G A SNP - - - - - - - - - - - - - - - tier3 912 8 0.87 1094 676 38.19 0 0 NA 709968 TCGA-AB-2994 AML09 10 92326388 92326388 C A SNP - - - - - - - - - - - - - - - tier3 1329 14 1.04 1388 779 35.87 0 0 NA 709968 TCGA-AB-2994 AML09 10 111427349 111427349 C G SNP LOC100132843 XR_037957.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.104 - - - pseudogene tier3 2128 47 2.16 2154 1187 35.52 0 0 NA 709968 TCGA-AB-2994 AML09 10 113724112 113724112 A G SNP - - - - - - - - - - - - - - - tier3 1115 30 2.62 1175 625 34.7 0 0 NA 709968 TCGA-AB-2994 AML09 10 132069924 132069924 G A SNP - - - - - - - - - - - - - - - tier3 978 24 2.4 752 441 36.93 0 0 NA 709968 TCGA-AB-2994 AML09 11 17501723 17501723 C T SNP - - - - - - - - - - - - - - - tier3 2253 50 2.17 1796 991 35.56 0 0 NA 709968 TCGA-AB-2994 AML09 11 27834171 27834171 G T SNP - - - - - - - - - - - - - - - tier3 811 7 0.86 617 272 30.6 0 0 NA 709968 TCGA-AB-2994 AML09 11 30795824 30795824 T C SNP - - - - - - - - - - - - - - - tier3 2080 49 2.3 1435 743 34.07 0 0 NA 709968 TCGA-AB-2994 AML09 11 68923581 68923581 C G SNP - - - - - - - - - - - - - - - tier3 2784 56 1.97 1277 686 34.89 0 0 NA 709968 TCGA-AB-2994 AML09 11 74975387 74975387 G A SNP - - - - - - - - - - - - - - - tier3 1614 16 0.98 1026 593 36.6 0 0 NA 709968 TCGA-AB-2994 AML09 11 94047070 94047070 C T SNP - - - - - - - - - - - - - - - tier3 1892 17 0.89 1476 475 24.35 0 0 NA 709968 TCGA-AB-2994 AML09 11 114388605 114388605 C T SNP - - - - - - - - - - - - - - - tier3 1333 32 2.34 1180 848 41.77 0 0 NA 709968 TCGA-AB-2994 AML09 11 125068280 125068280 G A SNP ACRV1 NM_001612.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12395 NULL 0.005 - - - no_errors tier3 2030 30 1.46 1124 659 36.96 0 0 NA 709968 TCGA-AB-2994 AML09 11 133037103 133037103 C A SNP - - - - - - - - - - - - - - - tier3 1239 25 1.98 1191 656 35.48 0 0 NA 709968 TCGA-AB-2994 AML09 11 134287163 134287163 A T SNP - - - - - - - - - - - - - - - tier3 1367 30 2.15 1101 546 33.15 0 0 NA 709968 TCGA-AB-2994 AML09 12 4574069 4574069 G A SNP DYRK4 NM_003845.1 human genbank 54_36p 1 provisional intronic c.282+1477 e2+1477 0.061 - - - no_errors tier3 900 18 1.96 829 426 33.92 0 0 NA 709968 TCGA-AB-2994 AML09 12 22358975 22358975 C T SNP ST8SIA1 NM_003034.3 human genbank 54_36p -1 reviewed intronic c.236+19223 e1+19223 0 - - - no_errors tier3 1531 20 1.29 1058 604 36.34 0 0 0 709968 TCGA-AB-2994 AML09 12 23580673 23580673 G A SNP SOX5 NM_006940.4 human genbank 54_36p -1 reviewed missense c.1969 p.R657W 1 NULL "HMMPfam_HMG_box,HMMSmart_SM00398,superfamily_HMG-box,PatternScan_TONB_DEPENDENT_REC_1" - no_errors tier1 781 26 3.22 1133 368 24.52 NA 709968 TCGA-AB-2994 AML09 12 37897894 37897894 G A SNP - - - - - - - - - - - - - - - tier3 1107 18 1.6 1382 783 36.15 0 0 NA 709968 TCGA-AB-2994 AML09 12 68606785 68606785 C T SNP C12orf28 XM_001718908.1 human genbank 54_36p 1 model splice_region c.1952+4 e16+4 0 - - - no_errors tier3 1685 17 1 1297 425 24.67 0 0 NA 709968 TCGA-AB-2994 AML09 12 69327018 69327018 G A SNP PTPRR NM_002849.2 human genbank 54_36p -1 reviewed intronic c.1881-7694 e14-7694 0 - - - no_errors tier3 594 7 1.16 667 328 32.96 0 0 0 709968 TCGA-AB-2994 AML09 12 72627229 72627229 G A SNP ENSG00000215944 ENST00000401125 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47230 NULL 0 - - - no_errors tier3 1256 21 1.64 1574 857 35.21 0 0 NA 709968 TCGA-AB-2994 AML09 12 82158727 82158727 G A SNP - - - - - - - - - - - - - - - tier3 356 4 1.11 660 369 35.86 0 0 NA 709968 TCGA-AB-2994 AML09 12 94071124 94071124 G A SNP FGD6 NM_018351.3 human genbank 54_36p -1 validated intronic c.2587-224 e4-224 0.002 - - - no_errors tier2 1098 23 2.05 851 464 35.29 0 0 0 709968 TCGA-AB-2994 AML09 12 96599344 96599344 C T SNP RNU6-2 ENST00000384172 human ensembl 54_36p 1 known 5_prime_flanking_region c.-40281 NULL 0 - - - no_errors tier2 674 10 1.46 1188 609 33.85 0 0 NA 709968 TCGA-AB-2994 AML09 12 106910396 106910396 T A SNP LOC100129448 XM_001715530.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-12119 NULL 0.093 - - - no_errors tier3 1709 46 2.62 2750 1366 33.17 0 0 NA 709968 TCGA-AB-2994 AML09 12 108471382 108471382 C T SNP MVK NM_000431.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25629 NULL 0.052 - - - no_errors tier3 564 10 1.74 496 249 33.42 0 0 NA 709968 TCGA-AB-2994 AML09 12 123868089 123868089 C T SNP SCARB1 NM_005505.1 human genbank 54_36p -1 validated missense c.244 p.E82K 0.995 HMMPfam_CD36 HMMPfam_CD36 - no_errors tier1 1377 11 0.79 703 379 35 14 3 17.65 709968 TCGA-AB-2994 AML09 12 128236711 128236711 G T SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1443+23307 e5+23307 0.001 - - - no_errors tier3 1143 20 1.72 777 252 24.47 0 0 NA 709968 TCGA-AB-2994 AML09 13 20328256 20328256 C T SNP XPO4 NM_022459.4 human genbank 54_36p -1 validated intronic c.318-352 e4-352 0 - - - no_errors tier3 1399 17 1.2 1676 797 32.22 6 6 50 709968 TCGA-AB-2994 AML09 13 27205921 27205921 G T SNP ENSG00000220042 ENST00000404181 human ensembl 54_36p -1 known 5_prime_flanking_region c.-36580 NULL 0.04 - - - no_coding_region:pseudogene tier3 1150 15 1.29 785 445 36.18 0 0 NA 709968 TCGA-AB-2994 AML09 13 27506255 27506256 - ATCATATTCATATTCTCTGAA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1801_1800 p.600in_frame_insFREYEYD 1.000:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 709968 TCGA-AB-2994 AML09 13 38074808 38074808 T C SNP ENSG00000216558 ENST00000404132 human ensembl 54_36p -1 known 3_prime_flanking_region c.*14748 NULL 0 - - - no_coding_region:pseudogene tier3 1102 18 1.61 1142 685 37.47 0 0 NA 709968 TCGA-AB-2994 AML09 13 38619139 38619139 C A SNP ENSG00000214823 ENST00000399049 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*22627 NULL 0.022 - - - no_coding_region:pseudogene tier3 1176 21 1.75 782 455 36.75 0 0 NA 709968 TCGA-AB-2994 AML09 13 42279884 42279884 G A SNP C13orf30 NM_182508.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*18958 NULL 0 - - - no_errors tier3 1811 25 1.36 1844 955 34.11 0 0 NA 709968 TCGA-AB-2994 AML09 13 47177992 47177992 T C SNP - - - - - - - - - - - - - - - tier3 1837 25 1.34 1137 741 39.46 0 0 NA 709968 TCGA-AB-2994 AML09 13 57286612 57286612 C A SNP - - - - - - - - - - - - - - - tier3 462 5 1.07 799 252 23.98 0 0 NA 709968 TCGA-AB-2994 AML09 13 61311172 61311172 G A SNP ENSG00000217192 ENST00000407335 human ensembl 54_36p 1 known 3_prime_flanking_region c.*33362 NULL 0.027 - - - no_coding_region:pseudogene tier2 673 7 1.03 939 484 33.94 0 0 NA 709968 TCGA-AB-2994 AML09 13 77697162 77697162 C T SNP - - - - - - - - - - - - - - - tier3 1493 20 1.32 1492 761 33.78 0 0 NA 709968 TCGA-AB-2994 AML09 14 47938323 47938323 T C SNP - - - - - - - - - - - - - - - tier3 1436 19 1.31 1441 891 38.19 0 0 NA 709968 TCGA-AB-2994 AML09 14 68987327 68987327 T A SNP SLC39A9 NM_018375.3 human genbank 54_36p 1 validated intronic c.404-2384 e4-2384 0.101 - - - no_errors tier3 1019 16 1.55 1164 616 34.59 5 1 16.67 709968 TCGA-AB-2994 AML09 14 96098409 96098409 T A SNP PAPOLA NM_032632.3 human genbank 54_36p 1 validated intronic c.2068-500 e21-500 0.016 - - - no_errors tier3 705 3 0.42 528 286 35.14 0 2 100 709968 TCGA-AB-2994 AML09 14 96106390 96106390 C T SNP PAPOLA NM_032632.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*5250 NULL 0 - - - no_errors tier3 520 7 1.33 425 165 27.87 0 1 100 709968 TCGA-AB-2994 AML09 14 97358480 97358480 C A SNP - - - - - - - - - - - - - - - tier3 1910 29 1.49 1297 740 36.33 0 0 NA 709968 TCGA-AB-2994 AML09 15 35990674 35990674 G T SNP TMCO5A NM_152453.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-25143 NULL 0.006 - - - no_errors tier3 1051 13 1.22 1398 774 35.57 0 0 NA 709968 TCGA-AB-2994 AML09 15 48765677 48765677 G A SNP TRPM7 NM_017672.3 human genbank 54_36p -1 validated intronic c.3+343 e1+343 0.161 - - - no_errors tier2 1034 27 2.54 639 348 35.22 0 0 0 709968 TCGA-AB-2994 AML09 15 85568008 85568008 A G SNP - - - - - - - - - - - - - - - tier3 875 18 2.02 1608 502 23.78 0 0 NA 709968 TCGA-AB-2994 AML09 15 93416999 93416999 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 709968 TCGA-AB-2994 AML09 16 1776558 1776558 C T SNP NUBP2 NM_012225.2 human genbank 54_36p 1 validated silent c.36 p.G12 0.837 superfamily_SSF52540 "PatternScan_MRP,HMMPfam_ParA,superfamily_SSF52540" - no_errors tier1 205 5 2.38 127 88 40.93 13 11 45.83 709968 TCGA-AB-2994 AML09 16 11833886 11833886 A C SNP ZC3H7A NM_014153.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-50175 NULL 0.003 - - - no_errors tier3 985 12 1.2 543 289 34.74 0 0 NA 709968 TCGA-AB-2994 AML09 16 12927077 12927077 C T SNP - - - - - - - - - - - - - - - tier3 1455 30 2.02 1196 606 33.61 0 0 NA 709968 TCGA-AB-2994 AML09 16 23767444 23767444 C T SNP PRKCB NM_002738.6 human genbank 54_36p 1 reviewed intronic c.205+11216 e2+11216 0.079 - - - no_errors tier3 1655 36 2.13 1349 420 23.73 8 10 55.56 709968 TCGA-AB-2994 AML09 16 25962794 25962794 G A SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.735-91640 e2-91640 0.052 - - - no_errors tier3 1249 10 0.79 878 472 34.96 0 0 NA 709968 TCGA-AB-2994 AML09 16 31414446 31414446 T C SNP LOC100128371 XM_001725757.1 human genbank 54_36p -1 model missense c.250 p.T84A 0.004 NULL NULL - no_errors tier1 1471 22 1.47 620 347 35.85 1 100 709968 TCGA-AB-2994 AML09 16 34275855 34275855 C T SNP LOC100131688 XM_001718246.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-38307 NULL 0 - - - no_errors tier3 256 3 1.16 260 77 22.85 0 0 NA 709968 TCGA-AB-2994 AML09 16 63763334 63763334 G A SNP CDH11 NM_001797.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-167061 NULL 0 - - - no_errors tier3 2041 22 1.07 2117 1158 35.35 0 0 NA 709968 TCGA-AB-2994 AML09 16 69535291 69535291 G A SNP HYDIN NM_032821.2 human genbank 54_36p -1 validated silent c.6591 p.V2197 0.016 superfamily_P-loop containing nucleoside triphosphate hydrolases "superfamily_PapD-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 948 11 1.14 1795 493 21.53 NA 709968 TCGA-AB-2994 AML09 17 5191814 5191814 T C SNP RABEP1 NM_004703.1 human genbank 54_36p 1 validated intronic c.784+870 e6+870 0 - - - no_errors tier3 506 8 1.56 805 425 34.52 3 3 50 709968 TCGA-AB-2994 AML09 17 10297482 10297482 C G SNP MYH4 NM_017533.2 human genbank 54_36p -1 validated intronic c.2935-112 e22-112 0.001 - - - no_errors tier3 1065 16 1.48 737 460 38.4 0 0 NA 709968 TCGA-AB-2994 AML09 18 47002133 47002133 T C SNP MEX3C NM_016626.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-24445 NULL 0.004 - - - no_errors tier3 3068 53 1.7 2950 934 24 0 0 NA 709968 TCGA-AB-2994 AML09 18 55350737 55350737 C A SNP CCBE1 NM_133459.1 human genbank 54_36p -1 provisional intronic c.213-52287 e3-52287 0.001 - - - no_errors tier3 1057 11 1.03 1124 382 25.37 0 0 NA 709968 TCGA-AB-2994 AML09 18 55538356 55538356 G A SNP CCBE1 NM_133459.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-22802 NULL 0.003 - - - no_errors tier3 758 19 2.44 509 321 38.58 0 0 NA 709968 TCGA-AB-2994 AML09 18 59545741 59545741 C G SNP SERPINB7 NM_001040147.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-54846 NULL 0.004 - - - no_errors tier3 1288 39 2.94 1332 780 36.91 0 0 NA 709968 TCGA-AB-2994 AML09 18 60806355 60806355 C T SNP - - - - - - - - - - - - - - - tier3 79 6 7.06 92 215 69.35 0 0 NA 709968 TCGA-AB-2994 AML09 18 65041541 65041541 T C SNP - - - - - - - - - - - - - - - tier3 766 18 2.3 849 444 34.29 0 0 NA 709968 TCGA-AB-2994 AML09 18 67951599 67951599 A G SNP - - - - - - - - - - - - - - - tier3 889 25 2.74 866 486 35.95 0 0 NA 709968 TCGA-AB-2994 AML09 18 74883862 74883862 T C SNP ATP9B NM_198531.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46537 NULL 0.012 - - - no_errors tier2 225 2 0.88 117 133 53.2 0 0 NA 709968 TCGA-AB-2994 AML09 18 75665733 75665733 C A SNP LOC100132893 XM_001717932.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-48637 NULL 0.002 - - - no_errors tier3 1319 36 2.66 1070 513 32.39 1 1 50 709968 TCGA-AB-2994 AML09 19 2674470 2674470 G A SNP DIRAS1 NM_145173.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5666 NULL 0 - - - no_errors tier3 905 11 1.2 257 122 32.11 0 0 NA 709968 TCGA-AB-2994 AML09 19 36099839 36099839 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 709968 TCGA-AB-2994 AML09 19 50375187 50375187 C T SNP NKPD1 NM_198478.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-26319 NULL 0.01 - - - no_errors tier3 765 6 0.78 621 307 33.01 7 8 53.33 709968 TCGA-AB-2994 AML09 19 55412628 55412628 C T SNP MYH14 NM_001077186.1 human genbank 54_36p 1 reviewed intronic c.406-56 e2-56 0.001 - - - no_errors tier2 969 12 1.22 773 463 37.46 0 0 NA 709968 TCGA-AB-2994 AML09 20 9361315 9361315 C A SNP PLCB4 NM_000933.2 human genbank 54_36p 1 reviewed intronic c.2489-2892 e25-2892 0 - - - no_errors tier3 961 4 0.41 920 292 24.09 0 0 NA 709968 TCGA-AB-2994 AML09 20 21691754 21691754 C T SNP SLC25A6P1 ENST00000402848 human ensembl 54_36p -1 known 5_prime_flanking_region c.-20039 NULL 0 - - - no_coding_region:pseudogene tier3 726 23 3.06 1164 612 34.44 0 0 NA 709968 TCGA-AB-2994 AML09 20 22449610 22449610 A G SNP - - - - - - - - - - - - - - - tier2 2318 39 1.65 1889 1198 38.77 0 0 NA 709968 TCGA-AB-2994 AML09 20 37214333 37214333 C T SNP - - - - - - - - - - - - - - - tier3 700 50 6.66 959 291 23.24 0 0 NA 709968 TCGA-AB-2994 AML09 20 37563919 37563919 A G SNP - - - - - - - - - - - - - - - tier3 1528 29 1.86 1679 772 31.47 0 0 NA 709968 TCGA-AB-2994 AML09 20 43254762 43254762 G C SNP SEMG2 NM_003008.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28683 NULL 0.014 - - - no_errors tier3 872 17 1.91 1024 618 37.61 0 0 NA 709968 TCGA-AB-2994 AML09 20 53784450 53784450 G A SNP - - - - - - - - - - - - - - - tier2 2195 18 0.81 1768 589 24.99 0 0 NA 709968 TCGA-AB-2994 AML09 20 59122635 59122635 G A SNP - - - - - - - - - - - - - - - tier3 1328 15 1.12 903 499 35.54 0 0 NA 709968 TCGA-AB-2994 AML09 21 42550695 42550695 G A SNP ABCG1 NM_004915.3 human genbank 54_36p 1 reviewed intronic c.287-13554 e3-13554 0.001 - - - no_errors tier3 4371 88 1.97 2312 1273 35.49 0 0 0 709968 TCGA-AB-2994 AML09 22 18554768 18554768 G C SNP LOC388849 XM_373945.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23637 NULL 0.002 - - - no_errors tier3 828 13 1.54 365 200 35.4 0 0 NA 709968 TCGA-AB-2994 AML09 22 25695131 25695131 G A SNP - - - - - - - - - - - - - - - tier2 2662 59 2.17 1801 1003 35.77 0 0 NA 709968 TCGA-AB-2994 AML09 22 25816189 25816189 C A SNP - - - - - - - - - - - - - - - tier3 5318 53 0.99 2934 1494 33.69 0 0 NA 709968 TCGA-AB-2994 AML09 22 34597706 34597706 C T SNP RBM9 NM_001082578.2 human genbank 54_36p -1 reviewed intronic c.238-61709 e3-61709 0 - - - no_errors tier3 1479 20 1.33 1430 810 36.16 0 0 NA 709968 TCGA-AB-2994 AML09 22 42237246 42237246 G A SNP EFCAB6 NM_022785.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*18820 NULL 0.154 - - - no_errors tier3 115 1 0.86 75 35 31.53 0 0 NA 709968 TCGA-AB-2994 AML09 22 48320515 48320515 G A SNP FLJ44385 XR_041678.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-12930 NULL 0.003 - - - no_errors tier3 895 5 0.56 690 373 35.02 0 1 100 991612 TCGA-AB-2995 AML46 X 3376057 3376057 C T SNP - - - - - - - - - - - - - - - tier3 138 0 0 646 386 37.29 0 0 NA 991612 TCGA-AB-2995 AML46 X 25095871 25095871 C T SNP ENSG00000212075 ENST00000390786 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*38537 NULL 0.004 - - - no_errors tier3 166 0 0 437 270 38.08 0 0 NA 991612 TCGA-AB-2995 AML46 X 26314255 26314255 A G SNP ENSG00000216472 ENST00000404628 human ensembl 54_36p 1 known 3_prime_flanking_region c.*39975 NULL 0.079 - - - no_coding_region:pseudogene tier3 70 0 0 256 190 42.6 0 0 NA 991612 TCGA-AB-2995 AML46 X 26540559 26540559 G A SNP ENSG00000217953 ENST00000407620 human ensembl 54_36p -1 known 3_prime_flanking_region c.*44770 NULL 0 - - - no_coding_region:pseudogene tier3 198 0 0 482 336 40.98 0 0 NA 991612 TCGA-AB-2995 AML46 X 31995370 31995370 C A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6439-98818 e45-98818 0.001 - - - no_errors tier3 92 0 0 296 75 20.22 0 0 NA 991612 TCGA-AB-2995 AML46 X 37673547 37673547 A G SNP ENSG00000220615 ENST00000405464 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16534 NULL 0.035 - - - no_coding_region:pseudogene tier3 110 0 0 213 148 41 0 0 NA 991612 TCGA-AB-2995 AML46 X 49846701 49846701 G A SNP AKAP4 NM_003886.2 human genbank 54_36p -1 reviewed intronic c.277-874 e5-874 0.009 - - - no_errors tier3 167 0 0 697 491 41.19 0 0 NA 991612 TCGA-AB-2995 AML46 X 61966460 61966460 C T SNP ENSG00000218162 ENST00000404359 human ensembl 54_36p 1 known 5_prime_flanking_region c.-12277 NULL 0.008 - - - no_coding_region:pseudogene tier3 399 0 0 645 493 43.32 0 0 NA 991612 TCGA-AB-2995 AML46 X 63821563 63821563 A T SNP ENSG00000218277 ENST00000402821 human ensembl 54_36p -1 known 3_prime_flanking_region c.*12920 NULL 0.148 - - - no_coding_region:pseudogene tier3 360 1 0.28 1160 298 20.4 0 0 NA 991612 TCGA-AB-2995 AML46 X 108521063 108521063 C T SNP GUCY2F NM_001522.2 human genbank 54_36p -1 reviewed intronic c.2781+733 e13+733 0.006 - - - no_errors tier3 328 0 0 1159 663 36.35 0 0 NA 991612 TCGA-AB-2995 AML46 X 111317261 111317261 C A SNP ZCCHC16 NM_001004308.2 human genbank 54_36p 1 validated intronic c.1+56276 e0+56276 0 - - - no_errors tier3 339 1 0.29 778 117 13.07 0 0 NA 991612 TCGA-AB-2995 AML46 X 143923410 143923410 G A SNP ENSG00000201912 ENST00000365042 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-22910 NULL 0 - - - no_errors tier3 230 0 0 566 439 43.68 0 0 NA 991612 TCGA-AB-2995 AML46 1 22880822 22880822 C T SNP EPHB2 NM_004442.6 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29241 NULL 0 - - - no_errors tier3 233 0 0 658 74 10.1 0 0 NA 991612 TCGA-AB-2995 AML46 1 47952493 47952493 C T SNP - - - - - - - - - - - - - - - tier3 441 0 0 792 221 21.79 0 0 NA 991612 TCGA-AB-2995 AML46 1 57093884 57093884 G A SNP C8A NM_000562.2 human genbank 54_36p 1 reviewed intronic c.77+645 e1+645 0 - - - no_errors tier3 97 0 0 381 98 20.46 0 0 NA 991612 TCGA-AB-2995 AML46 1 61658041 61658041 C A SNP NFIA NM_005595.3 human genbank 54_36p 1 reviewed intronic c.1420+13054 e9+13054 0.478 - - - no_errors tier3 272 0 0 1620 368 18.5 0 1 100 991612 TCGA-AB-2995 AML46 1 65965049 65965049 C A SNP ENSG00000222443 ENST00000410511 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*34282 NULL 0 - - - no_errors tier3 268 0 0 1177 288 19.62 0 0 NA 991612 TCGA-AB-2995 AML46 1 68678695 68678695 T C SNP RPE65 NM_000329.2 human genbank 54_36p -1 reviewed intronic c.643+429 e6+429 0.001 - - - no_errors tier3 262 0 0 1371 323 19.04 0 0 NA 991612 TCGA-AB-2995 AML46 1 77720669 77720669 G A SNP AK5 NM_174858.2 human genbank 54_36p 1 reviewed intronic c.1060-921 e9-921 0.013 - - - no_errors tier3 55 0 0 313 117 27.21 0 0 NA 991612 TCGA-AB-2995 AML46 1 102947494 102947494 G T SNP - - - - - - - - - - - - - - - tier3 198 0 0 480 128 21.02 0 0 NA 991612 TCGA-AB-2995 AML46 1 103133146 103133146 G A SNP COL11A1 NM_080629.3 human genbank 54_36p -1 reviewed intronic c.4338+3123 e57+3123 0.001 - - - no_errors tier3 121 2 1.63 845 296 25.92 0 0 NA 991612 TCGA-AB-2995 AML46 1 107344921 107344921 G A SNP - - - - - - - - - - - - - - - tier3 419 0 0 1662 465 21.84 0 0 NA 991612 TCGA-AB-2995 AML46 1 110082336 110082336 C A SNP GSTM3 NM_000849.4 human genbank 54_36p -1 reviewed missense c.272 p.C91F 1 superfamily_Glutathione S-transferase (GST) C-terminal domain "HMMPfam_GST_N,HMMPfam_GST_C,superfamily_Glutathione S-transferase (GST) C-terminal domain,superfamily_Thioredoxin-like" - no_errors tier1 324 0 917 207 18.4 16 26 61.9 991612 TCGA-AB-2995 AML46 1 113720466 113720466 G C SNP MAGI3 NM_152900.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14713 NULL 0.347 - - - no_errors tier3 234 0 0 919 210 18.53 0 0 NA 991612 TCGA-AB-2995 AML46 1 149066074 149066074 C T SNP ARNT NM_001668.2 human genbank 54_36p -1 reviewed intronic c.1168-357 e13-357 0.002 - - - no_errors tier3 59 0 0 677 158 18.9 1 1 50 991612 TCGA-AB-2995 AML46 1 150264199 150264199 C T SNP S100A10 NM_002966.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-38869 NULL 0.17 - - - no_errors tier3 421 0 0 545 128 19.02 0 0 NA 991612 TCGA-AB-2995 AML46 1 162989595 162989595 T C SNP PBX1 NM_002585.2 human genbank 54_36p 1 validated intronic c.266-38760 e3-38760 0.005 - - - no_errors tier3 277 0 0 1359 405 22.92 0 1 100 991612 TCGA-AB-2995 AML46 1 173819075 173819075 C A SNP TNR NM_003285.2 human genbank 54_36p -1 validated intronic c.1-54947 e1-54947 0.003 - - - no_errors tier3 748 2 0.27 982 99 9.16 0 0 NA 991612 TCGA-AB-2995 AML46 1 177195254 177195254 C G SNP RALGPS2 NM_152663.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*43137 NULL 0.001 - - - no_errors tier3 368 0 0 853 272 24.11 0 0 NA 991612 TCGA-AB-2995 AML46 1 190841029 190841029 T A SNP RGS13 NM_002927.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-39059 NULL 0.001 - - - no_errors tier3 113 0 0 1137 309 21.34 0 0 NA 991612 TCGA-AB-2995 AML46 1 205081357 205081357 T A SNP IL19 NM_153758.2 human genbank 54_36p 1 reviewed intronic c.552+311 e5+311 0 - - - no_errors tier3 701 0 0 1345 338 20.05 0 0 NA 991612 TCGA-AB-2995 AML46 1 225359437 225359437 T C SNP CDC42BPA NM_003607.3 human genbank 54_36p -1 reviewed intronic c.2002-3874 e15-3874 0.03 - - - no_errors tier3 114 0 0 487 124 20.23 0 1 100 991612 TCGA-AB-2995 AML46 2 1524677 1524677 C T SNP TPO NM_000547.4 human genbank 54_36p 1 reviewed intronic c.2749-523 e16-523 0.011 - - - no_errors tier3 185 1 0.54 366 35 8.66 0 0 NA 991612 TCGA-AB-2995 AML46 2 21123345 21123345 C T SNP APOB NM_000384.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3023 NULL 0.001 - - - no_errors tier3 204 0 0 506 137 21.27 0 0 NA 991612 TCGA-AB-2995 AML46 2 36686662 36686662 T G SNP FEZ2 NM_001042548.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7873 NULL 0.073 - - - no_errors tier3 55 1 1.79 140 76 35.19 0 0 NA 991612 TCGA-AB-2995 AML46 2 38962603 38962603 T - DEL MORN2 ENST00000340556 human ensembl 54_36p 1 known intronic c.137+380 e1+380 0.045 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 991612 TCGA-AB-2995 AML46 2 56250436 56250436 C T SNP CCDC85A NM_001080433.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-14828 NULL 0 - - - no_errors tier3 437 0 0 972 237 19.6 0 0 NA 991612 TCGA-AB-2995 AML46 2 85332807 85332807 G A SNP TCF7L1 NM_031283.1 human genbank 54_36p 1 provisional intronic c.442-31322 e4-31322 0.003 - - - no_errors tier3 246 1 0.4 796 192 19.39 0 0 NA 991612 TCGA-AB-2995 AML46 2 94897289 94897289 A G SNP TEKT4 NM_144705.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-3763 NULL 0.021 - - - no_errors tier3 44 0 0 338 88 20.61 0 0 NA 991612 TCGA-AB-2995 AML46 2 114925684 114925684 C T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.60+8799 e1+8799 0 - - - no_errors tier3 249 0 0 1180 364 23.51 0 0 NA 991612 TCGA-AB-2995 AML46 2 130486220 130486220 G A SNP LOC100131320 XM_001723688.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-32113 NULL 0 - - - no_errors tier3 78 0 0 311 91 22.64 0 0 NA 991612 TCGA-AB-2995 AML46 2 139800381 139800381 C G SNP - - - - - - - - - - - - - - - tier3 217 0 0 1070 143 11.78 0 0 NA 991612 TCGA-AB-2995 AML46 2 140791889 140791889 G A SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.12641-2751 e83-2751 0.001 - - - no_errors tier3 189 0 0 939 225 19.31 0 0 NA 991612 TCGA-AB-2995 AML46 2 140930810 140930810 T A SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.9815-168 e62-168 0.004 - - - no_errors tier3 103 0 0 369 81 18 0 0 NA 991612 TCGA-AB-2995 AML46 2 147471866 147471866 T C SNP - - - - - - - - - - - - - - - tier3 306 0 0 1363 388 22.15 0 0 NA 991612 TCGA-AB-2995 AML46 2 151193134 151193134 T G SNP - - - - - - - - - - - - - - - tier3 268 0 0 664 180 21.33 0 0 NA 991612 TCGA-AB-2995 AML46 2 163227926 163227926 G A SNP KCNH7 NM_033272.2 human genbank 54_36p -1 reviewed intronic c.308-126090 e3-126090 0.014 - - - no_errors tier3 457 0 0 1671 429 20.42 0 0 NA 991612 TCGA-AB-2995 AML46 2 169677766 169677766 G C SNP LRP2 NM_004525.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*15653 NULL 0.007 - - - no_errors tier3 309 0 0 999 245 19.63 0 0 NA 991612 TCGA-AB-2995 AML46 2 182241922 182241922 T A SNP CERKL NM_201548.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11944 NULL 0.011 - - - no_errors tier3 387 1 0.26 877 248 22.04 0 0 NA 991612 TCGA-AB-2995 AML46 2 188315154 188315154 G A SNP - - - - - - - - - - - - - - - tier3 37 0 0 262 65 19.82 0 0 NA 991612 TCGA-AB-2995 AML46 2 192062001 192062001 T C SNP - - - - - - - - - - - - - - - tier3 111 0 0 297 80 21.11 0 0 NA 991612 TCGA-AB-2995 AML46 2 208048476 208048477 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 991612 TCGA-AB-2995 AML46 2 210175722 210175722 T G SNP MAP2 NM_002374.1 human genbank 54_36p 1 reviewed intronic c.1-22300 e1-22300 0.001 - - - no_errors tier3 198 0 0 444 151 25.29 0 0 NA 991612 TCGA-AB-2995 AML46 2 211615012 211615012 C G SNP - - - - - - - - - - - - - - - tier3 56 0 0 275 101 26.86 0 0 NA 991612 TCGA-AB-2995 AML46 2 215677037 215677037 C T SNP ABCA12 NM_173076.3 human genbank 54_36p -1 reviewed intronic c.163+7528 e2+7528 0.032 - - - no_errors tier3 332 0 0 611 165 21.18 0 0 NA 991612 TCGA-AB-2995 AML46 2 216815313 216815313 G A SNP XRCC5 NM_021141.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*37143 NULL 0.006 - - - no_errors tier3 853 4 0.47 1911 472 19.79 1 0 0 991612 TCGA-AB-2995 AML46 2 229148074 229148074 A T SNP - - - - - - - - - - - - - - - tier3 57 0 0 661 154 18.87 0 0 NA 991612 TCGA-AB-2995 AML46 2 235025381 235025381 A G SNP LOC727890 XM_001714076.1 human genbank 54_36p 1 model intronic c.356-8580 e4-8580 0.001 - - - no_errors tier3 408 0 0 1029 251 19.59 1 0 0 991612 TCGA-AB-2995 AML46 2 241391972 241391972 C G SNP KIF1A NM_004321.4 human genbank 54_36p -1 reviewed intronic c.1-6070 e1-6070 0.003 - - - no_errors tier3 53 0 0 135 30 18.18 0 0 NA 991612 TCGA-AB-2995 AML46 3 24063704 24063704 C T SNP - - - - - - - - - - - - - - - tier3 165 7 4.07 778 435 35.77 0 0 NA 991612 TCGA-AB-2995 AML46 3 25137841 25137841 C T SNP - - - - - - - - - - - - - - - tier3 262 0 0 643 142 18.04 0 0 NA 991612 TCGA-AB-2995 AML46 3 27830309 27830309 C T SNP - - - - - - - - - - - - - - - tier3 117 0 0 764 161 17.41 0 0 NA 991612 TCGA-AB-2995 AML46 3 47070559 47070559 T A SNP SETD2 NM_014159.6 human genbank 54_36p -1 reviewed intronic c.5454+2756 e13+2756 0.005 - - - no_errors tier3 101 0 0 746 164 18 1 2 66.67 991612 TCGA-AB-2995 AML46 3 54370198 54370198 A G SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.322-25584 e4-25584 0.077 - - - no_errors tier3 219 0 0 1283 344 21.13 0 0 NA 991612 TCGA-AB-2995 AML46 3 54880564 54880564 G A SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.1627-42 e18-42 0.001 - - - no_errors tier3 360 1 0.28 829 217 20.69 0 0 NA 991612 TCGA-AB-2995 AML46 3 62139283 62139283 G A SNP PTPRG NM_002841.3 human genbank 54_36p 1 reviewed intronic c.1033+10406 e8+10406 0.052 - - - no_errors tier3 583 1 0.17 1208 306 20.21 0 0 NA 991612 TCGA-AB-2995 AML46 3 76094280 76094280 C T SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.109+24837 e1+24837 0.001 - - - no_stop_codon:overly_large_intron tier3 188 0 0 1265 301 19.18 0 0 NA 991612 TCGA-AB-2995 AML46 3 84104412 84104412 G A SNP - - - - - - - - - - - - - - - tier3 215 0 0 1547 166 9.68 0 0 NA 991612 TCGA-AB-2995 AML46 3 100660217 100660217 C T SNP - - - - - - - - - - - - - - - tier3 267 0 0 1182 317 21.12 0 0 NA 991612 TCGA-AB-2995 AML46 3 100920378 100920378 C G SNP COL8A1 NM_001850.3 human genbank 54_36p 1 reviewed intronic c.1-26053 e1-26053 0.002 - - - no_errors tier3 238 0 0 941 267 22.08 0 0 NA 991612 TCGA-AB-2995 AML46 3 111955163 111955163 G T SNP ENSG00000201426 ENST00000364556 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*26505 NULL 0.077 - - - no_errors tier3 239 0 0 965 207 17.65 0 0 NA 991612 TCGA-AB-2995 AML46 3 135162631 135162631 G A SNP SLCO2A1 NM_005630.2 human genbank 54_36p -1 validated intronic c.398-5904 e4-5904 0.004 - - - no_errors tier3 275 0 0 910 293 24.3 0 0 NA 991612 TCGA-AB-2995 AML46 3 138736904 138736904 C T SNP ENSG00000201325 ENST00000364455 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-17117 NULL 0.013 - - - no_errors tier3 114 0 0 587 157 21.1 0 0 NA 991612 TCGA-AB-2995 AML46 3 155301424 155301424 A C SNP uc003ezv.1 ENST00000356448 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21048 NULL 0.004 - - - no_errors tier3 518 0 0 1072 296 21.62 1 0 0 991612 TCGA-AB-2995 AML46 3 192082796 192082796 C T SNP LOC647309 XM_930379.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-19151 NULL 0 - - - no_errors tier3 122 0 0 968 106 9.86 0 0 NA 991612 TCGA-AB-2995 AML46 4 3271977 3271977 G A SNP RGS12 NM_198229.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15719 NULL 0.012 - - - no_errors tier3 74 0 0 154 44 22.22 1 0 0 991612 TCGA-AB-2995 AML46 4 20740567 20740567 G A SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.100+173961 e1+173961 0.439 - - - no_errors tier3 152 0 0 1009 299 22.86 0 0 NA 991612 TCGA-AB-2995 AML46 4 35471340 35471340 G A SNP - - - - - - - - - - - - - - - tier3 228 0 0 681 164 19.41 0 0 NA 991612 TCGA-AB-2995 AML46 4 61778714 61778714 A G SNP - - - - - - - - - - - - - - - tier3 110 0 0 574 157 21.48 0 0 NA 991612 TCGA-AB-2995 AML46 4 65157430 65157430 C T SNP ENSG00000210717 ENST00000387982 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1419 NULL 0.338 - - - pseudogene tier3 129 0 0 641 149 18.84 0 0 NA 991612 TCGA-AB-2995 AML46 4 86320148 86320148 G A SNP - - - - - - - - - - - - - - - tier3 208 1 0.48 1464 178 10.81 0 0 NA 991612 TCGA-AB-2995 AML46 4 95372643 95372643 A G SNP SMARCAD1 NM_020159.1 human genbank 54_36p 1 validated intronic c.369-1485 e3-1485 0.002 - - - no_errors tier3 250 0 0 1654 353 17.57 3 3 50 991612 TCGA-AB-2995 AML46 4 108946881 108946881 T G SNP SGMS2 ENST00000394684 human ensembl 54_36p 1 known 5_prime_flanking_region c.-89278 NULL 0.937 - - - no_errors tier3 294 0 0 700 187 21.08 0 0 NA 991612 TCGA-AB-2995 AML46 4 122519452 122519452 A G SNP QRFPR NM_198179.2 human genbank 54_36p -1 validated intronic c.340+1461 e1+1461 0 - - - no_errors tier3 208 0 0 609 176 22.39 0 0 NA 991612 TCGA-AB-2995 AML46 4 122595852 122595852 C T SNP LOC729112 XM_001132973.1 human genbank 54_36p 1 model intronic c.127+5136 e1+5136 0 - - - no_errors tier3 207 0 0 823 97 10.53 0 0 NA 991612 TCGA-AB-2995 AML46 4 138583940 138583940 G A SNP ENSG00000213448 ENST00000394245 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-4751 NULL 0 - - - no_coding_region:pseudogene tier3 166 0 0 703 177 20.09 0 0 NA 991612 TCGA-AB-2995 AML46 4 139824277 139824277 C G SNP - - - - - - - - - - - - - - - tier3 374 0 0 1329 285 17.59 0 0 NA 991612 TCGA-AB-2995 AML46 4 155316436 155316436 G T SNP - - - - - - - - - - - - - - - tier3 163 0 0 957 228 19.22 0 0 NA 991612 TCGA-AB-2995 AML46 4 155513219 155513219 A G SNP DCHS2 NM_017639.1 human genbank 54_36p -1 validated intronic c.462+1303 e4+1303 0 - - - no_errors tier3 256 4 1.54 979 304 23.68 0 0 NA 991612 TCGA-AB-2995 AML46 4 156156463 156156463 G A SNP - - - - - - - - - - - - - - - tier3 240 0 0 1093 252 18.74 0 0 NA 991612 TCGA-AB-2995 AML46 4 165703520 165703520 T G SNP - - - - - - - - - - - - - - - tier3 236 0 0 769 250 24.53 0 0 NA 991612 TCGA-AB-2995 AML46 4 190499233 190499233 G A SNP - - - - - - - - - - - - - - - tier3 1685 5 0.3 885 260 22.67 2 10 83.33 991612 TCGA-AB-2995 AML46 5 2451638 2451638 G A SNP - - - - - - - - - - - - - - - tier3 201 0 0 577 63 9.81 0 0 NA 991612 TCGA-AB-2995 AML46 5 9256712 9256712 C T SNP SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.647-1360 e7-1360 0 - - - no_errors tier3 168 0 0 763 195 20.33 0 0 NA 991612 TCGA-AB-2995 AML46 5 15903163 15903163 G A SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.128-77836 e3-77836 0 - - - no_errors tier3 179 0 0 670 218 24.52 0 0 NA 991612 TCGA-AB-2995 AML46 5 19571462 19571462 G T SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed intronic c.1390+8273 e7+8273 0.002 - - - no_errors tier3 146 0 0 1207 135 10.05 0 0 NA 991612 TCGA-AB-2995 AML46 5 19952779 19952779 G A SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed intronic c.1+64147 e0+64147 0.061 - - - no_errors tier3 115 0 0 908 205 18.42 0 0 NA 991612 TCGA-AB-2995 AML46 5 64123089 64123089 G T SNP SDCCAG10 NM_005869.2 human genbank 54_36p 1 validated intronic c.669+2486 e7+2486 0.005 - - - no_errors tier3 123 0 0 727 178 19.67 0 0 0 991612 TCGA-AB-2995 AML46 5 86306979 86306979 T A SNP - - - - - - - - - - - - - - - tier3 406 0 0 1426 353 19.83 0 0 NA 991612 TCGA-AB-2995 AML46 5 102339324 102339324 A G SNP PAM NM_000919.2 human genbank 54_36p 1 reviewed intronic c.1483+1285 e14+1285 0 - - - no_errors tier3 196 0 0 1261 409 24.49 9 3 25 991612 TCGA-AB-2995 AML46 5 105269871 105269871 G A SNP ENSG00000201790 ENST00000364920 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*16723 NULL 0.002 - - - no_errors tier3 96 0 0 689 180 20.71 0 0 NA 991612 TCGA-AB-2995 AML46 5 105819628 105819628 C A SNP - - - - - - - - - - - - - - - tier3 64 0 0 557 143 20.43 0 0 NA 991612 TCGA-AB-2995 AML46 5 122580220 122580220 G T SNP ENSG00000213655 ENST00000395448 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19448 NULL 0 - - - no_coding_region:pseudogene tier3 230 0 0 1184 271 18.63 0 0 NA 991612 TCGA-AB-2995 AML46 5 122837301 122837301 G A SNP CSNK1G3 NM_001044723.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-71956 NULL 0 - - - no_errors tier3 215 0 0 632 124 16.38 0 0 NA 991612 TCGA-AB-2995 AML46 5 129055788 129055788 T G SNP ADAMTS19 NM_133638.3 human genbank 54_36p 1 reviewed intronic c.2801-2524 e19-2524 0.002 - - - no_errors tier3 72 0 0 472 135 22.24 0 0 NA 991612 TCGA-AB-2995 AML46 5 176871976 176871976 C T SNP DDX41 NM_016222.2 human genbank 54_36p -1 reviewed missense c.1574 p.R525H 1 "HMMPfam_Helicase_C,HMMSmart_SM00490,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_zf-CCHC,HMMPfam_DEAD,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 94 0 222 61 21.48 77 48 38.4 991612 TCGA-AB-2995 AML46 6 22780654 22780654 A G SNP LOC389370 XM_374162.1 human genbank 54_36p -1 model intronic c.47-5407 e2-5407 0 - - - no_errors tier3 125 0 0 190 41 17.67 0 0 NA 991612 TCGA-AB-2995 AML46 6 57716454 57716454 C T SNP - - - - - - - - - - - - - - - tier3 274 0 0 1233 325 20.83 0 0 NA 991612 TCGA-AB-2995 AML46 6 64493182 64493182 A C SNP ENSG00000118487 ENST00000237261 human ensembl 54_36p -1 known 5_prime_flanking_region c.-3532 NULL 0.001 - - - no_start_codon tier3 132 0 0 861 208 19.42 6 4 40 991612 TCGA-AB-2995 AML46 6 68205624 68205624 G A SNP ENSG00000211117 ENST00000388382 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*28207 NULL 0.012 - - - pseudogene tier3 62 0 0 463 92 16.52 0 0 NA 991612 TCGA-AB-2995 AML46 6 70735222 70735222 G T SNP COL19A1 NM_001858.4 human genbank 54_36p 1 reviewed intronic c.1026+5739 e10+5739 0.003 - - - no_errors tier3 131 1 0.76 299 73 19.62 0 0 0 991612 TCGA-AB-2995 AML46 6 74734479 74734479 T C SNP ENSG00000217268 ENST00000406296 human ensembl 54_36p -1 known 3_prime_flanking_region c.*36477 NULL 0 - - - no_coding_region:pseudogene tier3 266 0 0 898 274 23.38 0 0 NA 991612 TCGA-AB-2995 AML46 6 86728160 86728160 T C SNP ENSG00000202103 ENST00000365233 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*31298 NULL 0.003 - - - no_errors tier3 91 0 0 644 216 25.03 0 0 NA 991612 TCGA-AB-2995 AML46 6 93342154 93342154 G A SNP - - - - - - - - - - - - - - - tier3 192 0 0 954 214 18.31 0 0 NA 991612 TCGA-AB-2995 AML46 6 94378279 94378279 A C SNP - - - - - - - - - - - - - - - tier3 115 0 0 547 120 17.99 0 0 NA 991612 TCGA-AB-2995 AML46 6 104152500 104152500 T C SNP ENSG00000202283 ENST00000365413 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*14664 NULL 0.003 - - - no_errors tier3 121 1 0.82 1141 147 11.4 0 0 NA 991612 TCGA-AB-2995 AML46 6 116042910 116042910 T A SNP - - - - - - - - - - - - - - - tier3 290 1 0.34 1040 304 22.6 0 0 NA 991612 TCGA-AB-2995 AML46 6 118303702 118303702 G C SNP SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-31881 NULL 0.018 - - - no_errors tier3 193 1 0.52 934 119 11.3 0 0 NA 991612 TCGA-AB-2995 AML46 6 119966853 119966853 G A SNP LOC728727 XM_001128292.2 human genbank 54_36p 1 model intronic c.225+53594 e3+53594 0 - - - no_errors tier3 62 0 0 453 109 19.4 0 1 100 991612 TCGA-AB-2995 AML46 6 124435724 124435724 A G SNP NKAIN2 NM_001040214.1 human genbank 54_36p 1 validated intronic c.55-210126 e2-210126 0 - - - no_errors tier3 171 0 0 850 237 21.8 1 0 0 991612 TCGA-AB-2995 AML46 6 143250658 143250658 G A SNP HIVEP2 NM_006734.3 human genbank 54_36p -1 provisional intronic c.1-50781 e1-50781 0 - - - no_errors tier3 124 0 0 777 148 15.98 0 0 0 991612 TCGA-AB-2995 AML46 7 1517373 1517373 C T SNP LOC100134722 XM_001725218.1 human genbank 54_36p -1 model 5_prime_untranslated_region c.-388 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 241 11 4.37 17 22 56.41 1 1 50 991612 TCGA-AB-2995 AML46 7 18863065 18863065 G A SNP HDAC9 NM_178425.1 human genbank 54_36p 1 reviewed intronic c.2685-17561 e21-17561 0.001 - - - no_errors tier3 506 0 0 1411 382 21.28 0 0 0 991612 TCGA-AB-2995 AML46 7 41005536 41005536 C T SNP - - - - - - - - - - - - - - - tier3 350 0 0 898 260 22.43 0 0 NA 991612 TCGA-AB-2995 AML46 7 42343480 42343480 C T SNP - - - - - - - - - - - - - - - tier3 459 0 0 1287 171 11.66 0 0 NA 991612 TCGA-AB-2995 AML46 7 52248965 52248965 G A SNP - - - - - - - - - - - - - - - tier3 96 0 0 418 128 23.44 0 0 NA 991612 TCGA-AB-2995 AML46 7 67304862 67304862 G A SNP - - - - - - - - - - - - - - - tier3 319 0 0 614 159 20.54 0 0 NA 991612 TCGA-AB-2995 AML46 7 101227237 101227237 A T SNP CUX1 NM_181552.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20403 NULL 0.006 - - - no_errors tier3 890 14 1.55 815 233 22.21 0 0 NA 991612 TCGA-AB-2995 AML46 7 118986323 118986323 C T SNP ENSG00000203365 ENST00000355604 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29174 NULL 0 - - - no_coding_region:pseudogene tier3 127 0 0 627 127 16.84 0 0 NA 991612 TCGA-AB-2995 AML46 7 131217735 131217735 C T SNP - - - - - - - - - - - - - - - tier3 411 2 0.48 971 121 11 0 0 NA 991612 TCGA-AB-2995 AML46 7 147828969 147828969 C T SNP - - - - - - - - - - - - - - - tier3 212 0 0 532 163 23.42 0 0 NA 991612 TCGA-AB-2995 AML46 7 158805112 158805112 T A SNP - - - - - - - - - - - - - - - tier3 62 0 0 366 125 25.46 0 0 NA 991612 TCGA-AB-2995 AML46 8 2068531 2068531 G T SNP MYOM2 NM_003970.2 human genbank 54_36p 1 validated intronic c.3800+3904 e31+3904 0.001 - - - no_errors tier3 344 0 0 1706 385 18.41 1 0 0 991612 TCGA-AB-2995 AML46 8 2458229 2458229 T C SNP - - - - - - - - - - - - - - - tier3 59 0 0 304 131 30.05 0 1 100 991612 TCGA-AB-2995 AML46 8 32033198 32033198 C T SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.745+415411 e1+415411 0.025 - - - overly_large_intron tier3 346 1 0.29 1864 520 21.77 0 0 NA 991612 TCGA-AB-2995 AML46 8 37624939 37624939 G T SNP ZNF703 NM_025069.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-47717 NULL 0 - - - no_errors tier3 221 0 0 670 186 21.73 0 0 NA 991612 TCGA-AB-2995 AML46 8 72642291 72642291 A G SNP LOC100132809 XM_001715796.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10481 NULL 0.004 - - - no_errors tier3 155 0 0 411 55 11.78 0 0 NA 991612 TCGA-AB-2995 AML46 8 100243564 100243564 T A SNP VPS13B NM_017890.2 human genbank 54_36p 1 reviewed intronic c.2208+5417 e14+5417 0.056 - - - no_errors tier3 83 0 0 454 101 18.17 1 1 50 991612 TCGA-AB-2995 AML46 8 103234173 103234173 C T SNP NCALD NM_001040624.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-433140 NULL 0 - - - no_errors tier3 208 0 0 722 142 16.42 0 0 NA 991612 TCGA-AB-2995 AML46 8 109133052 109133052 T C SNP RSPO2 NM_178565.4 human genbank 54_36p -1 validated intronic c.94+30897 e1+30897 0.015 - - - no_errors tier3 395 1 0.25 1637 397 19.52 0 0 NA 991612 TCGA-AB-2995 AML46 8 112069054 112069054 A T SNP - - - - - - - - - - - - - - - tier3 145 1 0.68 914 270 22.8 0 0 NA 991612 TCGA-AB-2995 AML46 8 122077579 122077579 C T SNP - - - - - - - - - - - - - - - tier3 128 0 0 488 99 16.84 0 0 NA 991612 TCGA-AB-2995 AML46 8 133489851 133489851 G A SNP KCNQ3 NM_004519.2 human genbank 54_36p -1 reviewed intronic c.386+71725 e1+71725 0.002 - - - no_errors tier3 546 24 4.21 928 499 34.94 0 0 NA 991612 TCGA-AB-2995 AML46 8 134251484 134251484 C T SNP WISP1 NM_003882.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-21086 NULL 0 - - - no_errors tier3 408 1 0.24 1737 429 19.79 0 0 NA 991612 TCGA-AB-2995 AML46 8 136431146 136431146 T C SNP - - - - - - - - - - - - - - - tier3 552 0 0 1107 353 24.11 0 0 NA 991612 TCGA-AB-2995 AML46 8 137618605 137618605 C T SNP - - - - - - - - - - - - - - - tier3 186 0 0 216 32 12.9 0 0 NA 991612 TCGA-AB-2995 AML46 8 140379139 140379139 C T SNP - - - - - - - - - - - - - - - tier3 269 1 0.37 1122 340 23.22 0 0 NA 991612 TCGA-AB-2995 AML46 9 9243219 9243219 G A SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-69856 e1-69856 0.002 - - - no_errors tier3 123 1 0.8 483 125 20.53 0 0 NA 991612 TCGA-AB-2995 AML46 9 16654322 16654322 C T SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated intronic c.330+63473 e3+63473 0.001 - - - no_errors tier3 255 0 0 1377 378 21.53 0 0 NA 991612 TCGA-AB-2995 AML46 9 76097398 76097398 T A SNP - - - - - - - - - - - - - - - tier3 174 1 0.57 563 185 24.7 0 0 NA 991612 TCGA-AB-2995 AML46 9 78280736 78280736 C G SNP GCNT1 NM_001097633.1 human genbank 54_36p 1 reviewed intronic c.1+16695 e0+16695 0 - - - no_errors tier3 149 1 0.67 986 295 23.01 2 1 33.33 991612 TCGA-AB-2995 AML46 9 81384234 81384234 A C SNP TLE4 NM_007005.3 human genbank 54_36p 1 validated intronic c.252+3322 e4+3322 0.07 - - - no_errors tier3 146 1 0.68 391 125 24.22 2 3 60 991612 TCGA-AB-2995 AML46 9 107488924 107488924 T G SNP TMEM38B NM_018112.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-7839 NULL 0.004 - - - no_errors tier3 386 0 0 533 107 16.69 0 0 NA 991612 TCGA-AB-2995 AML46 9 108734158 108734158 A G SNP ZNF462 NM_021224.4 human genbank 54_36p 1 validated intronic c.6013-390 e4-390 0.001 - - - no_errors tier3 207 0 0 647 152 19.02 2 1 33.33 991612 TCGA-AB-2995 AML46 9 111796334 111796334 G A SNP PALM2-AKAP2 NM_007203.3 human genbank 54_36p 1 validated intronic c.497-21721 e7-21721 0.661 - - - no_errors tier3 245 0 0 873 224 20.4 0 0 NA 991612 TCGA-AB-2995 AML46 9 118231906 118231906 T A SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.3783-3718 e23-3718 0 - - - no_errors tier3 313 0 0 973 239 19.69 1 1 50 991612 TCGA-AB-2995 AML46 10 4053637 4053637 G A SNP - - - - - - - - - - - - - - - tier3 157 0 0 662 118 15.09 0 0 NA 991612 TCGA-AB-2995 AML46 10 19152410 19152410 G C SNP - - - - - - - - - - - - - - - tier3 132 0 0 715 229 24.23 0 0 NA 991612 TCGA-AB-2995 AML46 10 33932396 33932396 C G SNP - - - - - - - - - - - - - - - tier3 102 0 0 578 132 18.57 0 0 NA 991612 TCGA-AB-2995 AML46 10 37132100 37132100 A T SNP - - - - - - - - - - - - - - - tier3 222 0 0 489 152 23.71 0 0 NA 991612 TCGA-AB-2995 AML46 10 38446452 38446452 A G SNP ZNF37A NM_001007094.1 human genbank 54_36p 1 validated missense c.367 p.N123D 0.808 NULL "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 135 0 536 156 22.48 8 8 50 991612 TCGA-AB-2995 AML46 10 74784244 74784244 C T SNP TTC18 NM_145170.2 human genbank 54_36p -1 provisional intronic c.63+254 e1+254 0 - - - no_errors tier3 140 0 0 692 206 22.86 2 0 0 991612 TCGA-AB-2995 AML46 10 80157316 80157316 T C SNP ENSG00000223243 ENST00000411311 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23049 NULL 0 - - - no_errors tier3 1134 2 0.18 1779 540 23.24 0 0 NA 991612 TCGA-AB-2995 AML46 10 85669962 85669962 G A SNP - - - - - - - - - - - - - - - tier3 141 0 0 423 110 20.56 0 0 NA 991612 TCGA-AB-2995 AML46 10 125388435 125388435 A G SNP GPR26 NM_153442.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27479 NULL 0.001 - - - no_errors tier3 218 2 0.91 703 204 22.47 0 0 NA 991612 TCGA-AB-2995 AML46 11 12854379 12854379 T G SNP TEAD1 NM_021961.4 human genbank 54_36p 1 validated intronic c.286-3452 e4-3452 0.004 - - - no_errors tier3 196 0 0 1049 328 23.77 0 0 NA 991612 TCGA-AB-2995 AML46 11 38737470 38737470 C T SNP - - - - - - - - - - - - - - - tier3 243 0 0 1165 295 20.19 0 0 NA 991612 TCGA-AB-2995 AML46 11 51283520 51283520 A G SNP OR4A5 NM_001005272.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-14549 NULL 0.002 - - - no_errors tier3 206 0 0 1048 254 19.49 0 0 NA 991612 TCGA-AB-2995 AML46 11 79238631 79238631 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 991612 TCGA-AB-2995 AML46 11 120233323 120233323 G A SNP GRIK4 NM_014619.2 human genbank 54_36p 1 reviewed intronic c.745-4555 e7-4555 0 - - - no_errors tier3 714 2 0.28 1946 238 10.84 0 0 0 991612 TCGA-AB-2995 AML46 12 17393867 17393867 T C SNP - - - - - - - - - - - - - - - tier3 169 0 0 868 217 20 0 0 NA 991612 TCGA-AB-2995 AML46 12 17553112 17553113 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 991612 TCGA-AB-2995 AML46 12 21472346 21472346 A - DEL SLCO1A2 NM_134431.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-93498 NULL 0.015 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 991612 TCGA-AB-2995 AML46 12 42595268 42595268 C T SNP TMEM117 NM_032256.1 human genbank 54_36p 1 provisional intronic c.278-29012 e2-29012 0.008 - - - no_errors tier3 414 0 0 1989 531 21.01 1 0 0 991612 TCGA-AB-2995 AML46 12 46170111 46170111 C T SNP - - - - - - - - - - - - - - - tier3 254 0 0 1054 265 20.06 0 0 NA 991612 TCGA-AB-2995 AML46 12 77644709 77644709 T C SNP - - - - - - - - - - - - - - - tier3 133 0 0 744 210 22.01 0 0 NA 991612 TCGA-AB-2995 AML46 12 82099753 82099753 A G SNP TMTC2 NM_152588.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*49454 NULL 0 - - - no_errors tier3 251 0 0 1328 336 20.13 0 0 NA 991612 TCGA-AB-2995 AML46 12 82981165 82981165 A G SNP - - - - - - - - - - - - - - - tier3 73 0 0 549 171 23.75 0 0 NA 991612 TCGA-AB-2995 AML46 12 83048156 83048156 G C SNP - - - - - - - - - - - - - - - tier3 78 2 2.5 493 165 25.08 0 0 NA 991612 TCGA-AB-2995 AML46 12 83054785 83054785 G C SNP ENSG00000221148 ENST00000408221 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46449 NULL 0.119 - - - no_errors tier3 234 0 0 793 209 20.84 0 0 NA 991612 TCGA-AB-2995 AML46 12 90499298 90499298 C T SNP - - - - - - - - - - - - - - - tier3 60 0 0 414 62 13 0 0 NA 991612 TCGA-AB-2995 AML46 12 99584899 99584899 T C SNP GAS2L3 NM_174942.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*42100 NULL 0.007 - - - no_errors tier3 383 0 0 889 198 18.22 0 0 NA 991612 TCGA-AB-2995 AML46 12 114704683 114704683 G A SNP - - - - - - - - - - - - - - - tier3 410 7 1.68 804 393 32.8 0 0 NA 991612 TCGA-AB-2995 AML46 12 116314746 116314746 A T SNP NOS1 NM_000620.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-61489 NULL 0 - - - no_errors tier3 534 0 0 755 165 17.93 0 0 NA 991612 TCGA-AB-2995 AML46 12 116901505 116901505 G A SNP RFC5 NM_007370.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-37511 NULL 0 - - - no_errors tier3 127 0 0 306 77 20 0 0 NA 991612 TCGA-AB-2995 AML46 13 54846401 54846401 G A SNP - - - - - - - - - - - - - - - tier3 99 0 0 854 245 22.25 0 0 NA 991612 TCGA-AB-2995 AML46 13 106919236 106919236 C G SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.916-258132 e2-258132 0.001 - - - no_errors tier3 71 0 0 400 55 12.09 0 0 NA 991612 TCGA-AB-2995 AML46 13 107295234 107295234 G T SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.915+20797 e1+20797 0 - - - no_errors tier3 154 0 0 415 133 24.27 0 0 NA 991612 TCGA-AB-2995 AML46 14 37471032 37471032 C T SNP - - - - - - - - - - - - - - - tier3 419 1 0.24 1510 368 19.55 0 0 NA 991612 TCGA-AB-2995 AML46 14 51149381 51149381 A C SNP FRMD6 NM_001042481.1 human genbank 54_36p 1 validated intronic c.1+42503 e0+42503 0 - - - no_errors tier3 273 0 0 784 270 25.62 0 0 NA 991612 TCGA-AB-2995 AML46 14 56397099 56397099 C T SNP ENSG00000223234 ENST00000411302 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35972 NULL 0.002 - - - no_errors tier3 509 2 0.39 1676 584 25.81 0 0 NA 991612 TCGA-AB-2995 AML46 14 62517600 62517600 C T SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed missense c.685 p.A229T 1 superfamily_Voltage-gated potassium channels "HMMPfam_cNMP_binding,HMMSmart_SM00100,HMMSmart_SM00086,HMMPfam_Ion_trans,HMMPfam_PAS,superfamily_cAMP-binding domain-like,superfamily_PYP-like sensor domain (PAS domain),superfamily_Voltage-gated potassium channels" - no_errors tier1 217 0 1499 443 22.66 NA 991612 TCGA-AB-2995 AML46 14 86080961 86080961 G A SNP - - - - - - - - - - - - - - - tier3 115 0 0 437 93 17.55 0 0 NA 991612 TCGA-AB-2995 AML46 15 21386171 21386171 G A SNP MKRN3 NM_005664.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*22625 NULL 0.009 - - - no_errors tier3 362 0 0 1249 331 20.94 0 0 NA 991612 TCGA-AB-2995 AML46 15 24071270 24071270 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 991612 TCGA-AB-2995 AML46 15 24899650 24899650 G T SNP GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.270+44936 e3+44936 0.001 - - - no_errors tier3 105 0 0 411 88 17.6 0 0 NA 991612 TCGA-AB-2995 AML46 15 31185268 31185268 G A SNP FMN1 NM_001103184.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-37891 NULL 0.608 - - - no_errors tier3 387 0 0 1082 256 19.09 0 0 NA 991612 TCGA-AB-2995 AML46 15 41520754 41520754 A G SNP TP53BP1 NM_005657.1 human genbank 54_36p -1 validated intronic c.3083+262 e14+262 0 - - - no_errors tier3 185 0 0 835 195 18.9 1 2 66.67 991612 TCGA-AB-2995 AML46 15 47495648 47495648 C T SNP C15orf33 NM_152647.2 human genbank 54_36p -1 validated intronic c.1013-44760 e11-44760 0 - - - no_errors tier3 217 0 0 634 218 25.53 0 0 NA 991612 TCGA-AB-2995 AML46 15 51192393 51192393 G A SNP - - - - - - - - - - - - - - - tier3 193 0 0 1497 408 21.38 0 0 NA 991612 TCGA-AB-2995 AML46 15 52487879 52487879 T A SNP UNC13C NM_001080534.1 human genbank 54_36p 1 provisional intronic c.4848-6593 e18-6593 0.003 - - - no_errors tier3 172 0 0 955 225 19.05 0 0 NA 991612 TCGA-AB-2995 AML46 15 60895687 60895687 G T SNP TLN2 NM_015059.2 human genbank 54_36p 1 reviewed intronic c.6772-3081 e50-3081 0.021 - - - no_errors tier3 182 0 0 643 163 20.22 0 0 0 991612 TCGA-AB-2995 AML46 15 63748681 63748681 T G SNP DENND4A NM_005848.1 human genbank 54_36p -1 validated intronic c.4655+490 e24+490 0.009 - - - no_errors tier3 81 0 0 575 135 19.01 14 4 22.22 991612 TCGA-AB-2995 AML46 15 65695255 65695255 C G SNP MAP2K5 NM_145160.2 human genbank 54_36p 1 reviewed intronic c.546-15025 e9-15025 0.008 - - - no_errors tier3 196 0 0 935 273 22.54 2 1 33.33 991612 TCGA-AB-2995 AML46 15 87321423 87321423 G C SNP LOC100129942 XR_038237.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*12221 NULL 0.04 - - - pseudogene tier3 142 0 0 842 224 20.99 0 0 NA 991612 TCGA-AB-2995 AML46 15 91779076 91779076 C T SNP ENSG00000208918 ENST00000386183 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14503 NULL 0 - - - pseudogene tier3 94 0 0 580 135 18.78 0 0 NA 991612 TCGA-AB-2995 AML46 15 99045170 99045170 G A SNP ASB7 NM_198243.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*38980 NULL 0 - - - no_errors tier3 125 1 0.79 626 68 9.78 0 0 NA 991612 TCGA-AB-2995 AML46 16 45392254 45392254 A C SNP C16orf87 NM_001001436.2 human genbank 54_36p -1 predicted 3_prime_flanking_region c.*2111 NULL 0.069 - - - no_errors tier3 92 0 0 514 146 22.09 0 1 100 991612 TCGA-AB-2995 AML46 16 58335874 58335874 G T SNP ENSG00000200911 ENST00000364041 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13005 NULL 0 - - - no_errors tier3 41 0 0 429 225 34.35 0 0 NA 991612 TCGA-AB-2995 AML46 16 58830548 58830548 G A SNP - - - - - - - - - - - - - - - tier3 189 0 0 809 130 13.84 0 0 NA 991612 TCGA-AB-2995 AML46 16 83702528 83702528 G A SNP FAM92B NM_198491.1 human genbank 54_36p -1 predicted intronic c.20+912 e1+912 0.001 - - - no_errors tier3 244 1 0.41 420 94 18.25 0 0 NA 991612 TCGA-AB-2995 AML46 17 11513510 11513510 C T SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed silent c.3027 p.T1009 0.907 NULL "HMMSmart_SM00382,HMMPfam_Dynein_heavy,PatternScan_CPSASE_2,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 314 0 1210 325 21.1 NA 991612 TCGA-AB-2995 AML46 17 32452469 32452469 G A SNP AATF NM_012138.3 human genbank 54_36p 1 reviewed intronic c.1547+43 e10+43 0 - - - no_errors tier3 131 0 0 910 188 17.09 2 1 33.33 991612 TCGA-AB-2995 AML46 17 50117671 50117671 G A SNP - - - - - - - - - - - - - - - tier3 125 0 0 610 59 8.82 0 0 NA 991612 TCGA-AB-2995 AML46 17 70634046 70634046 C T SNP ARMC7 NM_024585.2 human genbank 54_36p 1 provisional intronic c.236-2321 e3-2321 0.002 - - - no_errors tier3 105 0 0 346 90 20.64 2 1 33.33 991612 TCGA-AB-2995 AML46 18 8210981 8210981 T C SNP PTPRM NM_001105244.1 human genbank 54_36p 1 reviewed intronic c.2301-23075 e15-23075 0.002 - - - no_errors tier3 414 0 0 1821 441 19.49 0 0 0 991612 TCGA-AB-2995 AML46 18 17749734 17749734 G A SNP MIB1 NM_020774.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*51109 NULL 0 - - - no_errors tier3 321 0 0 1074 274 20.28 0 0 NA 991612 TCGA-AB-2995 AML46 18 43407674 43407674 G A SNP ENSG00000184125 ENST00000328279 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2807 NULL 0.001 - - - no_coding_region:pseudogene tier3 333 1 0.3 885 227 20.36 0 0 NA 991612 TCGA-AB-2995 AML46 18 69629230 69629230 G A SNP - - - - - - - - - - - - - - - tier3 107 0 0 651 55 7.79 0 0 NA 991612 TCGA-AB-2995 AML46 19 56025435 56025435 G A SNP KLK15 NM_017509.2 human genbank 54_36p -1 reviewed intronic c.43+1083 e1+1083 0.053 - - - no_errors tier3 557 0 0 744 157 17.39 0 0 NA 991612 TCGA-AB-2995 AML46 20 662737 662737 C T SNP C20orf54 NM_033409.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*26933 NULL 0.992 - - - no_errors tier3 179 0 0 338 73 17.51 0 0 NA 991612 TCGA-AB-2995 AML46 20 5777442 5777442 G A SNP C20orf196 NM_152504.2 human genbank 54_36p 1 predicted intronic c.179-14228 e2-14228 0.001 - - - no_errors tier3 173 0 0 718 173 19.37 3 0 0 991612 TCGA-AB-2995 AML46 20 10103957 10103957 G C SNP LOC100131208 XM_001725409.1 human genbank 54_36p -1 model intronic c.22+21509 e1+21509 0.009 - - - no_errors tier3 281 0 0 1063 266 19.98 0 0 NA 991612 TCGA-AB-2995 AML46 20 29882538 29882538 G T SNP MYLK2 NM_033118.3 human genbank 54_36p 1 reviewed missense c.1357 p.V453L 1 "HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase" "HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 226 0 511 107 17.29 NA 991612 TCGA-AB-2995 AML46 21 13601436 13601436 A G SNP LOC100129305 XM_001714760.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-7198 NULL 0.01 - - - no_errors tier3 106 1 0.93 558 146 20.74 0 0 NA 991612 TCGA-AB-2995 AML46 21 16420892 16420892 A G SNP C21orf34 NM_001005732.1 human genbank 54_36p 1 validated intronic c.225-54890 e2-54890 0.032 - - - no_errors tier3 41 0 0 164 39 19.21 0 0 NA 991612 TCGA-AB-2995 AML46 21 30628389 30628389 C T SNP KRTAP26-1 NM_203405.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-14165 NULL 0 - - - no_errors tier3 478 0 0 1393 352 20.11 0 0 NA 991612 TCGA-AB-2995 AML46 21 36977671 36977671 T C SNP SIM2 NM_005069.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-16246 NULL 0.018 - - - no_errors tier3 603 0 0 1136 310 21.41 0 0 NA 991612 TCGA-AB-2995 AML46 22 29161774 29161774 C T SNP LOC646513 XM_001132717.1 human genbank 54_36p 1 model silent c.144 p.L48 0.056 NULL NULL - no_errors tier1 545 0 722 148 16.99 1 2 66.67 991612 TCGA-AB-2995 AML46 22 33034161 33034161 C T SNP - - - - - - - - - - - - - - - tier3 406 2 0.49 917 207 18.32 0 0 NA 991612 TCGA-AB-2995 AML46 22 35927832 35927832 G A SNP C1QTNF6 NM_031910.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-13633 NULL 0.031 - - - no_errors tier3 206 0 0 472 83 14.93 0 0 NA 991612 TCGA-AB-2995 AML46 22 47701859 47701859 G T SNP LOC100128946 XM_001725064.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*24820 NULL 0.002 - - - no_errors tier3 167 0 0 576 189 24.67 0 0 NA 445045 TCGA-AB-2996 AML30 X 1830396 1830396 C T SNP LOC100130227 XM_001713694.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-33216 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 246 7 2.77 129 106 44.54 0 0 NA 445045 TCGA-AB-2996 AML30 X 23611257 23611257 A G SNP PRDX4 NM_006406.1 human genbank 54_36p 1 reviewed intronic c.731-452 e6-452 0.962 - - - no_errors tier3 83 2 2.35 13 96 88.07 0 0 0 445045 TCGA-AB-2996 AML30 X 42061453 42061453 C A SNP ENSG00000212635 ENST00000391331 human ensembl 54_36p 1 known intronic c.375+31554 e1+31554 0.001 - - - no_errors tier3 155 6 3.73 31 146 82.02 0 0 NA 445045 TCGA-AB-2996 AML30 X 105080567 105080567 G A SNP NRK ENST00000243300 human ensembl 54_36p 1 known intronic c.4516+185 e27+185 0 - - - no_errors tier3 57 4 6.56 15 82 84.54 0 0 NA 445045 TCGA-AB-2996 AML30 X 109119780 109119780 G C SNP TMEM164 NM_032227.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-13879 NULL 0.071 - - - no_errors tier3 236 15 5.98 34 165 82.91 0 0 NA 445045 TCGA-AB-2996 AML30 X 122307084 122307084 G A SNP GRIA3 NM_000828.4 human genbank 54_36p 1 reviewed intronic c.697-9358 e5-9358 0.001 - - - no_errors tier3 236 7 2.88 20 268 93.06 0 0 NA 445045 TCGA-AB-2996 AML30 X 131603921 131603921 C T SNP HS6ST2 ENST00000319809 human ensembl 54_36p -1 known intronic c.1062-13119 e7-13119 0 - - - no_errors tier3 174 10 5.43 26 232 89.92 0 0 NA 445045 TCGA-AB-2996 AML30 X 142006671 142006671 G A SNP ENSG00000202473 ENST00000365603 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*542 NULL 0 - - - no_errors tier3 77 2 2.53 29 182 86.26 0 0 NA 445045 TCGA-AB-2996 AML30 X 144020813 144020813 T C SNP ENSG00000218657 ENST00000403711 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44981 NULL 0.004 - - - no_coding_region:pseudogene tier3 135 2 1.46 25 114 82.01 0 0 NA 445045 TCGA-AB-2996 AML30 1 18534084 18534084 C T SNP IGSF21 NM_032880.2 human genbank 54_36p 1 provisional silent c.417 p.N139 0.998 "HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726" "HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726" - no_errors tier1 486 9 1.82 315 252 44.37 1 0 445045 TCGA-AB-2996 AML30 1 18612778 18612778 C A SNP IGSF21 NM_032880.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*35371 NULL 0.738 - - - no_errors tier3 509 8 1.54 182 127 41.1 0 0 NA 445045 TCGA-AB-2996 AML30 1 31090539 31090539 C T SNP SDC3 NM_014654.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*28106 NULL 0.001 - - - no_errors tier3 210 1 0.47 263 199 43.07 0 0 NA 445045 TCGA-AB-2996 AML30 1 36975587 36975587 G A SNP - - - - - - - - - - - - - - - tier3 816 17 2.04 260 186 41.7 0 0 NA 445045 TCGA-AB-2996 AML30 1 40279765 40279765 G A SNP CAP1 NM_001105530.1 human genbank 54_36p 1 reviewed intronic c.1+723 e0+723 0 - - - no_errors tier3 194 5 2.51 107 79 42.47 0 0 0 445045 TCGA-AB-2996 AML30 1 43590992 43590992 C G SNP MPL NM_005373.2 human genbank 54_36p 1 reviewed missense c.1870 p.H624D 0.996 NULL "PatternScan_HEMATOPO_REC_L_F1,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_EpoR_lig-bind" - no_errors tier1 342 8 2.29 148 145 49.49 42 40 48.19 445045 TCGA-AB-2996 AML30 1 56644830 56644830 A G SNP - - - - - - - - - - - - - - - tier3 410 6 1.44 411 380 48.04 0 0 NA 445045 TCGA-AB-2996 AML30 1 69976403 69976403 G A SNP LRRC7 ENST00000310961 human ensembl 54_36p 1 known intronic c.1+21914 e1+21914 0 - - - no_errors tier3 132 1 0.75 164 125 43.25 0 0 NA 445045 TCGA-AB-2996 AML30 1 79892331 79892331 G A SNP - - - - - - - - - - - - - - - tier3 75 0 0 193 113 36.81 0 0 NA 445045 TCGA-AB-2996 AML30 1 80480776 80480776 C A SNP ENSG00000218484 ENST00000402916 human ensembl 54_36p 1 known 5_prime_flanking_region c.-40849 NULL 0.035 - - - no_coding_region:pseudogene tier3 258 4 1.53 210 162 43.55 0 0 NA 445045 TCGA-AB-2996 AML30 1 82872246 82872246 A G SNP - - - - - - - - - - - - - - - tier3 161 6 3.59 162 122 42.96 0 0 NA 445045 TCGA-AB-2996 AML30 1 86678781 86678781 G T SNP CLCA2 NM_006536.5 human genbank 54_36p 1 reviewed intronic c.1381+185 e8+185 0 - - - no_errors tier3 324 3 0.92 248 188 43.12 0 0 NA 445045 TCGA-AB-2996 AML30 1 87401579 87401579 G A SNP HS2ST1 ENST00000370548 human ensembl 54_36p 1 known intronic c.872-4828 e8-4828 0.029 - - - no_errors tier3 410 13 3.07 237 203 46.14 0 0 0 445045 TCGA-AB-2996 AML30 1 91984763 91984764 - T INS TGFBR3 NM_003243.3 human genbank 54_36p -1 validated intronic c.385-11660_385-11659 e4-11659 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 1 102716033 102716033 T C SNP - - - - - - - - - - - - - - - tier3 100 0 0 56 45 44.55 0 0 NA 445045 TCGA-AB-2996 AML30 1 112856989 112856989 G A SNP WNT2B NM_024494.3 human genbank 54_36p 1 reviewed intronic c.183-2030 e2-2030 0 - - - no_errors tier3 557 10 1.76 152 79 34.2 0 0 NA 445045 TCGA-AB-2996 AML30 1 114494708 114494708 G C SNP SYT6 NM_205848.2 human genbank 54_36p -1 validated intronic c.1+3047 e0+3047 0 - - - no_errors tier3 600 5 0.83 246 162 39.71 0 0 NA 445045 TCGA-AB-2996 AML30 1 151051691 151051691 G T SNP LCE1B NM_178349.1 human genbank 54_36p 1 validated nonsense c.145 p.G49* 0.991 NULL NULL - no_errors tier1 70 2 2.78 91 67 41.88 NA 445045 TCGA-AB-2996 AML30 1 157516879 157516879 C G SNP OR10J5 ENST00000389011 human ensembl 54_36p -1 known intronic c.502-490 e2-490 0 - - - no_stop_codon tier3 171 3 1.72 329 221 40.18 0 0 NA 445045 TCGA-AB-2996 AML30 1 160531808 160531808 T G SNP NOS1AP NM_014697.1 human genbank 54_36p 1 reviewed intronic c.271-5239 e4-5239 0.01 - - - no_errors tier3 376 3 0.79 204 154 43.02 0 0 0 445045 TCGA-AB-2996 AML30 1 175357105 175357105 C T SNP ASTN1 NM_004319.1 human genbank 54_36p -1 validated intronic c.283+43048 e1+43048 0.003 - - - no_errors tier3 351 5 1.4 190 138 41.95 0 0 NA 445045 TCGA-AB-2996 AML30 1 181352534 181352534 T C SNP LAMC1 NM_002293.3 human genbank 54_36p 1 reviewed silent c.1437 p.P479 1 "HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,PatternScan_EGF_LAM_1,superfamily_Grow_fac_recept,superfamily_SSF57196" "HMMPfam_Laminin_B,HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,PatternScan_EGF_LAM_1,HMMPfam_Laminin_N,HMMSmart_LamNT,superfamily_Grow_fac_recept,PatternScan_EGF_1,PatternScan_EGF_2,HMMSmart_LamB,superfamily_SSF57196" - no_errors tier1 196 0 195 167 46.13 1 0 445045 TCGA-AB-2996 AML30 1 203684974 203684974 A G SNP LEMD1 ENST00000367154 human ensembl 54_36p -1 known intronic c.1+645 e0+645 0.008 - - - no_errors tier3 1417 15 1.05 319 242 43.06 0 0 NA 445045 TCGA-AB-2996 AML30 1 208337457 208337457 G A SNP SYT14 NM_153262.2 human genbank 54_36p 1 validated intronic c.715-2523 e6-2523 0 - - - no_errors tier3 248 13 4.98 125 108 46.35 0 0 NA 445045 TCGA-AB-2996 AML30 1 210747240 210747240 G A SNP ENSG00000203259 ENST00000366090 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2204 NULL 0.004 - - - no_coding_region:pseudogene tier3 344 11 3.1 177 147 45.37 0 0 NA 445045 TCGA-AB-2996 AML30 1 214161442 214161442 T - DEL USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.7300+13139 e37+13139 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 1 217132689 217132689 T A SNP ENSG00000218763 ENST00000407979 human ensembl 54_36p -1 known 5_prime_flanking_region c.-10074 NULL 0.114 - - - no_coding_region:pseudogene tier3 107 0 0 120 96 44.44 0 0 NA 445045 TCGA-AB-2996 AML30 1 234820150 234820150 C T SNP HEATR1 NM_018072.4 human genbank 54_36p -1 validated intronic c.1530+620 e11+620 0.045 - - - no_errors tier3 71 2 2.74 150 113 42.97 0 1 100 445045 TCGA-AB-2996 AML30 1 234985448 234985448 G A SNP ACTN2 NM_001103.2 human genbank 54_36p 1 reviewed intronic c.2154+327 e17+327 0.001 - - - no_errors tier3 176 14 7.37 216 159 42.4 0 0 NA 445045 TCGA-AB-2996 AML30 2 2271215 2271215 G A SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.1-3933 e1-3933 0.001 - - - no_errors tier3 202 1 0.49 179 149 45.43 0 0 NA 445045 TCGA-AB-2996 AML30 2 2988302 2988302 A G SNP - - - - - - - - - - - - - - - tier3 333 6 1.76 322 213 39.81 0 0 NA 445045 TCGA-AB-2996 AML30 2 4833382 4833382 G A SNP ENSG00000210527 ENST00000387792 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19084 NULL 0 - - - pseudogene tier3 141 0 0 293 190 39.26 0 0 NA 445045 TCGA-AB-2996 AML30 2 5406497 5406497 G A SNP ENSG00000219497 ENST00000407903 human ensembl 54_36p -1 known 5_prime_flanking_region c.-34779 NULL 0.025 - - - no_coding_region:pseudogene tier3 177 6 3.28 249 164 39.71 0 0 NA 445045 TCGA-AB-2996 AML30 2 8698300 8698300 A C SNP ID2 NM_002166.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-41447 NULL 0.002 - - - no_errors tier3 426 18 4.04 131 86 39.63 0 0 NA 445045 TCGA-AB-2996 AML30 2 15198202 15198202 A G SNP NBAS NM_015909.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*26421 NULL 0.007 - - - no_errors tier3 424 4 0.93 246 162 39.71 0 0 NA 445045 TCGA-AB-2996 AML30 2 16007044 16007044 G A SNP LOC100129296 XM_001715416.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-5901 NULL 0.008 - - - no_errors tier3 210 3 1.4 168 113 40.21 0 0 NA 445045 TCGA-AB-2996 AML30 2 17428942 17428942 G A SNP LOC388925 XR_016133.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-881 NULL 0 - - - pseudogene tier3 162 0 0 167 114 40.57 0 0 NA 445045 TCGA-AB-2996 AML30 2 24318717 24318717 T C SNP ITSN2 NM_006277.2 human genbank 54_36p -1 reviewed intronic c.3574+3785 e28+3785 0.003 - - - no_errors tier3 93 0 0 145 128 46.89 5 1 16.67 445045 TCGA-AB-2996 AML30 2 29718443 29718443 A T SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.952+52777 e3+52777 0.001 - - - no_errors tier3 447 3 0.67 584 500 45.91 0 0 NA 445045 TCGA-AB-2996 AML30 2 32892381 32892381 T C SNP TTC27 NM_017735.3 human genbank 54_36p 1 provisional intronic c.2308+1195 e18+1195 0.011 - - - no_errors tier3 239 0 0 163 130 44.37 3 3 50 445045 TCGA-AB-2996 AML30 2 35049879 35049879 T A SNP - - - - - - - - - - - - - - - tier3 243 7 2.8 127 107 45.73 0 0 NA 445045 TCGA-AB-2996 AML30 2 42758962 42758962 G A SNP MTA3 NM_020744.2 human genbank 54_36p 1 provisional intronic c.703-4083 e9-4083 0 - - - no_errors tier3 118 1 0.84 153 105 40.7 0 0 0 445045 TCGA-AB-2996 AML30 2 44850322 44850322 C T SNP C2orf34 NM_024766.3 human genbank 54_36p 1 validated intronic c.895-2357 e11-2357 0 - - - no_errors tier3 183 5 2.66 145 106 42.23 0 0 0 445045 TCGA-AB-2996 AML30 2 62112699 62112699 A G SNP COMMD1 NM_152516.2 human genbank 54_36p 1 validated intronic c.462+31078 e2+31078 0.205 - - - no_errors tier3 168 2 1.17 140 83 37.22 1 4 80 445045 TCGA-AB-2996 AML30 2 66052706 66052706 A G SNP - - - - - - - - - - - - - - - tier3 448 14 3.03 274 242 46.72 0 0 NA 445045 TCGA-AB-2996 AML30 2 71863335 71863335 C T SNP - - - - - - - - - - - - - - - tier3 563 4 0.7 173 129 42.57 0 0 NA 445045 TCGA-AB-2996 AML30 2 78045344 78045344 C A SNP - - - - - - - - - - - - - - - tier3 83 6 6.74 196 157 44.48 0 0 NA 445045 TCGA-AB-2996 AML30 2 79405698 79405698 G C SNP LOC100132577 XM_001726289.1 human genbank 54_36p 1 model intronic c.142+5159 e3+5159 0.069 - - - no_errors tier3 207 2 0.96 179 135 42.99 0 0 NA 445045 TCGA-AB-2996 AML30 2 80717186 80717186 G A SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.2434-11035 e17-11035 0 - - - no_errors tier3 198 2 1 203 136 40.12 0 0 NA 445045 TCGA-AB-2996 AML30 2 104479474 104479474 T A SNP ENSG00000199727 ENST00000362857 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36189 NULL 0 - - - no_errors tier3 146 0 0 152 131 46.29 0 0 NA 445045 TCGA-AB-2996 AML30 2 107304741 107304741 C G SNP - - - - - - - - - - - - - - - tier3 219 16 6.78 282 220 43.82 0 0 NA 445045 TCGA-AB-2996 AML30 2 115955577 115955577 A T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.272-17979 e4-17979 0 - - - no_errors tier3 267 1 0.37 328 264 44.59 0 0 NA 445045 TCGA-AB-2996 AML30 2 116643665 116643665 T C SNP - - - - - - - - - - - - - - - tier3 199 0 0 178 123 40.86 0 0 NA 445045 TCGA-AB-2996 AML30 2 117878014 117878014 T A SNP - - - - - - - - - - - - - - - tier3 266 2 0.75 269 251 48.27 0 0 NA 445045 TCGA-AB-2996 AML30 2 123499931 123499931 A G SNP - - - - - - - - - - - - - - - tier3 144 0 0 184 112 37.84 0 0 NA 445045 TCGA-AB-2996 AML30 2 126113387 126113387 T A SNP - - - - - - - - - - - - - - - tier3 191 1 0.52 273 217 44.29 0 0 NA 445045 TCGA-AB-2996 AML30 2 133037078 133037078 G C SNP GPR39 NM_001508.2 human genbank 54_36p 1 validated intronic c.857-82066 e2-82066 0.001 - - - no_errors tier3 180 1 0.55 246 203 45.21 0 0 NA 445045 TCGA-AB-2996 AML30 2 133207040 133207040 G T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.5129-946 e15-946 0 - - - no_errors tier3 251 6 2.33 317 306 49.12 0 0 NA 445045 TCGA-AB-2996 AML30 2 133623504 133623504 C G SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.208-19351 e4-19351 0.004 - - - no_errors tier3 157 0 0 432 331 43.32 0 0 NA 445045 TCGA-AB-2996 AML30 2 134306280 134306280 G A SNP - - - - - - - - - - - - - - - tier3 131 2 1.5 171 123 41.84 0 0 NA 445045 TCGA-AB-2996 AML30 2 139881418 139881418 A T SNP - - - - - - - - - - - - - - - tier3 167 1 0.6 92 79 45.66 0 0 NA 445045 TCGA-AB-2996 AML30 2 142259671 142259671 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.205+24647 e2+24647 0.004 - - - no_errors tier3 202 5 2.42 230 166 41.81 0 0 NA 445045 TCGA-AB-2996 AML30 2 146495054 146495054 A G SNP - - - - - - - - - - - - - - - tier3 200 6 2.91 183 158 46.33 0 0 NA 445045 TCGA-AB-2996 AML30 2 151183536 151183536 G A SNP - - - - - - - - - - - - - - - tier3 175 3 1.69 237 172 42.05 0 0 NA 445045 TCGA-AB-2996 AML30 2 163951540 163951540 G A SNP - - - - - - - - - - - - - - - tier3 261 17 6.12 336 239 41.57 0 0 NA 445045 TCGA-AB-2996 AML30 2 170923986 170923986 C T SNP MYO3B NM_138995.1 human genbank 54_36p 1 provisional intronic c.816-9992 e9-9992 0 - - - no_errors tier3 285 7 2.4 241 176 42.21 0 0 NA 445045 TCGA-AB-2996 AML30 2 204205384 204205384 T A SNP ENSG00000187543 ENST00000338769 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*2853 NULL 0 - - - no_coding_region:pseudogene tier3 236 2 0.84 135 127 48.47 0 0 NA 445045 TCGA-AB-2996 AML30 2 204654505 204654505 C T SNP - - - - - - - - - - - - - - - tier3 304 3 0.98 272 232 45.94 0 0 NA 445045 TCGA-AB-2996 AML30 2 208208401 208208401 G A SNP FAM119A NM_145280.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11057 NULL 0 - - - no_errors tier3 204 2 0.97 119 98 45.16 0 0 NA 445045 TCGA-AB-2996 AML30 2 212207623 212207623 G C SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.1947-4059 e17-4059 0.002 - - - no_errors tier3 109 0 0 115 92 44.44 0 0 NA 445045 TCGA-AB-2996 AML30 2 218523911 218523911 C T SNP TNS1 NM_022648.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-52978 NULL 0 - - - no_errors tier3 582 5 0.85 106 96 47.52 0 0 0 445045 TCGA-AB-2996 AML30 2 219271843 219271843 A G SNP STK36 NM_015690.3 human genbank 54_36p 1 validated missense c.3332 p.Y1111C 1 superfamily_ARM repeat "HMMPfam_HEAT,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 331 2 0.6 175 140 44.44 1 6 85.71 445045 TCGA-AB-2996 AML30 2 220011004 220011004 G A SNP SPEG NM_005876.4 human genbank 54_36p 1 validated intronic c.388+2673 e1+2673 0.145 - - - no_errors tier3 594 4 0.67 132 113 46.12 0 0 NA 445045 TCGA-AB-2996 AML30 2 222736471 222736471 G A SNP PAX3 NM_181459.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*37666 NULL 0.001 - - - no_errors tier3 189 2 1.05 127 121 48.79 0 0 NA 445045 TCGA-AB-2996 AML30 2 225934129 225934129 G A SNP KIAA1486 NM_020864.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-47712 NULL 0 - - - no_errors tier3 323 1 0.31 421 330 43.88 0 0 NA 445045 TCGA-AB-2996 AML30 2 229471340 229471340 C T SNP - - - - - - - - - - - - - - - tier3 346 11 3.08 144 123 46.07 0 0 NA 445045 TCGA-AB-2996 AML30 2 240860809 240860809 G A SNP ENSG00000212449 ENST00000391147 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16497 NULL 0.002 - - - no_errors tier3 96 0 0 56 43 43.43 0 0 0 445045 TCGA-AB-2996 AML30 3 434341 434341 C T SNP CHL1 NM_006614.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*11947 NULL 0.002 - - - no_errors tier3 419 4 0.95 243 154 38.69 0 0 NA 445045 TCGA-AB-2996 AML30 3 2341520 2341520 G A SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.1-14342 e1-14342 0.001 - - - no_errors tier3 102 0 0 94 53 35.81 0 0 NA 445045 TCGA-AB-2996 AML30 3 5490053 5490053 C T SNP - - - - - - - - - - - - - - - tier3 285 3 1.04 280 241 46.17 0 0 NA 445045 TCGA-AB-2996 AML30 3 7628788 7628788 T A SNP GRM7 NM_181874.2 human genbank 54_36p 1 reviewed intronic c.2451+32744 e8+32744 0.005 - - - no_errors tier3 302 2 0.66 307 298 49.26 0 0 NA 445045 TCGA-AB-2996 AML30 3 8232391 8232391 T C SNP - - - - - - - - - - - - - - - tier2 162 1 0.61 185 126 40.51 0 0 NA 445045 TCGA-AB-2996 AML30 3 10468995 10468995 C T SNP ATP2B2 ENST00000383800 human ensembl 54_36p -1 known intronic c.1-2449 e1-2449 0.001 - - - no_errors tier3 317 6 1.85 126 92 42.2 0 0 NA 445045 TCGA-AB-2996 AML30 3 14763200 14763200 C A SNP C3orf20 NM_032137.3 human genbank 54_36p 1 predicted intronic c.1941-10682 e11-10682 0.083 - - - no_errors tier3 256 2 0.78 185 119 39.14 0 0 NA 445045 TCGA-AB-2996 AML30 3 21822402 21822402 T A SNP ENSG00000221384 ENST00000408457 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23832 NULL 0.001 - - - no_errors tier3 251 6 2.33 231 196 45.9 2 0 0 445045 TCGA-AB-2996 AML30 3 26221177 26221177 C T SNP LOC645101 XR_016793.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-11640 NULL 0 - - - no_errors tier3 384 2 0.52 180 202 52.74 0 0 NA 445045 TCGA-AB-2996 AML30 3 30330519 30330519 A G SNP ENSG00000199927 ENST00000363057 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9488 NULL 0.026 - - - no_errors tier3 178 6 3.26 346 276 44.37 0 0 NA 445045 TCGA-AB-2996 AML30 3 48809948 48809948 C G SNP PRKAR2A NM_004157.2 human genbank 54_36p -1 reviewed intronic c.299-3462 e3-3462 0.032 - - - no_errors tier3 354 6 1.67 208 210 50.24 2 0 0 445045 TCGA-AB-2996 AML30 3 53129159 53129159 T C SNP RFT1 NM_052859.3 human genbank 54_36p -1 reviewed intronic c.559-82 e6-82 0.001 - - - no_errors tier3 169 3 1.74 152 58 27.62 0 0 0 445045 TCGA-AB-2996 AML30 3 59879322 59879322 C T SNP FHIT NM_002012.2 human genbank 54_36p -1 reviewed intronic c.348+3790 e4+3790 0.004 - - - no_errors tier3 435 3 0.68 423 276 39.32 0 0 0 445045 TCGA-AB-2996 AML30 3 62256815 62256815 G A SNP C3orf14 NM_020685.3 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-24372 NULL 1 - - - no_errors tier3 144 1 0.69 154 124 44.6 1 0 0 445045 TCGA-AB-2996 AML30 3 62606732 62606732 T C SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.1204-174 e6-174 0 - - - no_errors tier3 376 8 2.08 250 188 42.92 0 0 NA 445045 TCGA-AB-2996 AML30 3 64159031 64159031 A T SNP PRICKLE2 NM_198859.3 human genbank 54_36p -1 validated intronic c.144+469 e1+469 0.201 - - - no_errors tier3 109 0 0 125 101 44.69 0 0 NA 445045 TCGA-AB-2996 AML30 3 64652721 64652721 G A SNP LOC730057 XM_001132251.1 human genbank 54_36p 1 model intronic c.79+729 e1+729 0 - - - no_errors tier3 248 4 1.58 158 125 44.17 0 0 NA 445045 TCGA-AB-2996 AML30 3 64849264 64849264 G A SNP - - - - - - - - - - - - - - - tier3 145 3 2.03 272 191 41.25 0 0 NA 445045 TCGA-AB-2996 AML30 3 65069095 65069095 A G SNP - - - - - - - - - - - - - - - tier3 403 6 1.46 166 133 44.19 0 0 NA 445045 TCGA-AB-2996 AML30 3 73458475 73458475 C A SNP - - - - - - - - - - - - - - - tier3 315 2 0.63 237 240 50.31 0 0 NA 445045 TCGA-AB-2996 AML30 3 74502529 74502529 C T SNP CNTN3 NM_020872.1 human genbank 54_36p -1 validated intronic c.658+508 e5+508 0 - - - no_errors tier3 237 9 3.66 281 173 38.11 0 0 NA 445045 TCGA-AB-2996 AML30 3 79397664 79397664 T A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-140285 e2-140285 0.025 - - - no_errors tier3 61 3 4.69 79 54 40.6 0 0 NA 445045 TCGA-AB-2996 AML30 3 79464300 79464300 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-206921 e2-206921 0 - - - no_errors tier3 283 4 1.39 258 183 41.5 0 0 NA 445045 TCGA-AB-2996 AML30 3 79614960 79614960 C A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.88+106704 e1+106704 0.001 - - - no_errors tier3 140 0 0 142 123 46.42 0 0 NA 445045 TCGA-AB-2996 AML30 3 80541873 80541873 T C SNP - - - - - - - - - - - - - - - tier3 74 1 1.33 124 99 44.2 0 0 NA 445045 TCGA-AB-2996 AML30 3 96109116 96109116 C G SNP WDR82P1 ENST00000332119 human ensembl 54_36p -1 known 3_prime_flanking_region c.*29504 NULL 0 - - - no_coding_region:pseudogene tier3 161 1 0.62 132 112 45.71 0 0 NA 445045 TCGA-AB-2996 AML30 3 97506284 97506284 T C SNP LOC644063 XR_016547.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-44610 NULL 0 - - - pseudogene tier3 55 0 0 82 61 42.66 0 0 NA 445045 TCGA-AB-2996 AML30 3 106080991 106080991 G A SNP - - - - - - - - - - - - - - - tier3 124 3 2.31 177 138 42.86 0 0 NA 445045 TCGA-AB-2996 AML30 3 106258137 106258137 A T SNP - - - - - - - - - - - - - - - tier3 60 6 9.09 95 63 39.87 0 0 NA 445045 TCGA-AB-2996 AML30 3 109914910 109914910 C T SNP DZIP3 NM_014648.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*22476 NULL 0.98 - - - no_errors tier3 182 1 0.55 208 128 38.1 0 0 NA 445045 TCGA-AB-2996 AML30 3 119457502 119457502 A C SNP - - - - - - - - - - - - - - - tier3 220 10 4.33 120 71 37.17 0 0 NA 445045 TCGA-AB-2996 AML30 3 132753774 132753774 G A SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.1168+200 e12+200 0.075 - - - no_errors tier3 159 3 1.85 240 223 48.16 0 0 NA 445045 TCGA-AB-2996 AML30 3 133957116 133957116 C A SNP NCRNA00119 NR_002811.1 human genbank 54_36p 1 provisional intronic c.NULL NULL 0.006 - - - no_errors tier3 105 1 0.94 144 101 41.06 0 0 NA 445045 TCGA-AB-2996 AML30 3 141940045 141940045 C T SNP TRIM42 NM_152616.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*37539 NULL 0 - - - no_errors tier3 441 6 1.34 215 171 44.3 0 0 NA 445045 TCGA-AB-2996 AML30 3 146474603 146474603 T A SNP - - - - - - - - - - - - - - - tier3 87 1 1.14 76 90 53.57 0 0 NA 445045 TCGA-AB-2996 AML30 3 148442557 148442557 G A SNP ENSG00000214250 ENST00000327215 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-34688 NULL 0 - - - no_coding_region:pseudogene tier3 135 3 2.17 136 130 48.87 0 0 NA 445045 TCGA-AB-2996 AML30 3 148989506 148989506 G C SNP - - - - - - - - - - - - - - - tier3 115 0 0 210 142 40.34 0 0 NA 445045 TCGA-AB-2996 AML30 3 157113991 157113991 A C SNP GMPS NM_003875.2 human genbank 54_36p 1 reviewed intronic c.887-911 e8-911 0.147 - - - no_errors tier3 234 9 3.7 346 253 42.24 0 0 0 445045 TCGA-AB-2996 AML30 3 157207814 157207814 T C SNP CASRL1 ENST00000312652 human ensembl 54_36p 1 known 5_prime_flanking_region c.-11427 NULL 0.077 - - - no_errors tier3 234 10 4.1 225 206 47.8 0 0 NA 445045 TCGA-AB-2996 AML30 3 159778004 159778004 C T SNP MLF1 NM_022443.1 human genbank 54_36p 1 validated intronic c.47+6174 e1+6174 0 - - - no_errors tier3 48 0 0 27 24 47.06 0 0 NA 445045 TCGA-AB-2996 AML30 3 164850899 164850899 G A SNP - - - - - - - - - - - - - - - tier3 141 2 1.4 92 56 37.84 0 0 NA 445045 TCGA-AB-2996 AML30 3 165369105 165369105 A G SNP MIRN1263 ENST00000408324 human ensembl 54_36p -1 known 3_prime_flanking_region c.*2848 NULL 0.01 - - - no_errors tier3 149 1 0.67 158 125 44.17 0 0 NA 445045 TCGA-AB-2996 AML30 3 168616113 168616113 G A SNP ZBBX NM_024687.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42730 NULL 0.002 - - - no_errors tier3 424 6 1.4 417 338 44.77 0 0 NA 445045 TCGA-AB-2996 AML30 3 171682755 171682755 G A SNP SLC7A14 NM_020949.2 human genbank 54_36p -1 validated intronic c.1115+1042 e5+1042 0.014 - - - no_errors tier3 193 6 3 142 114 44.36 0 0 NA 445045 TCGA-AB-2996 AML30 3 174672640 174672640 C A SNP NLGN1 NM_014932.2 human genbank 54_36p 1 reviewed intronic c.1+37078 e0+37078 0.002 - - - no_errors tier3 322 1 0.31 166 112 40.29 0 0 NA 445045 TCGA-AB-2996 AML30 3 185435860 185435860 C T SNP ENSG00000214162 ENST00000397690 human ensembl 54_36p 1 known intronic c.310+4461 e2+4461 0.218 - - - no_stop_codon tier3 127 0 0 69 57 44.88 0 0 NA 445045 TCGA-AB-2996 AML30 3 190476492 190476492 G A SNP TPRG1 NM_198485.3 human genbank 54_36p 1 validated intronic c.480-34377 e4-34377 0.001 - - - no_errors tier3 403 5 1.22 294 231 44 0 0 NA 445045 TCGA-AB-2996 AML30 3 193461107 193461107 T C SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed intronic c.414+74737 e3+74737 0.003 - - - no_errors tier3 220 5 2.22 379 247 39.46 0 0 NA 445045 TCGA-AB-2996 AML30 4 884287 884287 T C SNP GAK NM_005255.2 human genbank 54_36p -1 validated intronic c.526-2341 e6-2341 0.002 - - - no_errors tier3 172 2 1.15 142 112 43.92 2 1 33.33 445045 TCGA-AB-2996 AML30 4 8762664 8762664 C T SNP - - - - - - - - - - - - - - - tier3 257 4 1.53 94 57 37.75 0 0 NA 445045 TCGA-AB-2996 AML30 4 9743365 9743365 A T SNP WDR1 NM_017491.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15977 NULL 0.002 - - - no_errors tier3 203 1 0.49 164 120 42.25 0 0 NA 445045 TCGA-AB-2996 AML30 4 11094338 11094338 A - DEL LOC730845 XM_001721817.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-15261 NULL 0.004 - - - no_start_codon:pseudogene:no_stop_codon tier2 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 4 21835766 21835766 C T SNP - - - - - - - - - - - - - - - tier3 474 17 3.46 284 269 48.64 0 0 NA 445045 TCGA-AB-2996 AML30 4 23092976 23092976 A G SNP - - - - - - - - - - - - - - - tier3 250 5 1.95 228 215 48.42 0 0 NA 445045 TCGA-AB-2996 AML30 4 26975936 26975936 C T SNP - - - - - - - - - - - - - - - tier3 132 5 3.65 178 159 47.18 0 0 NA 445045 TCGA-AB-2996 AML30 4 28489135 28489135 G T SNP - - - - - - - - - - - - - - - tier3 222 8 3.48 179 125 40.98 0 0 NA 445045 TCGA-AB-2996 AML30 4 31040556 31040557 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 4 31239842 31239842 T A SNP - - - - - - - - - - - - - - - tier3 113 2 1.74 127 80 38.65 0 0 NA 445045 TCGA-AB-2996 AML30 4 32586262 32586262 G A SNP - - - - - - - - - - - - - - - tier3 169 2 1.16 290 174 37.5 0 0 NA 445045 TCGA-AB-2996 AML30 4 33265848 33265848 G A SNP - - - - - - - - - - - - - - - tier3 146 1 0.68 232 151 39.43 0 0 NA 445045 TCGA-AB-2996 AML30 4 33933757 33933758 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 4 34746333 34746333 G A SNP - - - - - - - - - - - - - - - tier3 130 1 0.76 127 110 46.41 0 0 NA 445045 TCGA-AB-2996 AML30 4 37002529 37002529 A T SNP ENSG00000215243 ENST00000389006 human ensembl 54_36p 1 known intronic c.1-1424 e1-1424 0 - - - no_start_codon:no_stop_codon tier3 313 0 0 286 201 41.27 0 0 NA 445045 TCGA-AB-2996 AML30 4 42578529 42578529 T A SNP GRXCR1 NM_001080476.1 human genbank 54_36p 1 inferred 5_prime_flanking_region c.-11512 NULL 0.04 - - - no_errors tier3 95 1 1.04 271 198 42.22 0 0 NA 445045 TCGA-AB-2996 AML30 4 42686508 42686508 C - DEL GRXCR1 NM_001080476.1 human genbank 54_36p 1 inferred intronic c.627+26600 e2+26600 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 4 55883644 55883644 A G SNP SRD5A3 NM_024592.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-23617 NULL 0.005 - - - no_errors tier3 153 3 1.92 208 168 44.68 0 0 NA 445045 TCGA-AB-2996 AML30 4 67410281 67410281 C T SNP - - - - - - - - - - - - - - - tier3 157 3 1.88 177 115 39.25 0 0 NA 445045 TCGA-AB-2996 AML30 4 73384887 73384887 A G SNP ADAMTS3 NM_014243.1 human genbank 54_36p -1 reviewed intronic c.2425-1864 e18-1864 0.001 - - - no_errors tier3 244 4 1.61 393 287 42.21 0 0 NA 445045 TCGA-AB-2996 AML30 4 80143237 80143238 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 4 81973101 81973101 C A SNP C4orf22 NM_152770.1 human genbank 54_36p 1 predicted intronic c.334-37070 e4-37070 0.001 - - - no_errors tier3 92 2 2.13 137 114 45.42 0 0 NA 445045 TCGA-AB-2996 AML30 4 89239957 89239957 C T SNP ABCG2 NM_004827.2 human genbank 54_36p -1 reviewed intronic c.1368-333 e11-333 0 - - - no_errors tier3 272 2 0.73 279 235 45.54 0 0 0 445045 TCGA-AB-2996 AML30 4 90356951 90356951 G A SNP GPRIN3 NM_198281.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*31003 NULL 0 - - - no_errors tier3 253 8 3.07 302 225 42.69 0 0 NA 445045 TCGA-AB-2996 AML30 4 90945731 90945731 G A SNP SNCA NM_000345.3 human genbank 54_36p -1 reviewed intronic c.306+16689 e3+16689 0.013 - - - no_errors tier3 157 2 1.26 216 188 46.42 13 13 50 445045 TCGA-AB-2996 AML30 4 93314884 93314884 C T SNP ENSG00000214910 ENST00000399219 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*7762 NULL 0.001 - - - no_coding_region:pseudogene tier3 97 0 0 111 76 40.64 0 0 NA 445045 TCGA-AB-2996 AML30 4 97244413 97244413 C T SNP ENSG00000201744 ENST00000364874 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*48058 NULL 0.998 - - - no_errors tier3 152 0 0 197 166 45.73 0 0 NA 445045 TCGA-AB-2996 AML30 4 98252977 98252977 C T SNP - - - - - - - - - - - - - - - tier3 114 8 6.56 198 148 42.77 0 0 NA 445045 TCGA-AB-2996 AML30 4 102535494 102535494 T A SNP PPP3CA NM_000944.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-48518 NULL 0 - - - no_errors tier3 346 5 1.42 227 145 38.98 0 0 NA 445045 TCGA-AB-2996 AML30 4 104983807 104983807 G A SNP - - - - - - - - - - - - - - - tier3 141 4 2.76 129 112 46.47 0 0 NA 445045 TCGA-AB-2996 AML30 4 106410231 106410232 AG - DEL TET2 ENST00000265149 human ensembl 54_36p 1 known frame_shift_del c.466_467 p.R156fs 1.000:1.000 NULL NULL - no_start_codon tier1 NA NA NA NA NA NA NA 445045 TCGA-AB-2996 AML30 4 106416718 106416718 C T SNP TET2 ENST00000265149 human ensembl 54_36p 1 known missense c.2008 p.H670Y 1 NULL NULL - no_start_codon tier1 119 2 1.65 274 197 41.83 32 33 50.77 445045 TCGA-AB-2996 AML30 4 106446861 106446861 G A SNP ENSG00000211283 ENST00000388548 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*12317 NULL 0.001 - - - pseudogene tier3 152 3 1.94 306 257 45.57 0 0 NA 445045 TCGA-AB-2996 AML30 4 116231983 116231983 A G SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.1-14096 e1-14096 0.001 - - - no_errors tier3 116 3 2.52 153 111 42.05 0 0 NA 445045 TCGA-AB-2996 AML30 4 118011472 118011472 C T SNP ENSG00000201752 ENST00000364882 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*31483 NULL 0 - - - no_errors tier3 69 1 1.43 192 133 40.92 0 0 NA 445045 TCGA-AB-2996 AML30 4 128376191 128376191 T A SNP - - - - - - - - - - - - - - - tier3 109 8 6.84 154 172 52.76 0 0 NA 445045 TCGA-AB-2996 AML30 4 133406805 133406805 G A SNP - - - - - - - - - - - - - - - tier3 108 2 1.82 112 111 49.78 0 0 NA 445045 TCGA-AB-2996 AML30 4 134321422 134321422 T A SNP PCDH10 NM_032961.1 human genbank 54_36p 1 reviewed intronic c.3104-9324 e5-9324 0 - - - no_errors tier3 53 1 1.85 52 32 38.1 0 0 NA 445045 TCGA-AB-2996 AML30 4 138987316 138987316 T C SNP - - - - - - - - - - - - - - - tier3 96 8 7.69 144 111 43.53 0 0 NA 445045 TCGA-AB-2996 AML30 4 148237442 148237442 C T SNP - - - - - - - - - - - - - - - tier3 158 5 3.07 194 145 42.77 0 0 NA 445045 TCGA-AB-2996 AML30 4 162811625 162811626 - A INS FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.728-14530_728-14529 e6-14529 0.993:0.981 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 4 165109659 165109659 C T SNP ENSG00000177803 ENST00000317414 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*35805 NULL 0.002 - - - no_coding_region:pseudogene tier3 308 5 1.6 216 180 45.45 0 0 NA 445045 TCGA-AB-2996 AML30 4 174183610 174183610 A T SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.1638+4259 e11+4259 0.034 - - - no_errors tier3 311 12 3.72 278 285 50.62 0 0 NA 445045 TCGA-AB-2996 AML30 4 174332085 174332085 G C SNP GALNT7 NM_017423.2 human genbank 54_36p 1 reviewed intronic c.126+5398 e1+5398 0.009 - - - no_errors tier3 516 12 2.27 152 127 45.52 2 3 60 445045 TCGA-AB-2996 AML30 4 176669556 176669556 T A SNP ENSG00000221136 ENST00000408209 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*38303 NULL 0 - - - no_errors tier3 69 0 0 118 89 43 0 0 NA 445045 TCGA-AB-2996 AML30 4 178525683 178525683 G A SNP NEIL3 NM_018248.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*5064 NULL 0 - - - no_errors tier3 129 5 3.73 185 121 39.41 0 0 NA 445045 TCGA-AB-2996 AML30 4 179378906 179378906 A G SNP - - - - - - - - - - - - - - - tier3 88 2 2.22 91 91 50 0 0 NA 445045 TCGA-AB-2996 AML30 4 180890143 180890143 G A SNP - - - - - - - - - - - - - - - tier3 161 4 2.42 159 115 41.97 0 0 NA 445045 TCGA-AB-2996 AML30 4 183731427 183731427 C T SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.512-27644 e3-27644 0 - - - no_errors tier3 123 0 0 159 119 42.81 0 0 NA 445045 TCGA-AB-2996 AML30 4 187996586 187996586 C T SNP - - - - - - - - - - - - - - - tier3 317 14 4.23 241 206 46.09 0 0 NA 445045 TCGA-AB-2996 AML30 4 188893173 188893173 C T SNP ENSG00000214607 ENST00000398655 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*11130 NULL 0.005 - - - no_coding_region:pseudogene tier3 451 10 2.17 166 162 49.39 0 0 NA 445045 TCGA-AB-2996 AML30 4 189751169 189751169 G T SNP - - - - - - - - - - - - - - - tier3 233 2 0.85 202 142 41.16 0 0 NA 445045 TCGA-AB-2996 AML30 4 190144239 190144239 C A SNP - - - - - - - - - - - - - - - tier3 47 2 4.08 53 36 40.45 0 0 NA 445045 TCGA-AB-2996 AML30 5 2183825 2183825 G A SNP - - - - - - - - - - - - - - - tier3 176 2 1.12 140 111 44.05 0 0 NA 445045 TCGA-AB-2996 AML30 5 3012948 3012948 G A SNP - - - - - - - - - - - - - - - tier3 181 0 0 220 168 43.3 0 0 NA 445045 TCGA-AB-2996 AML30 5 3211700 3211700 G T SNP - - - - - - - - - - - - - - - tier3 511 9 1.73 280 217 43.66 0 0 NA 445045 TCGA-AB-2996 AML30 5 9278058 9278058 T G SNP SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.433-59 e6-59 0 - - - no_errors tier3 212 8 3.64 248 267 51.84 0 0 NA 445045 TCGA-AB-2996 AML30 5 15257173 15257173 G A SNP - - - - - - - - - - - - - - - tier3 290 3 1.02 327 215 39.67 0 0 NA 445045 TCGA-AB-2996 AML30 5 15403247 15403247 G A SNP - - - - - - - - - - - - - - - tier3 163 2 1.21 205 166 44.74 0 0 NA 445045 TCGA-AB-2996 AML30 5 15417511 15417511 G T SNP - - - - - - - - - - - - - - - tier3 293 5 1.68 219 132 37.61 0 0 NA 445045 TCGA-AB-2996 AML30 5 24121207 24121207 G T SNP - - - - - - - - - - - - - - - tier3 94 1 1.05 226 157 40.99 0 0 NA 445045 TCGA-AB-2996 AML30 5 25994801 25994801 A G SNP LOC100133558 XM_001716419.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37248 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 99 7 6.6 200 183 47.78 0 0 NA 445045 TCGA-AB-2996 AML30 5 29034901 29034901 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 5 39121124 39121124 C T SNP RICTOR NM_152756.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-10888 NULL 0.005 - - - no_errors tier3 69 1 1.43 101 77 43.26 0 0 NA 445045 TCGA-AB-2996 AML30 5 40544723 40544723 G A SNP - - - - - - - - - - - - - - - tier3 90 3 3.23 127 116 47.74 0 0 NA 445045 TCGA-AB-2996 AML30 5 44377538 44377538 G T SNP FGF10 NM_004465.1 human genbank 54_36p -1 reviewed intronic c.326-31149 e2-31149 0 - - - no_errors tier3 231 3 1.28 282 219 43.71 0 0 NA 445045 TCGA-AB-2996 AML30 5 44655696 44655696 G A SNP - - - - - - - - - - - - - - - tier3 107 4 3.6 137 125 47.71 0 0 NA 445045 TCGA-AB-2996 AML30 5 50406898 50406898 C T SNP ENSG00000207060 ENST00000384332 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19848 NULL 0 - - - no_errors tier3 100 1 0.99 168 117 41.05 0 0 NA 445045 TCGA-AB-2996 AML30 5 57661603 57661603 C T SNP - - - - - - - - - - - - - - - tier3 127 5 3.79 153 110 41.83 0 0 NA 445045 TCGA-AB-2996 AML30 5 66061725 66061725 G A SNP MAST4 NM_198828.1 human genbank 54_36p 1 validated intronic c.364-29568 e2-29568 0.014 - - - no_errors tier3 376 8 2.08 661 485 42.32 0 0 0 445045 TCGA-AB-2996 AML30 5 85043696 85043696 C T SNP - - - - - - - - - - - - - - - tier3 54 0 0 75 39 34.21 0 0 NA 445045 TCGA-AB-2996 AML30 5 101344497 101344497 T C SNP - - - - - - - - - - - - - - - tier3 217 3 1.36 144 115 44.4 0 0 NA 445045 TCGA-AB-2996 AML30 5 104551674 104551674 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 5 104762621 104762621 A T SNP - - - - - - - - - - - - - - - tier3 131 0 0 151 106 41.25 0 0 NA 445045 TCGA-AB-2996 AML30 5 105400545 105400545 G A SNP - - - - - - - - - - - - - - - tier3 50 1 1.96 124 93 42.86 0 0 NA 445045 TCGA-AB-2996 AML30 5 108935353 108935353 C G SNP KRT18P42 XR_016386.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-16586 NULL 0 - - - pseudogene tier3 143 2 1.38 172 138 44.37 0 0 NA 445045 TCGA-AB-2996 AML30 5 109460690 109460690 A G SNP - - - - - - - - - - - - - - - tier3 334 7 2.05 187 119 38.89 0 0 NA 445045 TCGA-AB-2996 AML30 5 110607256 110607256 G A SNP CAMK4 NM_001744.3 human genbank 54_36p 1 reviewed intronic c.161+19015 e1+19015 0.01 - - - no_errors tier3 168 2 1.18 157 125 44.33 0 0 0 445045 TCGA-AB-2996 AML30 5 113178888 113178888 G T SNP - - - - - - - - - - - - - - - tier3 240 5 2.04 251 209 45.43 0 0 NA 445045 TCGA-AB-2996 AML30 5 114024517 114024517 C T SNP - - - - - - - - - - - - - - - tier3 248 6 2.36 211 181 46.17 0 0 NA 445045 TCGA-AB-2996 AML30 5 114471396 114471396 A G SNP TRIM36 NM_018700.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*18703 NULL 0.002 - - - no_errors tier3 244 7 2.79 285 158 35.67 0 0 NA 445045 TCGA-AB-2996 AML30 5 116620055 116620055 G T SNP - - - - - - - - - - - - - - - tier3 181 2 1.09 213 193 47.42 0 0 NA 445045 TCGA-AB-2996 AML30 5 119503389 119503389 C T SNP - - - - - - - - - - - - - - - tier3 209 7 3.23 160 172 51.81 0 0 NA 445045 TCGA-AB-2996 AML30 5 132817523 132817523 C T SNP FSTL4 NM_015082.1 human genbank 54_36p -1 validated intronic c.161-52946 e3-52946 0.271 - - - no_errors tier3 302 5 1.63 238 179 42.93 0 0 NA 445045 TCGA-AB-2996 AML30 5 132889134 132889134 G A SNP FSTL4 NM_015082.1 human genbank 54_36p -1 validated intronic c.160+41642 e2+41642 0 - - - no_errors tier3 164 1 0.61 267 166 38.34 0 0 NA 445045 TCGA-AB-2996 AML30 5 136380667 136380667 C T SNP SPOCK1 NM_004598.3 human genbank 54_36p -1 reviewed intronic c.590-24479 e6-24479 0 - - - no_errors tier3 361 4 1.1 493 322 39.51 0 0 0 445045 TCGA-AB-2996 AML30 5 140699526 140699526 C T SNP PCDHGA2 NM_018915.2 human genbank 54_36p 1 reviewed silent c.804 p.D268 0.635 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 247 2 0.8 171 137 44.48 NA 445045 TCGA-AB-2996 AML30 5 146240618 146240618 G C SNP PPP2R2B NM_181676.1 human genbank 54_36p -1 reviewed intronic c.79+174803 e1+174803 0.002 - - - no_errors tier3 399 3 0.74 187 139 42.51 0 0 NA 445045 TCGA-AB-2996 AML30 5 150495369 150495369 A G SNP ANXA6 NM_001155.3 human genbank 54_36p -1 reviewed intronic c.489+641 e6+641 0.004 - - - no_errors tier3 788 9 1.13 201 163 44.78 0 0 0 445045 TCGA-AB-2996 AML30 5 151122431 151122431 G A SNP G3BP1 NM_005754.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23944 NULL 0.003 - - - no_errors tier3 159 0 0 87 50 36.5 0 0 NA 445045 TCGA-AB-2996 AML30 5 152128788 152128788 G A SNP - - - - - - - - - - - - - - - tier3 110 2 1.79 156 133 46.02 0 0 NA 445045 TCGA-AB-2996 AML30 5 155830554 155830555 - T INS SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.193-37635_193-37634 e3-37634 0.005:0.029 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 5 158209905 158209905 G T SNP EBF1 NM_024007.3 human genbank 54_36p -1 validated intronic c.555-10209 e7-10209 0 - - - no_errors tier3 86 3 3.37 49 35 41.67 0 0 0 445045 TCGA-AB-2996 AML30 5 163747759 163747759 C T SNP - - - - - - - - - - - - - - - tier3 221 2 0.9 246 188 43.32 0 0 NA 445045 TCGA-AB-2996 AML30 5 164605423 164605423 T C SNP - - - - - - - - - - - - - - - tier3 418 6 1.42 187 211 53.02 0 0 NA 445045 TCGA-AB-2996 AML30 5 165253346 165253346 T A SNP - - - - - - - - - - - - - - - tier3 189 3 1.56 324 233 41.76 0 0 NA 445045 TCGA-AB-2996 AML30 5 168374835 168374835 G A SNP SLIT3 NM_003062.2 human genbank 54_36p -1 validated intronic c.414-131916 e5-131916 0.003 - - - no_errors tier3 567 6 1.05 385 237 38.04 0 0 NA 445045 TCGA-AB-2996 AML30 5 172601476 172601476 T G SNP NKX2-5 NM_004387.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-6784 NULL 0.056 - - - no_errors tier3 153 1 0.65 111 60 34.88 0 0 NA 445045 TCGA-AB-2996 AML30 5 173848899 173848899 C T SNP ENSG00000213376 ENST00000393755 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24018 NULL 0 - - - no_coding_region:pseudogene tier3 357 5 1.38 256 206 44.59 0 0 NA 445045 TCGA-AB-2996 AML30 5 178685734 178685734 G A SNP ADAMTS2 NM_014244.2 human genbank 54_36p -1 reviewed intronic c.534+17640 e2+17640 0.3 - - - no_errors tier3 380 7 1.81 74 45 37.82 0 0 0 445045 TCGA-AB-2996 AML30 6 7685548 7685548 C T SNP BMP6 NM_001718.4 human genbank 54_36p 1 reviewed intronic c.664+12697 e1+12697 0.068 - - - no_errors tier3 361 5 1.37 280 223 44.33 0 0 NA 445045 TCGA-AB-2996 AML30 6 11437073 11437073 C T SNP LOC100129322 XM_001720477.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*22129 NULL 0.01 - - - no_errors tier3 378 3 0.79 343 281 45.03 0 0 0 445045 TCGA-AB-2996 AML30 6 16309837 16309837 G A SNP GMPR NM_006877.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37067 NULL 0.005 - - - no_errors tier3 159 2 1.24 126 117 48.15 0 0 NA 445045 TCGA-AB-2996 AML30 6 20614407 20614407 C T SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40154 NULL 0 - - - no_errors tier3 519 8 1.52 283 257 47.5 0 0 NA 445045 TCGA-AB-2996 AML30 6 20760839 20760839 C - DEL CDKAL1 NM_017774.2 human genbank 54_36p 1 validated intronic c.371+3252 e3+3252 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 6 33984391 33984391 T C SNP LOC100132252 XM_001724521.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*25189 NULL 0.003 - - - no_errors tier3 527 5 0.94 208 163 43.94 0 0 NA 445045 TCGA-AB-2996 AML30 6 36478059 36478059 T C SNP KCTD20 NM_173562.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-67794 NULL 0.027 - - - no_errors tier3 292 0 0 101 77 43.26 0 0 NA 445045 TCGA-AB-2996 AML30 6 41088655 41088655 G - DEL APOBEC2 NM_006789.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40410 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 6 42940470 42940470 A G SNP KIAA0240 NM_015349.1 human genbank 54_36p 1 validated missense c.2548 p.S850G 0.002 NULL NULL - no_errors tier1 234 6 2.5 184 181 49.59 20 16 44.44 445045 TCGA-AB-2996 AML30 6 49525146 49525146 G A SNP MUT NM_000255.2 human genbank 54_36p -1 reviewed intronic c.1333-547 e6-547 0 - - - no_errors tier3 88 3 3.3 96 108 52.94 0 0 0 445045 TCGA-AB-2996 AML30 6 50604112 50604112 T C SNP - - - - - - - - - - - - - - - tier3 314 0 0 256 215 45.65 0 0 NA 445045 TCGA-AB-2996 AML30 6 55817158 55817158 G A SNP BMP5 NM_021073.2 human genbank 54_36p -1 reviewed intronic c.491-24554 e2-24554 0.011 - - - no_errors tier3 121 0 0 125 118 48.56 0 0 0 445045 TCGA-AB-2996 AML30 6 64281917 64281917 C T SNP LOC441154 XR_016183.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*34581 NULL 0.014 - - - pseudogene tier3 49 1 2 41 17 29.31 0 0 NA 445045 TCGA-AB-2996 AML30 6 78572810 78572810 C A SNP ENSG00000214481 ENST00000398401 human ensembl 54_36p 1 known intronic c.775-22557 e4-22557 0 - - - no_stop_codon tier3 115 2 1.71 173 86 33.2 0 0 NA 445045 TCGA-AB-2996 AML30 6 87549639 87549639 C T SNP ENSG00000219190 ENST00000402173 human ensembl 54_36p -1 known 5_prime_flanking_region c.-14270 NULL 0 - - - no_coding_region:pseudogene tier3 129 3 2.26 244 178 42.18 0 0 NA 445045 TCGA-AB-2996 AML30 6 88585458 88585458 G A SNP ENSG00000223226 ENST00000411294 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-26629 NULL 0.001 - - - no_errors tier3 328 3 0.91 324 313 49.14 0 0 NA 445045 TCGA-AB-2996 AML30 6 92962286 92962286 T C SNP - - - - - - - - - - - - - - - tier3 120 3 2.44 202 100 33.11 0 0 NA 445045 TCGA-AB-2996 AML30 6 93434170 93434170 A T SNP - - - - - - - - - - - - - - - tier3 146 0 0 115 104 47.49 0 0 NA 445045 TCGA-AB-2996 AML30 6 95159491 95159491 T C SNP ENSG00000220370 ENST00000404458 human ensembl 54_36p 1 known 3_prime_flanking_region c.*48090 NULL 0.026 - - - no_coding_region:pseudogene tier3 213 7 3.18 199 126 38.53 0 0 NA 445045 TCGA-AB-2996 AML30 6 99587349 99587349 A T SNP - - - - - - - - - - - - - - - tier3 406 8 1.93 216 186 46.27 0 0 NA 445045 TCGA-AB-2996 AML30 6 102422230 102422230 A T SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.1524+8169 e10+8169 0.013 - - - no_errors tier3 46 1 2.13 81 68 45.64 0 0 NA 445045 TCGA-AB-2996 AML30 6 105942797 105942797 G T SNP PREP NM_002726.3 human genbank 54_36p -1 reviewed intronic c.120+9624 e2+9624 0.003 - - - no_errors tier3 137 1 0.72 133 119 47.22 1 0 0 445045 TCGA-AB-2996 AML30 6 107673282 107673282 G A SNP PDSS2 NM_020381.3 human genbank 54_36p -1 validated intronic c.702+163 e4+163 0.997 - - - no_errors tier3 95 2 2.06 101 55 35.26 1 1 50 445045 TCGA-AB-2996 AML30 6 112431387 112431387 T C SNP - - - - - - - - - - - - - - - tier3 1057 7 0.66 507 337 39.93 0 0 NA 445045 TCGA-AB-2996 AML30 6 125801336 125801336 A C SNP - - - - - - - - - - - - - - - tier3 420 7 1.64 446 323 42 0 0 NA 445045 TCGA-AB-2996 AML30 6 128189729 128189729 A G SNP C6orf190 NM_001010923.1 human genbank 54_36p -1 validated intronic c.709+2585 e3+2585 0 - - - no_errors tier3 183 1 0.54 163 133 44.93 1 0 0 445045 TCGA-AB-2996 AML30 6 128773291 128773291 T C SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.101-12765 e2-12765 0 - - - no_errors tier3 309 2 0.64 170 149 46.71 0 0 NA 445045 TCGA-AB-2996 AML30 6 133701877 133701877 G A SNP EYA4 NM_004100.4 human genbank 54_36p 1 reviewed intronic c.34-43346 e2-43346 0.001 - - - no_errors tier3 71 1 1.39 101 92 47.67 0 0 NA 445045 TCGA-AB-2996 AML30 6 139418457 139418457 C T SNP C6orf115 NM_021243.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*12724 NULL 0 - - - no_errors tier3 162 7 4.09 240 177 42.34 0 0 NA 445045 TCGA-AB-2996 AML30 6 147084062 147084062 C T SNP C6orf103 ENST00000326929 human ensembl 54_36p 1 known intronic c.1993-170 e17-170 0.01 - - - no_errors tier3 177 3 1.66 270 253 48.37 0 0 NA 445045 TCGA-AB-2996 AML30 6 147794901 147794901 G A SNP STXBP5 NM_139244.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*47317 NULL 0.003 - - - no_errors tier3 227 8 3.4 216 162 42.86 0 0 NA 445045 TCGA-AB-2996 AML30 6 151021056 151021056 G A SNP PLEKHG1 NM_001029884.1 human genbank 54_36p 1 provisional intronic c.1+7441 e0+7441 0.006 - - - no_errors tier3 222 5 2.2 305 225 42.45 2 0 0 445045 TCGA-AB-2996 AML30 6 162549863 162549863 G A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.413-7589 e4-7589 0.001 - - - no_errors tier3 149 4 2.61 132 108 45 0 0 0 445045 TCGA-AB-2996 AML30 7 3619382 3619382 C T SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.299-5856 e2-5856 0 - - - no_errors tier3 271 3 1.09 225 203 47.43 0 0 NA 445045 TCGA-AB-2996 AML30 7 5817899 5817899 C T SNP RNF216 NM_207111.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-50673 NULL 0.005 - - - no_errors tier3 183 4 2.14 74 53 41.73 0 0 NA 445045 TCGA-AB-2996 AML30 7 6099233 6099233 T C SNP EIF2AK1 NM_014413.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33993 NULL 0.09 - - - no_errors tier3 276 5 1.78 126 95 42.99 0 0 NA 445045 TCGA-AB-2996 AML30 7 10779319 10779319 T G SNP LOC100134489 XM_001723806.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*28928 NULL 0.994 - - - no_start_codon:pseudogene:no_stop_codon tier3 352 10 2.76 145 84 36.68 0 0 NA 445045 TCGA-AB-2996 AML30 7 24755244 24755244 C T SNP DFNA5 NM_004403.1 human genbank 54_36p -1 reviewed intronic c.211+464 e1+464 0.001 - - - no_errors tier3 222 4 1.77 112 100 47.17 0 0 NA 445045 TCGA-AB-2996 AML30 7 26716219 26716219 C T SNP SKAP2 NM_003930.3 human genbank 54_36p -1 reviewed intronic c.796+15353 e9+15353 0.011 - - - no_errors tier3 198 3 1.49 120 86 41.75 2 8 80 445045 TCGA-AB-2996 AML30 7 26931093 26931093 G A SNP ENSG00000213787 ENST00000396363 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*2037 NULL 0 - - - no_coding_region:pseudogene tier3 146 1 0.68 225 174 43.61 0 0 NA 445045 TCGA-AB-2996 AML30 7 34020846 34020846 A G SNP BMPER NM_133468.3 human genbank 54_36p 1 validated intronic c.577-31597 e7-31597 0.116 - - - no_errors tier3 204 0 0 158 91 36.55 0 0 0 445045 TCGA-AB-2996 AML30 7 49298722 49298722 G A SNP LOC100134791 XM_001726801.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*16303 NULL 0.009 - - - no_start_codon:pseudogene:no_stop_codon tier3 386 3 0.77 332 259 43.82 0 0 NA 445045 TCGA-AB-2996 AML30 7 51524034 51524034 A G SNP - - - - - - - - - - - - - - - tier3 137 4 2.84 182 123 40.33 0 0 NA 445045 TCGA-AB-2996 AML30 7 51658194 51658194 A G SNP LOC100134540 XR_039782.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*3784 NULL 0.004 - - - pseudogene tier3 446 2 0.45 201 129 39.09 0 0 NA 445045 TCGA-AB-2996 AML30 7 53837150 53837150 A G SNP FLJ45974 XR_040790.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 77 1 1.28 114 96 45.71 0 0 NA 445045 TCGA-AB-2996 AML30 7 54940199 54940199 A T SNP ENSG00000218586 ENST00000407916 human ensembl 54_36p 1 known 5_prime_flanking_region c.-28441 NULL 0.006 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 105 1 0.94 67 79 54.11 0 0 NA 445045 TCGA-AB-2996 AML30 7 56577105 56577105 G T SNP LOC100128867 XR_037006.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*49582 NULL 0 - - - pseudogene tier3 116 2 1.69 177 114 39.18 0 0 0 445045 TCGA-AB-2996 AML30 7 66814520 66814520 T C SNP - - - - - - - - - - - - - - - tier3 637 8 1.24 281 221 43.94 0 0 NA 445045 TCGA-AB-2996 AML30 7 67235314 67235314 C T SNP ENSG00000211250 ENST00000388515 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-34566 NULL 0 - - - pseudogene tier3 318 2 0.62 209 206 49.64 0 0 NA 445045 TCGA-AB-2996 AML30 7 67370564 67370564 G A SNP - - - - - - - - - - - - - - - tier3 337 1 0.3 338 236 41.04 0 0 NA 445045 TCGA-AB-2996 AML30 7 79765689 79765689 G T SNP ENSG00000209130 ENST00000386395 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19816 NULL 0.374 - - - pseudogene tier3 193 2 1.03 220 160 42.11 0 0 NA 445045 TCGA-AB-2996 AML30 7 83840538 83840538 A C SNP - - - - - - - - - - - - - - - tier3 83 3 3.49 107 110 50.46 0 0 NA 445045 TCGA-AB-2996 AML30 7 94214777 94214777 C T SNP ENSG00000208971 ENST00000386236 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-7055 NULL 0 - - - pseudogene tier3 250 9 3.47 173 147 45.94 0 0 NA 445045 TCGA-AB-2996 AML30 7 104093601 104093601 C T SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed intronic c.446-70757 e2-70757 0 - - - no_errors tier3 161 6 3.59 199 187 48.45 0 0 NA 445045 TCGA-AB-2996 AML30 7 113800045 113800045 C T SNP FOXP2 NM_148898.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-53758 NULL 0.001 - - - no_errors tier3 147 3 2 144 95 39.75 0 0 NA 445045 TCGA-AB-2996 AML30 7 115211859 115211859 G T SNP ENSG00000199224 ENST00000362354 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*48703 NULL 0.013 - - - no_errors tier3 191 15 7.28 126 79 38.54 0 0 NA 445045 TCGA-AB-2996 AML30 7 122035776 122035776 G C SNP CADPS2 NM_017954.2 human genbank 54_36p -1 validated intronic c.1223+6695 e6+6695 0.003 - - - no_errors tier3 341 8 2.29 311 220 41.35 0 0 NA 445045 TCGA-AB-2996 AML30 7 130964010 130964010 C T SNP LOC647030 XR_017470.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*33164 NULL 0 - - - no_errors tier3 1156 11 0.94 437 335 43.34 0 0 NA 445045 TCGA-AB-2996 AML30 7 135747710 135747710 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 7 135920799 135920799 G A SNP - - - - - - - - - - - - - - - tier3 291 0 0 190 153 44.48 0 0 NA 445045 TCGA-AB-2996 AML30 7 136384880 136384880 C T SNP LOC100128744 XM_001718911.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24121 NULL 0.058 - - - no_errors tier3 194 7 3.48 224 168 42.86 0 0 NA 445045 TCGA-AB-2996 AML30 7 136904164 136904164 C T SNP DGKI NM_004717.2 human genbank 54_36p -1 reviewed intronic c.1947+2297 e19+2297 0.001 - - - no_errors tier3 91 0 0 30 13 30.23 0 0 NA 445045 TCGA-AB-2996 AML30 7 149136237 149136237 C T SNP SSPO NM_198455.2 human genbank 54_36p 1 provisional intronic c.8911-42 e58-42 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 560 12 2.09 77 60 43.8 0 0 0 445045 TCGA-AB-2996 AML30 7 152077888 152077888 T C SNP ACTR3B NM_020445.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-10013 NULL 0.926 - - - no_errors tier3 140 3 2.1 54 52 49.06 0 0 NA 445045 TCGA-AB-2996 AML30 7 153012537 153012537 G T SNP LOC100130228 XM_001721136.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40049 NULL 0.003 - - - no_errors tier3 296 7 2.31 218 151 40.92 0 0 NA 445045 TCGA-AB-2996 AML30 7 154472490 154472490 C G SNP PAXIP1 NM_007349.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-46918 NULL 0.401 - - - no_errors tier3 366 1 0.27 146 125 46.13 0 0 NA 445045 TCGA-AB-2996 AML30 7 157608292 157608292 G A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1556+10838 e9+10838 0.001 - - - no_errors tier3 129 1 0.77 111 107 48.86 0 0 NA 445045 TCGA-AB-2996 AML30 7 158058368 158058368 T G SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.112+14643 e1+14643 0.613 - - - no_errors tier3 80 2 2.44 87 50 36.5 0 0 NA 445045 TCGA-AB-2996 AML30 7 158088345 158088345 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15223 NULL 0.002 - - - no_errors tier3 310 3 0.96 62 45 42.06 0 0 NA 445045 TCGA-AB-2996 AML30 8 4587733 4587733 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.86-105245 e2-105245 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 140 2 1.4 143 87 37.83 0 0 NA 445045 TCGA-AB-2996 AML30 8 21164209 21164209 C T SNP - - - - - - - - - - - - - - - tier3 121 8 6.2 265 236 47.11 0 0 NA 445045 TCGA-AB-2996 AML30 8 23876400 23876400 G A SNP - - - - - - - - - - - - - - - tier3 239 1 0.42 165 123 42.71 0 0 NA 445045 TCGA-AB-2996 AML30 8 24396746 24396746 C T SNP ADAM7 NM_003817.2 human genbank 54_36p 1 validated intronic c.875+1032 e9+1032 0.001 - - - no_errors tier3 133 2 1.48 176 128 42.11 0 0 NA 445045 TCGA-AB-2996 AML30 8 32445616 32445616 G A SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.746-127272 e2-127272 0 - - - overly_large_intron tier3 258 6 2.27 115 110 48.89 0 0 NA 445045 TCGA-AB-2996 AML30 8 38417744 38417744 C T SNP FGFR1 NM_023110.3 human genbank 54_36p -1 reviewed intronic c.92-11121 e2-11121 0.937 - - - no_errors tier3 483 5 1.02 160 154 49.04 0 0 NA 445045 TCGA-AB-2996 AML30 8 39080390 39080390 C G SNP ADAM9 NM_003816.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*14 NULL 0 - - - no_errors tier3 93 0 0 121 93 43.46 20 12 37.5 445045 TCGA-AB-2996 AML30 8 43272205 43272205 G A SNP POTEA NM_001005365.1 human genbank 54_36p 1 provisional intronic c.588+446 e3+446 0 - - - no_errors tier3 92 2 2.13 83 58 41.13 0 0 NA 445045 TCGA-AB-2996 AML30 8 50713847 50713847 T C SNP - - - - - - - - - - - - - - - tier3 168 3 1.75 202 185 47.8 0 0 NA 445045 TCGA-AB-2996 AML30 8 51827083 51827083 C T SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1285-31 e16-31 0.103 - - - no_errors tier3 101 1 0.98 269 203 43.01 0 0 NA 445045 TCGA-AB-2996 AML30 8 52786758 52786758 T A SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.165-56885 e2-56885 0 - - - no_errors tier3 137 1 0.72 106 73 40.78 0 0 NA 445045 TCGA-AB-2996 AML30 8 53562225 53562225 A - DEL FAM150A NM_207413.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*51331 NULL 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 8 60266832 60266832 C T SNP - - - - - - - - - - - - - - - tier3 267 1 0.37 312 223 41.68 0 0 NA 445045 TCGA-AB-2996 AML30 8 62096184 62096184 G A SNP - - - - - - - - - - - - - - - tier3 236 2 0.84 149 157 51.31 0 0 NA 445045 TCGA-AB-2996 AML30 8 63904724 63904724 A C SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.471+82482 e4+82482 0.003 - - - no_errors tier3 80 0 0 298 215 41.91 0 0 NA 445045 TCGA-AB-2996 AML30 8 64819121 64819121 G C SNP - - - - - - - - - - - - - - - tier3 271 5 1.81 284 232 44.96 0 0 NA 445045 TCGA-AB-2996 AML30 8 69904311 69904311 T - DEL C8orf34 NM_052958.1 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*11276 NULL 0.478 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 8 70388699 70388699 T C SNP - - - - - - - - - - - - - - - tier3 315 6 1.87 122 104 46.02 0 0 NA 445045 TCGA-AB-2996 AML30 8 72830845 72830845 T G SNP - - - - - - - - - - - - - - - tier3 1751 9 0.51 427 322 42.93 0 0 NA 445045 TCGA-AB-2996 AML30 8 73158767 73158767 A T SNP TRPA1 NM_007332.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-8569 NULL 0.023 - - - no_errors tier3 71 2 2.74 142 65 31.4 0 0 NA 445045 TCGA-AB-2996 AML30 8 74316291 74316291 G T SNP LOC100130301 XM_001721302.1 human genbank 54_36p -1 model silent c.441 p.T147 0 NULL NULL - no_errors tier1 93 6 6.06 125 102 44.93 NA 445045 TCGA-AB-2996 AML30 8 75651889 75651889 G T SNP FLJ39080 XM_499117.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-35769 NULL 0.014 - - - no_errors tier3 230 5 2.13 145 119 45.08 0 0 NA 445045 TCGA-AB-2996 AML30 8 84378353 84378353 C T SNP - - - - - - - - - - - - - - - tier3 150 0 0 94 67 41.61 0 0 NA 445045 TCGA-AB-2996 AML30 8 88169441 88169441 C T SNP CNBD1 NM_173538.2 human genbank 54_36p 1 provisional intronic c.432-117896 e5-117896 0 - - - no_errors tier3 70 2 2.78 120 120 50 0 0 NA 445045 TCGA-AB-2996 AML30 8 114045995 114045995 T C SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1343-9829 e8-9829 0.016 - - - no_errors tier3 102 0 0 109 88 44.67 0 0 NA 445045 TCGA-AB-2996 AML30 8 132358383 132358383 G A SNP - - - - - - - - - - - - - - - tier3 327 3 0.91 243 178 42.28 0 0 NA 445045 TCGA-AB-2996 AML30 8 133415957 133415957 C T SNP KCNQ3 NM_004519.2 human genbank 54_36p -1 reviewed intronic c.386+145619 e1+145619 0.001 - - - no_errors tier3 707 4 0.56 262 174 39.91 0 0 NA 445045 TCGA-AB-2996 AML30 8 140611376 140611376 C A SNP - - - - - - - - - - - - - - - tier3 265 2 0.75 152 106 41.09 0 0 NA 445045 TCGA-AB-2996 AML30 9 254128 254128 A G SNP DOCK8 NM_203447.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22381 NULL 0.007 - - - no_errors tier3 214 9 4.04 222 250 52.97 5 10 66.67 445045 TCGA-AB-2996 AML30 9 3088219 3088219 A G SNP - - - - - - - - - - - - - - - tier3 126 4 3.08 106 93 46.73 0 0 NA 445045 TCGA-AB-2996 AML30 9 9408008 9408008 T C SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-20526 e1-20526 0 - - - no_errors tier3 238 3 1.24 134 85 38.46 0 0 NA 445045 TCGA-AB-2996 AML30 9 11192581 11192581 G A SNP - - - - - - - - - - - - - - - tier3 191 0 0 140 97 40.93 0 0 NA 445045 TCGA-AB-2996 AML30 9 13697655 13697655 G T SNP - - - - - - - - - - - - - - - tier3 92 3 3.12 163 108 39.85 0 0 NA 445045 TCGA-AB-2996 AML30 9 16679249 16679249 G A SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated intronic c.330+38546 e3+38546 0 - - - no_errors tier3 318 1 0.31 190 144 43.11 0 0 NA 445045 TCGA-AB-2996 AML30 9 17006967 17006967 C T SNP ENSG00000223340 ENST00000411408 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36932 NULL 0 - - - no_errors tier3 158 2 1.25 178 140 44.03 0 0 NA 445045 TCGA-AB-2996 AML30 9 17620601 17620601 C A SNP SH3GL2 NM_003026.2 human genbank 54_36p 1 validated intronic c.45+51316 e1+51316 0.014 - - - no_errors tier3 199 0 0 264 187 41.46 0 0 NA 445045 TCGA-AB-2996 AML30 9 18629381 18629381 G T SNP ADAMTSL1 NM_001040272.4 human genbank 54_36p 1 validated missense c.806 p.G269V 1 NULL "HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_PLAC,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 167 8 4.57 278 256 47.85 NA 445045 TCGA-AB-2996 AML30 9 24202258 24202258 G A SNP - - - - - - - - - - - - - - - tier3 143 3 2.05 98 69 41.32 0 0 NA 445045 TCGA-AB-2996 AML30 9 24234197 24234197 A G SNP - - - - - - - - - - - - - - - tier3 270 5 1.82 145 97 40.08 0 0 NA 445045 TCGA-AB-2996 AML30 9 25485070 25485070 T A SNP - - - - - - - - - - - - - - - tier3 132 1 0.75 173 108 38.43 0 0 NA 445045 TCGA-AB-2996 AML30 9 25828077 25828077 G T SNP - - - - - - - - - - - - - - - tier3 187 1 0.53 240 164 40.59 0 0 NA 445045 TCGA-AB-2996 AML30 9 31596808 31596808 C A SNP ENSG00000217739 ENST00000402171 human ensembl 54_36p -1 known 3_prime_flanking_region c.*37770 NULL 0.01 - - - no_coding_region:pseudogene tier3 140 9 6.04 197 145 42.27 0 0 NA 445045 TCGA-AB-2996 AML30 9 44808155 44808155 G A SNP ENSG00000204814 ENST00000377548 human ensembl 54_36p 1 known intronic c.1+400 e0+400 0.018 - - - no_errors tier3 247 1 0.4 44 44 50 0 0 NA 445045 TCGA-AB-2996 AML30 9 73291061 73291061 G T SNP TRPM3 ENST00000357533 human ensembl 54_36p -1 known 5_prime_flanking_region c.-39490 NULL 0.005 - - - no_errors tier3 224 4 1.75 185 147 44.14 0 0 NA 445045 TCGA-AB-2996 AML30 9 76359588 76359588 A G SNP RORB NM_006914.3 human genbank 54_36p 1 reviewed intronic c.7+56869 e1+56869 1 - - - no_errors tier2 267 4 1.48 367 317 46.35 0 0 NA 445045 TCGA-AB-2996 AML30 9 83401816 83401816 G A SNP TLE1 NM_005077.3 human genbank 54_36p -1 provisional intronic c.1332-3807 e15-3807 0 - - - no_errors tier3 411 0 0 242 140 36.65 0 0 0 445045 TCGA-AB-2996 AML30 9 86644594 86644594 G A SNP NTRK2 NM_006180.1 human genbank 54_36p 1 reviewed intronic c.1397-21181 e12-21181 0.702 - - - no_errors tier3 588 8 1.34 676 548 44.77 0 0 NA 445045 TCGA-AB-2996 AML30 9 87020307 87020307 G A SNP - - - - - - - - - - - - - - - tier3 484 8 1.63 420 343 44.95 0 0 NA 445045 TCGA-AB-2996 AML30 9 92205763 92205763 G A SNP - - - - - - - - - - - - - - - tier3 194 0 0 308 217 41.33 0 0 NA 445045 TCGA-AB-2996 AML30 9 101144640 101144640 G A SNP KRT8P11 ENST00000410082 human ensembl 54_36p 1 known 3_prime_flanking_region c.*35926 NULL 0.038 - - - no_coding_region:pseudogene tier3 348 0 0 266 200 42.92 0 0 NA 445045 TCGA-AB-2996 AML30 9 105633874 105633874 G A SNP - - - - - - - - - - - - - - - tier3 253 0 0 144 124 46.27 0 0 NA 445045 TCGA-AB-2996 AML30 9 108978337 108978337 C T SNP ENSG00000214180 ENST00000397723 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5087 NULL 0.135 - - - no_coding_region:pseudogene tier3 222 5 2.19 97 106 52.22 0 0 NA 445045 TCGA-AB-2996 AML30 9 111247293 111247293 T C SNP PTPN3 NM_002829.1 human genbank 54_36p -1 reviewed intronic c.466+48 e6+48 0 - - - no_errors tier3 211 3 1.4 224 211 48.51 0 0 0 445045 TCGA-AB-2996 AML30 9 113234863 113234863 T C SNP KIAA0368 NM_001080398.1 human genbank 54_36p -1 provisional intronic c.1382+471 e9+471 0.149 - - - no_errors tier3 115 4 3.36 115 95 45.24 0 0 0 445045 TCGA-AB-2996 AML30 9 118934684 118934684 A G SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.1168+8742 e4+8742 1 - - - no_errors tier3 273 11 3.87 206 144 41.14 0 0 NA 445045 TCGA-AB-2996 AML30 9 120854691 120854691 G A SNP - - - - - - - - - - - - - - - tier3 209 4 1.88 153 178 53.61 0 0 NA 445045 TCGA-AB-2996 AML30 9 133993062 133993062 G A SNP MED27 NM_004269.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-48010 NULL 0.001 - - - no_errors tier3 953 13 1.35 224 136 37.78 0 0 NA 445045 TCGA-AB-2996 AML30 9 136443879 136443879 C T SNP RXRA NM_002957.4 human genbank 54_36p 1 reviewed intronic c.610+3093 e4+3093 0.009 - - - no_errors tier3 464 0 0 83 95 53.37 1 0 0 445045 TCGA-AB-2996 AML30 9 138899271 138899271 C T SNP TRAF2 NM_021138.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13743 NULL 0 - - - no_errors tier3 162 0 0 38 39 50.65 0 0 NA 445045 TCGA-AB-2996 AML30 10 2946400 2946400 G - DEL ENSG00000218235 ENST00000404097 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21813 NULL 0.031 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 10 3838374 3838374 C T SNP KLF6 NM_001300.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-21168 NULL 0 - - - no_errors tier3 257 4 1.53 186 164 46.72 0 0 NA 445045 TCGA-AB-2996 AML30 10 10119079 10119079 T C SNP - - - - - - - - - - - - - - - tier3 187 8 4.1 233 193 45.31 0 0 NA 445045 TCGA-AB-2996 AML30 10 14454293 14454293 C T SNP FRMD4A NM_018027.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-42186 NULL 0.002 - - - no_errors tier3 657 12 1.79 293 239 44.84 0 0 NA 445045 TCGA-AB-2996 AML30 10 15330670 15330670 G A SNP FAM171A1 NM_001010924.1 human genbank 54_36p -1 validated missense c.728 p.A243V 0.765 HMMPfam_UPF0560 HMMPfam_UPF0560 - no_errors tier1 246 0 267 212 44.26 3 7 70 445045 TCGA-AB-2996 AML30 10 15698530 15698530 G A SNP ITGA8 NM_003638.1 human genbank 54_36p -1 provisional silent c.1434 p.V478 0.954 "HMMSmart_Int_alpha,superfamily_SSF69318" "HMMPfam_Integrin_alpha,HMMPfam_FG-GAP,HMMSmart_Int_alpha,HMMPfam_Integrin_alpha2,PatternScan_INTEGRIN_ALPHA,superfamily_SSF69179,superfamily_SSF69318" - no_errors tier1 270 3 1.1 258 219 45.82 6 0 445045 TCGA-AB-2996 AML30 10 24601554 24601554 C T SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated intronic c.354+52710 e2+52710 0.824 - - - no_errors tier3 256 5 1.92 315 235 42.73 1 0 0 445045 TCGA-AB-2996 AML30 10 28063581 28063581 G C SNP MKX NM_173576.2 human genbank 54_36p -1 validated silent c.648 p.P216 0.635 NULL "HMMPfam_Homeobox,HMMSmart_HOX,superfamily_Homeodomain_like,PatternScan_HOMEOBOX_1" - no_errors tier1 257 5 1.91 131 137 50.93 NA 445045 TCGA-AB-2996 AML30 10 34287166 34287166 G A SNP - - - - - - - - - - - - - - - tier3 129 2 1.53 214 157 42.32 0 0 NA 445045 TCGA-AB-2996 AML30 10 36516952 36516952 T C SNP - - - - - - - - - - - - - - - tier3 146 2 1.35 167 139 45.42 0 0 NA 445045 TCGA-AB-2996 AML30 10 43509319 43509319 T C SNP ZNF32 NM_001005368.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-47732 NULL 0 - - - no_errors tier3 359 2 0.55 175 195 52.7 0 0 NA 445045 TCGA-AB-2996 AML30 10 56218031 56218031 G T SNP PCDH15 NM_033056.1 human genbank 54_36p -1 reviewed intronic c.1+12660 e0+12660 0.001 - - - no_errors tier3 194 1 0.51 194 111 36.39 0 0 NA 445045 TCGA-AB-2996 AML30 10 58291641 58291641 T A SNP - - - - - - - - - - - - - - - tier3 108 0 0 149 91 37.92 0 0 NA 445045 TCGA-AB-2996 AML30 10 63026199 63026199 G A SNP - - - - - - - - - - - - - - - tier3 266 7 2.55 239 182 43.23 0 0 NA 445045 TCGA-AB-2996 AML30 10 69258138 69258138 A G SNP DNAJC12 NM_021800.2 human genbank 54_36p -1 reviewed intronic c.79-4982 e2-4982 0.179 - - - no_errors tier3 247 11 4.26 269 206 43.37 0 0 0 445045 TCGA-AB-2996 AML30 10 72621148 72621148 C T SNP UNC5B NM_170744.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21601 NULL 0 - - - no_errors tier3 249 3 1.19 221 142 39.01 0 0 NA 445045 TCGA-AB-2996 AML30 10 73444221 73444221 C T SNP CHST3 NM_004273.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*5986 NULL 0 - - - no_errors tier3 198 10 4.81 45 65 59.09 0 0 NA 445045 TCGA-AB-2996 AML30 10 85910103 85910103 G T SNP PCDH21 NM_033100.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34394 NULL 0.007 - - - no_errors tier3 100 7 6.54 133 100 42.92 0 0 NA 445045 TCGA-AB-2996 AML30 10 86310725 86310725 G C SNP LOC100131699 XM_001723921.1 human genbank 54_36p -1 model missense c.176 p.S59W 1 NULL NULL - no_errors tier1 107 4 3.6 135 109 44.67 330 1 0.3 445045 TCGA-AB-2996 AML30 10 86805062 86805062 C T SNP - - - - - - - - - - - - - - - tier3 404 3 0.74 319 258 44.71 0 0 NA 445045 TCGA-AB-2996 AML30 10 88484122 88484122 C T SNP LDB3 NM_007078.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*1409 NULL 0 - - - no_errors tier3 394 5 1.25 155 145 48.33 0 0 NA 445045 TCGA-AB-2996 AML30 10 107034495 107034495 C A SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*21373 NULL 0.002 - - - no_errors tier3 99 2 1.98 198 133 40.06 0 0 NA 445045 TCGA-AB-2996 AML30 10 119663071 119663071 A G SNP - - - - - - - - - - - - - - - tier3 259 1 0.38 287 240 45.54 0 0 NA 445045 TCGA-AB-2996 AML30 10 127873288 127873288 A G SNP ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed intronic c.261-39424 e4-39424 0 - - - no_errors tier3 205 4 1.91 203 138 40.47 0 0 NA 445045 TCGA-AB-2996 AML30 10 129008202 129008202 G A SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.3180-19058 e31-19058 0 - - - no_errors tier3 426 6 1.39 331 237 41.73 0 0 NA 445045 TCGA-AB-2996 AML30 10 130962877 130962877 T C SNP - - - - - - - - - - - - - - - tier3 300 6 1.96 360 336 48.28 0 0 NA 445045 TCGA-AB-2996 AML30 10 132754384 132754384 T C SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*27031 NULL 0 - - - no_errors tier3 126 0 0 97 75 43.6 0 0 NA 445045 TCGA-AB-2996 AML30 11 1617276 1617276 C T SNP KRTAP5-3 NM_001012708.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31085 NULL 0.022 - - - no_errors tier3 194 2 1.02 128 44 25.58 0 0 NA 445045 TCGA-AB-2996 AML30 11 2064177 2064177 C T SNP IGF2 NM_000612.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*46616 NULL 0.031 - - - no_errors tier3 593 4 0.67 88 103 53.65 0 0 NA 445045 TCGA-AB-2996 AML30 11 9474167 9474167 C T SNP ZNF143 NM_003442.4 human genbank 54_36p 1 validated intronic c.766-259 e8-259 0.005 - - - no_errors tier3 228 1 0.44 266 188 41.41 0 0 0 445045 TCGA-AB-2996 AML30 11 26168716 26168717 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 11 27927566 27927566 C A SNP - - - - - - - - - - - - - - - tier3 431 7 1.6 318 263 45.19 0 1 100 445045 TCGA-AB-2996 AML30 11 28720987 28720987 G T SNP - - - - - - - - - - - - - - - tier3 333 1 0.3 204 198 49.25 0 0 NA 445045 TCGA-AB-2996 AML30 11 36337646 36337646 A G SNP FLJ14213 NM_024841.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-41602 NULL 0.081 - - - no_errors tier3 290 2 0.68 158 79 33.33 0 0 NA 445045 TCGA-AB-2996 AML30 11 39538272 39538272 G C SNP - - - - - - - - - - - - - - - tier3 203 10 4.69 219 198 47.48 0 0 NA 445045 TCGA-AB-2996 AML30 11 40954682 40954682 G A SNP - - - - - - - - - - - - - - - tier3 202 4 1.94 321 230 41.74 0 0 NA 445045 TCGA-AB-2996 AML30 11 41063984 41063984 C T SNP ENSG00000209683 ENST00000386948 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*37061 NULL 0 - - - pseudogene tier3 125 0 0 144 125 46.47 0 0 NA 445045 TCGA-AB-2996 AML30 11 49234141 49234141 C T SNP FOLH1 NM_004476.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-47604 NULL 0 - - - no_errors tier3 229 1 0.43 203 142 41.16 0 0 NA 445045 TCGA-AB-2996 AML30 11 56051119 56051119 C A SNP OR5M5P ENST00000341231 human ensembl 54_36p -1 known missense c.196 p.A66S 0.001 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 282 2 0.7 223 181 44.8 NA 445045 TCGA-AB-2996 AML30 11 69065186 69065186 C A SNP - - - - - - - - - - - - - - - tier3 645 20 3 150 109 41.92 0 0 NA 445045 TCGA-AB-2996 AML30 11 71056662 71056662 C T SNP ENSG00000221458 ENST00000408531 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5273 NULL 0 - - - no_errors tier3 413 6 1.43 396 305 43.45 0 0 NA 445045 TCGA-AB-2996 AML30 11 74824213 74824213 C T SNP GDPD5 NM_030792.6 human genbank 54_36p -1 validated missense c.1805 p.R602Q 0.235 NULL "HMMPfam_GDPD,superfamily_PLC-like phosphodiesterases" - no_errors tier1 474 13 2.67 90 74 45.12 14 8 36.36 445045 TCGA-AB-2996 AML30 11 82144800 82144800 C T SNP FAM181B NM_175885.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22381 NULL 0.211 - - - no_errors tier3 213 1 0.47 139 105 43.03 0 0 NA 445045 TCGA-AB-2996 AML30 11 86583188 86583188 T C SNP TMEM135 NM_022918.2 human genbank 54_36p 1 provisional intronic c.462+37092 e5+37092 0.017 - - - no_errors tier3 169 2 1.17 302 191 38.74 1 2 66.67 445045 TCGA-AB-2996 AML30 11 100826735 100826735 T A SNP TRPC6 NM_004621.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*2161 NULL 0.002 - - - no_errors tier3 127 4 3.05 203 142 41.16 0 0 NA 445045 TCGA-AB-2996 AML30 11 102922711 102922711 G T SNP - - - - - - - - - - - - - - - tier3 162 5 2.98 106 101 48.79 0 0 NA 445045 TCGA-AB-2996 AML30 11 113809454 113809454 T G SNP REXO2 NM_015523.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-6007 NULL 0.04 - - - no_errors tier3 230 2 0.86 116 64 35.56 0 0 NA 445045 TCGA-AB-2996 AML30 11 120352146 120352146 A G SNP GRIK4 NM_014619.2 human genbank 54_36p 1 reviewed intronic c.2396-5879 e18-5879 0.001 - - - no_errors tier3 605 11 1.79 231 196 45.9 0 0 NA 445045 TCGA-AB-2996 AML30 11 124858738 124858738 C T SNP FEZ1 NM_005103.3 human genbank 54_36p -1 reviewed intronic c.312-1999 e2-1999 0 - - - no_errors tier3 259 2 0.77 190 161 45.87 0 0 0 445045 TCGA-AB-2996 AML30 11 129058944 129058944 C T SNP - - - - - - - - - - - - - - - tier3 324 4 1.22 203 154 43.14 0 0 NA 445045 TCGA-AB-2996 AML30 11 130206661 130206661 G - DEL SNX19 NM_014758.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*46866 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 11 131364070 131364070 A G SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.167+77318 e2+77318 0.015 - - - no_errors tier3 475 9 1.86 171 155 47.55 0 0 NA 445045 TCGA-AB-2996 AML30 12 904093 904093 C T SNP RAD52 NM_134424.2 human genbank 54_36p -1 reviewed intronic c.543+784 e6+784 0.004 - - - no_errors tier3 710 23 3.14 281 230 45.01 10 6 37.5 445045 TCGA-AB-2996 AML30 12 5638608 5638608 C T SNP ANO2 NM_020373.2 human genbank 54_36p -1 validated intronic c.1549-11380 e17-11380 0.002 - - - no_errors tier3 773 2 0.26 281 248 46.79 0 0 NA 445045 TCGA-AB-2996 AML30 12 10044493 10044493 C A SNP CLEC12A ENST00000396507 human ensembl 54_36p 1 known intronic c.254-14585 e4-14585 0 - - - no_stop_codon tier3 255 6 2.29 215 150 41.1 1 1 50 445045 TCGA-AB-2996 AML30 12 11542011 11542011 G A SNP ENSG00000221128 ENST00000408201 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*44113 NULL 0 - - - no_errors tier3 417 3 0.71 117 114 49.35 1 1 50 445045 TCGA-AB-2996 AML30 12 16168437 16168437 C T SNP - - - - - - - - - - - - - - - tier3 546 8 1.44 274 219 44.42 0 0 NA 445045 TCGA-AB-2996 AML30 12 36246864 36246864 G A SNP - - - - - - - - - - - - - - - tier2 594 6 1 195 180 48 0 0 NA 445045 TCGA-AB-2996 AML30 12 36923827 36923827 G T SNP ENSG00000221341 ENST00000408414 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40760 NULL 0 - - - no_errors tier3 141 6 4.08 120 86 41.75 0 0 NA 445045 TCGA-AB-2996 AML30 12 46387662 46387662 G A SNP RPAP3 NM_024604.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4772 NULL 0.191 - - - no_errors tier3 321 2 0.62 195 163 45.53 0 1 100 445045 TCGA-AB-2996 AML30 12 51050406 51050406 C T SNP KRT85 NM_002283.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2950 NULL 0 - - - no_errors tier3 378 3 0.79 232 208 47.27 0 0 NA 445045 TCGA-AB-2996 AML30 12 53273429 53273429 C T SNP PPP1R1A NM_006741.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-4890 NULL 0.001 - - - no_errors tier3 770 16 2.04 158 127 44.41 0 0 NA 445045 TCGA-AB-2996 AML30 12 57914889 57914889 G A SNP - - - - - - - - - - - - - - - tier3 175 5 2.78 256 190 42.6 0 0 NA 445045 TCGA-AB-2996 AML30 12 58295370 58295370 C T SNP ENSG00000202471 ENST00000365601 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-28379 NULL 0 - - - no_errors tier3 254 0 0 264 223 45.79 1 0 0 445045 TCGA-AB-2996 AML30 12 63893812 63893812 G A SNP LEMD3 NM_014319.3 human genbank 54_36p 1 validated intronic c.1561-2212 e3-2212 0.086 - - - no_errors tier3 154 2 1.28 333 252 43.08 1 0 0 445045 TCGA-AB-2996 AML30 12 68684034 68684034 C T SNP C12orf28 XM_001718908.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*45456 NULL 0.002 - - - no_errors tier3 264 6 2.22 160 123 43.46 0 0 NA 445045 TCGA-AB-2996 AML30 12 70722382 70722382 A T SNP TPH2 NM_173353.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*10640 NULL 0 - - - no_errors tier3 163 1 0.61 295 234 44.23 0 0 NA 445045 TCGA-AB-2996 AML30 12 77091567 77091567 A C SNP NAV3 NM_014903.4 human genbank 54_36p 1 validated intronic c.4982-1650 e25-1650 0 - - - no_errors tier3 124 1 0.79 205 170 45.33 0 0 NA 445045 TCGA-AB-2996 AML30 12 81019523 81019523 A C SNP - - - - - - - - - - - - - - - tier3 183 2 1.08 201 159 44.17 0 0 NA 445045 TCGA-AB-2996 AML30 12 90828381 90828381 A C SNP - - - - - - - - - - - - - - - tier3 327 2 0.61 139 98 41.35 0 0 NA 445045 TCGA-AB-2996 AML30 12 91470546 91470546 A T SNP - - - - - - - - - - - - - - - tier3 713 1 0.14 576 489 45.92 0 0 NA 445045 TCGA-AB-2996 AML30 12 102168836 102168836 C T SNP LOC728545 XM_001127727.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*11466 NULL 0.069 - - - no_errors tier3 294 5 1.67 374 264 41.38 0 0 0 445045 TCGA-AB-2996 AML30 12 102242367 102242367 G A SNP C12orf42 NM_001099336.1 human genbank 54_36p -1 validated intronic c.260-18114 e4-18114 0.001 - - - no_errors tier3 186 0 0 93 86 48.04 0 0 NA 445045 TCGA-AB-2996 AML30 12 102944379 102944379 T C SNP GLT8D2 NM_031302.3 human genbank 54_36p -1 provisional intronic c.1-4980 e1-4980 0.004 - - - no_errors tier3 437 1 0.23 143 117 45 0 0 NA 445045 TCGA-AB-2996 AML30 12 104253069 104253069 G A SNP - - - - - - - - - - - - - - - tier3 130 4 2.99 80 62 43.66 0 0 0 445045 TCGA-AB-2996 AML30 12 106671539 106671539 G T SNP PRDM4 NM_012406.3 human genbank 54_36p -1 reviewed intronic c.331+292 e3+292 0 - - - no_errors tier3 200 2 0.99 111 108 49.32 2 1 33.33 445045 TCGA-AB-2996 AML30 12 109297133 109297133 A G SNP ANAPC7 NM_016238.1 human genbank 54_36p -1 reviewed intronic c.1509-612 e11-612 0.002 - - - no_errors tier3 409 8 1.92 282 213 43.03 0 1 100 445045 TCGA-AB-2996 AML30 12 111480247 111480247 T C SNP PTPN11 NM_002834.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*53296 NULL 0.462 - - - no_errors tier3 294 6 2 201 185 47.93 0 0 NA 445045 TCGA-AB-2996 AML30 12 118256590 118256590 C T SNP CCDC60 NM_178499.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-775 NULL 0.001 - - - no_errors tier3 331 3 0.9 124 144 53.73 0 0 NA 445045 TCGA-AB-2996 AML30 12 127998249 127998249 G T SNP GLT1D1 NM_144669.1 human genbank 54_36p 1 provisional intronic c.540+293 e6+293 0 - - - no_errors tier3 218 2 0.91 87 76 46.63 0 0 0 445045 TCGA-AB-2996 AML30 12 130209423 130209423 G A SNP ENSG00000204603 ENST00000376678 human ensembl 54_36p 1 known 5_prime_flanking_region c.-6198 NULL 0 - - - no_errors tier3 172 2 1.15 61 56 47.86 0 0 NA 445045 TCGA-AB-2996 AML30 13 21262213 21262213 G A SNP ENSG00000222286 ENST00000410354 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-463 NULL 0 - - - no_errors tier3 259 1 0.38 236 168 41.58 0 0 NA 445045 TCGA-AB-2996 AML30 13 21283356 21283356 G A SNP ENSG00000222286 ENST00000410354 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*20374 NULL 0.005 - - - no_errors tier3 211 3 1.4 164 128 43.69 0 0 NA 445045 TCGA-AB-2996 AML30 13 21544356 21544356 G A SNP ENSG00000217355 ENST00000402362 human ensembl 54_36p -1 known 3_prime_flanking_region c.*26946 NULL 0 - - - no_coding_region:pseudogene tier3 263 11 4.01 254 160 38.55 0 0 NA 445045 TCGA-AB-2996 AML30 13 30828650 30828650 C T SNP B3GALTL NM_194318.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*26845 NULL 0.003 - - - no_errors tier3 553 8 1.42 171 137 44.48 0 0 NA 445045 TCGA-AB-2996 AML30 13 36018726 36018726 C T SNP - - - - - - - - - - - - - - - tier3 398 19 4.56 280 256 47.76 0 0 NA 445045 TCGA-AB-2996 AML30 13 37345487 37345487 A G SNP TRPC4 NM_016179.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-90017 NULL 0 - - - no_errors tier3 102 0 0 90 55 37.93 0 0 NA 445045 TCGA-AB-2996 AML30 13 47581640 47581640 C T SNP MED4 NM_014166.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-14425 NULL 0.002 - - - no_errors tier3 220 2 0.9 122 90 42.45 0 0 NA 445045 TCGA-AB-2996 AML30 13 52846656 52846656 C - DEL ENSG00000220990 ENST00000408063 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-6564 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 13 52993239 52993239 C T SNP - - - - - - - - - - - - - - - tier3 169 4 2.31 276 186 40.26 0 0 NA 445045 TCGA-AB-2996 AML30 13 57487446 57487446 T C SNP ENSG00000202422 ENST00000365552 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23847 NULL 0.001 - - - no_errors tier3 100 2 1.96 99 74 42.77 0 0 NA 445045 TCGA-AB-2996 AML30 13 59117065 59117065 C T SNP DIAPH3 NM_001042517.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*21654 NULL 0 - - - no_errors tier3 337 8 2.32 354 284 44.51 0 0 NA 445045 TCGA-AB-2996 AML30 13 62363778 62363779 AC - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 13 68803677 68803677 G A SNP - - - - - - - - - - - - - - - tier3 166 0 0 197 138 41.07 0 0 NA 445045 TCGA-AB-2996 AML30 13 71418123 71418123 T C SNP ENSG00000200037 ENST00000363167 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32104 NULL 0.003 - - - no_errors tier3 371 7 1.85 200 161 44.6 0 0 NA 445045 TCGA-AB-2996 AML30 13 76706351 76706351 C T SNP MYCBP2 NM_015057.3 human genbank 54_36p -1 validated intronic c.2516-952 e18-952 0 - - - no_errors tier3 66 3 4.35 97 77 44.25 1 2 66.67 445045 TCGA-AB-2996 AML30 13 83411320 83411320 G T SNP ENSG00000220449 ENST00000403715 human ensembl 54_36p -1 known 5_prime_flanking_region c.-31403 NULL 0.584 - - - no_coding_region:pseudogene tier3 241 5 2.03 243 169 41.02 0 0 NA 445045 TCGA-AB-2996 AML30 13 83854742 83854742 G A SNP - - - - - - - - - - - - - - - tier3 204 3 1.45 168 148 46.84 0 0 NA 445045 TCGA-AB-2996 AML30 13 87411327 87411327 T C SNP - - - - - - - - - - - - - - - tier3 117 1 0.85 91 74 44.85 0 0 NA 445045 TCGA-AB-2996 AML30 13 90795213 90795213 C G SNP MIRHG1 ENST00000400280 human ensembl 54_36p 1 known 5_prime_flanking_region c.-5231 NULL 0.001 - - - no_errors tier3 50 0 0 59 30 33.71 0 0 NA 445045 TCGA-AB-2996 AML30 13 97112316 97112316 G A SNP - - - - - - - - - - - - - - - tier3 181 1 0.55 205 150 42.25 0 0 NA 445045 TCGA-AB-2996 AML30 13 100845643 100845643 G A SNP NALCN NM_052867.2 human genbank 54_36p -1 validated silent c.183 p.F61 1 superfamily_Voltage-gated potassium channels "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" - no_errors tier1 131 4 2.96 228 186 44.93 NA 445045 TCGA-AB-2996 AML30 13 105433058 105433058 T A SNP - - - - - - - - - - - - - - - tier3 170 3 1.73 210 129 37.94 0 0 NA 445045 TCGA-AB-2996 AML30 13 106110318 106110318 T A SNP LOC390424 XR_016535.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-3468 NULL 0 - - - no_errors tier3 141 3 2.08 226 173 43.36 0 0 NA 445045 TCGA-AB-2996 AML30 13 109847475 109847475 G A SNP COL4A2 NM_001846.2 human genbank 54_36p 1 reviewed intronic c.181-27607 e4-27607 0.99 - - - no_errors tier3 291 5 1.69 145 150 50.85 0 0 NA 445045 TCGA-AB-2996 AML30 13 110668246 110668246 G T SNP ARHGEF7 NM_145735.1 human genbank 54_36p 1 reviewed intronic c.670+18 e5+18 0 - - - no_errors tier3 144 2 1.37 223 245 52.35 1 1 50 445045 TCGA-AB-2996 AML30 14 19442863 19442863 C T SNP OR4K5 NM_001005483.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-15743 NULL 0.029 - - - no_errors tier3 317 6 1.86 498 230 31.59 0 0 NA 445045 TCGA-AB-2996 AML30 14 28052642 28052642 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 14 29406944 29406944 T C SNP PRKD1 NM_002742.2 human genbank 54_36p -1 validated intronic c.264+59262 e1+59262 0.129 - - - no_errors tier3 305 5 1.61 265 193 42.14 0 0 NA 445045 TCGA-AB-2996 AML30 14 55522121 55522121 C T SNP ENSG00000213622 ENST00000395298 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*12564 NULL 0.568 - - - no_coding_region:pseudogene tier3 231 2 0.86 346 252 42.14 0 0 NA 445045 TCGA-AB-2996 AML30 14 62580926 62580926 C T SNP KCNH5 NM_139318.3 human genbank 54_36p -1 reviewed intronic c.73+659 e1+659 0.014 - - - no_errors tier3 154 2 1.28 109 120 52.4 0 0 NA 445045 TCGA-AB-2996 AML30 14 64755357 64755357 A G SNP LOC100128233 XM_001724610.1 human genbank 54_36p -1 model intronic c.84-191 e2-191 0 - - - no_errors tier3 311 11 3.42 314 227 41.96 0 0 NA 445045 TCGA-AB-2996 AML30 14 78263913 78263913 G A SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.925+12678 e3+12678 0.013 - - - no_errors tier3 738 4 0.54 347 270 43.76 0 0 NA 445045 TCGA-AB-2996 AML30 14 78362965 78362965 C T SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.1156+16525 e5+16525 0 - - - no_errors tier3 131 1 0.76 194 174 47.28 2 0 0 445045 TCGA-AB-2996 AML30 14 78992069 78992069 C T SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2144-11248 e11-11248 0.011 - - - no_errors tier3 132 2 1.49 100 81 44.75 0 0 NA 445045 TCGA-AB-2996 AML30 14 88057874 88057874 C T SNP PTPN21 NM_007039.3 human genbank 54_36p -1 reviewed intronic c.181-4516 e2-4516 0.964 - - - no_errors tier3 120 5 4 120 103 45.98 0 0 NA 445045 TCGA-AB-2996 AML30 14 99359480 99359480 G T SNP EML1 NM_001008707.1 human genbank 54_36p 1 reviewed intronic c.68-27463 e2-27463 0 - - - no_errors tier3 320 1 0.31 294 248 45.76 0 0 NA 445045 TCGA-AB-2996 AML30 15 19976403 19976403 G A SNP LOC642131 XM_001716834.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-1665 NULL 0.001 - - - no_errors tier3 312 1 0.32 262 59 18.38 0 0 0 445045 TCGA-AB-2996 AML30 15 20365357 20365357 C G SNP TUBGCP5 NM_001102610.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-19609 NULL 0 - - - no_errors tier3 90 2 2.17 74 44 37.29 0 0 NA 445045 TCGA-AB-2996 AML30 15 22199469 22199469 A G SNP - - - - - - - - - - - - - - - tier3 131 4 2.96 159 82 34.02 0 0 NA 445045 TCGA-AB-2996 AML30 15 22283089 22283089 C T SNP - - - - - - - - - - - - - - - tier3 145 1 0.68 141 83 37.05 0 0 NA 445045 TCGA-AB-2996 AML30 15 23800436 23800436 G A SNP LOC100128714 XM_001723960.1 human genbank 54_36p 1 model intronic c.184-11138 e2-11138 0 - - - no_errors tier3 415 8 1.89 190 164 46.33 0 0 NA 445045 TCGA-AB-2996 AML30 15 25658760 25658760 C T SNP ENSG00000210015 ENST00000387280 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-12066 NULL 0.001 - - - pseudogene tier3 266 0 0 156 126 44.68 0 0 NA 445045 TCGA-AB-2996 AML30 15 35331951 35331951 G A SNP - - - - - - - - - - - - - - - tier3 197 4 1.99 160 179 52.8 0 0 NA 445045 TCGA-AB-2996 AML30 15 47704119 47704119 T G SNP DTWD1 NM_020234.1 human genbank 54_36p 1 validated intronic c.1-483 e1-483 0.004 - - - no_errors tier3 130 1 0.76 123 106 46.29 1 0 0 445045 TCGA-AB-2996 AML30 15 53819353 53819353 A G SNP PRTG NM_173814.4 human genbank 54_36p -1 validated intronic c.397+519 e2+519 0.644 - - - no_errors tier3 268 5 1.83 181 148 44.85 2 0 0 445045 TCGA-AB-2996 AML30 15 53943101 53943101 C T SNP NEDD4 NM_198400.2 human genbank 54_36p -1 validated intronic c.1549-532 e2-532 0.002 - - - no_errors tier3 114 2 1.72 87 56 38.89 0 0 0 445045 TCGA-AB-2996 AML30 15 55041824 55041824 C G SNP TCF12 NM_207036.3 human genbank 54_36p 1 reviewed intronic c.148+41236 e2+41236 0 - - - no_errors tier3 165 3 1.79 149 111 42.53 1 5 83.33 445045 TCGA-AB-2996 AML30 15 71876815 71876815 G A SNP C15orf59 NM_001039614.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-46291 NULL 0.001 - - - no_errors tier3 583 2 0.34 191 153 44.35 0 0 NA 445045 TCGA-AB-2996 AML30 15 75881377 75881377 G A SNP - - - - - - - - - - - - - - - tier3 1097 19 1.7 178 146 44.92 0 0 NA 445045 TCGA-AB-2996 AML30 15 91543819 91543819 G A SNP UNQ9370 XR_041834.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-6608 NULL 0 - - - no_errors tier3 145 5 3.33 195 166 45.98 0 0 NA 445045 TCGA-AB-2996 AML30 15 96152678 96152678 C A SNP - - - - - - - - - - - - - - - tier3 455 3 0.66 209 154 42.42 0 0 0 445045 TCGA-AB-2996 AML30 16 3128460 3128460 G A SNP ZNF213 NM_004220.1 human genbank 54_36p 1 validated missense c.440 p.R147Q 0.001 NULL "HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_SCAN,HMMSmart_SM00431,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 217 0 171 160 47.76 4 4 50 445045 TCGA-AB-2996 AML30 16 6129458 6129458 C T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+119464 e0+119464 0 - - - no_errors tier3 494 9 1.79 411 345 45.57 0 0 NA 445045 TCGA-AB-2996 AML30 16 6474313 6474314 AT - DEL A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+167254_167255 e0+167254 0.003:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 16 20463925 20463925 G A SNP ACSM2B NM_001105069.1 human genbank 54_36p -1 validated intronic c.1281+55 e9+55 0 - - - no_errors tier3 323 6 1.82 241 209 46.44 0 0 NA 445045 TCGA-AB-2996 AML30 16 29009518 29009518 T - DEL ENSG00000103472 ENST00000219758 human ensembl 54_36p 1 known intronic c.1-44 e1-44 0.077 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 16 34330958 34330958 C T SNP ENSG00000221532 ENST00000408605 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-37406 NULL 0 - - - no_errors tier3 206 5 2.37 67 55 45.08 0 0 NA 445045 TCGA-AB-2996 AML30 16 49325201 49325201 G A SNP CYLD NM_015247.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15910 NULL 0.001 - - - no_errors tier3 391 1 0.26 160 152 48.72 1 1 50 445045 TCGA-AB-2996 AML30 16 55037318 55037318 C A SNP NUDT21 NM_007006.2 human genbank 54_36p -1 reviewed intronic c.381+721 e3+721 0.106 - - - no_errors tier3 117 5 4.1 68 41 37.61 1 0 0 445045 TCGA-AB-2996 AML30 16 56625680 56625680 G A SNP MMP15 NM_002428.2 human genbank 54_36p 1 reviewed intronic c.163-3197 e2-3197 0 - - - no_errors tier3 161 1 0.62 62 47 43.12 0 0 NA 445045 TCGA-AB-2996 AML30 16 67390717 67390717 G - DEL CDH1 NM_004360.3 human genbank 54_36p 1 reviewed intronic c.164-2357 e3-2357 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 16 69516466 69516466 C T SNP HYDIN NM_032821.2 human genbank 54_36p -1 validated intronic c.7156-3845 e45-3845 0.008 - - - no_errors tier3 573 6 1.04 421 120 22.18 0 0 NA 445045 TCGA-AB-2996 AML30 16 75128676 75128676 C A SNP CNTNAP4 NM_138994.3 human genbank 54_36p 1 validated intronic c.2777-838 e18-838 0 - - - no_errors tier3 116 3 2.52 131 96 42.29 0 0 NA 445045 TCGA-AB-2996 AML30 16 81307075 81307075 C A SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.45+88832 e1+88832 0 - - - no_errors tier3 413 4 0.96 184 140 43.21 0 0 NA 445045 TCGA-AB-2996 AML30 16 81630115 81630115 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.366+6791 e3+6791 0.001 - - - no_errors tier3 310 4 1.27 446 305 40.61 0 0 NA 445045 TCGA-AB-2996 AML30 16 83620581 83620581 C T SNP KIAA0513 NM_014732.2 human genbank 54_36p 1 validated intronic c.1+1623 e0+1623 0 - - - no_errors tier3 678 16 2.31 222 191 46.14 1 1 50 445045 TCGA-AB-2996 AML30 17 9073905 9073905 G A SNP NTN1 NM_004822.2 human genbank 54_36p 1 reviewed intronic c.1486+8621 e5+8621 0.001 - - - no_errors tier3 880 3 0.34 106 72 40.45 0 1 100 445045 TCGA-AB-2996 AML30 17 12918832 12918832 C T SNP LOC100134387 XM_001717070.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*32620 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 283 0 0 223 189 45.87 0 0 NA 445045 TCGA-AB-2996 AML30 17 26795545 26795545 G A SNP RAB11FIP4 NM_032932.3 human genbank 54_36p 1 validated intronic c.336+10279 e3+10279 0 - - - no_errors tier3 344 1 0.29 267 175 39.59 0 0 NA 445045 TCGA-AB-2996 AML30 17 29292352 29292352 T C SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.555+214758 e1+214758 0.001 - - - overly_large_intron tier3 333 3 0.89 183 118 39.2 0 0 NA 445045 TCGA-AB-2996 AML30 17 53256723 53256723 C T SNP LOC100128440 XM_001726725.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37339 NULL 0.005 - - - no_errors tier3 176 6 3.3 121 83 40.69 0 0 NA 445045 TCGA-AB-2996 AML30 17 53596574 53596574 G A SNP EPX NM_000502.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28633 NULL 0.724 - - - no_errors tier3 367 8 2.13 197 141 41.72 0 0 NA 445045 TCGA-AB-2996 AML30 17 67277057 67277057 C T SNP - - - - - - - - - - - - - - - tier3 276 2 0.72 218 122 35.88 0 0 NA 445045 TCGA-AB-2996 AML30 18 4149108 4149108 C T SNP - - - - - - - - - - - - - - - tier3 131 4 2.96 307 238 43.67 0 0 NA 445045 TCGA-AB-2996 AML30 18 4285200 4285200 G A SNP LOC284215 XM_001127273.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*1747 NULL 0.003 - - - no_errors tier3 155 1 0.64 291 196 40.25 0 0 NA 445045 TCGA-AB-2996 AML30 18 14197801 14197802 AT - DEL ENSG00000215525 ENST00000344538 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13941 NULL 0.000:0.001 - - - no_start_codon:no_stop_codon tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 18 22618823 22618824 - T INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 18 23442505 23442505 G A SNP FLJ45994 XR_040238.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13379 NULL 0.003 - - - no_errors tier3 59 2 3.28 123 91 42.52 0 0 NA 445045 TCGA-AB-2996 AML30 18 26975415 26975415 G A SNP DSC1 NM_024421.3 human genbank 54_36p -1 reviewed intronic c.1260+545 e9+545 0.001 - - - no_errors tier3 142 0 0 109 90 45.23 0 0 NA 445045 TCGA-AB-2996 AML30 18 27644025 27644026 - G INS MCART2 NM_001034172.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49403 NULL 0.013:0.014 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 18 27689854 27689854 A C SNP KIAA1012 NM_014939.3 human genbank 54_36p -1 validated intronic c.3189-86 e21-86 0.004 - - - no_errors tier3 118 2 1.67 165 111 40.22 1 0 0 445045 TCGA-AB-2996 AML30 18 27779482 27779482 A G SNP KIAA1012 NM_014939.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2757 NULL 0.062 - - - no_errors tier3 112 1 0.88 48 37 43.53 0 0 NA 445045 TCGA-AB-2996 AML30 18 29741495 29741495 C G SNP NOL4 NM_003787.3 human genbank 54_36p -1 validated intronic c.1543-24109 e10-24109 0 - - - no_errors tier3 66 2 2.9 122 82 40.2 0 0 NA 445045 TCGA-AB-2996 AML30 18 30495423 30495423 C T SNP DTNA NM_032975.1 human genbank 54_36p 1 reviewed intronic c.1-18007 e1-18007 0 - - - no_errors tier3 173 0 0 170 166 49.4 0 0 NA 445045 TCGA-AB-2996 AML30 18 32514852 32514852 T A SNP FHOD3 NM_025135.2 human genbank 54_36p 1 validated intronic c.1311-545 e12-545 0.01 - - - no_errors tier3 155 3 1.9 135 103 43.28 0 0 NA 445045 TCGA-AB-2996 AML30 18 34758715 34758715 C T SNP - - - - - - - - - - - - - - - tier3 267 0 0 221 204 48 0 0 NA 445045 TCGA-AB-2996 AML30 18 35459844 35459844 C T SNP - - - - - - - - - - - - - - - tier3 390 10 2.5 157 127 44.72 0 1 100 445045 TCGA-AB-2996 AML30 18 48155790 48155790 G C SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.91+34544 e1+34544 0.007 - - - no_errors tier3 123 1 0.8 102 98 49 0 0 NA 445045 TCGA-AB-2996 AML30 18 48844358 48844358 G T SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.1140+531 e6+531 0 - - - no_errors tier3 221 1 0.45 224 159 41.51 0 0 NA 445045 TCGA-AB-2996 AML30 18 58899212 58899212 A G SNP BCL2 NM_000633.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*47626 NULL 0.002 - - - no_errors tier3 271 2 0.73 151 116 43.28 0 0 NA 445045 TCGA-AB-2996 AML30 18 61594005 61594005 A G SNP CDH7 NM_004361.2 human genbank 54_36p 1 reviewed intronic c.210+12737 e1+12737 0.001 - - - no_errors tier3 207 4 1.9 331 260 43.99 0 0 NA 445045 TCGA-AB-2996 AML30 18 63637048 63637048 C T SNP - - - - - - - - - - - - - - - tier3 149 2 1.32 117 76 39.38 0 0 NA 445045 TCGA-AB-2996 AML30 18 67022641 67022641 T G SNP - - - - - - - - - - - - - - - tier3 212 1 0.47 85 107 55.73 0 0 NA 445045 TCGA-AB-2996 AML30 18 68353705 68353705 A G SNP CBLN2 NM_182511.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*2686 NULL 0.001 - - - no_errors tier3 210 2 0.94 82 79 48.77 0 0 NA 445045 TCGA-AB-2996 AML30 18 68890679 68890679 C T SNP - - - - - - - - - - - - - - - tier3 345 2 0.58 303 241 44.3 0 0 NA 445045 TCGA-AB-2996 AML30 19 8857309 8857309 A C SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated intronic c.41251+12 e61+12 0.001 - - - no_errors tier3 2327 21 0.89 520 371 41.64 0 0 NA 445045 TCGA-AB-2996 AML30 19 17331747 17331747 C T SNP PLVAP NM_031310.1 human genbank 54_36p -1 provisional intronic c.1322+590 e5+590 0.014 - - - no_errors tier3 790 16 1.98 209 141 40.29 0 0 0 445045 TCGA-AB-2996 AML30 19 33322024 33322024 C T SNP - - - - - - - - - - - - - - - tier3 557 21 3.63 314 263 45.58 0 0 NA 445045 TCGA-AB-2996 AML30 19 39145938 39145938 C T SNP ENSG00000222442 ENST00000410510 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35568 NULL 0 - - - no_errors tier3 569 1 0.18 227 185 44.9 0 0 NA 445045 TCGA-AB-2996 AML30 19 50526472 50526472 C T SNP KLC3 NM_177417.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-14168 NULL 0 - - - no_errors tier3 363 3 0.82 81 47 36.72 0 0 NA 445045 TCGA-AB-2996 AML30 19 55723998 55723998 G A SNP LRRC4B NM_001080457.1 human genbank 54_36p -1 provisional intronic c.298-9514 e2-9514 0 - - - no_errors tier3 788 14 1.75 115 89 43.63 0 0 NA 445045 TCGA-AB-2996 AML30 19 57240753 57240753 A G SNP ZNF432 NM_014650.2 human genbank 54_36p -1 provisional intronic c.15+1166 e1+1166 0.003 - - - no_errors tier3 121 0 0 144 113 43.8 0 0 0 445045 TCGA-AB-2996 AML30 19 57310035 57310035 G T SNP ZNF616 NM_178523.3 human genbank 54_36p -1 validated missense c.2194 p.L732I 0.066 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 234 3 1.27 116 109 48.44 4 2 33.33 445045 TCGA-AB-2996 AML30 19 62653250 62653250 G A SNP ZNF419 NM_001098491.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37881 NULL 0.003 - - - no_errors tier3 335 3 0.89 325 235 41.89 0 3 100 445045 TCGA-AB-2996 AML30 20 15315837 15315837 A G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.541-44213 e7-44213 0.006 - - - no_errors tier3 301 11 3.53 245 258 51.29 0 0 NA 445045 TCGA-AB-2996 AML30 20 15988739 15988739 C T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*10218 NULL 0 - - - no_errors tier3 320 2 0.62 263 233 46.88 0 0 NA 445045 TCGA-AB-2996 AML30 20 54198422 54198422 C T SNP ENSG00000222118 ENST00000410186 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*15095 NULL 0.031 - - - no_errors tier3 172 5 2.82 166 119 41.75 0 0 NA 445045 TCGA-AB-2996 AML30 20 54239261 54239261 C T SNP MC3R NM_019888.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17935 NULL 0.797 - - - no_errors tier3 180 3 1.64 269 201 42.77 0 0 NA 445045 TCGA-AB-2996 AML30 20 54841934 54841934 C T SNP ENSG00000207158 ENST00000384429 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-47384 NULL 0.001 - - - no_errors tier3 592 5 0.84 128 95 42.6 0 0 NA 445045 TCGA-AB-2996 AML30 20 55015266 55015266 C T SNP - - - - - - - - - - - - - - - tier3 770 8 1.03 168 137 44.92 0 0 NA 445045 TCGA-AB-2996 AML30 20 55607559 55607559 C T SNP PCK1 NM_002591.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*33293 NULL 0.354 - - - no_errors tier3 842 3 0.35 262 179 40.59 0 0 NA 445045 TCGA-AB-2996 AML30 20 58722587 58722587 C T SNP - - - - - - - - - - - - - - - tier3 264 3 1.12 120 115 48.94 0 0 NA 445045 TCGA-AB-2996 AML30 20 61724689 61724689 C T SNP GMEB2 ENST00000370077 human ensembl 54_36p -1 known intronic c.1-3438 e1-3438 0 - - - no_errors tier3 150 0 0 75 51 40.48 3 1 25 445045 TCGA-AB-2996 AML30 21 15263429 15263429 C T SNP NRIP1 ENST00000318948 human ensembl 54_36p -1 known intronic c.1-711 e1-711 0.028 - - - no_errors tier3 175 1 0.57 304 244 44.53 3 0 0 445045 TCGA-AB-2996 AML30 21 22126730 22126730 T A SNP - - - - - - - - - - - - - - - tier3 120 1 0.83 93 67 41.61 0 0 NA 445045 TCGA-AB-2996 AML30 21 22422915 22422915 G A SNP C21orf74 ENST00000333482 human ensembl 54_36p 1 known 3_prime_flanking_region c.*13888 NULL 0.002 - - - no_errors tier3 101 5 4.72 90 64 41.56 0 0 NA 445045 TCGA-AB-2996 AML30 21 25478386 25478386 C T SNP ENSG00000222042 ENST00000409758 human ensembl 54_36p -1 known intronic c.1-8756 e1-8756 0 - - - no_errors tier3 141 2 1.4 226 176 43.78 0 0 NA 445045 TCGA-AB-2996 AML30 21 25554163 25554163 G C SNP ENSG00000222042 ENST00000409758 human ensembl 54_36p -1 known intronic c.1+73759 e0+73759 0.004 - - - no_errors tier3 242 6 2.42 258 197 43.3 0 0 NA 445045 TCGA-AB-2996 AML30 21 26429738 26429738 G A SNP APP NM_000484.2 human genbank 54_36p -1 reviewed intronic c.58-23404 e2-23404 0 - - - no_errors tier3 157 1 0.63 146 148 50.34 0 1 100 445045 TCGA-AB-2996 AML30 21 43397525 43397525 G A SNP U2AF1 NM_001025203.1 human genbank 54_36p -1 reviewed missense c.101 p.S34F 1 "HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1" "HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928" - no_errors tier1 220 7 3.08 83 61 42.36 71 77 51.68 445045 TCGA-AB-2996 AML30 21 44531453 44531453 C T SNP AIRE NM_000383.2 human genbank 54_36p 1 reviewed splice_region c.463+9 e3+9 0.006 - - - no_errors tier3 127 2 1.55 26 31 54.39 0 0 NA 445045 TCGA-AB-2996 AML30 22 16174456 16174456 C T SNP ENSG00000209324 ENST00000386589 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*39315 NULL 0.111 - - - pseudogene tier3 333 3 0.89 215 152 41.42 0 0 NA 445045 TCGA-AB-2996 AML30 22 19051275 19051275 G A SNP USP41 XM_036729.1 human genbank 54_36p -1 model intronic c.631-251 e8-251 0 - - - no_errors tier3 189 0 0 80 70 46.67 0 0 0 445045 TCGA-AB-2996 AML30 22 21329349 21329349 C T SNP ENSG00000183169 ENST00000402027 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12793 NULL 0.068 - - - no_errors tier3 308 7 2.22 185 129 41.08 0 0 0 445045 TCGA-AB-2996 AML30 22 36497350 36497350 G - DEL TRIOBP NM_001039141.2 human genbank 54_36p 1 reviewed intronic c.6850-253 e20-253 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 445045 TCGA-AB-2996 AML30 22 46456791 46456791 C A SNP ENSG00000216847 ENST00000403781 human ensembl 54_36p -1 known 5_prime_flanking_region c.-18775 NULL 0.017 - - - no_coding_region:pseudogene tier3 463 10 2.11 299 245 44.95 0 0 NA 445045 TCGA-AB-2996 AML30 22 46603879 46603879 C G SNP - - - - - - - - - - - - - - - tier3 270 2 0.74 312 212 40.38 0 0 NA 445045 TCGA-AB-2996 AML30 22 46927472 46927472 C G SNP - - - - - - - - - - - - - - - tier3 180 2 1.1 128 98 43.36 0 0 NA 445045 TCGA-AB-2996 AML30 22 47897304 47897304 C T SNP - - - - - - - - - - - - - - - tier3 248 3 1.2 176 139 44.13 0 0 NA 758168 TCGA-AB-2997 AML15 X 6322152 6322152 T C SNP ENSG00000217694 ENST00000405313 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12467 NULL 0.001 - - - no_coding_region:pseudogene tier3 1383 89 6.05 820 566 40.81 NA NA NA 758168 TCGA-AB-2997 AML15 X 13117926 13117926 G A SNP - - - - - - - - - - - - - - - tier3 1007 58 5.44 928 677 42.15 NA NA NA 758168 TCGA-AB-2997 AML15 X 21537732 21537732 T C SNP CNKSR2 NM_014927.2 human genbank 54_36p 1 provisional intronic c.2692+76 e20+76 0.457 - - - no_errors tier3 522 52 9.06 395 276 41.13 NA NA NA 758168 TCGA-AB-2997 AML15 X 21592423 21592423 A T SNP KLHL34 NM_153270.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-6596 NULL 0.027 - - - no_errors tier3 1206 100 7.66 492 350 41.52 NA NA NA 758168 TCGA-AB-2997 AML15 X 26022927 26022927 C T SNP MAGEB18 NM_173699.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-44097 NULL 0 - - - no_errors tier3 669 49 6.82 395 332 45.67 NA NA NA 758168 TCGA-AB-2997 AML15 X 27627740 27627740 C G SNP ENSG00000218243 ENST00000404403 human ensembl 54_36p -1 known 3_prime_flanking_region c.*47194 NULL 0.099 - - - no_coding_region:pseudogene tier3 1689 151 8.2 1081 664 38.05 NA NA NA 758168 TCGA-AB-2997 AML15 X 29598897 29598897 C T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.778+2355 e5+2355 0.001 - - - no_errors tier3 630 26 3.96 439 368 45.54 NA NA NA 758168 TCGA-AB-2997 AML15 X 32610216 32610216 T C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.960+15692 e9+15692 0.004 - - - no_errors tier3 922 69 6.96 530 454 46.14 NA NA NA 758168 TCGA-AB-2997 AML15 X 34772060 34772060 G C SNP - - - - - - - - - - - - - - - tier3 1036 71 6.41 488 369 43.06 NA NA NA 758168 TCGA-AB-2997 AML15 X 39397156 39397156 A - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 X 95115225 95115225 G A SNP LOC648927 XR_038906.1 human genbank 54_36p -1 model rna NULL NULL 0.998 - - - pseudogene tier1 958 62 6.08 399 309 43.64 NA NA NA 758168 TCGA-AB-2997 AML15 X 103800606 103800606 A C SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.82+10274 e1+10274 0 - - - no_errors tier3 1899 143 7 1522 1194 43.93 NA NA NA 758168 TCGA-AB-2997 AML15 X 123754185 123754185 C G SNP ODZ1 NM_014253.2 human genbank 54_36p -1 provisional intronic c.536-55457 e4-55457 0.746 - - - no_errors tier2 989 48 4.63 788 562 41.6 NA NA NA 758168 TCGA-AB-2997 AML15 X 125327309 125327309 T A SNP - - - - - - - - - - - - - - - tier2 637 30 4.5 512 296 36.59 NA NA NA 758168 TCGA-AB-2997 AML15 1 7784722 7784722 T C SNP PER3 NM_016831.1 human genbank 54_36p 1 reviewed intronic c.869+884 e7+884 0.004 - - - no_errors tier3 295 35 10.61 230 192 45.5 NA NA NA 758168 TCGA-AB-2997 AML15 1 9292525 9292525 G C SNP SPSB1 NM_025106.3 human genbank 54_36p 1 validated intronic c.1+16808 e0+16808 0.008 - - - no_errors tier3 668 42 5.91 194 156 44.44 NA NA NA 758168 TCGA-AB-2997 AML15 1 16912831 16912831 G A SNP ESPNP ENST00000270691 human ensembl 54_36p -1 known intronic c.195-5671 e2-5671 0.003 - - - no_start_codon tier3 3428 82 2.33 361 91 20.13 NA NA NA 758168 TCGA-AB-2997 AML15 1 36221858 36221858 C G SNP EIF2C3 NM_024852.2 human genbank 54_36p 1 reviewed intronic c.658+10159 e5+10159 0 - - - no_errors tier3 1725 139 7.45 768 754 49.54 NA NA NA 758168 TCGA-AB-2997 AML15 1 65105070 65105071 - G INS JAK1 NM_002227.2 human genbank 54_36p -1 reviewed intronic c.990+66_990+65 e6+66 0.007:0.005 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 1 79695278 79695278 A G SNP - - - - - - - - - - - - - - - tier3 902 49 5.15 408 277 40.38 NA NA NA 758168 TCGA-AB-2997 AML15 1 90765265 90765265 G T SNP - - - - - - - - - - - - - - - tier3 983 60 5.75 748 718 48.98 NA NA NA 758168 TCGA-AB-2997 AML15 1 101795228 101795228 C T SNP - - - - - - - - - - - - - - - tier3 693 45 6.1 541 445 45.13 NA NA NA 758168 TCGA-AB-2997 AML15 1 108075256 108075256 C T SNP VAV3 NM_006113.1 human genbank 54_36p -1 reviewed intronic c.1502+17857 e15+17857 0.311 - - - no_errors tier3 686 58 7.8 782 588 42.83 NA NA NA 758168 TCGA-AB-2997 AML15 1 144426616 144426616 A G SNP CD160 NM_007053.2 human genbank 54_36p -1 validated intronic c.1+267 e0+267 0.021 - - - no_errors tier3 688 74 9.71 402 345 46.18 NA NA NA 758168 TCGA-AB-2997 AML15 1 145272658 145272658 T C SNP CHD1L NM_004284.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*38844 NULL 0.001 - - - no_errors tier3 1423 122 7.89 938 732 43.83 NA NA NA 758168 TCGA-AB-2997 AML15 1 157535832 157535832 C T SNP FCER1A NM_002001.2 human genbank 54_36p 1 reviewed intronic c.1-2888 e1-2888 0.001 - - - no_errors tier3 657 55 7.7 490 446 47.65 NA NA NA 758168 TCGA-AB-2997 AML15 1 161210083 161210083 C T SNP ENSG00000219987 ENST00000405744 human ensembl 54_36p -1 known 3_prime_flanking_region c.*5882 NULL 0.002 - - - no_coding_region:pseudogene tier3 1731 106 5.76 920 666 41.99 NA NA NA 758168 TCGA-AB-2997 AML15 1 162672026 162672026 C T SNP - - - - - - - - - - - - - - - tier3 95 12 11.21 43 29 40.28 NA NA NA 758168 TCGA-AB-2997 AML15 1 176722320 176722320 C G SNP C1orf49 NM_032126.3 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-26627 NULL 0.002 - - - no_errors tier2 470 35 6.92 289 200 40.73 NA NA NA 758168 TCGA-AB-2997 AML15 1 182681055 182681055 T G SNP C1orf21 NM_030806.3 human genbank 54_36p 1 validated intronic c.1-32088 e1-32088 0.001 - - - no_errors tier3 803 84 9.45 526 440 45.55 NA NA NA 758168 TCGA-AB-2997 AML15 1 213699271 213699271 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 1 227069729 227069729 G A SNP - - - - - - - - - - - - - - - tier3 1336 92 6.43 540 499 47.98 NA NA NA 758168 TCGA-AB-2997 AML15 1 227086932 227086932 T C SNP - - - - - - - - - - - - - - - tier3 1273 94 6.88 624 543 46.49 NA NA NA 758168 TCGA-AB-2997 AML15 2 1604624 1604624 G A SNP LOC100133877 XM_001722039.1 human genbank 54_36p -1 model intronic c.291-44566 e3-44566 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 576 43 6.94 367 323 46.68 NA NA NA 758168 TCGA-AB-2997 AML15 2 3653144 3653144 A G SNP COLEC11 NM_024027.3 human genbank 54_36p 1 validated intronic c.203-9854 e3-9854 0.957 - - - no_errors tier2 933 56 5.66 509 480 48.48 NA NA NA 758168 TCGA-AB-2997 AML15 2 5275186 5275186 A T SNP - - - - - - - - - - - - - - - tier3 733 49 6.27 484 331 40.61 NA NA NA 758168 TCGA-AB-2997 AML15 2 12812570 12812570 C T SNP TRIB2 NM_021643.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*14199 NULL 0.001 - - - no_errors tier3 785 60 7.1 374 331 46.95 NA NA NA 758168 TCGA-AB-2997 AML15 2 23020073 23020073 C A SNP - - - - - - - - - - - - - - - tier3 467 30 6.02 434 380 46.68 NA NA NA 758168 TCGA-AB-2997 AML15 2 32298967 32298967 A G SNP SLC30A6 NM_017964.2 human genbank 54_36p 1 provisional missense c.1067 p.H356R 1 NULL HMMPfam_Cation_efflux - no_errors tier1 926 63 6.37 569 418 42.31 NA NA NA 758168 TCGA-AB-2997 AML15 2 52295638 52295638 A G SNP - - - - - - - - - - - - - - - tier3 903 63 6.52 478 420 46.61 NA NA NA 758168 TCGA-AB-2997 AML15 2 79610921 79610921 A - DEL CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1+17080 e0+17080 0 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 2 100377523 100377523 C T SNP CHST10 NM_004854.3 human genbank 54_36p -1 validated intronic c.534-847 e5-847 0 - - - no_errors tier3 1306 122 8.54 985 817 45.29 NA NA NA 758168 TCGA-AB-2997 AML15 2 106517597 106517597 G A SNP CD8BP ENST00000303432 human ensembl 54_36p 1 known 3_prime_flanking_region c.*30096 NULL 0 - - - no_errors tier2 1435 100 6.51 467 433 48.11 NA NA NA 758168 TCGA-AB-2997 AML15 2 109210679 109210679 T A SNP SH3RF3 NM_001099289.1 human genbank 54_36p 1 provisional intronic c.573+97678 e1+97678 0.002 - - - no_stop_codon tier3 615 43 6.53 463 407 46.78 NA NA NA 758168 TCGA-AB-2997 AML15 2 112581114 112581114 G C SNP TMEM87B NM_032824.2 human genbank 54_36p 1 validated intronic c.1525-722 e17-722 0.097 - - - no_errors tier3 1069 74 6.47 623 546 46.67 NA NA NA 758168 TCGA-AB-2997 AML15 2 119959157 119959157 C T SNP SCTR NM_002980.2 human genbank 54_36p -1 reviewed intronic c.194-6193 e3-6193 0 - - - no_errors tier3 1659 113 6.37 808 653 44.51 NA NA NA 758168 TCGA-AB-2997 AML15 2 123733119 123733119 C T SNP - - - - - - - - - - - - - - - tier3 1599 103 6.05 728 540 42.59 NA NA NA 758168 TCGA-AB-2997 AML15 2 133290595 133290595 G A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.808-19823 e10-19823 0 - - - no_errors tier3 659 34 4.91 541 507 48.38 NA NA NA 758168 TCGA-AB-2997 AML15 2 164545173 164545173 G A SNP - - - - - - - - - - - - - - - tier3 596 50 7.74 597 397 39.94 NA NA NA 758168 TCGA-AB-2997 AML15 2 165489935 165489935 G A SNP SLC38A11 NM_173512.1 human genbank 54_36p -1 provisional intronic c.384-9206 e5-9206 0 - - - no_errors tier3 1709 103 5.67 1065 651 37.87 NA NA NA 758168 TCGA-AB-2997 AML15 2 193658805 193658805 A T SNP - - - - - - - - - - - - - - - tier3 620 42 6.34 506 385 43.16 NA NA NA 758168 TCGA-AB-2997 AML15 2 200990862 200990862 G A SNP LOC26010 NM_001100422.1 human genbank 54_36p 1 validated intronic c.199-1356 e4-1356 0 - - - no_errors tier2 905 79 8.02 461 368 44.39 NA NA NA 758168 TCGA-AB-2997 AML15 2 207420782 207420782 G A SNP - - - - - - - - - - - - - - - tier3 1000 82 7.58 579 560 49.08 NA NA NA 758168 TCGA-AB-2997 AML15 2 225157935 225157935 C A SNP CUL3 NM_003590.3 human genbank 54_36p -1 validated missense c.36 p.K12N 1 NULL "HMMPfam_Cullin,PatternScan_CULLIN_1,HMMSmart_SM00182,superfamily_Cullin homology domain,superfamily_Cullin repeat,HMMPfam_Cullin_Nedd8,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 110 12 9.84 41 52 55.91 NA NA NA 758168 TCGA-AB-2997 AML15 3 6639859 6639859 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 3 11753564 11753564 G A SNP VGLL4 NM_014667.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-34056 NULL 0 - - - no_errors tier3 1840 149 7.48 618 527 45.83 NA NA NA 758168 TCGA-AB-2997 AML15 3 18036353 18036353 G A SNP - - - - - - - - - - - - - - - tier3 2714 265 8.89 1070 952 47.08 NA NA NA 758168 TCGA-AB-2997 AML15 3 18385519 18385519 C T SNP SATB1 NM_002971.1 human genbank 54_36p -1 validated intronic c.1575+9147 e8+9147 0.005 - - - no_errors tier3 1031 96 8.5 505 440 46.56 NA NA NA 758168 TCGA-AB-2997 AML15 3 27672345 27672345 A G SNP LOC643634 XR_016808.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*20423 NULL 0.002 - - - pseudogene tier3 1187 81 6.39 562 441 43.92 NA NA NA 758168 TCGA-AB-2997 AML15 3 28052846 28052846 G T SNP - - - - - - - - - - - - - - - tier3 443 36 7.52 198 166 45.6 NA NA NA 758168 TCGA-AB-2997 AML15 3 30888917 30888917 T C SNP GADL1 NM_207359.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22327 NULL 0.003 - - - no_errors tier2 1381 81 5.54 945 626 39.82 NA NA NA 758168 TCGA-AB-2997 AML15 3 49658255 49658255 C T SNP BSN NM_003458.3 human genbank 54_36p 1 validated intronic c.1518+2666 e3+2666 0.106 - - - no_errors tier3 414 26 5.91 251 192 43.24 NA NA NA 758168 TCGA-AB-2997 AML15 3 71150853 71150853 G A SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.870-3359 e7-3359 0.069 - - - no_errors tier3 1325 133 9.12 831 761 47.77 NA NA NA 758168 TCGA-AB-2997 AML15 3 77764726 77764726 G A SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.3761-1985 e24-1985 0.003 - - - no_errors tier3 706 42 5.6 568 365 39.08 NA NA NA 758168 TCGA-AB-2997 AML15 3 95742782 95742782 A G SNP LOC389137 XM_371655.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-33628 NULL 0 - - - no_errors tier3 360 14 3.74 302 220 42.15 NA NA NA 758168 TCGA-AB-2997 AML15 3 98050427 98050427 A T SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.386-17932 e2-17932 0.002 - - - no_errors tier3 391 21 5.1 343 269 43.95 NA NA NA 758168 TCGA-AB-2997 AML15 3 103284349 103284349 T A SNP ZPLD1 ENST00000394046 human ensembl 54_36p 1 known 5_prime_flanking_region c.-355673 NULL 0.005 - - - no_errors tier3 698 61 8.03 490 433 46.91 NA NA NA 758168 TCGA-AB-2997 AML15 3 117716339 117716339 G T SNP - - - - - - - - - - - - - - - tier2 510 33 6.08 288 201 41.1 NA NA NA 758168 TCGA-AB-2997 AML15 3 118059508 118059508 A G SNP - - - - - - - - - - - - - - - tier3 1243 95 7.09 751 676 47.34 NA NA NA 758168 TCGA-AB-2997 AML15 3 141518769 141518769 C T SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.233-86392 e3-86392 0.013 - - - no_errors tier3 898 78 7.99 554 398 41.81 NA NA NA 758168 TCGA-AB-2997 AML15 3 167344171 167344171 A C SNP ENSG00000208609 ENST00000385874 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17429 NULL 0 - - - pseudogene tier3 906 55 5.72 624 424 40.38 NA NA NA 758168 TCGA-AB-2997 AML15 3 184733470 184733470 A T SNP KLHL6 NM_130446.2 human genbank 54_36p -1 validated intronic c.294-4978 e2-4978 0 - - - no_errors tier3 3953 291 6.85 1539 1178 43.32 NA NA NA 758168 TCGA-AB-2997 AML15 4 6335563 6335563 G A SNP WFS1 NM_006005.1 human genbank 54_36p 1 reviewed intronic c.233-4158 e2-4158 0 - - - no_errors tier2 350 29 7.63 176 127 41.64 NA NA NA 758168 TCGA-AB-2997 AML15 4 23382337 23382337 G C SNP PPARGC1A NM_013261.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*24206 NULL 0.213 - - - no_errors tier3 1050 88 7.73 415 380 47.68 NA NA NA 758168 TCGA-AB-2997 AML15 4 25244945 25244945 G A SNP SLC34A2 NM_006424.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28276 NULL 0.019 - - - no_errors tier2 1558 129 7.65 477 425 47.07 NA NA NA 758168 TCGA-AB-2997 AML15 4 45315673 45315673 G C SNP - - - - - - - - - - - - - - - tier3 682 56 7.57 300 274 47.74 NA NA NA 758168 TCGA-AB-2997 AML15 4 75410336 75410336 G A SNP EREG NM_001432.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-39554 NULL 0 - - - no_errors tier3 682 40 5.53 432 332 43.46 NA NA NA 758168 TCGA-AB-2997 AML15 4 116142222 116142222 C T SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.979-24343 e2-24343 0 - - - no_errors tier3 204 12 5.56 107 78 42.16 NA NA NA 758168 TCGA-AB-2997 AML15 4 120767588 120767588 T C SNP PDE5A NM_001083.3 human genbank 54_36p -1 reviewed intronic c.152+1535 e1+1535 0 - - - no_errors tier2 267 11 3.96 163 115 41.37 NA NA NA 758168 TCGA-AB-2997 AML15 4 145108652 145108653 TT - DEL GYPB NM_002100.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*28250 NULL 0.009:0.003 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 4 156270550 156270550 C A SNP - - - - - - - - - - - - - - - tier3 949 55 5.48 453 361 44.24 NA NA NA 758168 TCGA-AB-2997 AML15 4 156831276 156831276 T C SNP GUCY1A3 NM_000856.4 human genbank 54_36p 1 validated intronic c.1-6082 e1-6082 0 - - - no_errors tier3 856 71 7.64 497 438 46.84 NA NA NA 758168 TCGA-AB-2997 AML15 4 188219693 188219693 C A SNP - - - - - - - - - - - - - - - tier3 541 33 5.75 538 328 37.83 NA NA NA 758168 TCGA-AB-2997 AML15 4 188388493 188388493 T C SNP - - - - - - - - - - - - - - - tier3 420 27 6.04 241 187 43.69 NA NA NA 758168 TCGA-AB-2997 AML15 5 2610120 2610120 C A SNP LOC100133292 XM_001715713.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*25178 NULL 0 - - - no_errors tier3 627 45 6.69 383 353 47.96 NA NA NA 758168 TCGA-AB-2997 AML15 5 22951039 22951039 C T SNP - - - - - - - - - - - - - - - tier2 1483 52 3.38 668 454 40.43 NA NA NA 758168 TCGA-AB-2997 AML15 5 35263858 35263858 T C SNP PRLR NM_000949.4 human genbank 54_36p -1 validated intronic c.1+2269 e0+2269 0 - - - no_errors tier3 1981 165 7.69 794 672 45.78 NA NA NA 758168 TCGA-AB-2997 AML15 5 62068029 62068029 A G SNP ISCA1L NM_001080540.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*40326 NULL 0.01 - - - no_errors tier3 807 63 7.23 535 471 46.77 NA NA NA 758168 TCGA-AB-2997 AML15 5 111485540 111485540 G A SNP SNORA13 NR_002922.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-39541 NULL 0.007 - - - no_errors tier3 1503 76 4.81 778 621 44.26 NA NA NA 758168 TCGA-AB-2997 AML15 5 116451537 116451537 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 5 134701238 134701238 T C SNP H2AFY NM_138610.1 human genbank 54_36p -1 reviewed intronic c.954-2508 e8-2508 0.002 - - - no_errors tier3 551 45 7.53 312 281 47.39 NA NA NA 758168 TCGA-AB-2997 AML15 5 168146460 168146460 C T SNP SLIT3 NM_003062.2 human genbank 54_36p -1 validated intronic c.1080-899 e12-899 0 - - - no_errors tier3 892 56 5.91 355 321 47.49 NA NA NA 758168 TCGA-AB-2997 AML15 5 169360334 169360334 A C SNP DOCK2 NM_004946.2 human genbank 54_36p 1 validated intronic c.3072+4588 e30+4588 0 - - - no_errors tier3 617 42 6.37 384 376 49.34 NA NA NA 758168 TCGA-AB-2997 AML15 5 179375837 179375837 A T SNP RNF130 NM_018434.4 human genbank 54_36p -1 reviewed intronic c.443-2920 e3-2920 0.003 - - - no_errors tier3 775 73 8.61 493 280 36.04 NA NA NA 758168 TCGA-AB-2997 AML15 6 322235 322235 T G SNP LOC730077 XM_001132307.2 human genbank 54_36p 1 model intronic c.173+74047 e1+74047 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 797 25 3.04 927 403 30.3 NA NA NA 758168 TCGA-AB-2997 AML15 6 19427793 19427793 A T SNP ENSG00000218643 ENST00000403848 human ensembl 54_36p 1 known 5_prime_flanking_region c.-28598 NULL 0.187 - - - no_coding_region:pseudogene tier3 1956 114 5.49 664 563 45.85 NA NA NA 758168 TCGA-AB-2997 AML15 6 42797361 42797361 G A SNP PRPH2 NM_000322.4 human genbank 54_36p -1 reviewed intronic c.581+109 e1+109 0.001 - - - no_errors tier3 1119 94 7.74 336 261 43.72 NA NA NA 758168 TCGA-AB-2997 AML15 6 77165181 77165181 T G SNP - - - - - - - - - - - - - - - tier3 1577 102 6.08 621 497 44.45 NA NA NA 758168 TCGA-AB-2997 AML15 6 91426599 91426599 C A SNP - - - - - - - - - - - - - - - tier3 937 60 6.02 569 528 48.09 NA NA NA 758168 TCGA-AB-2997 AML15 6 91783109 91783109 T C SNP - - - - - - - - - - - - - - - tier3 1462 106 6.76 1007 880 46.54 NA NA NA 758168 TCGA-AB-2997 AML15 6 93879979 93879979 T C SNP ENSG00000213187 ENST00000392786 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20689 NULL 0.001 - - - no_coding_region:pseudogene tier3 1465 147 9.11 951 825 46.37 NA NA NA 758168 TCGA-AB-2997 AML15 6 106364146 106364146 C A SNP - - - - - - - - - - - - - - - tier3 2668 206 7.16 907 785 46.34 NA NA NA 758168 TCGA-AB-2997 AML15 6 113063678 113063678 A T SNP ENSG00000213146 ENST00000392536 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18065 NULL 0.147 - - - no_coding_region:pseudogene tier3 1538 126 7.57 650 558 46.15 NA NA NA 758168 TCGA-AB-2997 AML15 6 134270886 134270886 G A SNP TBPL1 NM_004865.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-72071 NULL 0.106 - - - no_errors tier3 525 43 7.57 230 199 46.39 NA NA NA 758168 TCGA-AB-2997 AML15 6 162058578 162058578 G A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.871+68216 e7+68216 0 - - - no_errors tier3 817 60 6.84 329 305 48.11 NA NA NA 758168 TCGA-AB-2997 AML15 6 162536244 162536244 G A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.534+5909 e4+5909 0 - - - no_errors tier3 650 51 7.28 500 454 47.59 NA NA NA 758168 TCGA-AB-2997 AML15 7 6727252 6727252 A G SNP LOC100134687 XM_001725648.1 human genbank 54_36p -1 model missense c.313 p.W105R 0 NULL NULL - no_start_codon:pseudogene:no_stop_codon tier1 1306 108 7.61 343 241 41.13 NA NA NA 758168 TCGA-AB-2997 AML15 7 53417884 53417884 C T SNP LOC100129159 XM_001716383.1 human genbank 54_36p -1 model intronic c.70-1956 e2-1956 0 - - - no_errors tier3 280 18 6.02 288 248 46.27 NA NA NA 758168 TCGA-AB-2997 AML15 7 56078480 56078480 G C SNP PSPH NM_004577.3 human genbank 54_36p -1 reviewed intronic c.1+7845 e0+7845 0.002 - - - no_errors tier3 1488 107 6.71 445 355 44.38 NA NA NA 758168 TCGA-AB-2997 AML15 7 67591954 67591954 C T SNP - - - - - - - - - - - - - - - tier3 2777 160 5.45 797 668 45.6 NA NA NA 758168 TCGA-AB-2997 AML15 7 70611382 70611382 C T SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.963-62824 e6-62824 0 - - - no_errors tier3 908 92 9.2 495 449 47.56 NA NA NA 758168 TCGA-AB-2997 AML15 7 93194956 93194956 A T SNP - - - - - - - - - - - - - - - tier3 1396 105 7 962 745 43.64 NA NA NA 758168 TCGA-AB-2997 AML15 7 95390896 95390896 T C SNP DYNC1I1 NM_004411.1 human genbank 54_36p 1 validated intronic c.541+53650 e5+53650 0.998 - - - no_errors tier3 523 48 8.41 402 297 42.49 NA NA NA 758168 TCGA-AB-2997 AML15 7 101354947 101354947 T C SNP CUX1 NM_181552.2 human genbank 54_36p 1 reviewed intronic c.141+8722 e2+8722 0.012 - - - no_errors tier3 1262 119 8.61 559 465 45.37 NA NA NA 758168 TCGA-AB-2997 AML15 7 139293998 139293998 G A SNP TBXAS1 NM_001061.3 human genbank 54_36p 1 reviewed intronic c.454-5638 e6-5638 0 - - - no_errors tier3 1677 137 7.54 974 669 40.72 NA NA NA 758168 TCGA-AB-2997 AML15 7 156900510 156900510 C T SNP DNAJB6 NM_058246.2 human genbank 54_36p 1 reviewed intronic c.899-961 e9-961 0 - - - no_errors tier2 305 12 3.79 193 164 45.94 NA NA NA 758168 TCGA-AB-2997 AML15 8 10969176 10969176 C T SNP XKR6 NM_173683.3 human genbank 54_36p -1 provisional intronic c.764+126319 e1+126319 0 - - - no_errors tier3 407 23 5.35 267 220 45.17 NA NA NA 758168 TCGA-AB-2997 AML15 8 21825961 21825961 G A SNP DOK2 NM_003974.2 human genbank 54_36p -1 reviewed missense c.70 p.R24C 0.996 "HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729" "HMMPfam_PH,HMMSmart_PH,HMMPfam_IRS,HMMSmart_PTBI,superfamily_SSF50729" - no_errors tier1 187 21 10.05 51 50 49.02 NA NA NA 758168 TCGA-AB-2997 AML15 8 40348835 40348835 G A SNP - - - - - - - - - - - - - - - tier3 1496 110 6.85 821 726 46.9 NA NA NA 758168 TCGA-AB-2997 AML15 8 40824826 40824826 A C SNP ZMAT4 NM_024645.1 human genbank 54_36p -1 validated intronic c.1-22470 e1-22470 0.009 - - - no_errors tier3 1731 163 8.61 707 543 43.44 NA NA NA 758168 TCGA-AB-2997 AML15 8 52491260 52491260 T C SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.1796-2889 e15-2889 0 - - - no_errors tier3 656 44 6.27 322 315 49.45 NA NA NA 758168 TCGA-AB-2997 AML15 8 52967075 52967075 A G SNP PCMTD1 NM_052937.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-30811 NULL 0.001 - - - no_errors tier3 808 52 6.05 343 290 45.81 NA NA NA 758168 TCGA-AB-2997 AML15 8 54298129 54298129 C T SNP OPRK1 NM_000912.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*6281 NULL 0 - - - no_errors tier3 855 75 8.05 502 417 45.38 NA NA NA 758168 TCGA-AB-2997 AML15 8 62949307 62949307 C T SNP - - - - - - - - - - - - - - - tier3 637 50 7.28 475 339 41.65 NA NA NA 758168 TCGA-AB-2997 AML15 8 68841305 68841305 G A SNP CPA6 NM_020361.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20387 NULL 0.001 - - - no_errors tier3 1481 99 6.26 833 682 45.02 NA NA NA 758168 TCGA-AB-2997 AML15 8 72669371 72669371 C T SNP LOC100132809 XM_001715796.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37561 NULL 0 - - - no_errors tier3 510 51 9.09 347 271 43.85 NA NA NA 758168 TCGA-AB-2997 AML15 8 75296736 75296736 C T SNP JPH1 NM_020647.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*15276 NULL 0.001 - - - no_errors tier3 1317 32 2.37 482 293 37.81 NA NA NA 758168 TCGA-AB-2997 AML15 8 78108824 78108824 G T SNP PXMP3 NM_000318.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49855 NULL 0.106 - - - no_errors tier3 1071 52 4.63 611 488 44.4 NA NA NA 758168 TCGA-AB-2997 AML15 8 86583060 86583060 G A SNP LOC100132709 XM_001716234.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-18907 NULL 0.011 - - - no_errors tier3 1666 121 6.77 1139 827 42.07 NA NA NA 758168 TCGA-AB-2997 AML15 8 87369705 87369705 C A SNP - - - - - - - - - - - - - - - tier3 876 59 6.31 612 404 39.69 NA NA NA 758168 TCGA-AB-2997 AML15 8 106308953 106308953 A G SNP - - - - - - - - - - - - - - - tier3 1312 96 6.82 872 669 43.39 NA NA NA 758168 TCGA-AB-2997 AML15 8 106683844 106683844 G A SNP ZFPM2 NM_012082.3 human genbank 54_36p 1 reviewed intronic c.421-31806 e5-31806 0 - - - no_errors tier3 497 23 4.41 443 303 40.62 NA NA NA 758168 TCGA-AB-2997 AML15 8 113753710 113753710 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.2678-5890 e17-5890 0 - - - no_errors tier3 657 69 9.48 278 202 42 NA NA NA 758168 TCGA-AB-2997 AML15 8 137086395 137086395 G A SNP - - - - - - - - - - - - - - - tier2 2094 156 6.93 1108 956 46.32 NA NA NA 758168 TCGA-AB-2997 AML15 9 7577987 7577987 T C SNP LOC392285 XR_017134.2 human genbank 54_36p 1 model intronic c.NULL NULL 0.001 - - - pseudogene tier3 1363 76 5.28 759 628 45.24 NA NA NA 758168 TCGA-AB-2997 AML15 9 8463921 8463921 C T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.3414-2836 e20-2836 0 - - - no_errors tier3 2271 210 8.46 1150 1092 48.64 NA NA NA 758168 TCGA-AB-2997 AML15 9 11505134 11505134 C T SNP - - - - - - - - - - - - - - - tier3 775 51 6.17 577 437 43.1 NA NA NA 758168 TCGA-AB-2997 AML15 9 16618272 16618272 G A SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated intronic c.331-45189 e4-45189 0.996 - - - no_errors tier2 950 45 4.52 635 498 43.95 NA NA NA 758168 TCGA-AB-2997 AML15 9 35205813 35205813 G A SNP UNC13B NM_006377.3 human genbank 54_36p 1 reviewed intronic c.23-12199 e2-12199 0 - - - no_errors tier2 1036 63 5.73 509 522 50.53 NA NA NA 758168 TCGA-AB-2997 AML15 9 87534973 87534973 A G SNP AGTPBP1 NM_015239.2 human genbank 54_36p -1 validated intronic c.1+11537 e0+11537 0.001 - - - no_errors tier3 890 87 8.9 459 383 45.49 NA NA NA 758168 TCGA-AB-2997 AML15 9 104675905 104675905 C A SNP ENSG00000216733 ENST00000404477 human ensembl 54_36p 1 known 5_prime_flanking_region c.-48816 NULL 0.11 - - - no_coding_region:pseudogene tier3 996 90 8.28 713 498 41.12 NA NA NA 758168 TCGA-AB-2997 AML15 9 116137165 116137165 T C SNP AKNA NM_030767.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1990 NULL 0.001 - - - no_errors tier3 323 28 7.95 207 161 43.75 NA NA NA 758168 TCGA-AB-2997 AML15 9 123698954 123698954 G C SNP TTLL11 ENST00000373777 human ensembl 54_36p -1 known intronic c.705-26106 e6-26106 0.006 - - - no_errors tier2 2414 176 6.79 1106 794 41.61 NA NA NA 758168 TCGA-AB-2997 AML15 10 2824791 2824791 A G SNP - - - - - - - - - - - - - - - tier3 877 57 6.1 534 462 46.25 NA NA NA 758168 TCGA-AB-2997 AML15 10 3797379 3797379 C A SNP KLF6 NM_001300.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*14352 NULL 0.002 - - - no_errors tier2 1515 122 7.45 500 405 44.65 NA NA NA 758168 TCGA-AB-2997 AML15 10 8605762 8605762 C T SNP ENSG00000220584 ENST00000403012 human ensembl 54_36p -1 known 5_prime_flanking_region c.-8687 NULL 0 - - - no_coding_region:pseudogene tier3 1482 74 4.76 669 447 40.05 NA NA NA 758168 TCGA-AB-2997 AML15 10 16181275 16181275 A C SNP ENSG00000220680 ENST00000407829 human ensembl 54_36p -1 known 5_prime_flanking_region c.-27461 NULL 0.001 - - - no_coding_region:pseudogene tier3 459 16 3.37 514 458 47.12 NA NA NA 758168 TCGA-AB-2997 AML15 10 30326889 30326889 G A SNP KIAA1462 NM_020848.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*19929 NULL 0 - - - no_errors tier2 2749 176 6.01 1259 1038 45.13 NA NA NA 758168 TCGA-AB-2997 AML15 10 34059045 34059045 G A SNP - - - - - - - - - - - - - - - tier3 509 51 9.11 275 209 43.18 NA NA NA 758168 TCGA-AB-2997 AML15 10 37500984 37500984 A G SNP ANKRD30A NM_052997.2 human genbank 54_36p 1 validated intronic c.2090-1662 e22-1662 0 - - - no_errors tier3 658 16 2.37 659 116 14.97 NA NA NA 758168 TCGA-AB-2997 AML15 10 44603059 44603059 G C SNP ENSG00000220202 ENST00000407900 human ensembl 54_36p 1 known 5_prime_flanking_region c.-18838 NULL 0.001 - - - no_coding_region:pseudogene tier3 1738 69 3.81 1228 236 16.08 NA NA NA 758168 TCGA-AB-2997 AML15 10 58036972 58036972 C A SNP - - - - - - - - - - - - - - - tier3 590 63 9.65 357 337 48.49 NA NA NA 758168 TCGA-AB-2997 AML15 10 67368173 67368173 A - DEL CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.2401-17792 e17-17792 0.001 - - - no_errors tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 10 71282909 71282909 T A SNP COL13A1 NM_005203.1 human genbank 54_36p 1 reviewed intronic c.365-19029 e3-19029 0.755 - - - no_errors tier3 139 13 8.55 141 96 40.51 NA NA NA 758168 TCGA-AB-2997 AML15 10 82964741 82964741 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 10 83775798 83775798 A G SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.823+149899 e1+149899 0.03 - - - no_errors tier3 722 53 6.84 592 368 38.29 NA NA NA 758168 TCGA-AB-2997 AML15 10 88479977 88479977 A G SNP LDB3 NM_007078.1 human genbank 54_36p 1 reviewed intronic c.2095-2647 e13-2647 0 - - - no_errors tier3 816 68 7.68 281 271 49.09 NA NA NA 758168 TCGA-AB-2997 AML15 10 91676896 91676896 G A SNP - - - - - - - - - - - - - - - tier2 620 44 6.62 495 431 46.54 NA NA NA 758168 TCGA-AB-2997 AML15 10 101883080 101883080 A C SNP ENSG00000217969 ENST00000379159 human ensembl 54_36p -1 known 5_prime_flanking_region c.-18110 NULL 0 - - - no_coding_region:pseudogene tier3 703 30 4.09 352 262 42.6 NA NA NA 758168 TCGA-AB-2997 AML15 10 107559315 107559315 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 10 122985405 122985405 C G SNP LOC100129699 XM_001718711.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*47606 NULL 0 - - - no_errors tier3 2010 111 5.22 1067 765 41.67 NA NA NA 758168 TCGA-AB-2997 AML15 10 132611796 132611796 G A SNP - - - - - - - - - - - - - - - tier3 1276 121 8.66 536 410 43.29 NA NA NA 758168 TCGA-AB-2997 AML15 10 133034167 133034167 G A SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-34279 NULL 0.009 - - - no_errors tier3 926 54 5.5 632 437 40.88 NA NA NA 758168 TCGA-AB-2997 AML15 11 1229284 1229284 C T SNP MUC5B NM_002458.1 human genbank 54_36p 1 validated silent c.14607 p.T4869 0 NULL "HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_VWD,HMMSmart_SM00216,superfamily_Serine proterase inhibitors,HMMSmart_SM00041,PatternScan_CTCK_1,HMMPfam_Cys_knot,HMMSmart_SM00215,superfamily_PMP inhibitors,HMMPfam_C8,HMMPfam_TIL" - no_errors tier1 45 10 18.18 6 54 90 NA NA NA 758168 TCGA-AB-2997 AML15 11 27062649 27062649 C T SNP BBOX1 NM_003986.2 human genbank 54_36p 1 reviewed intronic c.335-8642 e3-8642 0 - - - no_errors tier3 1684 208 10.98 149 1215 89.01 NA NA NA 758168 TCGA-AB-2997 AML15 11 29918482 29918482 A T SNP - - - - - - - - - - - - - - - tier3 547 68 11.06 77 507 86.82 NA NA NA 758168 TCGA-AB-2997 AML15 11 40213930 40213930 G A SNP LRRC4C NM_020929.1 human genbank 54_36p -1 validated intronic c.1+56389 e0+56389 0 - - - no_errors tier3 771 124 13.84 125 1045 89.32 NA NA NA 758168 TCGA-AB-2997 AML15 11 99450197 99450197 C T SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed missense c.1541 p.S514F 0.995 "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,superfamily_Immunoglobulin" - no_errors tier1 391 26 6.24 414 344 45.38 NA NA NA 758168 TCGA-AB-2997 AML15 11 103263588 103263588 G T SNP PDGFD NM_025208.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*22044 NULL 0 - - - no_errors tier3 867 45 4.93 569 401 41.26 NA NA NA 758168 TCGA-AB-2997 AML15 11 117810868 117810868 G A SNP MLL NM_005933.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-1570 NULL 1 - - - no_errors tier2 1397 85 5.73 237 228 49.03 NA NA NA 758168 TCGA-AB-2997 AML15 11 130208081 130208081 G T SNP SNX19 NM_014758.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*45446 NULL 0.001 - - - no_errors tier3 542 28 4.91 332 239 41.86 NA NA NA 758168 TCGA-AB-2997 AML15 12 23485260 23485260 C T SNP - - - - - - - - - - - - - - - tier2 2176 134 5.8 856 662 43.58 NA NA NA 758168 TCGA-AB-2997 AML15 12 67574421 67574421 C T SNP CPM NM_001005502.2 human genbank 54_36p -1 reviewed intronic c.161-8485 e2-8485 0.002 - - - no_errors tier3 1529 113 6.88 776 555 41.64 NA NA NA 758168 TCGA-AB-2997 AML15 12 72713799 72713799 G A SNP - - - - - - - - - - - - - - - tier3 639 53 7.66 385 335 46.53 NA NA NA 758168 TCGA-AB-2997 AML15 12 77851066 77851066 C T SNP SYT1 ENST00000261205 human ensembl 54_36p 1 known intronic c.1-44644 e1-44644 0.009 - - - no_errors tier3 476 43 8.27 372 311 45.53 NA NA NA 758168 TCGA-AB-2997 AML15 12 105079083 105079083 T G SNP NUAK1 NM_014840.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22522 NULL 0.001 - - - no_errors tier3 1272 112 8.09 521 466 47.21 NA NA NA 758168 TCGA-AB-2997 AML15 13 18194366 18194366 C G SNP LOC100132598 XM_001714168.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-11524 NULL 0 - - - no_errors tier3 536 32 5.63 264 211 44.33 NA NA NA 758168 TCGA-AB-2997 AML15 13 18910252 18910252 C T SNP TPTE2 NM_199254.1 human genbank 54_36p -1 validated missense c.1015 p.E339K 0.271 superfamily_(Phosphotyrosine protein) phosphatases II "superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_PTEN_C2,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_Voltage-gated potassium channels" - no_errors tier1 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 13 24234864 24234864 C T SNP LOC100133947 XM_001715259.1 human genbank 54_36p 1 model intronic c.195-6490 e4-6490 0.016 - - - no_start_codon:pseudogene:no_stop_codon tier2 2198 63 2.78 522 425 44.78 NA NA NA 758168 TCGA-AB-2997 AML15 13 32762787 32762787 C G SNP STARD13 NM_178006.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5012 NULL 0 - - - no_errors tier3 1764 82 4.44 930 740 44.28 NA NA NA 758168 TCGA-AB-2997 AML15 13 34044835 34044835 G T SNP ENSG00000220002 ENST00000407757 human ensembl 54_36p -1 known 3_prime_flanking_region c.*1506 NULL 0 - - - no_coding_region:pseudogene tier3 791 55 6.49 456 401 46.74 NA NA NA 758168 TCGA-AB-2997 AML15 13 65766919 65766919 G T SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*9869 NULL 0 - - - no_errors tier3 1017 73 6.68 566 464 45.05 NA NA NA 758168 TCGA-AB-2997 AML15 13 71336488 71336488 G A SNP DACH1 NM_080759.4 human genbank 54_36p -1 reviewed intronic c.854+1567 e1+1567 0 - - - no_errors tier3 707 72 9.23 179 177 49.72 NA NA NA 758168 TCGA-AB-2997 AML15 13 72244339 72244339 C T SNP DIS3 NM_014953.1 human genbank 54_36p -1 validated missense c.1462 p.D488N 1 HMMPfam_RNB "HMMPfam_RNB,PatternScan_RIBONUCLEASE_II,HMMSmart_SM00670,superfamily_PIN domain-like" - no_errors tier1 714 34 4.55 519 414 44.37 NA NA NA 758168 TCGA-AB-2997 AML15 13 89938365 89938365 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 13 92080314 92080314 A C SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1562-236222 e8-236222 0 - - - no_errors tier3 579 33 5.39 450 308 40.58 NA NA NA 758168 TCGA-AB-2997 AML15 13 94678458 94678458 C T SNP ABCC4 NM_005845.1 human genbank 54_36p -1 reviewed intronic c.531+6407 e4+6407 0 - - - no_errors tier2 742 55 6.89 660 441 40.02 NA NA NA 758168 TCGA-AB-2997 AML15 13 102456951 102456951 G A SNP SLC10A2 NM_000452.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*39533 NULL 0.009 - - - no_errors tier3 1381 95 6.44 715 578 44.67 NA NA NA 758168 TCGA-AB-2997 AML15 14 39653662 39653662 T A SNP - - - - - - - - - - - - - - - tier3 910 50 5.2 550 400 42.11 NA NA NA 758168 TCGA-AB-2997 AML15 14 49588483 49588483 G A SNP C14orf182 NM_001012706.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-46216 NULL 0.069 - - - no_errors tier3 568 60 9.55 274 230 45.63 NA NA NA 758168 TCGA-AB-2997 AML15 14 77942449 77942449 C T SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.1+2475 e0+2475 0.001 - - - no_errors tier3 821 64 7.2 528 435 45.12 NA NA NA 758168 TCGA-AB-2997 AML15 14 82072551 82072551 C T SNP - - - - - - - - - - - - - - - tier2 1078 98 8.33 844 802 48.69 NA NA NA 758168 TCGA-AB-2997 AML15 14 95069562 95069562 C T SNP SNHG10 NR_003138.2 human genbank 54_36p -1 validated rna NULL NULL 1 - - - no_errors tier1 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 15 33923658 33923658 C G SNP - - - - - - - - - - - - - - - tier3 1113 68 5.75 605 450 42.65 NA NA NA 758168 TCGA-AB-2997 AML15 15 51192438 51192438 G A SNP - - - - - - - - - - - - - - - tier3 1242 74 5.62 973 672 40.85 NA NA NA 758168 TCGA-AB-2997 AML15 15 84063349 84063355 AAGATCA - DEL AKAP13 NM_006738.4 human genbank 54_36p 1 reviewed frame_shift_del c.6052_6058 p.K2018fs 1.000:1.000:1.000:1.000:1.000:1.000:1.000 "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain" "HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMPfam_PH,HMMSmart_PH,superfamily_ANK,HMMPfam_C1_1,HMMSmart_C1,PatternScan_ZF_DAG_PE_1,PatternScan_EF_HAND_1,HMMPfam_RII_binding_1,superfamily_SSF50729,superfamily_SSF57889" - no_errors tier1 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 15 91530325 91530325 T C SNP UNQ9370 XR_041834.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-20102 NULL 0.214 - - - no_errors tier3 1816 137 7.01 668 666 49.93 NA NA NA 758168 TCGA-AB-2997 AML15 15 96588459 96588459 G A SNP - - - - - - - - - - - - - - - tier3 1350 104 7.15 767 527 40.73 NA NA NA 758168 TCGA-AB-2997 AML15 16 6728056 6728056 T C SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+83404 e0+83404 0 - - - no_errors tier3 1100 81 6.86 584 464 44.19 NA NA NA 758168 TCGA-AB-2997 AML15 16 46232164 46232164 G C SNP PHKB NM_000293.2 human genbank 54_36p 1 validated intronic c.1459-283 e15-283 0.587 - - - no_errors tier3 1050 80 7.08 845 654 43.6 NA NA NA 758168 TCGA-AB-2997 AML15 16 46589196 46589196 C T SNP - - - - - - - - - - - - - - - tier3 1331 132 9.02 705 555 44.05 NA NA NA 758168 TCGA-AB-2997 AML15 16 47618839 47618839 T - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 16 61371424 61371424 A T SNP ENSG00000223123 ENST00000411191 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*45942 NULL 0 - - - no_errors tier3 316 21 6.21 228 181 44.15 NA NA NA 758168 TCGA-AB-2997 AML15 16 61970462 61970462 T G SNP LOC390735 XM_001129659.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-27908 NULL 0.068 - - - pseudogene tier3 720 46 6.01 585 448 43.16 NA NA NA 758168 TCGA-AB-2997 AML15 17 11513530 11513530 T G SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed missense c.3047 p.L1016R 1 NULL "HMMSmart_SM00382,HMMPfam_Dynein_heavy,PatternScan_CPSASE_2,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 1085 70 6.06 765 675 46.81 NA NA NA 758168 TCGA-AB-2997 AML15 17 21927249 21927249 C T SNP ENSG00000222865 ENST00000410933 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18216 NULL 0 - - - no_errors tier3 690 38 5.21 486 429 46.83 NA NA NA 758168 TCGA-AB-2997 AML15 17 22978938 22978938 G A SNP LGALS9 NM_009587.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3481 NULL 0.003 - - - no_errors tier3 641 70 9.85 451 330 42.15 NA NA NA 758168 TCGA-AB-2997 AML15 17 46647529 46647529 G A SNP MBTD1 NM_017643.2 human genbank 54_36p -1 validated intronic c.1+2165 e0+2165 0.008 - - - no_errors tier2 808 50 5.83 493 466 48.49 NA NA NA 758168 TCGA-AB-2997 AML15 18 3064471 3064471 T C SNP MYOM1 NM_003803.3 human genbank 54_36p -1 reviewed intronic c.4708+981 e35+981 0.023 - - - no_errors tier3 951 66 6.49 494 400 44.69 NA NA NA 758168 TCGA-AB-2997 AML15 18 8840453 8840453 G A SNP KIAA0802 NM_015210.3 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*21509 NULL 0 - - - no_errors tier3 905 68 6.99 430 411 48.87 NA NA NA 758168 TCGA-AB-2997 AML15 18 13532518 13532518 G T SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.182-78598 e3-78598 0 - - - no_errors tier3 489 32 6.13 445 321 41.91 NA NA NA 758168 TCGA-AB-2997 AML15 18 61800412 61800412 A G SNP - - - - - - - - - - - - - - - tier3 741 40 5.12 493 397 44.61 NA NA NA 758168 TCGA-AB-2997 AML15 18 63477988 63477988 T A SNP - - - - - - - - - - - - - - - tier3 1076 54 4.78 809 581 41.74 NA NA NA 758168 TCGA-AB-2997 AML15 18 73920029 73920029 C A SNP ENSG00000199728 ENST00000362858 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22196 NULL 0.151 - - - no_errors tier3 2384 186 7.24 1128 1134 50.11 NA NA NA 758168 TCGA-AB-2997 AML15 18 74365674 74365674 C G SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model missense c.975 p.S325R 0.005 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 19 5248118 5248118 G A SNP PTPRS NM_002850.3 human genbank 54_36p -1 reviewed intronic c.1-10873 e1-10873 0.011 - - - no_errors tier3 1047 89 7.83 248 190 43.28 NA NA NA 758168 TCGA-AB-2997 AML15 19 39057748 39057748 G A SNP - - - - - - - - - - - - - - - tier2 483 35 6.76 153 112 42.26 NA NA NA 758168 TCGA-AB-2997 AML15 19 39761080 39761080 C T SNP ZNF807 XM_001718828.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-0 NULL 0.003 - - - rna_with_coding_region tier3 725 92 11.18 414 294 41.29 NA NA NA 758168 TCGA-AB-2997 AML15 19 48131669 48131669 G T SNP PSG7 NM_002783.2 human genbank 54_36p -1 reviewed missense c.157 p.L53I 0.003 "HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin" "HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_V-set,HMMPfam_ig,superfamily_Immunoglobulin" - pseudogene tier1 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 20 41777325 41777325 G A SNP MYBL2 NM_002466.2 human genbank 54_36p 1 reviewed silent c.1962 p.T654 0 NULL "HMMSmart_SM00717,superfamily_Homeodomain-like,HMMPfam_Myb_DNA-binding,HMMPfam_Cmyb_C" - no_errors tier1 NA NA NA NA NA NA NA NA NA 758168 TCGA-AB-2997 AML15 20 56078527 56078527 C A SNP ENSG00000221385 ENST00000408458 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*2458 NULL 0.002 - - - no_errors tier3 1264 93 6.85 761 495 39.35 NA NA NA 758168 TCGA-AB-2997 AML15 20 56640598 56640598 G A SNP STX16 NM_001001433.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19871 NULL 0 - - - no_errors tier2 471 41 8.01 228 240 51.28 NA NA NA 758168 TCGA-AB-2997 AML15 21 21618540 21618540 G A SNP NCAM2 NM_004540.2 human genbank 54_36p 1 reviewed intronic c.620-34 e6-34 0 - - - no_errors tier3 630 41 6.11 487 365 42.84 NA NA NA 758168 TCGA-AB-2997 AML15 21 21760990 21760990 G T SNP NCAM2 NM_004540.2 human genbank 54_36p 1 reviewed intronic c.1774+73 e13+73 0.002 - - - no_errors tier3 318 19 5.64 262 202 43.53 NA NA NA 758168 TCGA-AB-2997 AML15 21 38710638 38710638 C A SNP ERG NM_182918.1 human genbank 54_36p -1 validated intronic c.388+6564 e3+6564 0.001 - - - no_errors tier3 1260 168 11.76 529 438 45.29 NA NA NA 758168 TCGA-AB-2997 AML15 22 24241650 24241650 T C SNP ADRBK2 NM_005160.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49358 NULL 0.46 - - - no_errors tier3 565 58 9.28 255 205 44.57 NA NA NA 758168 TCGA-AB-2997 AML15 22 45144326 45144326 G T SNP CELSR1 NM_014246.1 human genbank 54_36p -1 reviewed missense c.7799 p.P2600H 0.998 HMMPfam_7tm_2 "PatternScan_ASX_HYDROXYL,HMMPfam_GPS,HMMSmart_SM00303,HMMPfam_7tm_2,HMMSmart_SM00282,HMMPfam_HRM,HMMSmart_SM00008,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Cadherin-like,superfamily_EGF/Laminin" - no_errors tier1 84 7 7.69 104 84 44.68 NA NA NA 202127 TCGA-AB-2998 AML48 X 4066820 4066820 G T SNP - - - - - - - - - - - - - - - tier3 1635 9 0.55 811 672 45.31 0 0 NA 202127 TCGA-AB-2998 AML48 X 4438490 4438490 G T SNP - - - - - - - - - - - - - - - tier3 286 7 2.38 213 138 39.32 0 0 NA 202127 TCGA-AB-2998 AML48 X 5888633 5888633 A G SNP NLGN4X NM_020742.2 human genbank 54_36p -1 reviewed intronic c.626-51353 e3-51353 0.009 - - - no_errors tier3 587 3 0.51 368 334 47.58 0 0 NA 202127 TCGA-AB-2998 AML48 X 8425058 8425058 C T SNP KAL1 NM_000216.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*35978 NULL 0.008 - - - no_errors tier3 817 7 0.85 479 429 47.14 0 0 NA 202127 TCGA-AB-2998 AML48 X 14232403 14232403 G A SNP - - - - - - - - - - - - - - - tier3 641 13 1.98 500 439 46.75 0 0 NA 202127 TCGA-AB-2998 AML48 X 16802288 16802288 C T SNP RBBP7 NM_002893.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4191 NULL 0.02 - - - no_errors tier3 562 0 0 406 253 38.39 0 0 NA 202127 TCGA-AB-2998 AML48 X 16932603 16932603 T A SNP REPS2 NM_004726.1 human genbank 54_36p 1 reviewed intronic c.274-1662 e2-1662 0.002 - - - no_errors tier2 2034 10 0.49 1395 1181 45.78 0 0 0 202127 TCGA-AB-2998 AML48 X 32042252 32042252 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6438+102702 e44+102702 0 - - - no_errors tier3 1588 14 0.87 898 843 48.39 0 0 NA 202127 TCGA-AB-2998 AML48 X 32312924 32312924 G T SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.4674+1424 e33+1424 0 - - - no_errors tier3 487 4 0.81 308 187 37.78 0 0 NA 202127 TCGA-AB-2998 AML48 X 33173221 33173221 G A SNP DMD NM_000109.2 human genbank 54_36p -1 reviewed intronic c.7+94076 e1+94076 0 - - - no_errors tier3 549 2 0.36 307 230 42.83 0 0 NA 202127 TCGA-AB-2998 AML48 X 35249805 35249805 A T SNP - - - - - - - - - - - - - - - tier3 1185 9 0.75 686 606 46.83 0 0 NA 202127 TCGA-AB-2998 AML48 X 41218979 41218979 C T SNP NYX NM_022567.2 human genbank 54_36p 1 reviewed silent c.1329 p.S443 0 NULL "HMMPfam_LRRNT,HMMSmart_LRRNT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058" - no_errors tier1 134 2 1.46 103 95 47.74 NA 202127 TCGA-AB-2998 AML48 X 43267025 43267025 C T SNP - - - - - - - - - - - - - - - tier3 1039 10 0.95 656 565 46.27 0 0 NA 202127 TCGA-AB-2998 AML48 X 43323910 43323910 T C SNP - - - - - - - - - - - - - - - tier2 1545 20 1.28 898 674 42.82 0 0 NA 202127 TCGA-AB-2998 AML48 X 45183761 45183761 G A SNP - - - - - - - - - - - - - - - tier2 939 9 0.95 693 588 45.83 0 0 NA 202127 TCGA-AB-2998 AML48 X 64113227 64113227 T C SNP ZC4H2 ENST00000337990 human ensembl 54_36p -1 known intronic c.1-54379 e1-54379 0.849 - - - no_errors tier3 1211 11 0.9 586 547 48.28 0 0 NA 202127 TCGA-AB-2998 AML48 X 66242340 66242341 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 X 68227908 68227908 T C SNP - - - - - - - - - - - - - - - tier3 647 14 2.12 456 471 50.81 0 0 NA 202127 TCGA-AB-2998 AML48 X 78508296 78508296 C T SNP ITM2A NM_004867.3 human genbank 54_36p -1 validated intronic c.111+962 e1+962 0 - - - no_errors tier3 836 7 0.83 606 399 39.66 4 0 0 202127 TCGA-AB-2998 AML48 X 81671266 81671266 A T SNP ENSG00000202183 ENST00000365313 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32040 NULL 0 - - - no_errors tier3 2295 17 0.73 1280 949 42.52 0 0 NA 202127 TCGA-AB-2998 AML48 X 105304047 105304047 C T SNP MUM1L1 ENST00000357175 human ensembl 54_36p 1 known intronic c.1+2259 e0+2259 0.006 - - - no_errors tier3 637 8 1.24 437 406 48.16 0 0 NA 202127 TCGA-AB-2998 AML48 X 107439613 107439613 A T SNP COL4A6 NM_001847.2 human genbank 54_36p -1 reviewed intronic c.147+1021 e3+1021 0.052 - - - no_errors tier3 2386 20 0.83 1409 1229 46.57 0 0 NA 202127 TCGA-AB-2998 AML48 X 116788925 116788925 T C SNP - - - - - - - - - - - - - - - tier2 1075 12 1.1 800 698 46.6 0 0 NA 202127 TCGA-AB-2998 AML48 X 118051705 118051705 C G SNP LOC727838 XM_001125955.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-39512 NULL 0.001 - - - no_errors tier3 1696 6 0.35 1190 842 41.4 0 0 NA 202127 TCGA-AB-2998 AML48 X 118075508 118075508 A G SNP LOC727838 XM_001125955.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-15709 NULL 0.437 - - - no_errors tier3 898 8 0.88 507 533 51.25 0 0 NA 202127 TCGA-AB-2998 AML48 X 132929243 132929243 C T SNP GPC3 NM_004484.2 human genbank 54_36p -1 reviewed intronic c.176-14339 e2-14339 0.071 - - - no_errors tier3 1048 8 0.76 556 482 46.39 0 0 NA 202127 TCGA-AB-2998 AML48 X 132954248 132954248 G A SNP GPC3 NM_004484.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7106 NULL 0 - - - no_errors tier3 841 12 1.41 496 481 49.23 0 0 NA 202127 TCGA-AB-2998 AML48 X 136503107 136503107 G A SNP ENSG00000223314 ENST00000411382 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1983 NULL 0.761 - - - no_errors tier3 631 6 0.94 418 289 40.88 0 0 NA 202127 TCGA-AB-2998 AML48 X 140990139 140990139 G A SNP - - - - - - - - - - - - - - - tier3 951 7 0.73 685 377 35.5 0 0 NA 202127 TCGA-AB-2998 AML48 X 140990140 140990140 A T SNP - - - - - - - - - - - - - - - tier3 948 5 0.52 687 374 35.25 0 0 NA 202127 TCGA-AB-2998 AML48 X 144603806 144603806 C T SNP - - - - - - - - - - - - - - - tier3 689 5 0.72 506 397 43.96 0 0 NA 202127 TCGA-AB-2998 AML48 X 145566070 145566070 G A SNP - - - - - - - - - - - - - - - tier3 1945 16 0.82 1346 1128 45.48 0 0 NA 202127 TCGA-AB-2998 AML48 X 146879900 146879900 G T SNP FMR1NB NM_152578.1 human genbank 54_36p 1 provisional intronic c.277+9009 e1+9009 0.313 - - - no_errors tier3 563 5 0.88 509 409 44.55 0 0 NA 202127 TCGA-AB-2998 AML48 1 4910660 4910660 T - DEL LOC100133958 XM_001722033.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-43871 NULL 0.004 - - - no_start_codon:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 1 10765761 10765761 C T SNP CASZ1 NM_001079843.1 human genbank 54_36p -1 validated intronic c.1+13447 e0+13447 0.936 - - - no_errors tier2 772 5 0.64 490 445 47.54 0 0 NA 202127 TCGA-AB-2998 AML48 1 30382559 30382559 C T SNP - - - - - - - - - - - - - - - tier3 1084 7 0.64 711 565 44.24 0 0 NA 202127 TCGA-AB-2998 AML48 1 33875730 33875730 T C SNP CSMD2 NM_052896.3 human genbank 54_36p -1 validated intronic c.4655-989 e30-989 0.012 - - - no_errors tier3 1144 14 1.21 645 595 47.98 0 0 NA 202127 TCGA-AB-2998 AML48 1 34843895 34843895 G A SNP - - - - - - - - - - - - - - - tier3 1204 3 0.25 660 508 43.46 0 0 NA 202127 TCGA-AB-2998 AML48 1 43185447 43185447 T A SNP SLC2A1 NM_006516.2 human genbank 54_36p -1 reviewed intronic c.19-3868 e2-3868 0.001 - - - no_errors tier3 391 2 0.51 295 206 41.12 4 2 33.33 202127 TCGA-AB-2998 AML48 1 44254276 44254276 C T SNP SLC6A9 NM_201649.1 human genbank 54_36p -1 validated intronic c.87+1030 e1+1030 0.002 - - - no_errors tier3 304 0 0 295 229 43.62 1 0 0 202127 TCGA-AB-2998 AML48 1 44693868 44693868 T G SNP RNF220 NM_018150.2 human genbank 54_36p 1 validated intronic c.625+42887 e1+42887 0.024 - - - no_errors tier3 882 5 0.56 632 470 42.61 15 11 42.31 202127 TCGA-AB-2998 AML48 1 52387560 52387560 C T SNP ZFYVE9 NM_004799.2 human genbank 54_36p 1 reviewed intronic c.1+6897 e0+6897 0.042 - - - no_errors tier3 453 4 0.88 348 288 45.28 0 0 0 202127 TCGA-AB-2998 AML48 1 56092931 56092931 G A SNP - - - - - - - - - - - - - - - tier3 655 6 0.91 377 442 53.9 0 0 NA 202127 TCGA-AB-2998 AML48 1 59505949 59505949 A G SNP FGGY NM_018291.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-78581 NULL 0 - - - no_errors tier3 2117 14 0.66 1418 1191 45.61 0 0 NA 202127 TCGA-AB-2998 AML48 1 65045473 65045473 A G SNP RAVER2 NM_018211.3 human genbank 54_36p 1 validated splice_region c.1373-4 e9-4 0.121 - - - no_errors tier3 832 8 0.95 463 391 45.78 7 1 12.5 202127 TCGA-AB-2998 AML48 1 65896535 65896535 G A SNP LEPR NM_002303.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*21249 NULL 0.007 - - - no_errors tier3 1084 9 0.82 802 670 45.52 0 0 NA 202127 TCGA-AB-2998 AML48 1 66156038 66156039 - A INS PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.43-830_43-829 e2-829 0.002:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 1 66232726 66232726 T G SNP PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.281+75620 e2+75620 0.02 - - - no_errors tier3 970 10 1.02 607 494 44.83 0 0 NA 202127 TCGA-AB-2998 AML48 1 83262793 83262793 C T SNP - - - - - - - - - - - - - - - tier3 725 4 0.55 372 299 44.49 0 0 NA 202127 TCGA-AB-2998 AML48 1 88442374 88442374 T C SNP - - - - - - - - - - - - - - - tier3 1274 12 0.93 839 729 46.49 0 0 NA 202127 TCGA-AB-2998 AML48 1 106382201 106382201 A - DEL LOC126987 XR_016153.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*42556 NULL 0.017 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 1 106780802 106780802 A T SNP - - - - - - - - - - - - - - - tier3 968 12 1.22 504 591 53.97 0 0 NA 202127 TCGA-AB-2998 AML48 1 107395609 107395610 - A INS PRMT6 NM_018137.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-5429 NULL 0.005:0.011 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 1 119436168 119436168 T C SNP WARS2 NM_015836.3 human genbank 54_36p -1 reviewed intronic c.91-15415 e2-15415 0.99 - - - no_errors tier3 1409 17 1.19 1023 811 44.17 0 0 NA 202127 TCGA-AB-2998 AML48 1 145385701 145385701 C - DEL ENSG00000207209 ENST00000384480 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27050 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 1 150548358 150548358 G A SNP FLG NM_002016.1 human genbank 54_36p -1 provisional silent c.5628 p.D1876 0 HMMPfam_Filaggrin "PatternScan_S100_CABP,HMMPfam_Filaggrin,HMMPfam_S_100,PatternScan_EF_HAND_1,superfamily_SSF47473" - no_errors tier1 360 1 0.28 288 252 46.58 NA 202127 TCGA-AB-2998 AML48 1 151383673 151383673 G A SNP SPRR2G ENST00000290702 human ensembl 54_36p -1 known intronic c.43-3903 e2-3903 0 - - - no_errors tier3 1359 3 0.22 872 805 47.97 0 0 NA 202127 TCGA-AB-2998 AML48 1 156845018 156845018 G A SNP OR10X1 NM_001004477.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-28705 NULL 0 - - - no_errors tier2 970 7 0.72 723 619 46.02 0 0 NA 202127 TCGA-AB-2998 AML48 1 168915049 168915049 G C SNP PRRX1 NM_022716.3 human genbank 54_36p 1 reviewed intronic c.241+14825 e1+14825 0.001 - - - no_errors tier2 1057 4 0.38 659 604 47.82 0 0 NA 202127 TCGA-AB-2998 AML48 1 169221924 169221924 C A SNP C1orf129 NM_025063.2 human genbank 54_36p 1 validated intronic c.730-402 e9-402 0.006 - - - no_errors tier3 1094 10 0.91 1067 467 30.44 0 0 NA 202127 TCGA-AB-2998 AML48 1 169493748 169493748 C T SNP FMO1 ENST00000354841 human ensembl 54_36p 1 known 5_prime_untranslated_region c.-103 NULL 0.145 - - - no_errors tier3 726 5 0.68 565 422 42.71 0 0 NA 202127 TCGA-AB-2998 AML48 1 176213242 176213242 C T SNP SEC16B ENST00000354921 human ensembl 54_36p -1 known intronic c.1-4175 e1-4175 0.008 - - - no_errors tier2 923 3 0.32 598 535 47.22 0 0 0 202127 TCGA-AB-2998 AML48 1 179152977 179152977 C G SNP KIAA1614 NM_020950.1 human genbank 54_36p 1 validated intronic c.997+118 e2+118 0.002 - - - no_errors tier3 330 1 0.3 332 226 40.5 0 0 NA 202127 TCGA-AB-2998 AML48 1 180155455 180155455 G A SNP - - - - - - - - - - - - - - - tier3 1842 12 0.65 1116 961 46.27 0 0 NA 202127 TCGA-AB-2998 AML48 1 180965744 180965744 G A SNP - - - - - - - - - - - - - - - tier3 1006 7 0.69 536 501 48.31 0 0 NA 202127 TCGA-AB-2998 AML48 1 182429166 182429166 A G SNP ENSG00000199840 ENST00000362970 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-21586 NULL 0 - - - no_errors tier3 1350 16 1.17 865 712 45.12 0 0 NA 202127 TCGA-AB-2998 AML48 1 186857145 186857145 G T SNP ENSG00000217509 ENST00000404186 human ensembl 54_36p 1 known 5_prime_flanking_region c.-49962 NULL 0.002 - - - no_coding_region:pseudogene tier3 508 2 0.39 426 283 39.92 0 0 NA 202127 TCGA-AB-2998 AML48 1 188333917 188333917 G A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional missense c.2155 p.R719C 1 NULL "HMMPfam_MACPF,HMMSmart_SM00457" - no_errors tier1 1122 4 0.36 692 633 47.7 NA 202127 TCGA-AB-2998 AML48 1 190991014 190991014 T A SNP ENSG00000220372 ENST00000403417 human ensembl 54_36p 1 known 5_prime_flanking_region c.-41272 NULL 0.176 - - - no_coding_region:pseudogene tier3 742 10 1.33 520 417 44.5 0 0 NA 202127 TCGA-AB-2998 AML48 1 192725004 192725004 A C SNP ENSG00000208230 ENST00000385495 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1046 NULL 0.999 - - - pseudogene tier2 745 2 0.27 454 366 44.58 0 0 NA 202127 TCGA-AB-2998 AML48 1 199336470 199336470 G C SNP CACNA1S NM_000069.2 human genbank 54_36p -1 reviewed intronic c.259-6698 e3-6698 0.004 - - - no_errors tier2 526 5 0.94 419 306 42.21 0 0 NA 202127 TCGA-AB-2998 AML48 1 202326801 202326801 C T SNP SOX13 NM_005686.2 human genbank 54_36p 1 reviewed intronic c.1+17339 e0+17339 0.029 - - - no_errors tier3 1263 6 0.47 866 633 42.14 0 0 NA 202127 TCGA-AB-2998 AML48 1 205455534 205455534 A G SNP LOC100129101 XM_001716664.1 human genbank 54_36p -1 model intronic c.346-80786 e2-80786 0.001 - - - no_errors tier3 1297 10 0.76 928 758 44.96 0 0 NA 202127 TCGA-AB-2998 AML48 1 208184983 208184983 A T SNP SYT14 NM_153262.2 human genbank 54_36p 1 validated intronic c.13+6738 e1+6738 0 - - - no_errors tier3 746 4 0.53 443 351 44.1 0 0 NA 202127 TCGA-AB-2998 AML48 1 208972262 208972262 A G SNP KCNH1 NM_172362.3 human genbank 54_36p -1 reviewed intronic c.2112+43051 e10+43051 0 - - - no_errors tier3 1268 8 0.63 684 622 47.63 0 0 NA 202127 TCGA-AB-2998 AML48 1 217127280 217127280 T C SNP ENSG00000218763 ENST00000407979 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4665 NULL 0.011 - - - no_coding_region:pseudogene tier3 558 7 1.24 349 299 46.07 0 0 NA 202127 TCGA-AB-2998 AML48 1 223662190 223662190 T C SNP LBR NM_002296.2 human genbank 54_36p -1 reviewed intronic c.1315-1033 e10-1033 0.001 - - - no_errors tier3 947 8 0.84 643 624 49.25 7 12 63.16 202127 TCGA-AB-2998 AML48 1 237967852 237967852 G A SNP CHRM3 NM_000740.2 human genbank 54_36p 1 reviewed intronic c.1+59641 e0+59641 0 - - - no_errors tier3 984 4 0.4 731 516 41.38 0 0 NA 202127 TCGA-AB-2998 AML48 1 246367565 246367565 C - DEL OR2M2 NM_001004688.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-42346 NULL 1 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 2 2327413 2327413 T C SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-364857 NULL 0 - - - no_errors tier3 1237 4 0.32 808 717 46.99 0 0 NA 202127 TCGA-AB-2998 AML48 2 2711951 2711951 G A SNP - - - - - - - - - - - - - - - tier3 205 1 0.49 136 158 53.56 0 0 NA 202127 TCGA-AB-2998 AML48 2 4661457 4661457 T G SNP LOC727982 XR_039999.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.002 - - - no_errors tier2 955 2 0.21 594 444 42.77 0 0 NA 202127 TCGA-AB-2998 AML48 2 9333124 9333124 G A SNP ASAP2 NM_003887.1 human genbank 54_36p 1 reviewed intronic c.127-3773 e2-3773 0 - - - no_errors tier3 748 9 1.19 406 387 48.62 0 0 0 202127 TCGA-AB-2998 AML48 2 14164322 14164322 G A SNP - - - - - - - - - - - - - - - tier3 459 1 0.22 276 230 45.45 0 0 NA 202127 TCGA-AB-2998 AML48 2 14748600 14748601 - A INS LOC653602 XR_041665.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*40206 NULL 0.077:0.078 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 2 17794891 17794891 A T SNP SMC6 NM_024624.1 human genbank 54_36p -1 validated intronic c.1+3483 e0+3483 0.037 - - - no_errors tier3 719 5 0.69 533 447 45.61 4 6 60 202127 TCGA-AB-2998 AML48 2 23315322 23315322 C T SNP - - - - - - - - - - - - - - - tier2 1237 10 0.8 785 637 44.8 0 0 NA 202127 TCGA-AB-2998 AML48 2 25316840 25316840 G C SNP DNMT3A NM_022552.3 human genbank 54_36p -1 reviewed intronic c.2174-17 e18-17 0.398 - - - no_errors tier3 547 2 0.36 453 456 50.11 2 2 50 202127 TCGA-AB-2998 AML48 2 29781312 29781312 A T SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.788-9928 e3-9928 0.138 - - - no_errors tier3 497 8 1.58 364 333 47.78 0 0 NA 202127 TCGA-AB-2998 AML48 2 42349401 42349401 A G SNP EML4 NM_019063.1 human genbank 54_36p 1 validated intronic c.667+4026 e6+4026 0 - - - no_errors tier3 566 6 1.05 371 350 48.54 0 0 0 202127 TCGA-AB-2998 AML48 2 63458953 63458953 T - DEL C2orf86 NM_015910.1 human genbank 54_36p -1 validated intronic c.1748+72 e12+72 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 2 66827128 66827128 T A SNP - - - - - - - - - - - - - - - tier3 1647 12 0.72 999 799 44.39 0 0 NA 202127 TCGA-AB-2998 AML48 2 71175551 71175551 C T SNP MPHOSPH10 NM_005791.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35753 NULL 0.078 - - - no_errors tier3 816 11 1.33 662 624 48.45 0 0 NA 202127 TCGA-AB-2998 AML48 2 76409653 76409653 A T SNP - - - - - - - - - - - - - - - tier3 698 5 0.71 451 362 44.47 0 0 NA 202127 TCGA-AB-2998 AML48 2 82147552 82147552 C T SNP - - - - - - - - - - - - - - - tier3 929 3 0.32 924 146 13.64 0 0 NA 202127 TCGA-AB-2998 AML48 2 106831439 106831439 C G SNP ST6GAL2 NM_032528.1 human genbank 54_36p -1 validated intronic c.1-4517 e1-4517 0.001 - - - no_errors tier3 754 6 0.79 548 434 44.11 0 0 NA 202127 TCGA-AB-2998 AML48 2 114909957 114909957 A G SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6869 NULL 0.011 - - - no_errors tier2 560 4 0.71 328 306 48.26 0 0 NA 202127 TCGA-AB-2998 AML48 2 117243913 117243913 C T SNP - - - - - - - - - - - - - - - tier3 914 7 0.76 501 383 43.33 0 0 NA 202127 TCGA-AB-2998 AML48 2 119107387 119107387 T C SNP - - - - - - - - - - - - - - - tier3 793 10 1.25 435 401 47.91 0 0 NA 202127 TCGA-AB-2998 AML48 2 120285466 120285466 T A SNP PTPN4 NM_002830.2 human genbank 54_36p 1 reviewed intronic c.138+1429 e1+1429 0.012 - - - no_errors tier3 622 5 0.8 504 347 40.78 0 0 0 202127 TCGA-AB-2998 AML48 2 123264417 123264417 C T SNP - - - - - - - - - - - - - - - tier3 1280 5 0.39 1013 685 40.32 0 0 NA 202127 TCGA-AB-2998 AML48 2 123494383 123494383 G A SNP - - - - - - - - - - - - - - - tier3 777 4 0.51 631 484 43.41 0 0 NA 202127 TCGA-AB-2998 AML48 2 124943361 124943362 - T INS CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.919-5425_919-5424 e7-5424 0.001:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 2 125254789 125254789 C T SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.2749+7725 e17+7725 0.003 - - - no_errors tier3 1480 3 0.2 1029 800 43.67 0 0 NA 202127 TCGA-AB-2998 AML48 2 125728788 125728788 C T SNP - - - - - - - - - - - - - - - tier3 864 6 0.69 507 358 41.39 0 0 NA 202127 TCGA-AB-2998 AML48 2 127362418 127362418 G C SNP LOC339760 XM_295058.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-825 NULL 0.003 - - - no_errors tier3 843 5 0.59 922 860 48.26 0 0 NA 202127 TCGA-AB-2998 AML48 2 127555543 127555543 C T SNP BIN1 NM_139343.2 human genbank 54_36p -1 reviewed intronic c.85-4791 e2-4791 0 - - - no_errors tier3 492 4 0.8 323 261 44.69 0 0 0 202127 TCGA-AB-2998 AML48 2 133036472 133036472 T G SNP GPR39 NM_001508.2 human genbank 54_36p 1 validated intronic c.857-82672 e2-82672 0.001 - - - no_errors tier2 1435 9 0.62 952 721 43.04 0 0 NA 202127 TCGA-AB-2998 AML48 2 133963139 133963139 C T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.69+28360 e1+28360 0 - - - no_errors tier3 779 14 1.76 574 405 41.24 0 0 NA 202127 TCGA-AB-2998 AML48 2 146719001 146719001 C T SNP LOC100129653 XM_001717973.1 human genbank 54_36p 1 model intronic c.386+1675 e2+1675 0.975 - - - no_errors tier2 684 9 1.29 350 296 45.82 0 0 NA 202127 TCGA-AB-2998 AML48 2 148044029 148044029 G A SNP - - - - - - - - - - - - - - - tier3 2756 21 0.76 1661 1351 44.81 0 0 NA 202127 TCGA-AB-2998 AML48 2 148365444 148365444 C G SNP ACVR2A NM_001616.3 human genbank 54_36p 1 reviewed intronic c.56-4896 e2-4896 0.079 - - - no_errors tier3 1229 24 1.92 702 554 44 1 0 0 202127 TCGA-AB-2998 AML48 2 157753241 157753241 C T SNP ENSG00000213194 ENST00000392819 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*22023 NULL 0 - - - no_coding_region:pseudogene tier3 525 8 1.5 335 288 46.23 0 0 NA 202127 TCGA-AB-2998 AML48 2 163897303 163897303 G T SNP ENSG00000200902 ENST00000364032 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*43451 NULL 0 - - - no_errors tier3 1696 7 0.41 941 695 42.46 0 0 NA 202127 TCGA-AB-2998 AML48 2 166568485 166568485 A T SNP SCN1A NM_006920.4 human genbank 54_36p -1 validated intronic c.3970-976 e21-976 0.496 - - - no_errors tier3 1208 11 0.9 679 612 47.33 0 0 NA 202127 TCGA-AB-2998 AML48 2 174330823 174330823 A C SNP - - - - - - - - - - - - - - - tier2 1135 6 0.52 607 630 50.81 0 0 NA 202127 TCGA-AB-2998 AML48 2 196712283 196712283 G T SNP STK17B NM_004226.3 human genbank 54_36p -1 validated intronic c.836+306 e6+306 0.005 - - - no_errors tier3 431 1 0.23 306 203 39.88 4 3 42.86 202127 TCGA-AB-2998 AML48 2 210263300 210263300 C T SNP MAP2 NM_002374.1 human genbank 54_36p 1 reviewed intronic c.455-2294 e4-2294 0.995 - - - no_errors tier3 1171 9 0.76 729 596 44.98 0 0 NA 202127 TCGA-AB-2998 AML48 2 213306250 213306250 C A SNP ENSG00000221388 ENST00000408461 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*30289 NULL 0.084 - - - no_errors tier3 1108 9 0.81 660 486 42.41 0 0 NA 202127 TCGA-AB-2998 AML48 2 215677160 215677160 C T SNP ABCA12 NM_173076.3 human genbank 54_36p -1 reviewed intronic c.163+7405 e2+7405 0.124 - - - no_errors tier3 722 3 0.41 369 364 49.59 0 0 NA 202127 TCGA-AB-2998 AML48 2 215977022 215977022 G A SNP FN1 NM_212482.2 human genbank 54_36p -1 reviewed intronic c.3253+335 e20+335 0.005 - - - no_errors tier3 1163 7 0.6 632 583 47.9 0 0 NA 202127 TCGA-AB-2998 AML48 2 225345929 225345929 A T SNP DOCK10 NM_014689.2 human genbank 54_36p -1 validated intronic c.6204+189 e53+189 0 - - - no_errors tier3 916 6 0.65 664 621 48.33 3 2 40 202127 TCGA-AB-2998 AML48 2 233465502 233465502 A T SNP NGEF NM_019850.1 human genbank 54_36p -1 validated intronic c.1142+350 e6+350 0 - - - no_errors tier3 88 0 0 42 32 42.67 0 0 NA 202127 TCGA-AB-2998 AML48 2 236785234 236785234 C T SNP ASB18 NM_212556.2 human genbank 54_36p -1 provisional intronic c.1101+2510 e4+2510 0.002 - - - no_errors tier3 420 7 1.64 227 264 53.77 0 0 NA 202127 TCGA-AB-2998 AML48 2 239021026 239021026 G A SNP ASB1 NM_001040445.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*1135 NULL 0 - - - no_errors tier3 390 3 0.76 289 239 45.27 2 7 77.78 202127 TCGA-AB-2998 AML48 2 239085763 239085763 G A SNP - - - - - - - - - - - - - - - tier2 859 3 0.35 479 515 51.35 1 0 0 202127 TCGA-AB-2998 AML48 2 239501117 239501117 C T SNP FLJ43879 XR_041560.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 262 2 0.76 161 118 42.29 0 0 NA 202127 TCGA-AB-2998 AML48 3 6239096 6239096 T C SNP - - - - - - - - - - - - - - - tier3 793 5 0.63 493 429 46.53 0 0 NA 202127 TCGA-AB-2998 AML48 3 7683486 7683486 C G SNP GRM7 NM_181874.2 human genbank 54_36p 1 reviewed intronic c.2452-13250 e9-13250 0.005 - - - no_errors tier3 383 3 0.78 249 208 45.51 0 0 NA 202127 TCGA-AB-2998 AML48 3 9692265 9692265 C A SNP MTMR14 NM_001077525.1 human genbank 54_36p 1 validated intronic c.752-1736 e8-1736 0.004 - - - no_errors tier3 2169 21 0.96 1173 1101 48.4 2 2 50 202127 TCGA-AB-2998 AML48 3 18014328 18014328 A C SNP - - - - - - - - - - - - - - - tier3 727 9 1.22 606 628 50.89 0 0 0 202127 TCGA-AB-2998 AML48 3 22800348 22800348 G A SNP - - - - - - - - - - - - - - - tier3 1287 8 0.62 733 584 44.28 0 0 NA 202127 TCGA-AB-2998 AML48 3 27793925 27793925 G A SNP - - - - - - - - - - - - - - - tier3 1389 6 0.43 786 588 42.7 0 0 NA 202127 TCGA-AB-2998 AML48 3 37503122 37503122 G A SNP ITGA9 NM_002207.2 human genbank 54_36p 1 reviewed intronic c.544+5020 e4+5020 0 - - - no_errors tier3 1186 11 0.92 710 601 45.84 0 0 0 202127 TCGA-AB-2998 AML48 3 42222373 42222373 C T SNP TRAK1 NM_001042646.1 human genbank 54_36p 1 validated intronic c.1744+3125 e13+3125 0.001 - - - no_errors tier3 331 2 0.6 263 231 46.76 4 2 33.33 202127 TCGA-AB-2998 AML48 3 45006240 45006240 T A SNP EXOSC7 NM_015004.3 human genbank 54_36p 1 validated intronic c.254+100 e3+100 0.001 - - - no_errors tier3 936 10 1.06 639 595 48.06 0 2 100 202127 TCGA-AB-2998 AML48 3 50174331 50174331 G A SNP SEMA3F NM_004186.3 human genbank 54_36p 1 validated intronic c.112+2160 e1+2160 0 - - - no_errors tier3 249 0 0 231 208 46.85 1 0 0 202127 TCGA-AB-2998 AML48 3 54566211 54566211 G A SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.545-5656 e6-5656 0.113 - - - no_errors tier3 793 3 0.38 488 438 47.25 0 0 NA 202127 TCGA-AB-2998 AML48 3 55479686 55479686 A G SNP WNT5A NM_003392.3 human genbank 54_36p -1 reviewed intronic c.685-68 e5-68 0 - - - no_errors tier3 450 3 0.66 297 263 46.96 0 0 NA 202127 TCGA-AB-2998 AML48 3 55707623 55707623 T C SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2847+823 e15+823 0 - - - no_errors tier3 968 11 1.12 551 441 44.41 0 0 NA 202127 TCGA-AB-2998 AML48 3 60411840 60411840 A G SNP FHIT NM_002012.2 human genbank 54_36p -1 reviewed intronic c.103+85793 e1+85793 0 - - - no_errors tier3 1417 17 1.18 872 807 48.06 0 0 NA 202127 TCGA-AB-2998 AML48 3 61768627 61768627 G A SNP PTPRG NM_002841.3 human genbank 54_36p 1 reviewed intronic c.190+58931 e2+58931 0.314 - - - no_errors tier2 1344 11 0.81 817 643 44.04 0 0 0 202127 TCGA-AB-2998 AML48 3 62532911 62532911 G A SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.1578-1258 e9-1258 0 - - - no_errors tier2 840 4 0.47 501 448 47.21 0 0 NA 202127 TCGA-AB-2998 AML48 3 63179612 63179612 G A SNP - - - - - - - - - - - - - - - tier3 757 8 1.04 425 349 44.97 0 0 NA 202127 TCGA-AB-2998 AML48 3 70637605 70637605 G A SNP - - - - - - - - - - - - - - - tier2 1226 14 1.13 721 543 42.92 0 0 NA 202127 TCGA-AB-2998 AML48 3 79075715 79075715 A T SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.173-4948 e3-4948 0 - - - no_errors tier3 872 7 0.8 582 435 42.77 0 0 NA 202127 TCGA-AB-2998 AML48 3 79251334 79251334 T C SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.172+5962 e2+5962 0 - - - no_errors tier3 732 9 1.21 506 465 47.84 0 0 NA 202127 TCGA-AB-2998 AML48 3 84637309 84637309 G A SNP - - - - - - - - - - - - - - - tier3 351 1 0.28 233 164 41.31 0 0 NA 202127 TCGA-AB-2998 AML48 3 90084983 90084983 T A SNP - - - - - - - - - - - - - - - tier3 1247 5 0.4 737 597 44.72 0 0 NA 202127 TCGA-AB-2998 AML48 3 96428580 96428580 T A SNP - - - - - - - - - - - - - - - tier3 1069 6 0.56 657 525 44.42 0 0 NA 202127 TCGA-AB-2998 AML48 3 100404860 100404860 G A SNP - - - - - - - - - - - - - - - tier3 1025 6 0.58 693 569 45.02 0 0 NA 202127 TCGA-AB-2998 AML48 3 105096248 105096248 C A SNP - - - - - - - - - - - - - - - tier3 644 7 1.08 394 282 41.72 0 0 NA 202127 TCGA-AB-2998 AML48 3 111148521 111148521 C T SNP ENSG00000214380 ENST00000398237 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30044 NULL 0.033 - - - no_coding_region:pseudogene tier3 999 10 0.99 607 503 45.27 0 0 NA 202127 TCGA-AB-2998 AML48 3 111950313 111950313 A G SNP ENSG00000201426 ENST00000364556 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21655 NULL 0 - - - no_errors tier3 692 4 0.57 439 346 44.08 0 0 NA 202127 TCGA-AB-2998 AML48 3 113649213 113649213 G A SNP BTLA NM_181780.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*18432 NULL 0.013 - - - no_errors tier3 811 7 0.85 644 610 48.61 0 7 100 202127 TCGA-AB-2998 AML48 3 116405847 116405847 C T SNP - - - - - - - - - - - - - - - tier3 779 11 1.39 459 415 47.43 0 0 NA 202127 TCGA-AB-2998 AML48 3 132863291 132863291 T - DEL CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.681+7918 e6+7918 0.012 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 3 136526537 136526537 T C SNP - - - - - - - - - - - - - - - tier3 954 6 0.62 628 514 45.01 0 0 NA 202127 TCGA-AB-2998 AML48 3 136545083 136545083 C G SNP - - - - - - - - - - - - - - - tier3 1508 17 1.11 941 854 47.58 0 0 NA 202127 TCGA-AB-2998 AML48 3 136547308 136547308 G A SNP - - - - - - - - - - - - - - - tier2 1521 19 1.23 1122 840 42.79 0 0 NA 202127 TCGA-AB-2998 AML48 3 146292770 146292770 A T SNP - - - - - - - - - - - - - - - tier3 991 9 0.9 580 478 45.18 0 0 NA 202127 TCGA-AB-2998 AML48 3 156603303 156603303 G A SNP PLCH1 ENST00000232926 human ensembl 54_36p -1 known intronic c.1295-27031 e11-27031 0 - - - no_errors tier3 526 3 0.57 318 251 44.11 0 0 NA 202127 TCGA-AB-2998 AML48 3 166525919 166525919 G A SNP - - - - - - - - - - - - - - - tier2 296 5 1.66 201 147 42.24 0 0 NA 202127 TCGA-AB-2998 AML48 3 167573208 167573208 G A SNP - - - - - - - - - - - - - - - tier3 771 6 0.77 416 354 45.97 0 0 NA 202127 TCGA-AB-2998 AML48 3 176215283 176215283 C A SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated intronic c.44-81991 e2-81991 0.014 - - - no_errors tier3 639 4 0.62 383 328 46.13 0 0 NA 202127 TCGA-AB-2998 AML48 3 178446485 178446485 A G SNP TBL1XR1 NM_024665.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-181026 NULL 0 - - - no_errors tier3 495 7 1.39 361 299 45.3 0 1 100 202127 TCGA-AB-2998 AML48 3 180049145 180049145 C T SNP KCNMB2 NM_005832.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*5726 NULL 0 - - - no_errors tier2 1281 4 0.31 710 599 45.73 0 0 NA 202127 TCGA-AB-2998 AML48 3 184239131 184239131 G A SNP MCCC1 NM_020166.3 human genbank 54_36p -1 reviewed intronic c.1377+377 e12+377 0.005 - - - no_errors tier3 1472 8 0.54 887 733 45.22 4 5 55.56 202127 TCGA-AB-2998 AML48 3 187446236 187446236 T C SNP DGKG NM_001346.1 human genbank 54_36p -1 reviewed intronic c.1762-3185 e19-3185 0.002 - - - no_errors tier3 985 5 0.5 696 593 45.97 4 2 33.33 202127 TCGA-AB-2998 AML48 3 198208154 198208154 G A SNP LOC728126 XR_036926.1 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - pseudogene tier3 340 3 0.87 272 208 43.33 1 0 0 202127 TCGA-AB-2998 AML48 4 6469792 6469792 T C SNP PPP2R2C NM_020416.3 human genbank 54_36p -1 reviewed intronic c.71-36070 e2-36070 0.006 - - - no_errors tier3 266 6 2.05 167 143 44.14 0 2 100 202127 TCGA-AB-2998 AML48 4 16426051 16426051 G A SNP LDB2 NM_001290.1 human genbank 54_36p -1 validated intronic c.133-56070 e2-56070 0 - - - no_errors tier3 930 6 0.64 556 502 47.4 0 0 NA 202127 TCGA-AB-2998 AML48 4 16907785 16907785 G A SNP ENSG00000206780 ENST00000384053 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*23682 NULL 0.077 - - - no_errors tier3 1181 8 0.67 753 674 47.2 0 0 NA 202127 TCGA-AB-2998 AML48 4 18126621 18126621 G A SNP - - - - - - - - - - - - - - - tier2 1003 8 0.79 806 614 43.21 0 0 NA 202127 TCGA-AB-2998 AML48 4 21052314 21052314 T C SNP KCNIP4 NM_001035003.1 human genbank 54_36p -1 reviewed intronic c.88+255757 e1+255757 0 - - - no_errors tier3 1336 4 0.3 1473 209 12.42 0 0 NA 202127 TCGA-AB-2998 AML48 4 21452584 21452584 G T SNP KCNIP4 NM_025221.1 human genbank 54_36p -1 reviewed intronic c.61+106708 e1+106708 0.012 - - - overly_large_intron tier3 1005 4 0.4 614 518 45.72 0 0 NA 202127 TCGA-AB-2998 AML48 4 27818128 27818128 A G SNP - - - - - - - - - - - - - - - tier3 793 5 0.63 401 381 48.66 0 0 NA 202127 TCGA-AB-2998 AML48 4 28690677 28690677 G A SNP - - - - - - - - - - - - - - - tier3 398 0 0 247 164 39.9 0 0 NA 202127 TCGA-AB-2998 AML48 4 30211164 30211164 A G SNP - - - - - - - - - - - - - - - tier3 664 5 0.75 425 371 46.61 0 0 NA 202127 TCGA-AB-2998 AML48 4 30853826 30853826 T G SNP LOC645716 XM_933075.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*46729 NULL 0.023 - - - no_errors tier3 1117 7 0.62 615 556 47.44 0 0 NA 202127 TCGA-AB-2998 AML48 4 32048251 32048251 C A SNP - - - - - - - - - - - - - - - tier3 770 5 0.65 358 266 42.63 0 0 NA 202127 TCGA-AB-2998 AML48 4 34568154 34568154 G A SNP - - - - - - - - - - - - - - - tier3 950 20 2.06 561 491 46.63 0 0 NA 202127 TCGA-AB-2998 AML48 4 43027825 43027825 A G SNP - - - - - - - - - - - - - - - tier3 617 11 1.75 358 340 48.71 0 0 NA 202127 TCGA-AB-2998 AML48 4 44045593 44045593 C G SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated intronic c.961+98744 e1+98744 0 - - - no_errors tier3 1319 8 0.6 741 571 43.52 0 0 NA 202127 TCGA-AB-2998 AML48 4 45132294 45132294 A T SNP ENSG00000200720 ENST00000363850 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44510 NULL 0.005 - - - no_errors tier2 783 11 1.38 473 407 46.2 0 0 NA 202127 TCGA-AB-2998 AML48 4 45640675 45640675 T A SNP - - - - - - - - - - - - - - - tier2 1066 9 0.84 612 497 44.82 0 0 NA 202127 TCGA-AB-2998 AML48 4 46114826 46114826 A T SNP GABRA2 NM_000807.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29346 NULL 0.996 - - - no_errors tier2 2151 31 1.42 1244 1097 46.82 0 0 NA 202127 TCGA-AB-2998 AML48 4 48459191 48459191 T C SNP FRYL NM_015030.1 human genbank 54_36p -1 validated intronic c.1+17661 e0+17661 0.02 - - - no_errors tier3 876 10 1.13 541 566 51.04 1 0 0 202127 TCGA-AB-2998 AML48 4 60019539 60019539 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 4 60251519 60251519 C T SNP - - - - - - - - - - - - - - - tier3 943 2 0.21 650 476 42.27 0 0 NA 202127 TCGA-AB-2998 AML48 4 61543782 61543782 C T SNP - - - - - - - - - - - - - - - tier3 1306 8 0.61 779 633 44.77 0 0 NA 202127 TCGA-AB-2998 AML48 4 66939852 66939852 C T SNP - - - - - - - - - - - - - - - tier3 713 5 0.7 628 529 45.72 0 0 NA 202127 TCGA-AB-2998 AML48 4 67048456 67048456 C T SNP - - - - - - - - - - - - - - - tier3 821 6 0.73 578 484 45.49 0 0 NA 202127 TCGA-AB-2998 AML48 4 77204663 77204663 T C SNP CXCL10 NM_001565.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-41055 NULL 0.003 - - - no_errors tier3 948 10 1.04 571 519 47.57 0 0 NA 202127 TCGA-AB-2998 AML48 4 83247942 83247942 G A SNP - - - - - - - - - - - - - - - tier3 1827 14 0.76 1106 915 45.23 0 0 NA 202127 TCGA-AB-2998 AML48 4 101303204 101303204 A G SNP DDIT4L NM_145244.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*24653 NULL 0.001 - - - no_errors tier3 730 8 1.08 475 419 46.82 0 0 NA 202127 TCGA-AB-2998 AML48 4 106728377 106728377 A T SNP FLJ20184 NM_017700.1 human genbank 54_36p 1 predicted intronic c.197-1477 e2-1477 0.008 - - - no_errors tier3 1425 19 1.31 853 697 44.97 0 0 NA 202127 TCGA-AB-2998 AML48 4 108530041 108530041 C T SNP ENSG00000211308 ENST00000388573 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-45683 NULL 0 - - - pseudogene tier3 573 7 1.2 459 348 43.12 0 0 NA 202127 TCGA-AB-2998 AML48 4 114647808 114647808 C T SNP CAMK2D NM_001221.3 human genbank 54_36p -1 reviewed intronic c.984+2435 e13+2435 0 - - - no_errors tier3 388 7 1.77 220 131 37.32 0 0 NA 202127 TCGA-AB-2998 AML48 4 116126487 116126487 C T SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.979-8608 e2-8608 0 - - - no_errors tier3 1051 6 0.57 593 500 45.7 0 0 NA 202127 TCGA-AB-2998 AML48 4 117751270 117751270 A G SNP ENSG00000213493 ENST00000390009 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*11055 NULL 0 - - - no_coding_region:pseudogene tier3 337 2 0.59 173 144 45.43 0 0 NA 202127 TCGA-AB-2998 AML48 4 120244378 120244378 T C SNP MYOZ2 NM_016599.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-32751 NULL 0.001 - - - no_errors tier3 1537 9 0.58 1026 725 41.38 0 0 NA 202127 TCGA-AB-2998 AML48 4 122307018 122307018 A G SNP TNIP3 NM_024873.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2288 NULL 0 - - - no_errors tier2 1138 14 1.21 664 498 42.71 0 0 NA 202127 TCGA-AB-2998 AML48 4 129711788 129711789 - C INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 4 130851400 130851400 A T SNP - - - - - - - - - - - - - - - tier3 983 6 0.61 541 482 47.12 3 1 25 202127 TCGA-AB-2998 AML48 4 135490717 135490717 T C SNP - - - - - - - - - - - - - - - tier3 230 2 0.86 156 115 42.44 0 0 NA 202127 TCGA-AB-2998 AML48 4 137698473 137698473 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 4 139936568 139936568 C G SNP LOC100128578 XM_001718303.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*24100 NULL 0 - - - no_errors tier3 2261 27 1.18 1243 1102 46.97 0 0 NA 202127 TCGA-AB-2998 AML48 4 148429350 148429350 T G SNP - - - - - - - - - - - - - - - tier3 1168 6 0.51 719 613 45.95 0 0 NA 202127 TCGA-AB-2998 AML48 4 155616229 155616229 A G SNP DCHS2 ENST00000339452 human ensembl 54_36p -1 known intronic c.2052+13677 e1+13677 0 - - - no_errors tier3 688 8 1.15 419 340 44.74 0 0 NA 202127 TCGA-AB-2998 AML48 4 157670944 157670944 T A SNP - - - - - - - - - - - - - - - tier2 1187 8 0.67 855 773 47.48 0 0 NA 202127 TCGA-AB-2998 AML48 4 162064057 162064057 G T SNP - - - - - - - - - - - - - - - tier3 712 8 1.11 393 353 47.32 0 0 NA 202127 TCGA-AB-2998 AML48 4 163301868 163301868 T A SNP FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.1+2349 e0+2349 0.008 - - - no_errors tier3 931 4 0.43 448 436 49.32 0 0 NA 202127 TCGA-AB-2998 AML48 4 165649899 165649899 T A SNP - - - - - - - - - - - - - - - tier3 1220 6 0.49 766 716 48.18 0 0 NA 202127 TCGA-AB-2998 AML48 4 174734646 174734646 G A SNP HAND2 NM_021973.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-47631 NULL 0.002 - - - no_errors tier3 485 6 1.22 309 244 44.12 0 0 NA 202127 TCGA-AB-2998 AML48 4 175311132 175311132 T C SNP - - - - - - - - - - - - - - - tier3 644 7 1.08 376 324 46.22 0 0 NA 202127 TCGA-AB-2998 AML48 4 176429873 176429873 T G SNP - - - - - - - - - - - - - - - tier3 447 2 0.45 277 245 46.93 0 0 NA 202127 TCGA-AB-2998 AML48 4 177317936 177317936 G A SNP WDR17 NM_170710.3 human genbank 54_36p 1 reviewed intronic c.2598-203 e19-203 0 - - - no_errors tier3 851 4 0.47 487 363 42.71 0 0 NA 202127 TCGA-AB-2998 AML48 4 177602725 177602726 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 4 179802272 179802272 G T SNP ENSG00000212191 ENST00000390889 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*41762 NULL 0.001 - - - no_errors tier3 1627 19 1.15 1056 918 46.5 0 0 NA 202127 TCGA-AB-2998 AML48 4 182178007 182178007 G T SNP LOC728081 XM_001127776.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*44591 NULL 0 - - - no_errors tier3 609 7 1.14 392 284 42.01 0 0 NA 202127 TCGA-AB-2998 AML48 4 183566307 183566307 G T SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.511+61231 e2+61231 0.017 - - - no_errors tier3 738 7 0.94 501 426 45.91 0 0 NA 202127 TCGA-AB-2998 AML48 5 4776410 4776410 C T SNP LOC730926 XM_001129902.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*44351 NULL 0.007 - - - no_start_codon:pseudogene:no_stop_codon tier3 938 15 1.57 711 592 45.43 0 0 NA 202127 TCGA-AB-2998 AML48 5 9845664 9845664 G A SNP LOC100134212 XM_001714259.1 human genbank 54_36p 1 model intronic c.262-11084 e3-11084 0.234 - - - no_start_codon:pseudogene:no_stop_codon tier3 772 4 0.51 489 454 48.09 0 0 NA 202127 TCGA-AB-2998 AML48 5 12442237 12442237 G C SNP - - - - - - - - - - - - - - - tier3 891 8 0.89 613 480 43.92 0 0 NA 202127 TCGA-AB-2998 AML48 5 19501273 19501273 C T SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*7819 NULL 0 - - - no_errors tier3 737 3 0.4 503 384 43.29 0 0 NA 202127 TCGA-AB-2998 AML48 5 19505008 19505008 A G SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*4084 NULL 0.002 - - - no_errors tier3 417 9 2.11 262 239 47.7 0 0 NA 202127 TCGA-AB-2998 AML48 5 21794534 21794534 T C SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1633+1890 e9+1890 0.108 - - - no_errors tier3 1559 17 1.08 835 782 48.36 0 0 NA 202127 TCGA-AB-2998 AML48 5 22290179 22290179 T G SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1-41670 e1-41670 0 - - - no_errors tier3 341 1 0.29 213 150 41.32 0 0 NA 202127 TCGA-AB-2998 AML48 5 26102928 26102928 C T SNP - - - - - - - - - - - - - - - tier3 960 7 0.72 550 432 43.99 0 0 NA 202127 TCGA-AB-2998 AML48 5 30404029 30404029 G C SNP - - - - - - - - - - - - - - - tier3 1359 12 0.87 713 607 45.98 0 0 NA 202127 TCGA-AB-2998 AML48 5 38593791 38593791 C A SNP LIFR NM_002310.1 human genbank 54_36p -1 reviewed intronic c.1-27266 e1-27266 0.002 - - - no_errors tier2 584 8 1.35 387 328 45.87 0 0 NA 202127 TCGA-AB-2998 AML48 5 39223235 39223235 C T SNP FYB NM_001465.3 human genbank 54_36p -1 validated intronic c.1135+14450 e1+14450 0 - - - no_errors tier3 711 6 0.84 430 342 44.3 2 1 33.33 202127 TCGA-AB-2998 AML48 5 41684745 41684745 G C SNP - - - - - - - - - - - - - - - tier3 692 5 0.72 418 404 49.09 0 0 NA 202127 TCGA-AB-2998 AML48 5 42842101 42842101 G A SNP SEPP1 NM_001093726.1 human genbank 54_36p -1 reviewed intronic c.506+654 e3+654 0.151 - - - pseudogene tier3 937 4 0.42 539 410 43.2 0 2 100 202127 TCGA-AB-2998 AML48 5 52714248 52714248 T C SNP - - - - - - - - - - - - - - - tier3 1203 8 0.66 792 715 47.41 0 0 NA 202127 TCGA-AB-2998 AML48 5 57727657 57727657 G A SNP - - - - - - - - - - - - - - - tier2 1015 22 2.12 719 624 46.36 0 0 NA 202127 TCGA-AB-2998 AML48 5 59143115 59143115 A G SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.455+81637 e1+81637 0 - - - no_errors tier3 1263 10 0.78 888 672 43.05 3 2 40 202127 TCGA-AB-2998 AML48 5 61147893 61147893 G A SNP - - - - - - - - - - - - - - - tier3 787 15 1.87 397 308 43.69 0 0 NA 202127 TCGA-AB-2998 AML48 5 72365967 72365967 A G SNP FCHO2 NM_138782.1 human genbank 54_36p 1 provisional intronic c.797-273 e9-273 0.006 - - - no_errors tier3 1206 4 0.33 829 725 46.62 1 0 0 202127 TCGA-AB-2998 AML48 5 82619169 82619169 T - DEL XRCC4 NM_022406.3 human genbank 54_36p 1 reviewed intronic c.893+28917 e6+28917 0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 5 82998160 82998160 A G SNP HAPLN1 NM_001884.3 human genbank 54_36p -1 validated intronic c.100+6839 e1+6839 0 - - - no_errors tier3 318 3 0.93 156 114 42.07 0 0 NA 202127 TCGA-AB-2998 AML48 5 84624739 84624739 C A SNP - - - - - - - - - - - - - - - tier3 727 6 0.82 486 390 44.52 0 0 NA 202127 TCGA-AB-2998 AML48 5 85373083 85373083 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 5 87877560 87877560 G T SNP - - - - - - - - - - - - - - - tier2 1415 6 0.42 919 653 41.51 0 0 NA 202127 TCGA-AB-2998 AML48 5 92746576 92746576 T C SNP - - - - - - - - - - - - - - - tier3 1410 9 0.63 887 793 47.15 0 0 NA 202127 TCGA-AB-2998 AML48 5 93454639 93454639 A G SNP FAM172A ENST00000395965 human ensembl 54_36p -1 known intronic c.1+18333 e0+18333 0.041 - - - no_errors tier3 884 10 1.12 468 411 46.76 0 0 0 202127 TCGA-AB-2998 AML48 5 93952295 93952295 T A SNP C5orf36 NM_173665.1 human genbank 54_36p -1 validated intronic c.1-8251 e1-8251 0.053 - - - no_errors tier3 681 7 1.02 443 418 48.55 0 0 NA 202127 TCGA-AB-2998 AML48 5 100189081 100189082 - A INS ST8SIA4 NM_005668.4 human genbank 54_36p -1 reviewed intronic c.798-13350_798-13349 e5-13349 0.009:0.014 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 5 101114115 101114115 C T SNP - - - - - - - - - - - - - - - tier3 889 2 0.22 581 433 42.7 0 0 NA 202127 TCGA-AB-2998 AML48 5 103648573 103648573 G A SNP ENSG00000222401 ENST00000410469 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-24147 NULL 0.042 - - - no_errors tier3 992 11 1.1 592 425 41.75 0 0 NA 202127 TCGA-AB-2998 AML48 5 103710451 103710451 G C SNP - - - - - - - - - - - - - - - tier3 401 3 0.74 248 202 44.89 0 0 NA 202127 TCGA-AB-2998 AML48 5 104852511 104852511 A T SNP - - - - - - - - - - - - - - - tier3 765 3 0.39 636 251 28.3 0 0 NA 202127 TCGA-AB-2998 AML48 5 108179428 108179429 TT - DEL FER NM_005246.2 human genbank 54_36p 1 reviewed intronic c.208-16942_208-16941 e2-16941 0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 5 111602998 111602998 C T SNP EPB41L4A NM_022140.3 human genbank 54_36p -1 validated intronic c.965+258 e11+258 0.001 - - - no_errors tier3 983 4 0.41 630 527 45.51 0 0 NA 202127 TCGA-AB-2998 AML48 5 114044091 114044091 A G SNP - - - - - - - - - - - - - - - tier3 534 2 0.37 457 334 42.17 0 0 NA 202127 TCGA-AB-2998 AML48 5 117674024 117674024 C T SNP - - - - - - - - - - - - - - - tier3 897 8 0.88 537 444 45.21 0 0 NA 202127 TCGA-AB-2998 AML48 5 121212829 121212829 T A SNP FTMT NM_177478.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-2729 NULL 0.81 - - - no_errors tier2 735 2 0.27 541 425 43.95 0 0 NA 202127 TCGA-AB-2998 AML48 5 123544176 123544176 T A SNP ENSG00000214750 ENST00000398908 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*40320 NULL 0 - - - no_coding_region:pseudogene tier3 534 5 0.93 451 332 42.4 0 0 NA 202127 TCGA-AB-2998 AML48 5 123589833 123589833 C T SNP ENSG00000214750 ENST00000398908 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5185 NULL 0 - - - no_coding_region:pseudogene tier3 1227 2 0.16 743 544 42.27 0 0 NA 202127 TCGA-AB-2998 AML48 5 127766500 127766500 C T SNP FBN2 NM_001999.3 human genbank 54_36p -1 reviewed intronic c.1078+5766 e8+5766 0 - - - no_errors tier3 1236 11 0.88 981 671 40.57 0 0 0 202127 TCGA-AB-2998 AML48 5 140763027 140763027 C T SNP PCDHGA9 NM_018921.2 human genbank 54_36p 1 reviewed silent c.324 p.V108 0 "HMMSmart_SM00112,HMMPfam_Cadherin_2,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 236 1 0.42 214 119 35.74 NA 202127 TCGA-AB-2998 AML48 5 142397939 142397939 T C SNP ARHGAP26 NM_015071.1 human genbank 54_36p 1 validated intronic c.1210+920 e13+920 0.09 - - - no_errors tier3 948 8 0.84 537 580 51.92 2 0 0 202127 TCGA-AB-2998 AML48 5 143111750 143111750 C T SNP - - - - - - - - - - - - - - - tier3 737 3 0.4 316 297 48.14 0 0 NA 202127 TCGA-AB-2998 AML48 5 144956147 144956147 G A SNP - - - - - - - - - - - - - - - tier3 875 5 0.57 472 379 44.54 0 1 100 202127 TCGA-AB-2998 AML48 5 150079975 150079975 C T SNP DCTN4 NM_016221.1 human genbank 54_36p -1 validated intronic c.909-450 e10-450 0.054 - - - no_errors tier3 1118 8 0.71 685 703 50.61 6 8 57.14 202127 TCGA-AB-2998 AML48 5 157954211 157954211 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 5 158184860 158184860 C G SNP EBF1 NM_024007.3 human genbank 54_36p -1 validated intronic c.637-1957 e8-1957 0.001 - - - no_errors tier3 1290 7 0.54 598 493 45.15 0 0 NA 202127 TCGA-AB-2998 AML48 5 163724145 163724145 T C SNP - - - - - - - - - - - - - - - tier2 964 11 1.13 605 472 43.74 0 0 NA 202127 TCGA-AB-2998 AML48 5 165242968 165242968 T G SNP - - - - - - - - - - - - - - - tier3 1062 7 0.65 603 545 47.39 0 0 NA 202127 TCGA-AB-2998 AML48 5 166272967 166272967 T C SNP - - - - - - - - - - - - - - - tier3 1000 10 0.99 528 517 49.33 0 0 NA 202127 TCGA-AB-2998 AML48 5 175200495 175200495 G A SNP CPLX2 NM_006650.1 human genbank 54_36p 1 reviewed intronic c.1+31818 e0+31818 0 - - - no_errors tier2 727 10 1.36 486 401 44.8 0 0 NA 202127 TCGA-AB-2998 AML48 6 4064344 4064344 G C SNP PECI NM_006117.2 human genbank 54_36p -1 validated intronic c.795+75 e7+75 0.004 - - - no_errors tier3 372 5 1.33 263 237 47.4 1 2 66.67 202127 TCGA-AB-2998 AML48 6 4475875 4475875 G A SNP LOC100134205 XM_001716692.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-21260 NULL 1 - - - no_start_codon:pseudogene:no_stop_codon tier3 1052 12 1.13 563 571 50.26 0 0 NA 202127 TCGA-AB-2998 AML48 6 8750091 8750091 C T SNP - - - - - - - - - - - - - - - tier3 811 6 0.73 566 393 40.94 0 0 NA 202127 TCGA-AB-2998 AML48 6 10004572 10004572 C G SNP OFCC1 ENST00000316020 human ensembl 54_36p -1 known intronic c.831+518 e7+518 0.005 - - - no_errors tier3 1867 10 0.53 1246 1178 48.54 0 0 NA 202127 TCGA-AB-2998 AML48 6 13153361 13153361 G A SNP PHACTR1 NM_030948.1 human genbank 54_36p 1 validated intronic c.251-8222 e3-8222 0 - - - no_errors tier3 1988 31 1.53 1238 1125 47.59 3 1 25 202127 TCGA-AB-2998 AML48 6 16462067 16462067 A T SNP ATXN1 NM_000332.3 human genbank 54_36p -1 reviewed intronic c.1-25387 e1-25387 0.012 - - - no_errors tier3 1192 11 0.91 748 740 49.73 3 1 25 202127 TCGA-AB-2998 AML48 6 19286364 19286364 G A SNP LOC645157 XR_016770.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*33973 NULL 0 - - - pseudogene tier3 1199 13 1.07 782 716 47.77 0 0 NA 202127 TCGA-AB-2998 AML48 6 20966941 20966941 T C SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated intronic c.742+12553 e7+12553 0 - - - no_errors tier3 581 2 0.34 347 352 50.21 2 3 60 202127 TCGA-AB-2998 AML48 6 33889296 33889296 G A SNP MLN NM_002418.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12378 NULL 0 - - - no_errors tier3 584 2 0.34 418 343 44.78 0 0 NA 202127 TCGA-AB-2998 AML48 6 50732011 50732011 A G SNP - - - - - - - - - - - - - - - tier3 1233 13 1.04 821 739 47.28 0 0 NA 202127 TCGA-AB-2998 AML48 6 57141023 57141023 C T SNP ZNF451 NM_001031623.2 human genbank 54_36p 1 validated intronic c.3140-157 e15-157 0.016 - - - no_errors tier3 223 1 0.45 182 133 42.22 0 0 0 202127 TCGA-AB-2998 AML48 6 57464192 57464192 C T SNP PRIM2 ENST00000389488 human ensembl 54_36p 1 known intronic c.694-16055 e7-16055 0.017 - - - no_errors tier3 1246 10 0.8 1117 427 27.66 3 0 0 202127 TCGA-AB-2998 AML48 6 63919620 63919620 C T SNP ENSG00000217477 ENST00000403497 human ensembl 54_36p -1 known 3_prime_flanking_region c.*41302 NULL 0 - - - no_coding_region:pseudogene tier2 789 4 0.5 589 500 45.91 0 0 NA 202127 TCGA-AB-2998 AML48 6 67841437 67841437 G A SNP - - - - - - - - - - - - - - - tier3 667 7 1.04 462 357 43.59 0 0 NA 202127 TCGA-AB-2998 AML48 6 69345741 69345741 G T SNP ENSG00000218834 ENST00000406616 human ensembl 54_36p -1 known 3_prime_flanking_region c.*19076 NULL 0 - - - no_coding_region:pseudogene tier3 1196 5 0.42 676 473 41.13 0 0 NA 202127 TCGA-AB-2998 AML48 6 75134551 75134551 A T SNP - - - - - - - - - - - - - - - tier3 881 7 0.79 568 476 45.55 0 0 NA 202127 TCGA-AB-2998 AML48 6 76760583 76760583 T A SNP IMPG1 NM_001563.2 human genbank 54_36p -1 provisional intronic c.1291+8772 e12+8772 0.654 - - - no_errors tier3 764 7 0.91 459 392 46.01 0 0 NA 202127 TCGA-AB-2998 AML48 6 77532560 77532560 C T SNP - - - - - - - - - - - - - - - tier2 651 8 1.21 681 86 11.21 0 0 NA 202127 TCGA-AB-2998 AML48 6 92671306 92671306 G A SNP - - - - - - - - - - - - - - - tier2 1694 14 0.82 943 822 46.55 0 0 NA 202127 TCGA-AB-2998 AML48 6 93466037 93466037 A C SNP - - - - - - - - - - - - - - - tier3 683 2 0.29 376 354 48.49 0 0 NA 202127 TCGA-AB-2998 AML48 6 98262109 98262109 C T SNP - - - - - - - - - - - - - - - tier2 651 6 0.91 351 316 47.38 0 0 NA 202127 TCGA-AB-2998 AML48 6 100450337 100450337 T A SNP MCHR2 NM_001040179.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*25200 NULL 0.001 - - - no_errors tier3 828 7 0.84 540 496 47.83 0 0 NA 202127 TCGA-AB-2998 AML48 6 104623000 104623000 A - DEL ENSG00000214428 ENST00000398310 human ensembl 54_36p -1 known 5_prime_flanking_region c.-41669 NULL 0.004 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 6 104684184 104684184 G C SNP - - - - - - - - - - - - - - - tier3 1312 12 0.9 1003 811 44.66 0 0 NA 202127 TCGA-AB-2998 AML48 6 114451049 114451049 C T SNP ENSG00000216723 ENST00000404698 human ensembl 54_36p -1 known 5_prime_flanking_region c.-2709 NULL 0.001 - - - no_coding_region:pseudogene tier3 2562 12 0.47 1555 1210 43.68 0 0 NA 202127 TCGA-AB-2998 AML48 6 114483653 114483653 A - DEL ENSG00000216723 ENST00000404698 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35313 NULL 0.004 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 6 114788408 114788408 G A SNP ENSG00000218089 ENST00000406473 human ensembl 54_36p -1 known 5_prime_flanking_region c.-9903 NULL 0.006 - - - no_coding_region:pseudogene tier3 1588 10 0.63 731 573 43.91 0 0 NA 202127 TCGA-AB-2998 AML48 6 115053770 115053770 C T SNP - - - - - - - - - - - - - - - tier3 1719 14 0.81 1013 1044 50.73 0 0 NA 202127 TCGA-AB-2998 AML48 6 116268163 116268163 T A SNP - - - - - - - - - - - - - - - tier3 788 10 1.25 634 552 46.54 0 0 NA 202127 TCGA-AB-2998 AML48 6 119732830 119732830 G A SNP MAN1A1 NM_005907.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20901 NULL 0 - - - no_errors tier3 939 6 0.63 469 448 48.8 3 2 40 202127 TCGA-AB-2998 AML48 6 121801998 121801998 G A SNP GJA1 NM_000165.3 human genbank 54_36p 1 reviewed intronic c.1+3321 e0+3321 0.002 - - - no_errors tier3 360 1 0.28 219 180 45 0 0 NA 202127 TCGA-AB-2998 AML48 6 122677880 122677880 G A SNP - - - - - - - - - - - - - - - tier3 691 1 0.14 469 318 40.41 0 0 NA 202127 TCGA-AB-2998 AML48 6 123457137 123457137 A G SNP RLBP1L2 NM_001010852.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*30532 NULL 0.015 - - - no_errors tier2 1512 12 0.79 979 832 45.94 0 0 NA 202127 TCGA-AB-2998 AML48 6 124502332 124502332 A C SNP NKAIN2 NM_001040214.1 human genbank 54_36p 1 validated intronic c.55-143518 e2-143518 0.007 - - - no_errors tier3 708 6 0.84 556 441 44.23 0 0 NA 202127 TCGA-AB-2998 AML48 6 129344175 129344175 G A SNP LAMA2 NM_000426.3 human genbank 54_36p 1 reviewed intronic c.113-68581 e2-68581 0.001 - - - no_errors tier3 1760 14 0.79 949 815 46.2 0 0 NA 202127 TCGA-AB-2998 AML48 6 143126302 143126302 A T SNP HIVEP2 NM_006734.3 human genbank 54_36p -1 provisional intronic c.5518+1327 e3+1327 0.002 - - - no_errors tier2 662 9 1.34 423 381 47.27 1 3 75 202127 TCGA-AB-2998 AML48 6 145929608 145929608 A T SNP - - - - - - - - - - - - - - - tier3 983 8 0.81 614 523 46 0 0 NA 202127 TCGA-AB-2998 AML48 6 163909352 163909352 G T SNP QKI NM_206854.1 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*3620 NULL 0.002 - - - no_errors tier3 1022 12 1.16 652 573 46.78 8 9 52.94 202127 TCGA-AB-2998 AML48 6 165082554 165082554 G A SNP - - - - - - - - - - - - - - - tier3 1277 11 0.85 695 630 47.48 0 0 NA 202127 TCGA-AB-2998 AML48 6 166433301 166433301 G A SNP ENSG00000200442 ENST00000363572 human ensembl 54_36p 1 known 5_prime_flanking_region c.-30 NULL 0.001 - - - no_errors tier3 2108 19 0.89 1320 1138 46.24 0 0 NA 202127 TCGA-AB-2998 AML48 6 169459163 169459163 G A SNP ENSG00000219031 ENST00000406479 human ensembl 54_36p -1 known 5_prime_flanking_region c.-19184 NULL 0 - - - no_coding_region:pseudogene tier3 818 4 0.49 611 489 44.37 0 0 NA 202127 TCGA-AB-2998 AML48 7 1682555 1682555 G A SNP LOC100134769 XM_001715089.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-17868 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 270 6 2.17 240 252 50.91 0 0 NA 202127 TCGA-AB-2998 AML48 7 8476641 8476641 C T SNP NXPH1 NM_152745.2 human genbank 54_36p 1 reviewed intronic c.54+34719 e1+34719 0.007 - - - no_errors tier3 768 2 0.26 412 396 48.95 0 0 NA 202127 TCGA-AB-2998 AML48 7 9440110 9440110 T G SNP - - - - - - - - - - - - - - - tier3 1447 7 0.48 737 655 47.02 0 0 NA 202127 TCGA-AB-2998 AML48 7 10084112 10084112 C T SNP LOC340268 XR_041608.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 575 1 0.17 412 334 44.71 0 0 NA 202127 TCGA-AB-2998 AML48 7 25374764 25374764 C A SNP - - - - - - - - - - - - - - - tier3 1211 16 1.3 693 689 49.78 0 0 NA 202127 TCGA-AB-2998 AML48 7 31338089 31338089 A G SNP NEUROD6 NM_022728.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*6305 NULL 0.014 - - - no_errors tier3 587 6 1.01 425 354 45.44 0 0 NA 202127 TCGA-AB-2998 AML48 7 34029874 34029874 T C SNP BMPER NM_133468.3 human genbank 54_36p 1 validated intronic c.577-22569 e7-22569 0.001 - - - no_errors tier3 741 4 0.53 453 351 43.66 0 0 NA 202127 TCGA-AB-2998 AML48 7 35876269 35876269 C G SNP SEPT7 NM_001788.2 human genbank 54_36p 1 reviewed intronic c.277-2532 e5-2532 0.654 - - - no_errors tier2 727 1 0.14 446 285 38.99 1 3 75 202127 TCGA-AB-2998 AML48 7 41246826 41246826 C A SNP - - - - - - - - - - - - - - - tier3 1478 10 0.67 898 640 41.56 0 0 NA 202127 TCGA-AB-2998 AML48 7 43416128 43416128 C T SNP HECW1 NM_015052.3 human genbank 54_36p 1 validated intronic c.801+2273 e6+2273 0.004 - - - no_errors tier3 1004 8 0.79 599 631 51.13 0 0 NA 202127 TCGA-AB-2998 AML48 7 48897751 48897751 C A SNP CDC14C NR_003595.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-36952 NULL 0.001 - - - pseudogene tier3 1450 14 0.95 772 800 50.89 0 0 NA 202127 TCGA-AB-2998 AML48 7 56192813 56192813 A C SNP uc003tsb.2 ENST00000329309 human ensembl 54_36p -1 known 5_prime_flanking_region c.-41312 NULL 0.499 - - - no_errors tier3 535 7 1.29 344 268 43.79 0 0 NA 202127 TCGA-AB-2998 AML48 7 77980657 77980657 C T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.754+8026 e4+8026 0.009 - - - no_errors tier2 1729 14 0.8 925 691 42.76 0 0 NA 202127 TCGA-AB-2998 AML48 7 78192449 78192449 C T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.419-97958 e3-97958 0.009 - - - no_errors tier3 687 5 0.72 417 322 43.57 0 0 NA 202127 TCGA-AB-2998 AML48 7 81068297 81068297 T G SNP LOC100128317 XM_001717593.1 human genbank 54_36p -1 model intronic c.116-3219 e2-3219 0.003 - - - no_errors tier3 745 10 1.32 450 382 45.75 0 0 NA 202127 TCGA-AB-2998 AML48 7 83132053 83132053 C T SNP SEMA3E NM_012431.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-16259 NULL 0.906 - - - no_errors tier2 499 5 0.99 243 208 46.02 0 0 NA 202127 TCGA-AB-2998 AML48 7 83737423 83737423 A T SNP - - - - - - - - - - - - - - - tier3 1037 7 0.67 583 474 44.8 0 0 NA 202127 TCGA-AB-2998 AML48 7 85428958 85428958 C A SNP - - - - - - - - - - - - - - - tier3 328 3 0.91 260 134 34.01 0 0 NA 202127 TCGA-AB-2998 AML48 7 98560407 98560407 G A SNP SMURF1 NM_020429.1 human genbank 54_36p -1 reviewed intronic c.55+18878 e1+18878 0 - - - no_errors tier3 1287 19 1.45 825 722 46.64 5 5 50 202127 TCGA-AB-2998 AML48 7 110510419 110510419 G T SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional intronic c.240-119562 e3-119562 0 - - - no_errors tier3 617 3 0.48 340 346 50.44 0 0 NA 202127 TCGA-AB-2998 AML48 7 112751909 112751909 C T SNP - - - - - - - - - - - - - - - tier3 551 2 0.36 329 334 50.38 0 0 NA 202127 TCGA-AB-2998 AML48 7 114659181 114659181 G A SNP ENSG00000199764 ENST00000362894 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-23895 NULL 0.993 - - - no_errors tier2 969 6 0.61 646 644 49.88 0 0 NA 202127 TCGA-AB-2998 AML48 7 119719353 119719353 T A SNP KCND2 NM_012281.2 human genbank 54_36p 1 reviewed intronic c.1115+16316 e1+16316 0 - - - no_errors tier3 985 7 0.71 581 415 41.62 0 0 NA 202127 TCGA-AB-2998 AML48 7 121336391 121336391 C T SNP PTPRZ1 NM_002851.2 human genbank 54_36p 1 reviewed intronic c.59-19055 e2-19055 0.001 - - - no_errors tier3 626 0 0 371 227 37.96 0 0 NA 202127 TCGA-AB-2998 AML48 7 122505025 122505025 C T SNP SLC13A1 NM_022444.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*37783 NULL 0 - - - no_errors tier3 1140 5 0.44 715 557 43.79 0 0 NA 202127 TCGA-AB-2998 AML48 7 126830214 126830214 G C SNP ZNF800 NM_176814.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11367 NULL 0.022 - - - no_errors tier3 1158 9 0.77 619 540 46.55 0 0 NA 202127 TCGA-AB-2998 AML48 7 130341705 130341705 G C SNP ENSG00000199627 ENST00000362757 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*48480 NULL 0.009 - - - no_errors tier2 1117 8 0.71 720 509 41.42 11 5 31.25 202127 TCGA-AB-2998 AML48 7 133446671 133446671 C T SNP LRGUK NM_144648.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-15990 NULL 0.002 - - - no_errors tier3 1846 11 0.59 992 806 44.83 1 1 50 202127 TCGA-AB-2998 AML48 7 148630148 148630148 A T SNP ENSG00000218140 ENST00000406747 human ensembl 54_36p 1 known 5_prime_flanking_region c.-31900 NULL 0.02 - - - no_coding_region:pseudogene tier3 850 10 1.16 787 726 47.92 0 0 NA 202127 TCGA-AB-2998 AML48 7 151312576 151312576 G A SNP GALNTL5 NM_145292.2 human genbank 54_36p 1 provisional intronic c.535+1406 e3+1406 0.009 - - - no_errors tier3 888 13 1.44 599 515 46.19 0 0 NA 202127 TCGA-AB-2998 AML48 7 155607863 155607863 G A SNP LOC393076 XR_016902.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 822 4 0.48 603 537 47.11 0 0 NA 202127 TCGA-AB-2998 AML48 7 157082064 157082064 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.2419-1296 e17-1296 0 - - - no_errors tier3 808 11 1.34 553 396 41.73 0 0 0 202127 TCGA-AB-2998 AML48 8 3010270 3010270 T A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.5730-3064 e39-3064 0.003 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1118 7 0.62 650 594 47.75 0 0 NA 202127 TCGA-AB-2998 AML48 8 4206182 4206182 G C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.415+58701 e3+58701 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 540 3 0.55 296 242 44.98 0 0 NA 202127 TCGA-AB-2998 AML48 8 4738387 4738387 T A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+100875 e1+100875 0.002 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 478 2 0.42 272 194 41.45 0 0 NA 202127 TCGA-AB-2998 AML48 8 14447490 14447490 T C SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.234+9122 e2+9122 0 - - - no_errors tier3 648 4 0.61 352 254 41.91 0 0 NA 202127 TCGA-AB-2998 AML48 8 24910635 24910635 T C SNP NEFL ENST00000221169 human ensembl 54_36p -1 known 5_prime_flanking_region c.-40689 NULL 0.002 - - - no_errors tier3 543 3 0.55 375 325 46.43 0 0 NA 202127 TCGA-AB-2998 AML48 8 27227866 27227866 C T SNP PTK2B NM_004103.3 human genbank 54_36p 1 reviewed intronic c.1+1145 e0+1145 0 - - - no_errors tier3 72 0 0 72 58 44.62 0 0 NA 202127 TCGA-AB-2998 AML48 8 34698069 34698069 T A SNP - - - - - - - - - - - - - - - tier3 328 1 0.3 161 158 49.53 0 0 NA 202127 TCGA-AB-2998 AML48 8 51417327 51417327 G A SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1-51998 e1-51998 0.104 - - - no_errors tier3 592 3 0.5 353 344 49.35 0 0 NA 202127 TCGA-AB-2998 AML48 8 51900377 51900377 C T SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*32435 NULL 0 - - - no_errors tier3 923 5 0.54 540 399 42.45 0 0 NA 202127 TCGA-AB-2998 AML48 8 52044024 52044024 T A SNP ENSG00000201316 ENST00000364446 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46110 NULL 0.03 - - - no_errors tier3 1369 9 0.65 863 671 43.71 0 0 NA 202127 TCGA-AB-2998 AML48 8 58697371 58697371 C T SNP LOC100130588 XM_001719422.1 human genbank 54_36p -1 model intronic c.127-27796 e3-27796 0.001 - - - no_errors tier3 1444 11 0.75 1022 775 43.1 0 0 NA 202127 TCGA-AB-2998 AML48 8 63371816 63371816 A T SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.54+47576 e1+47576 0.006 - - - no_errors tier3 1148 9 0.78 795 560 41.33 0 0 NA 202127 TCGA-AB-2998 AML48 8 63534139 63534139 G A SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.55-120513 e2-120513 0.022 - - - no_errors tier3 680 11 1.59 415 384 48.06 0 0 NA 202127 TCGA-AB-2998 AML48 8 63869186 63869186 C T SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.471+46944 e4+46944 0.001 - - - no_errors tier2 1787 9 0.5 1266 888 41.19 0 0 NA 202127 TCGA-AB-2998 AML48 8 65505718 65505718 G C SNP - - - - - - - - - - - - - - - tier3 672 3 0.44 440 280 38.83 0 0 NA 202127 TCGA-AB-2998 AML48 8 65505727 65505727 A G SNP - - - - - - - - - - - - - - - tier3 577 4 0.69 383 244 38.92 0 0 NA 202127 TCGA-AB-2998 AML48 8 65597184 65597184 C T SNP LOC100129963 XM_001715427.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*32157 NULL 0.001 - - - no_errors tier3 689 4 0.58 437 363 45.38 0 0 NA 202127 TCGA-AB-2998 AML48 8 70264847 70264847 G T SNP ENSG00000211297 ENST00000388562 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29879 NULL 0.002 - - - pseudogene tier3 286 0 0 182 176 49.16 0 0 NA 202127 TCGA-AB-2998 AML48 8 72320536 72320536 G T SNP EYA1 NM_000503.4 human genbank 54_36p -1 reviewed intronic c.1051-1055 e10-1055 0 - - - no_errors tier3 946 8 0.84 540 413 43.34 0 0 NA 202127 TCGA-AB-2998 AML48 8 75850423 75850423 A G SNP PI15 NM_015886.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49617 NULL 0.007 - - - no_errors tier3 465 6 1.27 259 276 51.59 0 0 NA 202127 TCGA-AB-2998 AML48 8 76073566 76073566 A C SNP CRISPLD1 NM_031461.4 human genbank 54_36p 1 validated intronic c.258+12531 e1+12531 0 - - - no_errors tier3 2105 11 0.52 1016 819 44.58 0 0 NA 202127 TCGA-AB-2998 AML48 8 82962806 82962806 A G SNP SNX16 NM_022133.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-48030 NULL 0.098 - - - no_errors tier3 1128 6 0.53 572 480 45.58 0 0 NA 202127 TCGA-AB-2998 AML48 8 84445819 84445819 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 8 84687534 84687534 T A SNP - - - - - - - - - - - - - - - tier3 1043 5 0.48 909 762 45.57 0 0 NA 202127 TCGA-AB-2998 AML48 8 85227626 85227626 C A SNP RALYL NM_001100391.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-32163 NULL 0.104 - - - no_errors tier3 1404 6 0.43 1031 727 41.33 0 0 NA 202127 TCGA-AB-2998 AML48 8 85890367 85890367 T A SNP RALYL NM_001100391.1 human genbank 54_36p 1 validated intronic c.404+10775 e4+10775 0.003 - - - no_errors tier2 578 9 1.53 318 306 48.96 0 0 NA 202127 TCGA-AB-2998 AML48 8 97102261 97102261 C T SNP ENSG00000183663 ENST00000331024 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*47872 NULL 0.07 - - - no_coding_region:pseudogene tier2 1044 5 0.48 799 662 45.22 0 0 NA 202127 TCGA-AB-2998 AML48 8 108290382 108290382 G A SNP ENSG00000213707 ENST00000395823 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35169 NULL 0.001 - - - no_coding_region:pseudogene tier3 821 7 0.85 583 378 39.33 0 0 NA 202127 TCGA-AB-2998 AML48 8 109559739 109559739 C T SNP TTC35 NM_014673.3 human genbank 54_36p 1 provisional intronic c.703-672 e10-672 0 - - - no_errors tier3 490 8 1.6 386 280 41.92 2 1 33.33 202127 TCGA-AB-2998 AML48 8 113489340 113489340 T A SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.5605+383 e34+383 0.004 - - - no_errors tier3 734 3 0.41 439 338 43.44 0 0 NA 202127 TCGA-AB-2998 AML48 8 128697855 128697855 G C SNP - - - - - - - - - - - - - - - tier2 912 13 1.41 604 669 52.55 0 0 NA 202127 TCGA-AB-2998 AML48 8 129420191 129420191 C A SNP - - - - - - - - - - - - - - - tier3 1598 14 0.87 1137 799 41.23 0 0 NA 202127 TCGA-AB-2998 AML48 8 132019165 132019165 C T SNP ADCY8 NM_001115.2 human genbank 54_36p -1 reviewed intronic c.1354-537 e5-537 0.081 - - - no_errors tier2 552 4 0.72 348 346 49.86 0 0 NA 202127 TCGA-AB-2998 AML48 8 132428521 132428522 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 8 134921547 134921547 T C SNP - - - - - - - - - - - - - - - tier3 1292 9 0.69 1068 808 43.07 0 0 NA 202127 TCGA-AB-2998 AML48 8 139478043 139478043 A G SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.1-28616 e1-28616 0.001 - - - no_errors tier2 1245 9 0.72 789 637 44.67 0 0 NA 202127 TCGA-AB-2998 AML48 8 139983131 139983131 C T SNP COL22A1 NM_152888.1 human genbank 54_36p -1 validated intronic c.1+11913 e0+11913 0 - - - no_errors tier3 2108 17 0.8 1653 1140 40.79 0 0 NA 202127 TCGA-AB-2998 AML48 9 1038159 1038159 A T SNP DMRT2 NM_181872.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3455 NULL 0.001 - - - no_errors tier3 398 0 0 356 326 47.73 0 0 NA 202127 TCGA-AB-2998 AML48 9 7573293 7573293 T C SNP LOC392285 XR_017134.2 human genbank 54_36p 1 model intronic c.NULL NULL 0.017 - - - pseudogene tier3 1339 10 0.74 766 692 47.4 0 0 NA 202127 TCGA-AB-2998 AML48 9 11023967 11023967 G T SNP ENSG00000220830 ENST00000405905 human ensembl 54_36p 1 known 3_prime_flanking_region c.*20871 NULL 0.001 - - - no_coding_region:pseudogene tier3 562 8 1.4 310 204 39.69 0 0 NA 202127 TCGA-AB-2998 AML48 9 12394044 12394044 A G SNP - - - - - - - - - - - - - - - tier3 1456 9 0.61 1005 769 43.32 0 0 NA 202127 TCGA-AB-2998 AML48 9 23503823 23503823 T C SNP LOC100131398 XM_001716436.1 human genbank 54_36p 1 model intronic c.729-8073 e3-8073 0.093 - - - no_start_codon:pseudogene tier2 929 2 0.21 540 480 47.06 0 0 NA 202127 TCGA-AB-2998 AML48 9 23991567 23991567 G A SNP LOC286260 XM_001723591.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-0 NULL 0.055 - - - rna_with_coding_region tier3 438 2 0.45 301 292 49.24 0 0 NA 202127 TCGA-AB-2998 AML48 9 25520084 25520084 C A SNP - - - - - - - - - - - - - - - tier3 702 5 0.71 384 334 46.45 0 0 NA 202127 TCGA-AB-2998 AML48 9 25572748 25572748 G A SNP - - - - - - - - - - - - - - - tier2 897 1 0.11 524 488 48.17 0 0 NA 202127 TCGA-AB-2998 AML48 9 27284551 27284551 A G SNP C9orf11 NM_020641.1 human genbank 54_36p -1 provisional intronic c.203-151 e3-151 0 - - - no_errors tier2 542 5 0.91 444 319 41.75 0 0 NA 202127 TCGA-AB-2998 AML48 9 28389986 28389986 G A SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1-27120 e1-27120 0 - - - no_errors tier3 1538 14 0.9 761 599 44.04 0 0 NA 202127 TCGA-AB-2998 AML48 9 33400978 33400978 C A SNP AQP7 NM_001170.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-9718 NULL 0.001 - - - no_errors tier3 819 6 0.73 587 483 45.1 0 0 NA 202127 TCGA-AB-2998 AML48 9 33640640 33640640 G A SNP ENSG00000215206 ENST00000399779 human ensembl 54_36p 1 known intronic c.210+1169 e2+1169 0.022 - - - no_stop_codon tier3 1102 12 1.08 944 717 43.17 0 0 NA 202127 TCGA-AB-2998 AML48 9 93708210 93708210 G T SNP ROR2 NM_004560.2 human genbank 54_36p -1 reviewed intronic c.97+43760 e1+43760 0.006 - - - no_errors tier3 1651 12 0.72 1021 922 47.31 0 1 100 202127 TCGA-AB-2998 AML48 9 101194208 101194208 C T SNP - - - - - - - - - - - - - - - tier3 1282 11 0.85 874 700 44.47 0 0 NA 202127 TCGA-AB-2998 AML48 9 103746098 103746098 T C SNP - - - - - - - - - - - - - - - tier3 1365 10 0.73 837 740 46.89 0 0 NA 202127 TCGA-AB-2998 AML48 9 104225130 104225130 G T SNP - - - - - - - - - - - - - - - tier3 734 9 1.19 374 274 41.77 0 0 NA 202127 TCGA-AB-2998 AML48 9 111872563 111872563 T A SNP PALM2-AKAP2 NM_007203.3 human genbank 54_36p 1 validated intronic c.582+54423 e7+54423 0.04 - - - no_errors tier3 345 3 0.86 321 239 42.6 0 0 0 202127 TCGA-AB-2998 AML48 9 128553170 128553170 C T SNP - - - - - - - - - - - - - - - tier3 403 2 0.49 307 293 48.67 0 0 NA 202127 TCGA-AB-2998 AML48 9 132858453 132858453 G A SNP LAMC3 NM_006059.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15970 NULL 0.012 - - - no_errors tier3 1089 9 0.82 957 631 39.64 0 0 NA 202127 TCGA-AB-2998 AML48 9 138569622 138569622 C T SNP NOTCH1 NM_017617.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-9563 NULL 0.002 - - - no_errors tier2 102 2 1.92 89 67 42.95 0 0 NA 202127 TCGA-AB-2998 AML48 10 2212778 2212778 C A SNP LOC728347 XM_001714566.1 human genbank 54_36p -1 model intronic c.517+3556 e3+3556 0.004 - - - no_start_codon:pseudogene:no_stop_codon tier2 584 2 0.34 400 343 46.16 0 0 NA 202127 TCGA-AB-2998 AML48 10 2301562 2301562 G T SNP LOC728209 XM_001126868.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*47423 NULL 0.001 - - - no_errors tier3 895 8 0.88 475 373 43.93 0 0 NA 202127 TCGA-AB-2998 AML48 10 8604882 8604882 G A SNP ENSG00000220584 ENST00000403012 human ensembl 54_36p -1 known 5_prime_flanking_region c.-7807 NULL 0 - - - no_coding_region:pseudogene tier3 551 2 0.36 323 271 45.62 0 0 NA 202127 TCGA-AB-2998 AML48 10 9028206 9028206 T C SNP - - - - - - - - - - - - - - - tier3 1387 18 1.28 813 764 48.45 0 0 NA 202127 TCGA-AB-2998 AML48 10 10558206 10558206 C T SNP - - - - - - - - - - - - - - - tier3 789 1 0.13 335 262 43.89 0 0 NA 202127 TCGA-AB-2998 AML48 10 21184569 21184569 G A SNP NEBL NM_006393.2 human genbank 54_36p -1 validated intronic c.903+2606 e9+2606 0.001 - - - no_errors tier3 1157 10 0.86 688 646 48.39 0 0 NA 202127 TCGA-AB-2998 AML48 10 23909217 23909217 C T SNP LOC729432 XM_001130241.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-48495 NULL 0 - - - no_errors tier3 1502 15 0.99 963 846 46.77 0 0 NA 202127 TCGA-AB-2998 AML48 10 26197764 26197764 T C SNP ENSG00000209544 ENST00000386809 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49403 NULL 0.007 - - - pseudogene tier3 1307 10 0.76 873 716 45.03 0 0 NA 202127 TCGA-AB-2998 AML48 10 29268672 29268672 C T SNP LOC653665 XM_001723025.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-40292 NULL 0 - - - pseudogene tier3 1198 11 0.91 896 806 47.36 0 0 NA 202127 TCGA-AB-2998 AML48 10 34852412 34852412 A G SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional intronic c.223-6319 e3-6319 0.014 - - - no_errors tier3 1259 9 0.71 814 654 44.49 0 0 NA 202127 TCGA-AB-2998 AML48 10 37399092 37399092 T G SNP - - - - - - - - - - - - - - - tier3 513 3 0.58 418 323 43.59 0 0 NA 202127 TCGA-AB-2998 AML48 10 37965023 37965023 A G SNP ENSG00000216650 ENST00000407130 human ensembl 54_36p -1 known 5_prime_flanking_region c.-34721 NULL 0 - - - no_coding_region:pseudogene tier3 676 5 0.73 601 401 39.98 0 0 NA 202127 TCGA-AB-2998 AML48 10 46550312 46550312 G A SNP ENSG00000215065 ENST00000399538 human ensembl 54_36p 1 novel intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 1113 13 1.15 1104 285 20.49 0 0 0 202127 TCGA-AB-2998 AML48 10 48112066 48112066 C T SNP ENSG00000221361 ENST00000408434 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-35057 NULL 0.001 - - - no_errors tier3 452 2 0.44 289 243 45.68 0 0 NA 202127 TCGA-AB-2998 AML48 10 53717611 53717611 A G SNP PRKG1 NM_006258.1 human genbank 54_36p 1 validated intronic c.1710-881 e15-881 0.003 - - - no_errors tier3 1336 12 0.89 703 696 49.75 0 0 NA 202127 TCGA-AB-2998 AML48 10 57374751 57374751 G A SNP - - - - - - - - - - - - - - - tier3 849 8 0.93 404 372 47.88 0 0 NA 202127 TCGA-AB-2998 AML48 10 57644270 57644270 T C SNP - - - - - - - - - - - - - - - tier3 1238 2 0.16 1045 170 13.99 0 0 NA 202127 TCGA-AB-2998 AML48 10 57969106 57969106 T A SNP - - - - - - - - - - - - - - - tier3 635 4 0.62 443 341 43.49 0 0 NA 202127 TCGA-AB-2998 AML48 10 58142636 58142636 C T SNP - - - - - - - - - - - - - - - tier3 1503 10 0.66 951 760 44.39 0 0 NA 202127 TCGA-AB-2998 AML48 10 58180232 58180232 A G SNP - - - - - - - - - - - - - - - tier3 841 8 0.94 589 361 38 0 0 NA 202127 TCGA-AB-2998 AML48 10 59321160 59321160 T G SNP - - - - - - - - - - - - - - - tier3 1316 14 1.05 841 655 43.72 0 0 NA 202127 TCGA-AB-2998 AML48 10 61637123 61637123 T C SNP ANK3 NM_020987.2 human genbank 54_36p -1 reviewed intronic c.1194+677 e10+677 0 - - - no_errors tier3 797 13 1.6 569 424 42.66 0 0 0 202127 TCGA-AB-2998 AML48 10 61768866 61768867 - A INS ANK3 NM_020987.2 human genbank 54_36p -1 reviewed intronic c.114+50322_114+50321 e1+50322 0.901:0.592 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 10 84172759 84172759 T G SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.953+64155 e2+64155 0.001 - - - no_errors tier3 1130 7 0.62 889 673 43.06 0 0 NA 202127 TCGA-AB-2998 AML48 10 102646918 102646918 T C SNP FAM178A NM_018121.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-15940 NULL 0.013 - - - no_errors tier3 715 7 0.97 443 409 48 0 0 NA 202127 TCGA-AB-2998 AML48 10 107163227 107163227 G A SNP - - - - - - - - - - - - - - - tier3 524 5 0.95 352 205 36.8 0 0 NA 202127 TCGA-AB-2998 AML48 10 113625451 113625451 C T SNP - - - - - - - - - - - - - - - tier3 730 5 0.68 573 273 32.27 0 0 NA 202127 TCGA-AB-2998 AML48 10 122264578 122264578 C T SNP PPAPDC1A NM_001030059.1 human genbank 54_36p 1 validated intronic c.256+1075 e3+1075 0 - - - no_errors tier3 1260 7 0.55 819 712 46.51 0 0 NA 202127 TCGA-AB-2998 AML48 10 122479448 122479448 A G SNP - - - - - - - - - - - - - - - tier3 843 6 0.71 513 348 40.37 0 0 NA 202127 TCGA-AB-2998 AML48 10 123174084 123174084 G A SNP ENSG00000222979 ENST00000411047 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13380 NULL 0 - - - no_errors tier3 670 5 0.74 359 283 43.94 0 0 NA 202127 TCGA-AB-2998 AML48 10 128822847 128822847 C T SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.2784+6829 e27+6829 0 - - - no_errors tier3 1188 6 0.5 653 598 47.73 0 0 NA 202127 TCGA-AB-2998 AML48 10 129889105 129889105 C T SNP - - - - - - - - - - - - - - - tier3 931 9 0.96 561 437 43.79 0 0 NA 202127 TCGA-AB-2998 AML48 10 131061977 131061977 G C SNP - - - - - - - - - - - - - - - tier3 1209 16 1.31 890 588 39.76 0 0 NA 202127 TCGA-AB-2998 AML48 11 1616982 1616982 C T SNP KRTAP5-3 NM_001012708.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-30791 NULL 0.003 - - - no_errors tier3 624 5 0.79 619 522 45.71 0 0 NA 202127 TCGA-AB-2998 AML48 11 1937456 1937456 G A SNP MRPL23 ENST00000397297 human ensembl 54_36p 1 known intronic c.297+6795 e4+6795 0 - - - no_errors tier2 188 2 1.05 240 238 49.58 1 2 66.67 202127 TCGA-AB-2998 AML48 11 4950881 4950881 G A SNP OR51A5P ENST00000404120 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-4950881 NULL 0 - - - no_coding_region:pseudogene tier3 1483 13 0.87 781 703 47.34 0 0 NA 202127 TCGA-AB-2998 AML48 11 5662777 5662778 AA - DEL TRIM5 NM_033034.1 human genbank 54_36p -1 reviewed 5_prime_untranslated_region c.-4794 NULL 0.001:0.002 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 11 7213520 7213520 C A SNP SYT9 NM_175733.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-16474 NULL 0.01 - - - no_errors tier3 1477 11 0.74 913 851 48.19 0 0 NA 202127 TCGA-AB-2998 AML48 11 8139946 8139946 C T SNP RIC3 NM_024557.1 human genbank 54_36p -1 validated intronic c.124+7043 e1+7043 0.051 - - - no_errors tier3 4101 35 0.85 2447 1989 44.79 0 0 NA 202127 TCGA-AB-2998 AML48 11 13094056 13094056 G A SNP - - - - - - - - - - - - - - - tier3 1040 8 0.76 763 720 48.42 0 0 NA 202127 TCGA-AB-2998 AML48 11 14047009 14047009 G A SNP SPON1 ENST00000310358 human ensembl 54_36p 1 known intronic c.480-6459 e4-6459 0 - - - no_errors tier3 1667 22 1.3 1075 934 46.49 0 0 NA 202127 TCGA-AB-2998 AML48 11 28654769 28654769 C A SNP - - - - - - - - - - - - - - - tier2 1251 8 0.63 774 586 43.09 0 0 NA 202127 TCGA-AB-2998 AML48 11 32507064 32507064 G A SNP - - - - - - - - - - - - - - - tier3 765 4 0.52 445 393 46.79 0 0 NA 202127 TCGA-AB-2998 AML48 11 39753786 39753786 A - DEL ENSG00000209665 ENST00000386930 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-8711 NULL 0.026 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 11 49827907 49827907 T C SNP LOC387770 XR_017307.2 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - pseudogene tier3 352 3 0.85 271 237 46.56 0 0 NA 202127 TCGA-AB-2998 AML48 11 57060921 57060921 C T SNP TIMM10 NM_012456.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-6683 NULL 0.009 - - - no_errors tier3 291 2 0.68 202 191 48.11 0 1 100 202127 TCGA-AB-2998 AML48 11 57135442 57135442 T C SNP SERPING1 NM_000062.2 human genbank 54_36p 1 reviewed intronic c.1030-324 e6-324 0 - - - no_errors tier3 911 12 1.3 698 672 48.98 5 2 28.57 202127 TCGA-AB-2998 AML48 11 62038513 62038513 G A SNP AHNAK NM_024060.1 human genbank 54_36p -1 validated intronic c.342+20538 e2+20538 0 - - - no_errors tier3 1503 20 1.31 1119 961 46.2 0 0 0 202127 TCGA-AB-2998 AML48 11 73667951 73667951 T C SNP P4HA3 NM_182904.3 human genbank 54_36p -1 reviewed intronic c.1175+130 e8+130 0.008 - - - no_errors tier3 1426 14 0.97 895 819 47.76 0 0 NA 202127 TCGA-AB-2998 AML48 11 79274423 79274423 A T SNP - - - - - - - - - - - - - - - tier3 1594 11 0.68 1102 881 44.27 0 0 NA 202127 TCGA-AB-2998 AML48 11 79352173 79352173 G A SNP - - - - - - - - - - - - - - - tier3 2220 15 0.67 1188 1029 46.39 0 0 NA 202127 TCGA-AB-2998 AML48 11 80221204 80221204 C T SNP - - - - - - - - - - - - - - - tier3 828 4 0.48 468 475 50.37 0 0 NA 202127 TCGA-AB-2998 AML48 11 91818971 91818971 C G SNP FAT3 NM_001008781.2 human genbank 54_36p 1 validated intronic c.3293-78477 e2-78477 0 - - - no_errors tier3 1426 12 0.83 764 707 48.03 0 0 NA 202127 TCGA-AB-2998 AML48 11 98660996 98660996 G A SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1-40291 e1-40291 0.007 - - - no_errors tier3 408 0 0 323 129 28.48 0 0 NA 202127 TCGA-AB-2998 AML48 11 105431990 105431990 A C SNP KBTBD3 NM_152433.3 human genbank 54_36p -1 validated intronic c.234-1598 e2-1598 0.087 - - - no_errors tier2 572 3 0.52 303 281 48.12 0 0 0 202127 TCGA-AB-2998 AML48 11 110482101 110482101 A C SNP - - - - - - - - - - - - - - - tier3 1409 8 0.56 728 728 49.93 0 0 NA 202127 TCGA-AB-2998 AML48 11 110574123 110574123 T C SNP - - - - - - - - - - - - - - - tier2 1189 8 0.67 870 759 46.42 0 0 NA 202127 TCGA-AB-2998 AML48 11 118962695 118962695 G A SNP - - - - - - - - - - - - - - - tier3 466 1 0.21 340 262 43.45 0 0 NA 202127 TCGA-AB-2998 AML48 11 124460766 124460766 G A SNP SLC37A2 NM_198277.1 human genbank 54_36p 1 validated missense c.1411 p.V471I 0.02 superfamily_MFS_gen_substrate_transporter "HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter" - no_errors tier1 529 2 0.38 433 401 48.08 2 2 50 202127 TCGA-AB-2998 AML48 11 126028646 126028646 C T SNP KIRREL3 NM_032531.2 human genbank 54_36p -1 provisional intronic c.56-90629 e2-90629 0 - - - no_errors tier3 728 7 0.95 441 495 52.77 0 0 NA 202127 TCGA-AB-2998 AML48 11 127314335 127314335 A C SNP LOC387820 XR_017453.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*1013 NULL 0.044 - - - pseudogene tier3 1076 14 1.28 698 678 49.2 0 0 NA 202127 TCGA-AB-2998 AML48 11 131934560 131934560 A G SNP OPCML NM_002545.1 human genbank 54_36p -1 reviewed intronic c.401-30270 e3-30270 1 - - - no_errors tier2 546 1 0.18 235 287 54.98 0 0 NA 202127 TCGA-AB-2998 AML48 11 133038901 133038901 G A SNP - - - - - - - - - - - - - - - tier3 1598 12 0.75 884 779 46.81 0 0 NA 202127 TCGA-AB-2998 AML48 11 133845799 133845799 T G SNP ENSG00000216049 ENST00000401230 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19856 NULL 0.006 - - - no_errors tier3 610 8 1.29 500 348 40.94 0 0 NA 202127 TCGA-AB-2998 AML48 12 1532391 1532391 T C SNP FBXL14 NM_152441.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*13784 NULL 0.002 - - - no_errors tier3 1535 18 1.16 893 693 43.67 0 0 NA 202127 TCGA-AB-2998 AML48 12 12766924 12766924 A T SNP GPR19 ENST00000332427 human ensembl 54_36p -1 known 5_prime_flanking_region c.-60275 NULL 1 - - - no_errors tier3 602 3 0.5 400 324 44.69 2 2 50 202127 TCGA-AB-2998 AML48 12 22822031 22822031 G T SNP - - - - - - - - - - - - - - - tier2 1375 6 0.43 934 657 41.24 0 0 NA 202127 TCGA-AB-2998 AML48 12 32649817 32649817 A G SNP FGD4 NM_139241.2 human genbank 54_36p 1 reviewed intronic c.994-2341 e6-2341 0.037 - - - no_errors tier3 1045 7 0.66 589 462 43.92 0 0 0 202127 TCGA-AB-2998 AML48 12 36779939 36779939 C T SNP ENSG00000209796 ENST00000387061 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-37776 NULL 0 - - - pseudogene tier2 631 8 1.25 421 458 52.05 0 0 NA 202127 TCGA-AB-2998 AML48 12 39476306 39476306 A T SNP CNTN1 NM_001843.2 human genbank 54_36p 1 reviewed intronic c.1+103645 e0+103645 0.008 - - - no_errors tier3 1108 11 0.98 771 710 47.91 0 0 NA 202127 TCGA-AB-2998 AML48 12 47868189 47868189 C T SNP TUBA1A NM_006009.2 human genbank 54_36p -1 reviewed intronic c.3+838 e1+838 0.001 - - - no_errors tier2 1200 13 1.07 781 707 47.48 11 13 54.17 202127 TCGA-AB-2998 AML48 12 49344586 49344586 T C SNP DIP2B NM_173602.2 human genbank 54_36p 1 validated intronic c.427+4217 e4+4217 0.711 - - - no_errors tier3 943 10 1.05 684 586 46.14 2 1 33.33 202127 TCGA-AB-2998 AML48 12 53604301 53604301 T G SNP KIAA0748 NM_001098815.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*36919 NULL 0.073 - - - no_errors tier3 542 4 0.73 324 259 44.43 0 0 NA 202127 TCGA-AB-2998 AML48 12 54787269 54787269 G A SNP PA2G4 NM_006191.2 human genbank 54_36p 1 reviewed missense c.355 p.A119T 1 "HMMPfam_Peptidase_M24,superfamily_Peptidase_M24_cat_core,PatternScan_MAP_2" "HMMPfam_Peptidase_M24,superfamily_Peptidase_M24_cat_core,PatternScan_MAP_2,superfamily_SSF46785" - no_errors tier1 577 12 2.04 411 371 47.44 52 61 53.98 202127 TCGA-AB-2998 AML48 12 63232301 63232301 G A SNP ENSG00000223294 ENST00000411362 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23411 NULL 0.001 - - - no_errors tier3 1242 7 0.56 893 483 35.05 0 0 NA 202127 TCGA-AB-2998 AML48 12 68877301 68877301 T C SNP CNOT2 NM_014515.4 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-80973 NULL 0 - - - no_errors tier3 1016 6 0.59 588 611 50.96 0 2 100 202127 TCGA-AB-2998 AML48 12 72065294 72065294 G T SNP - - - - - - - - - - - - - - - tier3 1462 18 1.21 796 642 44.61 0 0 NA 202127 TCGA-AB-2998 AML48 12 74544802 74544802 C T SNP - - - - - - - - - - - - - - - tier3 2238 19 0.84 1393 1333 48.9 0 0 NA 202127 TCGA-AB-2998 AML48 12 82490623 82490623 T C SNP - - - - - - - - - - - - - - - tier3 1253 10 0.79 900 683 43.12 0 0 NA 202127 TCGA-AB-2998 AML48 12 83587369 83587369 T A SNP - - - - - - - - - - - - - - - tier3 509 5 0.97 307 270 46.79 0 0 NA 202127 TCGA-AB-2998 AML48 12 95158680 95158680 C G SNP ELK3 NM_005230.2 human genbank 54_36p 1 reviewed intronic c.208-6169 e2-6169 0 - - - no_errors tier3 908 6 0.65 466 506 52 0 0 0 202127 TCGA-AB-2998 AML48 12 96486953 96486954 - T INS MIRN135A2 ENST00000384854 human ensembl 54_36p 1 known 3_prime_flanking_region c.*5133 NULL 0.003:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 12 100147144 100147144 G A SNP SLC5A8 NM_145913.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19387 NULL 0 - - - no_errors tier3 603 4 0.66 349 313 47.28 0 0 NA 202127 TCGA-AB-2998 AML48 12 101316833 101316833 A T SNP IGF1 NM_000618.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*3582 NULL 0.763 - - - no_errors tier3 1582 14 0.88 1184 843 41.57 0 0 NA 202127 TCGA-AB-2998 AML48 12 102290580 102290580 T A SNP C12orf42 NM_001099336.1 human genbank 54_36p -1 validated intronic c.148-3674 e3-3674 0.004 - - - no_errors tier2 2331 12 0.51 1537 1424 47.95 0 0 NA 202127 TCGA-AB-2998 AML48 12 105290884 105290884 A G SNP POLR3B NM_018082.4 human genbank 54_36p 1 provisional intronic c.404+3293 e6+3293 0.172 - - - no_errors tier3 566 5 0.88 420 236 35.92 0 0 0 202127 TCGA-AB-2998 AML48 12 107080631 107080631 G C SNP WSCD2 NM_014653.2 human genbank 54_36p 1 validated intronic c.1-32558 e1-32558 0 - - - no_errors tier2 801 2 0.25 537 462 46.25 0 0 NA 202127 TCGA-AB-2998 AML48 12 112952529 112952529 G A SNP - - - - - - - - - - - - - - - tier2 344 2 0.58 178 136 43.17 0 0 NA 202127 TCGA-AB-2998 AML48 12 113105136 113105136 G A SNP - - - - - - - - - - - - - - - tier2 702 8 1.12 498 365 42.29 0 0 NA 202127 TCGA-AB-2998 AML48 12 130196691 130196691 T C SNP ENSG00000204603 ENST00000376678 human ensembl 54_36p 1 known 5_prime_flanking_region c.-18930 NULL 0 - - - no_errors tier3 74 0 0 64 51 44.35 0 0 NA 202127 TCGA-AB-2998 AML48 12 130297343 130297343 A G SNP LOC100128002 XM_001719995.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-49551 NULL 0 - - - no_errors tier3 240 1 0.41 173 120 40.82 0 0 NA 202127 TCGA-AB-2998 AML48 13 24912771 24912771 A G SNP ATP8A2 NM_016529.4 human genbank 54_36p 1 validated intronic c.77-28344 e2-28344 0 - - - no_errors tier3 2472 13 0.52 1523 1256 45.13 0 0 NA 202127 TCGA-AB-2998 AML48 13 26816433 26816433 G A SNP ENSG00000209438 ENST00000386703 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-552 NULL 0 - - - pseudogene tier3 1080 13 1.19 679 728 51.67 0 0 NA 202127 TCGA-AB-2998 AML48 13 27506255 27506256 - ATCATATTCATATTCTCTGAA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1801_1800 p.600in_frame_insFREYEYD 1.000:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 202127 TCGA-AB-2998 AML48 13 29188867 29188867 G A SNP UBL3 NM_007106.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*50525 NULL 0 - - - no_errors tier3 638 2 0.31 425 375 46.82 0 0 NA 202127 TCGA-AB-2998 AML48 13 33849294 33849294 T A SNP - - - - - - - - - - - - - - - tier3 1083 5 0.46 889 650 42.21 0 0 NA 202127 TCGA-AB-2998 AML48 13 46358116 46358116 C T SNP HTR2A NM_000621.2 human genbank 54_36p -1 validated intronic c.613+6410 e2+6410 0 - - - no_errors tier3 620 9 1.43 401 346 46.19 0 0 NA 202127 TCGA-AB-2998 AML48 13 52665698 52665698 G C SNP ENSG00000218221 ENST00000401786 human ensembl 54_36p 1 known 5_prime_flanking_region c.-6419 NULL 0.003 - - - no_coding_region:pseudogene tier3 731 6 0.81 507 417 45.13 0 0 NA 202127 TCGA-AB-2998 AML48 13 52952847 52952847 G T SNP - - - - - - - - - - - - - - - tier2 621 6 0.96 399 315 44.12 0 0 NA 202127 TCGA-AB-2998 AML48 13 54938095 54938095 C T SNP - - - - - - - - - - - - - - - tier3 1188 7 0.59 730 575 44.06 0 0 NA 202127 TCGA-AB-2998 AML48 13 57484623 57484623 G A SNP ENSG00000202422 ENST00000365552 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21024 NULL 0.001 - - - no_errors tier2 1295 2 0.15 693 566 44.89 0 0 NA 202127 TCGA-AB-2998 AML48 13 62193403 62193403 C A SNP - - - - - - - - - - - - - - - tier3 1195 5 0.42 810 601 42.59 0 0 NA 202127 TCGA-AB-2998 AML48 13 63805076 63805076 A T SNP - - - - - - - - - - - - - - - tier3 1417 12 0.84 731 692 48.53 0 0 NA 202127 TCGA-AB-2998 AML48 13 64856832 64856832 T A SNP - - - - - - - - - - - - - - - tier2 461 4 0.86 296 239 44.67 0 0 NA 202127 TCGA-AB-2998 AML48 13 79098382 79098382 A T SNP - - - - - - - - - - - - - - - tier3 628 2 0.32 384 295 43.45 0 0 NA 202127 TCGA-AB-2998 AML48 13 86518580 86518580 T C SNP - - - - - - - - - - - - - - - tier3 316 1 0.32 187 168 47.32 0 0 NA 202127 TCGA-AB-2998 AML48 13 89149161 89149161 C T SNP - - - - - - - - - - - - - - - tier3 349 1 0.29 239 174 42.03 0 0 NA 202127 TCGA-AB-2998 AML48 13 97782829 97782829 G T SNP FARP1 NM_005766.2 human genbank 54_36p 1 reviewed intronic c.172-11188 e2-11188 0 - - - no_errors tier3 1147 8 0.69 687 516 42.86 0 0 NA 202127 TCGA-AB-2998 AML48 13 100385454 100385454 T G SNP - - - - - - - - - - - - - - - tier3 1589 7 0.44 1023 774 43.07 0 0 NA 202127 TCGA-AB-2998 AML48 13 100489536 100489536 C A SNP NALCN NM_052867.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*16112 NULL 0 - - - no_errors tier2 1310 13 0.98 976 744 43.23 0 0 NA 202127 TCGA-AB-2998 AML48 13 103656331 103656331 A T SNP - - - - - - - - - - - - - - - tier3 452 2 0.44 250 204 44.93 0 0 NA 202127 TCGA-AB-2998 AML48 13 111686379 111686379 C T SNP - - - - - - - - - - - - - - - tier3 971 2 0.21 671 576 46.19 0 0 NA 202127 TCGA-AB-2998 AML48 13 113057166 113057166 A G SNP GRTP1 NM_024719.2 human genbank 54_36p -1 validated intronic c.340+473 e3+473 0.004 - - - no_errors tier3 281 1 0.35 220 138 38.55 0 0 0 202127 TCGA-AB-2998 AML48 14 29147066 29147066 C T SNP PRKD1 NM_002742.2 human genbank 54_36p -1 validated intronic c.1906-8292 e14-8292 0 - - - no_errors tier3 770 12 1.53 435 367 45.76 0 0 NA 202127 TCGA-AB-2998 AML48 14 29780317 29780317 G A SNP - - - - - - - - - - - - - - - tier3 636 2 0.31 399 410 50.68 0 0 NA 202127 TCGA-AB-2998 AML48 14 35972980 35972980 A C SNP SFTA3 NM_001101341.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*39834 NULL 0 - - - no_errors tier2 1158 8 0.68 771 731 48.67 0 0 NA 202127 TCGA-AB-2998 AML48 14 38779336 38779336 G A SNP MIA2 NM_054024.3 human genbank 54_36p 1 validated intronic c.250-180 e3-180 0 - - - no_errors tier3 475 1 0.21 344 230 40.07 0 0 0 202127 TCGA-AB-2998 AML48 14 39841960 39841960 G T SNP - - - - - - - - - - - - - - - tier3 707 4 0.56 419 342 44.94 0 0 NA 202127 TCGA-AB-2998 AML48 14 46422763 46422763 G T SNP MDGA2 NM_182830.1 human genbank 54_36p -1 validated intronic c.1345-1589 e7-1589 0.002 - - - no_errors tier3 585 3 0.51 307 208 40.39 0 0 NA 202127 TCGA-AB-2998 AML48 14 56598319 56598319 T G SNP LOC440180 XR_017569.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*19344 NULL 0 - - - pseudogene tier3 519 6 1.14 345 285 45.24 0 0 NA 202127 TCGA-AB-2998 AML48 14 62143166 62143166 T A SNP - - - - - - - - - - - - - - - tier2 1224 14 1.13 797 726 47.54 0 0 NA 202127 TCGA-AB-2998 AML48 14 80094083 80094083 G A SNP C14orf145 NM_152446.3 human genbank 54_36p -1 validated intronic c.2880+1293 e19+1293 0 - - - no_errors tier3 391 0 0 346 172 33.2 0 2 100 202127 TCGA-AB-2998 AML48 14 84709713 84709713 G C SNP ENSG00000222836 ENST00000410904 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-15280 NULL 0.892 - - - no_errors tier3 688 8 1.15 398 364 47.77 0 0 NA 202127 TCGA-AB-2998 AML48 14 87624158 87624158 C A SNP - - - - - - - - - - - - - - - tier3 1056 12 1.12 746 708 48.63 0 0 NA 202127 TCGA-AB-2998 AML48 14 93411032 93411032 A G SNP FAM181A NM_138344.3 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-50339 NULL 0.01 - - - no_errors tier3 1288 10 0.77 882 803 47.51 0 0 NA 202127 TCGA-AB-2998 AML48 14 93429708 93429708 G A SNP FAM181A NM_138344.3 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-31663 NULL 0.001 - - - no_errors tier2 805 1 0.12 488 420 46.26 0 0 NA 202127 TCGA-AB-2998 AML48 14 94531071 94531072 - A INS LOC730118 XM_001134296.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-32246 NULL 0.002:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 14 104765067 104765067 G A SNP BRF1 NM_001519.2 human genbank 54_36p -1 reviewed intronic c.789-925 e8-925 0 - - - no_errors tier3 246 3 1.2 57 60 51.28 2 0 0 202127 TCGA-AB-2998 AML48 15 21635550 21635550 C T SNP - - - - - - - - - - - - - - - tier3 820 5 0.61 415 400 49.02 0 0 NA 202127 TCGA-AB-2998 AML48 15 27276120 27276120 G A SNP uc010azk.1 ENST00000261275 human ensembl 54_36p -1 known 5_prime_flanking_region c.-75 NULL 0 - - - no_start_codon tier3 1507 12 0.79 1066 941 46.86 0 0 NA 202127 TCGA-AB-2998 AML48 15 27835387 27835387 T A SNP TJP1 NM_003257.3 human genbank 54_36p -1 validated intronic c.1010+5247 e8+5247 0.001 - - - no_errors tier3 898 5 0.55 600 543 47.42 0 0 NA 202127 TCGA-AB-2998 AML48 15 34105525 34105525 C A SNP - - - - - - - - - - - - - - - tier3 801 7 0.87 463 398 46.23 0 0 NA 202127 TCGA-AB-2998 AML48 15 35269319 35269319 A G SNP - - - - - - - - - - - - - - - tier3 1385 4 0.29 1118 173 13.37 0 0 NA 202127 TCGA-AB-2998 AML48 15 36173702 36173702 C T SNP LOC728288 XM_001128351.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*21001 NULL 0 - - - no_errors tier3 1653 9 0.54 947 700 42.4 0 0 NA 202127 TCGA-AB-2998 AML48 15 41613355 41613355 G C SNP HISPPD2A NM_014659.3 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*809 NULL 0.228 - - - no_errors tier3 482 4 0.82 352 314 47.15 8 6 42.86 202127 TCGA-AB-2998 AML48 15 43058360 43058360 G A SNP C15orf43 NM_152448.1 human genbank 54_36p 1 predicted 3_prime_untranslated_region c.*242 NULL 0.001 - - - no_errors tier3 681 4 0.58 464 345 42.44 0 0 NA 202127 TCGA-AB-2998 AML48 15 44300264 44300264 C T SNP - - - - - - - - - - - - - - - tier3 1431 15 1.04 885 788 47.07 0 0 NA 202127 TCGA-AB-2998 AML48 15 49179081 49179081 C T SNP TNFAIP8L3 NM_207381.2 human genbank 54_36p -1 provisional intronic c.173-4905 e2-4905 0.001 - - - no_errors tier3 1550 20 1.27 931 1055 53.12 0 0 NA 202127 TCGA-AB-2998 AML48 15 55725490 55725490 G A SNP GCOM1 NM_001018090.1 human genbank 54_36p 1 reviewed intronic c.1119+6455 e10+6455 0.006 - - - no_errors tier3 721 2 0.28 491 419 45.99 0 0 NA 202127 TCGA-AB-2998 AML48 15 59539845 59539845 C - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 15 61753611 61753611 C T SNP HERC1 NM_003922.3 human genbank 54_36p -1 reviewed missense c.7829 p.G2610E 1 NULL "HMMPfam_RCC1,PatternScan_RCC1_2,HMMPfam_HECT,HMMSmart_SM00119,superfamily_Hect E3 ligase catalytic domain,HMMSmart_SM00320,HMMPfam_SPRY,PatternScan_ARGINASE_2,PatternScan_PHOSPHOPANTETHEINE,superfamily_RCC1/BLIP-II,superfamily_WD40 repeat-like,HMMSmart_SM00449,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 1160 9 0.77 661 576 46.49 26 14 35 202127 TCGA-AB-2998 AML48 15 65448243 65448243 A G SNP IQCH NM_001031715.1 human genbank 54_36p 1 provisional intronic c.754-3260 e9-3260 0 - - - no_errors tier3 1041 6 0.57 686 499 42.07 1 0 0 202127 TCGA-AB-2998 AML48 15 67221824 67221824 G T SNP GLCE NM_015554.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-113376 NULL 0.019 - - - no_errors tier3 773 6 0.77 501 392 43.85 0 0 NA 202127 TCGA-AB-2998 AML48 15 69446421 69446421 G A SNP THSD4 NM_024817.2 human genbank 54_36p 1 provisional intronic c.1016-44659 e6-44659 0.001 - - - no_errors tier3 1565 15 0.95 908 989 52.11 0 0 NA 202127 TCGA-AB-2998 AML48 15 75583528 75583528 C A SNP HMG20A NM_018200.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*24816 NULL 0.002 - - - no_errors tier3 629 2 0.32 458 435 48.66 0 0 NA 202127 TCGA-AB-2998 AML48 15 75720964 75720964 C T SNP LINGO1 NM_032808.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9252 NULL 1 - - - no_errors tier2 341 6 1.73 262 242 47.92 0 0 NA 202127 TCGA-AB-2998 AML48 15 78579347 78579347 C G SNP ARNT2 NM_014862.3 human genbank 54_36p 1 reviewed intronic c.623-8205 e6-8205 0 - - - no_errors tier3 768 12 1.54 443 392 46.95 0 0 NA 202127 TCGA-AB-2998 AML48 15 84646492 84646492 A G SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.2236+6849 e15+6849 0.003 - - - no_errors tier3 565 5 0.88 346 299 46.36 0 0 NA 202127 TCGA-AB-2998 AML48 15 88010109 88010109 G T SNP PLIN NM_002666.1 human genbank 54_36p -1 reviewed silent c.1278 p.V426 0.001 NULL HMMPfam_Perilipin - no_errors tier1 185 4 2.12 127 119 48.37 NA 202127 TCGA-AB-2998 AML48 15 89479189 89479189 C T SNP SV2B ENST00000394232 human ensembl 54_36p 1 known intronic c.1+34592 e0+34592 0 - - - no_errors tier3 1854 13 0.69 1474 1165 44.13 0 0 NA 202127 TCGA-AB-2998 AML48 15 93537125 93537125 G C SNP - - - - - - - - - - - - - - - tier3 992 5 0.5 524 475 47.55 0 0 NA 202127 TCGA-AB-2998 AML48 15 95711713 95711713 C T SNP ENSG00000208890 ENST00000386155 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13753 NULL 0.021 - - - pseudogene tier3 501 11 2.15 268 313 53.69 0 0 NA 202127 TCGA-AB-2998 AML48 15 96040742 96040742 C T SNP - - - - - - - - - - - - - - - tier3 787 5 0.63 500 341 40.55 0 0 NA 202127 TCGA-AB-2998 AML48 15 98532482 98532482 G T SNP ADAMTS17 NM_139057.2 human genbank 54_36p -1 reviewed intronic c.1182-19434 e9-19434 0.001 - - - no_errors tier3 769 6 0.77 529 494 48.24 0 0 NA 202127 TCGA-AB-2998 AML48 16 7898026 7898026 T A SNP ENSG00000222109 ENST00000410177 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-8592 NULL 0.015 - - - no_errors tier3 588 3 0.51 444 284 38.96 0 0 NA 202127 TCGA-AB-2998 AML48 16 20806261 20806261 G A SNP DCUN1D3 NM_173475.2 human genbank 54_36p -1 validated intronic c.1+12766 e0+12766 0 - - - no_errors tier3 829 7 0.84 617 554 47.31 5 3 37.5 202127 TCGA-AB-2998 AML48 16 22860989 22860989 G C SNP HS3ST2 NM_006043.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*26605 NULL 1 - - - no_errors tier2 2188 31 1.4 1438 1208 45.65 0 0 NA 202127 TCGA-AB-2998 AML48 16 25875194 25875194 C T SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.735-179240 e2-179240 0.001 - - - no_errors tier3 925 5 0.54 675 622 47.88 0 0 NA 202127 TCGA-AB-2998 AML48 16 27839656 27839656 C G SNP GSG1L NM_001109763.1 human genbank 54_36p -1 validated intronic c.398-36196 e3-36196 0.002 - - - no_errors tier3 2205 31 1.39 1165 985 45.77 2 2 50 202127 TCGA-AB-2998 AML48 16 45657671 45657671 G A SNP NETO2 NM_018092.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*16962 NULL 0.003 - - - no_errors tier2 964 8 0.82 608 509 45.53 0 0 NA 202127 TCGA-AB-2998 AML48 16 54780607 54780607 G - DEL GNAO1 NM_020988.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3042 NULL 0.999 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 16 59370313 59370313 A G SNP - - - - - - - - - - - - - - - tier3 1067 10 0.93 549 440 44.49 0 0 NA 202127 TCGA-AB-2998 AML48 16 62681190 62681190 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 16 68042577 68042577 T A SNP CYB5B NM_030579.2 human genbank 54_36p 1 validated intronic c.333+3029 e3+3029 0.06 - - - no_errors tier2 555 1 0.18 402 355 46.9 3 9 75 202127 TCGA-AB-2998 AML48 16 69662674 69662674 A G SNP HYDIN NM_032821.2 human genbank 54_36p -1 validated intronic c.1739-1768 e13-1768 0.113 - - - no_errors tier3 1460 11 0.75 1391 405 22.51 0 0 NA 202127 TCGA-AB-2998 AML48 16 77325853 77325853 G A SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1056+301703 e8+301703 0.002 - - - no_errors tier3 1333 9 0.67 833 666 44.34 0 1 100 202127 TCGA-AB-2998 AML48 16 79798626 79798626 G A SNP PKD1L2 NM_001076780.1 human genbank 54_36p -1 reviewed silent c.876 p.D292 0.997 NULL "HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_C-type lectin-like" - no_errors tier1 679 2 0.29 425 299 41.3 NA 202127 TCGA-AB-2998 AML48 16 85048756 85048756 C T SNP LOC283904 XM_001719681.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*33339 NULL 0 - - - no_errors tier3 334 3 0.89 165 166 50.15 0 0 NA 202127 TCGA-AB-2998 AML48 17 5591262 5591262 G A SNP - - - - - - - - - - - - - - - tier3 1723 20 1.15 1291 995 43.49 0 0 NA 202127 TCGA-AB-2998 AML48 17 12394170 12394170 G A SNP ENSG00000179136 ENST00000313495 human ensembl 54_36p 1 known intronic c.1+51 e0+51 0 - - - no_errors tier3 633 4 0.63 467 331 41.43 0 0 NA 202127 TCGA-AB-2998 AML48 17 28611526 28611526 A G SNP ACCN1 NM_183377.4 human genbank 54_36p -1 reviewed intronic c.708+31013 e1+31013 0.001 - - - no_errors tier2 2921 27 0.91 1970 1971 49.94 0 0 NA 202127 TCGA-AB-2998 AML48 17 40549465 40549465 C T SNP PLCD3 ENST00000322765 human ensembl 54_36p -1 known intronic c.1413+60 e8+60 0 - - - no_errors tier2 403 3 0.74 362 349 48.88 0 1 100 202127 TCGA-AB-2998 AML48 17 42802781 42802781 T G SNP C17orf57 NM_152347.3 human genbank 54_36p 1 predicted intronic c.806-21 e8-21 0.003 - - - no_errors tier3 1261 6 0.47 793 682 46.21 1 1 50 202127 TCGA-AB-2998 AML48 17 48331465 48331465 G A SNP - - - - - - - - - - - - - - - tier3 752 8 1.05 455 346 43.2 0 0 NA 202127 TCGA-AB-2998 AML48 17 49920507 49920507 T C SNP - - - - - - - - - - - - - - - tier3 573 9 1.55 444 343 43.47 0 0 NA 202127 TCGA-AB-2998 AML48 17 51808047 51808047 C T SNP ANKFN1 NM_153228.2 human genbank 54_36p 1 validated intronic c.919+973 e7+973 0.004 - - - no_errors tier2 1350 11 0.81 832 694 45.42 0 0 NA 202127 TCGA-AB-2998 AML48 17 54542328 54542328 T G SNP FAM33A NM_182620.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*2092 NULL 0.003 - - - no_errors tier2 576 6 1.03 459 387 45.74 6 12 66.67 202127 TCGA-AB-2998 AML48 17 56916795 56916795 C G SNP TBX4 NM_018488.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*1136 NULL 0.909 - - - no_errors tier3 710 8 1.11 595 458 43.41 0 0 NA 202127 TCGA-AB-2998 AML48 17 63354125 63354125 C T SNP BPTF NM_182641.6 human genbank 54_36p 1 reviewed intronic c.5752-808 e16-808 0 - - - no_errors tier3 290 1 0.34 243 192 44.14 6 1 14.29 202127 TCGA-AB-2998 AML48 17 64344982 64344982 G A SNP ABCA8 NM_007168.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*30839 NULL 0 - - - no_errors tier3 1018 10 0.97 569 543 48.79 0 0 NA 202127 TCGA-AB-2998 AML48 18 3201478 3201478 C T SNP MYOM1 NM_003803.3 human genbank 54_36p -1 reviewed intronic c.290+3454 e1+3454 0.015 - - - no_errors tier3 656 6 0.91 528 456 46.34 0 0 0 202127 TCGA-AB-2998 AML48 18 12616307 12616307 C G SNP SPIRE1 NM_020148.1 human genbank 54_36p -1 validated intronic c.1+8754 e0+8754 0.004 - - - no_errors tier3 816 5 0.61 511 472 48.02 0 0 0 202127 TCGA-AB-2998 AML48 18 17903354 17903354 C T SNP - - - - - - - - - - - - - - - tier3 1916 19 0.98 1152 1045 47.37 0 0 NA 202127 TCGA-AB-2998 AML48 18 19511681 19511681 C T SNP LAMA3 NM_198129.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11965 NULL 0.002 - - - no_errors tier3 451 2 0.44 270 200 41.32 0 0 NA 202127 TCGA-AB-2998 AML48 18 23416581 23416581 C A SNP FLJ45994 XR_040238.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 670 5 0.74 409 359 46.74 0 0 NA 202127 TCGA-AB-2998 AML48 18 27278673 27278673 A G SNP DSG3 NM_001944.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3166 NULL 0 - - - no_errors tier3 1633 15 0.91 833 885 51.51 0 0 NA 202127 TCGA-AB-2998 AML48 18 27406586 27406586 T A SNP TTR NM_000371.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19278 NULL 0.003 - - - no_errors tier3 1020 6 0.58 501 434 46.32 0 0 NA 202127 TCGA-AB-2998 AML48 18 28917675 28917675 C T SNP C18orf34 NM_001105528.1 human genbank 54_36p -1 validated intronic c.2388+9048 e19+9048 0.014 - - - no_errors tier3 1054 5 0.47 742 595 44.5 0 0 NA 202127 TCGA-AB-2998 AML48 18 30478109 30478109 C T SNP DTNA NM_032975.1 human genbank 54_36p 1 reviewed intronic c.1-35321 e1-35321 0 - - - no_errors tier3 714 3 0.42 809 173 17.62 0 0 NA 202127 TCGA-AB-2998 AML48 18 31974644 31974644 T C SNP ELP2 NM_018255.1 human genbank 54_36p 1 provisional intronic c.524-454 e6-454 0.002 - - - no_errors tier3 840 1 0.12 644 458 41.56 2 1 33.33 202127 TCGA-AB-2998 AML48 18 36635636 36635636 T C SNP - - - - - - - - - - - - - - - tier3 856 3 0.35 469 418 47.13 0 0 NA 202127 TCGA-AB-2998 AML48 18 43002815 43002815 G A SNP FUSSEL18 XM_001715219.1 human genbank 54_36p -1 model intronic c.2918-2436 e6-2436 0.001 - - - no_errors tier3 1226 9 0.73 689 610 46.92 0 0 NA 202127 TCGA-AB-2998 AML48 18 49801574 49801574 T C SNP - - - - - - - - - - - - - - - tier3 827 5 0.6 502 529 51.26 0 0 NA 202127 TCGA-AB-2998 AML48 18 53728883 53728883 G A SNP - - - - - - - - - - - - - - - tier2 758 5 0.65 468 421 47.36 0 0 NA 202127 TCGA-AB-2998 AML48 18 61218165 61218165 T C SNP - - - - - - - - - - - - - - - tier3 818 5 0.61 492 370 42.92 0 0 NA 202127 TCGA-AB-2998 AML48 18 62963785 62963785 G A SNP - - - - - - - - - - - - - - - tier2 968 7 0.72 517 446 46.31 0 0 NA 202127 TCGA-AB-2998 AML48 18 63913931 63913931 A C SNP - - - - - - - - - - - - - - - tier2 1284 9 0.69 663 621 48.36 0 0 NA 202127 TCGA-AB-2998 AML48 18 65406554 65406554 C T SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.175-11046 e3-11046 0.001 - - - no_errors tier3 673 1 0.15 348 300 46.3 0 0 NA 202127 TCGA-AB-2998 AML48 18 68049780 68049780 A G SNP - - - - - - - - - - - - - - - tier3 804 6 0.74 422 297 41.31 0 0 NA 202127 TCGA-AB-2998 AML48 18 73143869 73143869 C - DEL GALR1 NM_001480.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*34023 NULL 0.01 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 18 74255527 74255527 T A SNP - - - - - - - - - - - - - - - tier3 743 4 0.54 528 529 50.05 0 0 NA 202127 TCGA-AB-2998 AML48 19 4817886 4817886 A - DEL M6PRBP1 NM_005817.3 human genbank 54_36p -1 reviewed intronic c.1+735 e0+735 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 19 7831223 7831223 C T SNP EVI5L NM_145245.2 human genbank 54_36p 1 provisional intronic c.1342-224 e12-224 0.006 - - - no_errors tier3 123 1 0.81 88 113 56.22 0 2 100 202127 TCGA-AB-2998 AML48 19 17287540 17287540 A C SNP DDA1 NM_024050.5 human genbank 54_36p 1 validated intronic c.137-203 e4-203 0 - - - no_errors tier3 224 3 1.3 243 194 43.69 1 3 75 202127 TCGA-AB-2998 AML48 19 33174778 33174778 C T SNP - - - - - - - - - - - - - - - tier2 739 6 0.8 541 446 45.14 0 0 NA 202127 TCGA-AB-2998 AML48 19 34717895 34717895 G A SNP VSTM2B XM_292785.1 human genbank 54_36p 1 model intronic c.1432+4858 e4+4858 0.001 - - - no_errors tier2 395 7 1.74 215 201 48.32 0 0 NA 202127 TCGA-AB-2998 AML48 19 37928150 37928150 G A SNP TDRD12 ENST00000311695 human ensembl 54_36p 1 known intronic c.440+2504 e4+2504 0 - - - no_stop_codon tier3 538 5 0.92 343 265 43.51 0 0 NA 202127 TCGA-AB-2998 AML48 19 46292210 46292210 C T SNP CYP2A13 NM_000766.3 human genbank 54_36p 1 reviewed intronic c.1161+33 e7+33 0 - - - no_errors tier3 490 7 1.41 395 407 50.62 0 0 NA 202127 TCGA-AB-2998 AML48 19 61951191 61951191 G A SNP ZIM2 NM_015363.3 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*26677 NULL 0.007 - - - no_errors tier3 892 3 0.34 663 542 44.94 0 0 NA 202127 TCGA-AB-2998 AML48 20 3289460 3289460 T C SNP C20orf194 NM_001009984.1 human genbank 54_36p -1 validated intronic c.613-1220 e7-1220 0.292 - - - no_errors tier3 866 3 0.34 598 415 40.93 9 2 18.18 202127 TCGA-AB-2998 AML48 20 5515832 5515832 C T SNP RP5-1022P6.2 NM_019593.3 human genbank 54_36p -1 validated intronic c.232-917 e4-917 0.02 - - - no_errors tier3 575 6 1.03 394 278 41.37 13 12 48 202127 TCGA-AB-2998 AML48 20 8957463 8957463 C T SNP PLCB4 ENST00000407043 human ensembl 54_36p 1 known 5_prime_flanking_region c.-278999 NULL 0 - - - no_stop_codon tier2 1296 12 0.92 802 621 43.49 0 0 NA 202127 TCGA-AB-2998 AML48 20 9242193 9242193 G A SNP PLCB4 NM_000933.2 human genbank 54_36p 1 reviewed intronic c.84+5648 e1+5648 0 - - - no_errors tier3 743 4 0.53 471 409 46.48 0 0 NA 202127 TCGA-AB-2998 AML48 20 15665946 15665946 A T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.646-125444 e9-125444 0.478 - - - no_errors tier3 1394 9 0.64 848 676 44.33 0 0 NA 202127 TCGA-AB-2998 AML48 20 19532651 19532651 G A SNP SLC24A3 NM_020689.3 human genbank 54_36p 1 validated intronic c.612+18463 e6+18463 0 - - - no_errors tier3 1976 15 0.75 1571 1547 49.55 1 0 0 202127 TCGA-AB-2998 AML48 20 21946694 21946694 T G SNP - - - - - - - - - - - - - - - tier3 1316 25 1.86 834 745 47.06 0 0 NA 202127 TCGA-AB-2998 AML48 20 24751891 24751891 G A SNP - - - - - - - - - - - - - - - tier3 429 3 0.69 195 146 42.69 0 0 NA 202127 TCGA-AB-2998 AML48 20 39778186 39778187 TA - DEL ENSG00000199287 ENST00000362417 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16417 NULL 0.097:0.090 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 20 53329244 53329244 C T SNP - - - - - - - - - - - - - - - tier3 1681 5 0.3 898 708 44.06 0 0 NA 202127 TCGA-AB-2998 AML48 20 54577526 54577526 C G SNP GCNT7 ENST00000243913 human ensembl 54_36p -1 known 5_prime_flanking_region c.-71821 NULL 0.002 - - - no_errors tier3 1261 12 0.94 646 548 45.9 0 0 NA 202127 TCGA-AB-2998 AML48 20 56860602 56860602 G A SNP GNAS NM_016592.4 human genbank 54_36p 1 reviewed intronic c.738+11266 e1+11266 0 - - - no_errors tier3 242 0 0 191 167 46.65 0 0 NA 202127 TCGA-AB-2998 AML48 20 57751439 57751439 T C SNP PHACTR3 NM_080672.3 human genbank 54_36p 1 reviewed intronic c.119-118 e2-118 0.002 - - - no_errors tier3 387 7 1.77 264 197 42.18 0 0 NA 202127 TCGA-AB-2998 AML48 20 58699721 58699721 T C SNP - - - - - - - - - - - - - - - tier3 1137 8 0.7 835 654 43.89 0 0 NA 202127 TCGA-AB-2998 AML48 21 18770516 18770516 T C SNP - - - - - - - - - - - - - - - tier3 784 6 0.76 529 343 39.33 0 0 NA 202127 TCGA-AB-2998 AML48 21 24163719 24163719 C T SNP - - - - - - - - - - - - - - - tier3 1114 7 0.62 600 637 51.45 0 0 NA 202127 TCGA-AB-2998 AML48 21 27515585 27515585 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 202127 TCGA-AB-2998 AML48 21 33481557 33481557 C T SNP IFNAR2 NM_207585.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-54541 NULL 0.002 - - - no_errors tier3 970 15 1.52 708 431 37.71 0 0 NA 202127 TCGA-AB-2998 AML48 21 41325759 41325759 A C SNP - - - - - - - - - - - - - - - tier3 1312 10 0.76 817 714 46.61 0 0 NA 202127 TCGA-AB-2998 AML48 22 25581158 25581158 T G SNP LOC100130624 XR_038453.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*31650 NULL 1 - - - pseudogene tier2 695 7 1 473 489 50.83 1 2 66.67 202127 TCGA-AB-2998 AML48 22 38972869 38972869 T G SNP TNRC6B NM_015088.1 human genbank 54_36p 1 validated intronic c.93+817 e2+817 0.4 - - - no_errors tier3 1028 13 1.25 520 457 46.78 0 3 100 202127 TCGA-AB-2998 AML48 22 43720893 43720893 C T SNP PHF21B NM_138415.1 human genbank 54_36p -1 validated intronic c.121-25859 e3-25859 0 - - - no_errors tier2 669 4 0.59 515 507 49.51 0 0 NA 202127 TCGA-AB-2998 AML48 22 46130543 46130543 C A SNP - - - - - - - - - - - - - - - tier3 762 5 0.65 471 456 49.14 0 0 NA 202127 TCGA-AB-2998 AML48 22 46328196 46328196 G A SNP - - - - - - - - - - - - - - - tier3 538 4 0.74 430 411 48.81 0 0 NA 202127 TCGA-AB-2998 AML48 22 46806195 46806195 A G SNP - - - - - - - - - - - - - - - tier3 548 2 0.36 369 292 44.04 0 0 NA 863018 TCGA-AB-2999 AML10 X 10630232 10630232 G T SNP MID1 NM_033290.2 human genbank 54_36p -1 reviewed intronic c.1+131362 e0+131362 1 - - - no_errors tier2 328 0 0 75 377 83.41 0 0 NA 863018 TCGA-AB-2999 AML10 X 13101409 13101409 C T SNP - - - - - - - - - - - - - - - tier3 1390 2 0.14 824 178 17.76 0 0 NA 863018 TCGA-AB-2999 AML10 X 43841031 43841031 C T SNP - - - - - - - - - - - - - - - tier3 1897 0 0 168 788 82.43 0 0 NA 863018 TCGA-AB-2999 AML10 X 57810263 57810263 G A SNP ENSG00000220247 ENST00000402843 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*57810263 NULL 0.91 - - - no_coding_region:pseudogene tier2 681 0 0 196 866 81.54 0 0 NA 863018 TCGA-AB-2999 AML10 X 103790827 103790827 G C SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.82+495 e1+495 0.2 - - - no_errors tier2 1188 0 0 201 1080 84.31 0 0 NA 863018 TCGA-AB-2999 AML10 X 138837703 138837703 G C SNP ATP11C ENST00000370557 human ensembl 54_36p -1 known intronic c.27+4138 e1+4138 0.001 - - - no_errors tier3 474 0 0 143 610 81.01 0 0 0 863018 TCGA-AB-2999 AML10 X 145054135 145054135 G A SNP - - - - - - - - - - - - - - - tier3 1117 0 0 84 541 86.56 0 0 NA 863018 TCGA-AB-2999 AML10 1 3104976 3104976 G A SNP PRDM16 NM_022114.2 human genbank 54_36p 1 reviewed intronic c.387+12078 e2+12078 0 - - - no_errors tier3 316 0 0 155 99 38.98 0 0 NA 863018 TCGA-AB-2999 AML10 1 5268500 5268500 G A SNP - - - - - - - - - - - - - - - tier2 1820 5 0.26 867 578 39.48 0 0 NA 863018 TCGA-AB-2999 AML10 1 5633581 5633581 C T SNP - - - - - - - - - - - - - - - tier3 1085 0 0 717 505 41.26 0 0 NA 863018 TCGA-AB-2999 AML10 1 16188608 16188608 C T SNP CLCNKA NM_004070.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33094 NULL 0 - - - no_errors tier3 192 0 0 48 35 42.17 0 0 NA 863018 TCGA-AB-2999 AML10 1 28325702 28325702 C A SNP EYA3 NM_001990.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-68578 NULL 0.007 - - - no_errors tier3 3161 3 0.09 865 619 41.71 0 0 NA 863018 TCGA-AB-2999 AML10 1 48773863 48773863 G A SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.1365-688 e13-688 0.002 - - - no_errors tier2 3128 1 0.03 1389 996 41.76 0 0 NA 863018 TCGA-AB-2999 AML10 1 49877667 49877667 A T SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.282+57905 e3+57905 0.042 - - - no_errors tier2 347 1 0.29 450 315 41.12 0 0 NA 863018 TCGA-AB-2999 AML10 1 58163298 58163298 C G SNP DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.1-40876 e1-40876 0 - - - no_errors tier2 890 0 0 1010 654 39.3 0 0 NA 863018 TCGA-AB-2999 AML10 1 64114081 64114081 C A SNP ROR1 NM_005012.1 human genbank 54_36p 1 validated intronic c.91+101314 e1+101314 0 - - - no_errors tier3 1960 1 0.05 864 512 37.16 0 0 NA 863018 TCGA-AB-2999 AML10 1 91881176 91881176 T C SNP HSP90B3P ENST00000370405 human ensembl 54_36p 1 known silent c.615 p.T205 0.99 "superfamily_Ribosomal_S5_D2-typ_fold,HMMPfam_HSP90" "superfamily_Ribosomal_S5_D2-typ_fold,HMMPfam_HSP90,superfamily_SSF110942" - no_errors tier1 1531 0 1050 690 39.66 121 0 863018 TCGA-AB-2999 AML10 1 93270901 93270901 G A SNP MTF2 NM_007358.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46771 NULL 0.006 - - - no_errors tier3 234 0 0 285 138 32.62 0 0 NA 863018 TCGA-AB-2999 AML10 1 95422913 95422913 G C SNP TMEM56 NM_152487.2 human genbank 54_36p 1 validated intronic c.474-6781 e6-6781 0 - - - no_errors tier3 1045 0 0 815 520 38.95 0 0 0 863018 TCGA-AB-2999 AML10 1 112370541 112370541 C T SNP KCND3 NM_004980.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43670 NULL 0.001 - - - no_errors tier3 2455 0 0 977 668 40.58 0 0 NA 863018 TCGA-AB-2999 AML10 1 160578057 160578057 T C SNP NOS1AP NM_014697.1 human genbank 54_36p 1 reviewed intronic c.454-2192 e6-2192 0.074 - - - no_errors tier3 1198 0 0 1286 825 39.08 0 0 NA 863018 TCGA-AB-2999 AML10 1 160997642 160997642 G A SNP DDR2 NM_001014796.1 human genbank 54_36p 1 reviewed missense c.873 p.M291I 1 NULL "HMMPfam_F5_F8_type_C,HMMSmart_FA58C,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_II,PatternScan_PROTEIN_KINASE_TYR,superfamily_Gal_bind_like,superfamily_Kinase_like" - no_errors tier1 1484 1 0.07 1076 845 43.99 NA 863018 TCGA-AB-2999 AML10 1 161167778 161167778 C T SNP ENSG00000219987 ENST00000405744 human ensembl 54_36p -1 known 3_prime_flanking_region c.*48187 NULL 0 - - - no_coding_region:pseudogene tier3 1099 0 0 927 664 41.73 0 0 NA 863018 TCGA-AB-2999 AML10 1 161255472 161255472 C T SNP RGS4 NM_001102445.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49877 NULL 0 - - - no_errors tier3 1775 0 0 1254 856 40.57 0 0 NA 863018 TCGA-AB-2999 AML10 1 171810034 171810034 C T SNP SLC9A11 NM_178527.3 human genbank 54_36p -1 validated intronic c.903-947 e8-947 0.001 - - - no_errors tier3 701 1 0.14 629 391 38.33 0 0 NA 863018 TCGA-AB-2999 AML10 1 174944968 174944968 C T SNP PAPPA2 NM_020318.2 human genbank 54_36p 1 validated intronic c.3458-774 e10-774 0 - - - no_errors tier3 2082 0 0 1362 939 40.81 0 0 NA 863018 TCGA-AB-2999 AML10 1 179838484 179838484 G A SNP CACNA1E NM_000721.2 human genbank 54_36p 1 reviewed intronic c.951+21949 e6+21949 0.002 - - - no_errors tier3 3752 1 0.03 1448 1078 42.66 0 0 NA 863018 TCGA-AB-2999 AML10 1 182893987 182893987 A G SNP EDEM3 NM_025191.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*35833 NULL 0 - - - no_errors tier3 647 0 0 746 446 37.38 0 0 NA 863018 TCGA-AB-2999 AML10 1 185984636 185984636 T C SNP ENSG00000216876 ENST00000402132 human ensembl 54_36p -1 known 5_prime_flanking_region c.-34147 NULL 0.012 - - - no_coding_region:pseudogene tier3 1172 0 0 860 567 39.73 0 0 NA 863018 TCGA-AB-2999 AML10 1 193137149 193137149 G T SNP - - - - - - - - - - - - - - - tier2 804 0 0 502 369 42.37 0 0 NA 863018 TCGA-AB-2999 AML10 1 209334890 209334890 G T SNP KCNH1 NM_172362.3 human genbank 54_36p -1 reviewed intronic c.311-4235 e4-4235 0.001 - - - no_errors tier3 697 0 0 1325 154 10.41 0 0 NA 863018 TCGA-AB-2999 AML10 1 212795076 212795076 G A SNP CENPF NM_016343.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-58645 NULL 0 - - - no_errors tier3 2542 6 0.23 1249 954 43.13 0 0 NA 863018 TCGA-AB-2999 AML10 1 213891287 213891287 G A SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.14134-521 e64-521 0.84 - - - no_errors tier2 1230 0 0 839 531 38.76 0 0 NA 863018 TCGA-AB-2999 AML10 1 215638359 215638359 A G SNP GPATCH2 NM_018040.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*32751 NULL 0.002 - - - no_errors tier3 1862 2 0.11 933 669 41.76 0 0 NA 863018 TCGA-AB-2999 AML10 1 219062887 219062887 T C SNP ENSG00000221571 ENST00000408644 human ensembl 54_36p 1 known 5_prime_flanking_region c.-2854 NULL 0 - - - no_errors tier3 2347 2 0.09 1104 657 37.31 2 5 71.43 863018 TCGA-AB-2999 AML10 1 227567130 227567130 C T SNP C1orf96 NM_145257.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22295 NULL 0 - - - no_errors tier3 1382 0 0 978 721 42.44 0 0 NA 863018 TCGA-AB-2999 AML10 1 234966998 234966998 G A SNP ACTN2 NM_001103.2 human genbank 54_36p 1 reviewed intronic c.784-47 e9-47 0 - - - no_errors tier2 1925 16 0.82 1271 971 43.31 0 0 NA 863018 TCGA-AB-2999 AML10 1 237787393 237787393 C G SNP - - - - - - - - - - - - - - - tier3 766 0 0 846 563 39.96 0 0 NA 863018 TCGA-AB-2999 AML10 1 240456233 240456233 G A SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.332-6193 e4-6193 0 - - - no_errors tier3 1013 0 0 629 467 42.61 0 0 NA 863018 TCGA-AB-2999 AML10 1 246382941 246382941 G T SNP OR2M2 NM_001004688.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-26970 NULL 0 - - - no_errors tier2 963 0 0 740 533 41.87 0 0 NA 863018 TCGA-AB-2999 AML10 2 3179284 3179284 G A SNP TSSC1 NM_003310.2 human genbank 54_36p -1 validated intronic c.653+375 e6+375 0 - - - no_errors tier3 332 1 0.3 185 142 43.43 0 0 0 863018 TCGA-AB-2999 AML10 2 4556148 4556148 T C SNP ENSG00000216435 ENST00000402611 human ensembl 54_36p -1 known 5_prime_flanking_region c.-15627 NULL 0.003 - - - no_coding_region:pseudogene tier3 996 0 0 822 532 39.26 0 0 NA 863018 TCGA-AB-2999 AML10 2 9225604 9225604 G A SNP ASAP2 NM_003887.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-39081 NULL 0.039 - - - no_errors tier3 827 0 0 390 272 41.03 0 0 NA 863018 TCGA-AB-2999 AML10 2 12690387 12690387 G A SNP - - - - - - - - - - - - - - - tier3 442 0 0 270 211 43.87 0 0 NA 863018 TCGA-AB-2999 AML10 2 15360903 15360903 G A SNP NBAS NM_015909.2 human genbank 54_36p -1 validated intronic c.4797+4888 e40+4888 0 - - - no_errors tier3 1065 0 0 855 552 39.23 0 2 100 863018 TCGA-AB-2999 AML10 2 22575837 22575837 G A SNP - - - - - - - - - - - - - - - tier3 1614 1 0.06 1087 727 40.08 0 0 NA 863018 TCGA-AB-2999 AML10 2 23136138 23136138 G T SNP - - - - - - - - - - - - - - - tier3 6680 0 0 2468 1767 41.71 0 0 NA 863018 TCGA-AB-2999 AML10 2 23315413 23315413 C T SNP - - - - - - - - - - - - - - - tier2 1823 0 0 831 591 41.56 0 0 NA 863018 TCGA-AB-2999 AML10 2 26761221 26761221 G A SNP KCNK3 NM_002246.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8027 NULL 0.002 - - - no_errors tier3 2995 0 0 1399 922 39.72 0 0 NA 863018 TCGA-AB-2999 AML10 2 30801106 30801106 C A SNP CAPN13 NM_144575.2 human genbank 54_36p -1 validated intronic c.2010-1500 e22-1500 0.005 - - - no_errors tier3 935 0 0 478 397 45.37 0 0 NA 863018 TCGA-AB-2999 AML10 2 34400755 34400755 T C SNP - - - - - - - - - - - - - - - tier3 1166 0 0 1311 1037 44.15 0 0 NA 863018 TCGA-AB-2999 AML10 2 39899785 39899785 C T SNP THUMPD2 NM_025264.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-39992 NULL 0.001 - - - no_errors tier3 1095 0 0 1288 1025 44.3 0 0 NA 863018 TCGA-AB-2999 AML10 2 51029360 51029360 G A SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.773-22763 e2-22763 0 - - - no_errors tier2 967 0 0 574 461 44.54 0 0 NA 863018 TCGA-AB-2999 AML10 2 67938909 67938909 C T SNP - - - - - - - - - - - - - - - tier3 1214 1 0.08 682 500 42.27 0 0 NA 863018 TCGA-AB-2999 AML10 2 80516512 80516512 G C SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1293+16275 e8+16275 0 - - - no_errors tier3 849 0 0 642 435 40.39 0 0 NA 863018 TCGA-AB-2999 AML10 2 99274496 99274496 C T SNP LYG1 NM_174898.2 human genbank 54_36p -1 validated intronic c.149-180 e3-180 0 - - - no_errors tier3 1396 1 0.07 670 586 46.62 0 0 0 863018 TCGA-AB-2999 AML10 2 100432799 100432799 T C SNP CHST10 NM_004854.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-43230 NULL 0.211 - - - no_errors tier3 2103 2 0.1 1377 959 41.05 0 0 NA 863018 TCGA-AB-2999 AML10 2 100973583 100973583 G T SNP NPAS2 NM_002518.3 human genbank 54_36p 1 reviewed intronic c.2019-91 e18-91 0.003 - - - no_errors tier2 1200 0 0 649 459 41.39 0 0 NA 863018 TCGA-AB-2999 AML10 2 111492418 111492418 T C SNP ACOXL NM_001105516.2 human genbank 54_36p 1 validated intronic c.1372-13257 e15-13257 0.001 - - - no_errors tier3 1704 0 0 851 544 39 0 0 NA 863018 TCGA-AB-2999 AML10 2 117409198 117409198 C T SNP - - - - - - - - - - - - - - - tier3 1957 2 0.1 1647 1101 40.05 0 0 NA 863018 TCGA-AB-2999 AML10 2 117410667 117410667 G A SNP - - - - - - - - - - - - - - - tier3 1744 0 0 2231 565 20.2 0 0 NA 863018 TCGA-AB-2999 AML10 2 133595096 133595096 C T SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.341+8924 e4+8924 0 - - - no_errors tier3 907 1 0.11 852 614 41.88 0 0 NA 863018 TCGA-AB-2999 AML10 2 139599861 139599861 G C SNP - - - - - - - - - - - - - - - tier3 304 7 2.25 458 88 16.12 0 0 NA 863018 TCGA-AB-2999 AML10 2 141501191 141501191 G T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.1790-7050 e12-7050 0.001 - - - no_errors tier3 438 0 0 358 210 36.91 0 0 NA 863018 TCGA-AB-2999 AML10 2 160722191 160722191 G C SNP ITGB6 NM_000888.3 human genbank 54_36p -1 provisional intronic c.1017+11778 e7+11778 0.003 - - - no_errors tier3 1217 1 0.08 958 720 42.88 0 0 0 863018 TCGA-AB-2999 AML10 2 162192234 162192234 T C SNP SLC4A10 NM_022058.3 human genbank 54_36p 1 validated intronic c.48+2912 e1+2912 0.001 - - - no_errors tier3 1211 0 0 719 590 45.04 0 0 NA 863018 TCGA-AB-2999 AML10 2 169716294 169716294 G A SNP LRP2 NM_004525.2 human genbank 54_36p -1 validated intronic c.12462-512 e68-512 0 - - - no_errors tier3 1314 1 0.08 899 567 38.62 0 0 NA 863018 TCGA-AB-2999 AML10 2 179976837 179976837 T A SNP ZNF385B NM_152520.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*39385 NULL 0.004 - - - no_errors tier3 543 0 0 467 370 44.21 0 0 NA 863018 TCGA-AB-2999 AML10 2 186434494 186434494 T C SNP FLJ44048 NM_207482.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*28296 NULL 0.001 - - - no_errors tier3 1046 2 0.19 784 527 40.05 0 1 100 863018 TCGA-AB-2999 AML10 2 214164125 214164125 T C SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1070+101066 e10+101066 0.001 - - - no_errors tier3 616 0 0 601 403 40.1 0 0 NA 863018 TCGA-AB-2999 AML10 2 226240668 226240668 G A SNP KIAA1486 NM_020864.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*16143 NULL 0 - - - no_errors tier3 1321 1 0.08 760 540 41.51 0 0 NA 863018 TCGA-AB-2999 AML10 2 227296358 227296358 A G SNP IRS1 NM_005544.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*71612 NULL 0 - - - no_errors tier3 2707 1 0.04 701 513 42.26 0 0 NA 863018 TCGA-AB-2999 AML10 2 229800582 229800582 A G SNP PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.123+35061 e1+35061 0 - - - no_errors tier3 1639 1 0.06 733 456 38.35 0 0 NA 863018 TCGA-AB-2999 AML10 2 237236303 237236303 C A SNP - - - - - - - - - - - - - - - tier3 1033 0 0 467 372 44.34 0 0 NA 863018 TCGA-AB-2999 AML10 2 241575124 241575124 C A SNP LOC728763 XR_037106.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - pseudogene tier3 293 0 0 166 140 45.75 0 0 NA 863018 TCGA-AB-2999 AML10 3 1148246 1148246 G T SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.1-16365 e1-16365 0.092 - - - no_errors tier3 862 0 0 773 279 26.52 0 0 NA 863018 TCGA-AB-2999 AML10 3 3646664 3646664 C T SNP ENSG00000223036 ENST00000411104 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16476 NULL 0.061 - - - no_errors tier3 1483 0 0 703 415 37.12 0 0 NA 863018 TCGA-AB-2999 AML10 3 5983635 5983635 C T SNP - - - - - - - - - - - - - - - tier3 2247 1 0.04 1221 884 41.98 0 0 NA 863018 TCGA-AB-2999 AML10 3 24982362 24982362 G A SNP - - - - - - - - - - - - - - - tier3 952 1 0.1 746 589 44.12 0 0 NA 863018 TCGA-AB-2999 AML10 3 28070610 28070610 G T SNP - - - - - - - - - - - - - - - tier3 869 0 0 760 478 38.58 0 0 NA 863018 TCGA-AB-2999 AML10 3 46878673 46878673 A G SNP MYL3 NM_000258.2 human genbank 54_36p -1 reviewed intronic c.129+1083 e1+1083 0 - - - no_errors tier3 2810 1 0.04 472 284 37.57 0 0 NA 863018 TCGA-AB-2999 AML10 3 54807908 54807908 G A SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.1381-18012 e14-18012 0.003 - - - no_errors tier3 1299 2 0.15 873 637 42.16 0 0 NA 863018 TCGA-AB-2999 AML10 3 59170484 59170484 A C SNP - - - - - - - - - - - - - - - tier3 903 0 0 702 546 43.75 0 0 NA 863018 TCGA-AB-2999 AML10 3 64224395 64224395 T C SNP PRICKLE2 NM_198859.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-64752 NULL 0 - - - no_errors tier3 2388 1 0.04 1125 939 45.45 0 0 NA 863018 TCGA-AB-2999 AML10 3 66683343 66683343 C T SNP LRIG1 NM_015541.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49822 NULL 0 - - - no_errors tier2 1393 0 0 1093 351 24.29 0 0 NA 863018 TCGA-AB-2999 AML10 3 66806028 66806028 T C SNP ENSG00000214560 ENST00000398581 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*35372 NULL 0.031 - - - no_coding_region:pseudogene tier3 1586 2 0.13 1403 937 40.04 0 0 NA 863018 TCGA-AB-2999 AML10 3 68360709 68360709 T A SNP FAM19A1 NM_213609.2 human genbank 54_36p 1 reviewed intronic c.119-188411 e2-188411 0 - - - no_errors tier3 1235 0 0 733 562 43.4 0 0 NA 863018 TCGA-AB-2999 AML10 3 71287430 71287430 C A SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.180+42613 e1+42613 0.002 - - - no_errors tier3 1144 0 0 594 400 40.2 0 2 100 863018 TCGA-AB-2999 AML10 3 72558291 72558291 T C SNP RYBP NM_012234.4 human genbank 54_36p -1 validated intronic c.126+20046 e1+20046 0.1 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 477 0 0 974 651 40.04 3 6 66.67 863018 TCGA-AB-2999 AML10 3 72949148 72949148 G C SNP SHQ1 NM_018130.2 human genbank 54_36p -1 validated missense c.805 p.R269G 0.063 HMMPfam_SHQ1 "HMMPfam_SHQ1,superfamily_HSP20_chap,HMMPfam_CS" - no_errors tier1 1359 0 892 555 38.36 14 10 41.67 863018 TCGA-AB-2999 AML10 3 73057387 73057387 T A SNP GLT8D4 NM_001080393.1 human genbank 54_36p 1 inferred intronic c.600+3211 e3+3211 0.074 - - - no_errors tier3 1223 0 0 646 504 43.83 0 0 0 863018 TCGA-AB-2999 AML10 3 73818604 73818604 T C SNP - - - - - - - - - - - - - - - tier3 2318 1 0.04 1047 854 44.9 0 0 NA 863018 TCGA-AB-2999 AML10 3 77039174 77039174 C T SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-190681 e2-190681 0 - - - no_stop_codon:overly_large_intron tier3 415 0 0 309 232 42.88 0 0 NA 863018 TCGA-AB-2999 AML10 3 96457785 96457785 T G SNP - - - - - - - - - - - - - - - tier3 260 0 0 275 157 36.34 0 0 NA 863018 TCGA-AB-2999 AML10 3 97927114 97927114 C G SNP - - - - - - - - - - - - - - - tier2 449 1 0.22 407 276 40.41 0 0 NA 863018 TCGA-AB-2999 AML10 3 100029025 100029025 G A SNP DCBLD2 NM_080927.3 human genbank 54_36p -1 validated intronic c.572-2125 e4-2125 0.001 - - - no_errors tier3 823 2 0.24 1018 816 44.47 0 0 NA 863018 TCGA-AB-2999 AML10 3 106118839 106118839 G A SNP - - - - - - - - - - - - - - - tier3 959 0 0 573 419 42.24 0 0 NA 863018 TCGA-AB-2999 AML10 3 108301260 108301260 C T SNP LOC344595 XM_001128525.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-30795 NULL 0 - - - no_errors tier3 1582 1 0.06 2461 707 22.3 0 0 NA 863018 TCGA-AB-2999 AML10 3 133199979 133199979 G A SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.1+36122 e0+36122 0.021 - - - no_errors tier3 1546 0 0 1036 723 41.06 0 0 NA 863018 TCGA-AB-2999 AML10 3 133211551 133211551 C A SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.1+24550 e0+24550 0 - - - no_errors tier3 948 1 0.11 814 610 42.81 0 0 NA 863018 TCGA-AB-2999 AML10 3 136717970 136717970 T G SNP - - - - - - - - - - - - - - - tier3 2152 1 0.05 1052 781 42.58 0 0 NA 863018 TCGA-AB-2999 AML10 3 151743353 151743353 G T SNP SERP1 NM_014445.3 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1582 NULL 0.062 - - - no_errors tier2 698 0 0 441 375 45.96 191 147 43.49 863018 TCGA-AB-2999 AML10 3 160673530 160673530 T G SNP SCHIP1 NM_014575.2 human genbank 54_36p 1 provisional intronic c.63+199164 e1+199164 0.011 - - - no_errors tier3 838 0 0 791 566 41.68 0 0 NA 863018 TCGA-AB-2999 AML10 3 170876625 170876625 T G SNP MDS1 NM_004991.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-12771 NULL 0.009 - - - no_errors tier3 974 1 0.1 1139 684 37.5 0 0 NA 863018 TCGA-AB-2999 AML10 3 179666432 179666432 C A SNP ENSG00000208463 ENST00000385728 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36661 NULL 0 - - - pseudogene tier3 1708 0 0 969 807 45.44 0 0 NA 863018 TCGA-AB-2999 AML10 3 180266693 180266693 G A SNP ZMAT3 NM_022470.2 human genbank 54_36p -1 reviewed intronic c.270+1272 e1+1272 0 - - - no_errors tier2 1629 0 0 906 704 43.73 0 0 0 863018 TCGA-AB-2999 AML10 3 181951305 181951305 C G SNP CCDC39 ENST00000273654 human ensembl 54_36p -1 known 5_prime_flanking_region c.-41998 NULL 0.053 - - - no_errors tier3 1884 1 0.05 718 490 40.56 0 0 NA 863018 TCGA-AB-2999 AML10 3 185929519 185929519 G A SNP MAGEF1 NM_022149.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-17216 NULL 0 - - - no_errors tier2 1471 0 0 1159 396 25.37 0 2 100 863018 TCGA-AB-2999 AML10 3 191703023 191703023 C T SNP IL1RAP NM_002182.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-61750 NULL 0.829 - - - no_errors tier2 1145 0 0 707 404 36.36 0 0 NA 863018 TCGA-AB-2999 AML10 3 195287087 195287087 G A SNP HES1 NM_005524.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-49777 NULL 0 - - - no_errors tier3 1505 2 0.13 656 463 41.34 0 0 NA 863018 TCGA-AB-2999 AML10 3 198223412 198223412 C T SNP MFI2 NM_005929.4 human genbank 54_36p -1 reviewed intronic c.1234-1350 e10-1350 0.008 - - - no_errors tier3 382 0 0 292 201 40.77 0 0 NA 863018 TCGA-AB-2999 AML10 4 7280077 7280077 T A SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.30+34323 e1+34323 0.007 - - - no_errors tier3 2537 1 0.04 467 387 45.32 0 0 NA 863018 TCGA-AB-2999 AML10 4 19321803 19321803 A G SNP - - - - - - - - - - - - - - - tier3 1711 0 0 1338 931 41.01 0 0 NA 863018 TCGA-AB-2999 AML10 4 20164709 20164709 G A SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.2725+20 e26+20 0 - - - no_errors tier3 593 0 0 469 355 43.03 0 0 NA 863018 TCGA-AB-2999 AML10 4 23067268 23067268 G A SNP - - - - - - - - - - - - - - - tier2 2199 3 0.14 1235 799 39.28 0 0 NA 863018 TCGA-AB-2999 AML10 4 30604884 30604884 T A SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3226+73819 e3+73819 0.001 - - - no_errors tier3 209 0 0 176 139 44.13 0 0 NA 863018 TCGA-AB-2999 AML10 4 32609450 32609450 C G SNP - - - - - - - - - - - - - - - tier3 725 0 0 507 363 41.72 0 0 NA 863018 TCGA-AB-2999 AML10 4 37384835 37384835 G A SNP RELL1 NM_001085399.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20531 NULL 0.009 - - - no_errors tier3 1210 1 0.08 789 569 41.81 0 0 NA 863018 TCGA-AB-2999 AML10 4 44881081 44881081 G A SNP - - - - - - - - - - - - - - - tier3 926 1 0.11 668 417 38.43 0 0 NA 863018 TCGA-AB-2999 AML10 4 68859475 68859475 C T SNP YTHDC1 NM_001031732.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*2937 NULL 0.002 - - - no_errors tier3 513 0 0 892 683 43.28 7 2 22.22 863018 TCGA-AB-2999 AML10 4 76710975 76710975 C T SNP CDKL2 NM_003948.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*15092 NULL 0.038 - - - no_errors tier3 672 0 0 482 362 42.89 0 0 NA 863018 TCGA-AB-2999 AML10 4 76832398 76832398 C T SNP USO1 NM_003715.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36630 NULL 0 - - - no_errors tier3 588 0 0 415 191 31.52 4 1 20 863018 TCGA-AB-2999 AML10 4 80321841 80321841 G A SNP - - - - - - - - - - - - - - - tier2 1412 14 0.98 948 728 43.38 0 0 NA 863018 TCGA-AB-2999 AML10 4 91826536 91826536 T C SNP KIAA1680 NM_207491.1 human genbank 54_36p 1 validated intronic c.1933-37552 e6-37552 0.013 - - - no_errors tier3 456 4 0.87 535 429 44.5 0 0 0 863018 TCGA-AB-2999 AML10 4 107593307 107593307 G - DEL ENSG00000222333 ENST00000410401 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36916 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 863018 TCGA-AB-2999 AML10 4 110007987 110007987 C G SNP COL25A1 NM_198721.2 human genbank 54_36p -1 validated intronic c.1083+1706 e19+1706 0 - - - no_errors tier3 896 0 0 721 380 34.51 0 0 NA 863018 TCGA-AB-2999 AML10 4 119149091 119149091 C T SNP NDST3 NM_004784.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45423 NULL 0.012 - - - no_errors tier3 1071 1 0.09 649 467 41.85 0 0 NA 863018 TCGA-AB-2999 AML10 4 119357833 119357833 T C SNP NDST3 NM_004784.2 human genbank 54_36p 1 reviewed intronic c.1540-7261 e6-7261 0 - - - no_errors tier3 1868 0 0 1694 1201 41.49 0 0 0 863018 TCGA-AB-2999 AML10 4 139976978 139976978 G A SNP LOC100128578 XM_001718303.1 human genbank 54_36p -1 model intronic c.248-16297 e4-16297 0.001 - - - no_errors tier3 2531 1 0.04 1655 606 26.8 0 0 NA 863018 TCGA-AB-2999 AML10 4 163653314 163653314 A T SNP - - - - - - - - - - - - - - - tier3 1820 0 0 1022 707 40.87 0 0 NA 863018 TCGA-AB-2999 AML10 4 165179458 165179458 A G SNP - - - - - - - - - - - - - - - tier3 540 1 0.18 668 501 42.82 0 0 NA 863018 TCGA-AB-2999 AML10 4 165874330 165874330 G T SNP LOC653794 XM_001718785.1 human genbank 54_36p 1 model intronic c.31+5668 e1+5668 0.001 - - - no_errors tier3 983 2 0.2 565 382 40.34 0 0 NA 863018 TCGA-AB-2999 AML10 4 166504734 166504734 A C SNP CPE NM_001873.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15090 NULL 0.004 - - - no_errors tier3 462 0 0 441 328 42.65 0 0 NA 863018 TCGA-AB-2999 AML10 4 166796991 166796991 A C SNP - - - - - - - - - - - - - - - tier3 647 0 0 782 569 42.12 0 0 NA 863018 TCGA-AB-2999 AML10 4 169680032 169680032 C T SNP PALLD NM_016081.3 human genbank 54_36p 1 validated intronic c.908+9894 e1+9894 0.03 - - - no_errors tier3 980 0 0 663 435 39.58 0 0 NA 863018 TCGA-AB-2999 AML10 4 172784029 172784029 G A SNP - - - - - - - - - - - - - - - tier3 805 3 0.37 665 448 40.22 0 0 NA 863018 TCGA-AB-2999 AML10 4 178062716 178062716 G T SNP - - - - - - - - - - - - - - - tier3 735 0 0 655 369 35.96 0 0 NA 863018 TCGA-AB-2999 AML10 4 183300622 183300622 C T SNP ENSG00000177822 ENST00000315302 human ensembl 54_36p -1 known 3_prime_untranslated_region c.*1 NULL 0 - - - no_errors tier2 162 0 0 255 205 44.57 0 0 NA 863018 TCGA-AB-2999 AML10 4 183740437 183740437 T A SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.512-18634 e3-18634 0.306 - - - no_errors tier3 835 0 0 534 374 41.19 0 0 NA 863018 TCGA-AB-2999 AML10 4 184087408 184087408 C A SNP DCTD NM_001012732.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11948 NULL 0.001 - - - no_errors tier3 1382 1 0.07 912 807 46.86 0 0 NA 863018 TCGA-AB-2999 AML10 4 187073856 187073856 C A SNP SORBS2 NM_021069.1 human genbank 54_36p -1 reviewed intronic c.1+40488 e0+40488 0 - - - no_errors tier3 760 0 0 530 395 42.7 0 0 NA 863018 TCGA-AB-2999 AML10 5 2332171 2332171 C G SNP - - - - - - - - - - - - - - - tier2 95 0 0 54 41 43.16 0 0 NA 863018 TCGA-AB-2999 AML10 5 3418819 3418819 G T SNP - - - - - - - - - - - - - - - tier3 1158 1 0.09 1018 829 44.84 0 0 NA 863018 TCGA-AB-2999 AML10 5 3579144 3579144 C T SNP - - - - - - - - - - - - - - - tier3 1760 0 0 985 722 42.25 0 0 NA 863018 TCGA-AB-2999 AML10 5 5062004 5062004 A T SNP ENSG00000215231 ENST00000399853 human ensembl 54_36p 1 known 5_prime_flanking_region c.-29630 NULL 0.003 - - - no_errors tier3 554 0 0 483 394 44.93 0 0 NA 863018 TCGA-AB-2999 AML10 5 7663033 7663033 G T SNP ADCY2 NM_020546.2 human genbank 54_36p 1 reviewed intronic c.571-16247 e4-16247 0 - - - no_errors tier3 1459 0 0 1067 859 44.6 0 0 NA 863018 TCGA-AB-2999 AML10 5 18366753 18366753 C G SNP - - - - - - - - - - - - - - - tier3 1879 0 0 716 494 40.83 0 0 NA 863018 TCGA-AB-2999 AML10 5 22502420 22502420 C T SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1+38716 e0+38716 0.003 - - - no_errors tier3 2211 3 0.14 940 643 40.57 0 0 NA 863018 TCGA-AB-2999 AML10 5 28126740 28126740 G T SNP - - - - - - - - - - - - - - - tier3 595 0 0 404 283 41.19 0 0 NA 863018 TCGA-AB-2999 AML10 5 29929709 29929709 C T SNP - - - - - - - - - - - - - - - tier3 1083 1 0.09 988 730 42.49 0 0 NA 863018 TCGA-AB-2999 AML10 5 34594454 34594454 A G SNP ENSG00000222261 ENST00000410329 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32291 NULL 0.308 - - - no_errors tier3 1185 0 0 755 482 38.87 0 0 NA 863018 TCGA-AB-2999 AML10 5 38004894 38004894 C T SNP - - - - - - - - - - - - - - - tier3 2184 1 0.05 1281 724 36.09 0 0 NA 863018 TCGA-AB-2999 AML10 5 44916551 44916551 C T SNP - - - - - - - - - - - - - - - tier3 620 0 0 666 384 36.57 0 0 NA 863018 TCGA-AB-2999 AML10 5 45029916 45029916 A C SNP ENSG00000222945 ENST00000411013 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*34439 NULL 0.01 - - - no_errors tier3 1394 0 0 606 475 43.86 0 0 NA 863018 TCGA-AB-2999 AML10 5 55814185 55814185 T G SNP LOC441073 XR_016376.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*21978 NULL 0.002 - - - pseudogene tier3 770 0 0 417 291 41.1 0 0 NA 863018 TCGA-AB-2999 AML10 5 58844233 58844233 T G SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.456-296682 e2-296682 0 - - - no_errors tier3 296 1 0.34 395 288 42.17 0 0 NA 863018 TCGA-AB-2999 AML10 5 58884854 58884854 G A SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.456-337303 e2-337303 0.858 - - - no_errors tier3 1436 2 0.14 658 420 38.92 0 0 NA 863018 TCGA-AB-2999 AML10 5 71893428 71893428 G A SNP LOC389300 XM_374124.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*12403 NULL 0 - - - no_errors tier3 3269 1 0.03 1370 864 38.68 0 0 NA 863018 TCGA-AB-2999 AML10 5 79037312 79037312 C T SNP CMYA5 NM_153610.3 human genbank 54_36p 1 validated intronic c.149+15677 e1+15677 0 - - - no_errors tier3 1388 1 0.07 845 603 41.64 0 0 NA 863018 TCGA-AB-2999 AML10 5 83616204 83616204 T C SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.68-30418 e2-30418 0.009 - - - no_errors tier3 343 0 0 469 314 40.05 0 0 NA 863018 TCGA-AB-2999 AML10 5 84152956 84152956 C T SNP - - - - - - - - - - - - - - - tier3 516 0 0 533 379 41.51 0 0 NA 863018 TCGA-AB-2999 AML10 5 85169363 85169363 C A SNP - - - - - - - - - - - - - - - tier3 755 1 0.13 1064 454 29.91 0 0 NA 863018 TCGA-AB-2999 AML10 5 92482393 92482393 G A SNP - - - - - - - - - - - - - - - tier3 951 0 0 716 537 42.82 0 0 NA 863018 TCGA-AB-2999 AML10 5 92638493 92638493 C T SNP LOC391811 XR_016127.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*8347 NULL 0 - - - pseudogene tier3 951 1 0.11 499 343 40.74 0 0 NA 863018 TCGA-AB-2999 AML10 5 98359677 98359677 G A SNP - - - - - - - - - - - - - - - tier2 1163 0 0 865 687 44.21 0 0 NA 863018 TCGA-AB-2999 AML10 5 98470040 98470040 A C SNP - - - - - - - - - - - - - - - tier3 545 0 0 529 285 35.01 0 0 NA 863018 TCGA-AB-2999 AML10 5 102151352 102151352 A G SNP - - - - - - - - - - - - - - - tier3 856 0 0 565 368 39.44 0 0 NA 863018 TCGA-AB-2999 AML10 5 106975103 106975103 T C SNP EFNA5 NM_001962.2 human genbank 54_36p -1 reviewed intronic c.125+58986 e1+58986 0 - - - no_errors tier3 755 0 0 517 377 42.08 0 0 NA 863018 TCGA-AB-2999 AML10 5 107378297 107378297 C T SNP FBXL17 NM_022824.1 human genbank 54_36p -1 provisional intronic c.628+6228 e5+6228 0.002 - - - no_errors tier3 466 0 0 457 279 37.91 1 0 0 863018 TCGA-AB-2999 AML10 5 110640317 110640317 T A SNP CAMK4 NM_001744.3 human genbank 54_36p 1 reviewed intronic c.161+52076 e1+52076 0 - - - no_errors tier3 320 0 0 174 105 37.63 0 0 NA 863018 TCGA-AB-2999 AML10 5 111298643 111298643 G A SNP - - - - - - - - - - - - - - - tier3 391 0 0 476 318 40.05 0 0 NA 863018 TCGA-AB-2999 AML10 5 117245001 117245001 T G SNP - - - - - - - - - - - - - - - tier3 334 0 0 557 348 38.45 0 0 0 863018 TCGA-AB-2999 AML10 5 124286119 124286119 A T SNP - - - - - - - - - - - - - - - tier2 534 0 0 430 346 44.59 0 0 NA 863018 TCGA-AB-2999 AML10 5 132736089 132736089 C T SNP FSTL4 NM_015082.1 human genbank 54_36p -1 validated intronic c.409+28240 e3+28240 0 - - - no_errors tier3 1018 0 0 570 405 41.54 0 0 NA 863018 TCGA-AB-2999 AML10 5 135279995 135279995 G A SNP IL9 NM_000590.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20591 NULL 0 - - - no_errors tier3 1179 5 0.42 502 309 38.01 0 0 NA 863018 TCGA-AB-2999 AML10 5 141973531 141973531 G T SNP FGF1 NM_000800.3 human genbank 54_36p -1 reviewed intronic c.169+177 e1+177 0 - - - no_errors tier2 1495 0 0 1218 853 41.17 0 0 NA 863018 TCGA-AB-2999 AML10 5 144758246 144758246 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 863018 TCGA-AB-2999 AML10 5 155025246 155025246 G A SNP - - - - - - - - - - - - - - - tier2 1003 1 0.1 936 697 42.66 0 0 NA 863018 TCGA-AB-2999 AML10 5 178098540 178098540 C T SNP ZNF354A NM_005649.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9911 NULL 0 - - - no_errors tier3 1374 1 0.07 641 444 40.88 0 0 NA 863018 TCGA-AB-2999 AML10 6 10960522 10960522 C T SNP MAK NM_005906.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-21655 NULL 0.001 - - - no_errors tier3 627 0 0 546 333 37.88 3 0 0 863018 TCGA-AB-2999 AML10 6 14905762 14905762 A G SNP - - - - - - - - - - - - - - - tier3 1742 0 0 964 289 23.03 0 0 NA 863018 TCGA-AB-2999 AML10 6 33259973 33259973 C T SNP COL11A2 NM_080680.2 human genbank 54_36p -1 reviewed missense c.1046 p.G349D 0.999 NULL "HMMPfam_COLFI,HMMSmart_SM00038,HMMSmart_SM00282,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2" - no_errors tier1 663 0 195 117 37.38 NA 863018 TCGA-AB-2999 AML10 6 37548352 37548352 C T SNP FTSJD2 NM_015050.2 human genbank 54_36p 1 validated intronic c.1689+111 e15+111 0 - - - no_errors tier2 2082 0 0 812 661 44.87 0 0 0 863018 TCGA-AB-2999 AML10 6 40339974 40339974 G A SNP - - - - - - - - - - - - - - - tier3 5420 3 0.06 1479 1115 42.98 0 0 NA 863018 TCGA-AB-2999 AML10 6 40744533 40744533 C T SNP - - - - - - - - - - - - - - - tier3 4032 1 0.02 1347 961 41.64 0 0 NA 863018 TCGA-AB-2999 AML10 6 42331435 42331435 T C SNP TRERF1 NM_033502.2 human genbank 54_36p -1 reviewed intronic c.2581-793 e9-793 0 - - - no_errors tier2 1566 0 0 544 336 38.18 1 5 83.33 863018 TCGA-AB-2999 AML10 6 46008658 46008658 C T SNP CLIC5 NM_016929.1 human genbank 54_36p -1 validated intronic c.406+8604 e4+8604 0.018 - - - no_errors tier3 1587 1 0.06 773 575 42.66 0 0 NA 863018 TCGA-AB-2999 AML10 6 48871727 48871727 G A SNP - - - - - - - - - - - - - - - tier2 471 0 0 474 370 43.84 0 0 NA 863018 TCGA-AB-2999 AML10 6 64495216 64495216 A T SNP ENSG00000118487 ENST00000237261 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5566 NULL 0.005 - - - no_start_codon tier3 861 1 0.12 691 442 39.01 2 2 50 863018 TCGA-AB-2999 AML10 6 81556783 81556783 T C SNP - - - - - - - - - - - - - - - tier2 594 3 0.5 740 504 40.51 0 0 NA 863018 TCGA-AB-2999 AML10 6 90146067 90146067 A T SNP RRAGD NM_021244.4 human genbank 54_36p -1 validated intronic c.645-291 e4-291 0 - - - no_errors tier3 1150 17 1.45 1234 1004 44.84 1 0 0 863018 TCGA-AB-2999 AML10 6 94256825 94256825 A C SNP - - - - - - - - - - - - - - - tier3 569 1 0.18 551 402 42.18 0 0 NA 863018 TCGA-AB-2999 AML10 6 99113589 99113589 C G SNP - - - - - - - - - - - - - - - tier2 945 0 0 661 457 40.88 0 0 NA 863018 TCGA-AB-2999 AML10 6 115334121 115334121 C T SNP ENSG00000208800 ENST00000386065 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-39288 NULL 0.001 - - - pseudogene tier3 2007 2 0.1 1097 818 42.69 0 0 NA 863018 TCGA-AB-2999 AML10 6 129611851 129611851 C T SNP LAMA2 NM_000426.3 human genbank 54_36p 1 reviewed intronic c.1783-1099 e13-1099 1 - - - no_errors tier3 1594 0 0 1099 796 41.98 0 0 NA 863018 TCGA-AB-2999 AML10 6 135480921 135480921 A T SNP - - - - - - - - - - - - - - - tier3 1666 1 0.06 909 620 40.55 0 0 NA 863018 TCGA-AB-2999 AML10 6 137788356 137788356 G A SNP - - - - - - - - - - - - - - - tier3 1916 1 0.05 789 674 46.04 0 0 NA 863018 TCGA-AB-2999 AML10 6 148483839 148483839 C T SNP - - - - - - - - - - - - - - - tier3 1016 0 0 587 406 40.89 0 0 NA 863018 TCGA-AB-2999 AML10 6 153530937 153530937 C T SNP RGS17 NM_012419.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-124091 NULL 0 - - - no_errors tier3 416 0 0 385 268 41.04 0 0 NA 863018 TCGA-AB-2999 AML10 7 2984655 2984655 C A SNP CARD11 NM_032415.3 human genbank 54_36p -1 validated intronic c.1-19864 e1-19864 0.003 - - - no_errors tier3 1685 3 0.18 1011 724 41.66 1 2 66.67 863018 TCGA-AB-2999 AML10 7 6169917 6169917 A C SNP CYTH3 NM_004227.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*1183 NULL 0.028 - - - no_errors tier3 676 1 0.15 595 432 42.06 10 3 23.08 863018 TCGA-AB-2999 AML10 7 14093313 14093313 T C SNP ENSG00000220499 ENST00000407541 human ensembl 54_36p -1 known 5_prime_flanking_region c.-15783 NULL 0.039 - - - no_coding_region:pseudogene tier3 980 0 0 613 395 39.19 0 0 NA 863018 TCGA-AB-2999 AML10 7 21715785 21715785 G A SNP DNAH11 ENST00000328843 human ensembl 54_36p 1 known intronic c.6705-911 e42-911 0 - - - no_errors tier3 1200 0 0 1266 918 42.03 0 0 NA 863018 TCGA-AB-2999 AML10 7 32557675 32557675 G T SNP AVL9 NM_015060.1 human genbank 54_36p 1 provisional intronic c.462+115 e5+115 0.008 - - - no_errors tier3 721 0 0 538 313 36.78 1 0 0 863018 TCGA-AB-2999 AML10 7 36907321 36907321 T C SNP ELMO1 NM_014800.1 human genbank 54_36p -1 reviewed intronic c.1438-6174 e16-6174 0.057 - - - no_errors tier3 2496 0 0 931 630 40.31 4 2 33.33 863018 TCGA-AB-2999 AML10 7 43958209 43958209 A G SNP UBE2D4 NM_015983.2 human genbank 54_36p 1 provisional intronic c.399-565 e7-565 0 - - - no_errors tier3 2049 1 0.05 1139 782 40.69 6 4 40 863018 TCGA-AB-2999 AML10 7 46885085 46885085 C A SNP - - - - - - - - - - - - - - - tier3 681 1 0.15 495 326 39.66 0 0 NA 863018 TCGA-AB-2999 AML10 7 52489106 52489106 T C SNP - - - - - - - - - - - - - - - tier3 1192 1 0.08 597 409 40.66 0 0 NA 863018 TCGA-AB-2999 AML10 7 55869714 55869714 C T SNP SEPT14 NM_207366.2 human genbank 54_36p -1 validated silent c.618 p.T206 0.808 "HMMPfam_Septin,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Septin,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 873 0 837 551 39.7 0 863018 TCGA-AB-2999 AML10 7 68096835 68096835 C T SNP - - - - - - - - - - - - - - - tier3 1500 0 0 742 551 42.61 0 0 NA 863018 TCGA-AB-2999 AML10 7 76639426 76639426 G A SNP CCDC146 NM_020879.2 human genbank 54_36p 1 validated intronic c.156+4349 e1+4349 0.006 - - - no_errors tier3 644 0 0 399 207 34.16 0 0 NA 863018 TCGA-AB-2999 AML10 7 87486004 87486004 G A SNP ADAM22 NM_021723.2 human genbank 54_36p 1 reviewed intronic c.323+40341 e3+40341 0.607 - - - no_errors tier3 727 0 0 728 546 42.86 0 0 0 863018 TCGA-AB-2999 AML10 7 94717425 94717425 A G SNP PPP1R9A NM_017650.2 human genbank 54_36p 1 validated missense c.2252 p.K751R 1 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMSmart_SM00454,superfamily_SAM/Pointed domain,HMMPfam_SAM_2" - no_errors tier1 1282 1 0.08 827 575 40.98 NA 863018 TCGA-AB-2999 AML10 7 96868386 96868386 C T SNP - - - - - - - - - - - - - - - tier3 635 0 0 525 374 41.6 0 0 NA 863018 TCGA-AB-2999 AML10 7 125150343 125150343 T A SNP - - - - - - - - - - - - - - - tier3 1174 0 0 514 454 46.9 0 0 NA 863018 TCGA-AB-2999 AML10 7 126565308 126565308 C A SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.511-31306 e2-31306 0.024 - - - no_errors tier3 1585 0 0 1087 815 42.83 0 0 NA 863018 TCGA-AB-2999 AML10 7 131901362 131901362 G A SNP PLXNA4 NM_020911.1 human genbank 54_36p -1 validated intronic c.1+10359 e0+10359 1 - - - no_errors tier2 374 1 0.27 87 62 41.61 0 0 NA 863018 TCGA-AB-2999 AML10 7 135961866 135961866 G A SNP - - - - - - - - - - - - - - - tier2 599 3 0.5 829 622 42.87 0 0 NA 863018 TCGA-AB-2999 AML10 7 139585346 139585346 G C SNP ENSG00000199283 ENST00000362413 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2793 NULL 0 - - - no_errors tier3 1361 0 0 510 306 37.5 0 0 NA 863018 TCGA-AB-2999 AML10 7 140872669 140872669 G A SNP AGK NM_018238.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29067 NULL 0.999 - - - no_errors tier3 1091 0 0 578 363 38.58 0 0 NA 863018 TCGA-AB-2999 AML10 7 141683049 141683049 G A SNP uc003vxy.2 ENST00000390359 human ensembl 54_36p 1 known 5_prime_flanking_region c.-37920 NULL 0.001 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 1430 0 0 774 529 40.6 1 0 0 863018 TCGA-AB-2999 AML10 7 154493826 154493826 C G SNP HTR5A NM_024012.2 human genbank 54_36p 1 reviewed missense c.284 p.P95R 0.994 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 584 0 378 248 39.62 NA 863018 TCGA-AB-2999 AML10 7 155375209 155375209 C T SNP LOC100132381 XM_001715638.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-2261 NULL 0 - - - no_errors tier3 342 0 0 90 69 43.4 0 0 NA 863018 TCGA-AB-2999 AML10 7 157978284 157978284 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.113-3046 e2-3046 0 - - - no_errors tier3 191 0 0 138 79 36.24 0 0 NA 863018 TCGA-AB-2999 AML10 8 4161659 4161659 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.415+103224 e3+103224 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 744 0 0 638 361 36.1 0 0 NA 863018 TCGA-AB-2999 AML10 8 12659374 12659374 A C SNP LONRF1 NM_152271.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-2074 NULL 0.548 - - - no_errors tier2 450 0 0 287 195 40.46 2 0 0 863018 TCGA-AB-2999 AML10 8 14071069 14071069 G A SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.425-4487 e5-4487 0.007 - - - no_errors tier3 1286 0 0 611 525 46.17 0 0 NA 863018 TCGA-AB-2999 AML10 8 15342471 15342471 C T SNP - - - - - - - - - - - - - - - tier3 1003 0 0 502 308 37.93 0 0 NA 863018 TCGA-AB-2999 AML10 8 15342473 15342473 T A SNP - - - - - - - - - - - - - - - tier3 988 0 0 505 310 37.99 0 0 NA 863018 TCGA-AB-2999 AML10 8 24846613 24846613 C A SNP LOC100129717 XM_001723212.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-0 NULL 0.001 - - - rna_with_coding_region tier3 2406 2 0.08 848 696 45.05 0 0 NA 863018 TCGA-AB-2999 AML10 8 36074393 36074393 G A SNP - - - - - - - - - - - - - - - tier3 3657 8 0.22 1278 951 42.65 0 0 NA 863018 TCGA-AB-2999 AML10 8 36329757 36329757 G T SNP ENSG00000206871 ENST00000384144 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43009 NULL 0.004 - - - no_errors tier2 1710 0 0 938 591 38.65 0 0 NA 863018 TCGA-AB-2999 AML10 8 37635492 37635492 G A SNP ZNF703 NM_025069.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-37164 NULL 0.001 - - - no_errors tier3 2902 1 0.03 1004 767 43.26 0 0 NA 863018 TCGA-AB-2999 AML10 8 53191132 53191132 C T SNP ST18 NM_014682.2 human genbank 54_36p -1 validated intronic c.3003+256 e19+256 0 - - - no_errors tier3 798 1 0.13 580 351 37.7 0 0 NA 863018 TCGA-AB-2999 AML10 8 57525490 57525490 G A SNP PENK NM_006211.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-4424 NULL 0.021 - - - no_errors tier3 675 0 0 509 372 42.22 0 0 NA 863018 TCGA-AB-2999 AML10 8 61146432 61146432 C T SNP - - - - - - - - - - - - - - - tier3 993 1 0.1 695 530 43.27 0 0 NA 863018 TCGA-AB-2999 AML10 8 62411333 62411333 G A SNP RLBP1L1 NM_173519.2 human genbank 54_36p 1 validated intronic c.455+35938 e1+35938 0.004 - - - no_errors tier3 1651 2 0.12 658 460 41.14 0 0 NA 863018 TCGA-AB-2999 AML10 8 63577299 63577299 A G SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.55-77353 e2-77353 0 - - - no_errors tier3 2083 8 0.38 1417 1199 45.83 0 0 NA 863018 TCGA-AB-2999 AML10 8 68505309 68505309 C T SNP CPA6 NM_020361.1 human genbank 54_36p -1 validated intronic c.1042-2389 e10-2389 0.016 - - - no_errors tier3 1154 1 0.09 549 348 38.75 0 0 0 863018 TCGA-AB-2999 AML10 8 71530452 71530452 C T SNP ENSG00000222928 ENST00000410996 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*24531 NULL 0 - - - no_errors tier3 461 0 0 805 505 38.46 0 0 NA 863018 TCGA-AB-2999 AML10 8 84711148 84711148 C T SNP - - - - - - - - - - - - - - - tier3 470 0 0 558 371 39.89 0 0 NA 863018 TCGA-AB-2999 AML10 8 84757021 84757021 C T SNP - - - - - - - - - - - - - - - tier3 968 0 0 444 357 44.51 0 0 NA 863018 TCGA-AB-2999 AML10 8 86572094 86572094 T G SNP CA2 NM_000067.2 human genbank 54_36p 1 reviewed intronic c.233-1080 e3-1080 0 - - - no_errors tier3 731 0 0 484 353 42.12 0 0 0 863018 TCGA-AB-2999 AML10 8 89522980 89522980 C T SNP ENSG00000209292 ENST00000386557 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45088 NULL 0.001 - - - pseudogene tier3 440 0 0 603 338 35.88 0 0 NA 863018 TCGA-AB-2999 AML10 8 95999443 95999443 T C SNP C8orf38 ENST00000396111 human ensembl 54_36p 1 known intronic c.1+22112 e0+22112 0.052 - - - no_errors tier3 784 0 0 492 416 45.71 2 3 60 863018 TCGA-AB-2999 AML10 8 107021601 107021601 T C SNP ENSG00000201627 ENST00000364757 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-10959 NULL 0.025 - - - no_errors tier3 520 0 0 484 324 40.1 0 0 NA 863018 TCGA-AB-2999 AML10 8 108245886 108245886 A C SNP ENSG00000213707 ENST00000395823 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8820 NULL 0.012 - - - no_coding_region:pseudogene tier3 1304 2 0.15 626 372 37.27 0 0 NA 863018 TCGA-AB-2999 AML10 8 113229273 113229273 A G SNP ENSG00000222146 ENST00000410214 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*818 NULL 0.024 - - - no_errors tier3 1091 0 0 898 699 43.77 0 0 NA 863018 TCGA-AB-2999 AML10 8 126949247 126949247 C T SNP ENSG00000206695 ENST00000383968 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33130 NULL 0 - - - no_errors tier2 1082 0 0 932 691 42.55 0 0 NA 863018 TCGA-AB-2999 AML10 8 135813120 135813120 G A SNP ZFAT NM_020863.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-18832 NULL 0.004 - - - no_errors tier3 777 0 0 624 425 40.48 0 0 NA 863018 TCGA-AB-2999 AML10 8 135999454 135999454 T C SNP - - - - - - - - - - - - - - - tier3 1024 1 0.1 356 316 47.02 0 0 NA 863018 TCGA-AB-2999 AML10 8 138583893 138583893 C T SNP - - - - - - - - - - - - - - - tier3 2226 0 0 1141 874 43.33 0 0 NA 863018 TCGA-AB-2999 AML10 8 142856927 142856927 G T SNP - - - - - - - - - - - - - - - tier3 1856 2 0.11 305 194 38.88 0 0 NA 863018 TCGA-AB-2999 AML10 8 143047994 143047994 G A SNP ENSG00000221123 ENST00000408196 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23101 NULL 1 - - - no_errors tier2 1578 0 0 1643 1169 41.56 0 0 0 863018 TCGA-AB-2999 AML10 8 143188790 143188790 G A SNP - - - - - - - - - - - - - - - tier3 2187 0 0 721 575 44.26 0 0 0 863018 TCGA-AB-2999 AML10 9 1458642 1458642 C T SNP LOC100134189 XM_001722214.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-46094 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1476 1 0.07 1122 757 40.29 0 0 NA 863018 TCGA-AB-2999 AML10 9 2087919 2087919 A T SNP SMARCA2 NM_003070.3 human genbank 54_36p 1 reviewed intronic c.3078+448 e20+448 0 - - - no_errors tier3 453 1 0.22 546 333 37.84 1 0 0 863018 TCGA-AB-2999 AML10 9 2586298 2586298 C G SNP VLDLR NM_003383.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25892 NULL 0.083 - - - no_errors tier3 1212 0 0 1127 698 38.25 0 0 NA 863018 TCGA-AB-2999 AML10 9 6155922 6155922 C T SNP ENSG00000218509 ENST00000404773 human ensembl 54_36p 1 known 5_prime_flanking_region c.-30012 NULL 0.021 - - - no_coding_region:pseudogene tier3 931 0 0 795 535 40.2 0 0 NA 863018 TCGA-AB-2999 AML10 9 27691353 27691353 G A SNP - - - - - - - - - - - - - - - tier3 693 1 0.14 579 445 43.46 0 0 NA 863018 TCGA-AB-2999 AML10 9 29323694 29323694 A T SNP LOC648294 XR_039095.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-39307 NULL 0.005 - - - pseudogene tier3 813 0 0 571 458 44.51 0 0 NA 863018 TCGA-AB-2999 AML10 9 32169294 32169294 C T SNP - - - - - - - - - - - - - - - tier3 996 5 0.5 1020 493 32.58 0 0 NA 863018 TCGA-AB-2999 AML10 9 35058998 35058998 T C SNP VCP NM_007126.3 human genbank 54_36p -1 reviewed intronic c.18-639 e2-639 0 - - - no_errors tier3 3439 1 0.03 942 706 42.81 9 18 66.67 863018 TCGA-AB-2999 AML10 9 35391603 35391603 G A SNP UNC13B NM_006377.3 human genbank 54_36p 1 reviewed intronic c.4237+1163 e36+1163 0.005 - - - no_errors tier3 3852 2 0.05 1430 1007 41.32 0 0 0 863018 TCGA-AB-2999 AML10 9 70881568 70881568 G A SNP LOC100131414 XM_001715469.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-44173 NULL 0.011 - - - no_errors tier2 1772 0 0 939 689 42.3 1 2 66.67 863018 TCGA-AB-2999 AML10 9 71268820 71268820 A T SNP APBA1 NM_001163.3 human genbank 54_36p -1 reviewed intronic c.1482+3739 e4+3739 0.001 - - - no_errors tier3 964 12 1.23 644 497 43.56 0 0 0 863018 TCGA-AB-2999 AML10 9 80499503 80499503 A G SNP ENSG00000211157 ENST00000388422 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-46632 NULL 0 - - - pseudogene tier2 1006 0 0 299 182 37.84 0 0 NA 863018 TCGA-AB-2999 AML10 9 88330213 88330213 T C SNP - - - - - - - - - - - - - - - tier3 589 3 0.51 456 347 43.16 0 0 NA 863018 TCGA-AB-2999 AML10 9 97274880 97274880 C T SNP PTCH1 NM_000264.3 human genbank 54_36p -1 reviewed intronic c.1729-2846 e13-2846 0 - - - no_errors tier3 2854 0 0 977 731 42.75 2 2 50 863018 TCGA-AB-2999 AML10 9 103203335 103203335 T C SNP ZNF189 NM_003452.2 human genbank 54_36p 1 validated intronic c.160+1222 e2+1222 0.019 - - - no_errors tier3 1262 4 0.32 1074 870 44.75 8 6 42.86 863018 TCGA-AB-2999 AML10 9 115301559 115301559 C T SNP RGS3 NM_144488.3 human genbank 54_36p 1 reviewed intronic c.897+1378 e10+1378 0.001 - - - no_errors tier2 1456 2 0.14 480 418 46.55 1 4 80 863018 TCGA-AB-2999 AML10 9 118811990 118811990 G A SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.1424-1631 e7-1631 0 - - - no_errors tier3 1709 0 0 992 318 24.27 0 0 NA 863018 TCGA-AB-2999 AML10 9 121912003 121912003 A G SNP - - - - - - - - - - - - - - - tier3 2804 0 0 1529 1140 42.71 0 0 NA 863018 TCGA-AB-2999 AML10 9 132750251 132750251 C T SNP ABL1 NM_007313.3 human genbank 54_36p 1 reviewed missense c.2810 p.P937L 0.837 NULL "HMMPfam_SH2,HMMSmart_SM00252,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_F_actin_bind,HMMSmart_SM00808,PatternScan_PROTEIN_KINASE_ATP,superfamily_SH2 domain" - no_errors tier1 380 0 298 207 40.75 18 14 43.75 863018 TCGA-AB-2999 AML10 9 133668726 133668726 C T SNP ENSG00000212395 ENST00000391093 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20522 NULL 0.003 - - - no_errors tier2 1599 2 0.12 445 352 44.11 0 0 NA 863018 TCGA-AB-2999 AML10 10 2906416 2906416 C G SNP - - - - - - - - - - - - - - - tier2 3106 0 0 1121 745 39.9 0 0 NA 863018 TCGA-AB-2999 AML10 10 5512701 5512701 A G SNP CALML3 NM_005185.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44348 NULL 0 - - - no_errors tier3 656 0 0 281 203 41.94 0 0 NA 863018 TCGA-AB-2999 AML10 10 8727349 8727349 G A SNP ENSG00000212505 ENST00000391203 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*11336 NULL 0.003 - - - no_errors tier2 2062 4 0.19 1267 856 40.3 0 0 NA 863018 TCGA-AB-2999 AML10 10 14695488 14695488 A G SNP FAM107B NM_031453.2 human genbank 54_36p -1 predicted intronic c.469+54151 e2+54151 0 - - - no_errors tier2 895 2 0.22 329 232 41.35 0 0 NA 863018 TCGA-AB-2999 AML10 10 19775562 19775562 C A SNP C10orf112 ENST00000377265 human ensembl 54_36p 1 known 5_prime_flanking_region c.-51860 NULL 0.043 - - - no_start_codon:no_stop_codon tier3 662 0 0 798 523 39.59 0 0 NA 863018 TCGA-AB-2999 AML10 10 20866823 20866823 G A SNP - - - - - - - - - - - - - - - tier3 316 0 0 136 343 71.46 0 0 NA 863018 TCGA-AB-2999 AML10 10 37096220 37096220 G T SNP - - - - - - - - - - - - - - - tier2 671 1 0.15 693 515 42.63 0 0 NA 863018 TCGA-AB-2999 AML10 10 54414387 54414387 T C SNP - - - - - - - - - - - - - - - tier3 1098 0 0 676 526 43.76 0 0 NA 863018 TCGA-AB-2999 AML10 10 67205341 67205341 A G SNP - - - - - - - - - - - - - - - tier3 568 0 0 379 274 41.96 0 0 NA 863018 TCGA-AB-2999 AML10 10 67511229 67511229 G A SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1978-11976 e14-11976 0 - - - no_errors tier2 147 0 0 118 102 46.36 0 0 NA 863018 TCGA-AB-2999 AML10 10 72725661 72725661 C T SNP UNC5B NM_170744.3 human genbank 54_36p 1 validated missense c.2263 p.R755C 1 NULL "HMMPfam_Death,HMMSmart_SM00005,HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_ZU5,HMMSmart_SM00218,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_DEATH domain,HMMPfam_I-set,superfamily_Immunoglobulin" - no_errors tier1 955 0 363 259 41.64 1 1 50 863018 TCGA-AB-2999 AML10 10 83698082 83698082 C T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.823+72183 e1+72183 0.001 - - - no_errors tier3 982 0 0 708 488 40.77 0 0 NA 863018 TCGA-AB-2999 AML10 10 84290003 84290003 A G SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.953+181399 e2+181399 0.001 - - - no_errors tier3 1027 0 0 1053 285 21.3 0 0 NA 863018 TCGA-AB-2999 AML10 10 84341643 84341643 C T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.954-146670 e3-146670 0 - - - no_errors tier3 874 0 0 836 356 29.87 0 0 NA 863018 TCGA-AB-2999 AML10 10 94354916 94354916 C T SNP KIF11 NM_004523.3 human genbank 54_36p 1 reviewed intronic c.78-1086 e2-1086 0.03 - - - no_errors tier3 545 0 0 514 367 41.56 2 0 0 863018 TCGA-AB-2999 AML10 10 100739463 100739463 G A SNP HPSE2 NM_021828.3 human genbank 54_36p -1 validated intronic c.610+154522 e3+154522 1 - - - no_errors tier2 2230 0 0 1102 726 39.72 0 0 NA 863018 TCGA-AB-2999 AML10 10 102555287 102555287 C A SNP PAX2 NM_003990.3 human genbank 54_36p 1 reviewed intronic c.686-890 e7-890 0 - - - no_errors tier2 3323 0 0 909 668 42.33 0 0 NA 863018 TCGA-AB-2999 AML10 10 103581584 103581584 T C SNP KCNIP2 NM_014591.4 human genbank 54_36p -1 reviewed intronic c.74-670 e2-670 0 - - - no_errors tier3 5738 1 0.02 1524 1002 39.62 2 2 50 863018 TCGA-AB-2999 AML10 10 104710316 104710316 C T SNP CNNM2 NM_017649.3 human genbank 54_36p 1 validated intronic c.1621+40468 e1+40468 0 - - - no_errors tier3 690 0 0 403 240 37.33 1 0 0 863018 TCGA-AB-2999 AML10 10 110391715 110391715 C T SNP - - - - - - - - - - - - - - - tier2 1944 1 0.05 1546 1049 40.41 0 0 NA 863018 TCGA-AB-2999 AML10 10 112092866 112092866 A C SNP SMNDC1 NM_005871.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-39531 NULL 0.011 - - - no_errors tier3 3664 2 0.05 959 646 40.25 0 0 NA 863018 TCGA-AB-2999 AML10 10 122244066 122244066 C T SNP PPAPDC1A NM_001030059.1 human genbank 54_36p 1 validated intronic c.57-9254 e2-9254 0.004 - - - no_errors tier3 2169 2 0.09 622 527 45.87 0 0 0 863018 TCGA-AB-2999 AML10 10 126063639 126063639 G A SNP OAT NM_000274.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*12862 NULL 0 - - - no_errors tier3 1567 0 0 861 621 41.9 0 0 NA 863018 TCGA-AB-2999 AML10 10 127099743 127099743 T C SNP - - - - - - - - - - - - - - - tier3 1590 0 0 1563 979 38.5 0 0 NA 863018 TCGA-AB-2999 AML10 10 127869283 127869283 C T SNP ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed intronic c.261-35419 e4-35419 0.005 - - - no_errors tier3 2737 1 0.04 585 450 43.44 0 0 NA 863018 TCGA-AB-2999 AML10 10 129333787 129333787 C T SNP - - - - - - - - - - - - - - - tier3 524 0 0 617 396 39.09 0 0 NA 863018 TCGA-AB-2999 AML10 11 8062369 8062369 T C SNP - - - - - - - - - - - - - - - tier3 397 0 0 247 195 44.02 0 0 NA 863018 TCGA-AB-2999 AML10 11 12981999 12981999 C - DEL RASSF10 NM_001080521.1 human genbank 54_36p 1 inferred 5_prime_flanking_region c.-5273 NULL 0.025 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 863018 TCGA-AB-2999 AML10 11 20830095 20830095 G T SNP - - - - - - - - - - - - - - - tier3 1292 0 0 785 609 43.66 0 0 NA 863018 TCGA-AB-2999 AML10 11 29556730 29556730 C T SNP - - - - - - - - - - - - - - - tier3 1827 0 0 706 506 41.71 0 0 NA 863018 TCGA-AB-2999 AML10 11 30249820 30249820 T C SNP - - - - - - - - - - - - - - - tier3 1390 1 0.07 1049 678 39.26 0 0 NA 863018 TCGA-AB-2999 AML10 11 30795453 30795453 C T SNP - - - - - - - - - - - - - - - tier2 2244 2 0.09 959 633 39.74 0 0 NA 863018 TCGA-AB-2999 AML10 11 35805237 35805237 T C SNP - - - - - - - - - - - - - - - tier3 910 1 0.11 655 468 41.67 0 0 NA 863018 TCGA-AB-2999 AML10 11 47376831 47376831 G A SNP - - - - - - - - - - - - - - - tier3 1035 1 0.1 525 361 40.74 0 0 NA 863018 TCGA-AB-2999 AML10 11 64590262 64590262 C T SNP - - - - - - - - - - - - - - - tier3 645 1 0.15 223 142 38.9 0 0 NA 863018 TCGA-AB-2999 AML10 11 76659860 76659860 C T SNP GDPD4 NM_182833.1 human genbank 54_36p -1 provisional nonsense c.363 p.W121* 0.997 NULL "HMMPfam_GDPD,superfamily_PLC-like_Pdiesterase_TIM-brl" - no_errors tier1 1967 1 0.05 1189 862 42.01 0 863018 TCGA-AB-2999 AML10 11 79777365 79777365 A G SNP - - - - - - - - - - - - - - - tier3 964 1 0.1 748 589 44.02 0 0 NA 863018 TCGA-AB-2999 AML10 11 96390344 96390344 G T SNP - - - - - - - - - - - - - - - tier2 868 0 0 648 403 38.34 0 0 NA 863018 TCGA-AB-2999 AML10 11 131222789 131222789 T G SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.83-63879 e2-63879 0.001 - - - no_errors tier2 3647 0 0 2016 1586 44.02 0 0 NA 863018 TCGA-AB-2999 AML10 11 134348750 134348750 C T SNP - - - - - - - - - - - - - - - tier3 734 0 0 439 336 43.35 0 0 NA 863018 TCGA-AB-2999 AML10 12 2126031 2126031 G A SNP CACNA1C NM_000719.6 human genbank 54_36p 1 reviewed intronic c.477+26174 e3+26174 0.002 - - - no_errors tier3 2145 20 0.92 627 469 42.75 0 0 NA 863018 TCGA-AB-2999 AML10 12 5610589 5610589 G A SNP ANO2 NM_020373.2 human genbank 54_36p -1 validated intronic c.1819+3990 e18+3990 0.001 - - - no_errors tier3 3450 0 0 1358 995 42.29 0 0 NA 863018 TCGA-AB-2999 AML10 12 15086670 15086670 T G SNP - - - - - - - - - - - - - - - tier3 1542 0 0 1058 1013 48.89 0 0 NA 863018 TCGA-AB-2999 AML10 12 28105957 28105957 T C SNP - - - - - - - - - - - - - - - tier3 1355 1 0.07 884 610 40.8 0 0 NA 863018 TCGA-AB-2999 AML10 12 74790577 74790577 G A SNP NAP1L1 NM_004537.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-36311 NULL 0 - - - no_errors tier2 1850 1 0.05 622 357 36.43 0 0 NA 863018 TCGA-AB-2999 AML10 12 76467295 76467295 G T SNP - - - - - - - - - - - - - - - tier3 492 0 0 643 487 43.06 0 0 NA 863018 TCGA-AB-2999 AML10 12 82059982 82059982 G A SNP ENSG00000213270 ENST00000393222 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-9259 NULL 0 - - - no_coding_region:pseudogene tier3 509 0 0 445 292 39.62 1 0 0 863018 TCGA-AB-2999 AML10 12 127282922 127282922 C G SNP - - - - - - - - - - - - - - - tier3 3120 0 0 1389 1032 42.63 0 0 NA 863018 TCGA-AB-2999 AML10 13 23619589 23619589 T C SNP SPATA13 NM_153023.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-102248 NULL 0 - - - no_errors tier3 1850 0 0 853 429 33.46 0 0 NA 863018 TCGA-AB-2999 AML10 13 33946694 33946694 C T SNP - - - - - - - - - - - - - - - tier3 1189 0 0 1415 387 21.46 0 0 NA 863018 TCGA-AB-2999 AML10 13 36705852 36705852 A C SNP ENSG00000218218 ENST00000406632 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12469 NULL 0.003 - - - no_coding_region:pseudogene tier3 887 0 0 593 383 39.16 0 0 NA 863018 TCGA-AB-2999 AML10 13 39334021 39334021 C T SNP ENSG00000212553 ENST00000391251 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4657 NULL 0.042 - - - no_errors tier2 1745 1 0.06 1182 902 43.26 0 0 NA 863018 TCGA-AB-2999 AML10 13 46601576 46601576 A T SNP - - - - - - - - - - - - - - - tier2 2429 0 0 1438 853 37.23 0 0 NA 863018 TCGA-AB-2999 AML10 13 65572611 65572611 C T SNP - - - - - - - - - - - - - - - tier3 832 1 0.12 860 587 40.57 0 0 NA 863018 TCGA-AB-2999 AML10 13 66082904 66082904 T C SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed intronic c.3340+20439 e3+20439 0.01 - - - no_errors tier3 441 0 0 330 244 42.51 0 0 NA 863018 TCGA-AB-2999 AML10 13 87229816 87229816 A C SNP - - - - - - - - - - - - - - - tier3 1297 1 0.08 579 402 40.9 0 0 NA 863018 TCGA-AB-2999 AML10 13 97488241 97488241 C A SNP IPO5 NM_002271.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*16164 NULL 0.361 - - - no_errors tier3 2882 0 0 903 601 39.93 0 0 NA 863018 TCGA-AB-2999 AML10 13 105856125 105856125 G A SNP ENSG00000174418 ENST00000310792 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19997 NULL 0.94 - - - no_coding_region:pseudogene tier2 1302 0 0 905 647 41.69 0 0 NA 863018 TCGA-AB-2999 AML10 13 106155882 106155882 C A SNP LOC390424 XR_016535.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*41581 NULL 0 - - - no_errors tier3 855 0 0 553 396 41.73 0 0 NA 863018 TCGA-AB-2999 AML10 13 109981699 109981699 C T SNP RAB20 NM_017817.1 human genbank 54_36p -1 provisional intronic c.173-7154 e2-7154 0.001 - - - no_errors tier3 585 0 0 416 236 36.14 0 0 0 863018 TCGA-AB-2999 AML10 14 28268590 28268590 G A SNP FOXG1 NM_005249.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-37647 NULL 0.003 - - - no_errors tier3 1126 0 0 864 585 40.37 0 0 NA 863018 TCGA-AB-2999 AML10 14 47428964 47428964 T A SNP - - - - - - - - - - - - - - - tier3 1971 0 0 1006 659 39.58 0 0 NA 863018 TCGA-AB-2999 AML10 14 53031331 53031331 A G SNP FAM30A XM_001725525.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40953 NULL 1 - - - no_start_codon:pseudogene:no_stop_codon tier2 2386 0 0 1135 863 43.17 0 0 0 863018 TCGA-AB-2999 AML10 14 57104565 57104565 G A SNP SLC35F4 NM_001080455.1 human genbank 54_36p -1 inferred intronic c.1235-1530 e7-1530 0.129 - - - no_errors tier3 1176 0 0 635 486 43.35 0 0 NA 863018 TCGA-AB-2999 AML10 14 60815641 60815641 A G SNP TMEM30B NM_001017970.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*922 NULL 0.002 - - - no_errors tier3 593 0 0 446 327 42.25 4 0 0 863018 TCGA-AB-2999 AML10 14 67280865 67280865 T A SNP ZFYVE26 ENST00000394455 human ensembl 54_36p -1 known intronic c.1989+6657 e13+6657 0.001 - - - no_errors tier3 401 0 0 282 200 41.49 2 4 66.67 863018 TCGA-AB-2999 AML10 14 70609786 70609786 G A SNP PCNX NM_014982.2 human genbank 54_36p 1 validated intronic c.4853-229 e27-229 0.083 - - - no_errors tier3 592 0 0 942 491 34.26 4 2 33.33 863018 TCGA-AB-2999 AML10 14 72444494 72444494 G A SNP WDR21A NM_015604.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29946 NULL 0.119 - - - no_errors tier2 1482 1 0.07 1192 659 35.58 0 0 NA 863018 TCGA-AB-2999 AML10 14 76780650 76780650 C T SNP TMEM63C NM_020431.2 human genbank 54_36p 1 validated intronic c.1448+99 e14+99 0.001 - - - no_errors tier3 517 0 0 147 124 45.76 0 0 NA 863018 TCGA-AB-2999 AML10 14 82769657 82769657 T A SNP - - - - - - - - - - - - - - - tier3 428 0 0 497 324 39.46 6 4 40 863018 TCGA-AB-2999 AML10 14 97729875 97729875 A G SNP - - - - - - - - - - - - - - - tier2 1996 0 0 925 615 39.94 0 0 NA 863018 TCGA-AB-2999 AML10 14 101273289 101273289 C T SNP LOC100132532 XM_001726536.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24695 NULL 0.002 - - - no_errors tier3 1008 0 0 436 307 41.32 0 0 NA 863018 TCGA-AB-2999 AML10 15 21441341 21441341 C T SNP MAGEL2 NM_019066.3 human genbank 54_36p -1 validated missense c.833 p.R278H 0.002 NULL HMMPfam_MAGE - no_errors tier1 276 0 584 304 34.16 NA 863018 TCGA-AB-2999 AML10 15 27679907 27679907 C T SNP LOC100130111 XM_001718651.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-35584 NULL 0.251 - - - no_errors tier3 1170 0 0 1021 738 41.93 0 0 NA 863018 TCGA-AB-2999 AML10 15 27950803 27950803 C T SNP TJP1 NM_003257.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49280 NULL 0 - - - no_errors tier3 1130 0 0 780 496 38.81 0 0 NA 863018 TCGA-AB-2999 AML10 15 31058509 31058509 T C SNP FMN1 NM_001103184.1 human genbank 54_36p -1 provisional intronic c.1555-9539 e4-9539 0.001 - - - no_errors tier3 970 0 0 522 378 41.95 0 0 NA 863018 TCGA-AB-2999 AML10 15 41999136 41999136 G A SNP FRMD5 NM_032892.3 human genbank 54_36p -1 validated intronic c.251-109 e4-109 0.067 - - - no_errors tier3 1512 0 0 794 584 42.35 0 0 NA 863018 TCGA-AB-2999 AML10 15 42038513 42038513 C G SNP FRMD5 NM_032892.3 human genbank 54_36p -1 validated intronic c.103-34714 e2-34714 0 - - - no_errors tier3 1409 1 0.07 1022 692 40.37 0 0 NA 863018 TCGA-AB-2999 AML10 15 44955336 44955336 C T SNP ENSG00000214983 ENST00000399372 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47886 NULL 0 - - - no_coding_region:pseudogene tier3 700 0 0 386 234 37.74 0 0 NA 863018 TCGA-AB-2999 AML10 15 63045889 63045889 T G SNP SPG21 NM_016630.1 human genbank 54_36p -1 reviewed intronic c.670-1035 e7-1035 0.143 - - - no_errors tier3 1129 1 0.09 626 404 39.19 0 1 100 863018 TCGA-AB-2999 AML10 15 63977422 63977422 G A SNP MEGF11 NM_032445.2 human genbank 54_36p -1 validated silent c.2814 p.Y938 1 NULL "HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_2,superfamily_SSF57196" - no_errors tier1 836 0 619 174 21.94 NA 863018 TCGA-AB-2999 AML10 15 66353946 66353946 A T SNP CLN6 NM_017882.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-44970 NULL 0 - - - no_errors tier3 1466 13 0.88 774 552 41.6 0 0 NA 863018 TCGA-AB-2999 AML10 15 67151443 67151443 A G SNP TMEM84 ENST00000391455 human ensembl 54_36p 1 known 5_prime_flanking_region c.-8819 NULL 0.002 - - - no_errors tier3 4105 1 0.02 953 659 40.88 0 0 NA 863018 TCGA-AB-2999 AML10 15 89833281 89833281 C T SNP - - - - - - - - - - - - - - - tier3 1600 0 0 854 607 41.52 0 0 NA 863018 TCGA-AB-2999 AML10 16 8324887 8324887 A T SNP - - - - - - - - - - - - - - - tier2 1215 0 0 914 605 39.78 0 0 NA 863018 TCGA-AB-2999 AML10 16 12318944 12318944 T G SNP SNX29 NM_001080530.2 human genbank 54_36p 1 provisional intronic c.628-38577 e8-38577 0.002 - - - no_errors tier3 2796 1 0.04 810 562 40.96 0 0 0 863018 TCGA-AB-2999 AML10 16 30908446 30908446 C T SNP STX4 NM_004604.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-44182 NULL 1 - - - no_errors tier2 1473 1 0.07 885 605 40.6 0 0 NA 863018 TCGA-AB-2999 AML10 16 46663127 46663127 C T SNP ABCC12 NM_033226.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*12000 NULL 0.429 - - - no_errors tier3 3591 0 0 773 615 44.21 0 0 NA 863018 TCGA-AB-2999 AML10 16 64792720 64792720 G A SNP - - - - - - - - - - - - - - - tier3 1934 0 0 1187 909 43.35 0 0 NA 863018 TCGA-AB-2999 AML10 16 74800130 74800130 T A SNP LOC441775 XR_042366.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*26311 NULL 0.633 - - - pseudogene tier3 698 0 0 520 346 39.91 0 0 NA 863018 TCGA-AB-2999 AML10 16 77749771 77749771 C T SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1057-53235 e9-53235 0.008 - - - no_errors tier3 4882 1 0.02 1791 1102 38.09 2 0 0 863018 TCGA-AB-2999 AML10 16 80712850 80712850 G A SNP ENSG00000210844 ENST00000388109 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1114 NULL 1 - - - pseudogene tier2 1155 1 0.09 502 331 39.69 0 0 NA 863018 TCGA-AB-2999 AML10 17 27476657 27476657 C T SNP RHOT1 NM_001033568.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17168 NULL 0.025 - - - no_errors tier3 1642 7 0.42 633 475 42.87 0 0 NA 863018 TCGA-AB-2999 AML10 17 32090356 32090356 G A SNP ENSG00000223276 ENST00000411344 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-22406 NULL 0 - - - no_errors tier3 4444 2 0.04 1015 893 46.8 0 0 NA 863018 TCGA-AB-2999 AML10 17 35296800 35296800 C T SNP IKZF3 NM_012481.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22895 NULL 0.047 - - - no_errors tier3 2259 0 0 811 628 43.64 0 0 NA 863018 TCGA-AB-2999 AML10 17 41166552 41166552 C T SNP - - - - - - - - - - - - - - - tier3 2507 1 0.04 828 596 41.82 0 0 NA 863018 TCGA-AB-2999 AML10 17 43955804 43955804 A G SNP LOC100131782 XM_001726546.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-33878 NULL 0 - - - no_errors tier3 4084 1 0.02 1122 857 43.3 0 0 NA 863018 TCGA-AB-2999 AML10 17 49542636 49542636 G A SNP - - - - - - - - - - - - - - - tier3 950 0 0 1150 376 24.64 0 0 NA 863018 TCGA-AB-2999 AML10 17 50868446 50868446 A C SNP MMD NM_012329.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-14391 NULL 0.02 - - - no_errors tier3 811 0 0 277 159 36.47 0 0 NA 863018 TCGA-AB-2999 AML10 17 51229795 51229795 G A SNP PCTP NM_021213.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*21335 NULL 0.044 - - - no_errors tier3 1647 6 0.36 854 611 41.71 0 0 NA 863018 TCGA-AB-2999 AML10 17 69211465 69211465 G A SNP C17orf54 ENST00000321800 human ensembl 54_36p -1 known 3_prime_flanking_region c.*46693 NULL 0 - - - no_errors tier3 2247 3 0.13 1047 667 38.89 0 0 NA 863018 TCGA-AB-2999 AML10 17 70285366 70285366 A T SNP TMEM104 NM_017728.3 human genbank 54_36p 1 validated intronic c.45+257 e1+257 0.003 - - - no_errors tier3 506 0 0 240 164 40.59 2 0 0 863018 TCGA-AB-2999 AML10 18 3309073 3309073 G A SNP MYL12B NM_033546.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*41138 NULL 0.001 - - - no_errors tier3 1764 3 0.17 1324 161 10.84 0 0 NA 863018 TCGA-AB-2999 AML10 18 4021339 4021339 A T SNP - - - - - - - - - - - - - - - tier3 816 0 0 396 275 40.98 0 0 NA 863018 TCGA-AB-2999 AML10 18 4757833 4757833 A C SNP - - - - - - - - - - - - - - - tier3 397 0 0 329 240 42.11 0 0 NA 863018 TCGA-AB-2999 AML10 18 25525942 25525942 G T SNP - - - - - - - - - - - - - - - tier3 945 0 0 586 422 41.87 0 0 NA 863018 TCGA-AB-2999 AML10 18 26176558 26176558 T C SNP - - - - - - - - - - - - - - - tier3 675 1 0.15 479 350 42.12 0 0 NA 863018 TCGA-AB-2999 AML10 18 31614918 31614918 T C SNP - - - - - - - - - - - - - - - tier3 1450 0 0 626 395 38.65 0 0 NA 863018 TCGA-AB-2999 AML10 18 33891815 33891815 C T SNP - - - - - - - - - - - - - - - tier3 1421 0 0 694 489 41.34 0 0 NA 863018 TCGA-AB-2999 AML10 18 37482817 37482817 G A SNP - - - - - - - - - - - - - - - tier3 802 0 0 882 499 36.13 0 0 NA 863018 TCGA-AB-2999 AML10 18 43186977 43186977 T C SNP - - - - - - - - - - - - - - - tier3 1119 2 0.18 472 333 41.37 0 0 NA 863018 TCGA-AB-2999 AML10 18 50008909 50008909 G A SNP MBD2 NM_003927.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3982 NULL 0.967 - - - no_errors tier3 973 0 0 630 365 36.65 0 0 NA 863018 TCGA-AB-2999 AML10 18 53997302 53997302 T C SNP NEDD4L NM_015277.1 human genbank 54_36p 1 validated intronic c.122+13211 e2+13211 0.122 - - - no_errors tier2 1841 0 0 638 354 35.69 0 0 NA 863018 TCGA-AB-2999 AML10 18 64988192 64988192 G A SNP - - - - - - - - - - - - - - - tier3 949 1 0.11 565 454 44.55 0 0 NA 863018 TCGA-AB-2999 AML10 18 69337209 69337209 C G SNP - - - - - - - - - - - - - - - tier3 3758 2 0.05 1522 1009 39.87 0 0 NA 863018 TCGA-AB-2999 AML10 18 71563052 71563052 C T SNP - - - - - - - - - - - - - - - tier3 1048 0 0 522 354 40.36 0 0 NA 863018 TCGA-AB-2999 AML10 19 800644 800644 C T SNP ELA2 NM_001972.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2685 NULL 0 - - - no_errors tier3 1281 0 0 298 228 43.26 0 0 NA 863018 TCGA-AB-2999 AML10 19 8021866 8021866 A G SNP ELAVL1 ENST00000351593 human ensembl 54_36p -1 known intronic c.1-59148 e1-59148 0 - - - no_errors tier2 928 0 0 379 275 42.05 0 0 NA 863018 TCGA-AB-2999 AML10 19 18277971 18277971 A C SNP JUND NM_005354.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24677 NULL 0.003 - - - no_errors tier3 2351 2 0.08 478 306 38.98 3 2 40 863018 TCGA-AB-2999 AML10 19 22498617 22498617 A G SNP ZNF729 ENST00000357491 human ensembl 54_36p 1 known intronic c.2644+52133 e5+52133 0.17 - - - no_stop_codon tier3 1597 5 0.31 516 411 44.34 0 1 100 863018 TCGA-AB-2999 AML10 19 34336438 34336438 C A SNP - - - - - - - - - - - - - - - tier3 3058 0 0 2047 1589 43.68 0 0 NA 863018 TCGA-AB-2999 AML10 19 34569692 34569692 G A SNP LOC284395 XM_378787.3 human genbank 54_36p -1 model 3_prime_flanking_region c.*25975 NULL 0 - - - no_errors tier3 1725 0 0 441 322 42.2 0 0 NA 863018 TCGA-AB-2999 AML10 19 40753869 40753869 G A SNP ATP4A NM_000704.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7498 NULL 0.003 - - - no_errors tier3 4089 2 0.05 1519 1093 41.83 0 0 NA 863018 TCGA-AB-2999 AML10 19 42198403 42198403 C A SNP - - - - - - - - - - - - - - - tier3 895 0 0 441 312 41.43 0 0 NA 863018 TCGA-AB-2999 AML10 19 53202730 53202730 A G SNP ELSPBP1 NM_022142.3 human genbank 54_36p 1 reviewed intronic c.1-990 e1-990 0.004 - - - no_errors tier3 2050 1 0.05 698 501 41.78 0 0 NA 863018 TCGA-AB-2999 AML10 20 2697029 2697029 C T SNP C20orf141 NM_080739.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46802 NULL 0.15 - - - no_errors tier3 881 0 0 449 268 37.38 0 0 NA 863018 TCGA-AB-2999 AML10 20 9718357 9718357 G A SNP PAK7 NM_020341.3 human genbank 54_36p -1 reviewed intronic c.1-5203 e1-5203 0 - - - no_errors tier3 1322 0 0 950 703 42.53 0 0 NA 863018 TCGA-AB-2999 AML10 20 17697792 17697792 T G SNP BANF2 NM_001014977.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*33336 NULL 0 - - - no_errors tier3 3989 2 0.05 1495 1065 41.57 0 0 NA 863018 TCGA-AB-2999 AML10 20 17702901 17702901 C G SNP BANF2 NM_001014977.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*38445 NULL 0 - - - no_errors tier2 4138 0 0 1590 1127 41.45 0 0 NA 863018 TCGA-AB-2999 AML10 20 33714036 33714036 T C SNP RBM12 NM_006047.4 human genbank 54_36p -1 reviewed intronic c.1+2060 e0+2060 0 - - - no_errors tier2 1444 0 0 808 553 40.6 7 6 46.15 863018 TCGA-AB-2999 AML10 20 36484550 36484550 C T SNP ENSG00000196756 ENST00000360896 human ensembl 54_36p -1 known intronic c.174-248 e3-248 0.002 - - - no_start_codon tier3 998 0 0 351 510 59.16 14 13 48.15 863018 TCGA-AB-2999 AML10 20 38268915 38268915 G A SNP - - - - - - - - - - - - - - - tier3 983 1 0.1 750 482 39.12 0 0 NA 863018 TCGA-AB-2999 AML10 20 38691810 38691810 C T SNP - - - - - - - - - - - - - - - tier3 1065 0 0 904 599 39.83 0 0 NA 863018 TCGA-AB-2999 AML10 20 48817056 48817056 C T SNP BCAS4 NM_017843.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27882 NULL 0.104 - - - no_errors tier3 1515 0 0 475 362 43.25 0 0 NA 863018 TCGA-AB-2999 AML10 20 49623889 49623889 T - DEL NFATC2 NM_173091.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31444 NULL 0.996 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 863018 TCGA-AB-2999 AML10 20 52415306 52415306 G A SNP - - - - - - - - - - - - - - - tier2 891 1 0.11 918 712 43.65 0 0 NA 863018 TCGA-AB-2999 AML10 20 55090186 55090186 G C SNP - - - - - - - - - - - - - - - tier3 1156 0 0 761 671 46.79 0 0 NA 863018 TCGA-AB-2999 AML10 20 55229328 55229328 G A SNP BMP7 NM_001719.2 human genbank 54_36p -1 reviewed intronic c.611+7364 e2+7364 0.034 - - - no_errors tier3 3029 3 0.1 1204 995 45.25 0 0 NA 863018 TCGA-AB-2999 AML10 20 61156492 61156492 C T SNP C20orf51 XR_040056.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.003 - - - no_errors tier3 341 1 0.29 589 401 40.46 0 0 NA 863018 TCGA-AB-2999 AML10 21 35548362 35548362 T G SNP - - - - - - - - - - - - - - - tier2 1232 0 0 1056 777 42.32 0 0 NA 863018 TCGA-AB-2999 AML10 21 40256480 40256480 G A SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*50351 NULL 0 - - - no_errors tier3 1171 0 0 841 513 37.86 0 0 NA 863018 TCGA-AB-2999 AML10 22 38237767 38237767 G A SNP SMCR7L NM_019008.4 human genbank 54_36p 1 validated intronic c.145-33 e2-33 0.002 - - - no_errors tier2 1504 0 0 690 457 39.74 3 0 0 863018 TCGA-AB-2999 AML10 22 48541981 48541981 G A SNP ENSG00000218799 ENST00000402476 human ensembl 54_36p -1 known 5_prime_flanking_region c.-3349 NULL 0.022 - - - no_coding_region:pseudogene tier3 569 2 0.35 318 218 40.6 2 0 0 273919 TCGA-AB-3000 AML25 X 9111367 9111367 G C SNP FAM9B ENST00000380975 human ensembl 54_36p -1 known 5_prime_flanking_region c.-150340 NULL 0 - - - no_errors tier3 1185 12 1 513 69 11.84 0 0 NA 273919 TCGA-AB-3000 AML25 X 102751098 102751098 A G SNP TCEAL3 NM_001006933.1 human genbank 54_36p 1 reviewed silent c.450 p.Q150 1 HMMPfam_TFA HMMPfam_TFA - no_errors tier1 839 161 16.02 393 160 28.83 16 0 273919 TCGA-AB-3000 AML25 X 141323751 141323751 G T SNP ENSG00000201000 ENST00000364130 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2754 NULL 1 - - - no_errors tier3 96 10 9.26 92 80 46.51 0 0 NA 273919 TCGA-AB-3000 AML25 1 11820095 11820095 G C SNP CLCN6 NM_001286.2 human genbank 54_36p 1 reviewed missense c.2247 p.Q749H 1 HMMPfam_CBS "HMMPfam_CBS,HMMSmart_SM00116,HMMPfam_Voltage_CLC,superfamily_Clc chloride channel,superfamily_CBS-domain" - no_errors tier1 1118 263 19.03 469 534 53.13 20 14 41.18 273919 TCGA-AB-3000 AML25 1 24545807 24545807 G A SNP GRHL3 NM_021180.2 human genbank 54_36p 1 reviewed intronic c.1558+89 e13+89 0.126 - - - no_errors tier3 186 29 13.36 52 36 40.91 0 0 NA 273919 TCGA-AB-3000 AML25 1 49611662 49611662 T A SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.283-127539 e4-127539 0.009 - - - no_errors tier3 957 48 4.73 832 162 16.28 0 0 NA 273919 TCGA-AB-3000 AML25 1 181027445 181027445 T C SNP NPL ENST00000367555 human ensembl 54_36p 1 known intronic c.1-545 e1-545 0.001 - - - no_errors tier3 697 106 13.12 273 300 52.36 3 0 0 273919 TCGA-AB-3000 AML25 1 193700168 193700168 G C SNP - - - - - - - - - - - - - - - tier3 782 161 17.06 713 665 48.26 0 0 NA 273919 TCGA-AB-3000 AML25 1 207560587 207560587 G A SNP - - - - - - - - - - - - - - - tier3 951 157 14.14 520 479 47.9 0 0 NA 273919 TCGA-AB-3000 AML25 1 208673385 208673385 A G SNP HHAT NM_018194.1 human genbank 54_36p 1 validated intronic c.856+15093 e6+15093 0 - - - no_errors tier3 1167 73 5.86 1183 267 18.41 0 0 0 273919 TCGA-AB-3000 AML25 2 71648884 71648884 C T SNP DYSF NM_003494.1 human genbank 54_36p 1 reviewed silent c.2718 p.D906 0.981 HMMSmart_SM00693 "HMMPfam_C2,HMMSmart_SM00239,HMMSmart_SM00693,HMMSmart_SM00694,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_FerA,HMMPfam_FerB,HMMPfam_FerI" - no_errors tier1 1456 383 20.76 379 319 45.64 17 16 48.48 273919 TCGA-AB-3000 AML25 2 102291912 102291912 A G SNP IL1RL1 NM_016232.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29245 NULL 0.047 - - - no_errors tier3 204 53 20.54 113 133 54.07 0 0 0 273919 TCGA-AB-3000 AML25 2 131532200 131532200 A C SNP FAM168B NM_001009993.2 human genbank 54_36p -1 validated intronic c.155-2462 e3-2462 0.041 - - - no_errors tier3 465 112 19.28 261 234 47.18 2 2 50 273919 TCGA-AB-3000 AML25 2 189335239 189335239 C T SNP DIRC1 NM_052952.2 human genbank 54_36p -1 validated intronic c.1-27318 e1-27318 0 - - - no_errors tier3 249 16 6.02 650 198 23.24 0 0 NA 273919 TCGA-AB-3000 AML25 2 219330818 219330818 C T SNP CYP27A1 NM_000784.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-24332 NULL 0.016 - - - no_errors tier3 1332 366 21.45 448 524 53.69 0 3 100 273919 TCGA-AB-3000 AML25 3 2385234 2385234 A T SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.1+29317 e0+29317 0 - - - no_errors tier3 1223 80 6.1 827 214 20.56 0 0 NA 273919 TCGA-AB-3000 AML25 3 15181516 15181516 C A SNP LOC344875 XM_497913.1 human genbank 54_36p -1 model missense c.2954 p.C985F 1 "HMMSmart_SM00327,superfamily_vWA-like" "HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like" - no_errors tier1 1399 351 20.01 669 546 44.94 NA 273919 TCGA-AB-3000 AML25 3 28400172 28400172 T A SNP ZCWPW2 ENST00000383768 human ensembl 54_36p 1 known intronic c.1-6821 e1-6821 0.002 - - - no_errors tier3 491 104 17.48 441 424 49.02 0 0 NA 273919 TCGA-AB-3000 AML25 3 36286849 36286849 G A SNP LOC100132360 XM_001717169.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-30317 NULL 0.004 - - - no_errors tier3 961 295 23.39 621 566 47.6 0 0 NA 273919 TCGA-AB-3000 AML25 3 78301778 78301778 C A SNP ENSG00000222574 ENST00000410642 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*7945 NULL 0.001 - - - no_errors tier3 454 15 3.16 407 90 18.11 0 0 NA 273919 TCGA-AB-3000 AML25 3 90061314 90061314 G A SNP - - - - - - - - - - - - - - - tier3 105 11 9.48 58 55 48.67 0 0 NA 273919 TCGA-AB-3000 AML25 4 9511236 9511236 G T SNP SLC2A9 NM_020041.1 human genbank 54_36p -1 reviewed intronic c.1113+7721 e8+7721 0.02 - - - no_errors tier3 841 233 21.57 387 385 49.74 0 0 0 273919 TCGA-AB-3000 AML25 4 11052843 11052843 T C SNP HS3ST1 NM_005114.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42116 NULL 0.092 - - - no_errors tier3 1209 341 21.96 549 556 50.27 0 0 NA 273919 TCGA-AB-3000 AML25 4 145185163 145185163 C G SNP GYPB NM_002100.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25273 NULL 0.001 - - - no_errors tier3 529 101 15.98 311 290 48.09 0 0 0 273919 TCGA-AB-3000 AML25 4 164565286 164565287 - T INS TKTL2 NM_032136.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*47170 NULL 0.019:0.019 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 273919 TCGA-AB-3000 AML25 4 181832146 181832146 T C SNP - - - - - - - - - - - - - - - tier3 1489 147 8.95 935 277 22.82 0 0 NA 273919 TCGA-AB-3000 AML25 4 181933067 181933067 G A SNP - - - - - - - - - - - - - - - tier3 954 192 16.67 741 675 47.64 0 0 NA 273919 TCGA-AB-3000 AML25 5 92515606 92515606 T C SNP - - - - - - - - - - - - - - - tier3 1645 327 16.54 728 635 46.55 0 0 NA 273919 TCGA-AB-3000 AML25 6 68277282 68277282 G T SNP ENSG00000201015 ENST00000364145 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-35983 NULL 0.001 - - - no_errors tier3 921 54 5.5 993 125 11.18 0 0 NA 273919 TCGA-AB-3000 AML25 6 115076943 115076943 G A SNP - - - - - - - - - - - - - - - tier3 1182 188 13.68 531 472 47.01 0 0 NA 273919 TCGA-AB-3000 AML25 6 119142299 119142299 T A SNP C6orf204 ENST00000392500 human ensembl 54_36p -1 known 5_prime_flanking_region c.-61662 NULL 0.012 - - - no_errors tier3 1272 316 19.84 857 771 47.33 0 0 NA 273919 TCGA-AB-3000 AML25 6 150942707 150942707 T A SNP PLEKHG1 NM_001029884.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-153804 NULL 0 - - - no_errors tier3 915 86 8.53 639 228 26.3 0 0 NA 273919 TCGA-AB-3000 AML25 6 152843753 152843753 T C SNP SYNE1 NM_182961.2 human genbank 54_36p -1 reviewed intronic c.1350+2160 e12+2160 0 - - - no_errors tier3 1438 230 13.76 1197 1124 48.28 0 0 NA 273919 TCGA-AB-3000 AML25 7 17628410 17628410 A G SNP - - - - - - - - - - - - - - - tier3 1115 244 17.86 617 615 49.8 0 0 NA 273919 TCGA-AB-3000 AML25 7 53490006 53490006 A C SNP ENSG00000222154 ENST00000410222 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*35329 NULL 0.002 - - - no_errors tier3 243 98 28.65 171 179 51.14 0 0 NA 273919 TCGA-AB-3000 AML25 7 103963615 103963615 C A SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed intronic c.446-200743 e2-200743 0 - - - no_errors tier3 1600 357 18.21 617 620 50.08 0 0 NA 273919 TCGA-AB-3000 AML25 8 67620024 67620024 A G SNP ENSG00000206949 ENST00000384222 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43924 NULL 0.004 - - - no_errors tier3 607 61 9.06 378 106 21.86 0 0 NA 273919 TCGA-AB-3000 AML25 8 132309048 132309048 A G SNP - - - - - - - - - - - - - - - tier3 199 53 20.95 292 193 39.79 0 0 NA 273919 TCGA-AB-3000 AML25 9 6533842 6533842 C G SNP GLDC NM_000170.2 human genbank 54_36p -1 validated intronic c.2570-3696 e22-3696 0.018 - - - no_errors tier3 1404 316 18.31 461 419 47.51 0 0 NA 273919 TCGA-AB-3000 AML25 9 25161799 25161799 C G SNP - - - - - - - - - - - - - - - tier3 546 25 4.36 702 131 15.71 0 0 NA 273919 TCGA-AB-3000 AML25 10 70924974 70924974 C T SNP TSPAN15 NM_012339.3 human genbank 54_36p 1 reviewed intronic c.358-382 e4-382 0 - - - no_errors tier3 1602 467 22.45 228 242 50.31 0 0 NA 273919 TCGA-AB-3000 AML25 11 14426684 14426684 G A SNP COPB1 NM_016451.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*9262 NULL 0.001 - - - no_errors tier3 1484 78 4.97 942 130 12.12 1 0 0 273919 TCGA-AB-3000 AML25 11 24578602 24578602 G A SNP LUZP2 NM_001009909.2 human genbank 54_36p 1 validated intronic c.62+103175 e1+103175 0.001 - - - no_errors tier3 338 43 11.26 419 299 41.64 0 0 NA 273919 TCGA-AB-3000 AML25 11 38560218 38560218 T C SNP - - - - - - - - - - - - - - - tier3 251 21 7.61 141 39 21.67 0 0 NA 273919 TCGA-AB-3000 AML25 11 59270792 59270792 G T SNP OR10V1 NM_001005324.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-32898 NULL 0.002 - - - no_errors tier3 936 183 16.21 340 293 46.21 0 0 NA 273919 TCGA-AB-3000 AML25 11 79023871 79023871 C A SNP - - - - - - - - - - - - - - - tier3 1306 274 17.25 930 727 43.85 0 0 NA 273919 TCGA-AB-3000 AML25 12 25824720 25824720 T C SNP ENSG00000222950 ENST00000411018 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-950 NULL 0.203 - - - no_errors tier3 1516 267 14.94 769 676 46.75 0 0 NA 273919 TCGA-AB-3000 AML25 12 30161642 30161642 C T SNP - - - - - - - - - - - - - - - tier3 1188 241 16.75 313 283 47.48 0 0 NA 273919 TCGA-AB-3000 AML25 12 62594679 62594679 T G SNP SRGAP1 NM_020762.2 human genbank 54_36p 1 validated intronic c.68-69315 e2-69315 0 - - - no_errors tier3 938 188 16.61 382 366 48.87 0 0 NA 273919 TCGA-AB-3000 AML25 12 130092470 130092470 G A SNP GPR133 NM_198827.3 human genbank 54_36p 1 validated intronic c.1473+27632 e13+27632 0.962 - - - no_errors tier3 338 72 17.52 199 156 43.7 0 0 NA 273919 TCGA-AB-3000 AML25 13 18434281 18434281 C T SNP ENSG00000218236 ENST00000405207 human ensembl 54_36p -1 known intronic c.NULL NULL 0.003 - - - no_coding_region:pseudogene tier3 358 47 11.55 90 104 53.61 0 0 NA 273919 TCGA-AB-3000 AML25 13 56936003 56936003 C A SNP - - - - - - - - - - - - - - - tier3 814 163 16.68 611 560 47.82 0 0 NA 273919 TCGA-AB-3000 AML25 13 59294309 59294309 T C SNP DIAPH3 NM_001042517.1 human genbank 54_36p -1 validated intronic c.3027+10933 e24+10933 0 - - - no_errors tier3 161 41 20.1 192 145 43.03 0 0 0 273919 TCGA-AB-3000 AML25 13 73799563 73799563 G A SNP ENSG00000206617 ENST00000383890 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-38211 NULL 0.044 - - - no_errors tier3 1149 225 16.32 984 924 48.38 0 0 NA 273919 TCGA-AB-3000 AML25 16 52228206 52228206 T C SNP RPGRIP1L NM_015272.1 human genbank 54_36p -1 reviewed intronic c.3221-281 e21-281 0 - - - no_errors tier3 116 11 8.66 70 61 46.56 0 0 0 273919 TCGA-AB-3000 AML25 17 11517867 11517867 C A SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed intronic c.3353+4031 e17+4031 0.021 - - - no_errors tier3 689 191 21.63 399 465 53.82 0 0 NA 273919 TCGA-AB-3000 AML25 18 19762964 19762964 C T SNP LAMA3 NM_198129.3 human genbank 54_36p 1 reviewed intronic c.8436+237 e64+237 0 - - - no_errors tier3 229 52 18.51 252 218 46.38 0 0 NA 273919 TCGA-AB-3000 AML25 18 64043906 64043906 G A SNP - - - - - - - - - - - - - - - tier3 274 36 11.58 286 184 39.15 0 0 NA 273919 TCGA-AB-3000 AML25 19 38484230 38484231 - CCA INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_ins c.931_930 p.310in_frame_insW 1.000:1.000 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 273919 TCGA-AB-3000 AML25 19 38484986 38484986 C A SNP CEBPA NM_004364.3 human genbank 54_36p -1 reviewed nonsense c.175 p.E59* 1 NULL "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 0 1 100 1 0 0 177 231 56.2 273919 TCGA-AB-3000 AML25 20 17654288 17654288 C T SNP BANF2 NM_001014977.2 human genbank 54_36p 1 provisional intronic c.126+492 e1+492 0.001 - - - no_errors tier3 935 76 7.5 748 175 18.88 0 0 NA 273919 TCGA-AB-3000 AML25 20 41307136 41307136 G A SNP ENSG00000222555 ENST00000410623 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22575 NULL 0 - - - no_errors tier3 2192 184 7.72 744 226 23.25 0 0 NA 273919 TCGA-AB-3000 AML25 21 9991853 9991853 G A SNP TPTE NM_199261.2 human genbank 54_36p -1 validated intronic c.119+27 e3+27 0 - - - no_errors tier3 4074 385 8.61 2717 870 24.2 0 0 0 273919 TCGA-AB-3000 AML25 21 17086645 17086645 C A SNP - - - - - - - - - - - - - - - tier3 452 69 13.19 385 326 45.85 0 0 NA 273919 TCGA-AB-3000 AML25 21 23307162 23307162 C A SNP - - - - - - - - - - - - - - - tier3 796 105 11.59 342 247 41.86 0 0 NA 273919 TCGA-AB-3000 AML25 21 34417728 34417728 T A SNP MRPS6 NM_032476.3 human genbank 54_36p 1 reviewed intronic c.46-1783 e2-1783 0 - - - no_errors tier3 774 62 7.32 788 195 19.84 2 1 33.33 273919 TCGA-AB-3000 AML25 21 41131088 41131088 C T SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.43+9327 e1+9327 0 - - - no_errors tier3 630 88 12.21 286 280 49.21 0 0 NA 273919 TCGA-AB-3000 AML25 22 14517177 14517177 G T SNP LOC644525 XM_927654.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-36635 NULL 0.002 - - - no_errors tier3 300 25 7.6 249 53 17.55 0 0 NA 321258 TCGA-AB-3001 AML14 X 793324 793324 C T SNP LOC728198 XM_001126120.2 human genbank 54_36p 1 model intronic c.482-129 e6-129 0.038 - - - no_start_codon:pseudogene:no_stop_codon tier3 408 0 0 309 148 31.36 0 0 NA 321258 TCGA-AB-3001 AML14 X 2404686 2404686 G A SNP DHRSX NM_145177.2 human genbank 54_36p -1 validated intronic c.109+24172 e1+24172 0 - - - no_errors tier3 455 4 0.87 371 97 20.73 4 0 0 321258 TCGA-AB-3001 AML14 X 4737108 4737108 C T SNP - - - - - - - - - - - - - - - tier3 704 7 0.98 491 176 26.39 0 0 NA 321258 TCGA-AB-3001 AML14 X 6662965 6662965 G T SNP - - - - - - - - - - - - - - - tier3 1609 2 0.12 1200 268 18.26 0 0 NA 321258 TCGA-AB-3001 AML14 X 8645578 8645578 A G SNP KAL1 NM_000216.2 human genbank 54_36p -1 reviewed intronic c.207+14293 e1+14293 0.012 - - - no_errors tier3 576 10 1.71 232 101 30.24 0 0 NA 321258 TCGA-AB-3001 AML14 X 14875381 14875381 G A SNP MOSPD2 NM_152581.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*27529 NULL 0.075 - - - no_errors tier2 893 3 0.33 807 354 30.49 0 0 NA 321258 TCGA-AB-3001 AML14 X 20898613 20898613 G A SNP - - - - - - - - - - - - - - - tier3 1075 11 1.01 480 177 26.94 0 0 NA 321258 TCGA-AB-3001 AML14 X 22074952 22074952 T A SNP PHEX NM_000444.4 human genbank 54_36p 1 reviewed intronic c.1404+13290 e12+13290 0.003 - - - no_errors tier3 334 2 0.6 132 59 30.89 0 0 NA 321258 TCGA-AB-3001 AML14 X 25852944 25852944 A T SNP - - - - - - - - - - - - - - - tier3 625 3 0.48 109 30 21.58 0 0 NA 321258 TCGA-AB-3001 AML14 X 31241780 31241780 T A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.9224+9856 e62+9856 0.001 - - - no_errors tier3 813 2 0.25 215 101 31.96 0 0 NA 321258 TCGA-AB-3001 AML14 X 31923106 31923106 G A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6439-26554 e45-26554 0 - - - no_errors tier3 1552 3 0.19 1022 271 20.93 0 0 NA 321258 TCGA-AB-3001 AML14 X 32871318 32871318 T C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.93+76859 e2+76859 0.001 - - - no_errors tier3 677 0 0 228 56 19.58 0 0 NA 321258 TCGA-AB-3001 AML14 X 33193243 33193243 A G SNP DMD NM_000109.2 human genbank 54_36p -1 reviewed intronic c.7+74054 e1+74054 0 - - - no_errors tier3 970 3 0.31 192 93 32.63 0 0 NA 321258 TCGA-AB-3001 AML14 X 33315126 33315126 A T SNP DMD NM_000109.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-47823 NULL 0.016 - - - no_errors tier3 775 6 0.77 338 148 30.39 0 0 NA 321258 TCGA-AB-3001 AML14 X 34540349 34540349 A T SNP TMEM47 NM_031442.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*18002 NULL 0.169 - - - no_errors tier3 1241 3 0.24 512 230 31 0 0 NA 321258 TCGA-AB-3001 AML14 X 36129230 36129230 A G SNP ENSG00000217194 ENST00000405251 human ensembl 54_36p 1 known 5_prime_flanking_region c.-9904 NULL 0 - - - no_coding_region:pseudogene tier2 825 5 0.6 368 132 26.4 0 0 NA 321258 TCGA-AB-3001 AML14 X 40895240 40895240 G A SNP USP9X NM_001039590.2 human genbank 54_36p 1 reviewed silent c.1749 p.A583 0.996 NULL "HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_Cysteine proteinases" - no_errors tier1 703 1 0.14 326 120 26.91 58 0 321258 TCGA-AB-3001 AML14 X 44008032 44008032 T C SNP EFHC2 NM_025184.3 human genbank 54_36p -1 validated intronic c.383-2544 e4-2544 0.196 - - - no_errors tier3 946 1 0.11 183 56 23.43 0 0 0 321258 TCGA-AB-3001 AML14 X 71058335 71058335 G A SNP ENSG00000201392 ENST00000364522 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*44212 NULL 0 - - - no_errors tier2 776 8 1.02 244 79 24.46 0 0 NA 321258 TCGA-AB-3001 AML14 X 77662386 77662386 G A SNP ENSG00000218439 ENST00000406177 human ensembl 54_36p -1 known 5_prime_flanking_region c.-47 NULL 0 - - - no_coding_region:pseudogene tier3 684 9 1.3 556 278 33.33 0 0 NA 321258 TCGA-AB-3001 AML14 X 85061261 85061261 A C SNP CHM NM_000390.2 human genbank 54_36p -1 reviewed intronic c.1167-8262 e9-8262 0.009 - - - no_errors tier3 417 5 1.18 144 52 26.53 0 0 0 321258 TCGA-AB-3001 AML14 X 103986563 103986563 C A SNP IL1RAPL2 NM_017416.1 human genbank 54_36p 1 reviewed intronic c.82+196231 e1+196231 0 - - - no_errors tier3 1984 4 0.2 990 396 28.53 0 0 NA 321258 TCGA-AB-3001 AML14 X 106550017 106550017 C G SNP ENSG00000207846 ENST00000385111 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8858 NULL 0 - - - no_errors tier3 1925 5 0.26 979 489 33.29 0 0 NA 321258 TCGA-AB-3001 AML14 X 111613638 111613638 G T SNP ZCCHC16 NM_001004308.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*28093 NULL 0.001 - - - no_errors tier3 1494 9 0.6 358 132 26.88 0 0 NA 321258 TCGA-AB-3001 AML14 X 113686552 113686552 A C SNP HTR2C NM_000868.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-181050 NULL 0.796 - - - no_errors tier2 818 0 0 250 28 10.07 0 0 NA 321258 TCGA-AB-3001 AML14 X 118669139 118669139 G A SNP SEPT6 NM_015129.5 human genbank 54_36p -1 reviewed intronic c.529-1050 e5-1050 0.001 - - - no_errors tier3 1457 29 1.95 820 380 31.67 4 0 0 321258 TCGA-AB-3001 AML14 X 120720437 120720437 C G SNP - - - - - - - - - - - - - - - tier3 1741 3 0.17 512 236 31.51 0 0 NA 321258 TCGA-AB-3001 AML14 X 123519508 123519508 G A SNP ODZ1 NM_014253.2 human genbank 54_36p -1 provisional intronic c.2434+3694 e14+3694 0 - - - no_errors tier3 1236 10 0.8 245 81 24.77 0 0 NA 321258 TCGA-AB-3001 AML14 X 125572776 125572776 A G SNP - - - - - - - - - - - - - - - tier3 729 0 0 199 33 14.22 0 0 0 321258 TCGA-AB-3001 AML14 X 125654349 125654349 T A SNP ENSG00000219741 ENST00000404361 human ensembl 54_36p 1 known 5_prime_flanking_region c.-36419 NULL 0 - - - no_coding_region:pseudogene tier3 894 1 0.11 128 27 17.42 0 0 0 321258 TCGA-AB-3001 AML14 X 131609209 131609209 T A SNP HS6ST2 ENST00000319809 human ensembl 54_36p -1 known intronic c.1062-18407 e7-18407 0.006 - - - no_errors tier3 1726 12 0.69 1125 479 29.86 0 0 NA 321258 TCGA-AB-3001 AML14 X 137224571 137224571 C T SNP - - - - - - - - - - - - - - - tier3 2062 8 0.39 1649 685 29.35 0 0 NA 321258 TCGA-AB-3001 AML14 X 142388326 142388326 G T SNP ENSG00000221505 ENST00000408578 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26538 NULL 0 - - - no_errors tier3 1555 3 0.19 696 305 30.47 0 0 NA 321258 TCGA-AB-3001 AML14 X 147657019 147657019 G A SNP AFF2 NM_002025.2 human genbank 54_36p 1 validated intronic c.1042-42073 e4-42073 0.931 - - - no_errors tier2 1210 1 0.08 211 84 28.47 0 5 100 321258 TCGA-AB-3001 AML14 X 147685327 147685327 C T SNP AFF2 NM_002025.2 human genbank 54_36p 1 validated intronic c.1042-13765 e4-13765 0.945 - - - no_errors tier3 564 1 0.18 170 51 23.08 0 3 100 321258 TCGA-AB-3001 AML14 X 147699135 147699135 G A SNP AFF2 NM_002025.2 human genbank 54_36p 1 validated missense c.1085 p.R362Q 1 HMMPfam_AF-4 HMMPfam_AF-4 - no_errors tier1 1422 7 0.49 387 121 23.82 252 0 321258 TCGA-AB-3001 AML14 X 149529797 149529797 G A SNP MTM1 NM_000252.2 human genbank 54_36p 1 reviewed intronic c.232-3923 e4-3923 0.554 - - - no_errors tier3 1268 2 0.16 649 159 19.68 6 0 0 321258 TCGA-AB-3001 AML14 X 151792502 151792502 C T SNP CETN2 NM_004344.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42592 NULL 0.002 - - - no_errors tier3 434 1 0.23 274 70 20.35 0 0 0 321258 TCGA-AB-3001 AML14 1 2072709 2072709 G C SNP PRKCZ NM_002744.1 human genbank 54_36p 1 reviewed intronic c.876+432 e9+432 0 - - - no_errors tier3 247 0 0 152 27 15.08 1 1 50 321258 TCGA-AB-3001 AML14 1 4308402 4308402 A G SNP - - - - - - - - - - - - - - - tier3 192 0 0 55 14 20.29 0 0 NA 321258 TCGA-AB-3001 AML14 1 11467864 11467864 C T SNP PTCHD2 NM_020780.1 human genbank 54_36p 1 validated intronic c.1+5848 e0+5848 0 - - - no_errors tier3 443 3 0.67 154 82 34.75 0 0 NA 321258 TCGA-AB-3001 AML14 1 26988878 26988878 A T SNP PIGV NM_017837.2 human genbank 54_36p 1 validated intronic c.1-959 e1-959 0 - - - no_errors tier3 1413 6 0.42 279 63 18.42 2 0 0 321258 TCGA-AB-3001 AML14 1 36119354 36119354 C T SNP EIF2C1 ENST00000373206 human ensembl 54_36p 1 known intronic c.1-7261 e1-7261 0.01 - - - no_errors tier3 1317 4 0.3 250 99 28.37 0 1 100 321258 TCGA-AB-3001 AML14 1 57455788 57455788 A C SNP DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.68-72098 e2-72098 0.012 - - - no_errors tier3 1055 25 2.31 381 79 17.17 0 0 NA 321258 TCGA-AB-3001 AML14 1 83152845 83152845 T G SNP - - - - - - - - - - - - - - - tier3 962 4 0.41 261 96 26.89 0 0 NA 321258 TCGA-AB-3001 AML14 1 84435523 84435523 A T SNP PRKACB NM_182948.2 human genbank 54_36p 1 reviewed intronic c.688-477 e7-477 0 - - - no_errors tier3 837 4 0.48 457 188 29.1 2 3 60 321258 TCGA-AB-3001 AML14 1 84992541 84992541 C T SNP ENSG00000222670 ENST00000410738 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*38795 NULL 0.042 - - - no_errors tier2 259 1 0.38 247 46 15.7 0 0 NA 321258 TCGA-AB-3001 AML14 1 89390535 89390535 A T SNP GBP7 NM_207398.2 human genbank 54_36p -1 validated splice_region c.625+4 e4+4 0.645 - - - no_errors tier3 1079 22 2 293 138 32.02 0 0 0 321258 TCGA-AB-3001 AML14 1 89834886 89834886 A C SNP LRRC8B ENST00000330947 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*3696 NULL 0.003 - - - no_errors tier3 1755 1 0.06 636 139 17.94 1 0 0 321258 TCGA-AB-3001 AML14 1 99509773 99509773 A G SNP LPPR4 NM_014839.3 human genbank 54_36p 1 reviewed intronic c.222+6958 e1+6958 0.014 - - - no_errors tier3 923 1 0.11 357 79 18.12 0 0 NA 321258 TCGA-AB-3001 AML14 1 102655825 102655825 C A SNP - - - - - - - - - - - - - - - tier3 1221 5 0.41 715 277 27.92 0 0 NA 321258 TCGA-AB-3001 AML14 1 106683695 106683695 C G SNP - - - - - - - - - - - - - - - tier3 1336 3 0.22 537 114 17.51 0 0 NA 321258 TCGA-AB-3001 AML14 1 107096348 107096348 G A SNP - - - - - - - - - - - - - - - tier3 911 1 0.11 144 58 28.71 0 0 NA 321258 TCGA-AB-3001 AML14 1 107481880 107481880 C G SNP NTNG1 NM_014917.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-10859 NULL 0.684 - - - no_errors tier3 484 1 0.21 95 53 35.81 0 0 NA 321258 TCGA-AB-3001 AML14 1 108310143 108310143 C A SNP VAV3 NM_006113.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-1129 NULL 0 - - - no_errors tier3 407 7 1.69 198 92 31.72 0 0 NA 321258 TCGA-AB-3001 AML14 1 113958918 113958918 A G SNP MAGI3 NM_152900.1 human genbank 54_36p 1 validated intronic c.1076+115 e7+115 0.001 - - - no_errors tier3 707 4 0.56 210 88 29.53 0 0 0 321258 TCGA-AB-3001 AML14 1 150977352 150977352 C G SNP LCE1E NM_178353.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49048 NULL 0.001 - - - no_errors tier3 1175 10 0.84 664 292 30.51 0 0 NA 321258 TCGA-AB-3001 AML14 1 158107252 158107252 G A SNP VSIG8 NM_001013661.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-8317 NULL 0.001 - - - no_errors tier3 1325 11 0.82 740 326 30.58 0 0 NA 321258 TCGA-AB-3001 AML14 1 175661539 175661539 C G SNP LOC400796 XM_001132413.2 human genbank 54_36p -1 model intronic c.198-31992 e3-31992 0 - - - no_errors tier3 978 0 0 538 79 12.8 2 0 0 321258 TCGA-AB-3001 AML14 1 180021175 180021175 C G SNP CACNA1E NM_000721.2 human genbank 54_36p 1 reviewed missense c.5677 p.Q1893E 1 HMMPfam_Ca_chan_IQ "HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels" - no_errors tier1 1466 6 0.41 878 377 30.04 NA 321258 TCGA-AB-3001 AML14 1 182380619 182380619 A T SNP ENSG00000199840 ENST00000362970 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*26852 NULL 0.002 - - - no_errors tier3 1223 7 0.57 594 189 24.14 0 0 NA 321258 TCGA-AB-3001 AML14 1 185114697 185114697 C T SNP PLA2G4A NM_024420.2 human genbank 54_36p 1 reviewed intronic c.115+8426 e2+8426 0.004 - - - no_errors tier3 386 2 0.52 59 10 14.49 0 0 NA 321258 TCGA-AB-3001 AML14 1 185534400 185534400 G T SNP - - - - - - - - - - - - - - - tier3 865 1 0.12 276 64 18.82 0 0 NA 321258 TCGA-AB-3001 AML14 1 185826908 185826908 T A SNP ENSG00000217211 ENST00000402196 human ensembl 54_36p 1 known 3_prime_flanking_region c.*27022 NULL 0.003 - - - no_coding_region:pseudogene tier3 818 1 0.12 149 63 29.72 0 0 NA 321258 TCGA-AB-3001 AML14 1 188687718 188687718 C A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional intronic c.236+2690 e1+2690 0.001 - - - no_errors tier3 492 0 0 132 51 27.57 0 0 NA 321258 TCGA-AB-3001 AML14 1 191498696 191498697 - A INS CDC73 NM_024529.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*12231 NULL 0.002:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 1 212010652 212010652 A G SNP - - - - - - - - - - - - - - - tier3 1254 13 1.03 609 254 29.43 0 0 NA 321258 TCGA-AB-3001 AML14 1 215658092 215658092 A T SNP GPATCH2 NM_018040.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*13018 NULL 0.909 - - - no_errors tier2 860 5 0.58 620 142 18.56 0 0 NA 321258 TCGA-AB-3001 AML14 1 217657547 217657547 T G SNP LOC728510 XM_001127601.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*17764 NULL 0.01 - - - no_errors tier3 1073 6 0.56 270 109 28.76 0 1 100 321258 TCGA-AB-3001 AML14 1 219622072 219622072 C T SNP - - - - - - - - - - - - - - - tier2 861 7 0.81 320 128 28.57 0 0 NA 321258 TCGA-AB-3001 AML14 1 224800919 224800919 A C SNP C1orf95 NM_001003665.2 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-2310 NULL 0.085 - - - no_errors tier3 421 4 0.94 208 59 22.1 0 0 NA 321258 TCGA-AB-3001 AML14 1 231924877 231924877 G T SNP - - - - - - - - - - - - - - - tier2 842 0 0 448 179 28.5 0 0 NA 321258 TCGA-AB-3001 AML14 1 235617654 235617654 C G SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.676+351 e9+351 0.002 - - - no_errors tier2 300 0 0 130 38 22.22 0 0 NA 321258 TCGA-AB-3001 AML14 1 237008538 237008538 C G SNP ENSG00000218598 ENST00000402695 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-237008538 NULL 0.852 - - - no_coding_region:pseudogene tier3 753 13 1.7 161 88 35.34 0 0 NA 321258 TCGA-AB-3001 AML14 1 238234559 238234559 C A SNP LOC645884 XR_017475.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-2888 NULL 0 - - - pseudogene tier2 954 6 0.62 411 72 14.91 0 0 NA 321258 TCGA-AB-3001 AML14 1 239060408 239060408 C T SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.610-3313 e9-3313 0 - - - no_errors tier3 1542 5 0.32 713 279 28.12 0 0 NA 321258 TCGA-AB-3001 AML14 2 1843620 1843620 G A SNP MYT1L NM_015025.2 human genbank 54_36p -1 validated intronic c.2706-9138 e14-9138 0.002 - - - no_errors tier3 205 1 0.49 143 60 29.56 0 0 NA 321258 TCGA-AB-3001 AML14 2 5096144 5096144 C A SNP - - - - - - - - - - - - - - - tier3 1364 3 0.22 1280 351 21.48 0 0 NA 321258 TCGA-AB-3001 AML14 2 11693513 11693513 G A SNP GREB1 NM_014668.3 human genbank 54_36p 1 reviewed intronic c.5346+531 e29+531 0.001 - - - no_errors tier3 680 2 0.29 464 128 21.62 0 0 0 321258 TCGA-AB-3001 AML14 2 20263134 20263134 C T SNP LOC100131373 XM_001720891.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-26596 NULL 0 - - - no_errors tier3 264 2 0.75 138 52 27.37 0 0 NA 321258 TCGA-AB-3001 AML14 2 22156422 22156422 C A SNP - - - - - - - - - - - - - - - tier3 1019 0 0 283 31 9.81 0 0 NA 321258 TCGA-AB-3001 AML14 2 23349051 23349051 C T SNP - - - - - - - - - - - - - - - tier3 975 3 0.31 518 223 30.09 0 0 NA 321258 TCGA-AB-3001 AML14 2 23880380 23880380 G T SNP ATAD2B NM_017552.1 human genbank 54_36p -1 validated intronic c.2455-5683 e19-5683 0 - - - no_errors tier3 772 7 0.9 456 95 17.24 1 0 0 321258 TCGA-AB-3001 AML14 2 27839358 27839358 T C SNP MRPL33 NM_004891.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8791 NULL 0.002 - - - no_errors tier2 1271 6 0.47 491 185 27.33 0 0 NA 321258 TCGA-AB-3001 AML14 2 33568467 33568467 G A SNP RASGRP3 NM_170672.1 human genbank 54_36p 1 validated intronic c.1-21814 e1-21814 0.005 - - - no_errors tier3 1989 3 0.15 1219 237 16.28 3 2 40 321258 TCGA-AB-3001 AML14 2 34064141 34064141 G A SNP - - - - - - - - - - - - - - - tier3 1452 2 0.14 1122 528 32 0 0 NA 321258 TCGA-AB-3001 AML14 2 34424679 34424679 G T SNP - - - - - - - - - - - - - - - tier3 1128 3 0.27 345 82 19.2 0 0 NA 321258 TCGA-AB-3001 AML14 2 50683314 50683314 C A SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.1320+17350 e7+17350 0.001 - - - no_errors tier3 920 3 0.33 390 152 28.04 0 0 NA 321258 TCGA-AB-3001 AML14 2 50853628 50853628 A C SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.832+148883 e4+148883 0 - - - no_errors tier3 1915 10 0.52 631 240 27.55 0 0 NA 321258 TCGA-AB-3001 AML14 2 52305197 52305197 C T SNP - - - - - - - - - - - - - - - tier3 859 2 0.23 441 162 26.87 0 0 NA 321258 TCGA-AB-3001 AML14 2 53579685 53579685 A G SNP ENSG00000212217 ENST00000390915 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-28414 NULL 0.15 - - - no_errors tier3 1162 5 0.43 365 163 30.87 0 0 NA 321258 TCGA-AB-3001 AML14 2 55010493 55010493 A G SNP EML6 XM_001725001.2 human genbank 54_36p 1 model intronic c.4019+1086 e27+1086 0 - - - no_errors tier3 649 6 0.92 111 44 28.39 0 0 NA 321258 TCGA-AB-3001 AML14 2 78164691 78164691 C A SNP - - - - - - - - - - - - - - - tier3 1031 1 0.1 380 77 16.85 0 0 NA 321258 TCGA-AB-3001 AML14 2 78519267 78519267 A T SNP ENSG00000214429 ENST00000398312 human ensembl 54_36p -1 known intronic c.1-25457 e1-25457 0.016 - - - no_errors tier3 1114 11 0.98 652 121 15.63 0 0 NA 321258 TCGA-AB-3001 AML14 2 84281192 84281192 G A SNP - - - - - - - - - - - - - - - tier3 1207 12 0.98 1014 226 18.2 0 0 NA 321258 TCGA-AB-3001 AML14 2 116406737 116406737 G A SNP - - - - - - - - - - - - - - - tier2 869 14 1.59 219 85 27.87 0 0 NA 321258 TCGA-AB-3001 AML14 2 123153787 123153787 C T SNP - - - - - - - - - - - - - - - tier2 885 4 0.45 389 126 24.42 0 0 NA 321258 TCGA-AB-3001 AML14 2 138360113 138360113 T C SNP - - - - - - - - - - - - - - - tier3 352 0 0 95 35 26.92 0 0 NA 321258 TCGA-AB-3001 AML14 2 164678849 164678849 G T SNP - - - - - - - - - - - - - - - tier3 413 0 0 84 41 32.8 0 0 NA 321258 TCGA-AB-3001 AML14 2 173690892 173690892 G A SNP ZAK NM_016653.2 human genbank 54_36p 1 reviewed intronic c.159+26728 e1+26728 0 - - - no_errors tier3 776 5 0.64 525 210 28.53 0 0 0 321258 TCGA-AB-3001 AML14 2 174198307 174198307 G A SNP - - - - - - - - - - - - - - - tier3 899 3 0.33 385 146 27.44 0 0 NA 321258 TCGA-AB-3001 AML14 2 199732710 199732710 C T SNP - - - - - - - - - - - - - - - tier3 1003 9 0.89 260 112 30.11 0 0 NA 321258 TCGA-AB-3001 AML14 2 201045842 201045842 G T SNP LOC26010 NM_001100422.1 human genbank 54_36p 1 validated missense c.1103 p.S368I 1 HMMPfam_DUF1387 HMMPfam_DUF1387 - no_errors tier1 980 2 0.2 514 113 18.02 8 2 20 321258 TCGA-AB-3001 AML14 2 205873212 205873212 G T SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated intronic c.2000-287 e16-287 0 - - - no_errors tier3 1207 3 0.25 485 182 27.25 0 0 NA 321258 TCGA-AB-3001 AML14 2 207320658 207320658 T A SNP MDH1B NM_001039845.1 human genbank 54_36p -1 validated intronic c.1217-1263 e8-1263 0 - - - no_errors tier3 764 3 0.39 683 187 21.47 0 0 NA 321258 TCGA-AB-3001 AML14 2 210408575 210408575 G T SNP uc002vdl.1 ENST00000272845 human ensembl 54_36p 1 known intronic c.566+596 e4+596 0 - - - no_start_codon tier3 572 1 0.17 212 40 15.87 0 0 NA 321258 TCGA-AB-3001 AML14 2 211412542 211412542 G C SNP - - - - - - - - - - - - - - - tier2 594 0 0 430 148 25.61 0 0 NA 321258 TCGA-AB-3001 AML14 2 211918217 211918217 C A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*38368 NULL 0.083 - - - no_errors tier3 746 0 0 420 77 15.49 0 0 NA 321258 TCGA-AB-3001 AML14 2 212596043 212596043 T A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.235-75457 e3-75457 0.007 - - - no_errors tier2 1538 7 0.45 714 155 17.82 0 0 NA 321258 TCGA-AB-3001 AML14 2 213751345 213751345 G A SNP IKZF2 NM_016260.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29747 NULL 0.01 - - - no_errors tier3 1244 2 0.16 645 60 8.51 0 0 NA 321258 TCGA-AB-3001 AML14 2 215002119 215002119 C A SNP VWC2L NM_001080500.2 human genbank 54_36p 1 provisional intronic c.391-7479 e2-7479 0.004 - - - no_errors tier3 771 1 0.13 240 99 29.2 0 0 NA 321258 TCGA-AB-3001 AML14 2 215417131 215417131 C T SNP BARD1 NM_000465.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-34593 NULL 0.001 - - - no_errors tier3 966 1 0.1 285 128 30.92 0 1 100 321258 TCGA-AB-3001 AML14 3 5373684 5373684 A G SNP - - - - - - - - - - - - - - - tier3 1361 8 0.58 469 169 26.49 0 0 NA 321258 TCGA-AB-3001 AML14 3 16183200 16183200 G C SNP GALNTL2 NM_054110.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-8463 NULL 0.055 - - - no_errors tier3 880 0 0 740 128 14.75 0 0 NA 321258 TCGA-AB-3001 AML14 3 21364297 21364297 A T SNP - - - - - - - - - - - - - - - tier2 1338 10 0.74 522 117 18.31 0 0 NA 321258 TCGA-AB-3001 AML14 3 22680990 22680990 A G SNP LOC731642 XR_039391.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-16439 NULL 0.008 - - - pseudogene tier3 1112 2 0.18 625 170 21.38 0 0 NA 321258 TCGA-AB-3001 AML14 3 26116482 26116482 G A SNP - - - - - - - - - - - - - - - tier3 1155 3 0.26 474 224 32 0 0 NA 321258 TCGA-AB-3001 AML14 3 35434476 35434476 C T SNP - - - - - - - - - - - - - - - tier3 669 1 0.15 413 158 27.67 0 0 NA 321258 TCGA-AB-3001 AML14 3 47450886 47450886 G A SNP SCAP NM_012235.2 human genbank 54_36p -1 reviewed intronic c.252+616 e2+616 0.009 - - - no_errors tier2 1192 6 0.5 551 220 28.5 3 0 0 321258 TCGA-AB-3001 AML14 3 54802307 54802307 G A SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.1381-23613 e14-23613 0 - - - no_errors tier3 1084 2 0.18 406 176 30.24 0 0 NA 321258 TCGA-AB-3001 AML14 3 56482872 56482872 C T SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-38797 NULL 0.001 - - - no_errors tier3 1065 7 0.65 265 43 13.96 0 0 NA 321258 TCGA-AB-3001 AML14 3 61092572 61092572 T A SNP FHIT NM_002012.2 human genbank 54_36p -1 reviewed intronic c.1+68759 e0+68759 0.001 - - - no_errors tier3 1233 0 0 827 119 12.58 1 0 0 321258 TCGA-AB-3001 AML14 3 62507829 62507829 C T SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.1966+2789 e11+2789 0 - - - no_errors tier2 1118 3 0.27 657 210 24.17 0 0 NA 321258 TCGA-AB-3001 AML14 3 62622876 62622876 A - DEL CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.969+153 e4+153 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 3 63095838 63095838 G T SNP - - - - - - - - - - - - - - - tier3 577 3 0.52 145 38 20.77 0 0 NA 321258 TCGA-AB-3001 AML14 3 65519815 65519815 C T SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.430+62872 e2+62872 0 - - - no_errors tier3 706 2 0.28 215 43 16.67 0 0 NA 321258 TCGA-AB-3001 AML14 3 65928714 65928714 T C SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.313+69997 e1+69997 0 - - - no_errors tier3 1075 0 0 612 272 30.77 0 0 NA 321258 TCGA-AB-3001 AML14 3 65937820 65937820 A G SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.313+60891 e1+60891 0 - - - no_errors tier3 1118 5 0.45 448 169 27.39 0 0 NA 321258 TCGA-AB-3001 AML14 3 67666259 67666259 T C SNP SUCLG2 NM_003848.2 human genbank 54_36p -1 validated intronic c.227-3959 e3-3959 0 - - - no_errors tier3 513 1 0.19 185 43 18.86 0 0 0 321258 TCGA-AB-3001 AML14 3 70233026 70233026 C T SNP - - - - - - - - - - - - - - - tier2 1042 8 0.76 290 89 23.42 0 0 NA 321258 TCGA-AB-3001 AML14 3 71091990 71091990 C G SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.1890-758 e16-758 1 - - - no_errors tier2 963 2 0.21 560 66 10.54 12 4 25 321258 TCGA-AB-3001 AML14 3 74888265 74888265 C T SNP - - - - - - - - - - - - - - - tier3 1178 6 0.51 212 77 26.64 0 0 NA 321258 TCGA-AB-3001 AML14 3 76648610 76648610 C G SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.109+579167 e1+579167 0.006 - - - no_stop_codon:overly_large_intron tier2 502 3 0.59 138 55 28.5 0 0 NA 321258 TCGA-AB-3001 AML14 3 77700485 77700485 T A SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.1971+210 e13+210 0 - - - no_errors tier3 662 2 0.3 90 32 26.23 0 0 NA 321258 TCGA-AB-3001 AML14 3 77758715 77758715 G T SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.3760+4442 e23+4442 0.009 - - - no_errors tier3 998 6 0.6 540 292 35.1 0 0 0 321258 TCGA-AB-3001 AML14 3 80011887 80011887 C A SNP - - - - - - - - - - - - - - - tier3 494 1 0.2 159 69 30.26 0 0 NA 321258 TCGA-AB-3001 AML14 3 97615241 97615241 T A SNP ENSG00000216136 ENST00000401317 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19608 NULL 0 - - - no_errors tier3 715 2 0.28 117 52 30.77 0 0 NA 321258 TCGA-AB-3001 AML14 3 133159084 133159084 C T SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.1-52106 e1-52106 0.003 - - - no_errors tier3 989 7 0.7 267 104 28.03 0 0 NA 321258 TCGA-AB-3001 AML14 3 148811578 148811578 G T SNP - - - - - - - - - - - - - - - tier3 232 0 0 142 24 14.46 0 0 NA 321258 TCGA-AB-3001 AML14 3 148882510 148882510 G C SNP - - - - - - - - - - - - - - - tier3 1177 3 0.25 390 84 17.72 0 0 NA 321258 TCGA-AB-3001 AML14 3 165878913 165878913 C A SNP - - - - - - - - - - - - - - - tier2 887 0 0 289 35 10.8 0 0 NA 321258 TCGA-AB-3001 AML14 3 166213499 166213499 G T SNP SI NM_001041.2 human genbank 54_36p -1 validated missense c.4025 p.T1342K 0.808 "HMMPfam_Glyco_hydro_31,superfamily_(Trans)glycosidases" "HMMPfam_Glyco_hydro_31,PatternScan_GLYCOSYL_HYDROL_F31_1,PatternScan_GLYCOSYL_HYDROL_F31_2,HMMPfam_Trefoil,HMMSmart_SM00018,superfamily_Trefoil,superfamily_(Trans)glycosidases,PatternScan_P_TREFOIL" - no_errors tier1 987 4 0.4 510 227 30.8 NA 321258 TCGA-AB-3001 AML14 3 167419302 167419302 G A SNP ENSG00000208601 ENST00000385866 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14388 NULL 0.001 - - - pseudogene tier3 640 6 0.93 227 57 20.07 0 0 NA 321258 TCGA-AB-3001 AML14 3 170304520 170304520 T A SNP EVI1 NM_001105077.2 human genbank 54_36p -1 validated intronic c.2233-1812 e10-1812 1 - - - no_errors tier2 742 4 0.54 410 186 31.16 0 0 NA 321258 TCGA-AB-3001 AML14 3 173282944 173282944 A G SNP FNDC3B ENST00000336824 human ensembl 54_36p 1 known intronic c.1-29992 e1-29992 1 - - - no_errors tier2 1032 9 0.86 556 258 31.7 8 15 65.22 321258 TCGA-AB-3001 AML14 3 176555316 176555316 G T SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated intronic c.1090+30508 e5+30508 0.005 - - - no_errors tier3 1484 3 0.2 725 185 20.33 0 0 NA 321258 TCGA-AB-3001 AML14 3 193588803 193588803 G A SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed intronic c.199+19705 e1+19705 0.001 - - - no_errors tier3 724 1 0.14 265 46 14.79 0 0 NA 321258 TCGA-AB-3001 AML14 4 19021366 19021366 T C SNP - - - - - - - - - - - - - - - tier3 923 5 0.54 132 49 27.07 0 0 NA 321258 TCGA-AB-3001 AML14 4 20080357 20080357 T G SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.467+1813 e5+1813 0.002 - - - no_errors tier3 600 3 0.5 137 34 19.88 0 0 NA 321258 TCGA-AB-3001 AML14 4 25938153 25938153 T C SNP RBPJ NM_005349.2 human genbank 54_36p 1 validated intronic c.59+6618 e1+6618 0 - - - no_errors tier3 732 5 0.68 204 65 24.16 0 0 0 321258 TCGA-AB-3001 AML14 4 28710964 28710964 T C SNP - - - - - - - - - - - - - - - tier3 585 6 1.02 88 45 33.83 0 0 NA 321258 TCGA-AB-3001 AML14 4 34743698 34743698 C A SNP - - - - - - - - - - - - - - - tier3 684 0 0 222 75 25.25 0 0 NA 321258 TCGA-AB-3001 AML14 4 43415281 43415281 G A SNP - - - - - - - - - - - - - - - tier3 842 3 0.36 265 103 27.99 0 0 NA 321258 TCGA-AB-3001 AML14 4 44209945 44209945 A C SNP - - - - - - - - - - - - - - - tier3 1123 3 0.27 608 278 31.38 0 0 NA 321258 TCGA-AB-3001 AML14 4 59876944 59876944 A G SNP - - - - - - - - - - - - - - - tier3 653 6 0.91 71 27 27.55 0 0 NA 321258 TCGA-AB-3001 AML14 4 66597337 66597337 C T SNP ENSG00000210740 ENST00000388005 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16358 NULL 0 - - - pseudogene tier3 1553 4 0.26 438 88 16.73 0 0 NA 321258 TCGA-AB-3001 AML14 4 71395039 71395039 C T SNP LOC100129410 XM_001714842.1 human genbank 54_36p -1 model intronic c.101-12974 e2-12974 0 - - - no_errors tier3 1634 5 0.3 651 218 25.06 0 0 NA 321258 TCGA-AB-3001 AML14 4 72452294 72452294 G A SNP SLC4A4 NM_001098484.2 human genbank 54_36p 1 reviewed intronic c.730+10526 e5+10526 1 - - - no_errors tier2 1146 0 0 1030 115 10.04 0 0 NA 321258 TCGA-AB-3001 AML14 4 74875845 74875845 G A SNP CXCL6 NM_002993.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45487 NULL 0 - - - no_errors tier3 940 4 0.42 107 16 13.01 0 0 NA 321258 TCGA-AB-3001 AML14 4 92063134 92063134 C G SNP - - - - - - - - - - - - - - - tier3 401 0 0 113 34 23.13 0 0 NA 321258 TCGA-AB-3001 AML14 4 97274980 97274980 C A SNP ENSG00000201744 ENST00000364874 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17491 NULL 0.002 - - - no_errors tier3 438 5 1.13 132 45 25.42 0 0 NA 321258 TCGA-AB-3001 AML14 4 105838889 105838889 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 4 120690333 120690333 C T SNP PDE5A NM_001083.3 human genbank 54_36p -1 reviewed intronic c.1396+2820 e9+2820 0.001 - - - no_errors tier3 1137 4 0.35 177 68 27.76 5 2 28.57 321258 TCGA-AB-3001 AML14 4 127109586 127109586 T G SNP - - - - - - - - - - - - - - - tier3 625 8 1.26 186 20 9.71 0 0 NA 321258 TCGA-AB-3001 AML14 4 129594350 129594350 C T SNP - - - - - - - - - - - - - - - tier2 1148 2 0.17 911 159 14.86 0 0 NA 321258 TCGA-AB-3001 AML14 4 137024445 137024445 G A SNP - - - - - - - - - - - - - - - tier3 868 3 0.34 407 163 28.6 0 0 NA 321258 TCGA-AB-3001 AML14 4 150832497 150832497 C T SNP LOC285423 XR_041269.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 1395 12 0.85 335 115 25.56 0 0 NA 321258 TCGA-AB-3001 AML14 4 155237361 155237361 T G SNP - - - - - - - - - - - - - - - tier3 1621 9 0.55 461 199 30.15 0 0 NA 321258 TCGA-AB-3001 AML14 4 161005486 161005486 G A SNP - - - - - - - - - - - - - - - tier3 767 7 0.9 172 81 32.02 0 0 NA 321258 TCGA-AB-3001 AML14 4 162207715 162207715 T A SNP - - - - - - - - - - - - - - - tier3 1074 1 0.09 336 95 22.04 0 0 NA 321258 TCGA-AB-3001 AML14 4 164226378 164226378 C G SNP LOC729971 XM_001131925.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-23048 NULL 0 - - - no_errors tier3 621 2 0.32 278 65 18.9 0 0 NA 321258 TCGA-AB-3001 AML14 4 164508443 164508443 G A SNP NPY1R NM_000909.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41287 NULL 0.008 - - - no_errors tier3 1542 7 0.45 587 115 16.38 0 0 NA 321258 TCGA-AB-3001 AML14 4 175272541 175272541 C T SNP - - - - - - - - - - - - - - - tier3 822 9 1.08 237 82 25.71 0 0 NA 321258 TCGA-AB-3001 AML14 4 176212257 176212257 T C SNP - - - - - - - - - - - - - - - tier3 574 4 0.69 139 50 26.46 0 0 NA 321258 TCGA-AB-3001 AML14 4 183635784 183635784 A G SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.512-123287 e3-123287 0.005 - - - no_errors tier3 390 0 0 79 23 22.55 0 0 NA 321258 TCGA-AB-3001 AML14 4 186270824 186270824 A T SNP SLC25A4 NM_001151.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30697 NULL 0 - - - no_errors tier3 534 3 0.56 209 88 29.53 0 0 NA 321258 TCGA-AB-3001 AML14 4 187565306 187565306 T C SNP - - - - - - - - - - - - - - - tier3 852 2 0.23 253 128 33.6 0 0 NA 321258 TCGA-AB-3001 AML14 4 188088806 188088806 G A SNP - - - - - - - - - - - - - - - tier3 493 1 0.2 193 70 26.62 0 0 NA 321258 TCGA-AB-3001 AML14 4 189292472 189292472 G A SNP TRIML1 NM_178556.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-5235 NULL 0.033 - - - no_errors tier3 716 8 1.1 25 16 39.02 0 0 NA 321258 TCGA-AB-3001 AML14 4 189297043 189297043 T A SNP TRIML1 NM_178556.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-664 NULL 0.001 - - - no_errors tier3 968 0 0 209 90 30.1 0 0 NA 321258 TCGA-AB-3001 AML14 5 8669159 8669159 T - DEL ENSG00000209933 ENST00000387198 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6024 NULL 0.001 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 5 9195051 9195051 G T SNP SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.1482-5318 e11-5318 0.057 - - - no_errors tier3 471 2 0.42 106 49 31.61 0 0 NA 321258 TCGA-AB-3001 AML14 5 13273206 13273206 G A SNP ENSG00000222717 ENST00000410785 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45246 NULL 0.002 - - - no_errors tier3 811 0 0 318 110 25.7 0 0 NA 321258 TCGA-AB-3001 AML14 5 13767001 13767001 C A SNP DNAH5 NM_001369.2 human genbank 54_36p -1 validated intronic c.13125+513 e75+513 0.003 - - - no_errors tier3 580 0 0 132 53 28.65 0 0 NA 321258 TCGA-AB-3001 AML14 5 20236784 20236784 C T SNP - - - - - - - - - - - - - - - tier3 615 3 0.48 54 20 27.03 0 0 NA 321258 TCGA-AB-3001 AML14 5 23361265 23361265 C A SNP LOC391771 XR_038806.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-20257 NULL 0 - - - pseudogene tier3 1581 1 0.06 622 165 20.97 0 0 NA 321258 TCGA-AB-3001 AML14 5 25277164 25277164 C A SNP LOC100133786 XM_001716394.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*26199 NULL 0.023 - - - no_start_codon:pseudogene:no_stop_codon tier3 499 0 0 219 65 22.89 0 0 NA 321258 TCGA-AB-3001 AML14 5 51319245 51319245 A T SNP - - - - - - - - - - - - - - - tier3 601 1 0.17 329 134 28.94 0 0 NA 321258 TCGA-AB-3001 AML14 5 56842762 56842762 G T SNP ACTBL2 NM_001017992.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-28471 NULL 0 - - - no_errors tier3 958 1 0.1 496 199 28.63 0 0 NA 321258 TCGA-AB-3001 AML14 5 62679888 62679888 C T SNP - - - - - - - - - - - - - - - tier3 542 2 0.37 267 89 25 0 0 NA 321258 TCGA-AB-3001 AML14 5 71342951 71342951 C A SNP - - - - - - - - - - - - - - - tier2 1459 8 0.54 648 183 22.02 0 0 NA 321258 TCGA-AB-3001 AML14 5 83503309 83503309 C T SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.355+8658 e4+8658 0.001 - - - no_errors tier3 440 0 0 86 15 14.85 0 0 0 321258 TCGA-AB-3001 AML14 5 89551827 89551827 G C SNP - - - - - - - - - - - - - - - tier2 1196 12 0.99 559 185 24.87 0 0 NA 321258 TCGA-AB-3001 AML14 5 90715595 90715595 T C SNP LOC100129716 XM_001716248.1 human genbank 54_36p 1 model intronic c.83+3098 e1+3098 0 - - - rna_with_coding_region tier3 991 1 0.1 159 66 29.33 1 1 50 321258 TCGA-AB-3001 AML14 5 91887865 91887865 A T SNP - - - - - - - - - - - - - - - tier3 1245 1 0.08 431 142 24.78 0 0 NA 321258 TCGA-AB-3001 AML14 5 91891631 91891631 C T SNP - - - - - - - - - - - - - - - tier3 773 8 1.02 156 25 13.81 0 0 NA 321258 TCGA-AB-3001 AML14 5 97293563 97293563 C T SNP - - - - - - - - - - - - - - - tier3 1001 1 0.1 271 109 28.61 0 0 NA 321258 TCGA-AB-3001 AML14 5 100615585 100615585 C T SNP - - - - - - - - - - - - - - - tier3 940 1 0.11 254 100 28.25 0 0 NA 321258 TCGA-AB-3001 AML14 5 103964103 103964103 T A SNP - - - - - - - - - - - - - - - tier3 262 0 0 22 15 40.54 0 0 NA 321258 TCGA-AB-3001 AML14 5 104863255 104863255 G T SNP - - - - - - - - - - - - - - - tier3 912 5 0.54 391 96 19.71 0 0 NA 321258 TCGA-AB-3001 AML14 5 112274305 112274305 A T SNP REEP5 NM_005669.4 human genbank 54_36p -1 validated intronic c.213-8191 e3-8191 0 - - - no_errors tier3 1133 9 0.79 451 172 27.52 0 0 0 321258 TCGA-AB-3001 AML14 5 113479828 113479828 A G SNP - - - - - - - - - - - - - - - tier2 1429 2 0.14 1250 565 31.13 0 0 NA 321258 TCGA-AB-3001 AML14 5 119893500 119893500 G A SNP PRR16 NM_016644.1 human genbank 54_36p 1 provisional intronic c.90+48613 e1+48613 0 - - - no_errors tier3 671 0 0 189 31 14.09 0 0 NA 321258 TCGA-AB-3001 AML14 5 128735720 128735720 A C SNP - - - - - - - - - - - - - - - tier3 629 4 0.63 421 169 28.64 0 0 NA 321258 TCGA-AB-3001 AML14 5 131469330 131469330 C T SNP IL3 NM_000588.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*42947 NULL 0.003 - - - no_errors tier3 755 2 0.26 619 117 15.88 0 0 NA 321258 TCGA-AB-3001 AML14 5 135772182 135772182 A C SNP ENSG00000213568 ENST00000394946 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20298 NULL 0.018 - - - no_coding_region:pseudogene tier3 1441 7 0.48 625 233 27.12 0 0 NA 321258 TCGA-AB-3001 AML14 5 165686157 165686157 C T SNP - - - - - - - - - - - - - - - tier3 1421 5 0.35 766 331 30.15 0 0 NA 321258 TCGA-AB-3001 AML14 5 168431480 168431480 G T SNP SLIT3 NM_003062.2 human genbank 54_36p -1 validated intronic c.413+121581 e4+121581 0.02 - - - no_errors tier3 903 1 0.11 554 241 30.31 0 0 NA 321258 TCGA-AB-3001 AML14 5 168646237 168646237 C T SNP SLIT3 NM_003062.2 human genbank 54_36p -1 validated intronic c.197+13858 e1+13858 0.747 - - - no_errors tier2 976 1 0.1 365 188 34 0 0 0 321258 TCGA-AB-3001 AML14 5 175649773 175649773 C T SNP C5orf25 NM_198567.4 human genbank 54_36p 1 validated missense c.583 p.R195C 0.021 NULL NULL - no_errors tier1 2500 13 0.52 693 305 30.53 6 17 73.91 321258 TCGA-AB-3001 AML14 5 178958402 178958402 C G SNP RUFY1 NM_025158.1 human genbank 54_36p 1 validated missense c.1735 p.L579V 1 NULL "HMMPfam_FYVE,HMMSmart_SM00064,HMMPfam_RUN,HMMSmart_SM00593,superfamily_FYVE/PHD zinc finger" - no_errors tier1 752 5 0.66 678 156 18.68 44 13 22.81 321258 TCGA-AB-3001 AML14 6 7896358 7896358 G T SNP TXNDC5 ENST00000358251 human ensembl 54_36p -1 known intronic c.135-46403 e3-46403 0.057 - - - no_errors tier3 1038 2 0.19 500 220 30.51 0 1 100 321258 TCGA-AB-3001 AML14 6 12230515 12230515 T C SNP HIVEP1 NM_002114.2 human genbank 54_36p 1 validated missense c.2501 p.L834S 0.997 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 1407 3 0.21 233 108 31.67 1 2 66.67 321258 TCGA-AB-3001 AML14 6 17659608 17659608 A T SNP CAP2 NM_006366.2 human genbank 54_36p 1 reviewed intronic c.1210-66 e11-66 0 - - - no_errors tier3 756 1 0.13 311 39 11.14 0 0 NA 321258 TCGA-AB-3001 AML14 6 22683493 22683493 T C SNP HDGFL1 NM_138574.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*4954 NULL 0 - - - no_errors tier3 1050 1 0.1 362 40 9.95 0 0 NA 321258 TCGA-AB-3001 AML14 6 37876684 37876684 C T SNP ZFAND3 NM_021943.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-19016 NULL 0.745 - - - no_errors tier3 1532 9 0.58 738 244 24.85 0 0 NA 321258 TCGA-AB-3001 AML14 6 46535605 46535605 G A SNP RCAN2 ENST00000306764 human ensembl 54_36p -1 known intronic c.1-2931 e1-2931 0.018 - - - no_errors tier3 467 1 0.21 232 108 31.76 0 0 NA 321258 TCGA-AB-3001 AML14 6 46999043 46999043 C T SNP GPR116 NM_015234.1 human genbank 54_36p -1 validated intronic c.1-16561 e1-16561 0.003 - - - no_errors tier3 2209 5 0.23 1020 439 30.07 0 0 NA 321258 TCGA-AB-3001 AML14 6 56572373 56572373 G T SNP DST NM_183380.1 human genbank 54_36p -1 reviewed intronic c.4803+453 e36+453 0.002 - - - no_errors tier3 816 12 1.45 339 155 31.38 0 0 0 321258 TCGA-AB-3001 AML14 6 69462745 69462745 C A SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.757+56700 e1+56700 0.825 - - - no_errors tier3 660 3 0.45 137 50 26.74 0 0 NA 321258 TCGA-AB-3001 AML14 6 74966566 74966566 T C SNP - - - - - - - - - - - - - - - tier3 935 9 0.95 916 363 28.38 0 0 NA 321258 TCGA-AB-3001 AML14 6 79148098 79148098 C G SNP - - - - - - - - - - - - - - - tier3 750 2 0.27 248 57 18.63 0 0 NA 321258 TCGA-AB-3001 AML14 6 80072959 80072959 A T SNP ENSG00000201464 ENST00000364594 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4457 NULL 1 - - - no_errors tier3 385 0 0 142 25 14.97 1 0 0 321258 TCGA-AB-3001 AML14 6 80745000 80745000 C G SNP ELOVL4 NM_022726.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31285 NULL 0 - - - no_errors tier2 756 1 0.13 491 159 24.42 0 0 NA 321258 TCGA-AB-3001 AML14 6 81658117 81658117 T A SNP - - - - - - - - - - - - - - - tier3 2098 2 0.1 1114 258 18.79 0 0 NA 321258 TCGA-AB-3001 AML14 6 91989560 91989560 C T SNP - - - - - - - - - - - - - - - tier3 1098 5 0.45 908 300 24.79 0 0 NA 321258 TCGA-AB-3001 AML14 6 92944538 92944538 A G SNP - - - - - - - - - - - - - - - tier3 1108 4 0.36 369 153 29.31 0 0 NA 321258 TCGA-AB-3001 AML14 6 95579739 95579739 T C SNP - - - - - - - - - - - - - - - tier2 873 0 0 196 65 24.9 0 0 NA 321258 TCGA-AB-3001 AML14 6 107091852 107091852 C T SNP AIM1 NM_001624.2 human genbank 54_36p 1 validated intronic c.3495-2119 e7-2119 0 - - - no_errors tier3 974 0 0 287 114 28.43 5 2 28.57 321258 TCGA-AB-3001 AML14 6 124784016 124784016 G C SNP NKAIN2 NM_001040214.1 human genbank 54_36p 1 validated intronic c.273+65824 e3+65824 0.003 - - - no_errors tier3 557 0 0 270 44 14.01 0 0 NA 321258 TCGA-AB-3001 AML14 6 133228812 133228812 T G SNP RPS12 NM_001016.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*48438 NULL 0.002 - - - no_errors tier3 1246 2 0.16 614 117 16.01 0 0 NA 321258 TCGA-AB-3001 AML14 6 143027393 143027393 A G SNP - - - - - - - - - - - - - - - tier3 1007 1 0.1 553 193 25.84 0 0 NA 321258 TCGA-AB-3001 AML14 6 159704797 159704797 G A SNP - - - - - - - - - - - - - - - tier3 1081 5 0.46 404 50 11.01 0 0 NA 321258 TCGA-AB-3001 AML14 6 168096020 168096020 T A SNP MLLT4 NM_001040001.1 human genbank 54_36p 1 validated intronic c.4809+304 e29+304 0.004 - - - no_errors tier3 505 0 0 146 66 31.13 0 0 0 321258 TCGA-AB-3001 AML14 7 11896666 11896666 A T SNP - - - - - - - - - - - - - - - tier3 722 7 0.96 220 102 31.68 0 0 NA 321258 TCGA-AB-3001 AML14 7 13134359 13134359 C A SNP - - - - - - - - - - - - - - - tier3 676 0 0 338 102 23.18 0 0 NA 321258 TCGA-AB-3001 AML14 7 16663305 16663305 G A SNP BZW2 NM_014038.1 human genbank 54_36p 1 provisional intronic c.1-8282 e1-8282 0 - - - no_errors tier3 353 2 0.56 54 21 28 0 1 100 321258 TCGA-AB-3001 AML14 7 20934224 20934224 T A SNP - - - - - - - - - - - - - - - tier3 1816 2 0.11 507 116 18.62 0 0 NA 321258 TCGA-AB-3001 AML14 7 27412066 27412066 C T SNP LOC100134624 XM_001726202.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-48640 NULL 0.253 - - - no_start_codon:pseudogene:no_stop_codon tier3 1181 3 0.25 623 123 16.49 0 0 NA 321258 TCGA-AB-3001 AML14 7 30098098 30098098 C T SNP PLEKHA8 ENST00000396257 human ensembl 54_36p 1 known intronic c.1362+17825 e13+17825 0 - - - no_errors tier3 1086 13 1.18 814 299 26.86 0 0 NA 321258 TCGA-AB-3001 AML14 7 38780134 38780134 T C SNP VPS41 NM_014396.3 human genbank 54_36p -1 reviewed intronic c.1012+106 e12+106 0.006 - - - no_errors tier3 1295 4 0.31 256 180 41.28 0 0 0 321258 TCGA-AB-3001 AML14 7 46848478 46848478 G A SNP - - - - - - - - - - - - - - - tier3 863 1 0.12 1002 449 30.92 0 0 NA 321258 TCGA-AB-3001 AML14 7 49115361 49115361 G A SNP LOC100134710 XR_038112.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*3010 NULL 0 - - - pseudogene tier3 678 5 0.73 370 142 27.63 0 0 NA 321258 TCGA-AB-3001 AML14 7 52999048 52999048 G A SNP - - - - - - - - - - - - - - - tier3 1039 1 0.1 654 308 32.02 0 0 NA 321258 TCGA-AB-3001 AML14 7 53767620 53767620 A G SNP ENSG00000205628 ENST00000380970 human ensembl 54_36p -1 known intronic c.525+32694 e3+32694 0.003 - - - no_errors tier3 585 2 0.34 37 11 22.92 0 0 NA 321258 TCGA-AB-3001 AML14 7 70304907 70304907 C T SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.238+68945 e1+68945 0 - - - no_errors tier3 546 1 0.18 126 38 23.03 0 0 NA 321258 TCGA-AB-3001 AML14 7 84356329 84356329 T C SNP HMGN2L11 ENST00000275609 human ensembl 54_36p 1 known 3_prime_flanking_region c.*12159 NULL 0.004 - - - no_coding_region:pseudogene tier3 680 0 0 78 7 8.24 0 0 NA 321258 TCGA-AB-3001 AML14 7 84779383 84779383 C A SNP - - - - - - - - - - - - - - - tier2 915 4 0.43 273 119 30.28 0 0 NA 321258 TCGA-AB-3001 AML14 7 110708939 110708939 G A SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional intronic c.239+205591 e2+205591 0 - - - no_errors tier3 2065 7 0.34 545 257 32.04 1 0 0 321258 TCGA-AB-3001 AML14 7 113523938 113523938 C T SNP ENSG00000208668 ENST00000385933 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-45255 NULL 0.241 - - - pseudogene tier3 896 1 0.11 85 22 20.56 0 0 NA 321258 TCGA-AB-3001 AML14 7 119896803 119896803 T G SNP KCND2 NM_012281.2 human genbank 54_36p 1 reviewed intronic c.1115+193766 e1+193766 0.421 - - - no_errors tier3 1058 1 0.09 477 192 28.7 0 0 NA 321258 TCGA-AB-3001 AML14 7 120044094 120044094 C G SNP KCND2 NM_012281.2 human genbank 54_36p 1 reviewed intronic c.1116-116099 e2-116099 0.005 - - - no_errors tier3 1108 6 0.54 552 192 25.77 0 0 NA 321258 TCGA-AB-3001 AML14 7 125566728 125566728 T A SNP - - - - - - - - - - - - - - - tier3 443 1 0.23 108 23 17.56 0 0 NA 321258 TCGA-AB-3001 AML14 7 125727811 125727811 C A SNP - - - - - - - - - - - - - - - tier3 719 2 0.28 387 132 25.43 0 0 NA 321258 TCGA-AB-3001 AML14 7 140516858 140516858 G A SNP LOC100129514 XM_001716072.1 human genbank 54_36p 1 model intronic c.383-42002 e2-42002 0.004 - - - no_errors tier3 804 6 0.74 353 159 31.05 0 0 NA 321258 TCGA-AB-3001 AML14 7 143313679 143313679 A T SNP OR6B1 NM_001005281.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-18344 NULL 1 - - - no_errors tier2 1268 6 0.47 625 257 29.11 0 0 NA 321258 TCGA-AB-3001 AML14 7 145872597 145872597 T C SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.98-229699 e2-229699 0.002 - - - no_errors tier3 834 0 0 427 76 15.11 0 0 NA 321258 TCGA-AB-3001 AML14 7 147207381 147207381 A T SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2099-24209 e14-24209 0.967 - - - no_errors tier3 1311 5 0.38 826 393 32.24 0 0 NA 321258 TCGA-AB-3001 AML14 7 157744703 157744703 G - DEL PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.278-53977 e4-53977 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 8 984068 984068 C T SNP C8orf68 XM_927505.1 human genbank 54_36p 1 model intronic c.71-90638 e3-90638 0 - - - no_errors tier3 265 1 0.38 60 26 30.23 0 0 NA 321258 TCGA-AB-3001 AML14 8 3615523 3615523 T C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.819-16551 e6-16551 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 988 8 0.8 990 410 29.29 0 0 NA 321258 TCGA-AB-3001 AML14 8 4303585 4303585 T C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.303-38590 e3-38590 0.008 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier2 1136 1 0.09 473 209 30.65 0 0 NA 321258 TCGA-AB-3001 AML14 8 6267405 6267405 G A SNP MCPH1 NM_024596.2 human genbank 54_36p 1 validated intronic c.233+7593 e3+7593 0 - - - no_errors tier3 1050 6 0.57 318 143 31.02 0 0 0 321258 TCGA-AB-3001 AML14 8 10655063 10655063 G A SNP SOX7 NM_031439.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29710 NULL 0 - - - no_errors tier3 1574 2 0.13 580 257 30.7 0 0 NA 321258 TCGA-AB-3001 AML14 8 16527789 16527789 G A SNP - - - - - - - - - - - - - - - tier2 1153 5 0.43 377 89 19.1 0 0 NA 321258 TCGA-AB-3001 AML14 8 25755647 25755647 A G SNP EBF2 NM_022659.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*2395 NULL 1 - - - no_errors tier2 1343 5 0.37 397 104 20.76 0 0 NA 321258 TCGA-AB-3001 AML14 8 32445350 32445350 G C SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.746-127538 e2-127538 0.257 - - - overly_large_intron tier3 1005 5 0.5 120 39 24.38 0 0 NA 321258 TCGA-AB-3001 AML14 8 32717666 32717666 A C SNP NRG1 NM_013956.2 human genbank 54_36p 1 reviewed intronic c.633-2069 e7-2069 0 - - - no_errors tier3 452 5 1.09 274 55 16.72 0 0 NA 321258 TCGA-AB-3001 AML14 8 35446578 35446578 G A SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.104-79774 e2-79774 0 - - - no_errors tier3 823 6 0.72 218 55 20.07 0 0 NA 321258 TCGA-AB-3001 AML14 8 39423363 39423363 G A SNP ADAM5P ENST00000399789 human ensembl 54_36p 1 known 3_prime_flanking_region c.*45326 NULL 0.014 - - - no_errors tier3 2390 6 0.25 1262 431 25.46 0 0 NA 321258 TCGA-AB-3001 AML14 8 40092706 40092706 T A SNP C8orf4 NM_020130.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-37503 NULL 0.009 - - - no_errors tier3 964 4 0.41 290 51 14.96 0 0 NA 321258 TCGA-AB-3001 AML14 8 51370765 51370765 A C SNP SNTG1 NM_018967.2 human genbank 54_36p 1 reviewed intronic c.1-98560 e1-98560 0.001 - - - no_errors tier3 920 0 0 429 137 24.2 0 0 NA 321258 TCGA-AB-3001 AML14 8 56439530 56439530 C T SNP XKR4 NM_052898.1 human genbank 54_36p 1 provisional intronic c.1006+6539 e2+6539 0 - - - no_errors tier2 1495 6 0.4 706 299 29.75 0 0 NA 321258 TCGA-AB-3001 AML14 8 63669651 63669651 A C SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.273+4744 e3+4744 0.074 - - - no_errors tier3 1015 6 0.59 278 119 29.97 0 0 NA 321258 TCGA-AB-3001 AML14 8 76879967 76879967 A T SNP ENSG00000221029 ENST00000408102 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18717 NULL 0.994 - - - no_errors tier2 401 3 0.74 227 51 18.35 0 0 NA 321258 TCGA-AB-3001 AML14 8 77103183 77103183 G C SNP - - - - - - - - - - - - - - - tier3 1574 3 0.19 740 158 17.59 0 0 NA 321258 TCGA-AB-3001 AML14 8 77463548 77463548 C A SNP - - - - - - - - - - - - - - - tier2 1349 3 0.22 665 148 18.2 0 0 NA 321258 TCGA-AB-3001 AML14 8 77672009 77672009 A G SNP - - - - - - - - - - - - - - - tier3 1251 8 0.64 250 74 22.84 0 0 NA 321258 TCGA-AB-3001 AML14 8 77837788 77837788 C A SNP ZFHX4 NM_024721.3 human genbank 54_36p 1 validated intronic c.3016-15211 e3-15211 0.001 - - - no_errors tier3 770 3 0.39 278 43 13.4 0 0 NA 321258 TCGA-AB-3001 AML14 8 88681283 88681283 G A SNP - - - - - - - - - - - - - - - tier2 376 1 0.26 322 75 18.84 0 0 NA 321258 TCGA-AB-3001 AML14 8 89678019 89678019 G C SNP - - - - - - - - - - - - - - - tier2 1110 5 0.45 505 226 30.92 0 0 NA 321258 TCGA-AB-3001 AML14 8 104879191 104879191 C T SNP RIMS2 NM_001100117.1 human genbank 54_36p 1 validated intronic c.698+31250 e3+31250 0 - - - no_errors tier3 831 1 0.12 167 55 24.77 0 0 NA 321258 TCGA-AB-3001 AML14 8 112307634 112307634 A C SNP - - - - - - - - - - - - - - - tier3 684 1 0.15 240 24 9.09 0 0 NA 321258 TCGA-AB-3001 AML14 8 116271017 116271017 G A SNP - - - - - - - - - - - - - - - tier3 1696 14 0.82 622 285 31.42 0 0 NA 321258 TCGA-AB-3001 AML14 8 126789065 126789065 T C SNP - - - - - - - - - - - - - - - tier3 1539 13 0.84 619 257 29.34 0 0 NA 321258 TCGA-AB-3001 AML14 8 132217348 132217348 G T SNP - - - - - - - - - - - - - - - tier3 1166 8 0.68 367 149 28.88 0 0 NA 321258 TCGA-AB-3001 AML14 8 138397237 138397237 C T SNP - - - - - - - - - - - - - - - tier2 1217 9 0.73 241 79 24.69 0 0 NA 321258 TCGA-AB-3001 AML14 8 138818818 138818818 A C SNP - - - - - - - - - - - - - - - tier3 509 1 0.2 132 23 14.84 0 0 NA 321258 TCGA-AB-3001 AML14 8 139367338 139367338 G A SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.158-20071 e3-20071 0 - - - no_errors tier3 815 9 1.09 234 110 31.98 0 0 NA 321258 TCGA-AB-3001 AML14 8 139984360 139984360 G A SNP COL22A1 NM_152888.1 human genbank 54_36p -1 validated intronic c.1+10684 e0+10684 0.001 - - - no_errors tier3 1379 3 0.22 585 301 33.97 0 0 NA 321258 TCGA-AB-3001 AML14 9 1789358 1789358 G T SNP - - - - - - - - - - - - - - - tier2 847 3 0.35 292 106 26.63 0 0 NA 321258 TCGA-AB-3001 AML14 9 9390922 9390922 G - DEL PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-3440 e1-3440 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 9 11765072 11765072 T C SNP - - - - - - - - - - - - - - - tier3 494 4 0.8 108 19 14.96 0 0 NA 321258 TCGA-AB-3001 AML14 9 13414877 13414877 C T SNP FLJ41200 XM_379623.1 human genbank 54_36p -1 model intronic c.199+6325 e1+6325 0.017 - - - no_errors tier3 1913 3 0.16 847 253 23 0 0 NA 321258 TCGA-AB-3001 AML14 9 17638277 17638277 A - DEL SH3GL2 NM_003026.2 human genbank 54_36p 1 validated intronic c.45+68992 e1+68992 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 9 22995520 22995520 G A SNP - - - - - - - - - - - - - - - tier2 1229 4 0.32 707 289 28.99 0 0 NA 321258 TCGA-AB-3001 AML14 9 25199833 25199833 T A SNP - - - - - - - - - - - - - - - tier3 686 3 0.43 246 118 32.42 0 0 NA 321258 TCGA-AB-3001 AML14 9 26011941 26011941 T G SNP ENSG00000196478 ENST00000359978 human ensembl 54_36p 1 known 5_prime_flanking_region c.-72652 NULL 0.002 - - - no_errors tier3 882 2 0.23 162 67 29.26 0 0 NA 321258 TCGA-AB-3001 AML14 9 29093047 29093047 A G SNP - - - - - - - - - - - - - - - tier3 642 2 0.31 340 46 11.92 0 0 NA 321258 TCGA-AB-3001 AML14 9 29398197 29398197 T C SNP - - - - - - - - - - - - - - - tier3 771 2 0.26 136 59 30.26 0 0 NA 321258 TCGA-AB-3001 AML14 9 71982714 71982714 T C SNP MAMDC2 NM_153267.4 human genbank 54_36p 1 validated intronic c.1651+7347 e11+7347 0 - - - no_errors tier3 997 9 0.89 217 89 29.08 15 21 58.33 321258 TCGA-AB-3001 AML14 9 78981286 78981286 A G SNP VPS13A NM_033305.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1155 NULL 0 - - - no_errors tier3 442 0 0 133 37 21.76 0 0 NA 321258 TCGA-AB-3001 AML14 9 79722746 79722746 C T SNP GNAQ NM_002072.2 human genbank 54_36p -1 provisional intronic c.321+4151 e2+4151 0.005 - - - no_errors tier2 1961 4 0.2 1193 533 30.88 5 3 37.5 321258 TCGA-AB-3001 AML14 9 83341957 83341957 G A SNP TLE1 NM_005077.3 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*46976 NULL 0.009 - - - no_errors tier3 1631 1 0.06 607 57 8.58 0 0 NA 321258 TCGA-AB-3001 AML14 9 84228084 84228084 C A SNP LOC442427 XR_037390.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*8540 NULL 0.003 - - - pseudogene tier3 812 1 0.12 580 232 28.57 0 0 NA 321258 TCGA-AB-3001 AML14 9 84228086 84228086 G T SNP LOC442427 XR_037390.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*8538 NULL 0 - - - pseudogene tier3 801 1 0.12 579 232 28.61 0 0 NA 321258 TCGA-AB-3001 AML14 9 97880902 97880902 G A SNP ENSG00000201938 ENST00000365068 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*24280 NULL 0 - - - no_errors tier3 758 5 0.65 296 141 32.12 0 0 NA 321258 TCGA-AB-3001 AML14 9 107869287 107869287 A G SNP - - - - - - - - - - - - - - - tier2 1728 7 0.4 408 140 25.55 0 0 NA 321258 TCGA-AB-3001 AML14 9 123248556 123248556 G C SNP ENSG00000222970 ENST00000411038 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48062 NULL 0.001 - - - no_errors tier3 1198 4 0.33 750 317 29.71 0 0 NA 321258 TCGA-AB-3001 AML14 9 126682407 126682407 T C SNP GOLGA1 NM_002077.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*223 NULL 0.688 - - - no_errors tier2 1038 7 0.67 615 224 26.7 16 10 38.46 321258 TCGA-AB-3001 AML14 9 127506694 127506694 T C SNP MAPKAP1 NM_001006617.1 human genbank 54_36p -1 reviewed intronic c.1+2377 e0+2377 0 - - - no_errors tier3 650 7 1.07 101 42 29.37 0 0 0 321258 TCGA-AB-3001 AML14 10 9057902 9057902 C A SNP - - - - - - - - - - - - - - - tier3 1226 7 0.57 978 187 16.02 0 0 NA 321258 TCGA-AB-3001 AML14 10 18729112 18729112 A G SNP CACNB2 NM_201596.3 human genbank 54_36p 1 validated intronic c.214-1747 e3-1747 0.005 - - - no_errors tier3 1284 9 0.7 379 94 19.87 0 0 NA 321258 TCGA-AB-3001 AML14 10 25911473 25911473 G A SNP GPR158 NM_020752.2 human genbank 54_36p 1 validated intronic c.1754-6469 e8-6469 0 - - - no_errors tier3 1550 14 0.89 546 190 25.82 0 0 NA 321258 TCGA-AB-3001 AML14 10 28945298 28945298 G A SNP WAC NM_016628.3 human genbank 54_36p 1 reviewed splice_site c.1746+1 e12+1 1 - - - no_errors tier1 746 4 0.53 685 303 30.67 6 1 14.29 321258 TCGA-AB-3001 AML14 10 32245231 32245231 C T SNP ARHGAP12 NM_018287.5 human genbank 54_36p -1 provisional intronic c.1-5734 e1-5734 0.004 - - - no_errors tier3 3139 11 0.35 736 189 20.43 1 1 50 321258 TCGA-AB-3001 AML14 10 52263560 52263560 C A SNP A1CF NM_138932.2 human genbank 54_36p -1 reviewed intronic c.604+2280 e4+2280 0 - - - no_errors tier3 987 1 0.1 612 181 22.82 0 0 NA 321258 TCGA-AB-3001 AML14 10 66080075 66080075 G T SNP ENSG00000216248 ENST00000405829 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29390 NULL 0 - - - no_coding_region:pseudogene tier3 834 3 0.36 628 149 19.18 0 0 NA 321258 TCGA-AB-3001 AML14 10 73224959 73224959 G T SNP CDH23 NM_022124.4 human genbank 54_36p 1 reviewed intronic c.6712+1556 e47+1556 0 - - - no_errors tier3 798 11 1.36 459 104 18.47 0 0 NA 321258 TCGA-AB-3001 AML14 10 85130177 85130177 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 10 107744809 107744809 G A SNP - - - - - - - - - - - - - - - tier2 1305 5 0.38 811 363 30.92 0 0 NA 321258 TCGA-AB-3001 AML14 10 107854550 107854550 T A SNP - - - - - - - - - - - - - - - tier3 351 0 0 91 23 20.18 0 0 NA 321258 TCGA-AB-3001 AML14 10 108071893 108071893 C A SNP - - - - - - - - - - - - - - - tier3 1104 1 0.09 663 162 19.61 0 0 NA 321258 TCGA-AB-3001 AML14 10 110868363 110868363 A T SNP - - - - - - - - - - - - - - - tier3 799 3 0.37 557 102 15.41 0 0 NA 321258 TCGA-AB-3001 AML14 10 115894360 115894360 G A SNP C10orf118 NM_018017.2 human genbank 54_36p -1 validated silent c.1107 p.G369 0.95 NULL superfamily_Prefoldin - no_errors tier1 643 8 1.23 92 21 18.58 8 4 33.33 321258 TCGA-AB-3001 AML14 10 116992114 116992114 G A SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.1687+610 e10+610 0 - - - no_errors tier3 278 2 0.71 123 25 16.89 0 0 NA 321258 TCGA-AB-3001 AML14 10 123230195 123230195 A G SNP FGFR2 NM_022970.4 human genbank 54_36p -1 reviewed intronic c.2305-670 e17-670 0 - - - no_errors tier3 711 0 0 192 40 17.24 0 0 NA 321258 TCGA-AB-3001 AML14 10 125307433 125307433 G A SNP - - - - - - - - - - - - - - - tier3 426 5 1.16 317 151 32.26 1 0 0 321258 TCGA-AB-3001 AML14 11 24716425 24716425 G C SNP LUZP2 NM_001009909.2 human genbank 54_36p 1 validated splice_site c.333+1 e4+1 0.994 - - - no_errors tier1 1289 5 0.39 1226 256 17.26 NA 321258 TCGA-AB-3001 AML14 11 26643125 26643125 C T SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*4558 NULL 0 - - - no_errors tier3 780 2 0.26 361 141 28.09 0 0 NA 321258 TCGA-AB-3001 AML14 11 27081800 27081800 T G SNP BBOX1 NM_003986.2 human genbank 54_36p 1 reviewed intronic c.533+10311 e3+10311 0.002 - - - no_errors tier3 645 3 0.46 57 20 25.97 0 0 NA 321258 TCGA-AB-3001 AML14 11 29471866 29471866 C T SNP LOC729560 XM_001130628.2 human genbank 54_36p -1 model intronic c.90+37545 e2+37545 0.949 - - - no_errors tier3 1100 0 0 436 104 19.22 0 0 NA 321258 TCGA-AB-3001 AML14 11 31121131 31121131 C T SNP uc001msu.1 ENST00000342355 human ensembl 54_36p -1 known intronic c.79-5224 e2-5224 0.001 - - - no_errors tier3 1009 0 0 350 137 28.07 0 0 NA 321258 TCGA-AB-3001 AML14 11 38623133 38623133 C G SNP - - - - - - - - - - - - - - - tier3 517 2 0.39 86 22 20.37 0 0 NA 321258 TCGA-AB-3001 AML14 11 40433989 40433989 C G SNP - - - - - - - - - - - - - - - tier3 1505 2 0.13 367 79 17.71 0 0 NA 321258 TCGA-AB-3001 AML14 11 49243852 49243852 A T SNP LOC729960 XR_016034.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-40041 NULL 0.001 - - - pseudogene tier3 702 5 0.71 107 48 30.97 0 0 NA 321258 TCGA-AB-3001 AML14 11 63277995 63277995 C T SNP RTN3 NM_201428.2 human genbank 54_36p 1 validated intronic c.2937+239 e6+239 0 - - - no_errors tier3 534 0 0 124 12 8.76 3 1 25 321258 TCGA-AB-3001 AML14 11 63971267 63971267 C T SNP ENSG00000181908 ENST00000316124 human ensembl 54_36p 1 known 5_prime_flanking_region c.-2326 NULL 0.01 - - - no_errors tier3 562 2 0.35 228 100 30.49 0 0 NA 321258 TCGA-AB-3001 AML14 11 70793355 70793355 C T SNP NADSYN1 NM_018161.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-48636 NULL 0.001 - - - no_errors tier3 559 3 0.53 259 40 13.33 0 0 NA 321258 TCGA-AB-3001 AML14 11 74338477 74338477 T A SNP SPCS2 NM_014752.2 human genbank 54_36p 1 validated intronic c.1+385 e0+385 0.004 - - - no_errors tier2 1713 10 0.58 1010 188 15.69 2 0 0 321258 TCGA-AB-3001 AML14 11 78432462 78432462 G T SNP ODZ4 ENST00000278550 human ensembl 54_36p -1 known intronic c.493+20969 e2+20969 0.017 - - - no_errors tier3 797 2 0.25 458 170 27.07 0 0 NA 321258 TCGA-AB-3001 AML14 11 79362172 79362172 C A SNP - - - - - - - - - - - - - - - tier3 944 3 0.32 886 425 32.42 0 0 NA 321258 TCGA-AB-3001 AML14 11 84414130 84414130 G T SNP DLG2 ENST00000376104 human ensembl 54_36p -1 known intronic c.357+86223 e4+86223 0.093 - - - no_errors tier3 622 1 0.16 165 44 21.05 1 0 0 321258 TCGA-AB-3001 AML14 11 90266254 90266254 C A SNP MIRN1261 ENST00000408659 human ensembl 54_36p -1 known 5_prime_flanking_region c.-24236 NULL 0 - - - no_errors tier2 1068 2 0.19 340 127 27.19 0 0 NA 321258 TCGA-AB-3001 AML14 11 96413703 96413703 A T SNP - - - - - - - - - - - - - - - tier3 499 0 0 268 72 21.18 0 0 NA 321258 TCGA-AB-3001 AML14 11 96825559 96825559 C T SNP - - - - - - - - - - - - - - - tier2 586 2 0.34 116 50 30.12 0 0 NA 321258 TCGA-AB-3001 AML14 11 99820404 99820404 C A SNP - - - - - - - - - - - - - - - tier3 197 1 0.51 99 17 14.66 0 0 NA 321258 TCGA-AB-3001 AML14 11 105359074 105359074 T A SNP GRIA4 NM_000829.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*3398 NULL 0 - - - no_errors tier3 1749 4 0.23 282 26 8.44 0 0 NA 321258 TCGA-AB-3001 AML14 11 112548141 112548141 C T SNP NCAM1 ENST00000404693 human ensembl 54_36p 1 known intronic c.1-30170 e1-30170 0 - - - no_errors tier3 1178 8 0.67 427 175 29.07 0 0 NA 321258 TCGA-AB-3001 AML14 11 133763559 133763559 G A SNP B3GAT1 NM_018644.3 human genbank 54_36p -1 reviewed intronic c.1-515 e1-515 0 - - - no_errors tier3 309 1 0.32 132 30 18.4 0 0 0 321258 TCGA-AB-3001 AML14 12 25593193 25593193 A C SNP IFLTD1 NM_152590.1 human genbank 54_36p -1 validated intronic c.247+334 e2+334 0.003 - - - no_errors tier2 885 7 0.78 287 125 30.34 0 0 NA 321258 TCGA-AB-3001 AML14 12 28670978 28670978 C T SNP - - - - - - - - - - - - - - - tier3 901 3 0.33 1009 373 26.97 0 0 NA 321258 TCGA-AB-3001 AML14 12 32812459 32812459 G A SNP YARS2 NM_001040436.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-12384 NULL 0.002 - - - no_errors tier3 746 0 0 299 50 14.29 0 0 NA 321258 TCGA-AB-3001 AML14 12 37359687 37359687 T A SNP CPNE8 NM_153634.2 human genbank 54_36p -1 reviewed intronic c.1272-2064 e17-2064 0.002 - - - no_errors tier3 628 2 0.32 158 45 22.17 1 0 0 321258 TCGA-AB-3001 AML14 12 40118468 40118468 C T SNP PDZRN4 NM_013377.3 human genbank 54_36p 1 validated intronic c.69+386 e1+386 1 - - - no_errors tier2 869 2 0.23 194 80 29.2 0 0 NA 321258 TCGA-AB-3001 AML14 12 41265754 41265754 G A SNP PRICKLE1 NM_153026.1 human genbank 54_36p -1 validated intronic c.1+3780 e0+3780 0.024 - - - no_errors tier3 612 9 1.45 201 101 33.33 1 2 66.67 321258 TCGA-AB-3001 AML14 12 57565928 57565928 C T SNP LRIG3 NM_153377.1 human genbank 54_36p -1 provisional missense c.1196 p.R399H 0.998 "HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00365,superfamily_RNI-like" "HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMSmart_SM00365,superfamily_Immunoglobulin,superfamily_RNI-like" - no_errors tier1 798 6 0.75 198 84 29.79 NA 321258 TCGA-AB-3001 AML14 12 64592059 64592059 T C SNP HMGA2 NM_003483.4 human genbank 54_36p 1 reviewed intronic c.250-39371 e4-39371 0 - - - no_errors tier2 1137 3 0.26 410 96 18.93 0 0 NA 321258 TCGA-AB-3001 AML14 12 72277107 72277107 A T SNP - - - - - - - - - - - - - - - tier2 727 0 0 350 103 22.74 0 0 NA 321258 TCGA-AB-3001 AML14 12 75207739 75207739 A G SNP ENSG00000223273 ENST00000411341 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-25923 NULL 0.029 - - - no_errors tier3 1283 4 0.31 1367 558 28.99 0 0 NA 321258 TCGA-AB-3001 AML14 12 75860549 75860549 A T SNP LOC727803 XR_015131.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*41125 NULL 0 - - - pseudogene tier3 1559 12 0.76 615 104 14.44 0 0 NA 321258 TCGA-AB-3001 AML14 12 76474017 76474017 C T SNP - - - - - - - - - - - - - - - tier2 527 2 0.38 211 60 22.14 0 0 NA 321258 TCGA-AB-3001 AML14 12 85087814 85087814 G T SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1-120182 e1-120182 0.001 - - - no_errors tier3 400 2 0.5 153 47 23.5 0 0 NA 321258 TCGA-AB-3001 AML14 12 86162143 86162143 A C SNP - - - - - - - - - - - - - - - tier2 1012 8 0.78 567 111 16.37 0 0 NA 321258 TCGA-AB-3001 AML14 12 98360943 98360943 C T SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.1575+639 e11+639 1 - - - no_errors tier2 1358 4 0.29 422 193 31.38 0 0 NA 321258 TCGA-AB-3001 AML14 12 98464564 98464564 G A SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.1273-42014 e10-42014 0.001 - - - no_errors tier3 1518 36 2.32 891 137 13.33 0 0 NA 321258 TCGA-AB-3001 AML14 12 119290047 119290047 G A SNP MSI1 NM_002442.2 human genbank 54_36p -1 reviewed intronic c.267+147 e4+147 0.469 - - - no_errors tier3 503 8 1.57 117 29 19.86 0 0 NA 321258 TCGA-AB-3001 AML14 12 125456871 125456871 C T SNP LOC100128554 XM_001719470.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-38594 NULL 0.023 - - - no_errors tier3 988 4 0.4 628 236 27.31 0 0 NA 321258 TCGA-AB-3001 AML14 12 128676495 128676495 C T SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.968+73813 e2+73813 0 - - - no_errors tier3 1303 7 0.53 628 233 27.06 0 0 NA 321258 TCGA-AB-3001 AML14 12 128841696 128841696 G A SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.80-90500 e2-90500 0 - - - no_errors tier3 1636 3 0.18 1030 221 17.67 0 0 NA 321258 TCGA-AB-3001 AML14 13 23456247 23456247 A G SNP FLJ46358 XM_001715330.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-36134 NULL 0.332 - - - no_errors tier2 1061 8 0.75 220 96 30.28 0 0 NA 321258 TCGA-AB-3001 AML14 13 26459490 26459490 C G SNP LOC100129306 XM_001719801.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*30198 NULL 0.005 - - - pseudogene tier3 1590 8 0.5 714 261 26.77 0 0 NA 321258 TCGA-AB-3001 AML14 13 37881843 37881843 A T SNP UFM1 NM_016617.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*48928 NULL 0 - - - no_errors tier3 522 1 0.19 204 37 15.35 0 0 NA 321258 TCGA-AB-3001 AML14 13 55692444 55692444 T G SNP ENSG00000219006 ENST00000404148 human ensembl 54_36p 1 known 3_prime_flanking_region c.*3367 NULL 0.001 - - - no_coding_region:pseudogene tier3 567 6 1.05 357 153 30 0 0 NA 321258 TCGA-AB-3001 AML14 13 69657321 69657321 C T SNP ATXN8OS NR_002717.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45759 NULL 0 - - - no_errors tier2 368 1 0.27 131 32 19.63 0 0 NA 321258 TCGA-AB-3001 AML14 13 74069805 74069805 A G SNP - - - - - - - - - - - - - - - tier3 1423 5 0.35 269 103 27.69 0 0 NA 321258 TCGA-AB-3001 AML14 13 84657776 84657776 G A SNP - - - - - - - - - - - - - - - tier3 2194 1 0.05 503 86 14.6 0 0 NA 321258 TCGA-AB-3001 AML14 13 84849240 84849240 T G SNP - - - - - - - - - - - - - - - tier3 854 0 0 255 60 19.05 0 0 NA 321258 TCGA-AB-3001 AML14 13 85313138 85313138 G T SNP SLITRK6 NM_032229.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44494 NULL 0.009 - - - no_errors tier3 726 1 0.14 137 44 24.31 0 0 NA 321258 TCGA-AB-3001 AML14 13 93268684 93268685 - T INS GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.320-11724_320-11723 e3-11723 0.000:0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 13 93639410 93639410 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.878-97194 e5-97194 0.674 - - - no_errors tier3 675 2 0.3 207 64 23.62 1 3 75 321258 TCGA-AB-3001 AML14 13 93763817 93763817 C T SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.1152+7439 e6+7439 0 - - - no_errors tier3 866 4 0.46 474 165 25.82 0 2 100 321258 TCGA-AB-3001 AML14 13 100559733 100559733 C A SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.2364+1238 e19+1238 0.001 - - - no_errors tier3 1385 7 0.5 591 236 28.54 0 0 NA 321258 TCGA-AB-3001 AML14 13 105455552 105455552 G T SNP - - - - - - - - - - - - - - - tier2 1095 1 0.09 396 73 15.57 0 0 NA 321258 TCGA-AB-3001 AML14 13 105455553 105455553 A T SNP - - - - - - - - - - - - - - - tier2 1085 1 0.09 397 72 15.35 0 0 NA 321258 TCGA-AB-3001 AML14 14 23088557 23088557 G A SNP THTPA NM_024328.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7250 NULL 0.014 - - - no_errors tier3 1822 8 0.44 158 24 13.19 0 0 0 321258 TCGA-AB-3001 AML14 14 26366465 26366465 T A SNP - - - - - - - - - - - - - - - tier3 982 3 0.3 302 72 19.25 0 0 NA 321258 TCGA-AB-3001 AML14 14 26922669 26922669 A - DEL LOC728755 XM_001128377.2 human genbank 54_36p -1 model intronic c.202-61482 e3-61482 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 14 27487698 27487698 A T SNP ENSG00000223164 ENST00000411232 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41353 NULL 0.011 - - - no_errors tier3 1129 12 1.05 424 158 27.15 1 0 0 321258 TCGA-AB-3001 AML14 14 28621397 28621397 A G SNP - - - - - - - - - - - - - - - tier3 943 0 0 413 199 32.46 0 0 NA 321258 TCGA-AB-3001 AML14 14 41941796 41941796 C G SNP - - - - - - - - - - - - - - - tier3 615 2 0.32 143 24 14.37 0 0 NA 321258 TCGA-AB-3001 AML14 14 44226405 44226405 C T SNP - - - - - - - - - - - - - - - tier2 1012 7 0.69 195 70 26.42 0 0 NA 321258 TCGA-AB-3001 AML14 14 45183483 45183483 G A SNP - - - - - - - - - - - - - - - tier3 627 4 0.63 101 35 25.74 0 0 NA 321258 TCGA-AB-3001 AML14 14 46910605 46910605 A C SNP MDGA2 ENST00000399232 human ensembl 54_36p -1 known intronic c.74-70102 e2-70102 0.001 - - - no_errors tier3 385 1 0.26 72 28 28 0 0 NA 321258 TCGA-AB-3001 AML14 14 61461743 61461743 C T SNP - - - - - - - - - - - - - - - tier3 904 3 0.33 249 108 30.25 0 0 NA 321258 TCGA-AB-3001 AML14 14 82144919 82144919 G A SNP - - - - - - - - - - - - - - - tier3 438 5 1.12 206 70 25.36 0 0 NA 321258 TCGA-AB-3001 AML14 14 83684273 83684273 C G SNP ENSG00000210415 ENST00000387680 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24580 NULL 0.037 - - - pseudogene tier3 546 5 0.91 146 38 20.65 0 0 NA 321258 TCGA-AB-3001 AML14 14 83897613 83897613 C A SNP - - - - - - - - - - - - - - - tier3 928 2 0.22 281 58 17.11 0 0 NA 321258 TCGA-AB-3001 AML14 14 97123415 97123415 A - DEL LOC730217 XM_001132986.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*29873 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 14 97557909 97557909 T C SNP - - - - - - - - - - - - - - - tier2 1357 1 0.07 520 173 24.96 0 0 NA 321258 TCGA-AB-3001 AML14 14 97810124 97810124 C G SNP - - - - - - - - - - - - - - - tier3 941 7 0.74 667 209 23.86 0 0 NA 321258 TCGA-AB-3001 AML14 15 29694299 29694299 G A SNP OTUD7A NM_130901.1 human genbank 54_36p -1 provisional intronic c.151+40292 e1+40292 0.025 - - - no_errors tier2 536 4 0.74 202 135 40.06 0 0 NA 321258 TCGA-AB-3001 AML14 15 40366233 40366233 C T SNP GANC NM_198141.2 human genbank 54_36p 1 reviewed intronic c.202-948 e4-948 0.001 - - - no_errors tier3 1091 0 0 347 152 30.4 3 2 40 321258 TCGA-AB-3001 AML14 15 43929383 43929383 A C SNP - - - - - - - - - - - - - - - tier3 1031 9 0.86 409 173 29.73 0 0 NA 321258 TCGA-AB-3001 AML14 15 47800831 47800831 T C SNP - - - - - - - - - - - - - - - tier3 1966 21 1.06 574 248 30.17 0 0 NA 321258 TCGA-AB-3001 AML14 15 60547276 60547276 G A SNP - - - - - - - - - - - - - - - tier3 1099 4 0.36 655 122 15.68 0 0 NA 321258 TCGA-AB-3001 AML14 15 85159672 85159672 G A SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.3083+141001 e21+141001 0 - - - no_errors tier3 699 10 1.41 234 98 29.52 0 0 NA 321258 TCGA-AB-3001 AML14 16 6195805 6195805 C G SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-111192 e1-111192 0.001 - - - no_errors tier3 1016 6 0.59 192 64 25 0 0 NA 321258 TCGA-AB-3001 AML14 16 6591673 6591673 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-52932 e1-52932 0 - - - no_errors tier3 1309 4 0.3 686 142 17.15 0 0 NA 321258 TCGA-AB-3001 AML14 16 9397545 9397545 C A SNP - - - - - - - - - - - - - - - tier3 485 2 0.41 201 52 20.55 0 0 NA 321258 TCGA-AB-3001 AML14 16 15025050 15025050 G A SNP PDXDC1 NM_015027.2 human genbank 54_36p 1 validated intronic c.1140+938 e13+938 0 - - - no_errors tier3 2637 34 1.27 1543 231 13.02 14 2 12.5 321258 TCGA-AB-3001 AML14 16 34233261 34233261 C A SNP LOC100131688 XM_001718246.1 human genbank 54_36p -1 model intronic c.83-3598 e2-3598 0 - - - no_errors tier3 518 2 0.38 393 178 31.17 0 0 NA 321258 TCGA-AB-3001 AML14 16 50731295 50731295 A T SNP - - - - - - - - - - - - - - - tier2 1301 1 0.08 642 157 19.65 0 0 NA 321258 TCGA-AB-3001 AML14 16 51403989 51403989 C T SNP - - - - - - - - - - - - - - - tier3 1246 1 0.08 1236 252 16.92 0 0 NA 321258 TCGA-AB-3001 AML14 16 53674164 53674164 G T SNP - - - - - - - - - - - - - - - tier2 838 1 0.12 560 189 25.23 0 0 NA 321258 TCGA-AB-3001 AML14 16 59757453 59757453 G T SNP - - - - - - - - - - - - - - - tier3 706 1 0.14 411 85 17.14 0 0 NA 321258 TCGA-AB-3001 AML14 16 60701368 60701368 A G SNP - - - - - - - - - - - - - - - tier3 854 1 0.12 219 92 29.49 0 0 NA 321258 TCGA-AB-3001 AML14 16 62123079 62123079 C A SNP - - - - - - - - - - - - - - - tier3 656 2 0.3 261 69 20.91 0 0 NA 321258 TCGA-AB-3001 AML14 16 63931458 63931458 C G SNP LOC283867 NM_001101346.1 human genbank 54_36p -1 inferred intronic c.126+14189 e3+14189 0.003 - - - no_errors tier2 805 0 0 691 64 8.48 0 0 NA 321258 TCGA-AB-3001 AML14 16 75569665 75569665 A T SNP - - - - - - - - - - - - - - - tier2 1208 6 0.49 611 243 28.39 0 0 NA 321258 TCGA-AB-3001 AML14 16 79020325 79020325 C A SNP LOC729847 XM_001131495.1 human genbank 54_36p -1 model intronic c.191+63643 e1+63643 0.001 - - - no_errors tier3 1241 1 0.08 534 62 10.4 0 0 NA 321258 TCGA-AB-3001 AML14 16 84578016 84578016 C T SNP LOC100131952 XM_001726876.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-49130 NULL 0.001 - - - no_errors tier2 816 10 1.21 1000 473 32.07 0 0 NA 321258 TCGA-AB-3001 AML14 16 84703810 84703810 G C SNP - - - - - - - - - - - - - - - tier2 368 3 0.81 261 82 23.91 0 0 NA 321258 TCGA-AB-3001 AML14 17 1508697 1508697 C T SNP PRPF8 NM_006445.3 human genbank 54_36p -1 reviewed missense c.5249 p.G1750E 0.997 NULL "HMMPfam_Mov34,HMMSmart_SM00232,HMMPfam_PRO8NT,HMMPfam_PROCN,HMMPfam_PROCT,HMMPfam_U6-snRNA_bdg,HMMPfam_U5_2-snRNA_bdg,HMMPfam_RRM_4" - no_errors tier1 1403 6 0.43 394 95 19.43 294 102 25.76 321258 TCGA-AB-3001 AML14 17 11198914 11198914 T C SNP uc002gna.2 ENST00000409168 human ensembl 54_36p 1 known intronic c.800-24542 e3-24542 0.048 - - - no_errors tier3 1555 3 0.19 630 71 10.13 0 0 NA 321258 TCGA-AB-3001 AML14 17 20808255 20808255 T A SNP LOC100128014 XM_001723607.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-25390 NULL 0.003 - - - no_errors tier3 829 3 0.36 184 66 26.4 0 0 NA 321258 TCGA-AB-3001 AML14 17 24234081 24234081 C T SNP FLOT2 NM_004475.2 human genbank 54_36p -1 reviewed intronic c.346+171 e4+171 0.015 - - - no_errors tier3 315 0 0 165 66 28.57 6 7 53.85 321258 TCGA-AB-3001 AML14 17 26838630 26838630 C T SNP RAB11FIP4 NM_032932.3 human genbank 54_36p 1 validated intronic c.337-30159 e4-30159 0.015 - - - no_errors tier3 410 6 1.44 193 97 33.45 0 0 NA 321258 TCGA-AB-3001 AML14 17 36745221 36745221 G C SNP ENSG00000216950 ENST00000406731 human ensembl 54_36p 1 known intronic c.NULL NULL 0.033 - - - no_coding_region:pseudogene tier3 506 7 1.36 535 240 30.97 0 0 NA 321258 TCGA-AB-3001 AML14 17 39167910 39167910 G A SNP ENSG00000215964 ENST00000401145 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13184 NULL 0 - - - no_errors tier3 815 7 0.85 238 110 31.52 0 0 NA 321258 TCGA-AB-3001 AML14 17 47071598 47071598 G A SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.635-3229 e7-3229 1 - - - no_errors tier2 1909 1 0.05 743 128 14.68 0 0 NA 321258 TCGA-AB-3001 AML14 17 47071652 47071652 T C SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.635-3283 e7-3283 0.998 - - - no_errors tier2 1521 1 0.07 673 127 15.86 0 0 NA 321258 TCGA-AB-3001 AML14 18 549878 549878 G A SNP CETN1 NM_004066.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20531 NULL 0.005 - - - no_errors tier3 269 0 0 33 8 19.51 0 0 NA 321258 TCGA-AB-3001 AML14 18 1187107 1187107 A G SNP LOC100130247 XM_001716684.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-20094 NULL 0.01 - - - no_errors tier2 788 0 0 767 75 8.91 0 0 NA 321258 TCGA-AB-3001 AML14 18 3258915 3258915 C T SNP MYL12B NM_033546.1 human genbank 54_36p 1 validated intronic c.1-3967 e1-3967 0.02 - - - no_errors tier3 851 5 0.58 196 29 12.89 2 3 60 321258 TCGA-AB-3001 AML14 18 19677706 19677706 G A SNP LAMA3 NM_198129.3 human genbank 54_36p 1 reviewed intronic c.3603+994 e29+994 0.004 - - - no_errors tier3 789 6 0.75 561 189 25.2 0 0 NA 321258 TCGA-AB-3001 AML14 18 21541729 21541729 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 321258 TCGA-AB-3001 AML14 18 23633944 23633944 C A SNP - - - - - - - - - - - - - - - tier3 693 3 0.43 413 97 19.02 0 0 NA 321258 TCGA-AB-3001 AML14 18 44225181 44225181 G A SNP LOC647055 XM_001715324.1 human genbank 54_36p 1 model intronic c.814-1893 e8-1893 0.004 - - - no_errors tier3 620 5 0.8 689 239 25.75 0 0 NA 321258 TCGA-AB-3001 AML14 18 56551488 56551488 T C SNP - - - - - - - - - - - - - - - tier3 766 3 0.39 174 87 33.21 0 0 NA 321258 TCGA-AB-3001 AML14 18 57120324 57120324 A G SNP - - - - - - - - - - - - - - - tier3 1211 5 0.41 1192 524 30.52 0 0 NA 321258 TCGA-AB-3001 AML14 18 61640291 61640291 T C SNP CDH7 NM_004361.2 human genbank 54_36p 1 reviewed splice_region c.626-6 e4-6 0.259 - - - no_errors tier2 958 1 0.1 504 134 21 0 0 NA 321258 TCGA-AB-3001 AML14 18 63998003 63998003 T C SNP - - - - - - - - - - - - - - - tier3 1065 7 0.65 177 70 28.34 0 0 NA 321258 TCGA-AB-3001 AML14 18 67799501 67799501 C A SNP - - - - - - - - - - - - - - - tier3 710 4 0.56 248 101 28.94 0 0 NA 321258 TCGA-AB-3001 AML14 18 68049097 68049097 G T SNP - - - - - - - - - - - - - - - tier3 175 1 0.56 53 35 39.77 0 0 NA 321258 TCGA-AB-3001 AML14 18 69603664 69603664 C T SNP ENSG00000222180 ENST00000410248 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*40220 NULL 0.001 - - - no_errors tier3 1378 3 0.22 396 115 22.5 0 0 NA 321258 TCGA-AB-3001 AML14 18 74511443 74511443 T A SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*28682 NULL 0 - - - no_errors tier3 611 2 0.33 571 122 17.58 0 0 NA 321258 TCGA-AB-3001 AML14 18 74791585 74791585 C G SNP SALL3 NM_171999.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49678 NULL 0 - - - no_errors tier3 1502 6 0.4 462 205 30.69 0 1 100 321258 TCGA-AB-3001 AML14 19 16279796 16279796 C T SNP KLF2 NM_016270.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-16939 NULL 0.009 - - - no_errors tier3 516 0 0 185 88 32.23 0 0 NA 321258 TCGA-AB-3001 AML14 19 23250321 23250321 G A SNP LOC100132815 XM_001726889.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13203 NULL 0 - - - no_errors tier2 667 2 0.3 119 23 16.2 0 0 0 321258 TCGA-AB-3001 AML14 19 38796445 38796445 T A SNP - - - - - - - - - - - - - - - tier3 687 1 0.14 307 133 30.23 0 0 NA 321258 TCGA-AB-3001 AML14 19 38872261 38872261 G A SNP CHST8 NM_022467.1 human genbank 54_36p 1 validated intronic c.130+124 e1+124 0 - - - no_errors tier3 373 0 0 494 223 31.1 0 0 NA 321258 TCGA-AB-3001 AML14 19 41678983 41678983 A G SNP LOC728752 XM_001128360.2 human genbank 54_36p 1 model intronic c.588-339 e3-339 0.461 - - - no_errors tier3 682 1 0.15 317 141 30.79 0 0 0 321258 TCGA-AB-3001 AML14 19 44808193 44808193 C A SNP LOC148003 XM_001721341.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-31615 NULL 0 - - - no_errors tier3 858 3 0.35 416 110 20.87 0 0 NA 321258 TCGA-AB-3001 AML14 20 9439343 9439343 C A SNP C20orf103 NM_012261.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-4157 NULL 0 - - - no_errors tier3 600 4 0.66 326 71 17.88 0 0 NA 321258 TCGA-AB-3001 AML14 20 15371644 15371644 C A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.571+11564 e7+11564 0 - - - no_errors tier3 627 1 0.16 123 50 28.9 0 0 0 321258 TCGA-AB-3001 AML14 20 21962741 21962741 C A SNP - - - - - - - - - - - - - - - tier3 700 1 0.14 414 79 15.99 0 0 NA 321258 TCGA-AB-3001 AML14 20 34868167 34868167 G A SNP C20orf117 NM_199181.2 human genbank 54_36p -1 predicted intronic c.2101-393 e8-393 0.001 - - - no_errors tier3 531 7 1.3 559 250 30.79 1 1 50 321258 TCGA-AB-3001 AML14 20 41005596 41005596 G A SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.89-57610 e2-57610 0 - - - no_errors tier3 1683 14 0.82 1175 513 30.28 0 0 NA 321258 TCGA-AB-3001 AML14 20 46154716 46154716 G A SNP LOC100130372 XM_001722388.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*27562 NULL 0 - - - no_errors tier3 1398 12 0.85 861 371 30.04 0 0 NA 321258 TCGA-AB-3001 AML14 21 15502460 15502460 C T SNP - - - - - - - - - - - - - - - tier3 788 3 0.38 313 80 20.36 0 0 NA 321258 TCGA-AB-3001 AML14 21 19010745 19010745 C T SNP - - - - - - - - - - - - - - - tier3 1142 2 0.17 360 100 21.74 0 0 NA 321258 TCGA-AB-3001 AML14 21 21757444 21757444 G T SNP NCAM2 NM_004540.2 human genbank 54_36p 1 reviewed intronic c.1655-3354 e13-3354 0.486 - - - no_errors tier2 656 5 0.76 189 54 22.13 0 0 NA 321258 TCGA-AB-3001 AML14 21 21962097 21962097 G C SNP ENSG00000198434 ENST00000358086 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33177 NULL 0.001 - - - no_coding_region:pseudogene tier3 1245 14 1.11 526 162 23.55 0 0 NA 321258 TCGA-AB-3001 AML14 21 22360782 22360782 G A SNP C21orf74 ENST00000333482 human ensembl 54_36p 1 known 5_prime_flanking_region c.-42876 NULL 0 - - - no_errors tier3 617 5 0.8 163 60 26.91 0 0 NA 321258 TCGA-AB-3001 AML14 21 23244057 23244057 G A SNP - - - - - - - - - - - - - - - tier3 1148 7 0.61 371 136 26.82 0 0 NA 321258 TCGA-AB-3001 AML14 21 25062393 25062393 C A SNP - - - - - - - - - - - - - - - tier2 362 1 0.28 107 28 20.74 0 0 NA 321258 TCGA-AB-3001 AML14 21 25356011 25356011 T C SNP ENSG00000222567 ENST00000410635 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-39305 NULL 0.001 - - - no_errors tier3 878 6 0.68 207 77 27.11 0 0 NA 321258 TCGA-AB-3001 AML14 21 26236086 26236086 C T SNP APP NM_000484.2 human genbank 54_36p -1 reviewed intronic c.1687+12689 e13+12689 0 - - - no_errors tier3 1415 4 0.28 694 256 26.92 1 1 50 321258 TCGA-AB-3001 AML14 21 41854327 41854327 C T SNP ENSG00000207503 ENST00000384772 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21204 NULL 0 - - - no_errors tier3 1509 18 1.18 1186 252 17.52 0 0 NA 321258 TCGA-AB-3001 AML14 21 46266501 46266501 G A SNP LOC100133289 XM_001716625.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37115 NULL 0.572 - - - no_errors tier3 598 4 0.66 276 96 25.81 0 0 NA 321258 TCGA-AB-3001 AML14 22 37753508 37753508 C T SNP APOBEC3D ENST00000216099 human ensembl 54_36p 1 known intronic c.606-1806 e5-1806 0.003 - - - no_errors tier3 702 6 0.85 316 157 33.19 3 0 0 321258 TCGA-AB-3001 AML14 22 46198302 46198302 G A SNP ENSG00000218357 ENST00000405369 human ensembl 54_36p -1 known 3_prime_flanking_region c.*37804 NULL 0 - - - no_errors tier3 1134 1 0.09 801 333 29.37 0 0 NA 426980 TCGA-AB-3002 AML28 Y 5180662 5180681 TTAAGAGTTTAACTTACCAT - DEL PCDH11Y NM_032973.1 human genbank 54_36p 1 reviewed intronic c.3129+151914_3129+151895 e2+151914 0.017:0.019:0.026:0.030:0.032:0.030:0.028:0.026:0.022:0.018:0.014:0.009:0.003:0.002:0.003:0.004:0.004:0.004:0.003:0.002 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 X 6192868 6192868 G A SNP NLGN4X NM_020742.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-113361 NULL 0.063 - - - no_errors tier3 182 7 3.7 18 156 89.66 0 0 NA 426980 TCGA-AB-3002 AML28 X 7410725 7410725 G A SNP - - - - - - - - - - - - - - - tier3 329 9 2.66 32 292 90.12 0 0 NA 426980 TCGA-AB-3002 AML28 Y 8195097 8195097 G T SNP RBMY2KP ENST00000404997 human ensembl 54_36p -1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 261 4 1.51 16 224 93.33 0 0 NA 426980 TCGA-AB-3002 AML28 Y 8487910 8487910 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 X 10294020 10294021 - T INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 X 11680134 11680134 C G SNP MSL3 NM_078629.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6170 NULL 0.007 - - - no_errors tier3 92 2 2.11 4 28 87.5 0 0 NA 426980 TCGA-AB-3002 AML28 Y 16229629 16229629 G T SNP ENSG00000219842 ENST00000401713 human ensembl 54_36p 1 known 3_prime_flanking_region c.*15024 NULL 0.001 - - - no_coding_region:pseudogene tier3 261 2 0.76 248 98 28.32 0 0 NA 426980 TCGA-AB-3002 AML28 Y 16302321 16302321 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 X 17368749 17368749 T C SNP NHS NM_198270.2 human genbank 54_36p 1 reviewed intronic c.565+64383 e1+64383 0.973 - - - no_errors tier3 380 5 1.3 20 204 91.07 0 0 NA 426980 TCGA-AB-3002 AML28 X 24850996 24850996 G A SNP POLA1 NM_016937.2 human genbank 54_36p 1 validated intronic c.4147-7495 e36-7495 0 - - - no_errors tier3 NA NA NA NA NA NA 1 0 0 426980 TCGA-AB-3002 AML28 X 27447388 27447388 C T SNP ENSG00000217246 ENST00000405939 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*27447388 NULL 0.999 - - - no_coding_region:pseudogene tier3 199 9 4.33 37 230 83.64 2 0 0 426980 TCGA-AB-3002 AML28 X 29590698 29590698 C T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.704-5770 e5-5770 0 - - - no_errors tier3 284 7 2.39 11 78 87.64 0 0 NA 426980 TCGA-AB-3002 AML28 X 32121858 32121858 G C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6438+23096 e44+23096 0 - - - no_errors tier3 161 4 2.42 19 192 91 0 0 NA 426980 TCGA-AB-3002 AML28 X 33727134 33727134 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 X 34820105 34820105 T G SNP - - - - - - - - - - - - - - - tier3 244 5 2.01 22 151 87.28 0 0 NA 426980 TCGA-AB-3002 AML28 X 35245727 35245727 T C SNP - - - - - - - - - - - - - - - tier3 344 8 2.27 19 193 91.04 0 0 NA 426980 TCGA-AB-3002 AML28 X 55215216 55215216 G A SNP LOC100129876 XM_001715675.1 human genbank 54_36p 1 model silent c.105 p.E35 0.007 NULL HMMPfam_GAGE - no_errors tier1 238 3 1.24 21 146 87.43 NA 426980 TCGA-AB-3002 AML28 X 81797394 81797394 G T SNP - - - - - - - - - - - - - - - tier3 222 5 2.2 64 446 87.45 0 0 NA 426980 TCGA-AB-3002 AML28 X 86716242 86716242 T C SNP KLHL4 NM_057162.4 human genbank 54_36p 1 reviewed intronic c.423-39294 e2-39294 0 - - - no_errors tier3 81 3 3.57 10 139 92.67 0 0 NA 426980 TCGA-AB-3002 AML28 X 97913227 97913227 G T SNP - - - - - - - - - - - - - - - tier3 81 1 1.22 2 25 92.59 0 0 NA 426980 TCGA-AB-3002 AML28 X 105876728 105876728 G A SNP RNF128 NM_194463.3 human genbank 54_36p 1 reviewed intronic c.484+19445 e1+19445 0.002 - - - no_errors tier2 200 5 2.44 16 132 89.19 0 0 NA 426980 TCGA-AB-3002 AML28 X 117622824 117622824 G A SNP DOCK11 NM_144658.3 human genbank 54_36p 1 validated intronic c.2563-405 e24-405 0.001 - - - no_errors tier3 785 15 1.88 112 870 88.59 1 4 80 426980 TCGA-AB-3002 AML28 X 135789240 135789240 C A SNP RBMX NM_002139.2 human genbank 54_36p -1 reviewed missense c.13 p.D5Y 1 NULL "HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00361,HMMPfam_RBM1CTR,superfamily_RNA-binding domain RBD" - no_errors tier1 307 4 1.28 21 99 81.82 8 143 94.08 426980 TCGA-AB-3002 AML28 X 141024741 141024741 G T SNP ENSG00000217283 ENST00000402189 human ensembl 54_36p -1 known 3_prime_flanking_region c.*38573 NULL 0.457 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 X 143123430 143123430 A C SNP - - - - - - - - - - - - - - - tier3 274 9 3.18 21 226 91.5 0 0 NA 426980 TCGA-AB-3002 AML28 X 144114037 144114037 T A SNP SPANXN1 NM_001009614.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22762 NULL 0.017 - - - no_errors tier3 165 1 0.6 13 160 92.49 0 0 NA 426980 TCGA-AB-3002 AML28 1 3628599 3628599 C T SNP TP73 NM_005427.1 human genbank 54_36p 1 reviewed missense c.584 p.P195L 1 "superfamily_p53-like transcription factors,HMMPfam_P53" "HMMSmart_SM00454,PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,superfamily_SAM/Pointed domain,HMMPfam_SAM_2,HMMPfam_P53" - no_errors tier1 62 1 1.59 16 6 27.27 NA 426980 TCGA-AB-3002 AML28 1 8610857 8610857 C A SNP RERE NM_001042681.1 human genbank 54_36p -1 reviewed intronic c.326-3831 e2-3831 0.001 - - - no_errors tier3 765 7 0.91 278 208 42.8 1 1 50 426980 TCGA-AB-3002 AML28 1 18730737 18730737 C T SNP KLHDC7A NM_152375.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*48341 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 21472135 21472135 C T SNP ECE1 NM_001397.1 human genbank 54_36p -1 validated intronic c.281-144 e4-144 0 - - - no_errors tier2 421 0 0 84 78 48.15 0 2 100 426980 TCGA-AB-3002 AML28 1 22831628 22831628 C T SNP C1QB NM_000491.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26909 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 24106057 24106057 C T SNP CNR2 NM_001841.2 human genbank 54_36p -1 reviewed intronic c.1+6266 e0+6266 0.003 - - - no_errors tier2 517 7 1.33 139 103 42.56 0 0 NA 426980 TCGA-AB-3002 AML28 1 27746319 27746319 C T SNP AHDC1 NM_001029882.2 human genbank 54_36p -1 validated intronic c.4812+40 e1+40 0.029 - - - no_errors tier3 188 1 0.53 122 108 46.35 0 3 100 426980 TCGA-AB-3002 AML28 1 29998919 29998919 G T SNP - - - - - - - - - - - - - - - tier3 533 10 1.84 274 185 40.31 0 0 NA 426980 TCGA-AB-3002 AML28 1 32266340 32266340 G T SNP KHDRBS1 NM_006559.1 human genbank 54_36p 1 provisional intronic c.383-2146 e2-2146 0.001 - - - no_errors tier3 266 0 0 40 28 41.18 0 0 0 426980 TCGA-AB-3002 AML28 1 34313330 34313330 G A SNP CSMD2 NM_052896.3 human genbank 54_36p -1 validated intronic c.284+13835 e2+13835 0.002 - - - no_errors tier3 698 3 0.43 351 301 46.09 0 0 NA 426980 TCGA-AB-3002 AML28 1 38002399 38002399 C T SNP EPHA10 NM_001099439.1 human genbank 54_36p -1 validated intronic c.106+821 e1+821 0.156 - - - no_errors tier2 1497 12 0.79 205 122 37.31 0 0 NA 426980 TCGA-AB-3002 AML28 1 41706896 41706896 T C SNP ENSG00000210279 ENST00000387544 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1611 NULL 0.002 - - - pseudogene tier3 264 2 0.75 183 111 37.76 0 0 NA 426980 TCGA-AB-3002 AML28 1 44238718 44238718 C T SNP SLC6A9 NM_201649.1 human genbank 54_36p -1 validated intronic c.1755+308 e12+308 0.03 - - - no_errors tier3 544 7 1.27 332 260 43.84 0 0 NA 426980 TCGA-AB-3002 AML28 1 46486887 46486887 G A SNP RAD54L NM_003579.1 human genbank 54_36p 1 reviewed intronic c.90+30 e2+30 0.001 - - - no_errors tier3 135 1 0.74 61 41 40.2 2 0 0 426980 TCGA-AB-3002 AML28 1 49353893 49353893 G A SNP AGBL4 ENST00000371839 human ensembl 54_36p -1 known intronic c.378-69834 e5-69834 0 - - - no_errors tier3 534 6 1.11 249 199 44.42 0 0 NA 426980 TCGA-AB-3002 AML28 1 57959013 57959013 G A SNP DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.1-71088 e1-71088 0 - - - no_errors tier3 684 9 1.3 190 131 40.68 0 0 NA 426980 TCGA-AB-3002 AML28 1 58062591 58062591 G A SNP DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.1+59668 e0+59668 0.003 - - - no_errors tier3 483 5 1.02 397 277 41.1 0 0 NA 426980 TCGA-AB-3002 AML28 1 62517067 62517067 T C SNP KANK4 NM_181712.4 human genbank 54_36p -1 validated intronic c.16+2742 e1+2742 0 - - - no_errors tier3 1006 9 0.89 381 323 45.88 0 0 NA 426980 TCGA-AB-3002 AML28 1 64758033 64758033 A G SNP CACHD1 NM_020925.2 human genbank 54_36p 1 validated intronic c.46-30832 e2-30832 0.002 - - - no_errors tier3 699 7 0.99 152 96 38.71 0 0 NA 426980 TCGA-AB-3002 AML28 1 66455603 66455603 C T SNP PDE4B NM_001037341.1 human genbank 54_36p 1 reviewed intronic c.282-30128 e3-30128 0.006 - - - no_errors tier3 1302 7 0.53 805 620 43.42 0 0 NA 426980 TCGA-AB-3002 AML28 1 68003365 68003365 T G SNP GNG12 NM_018841.4 human genbank 54_36p -1 validated intronic c.1+12364 e0+12364 0 - - - no_errors tier3 205 3 1.44 22 40 64.52 0 0 NA 426980 TCGA-AB-3002 AML28 1 70011661 70011661 G C SNP LRRC7 NM_020794.2 human genbank 54_36p 1 validated intronic c.189+12997 e1+12997 0.002 - - - no_errors tier3 399 3 0.75 434 318 42.23 0 0 NA 426980 TCGA-AB-3002 AML28 1 70313793 70313793 C T SNP LRRC7 NM_020794.2 human genbank 54_36p 1 validated intronic c.4117-555 e22-555 0 - - - no_errors tier3 469 3 0.63 251 174 40.85 0 0 NA 426980 TCGA-AB-3002 AML28 1 72971329 72971329 T G SNP ENSG00000212366 ENST00000391064 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-15289 NULL 0.001 - - - no_errors tier3 151 0 0 36 40 52.63 0 0 NA 426980 TCGA-AB-3002 AML28 1 76285296 76285296 C T SNP LOC729766 XM_001131228.1 human genbank 54_36p 1 model intronic c.463+5125 e3+5125 0 - - - no_errors tier3 547 1 0.18 517 445 46.26 0 0 NA 426980 TCGA-AB-3002 AML28 1 78098735 78098735 G A SNP FAM73A NM_198549.2 human genbank 54_36p 1 predicted intronic c.1275+336 e11+336 0 - - - no_errors tier3 504 10 1.95 238 199 45.54 3 0 0 426980 TCGA-AB-3002 AML28 1 80262063 80262063 C A SNP - - - - - - - - - - - - - - - tier3 251 4 1.57 96 69 41.82 0 0 NA 426980 TCGA-AB-3002 AML28 1 82981466 82981466 T G SNP - - - - - - - - - - - - - - - tier3 184 0 0 63 38 37.62 0 0 NA 426980 TCGA-AB-3002 AML28 1 87284832 87284832 C A SNP ENSG00000219673 ENST00000407455 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*87284832 NULL 1 - - - no_coding_region:pseudogene tier2 175 3 1.68 184 131 41.59 36 1 2.7 426980 TCGA-AB-3002 AML28 1 89433568 89433568 C A SNP GBP4 NM_052941.4 human genbank 54_36p -1 validated missense c.363 p.K121N 1 "HMMPfam_GBP,superfamily_SSF52540" "HMMPfam_GBP_C,HMMPfam_GBP,superfamily_GBP,superfamily_SSF52540" - no_errors tier1 NA NA NA NA NA NA 35 0 426980 TCGA-AB-3002 AML28 1 91498853 91498853 C T SNP ENSG00000206817 ENST00000384090 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-917 NULL 0.183 - - - no_errors tier2 77 0 0 36 34 48.57 0 0 NA 426980 TCGA-AB-3002 AML28 1 96777968 96777968 G A SNP ENSG00000211377 ENST00000388642 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-43388 NULL 0 - - - pseudogene tier3 631 10 1.56 498 349 41.2 0 0 NA 426980 TCGA-AB-3002 AML28 1 99828834 99828834 G A SNP - - - - - - - - - - - - - - - tier3 511 2 0.39 366 237 39.3 0 0 NA 426980 TCGA-AB-3002 AML28 1 101393361 101393361 C T SNP ENSG00000212577 ENST00000391275 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21878 NULL 0.972 - - - no_errors tier2 1063 7 0.65 523 377 41.89 0 0 NA 426980 TCGA-AB-3002 AML28 1 105143735 105143735 C G SNP - - - - - - - - - - - - - - - tier3 943 9 0.94 690 554 44.36 0 0 NA 426980 TCGA-AB-3002 AML28 1 118156398 118156398 C T SNP LOC100131261 XM_001720964.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-33747 NULL 0.006 - - - no_errors tier2 293 3 1.01 259 201 43.41 0 0 NA 426980 TCGA-AB-3002 AML28 1 119892131 119892131 G T SNP LOC644213 XR_016570.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10445 NULL 0.002 - - - pseudogene tier3 NA NA NA 1 0 0 0 0 NA 426980 TCGA-AB-3002 AML28 1 145465273 145465273 A C SNP BCL9 NM_004326.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-84987 NULL 0.006 - - - no_errors tier3 847 6 0.7 428 385 47.18 0 0 NA 426980 TCGA-AB-3002 AML28 1 145742928 145742928 G A SNP GJA5 NM_005266.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-44958 NULL 0.9 - - - no_errors tier3 451 4 0.88 304 207 40.51 0 0 NA 426980 TCGA-AB-3002 AML28 1 149937379 149937380 TC - DEL SNX27 NM_030918.5 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*4678 NULL 0.010:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 151632796 151632796 G A SNP S100A8 NM_002964.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3161 NULL 0.001 - - - no_errors tier3 697 11 1.54 505 349 40.87 0 0 NA 426980 TCGA-AB-3002 AML28 1 154189110 154189110 G T SNP ARHGEF2 NM_004723.2 human genbank 54_36p -1 reviewed silent c.1833 p.G611 0.971 NULL "HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_PH,HMMSmart_SM00233,HMMPfam_C1_1,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,superfamily_PH domain-like,superfamily_Cysteine-rich domain" - no_errors tier1 558 8 1.41 294 238 44.65 48 57 54.29 426980 TCGA-AB-3002 AML28 1 162390535 162390535 A G SNP - - - - - - - - - - - - - - - tier3 1309 14 1.06 599 481 44.54 0 0 NA 426980 TCGA-AB-3002 AML28 1 164527242 164527242 C T SNP LOC284685 XR_017685.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-13735 NULL 0.218 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 168963347 168963347 G A SNP PRRX1 NM_022716.3 human genbank 54_36p 1 reviewed intronic c.599+1181 e3+1181 0 - - - no_errors tier3 467 5 1.06 100 72 41.86 0 0 NA 426980 TCGA-AB-3002 AML28 1 175508370 175508370 C T SNP FAM5B NM_021165.2 human genbank 54_36p 1 provisional intronic c.670-877 e4-877 0.014 - - - no_errors tier3 454 5 1.09 301 247 45.07 0 0 NA 426980 TCGA-AB-3002 AML28 1 181141559 181141559 C T SNP C1orf14 NM_030933.2 human genbank 54_36p -1 validated intronic c.1183-152 e7-152 0.002 - - - no_errors tier3 220 0 0 130 99 43.04 0 0 NA 426980 TCGA-AB-3002 AML28 1 182353408 182353408 G C SNP TSEN15 NM_052965.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*44804 NULL 0.047 - - - no_errors tier3 543 6 1.09 345 246 41.62 0 1 100 426980 TCGA-AB-3002 AML28 1 184219659 184219659 A G SNP HMCN1 NM_031935.2 human genbank 54_36p 1 reviewed intronic c.2791-265 e19-265 0 - - - no_errors tier3 136 3 2.16 73 47 39.17 0 0 NA 426980 TCGA-AB-3002 AML28 1 185120932 185120932 G A SNP PLA2G4A NM_024420.2 human genbank 54_36p 1 reviewed intronic c.116-7834 e3-7834 0 - - - no_errors tier2 787 16 1.99 717 558 43.7 0 3 100 426980 TCGA-AB-3002 AML28 1 187595261 187595261 T C SNP - - - - - - - - - - - - - - - tier3 262 0 0 101 88 46.56 0 0 NA 426980 TCGA-AB-3002 AML28 1 187909251 187909251 G A SNP - - - - - - - - - - - - - - - tier3 244 5 2.01 90 88 49.44 0 0 NA 426980 TCGA-AB-3002 AML28 1 199529289 199529289 G A SNP PKP1 NM_000299.2 human genbank 54_36p 1 reviewed intronic c.203-404 e2-404 0 - - - no_errors tier3 864 12 1.37 248 203 45.01 0 0 NA 426980 TCGA-AB-3002 AML28 1 201235198 201235198 G A SNP TMEM183A NM_138391.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-8019 NULL 0.135 - - - no_errors tier2 493 9 1.79 126 105 45.26 0 0 NA 426980 TCGA-AB-3002 AML28 1 204839488 204839488 T C SNP LGTN NM_006893.2 human genbank 54_36p -1 reviewed missense c.1154 p.Y385C 1 superfamily_SWIB/MDM2 domain "HMMPfam_SUI1,superfamily_eIF1-like,HMMSmart_SM00359,superfamily_SWIB/MDM2 domain,superfamily_PUA domain-like" - no_errors tier1 539 11 2 335 305 47.51 47 50 51.55 426980 TCGA-AB-3002 AML28 1 207753849 207753849 G T SNP - - - - - - - - - - - - - - - tier2 1103 16 1.43 709 519 42.23 0 0 NA 426980 TCGA-AB-3002 AML28 1 211654724 211654724 T C SNP LOC643330 XM_926662.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*13950 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 212037538 212037538 C T SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 214814537 214814537 G A SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.590-6474 e4-6474 0 - - - no_errors tier3 245 2 0.81 77 58 42.96 0 0 NA 426980 TCGA-AB-3002 AML28 1 214823009 214823010 - A INS ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.590-14947_590-14946 e4-14946 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 215053873 215053873 G A SNP ESRRG NM_206594.1 human genbank 54_36p -1 validated intronic c.1+51153 e0+51153 0.99 - - - no_errors tier2 452 3 0.66 375 201 34.78 0 0 NA 426980 TCGA-AB-3002 AML28 1 216303921 216303921 T C SNP - - - - - - - - - - - - - - - tier2 635 8 1.24 287 202 41.22 0 0 NA 426980 TCGA-AB-3002 AML28 1 220229180 220229180 A C SNP ENSG00000212094 ENST00000390805 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23792 NULL 0.001 - - - no_errors tier3 1089 4 0.37 538 436 44.72 0 0 NA 426980 TCGA-AB-3002 AML28 1 224891642 224891642 G A SNP ITPKB NM_002221.3 human genbank 54_36p -1 reviewed intronic c.2625+361 e6+361 0.009 - - - no_errors tier2 NA NA NA NA NA NA 3 1 25 426980 TCGA-AB-3002 AML28 1 231376911 231376911 T A SNP PCNXL2 NM_014801.3 human genbank 54_36p -1 provisional intronic c.3273+3260 e17+3260 0.001 - - - no_errors tier3 248 1 0.4 111 99 47.14 0 0 0 426980 TCGA-AB-3002 AML28 1 231645734 231645734 G A SNP - - - - - - - - - - - - - - - tier3 522 9 1.69 199 136 40.6 0 0 NA 426980 TCGA-AB-3002 AML28 1 234870833 234870833 A G SNP ACTN2 NM_001103.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45764 NULL 0 - - - no_errors tier3 717 19 2.58 790 314 28.44 1 0 0 426980 TCGA-AB-3002 AML28 1 235735186 235735186 G A SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.2614-1447 e23-1447 0.001 - - - no_errors tier3 1 0 0 NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 1 236046085 236046085 C T SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.14434-2874 e101-2874 0.066 - - - no_errors tier2 274 1 0.36 237 211 47.1 0 0 NA 426980 TCGA-AB-3002 AML28 1 238987024 238987024 G A SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*19062 NULL 0 - - - no_errors tier3 296 3 1 146 140 48.95 0 0 NA 426980 TCGA-AB-3002 AML28 1 240678783 240678783 G A SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.1+75230 e0+75230 0.809 - - - no_errors tier3 627 0 0 305 230 42.99 0 0 NA 426980 TCGA-AB-3002 AML28 1 246896247 246896247 G A SNP OR2T35 NM_001001827.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-27065 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 680769 680769 C A SNP TMEM18 NM_152834.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-13424 NULL 0.004 - - - no_errors tier2 350 2 0.57 154 102 39.84 0 0 NA 426980 TCGA-AB-3002 AML28 2 2694285 2694285 G A SNP - - - - - - - - - - - - - - - tier3 823 3 0.36 339 281 45.25 0 0 NA 426980 TCGA-AB-3002 AML28 2 3907608 3907608 G A SNP - - - - - - - - - - - - - - - tier2 568 9 1.56 193 187 49.21 0 0 NA 426980 TCGA-AB-3002 AML28 2 4771422 4771422 C T SNP - - - - - - - - - - - - - - - tier3 381 8 2.05 430 386 47.19 0 0 NA 426980 TCGA-AB-3002 AML28 2 4951026 4951026 G T SNP ENSG00000207192 ENST00000384463 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19716 NULL 0 - - - no_errors tier3 1 0 0 NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 7652223 7652223 A T SNP ENSG00000221255 ENST00000408328 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*17677 NULL 0.004 - - - no_errors tier3 389 5 1.27 201 156 43.7 0 0 NA 426980 TCGA-AB-3002 AML28 2 10820130 10820130 C T SNP ATP6V1C2 NM_001039362.1 human genbank 54_36p 1 reviewed intronic c.284-1778 e4-1778 0.002 - - - no_errors tier3 568 10 1.73 275 231 45.65 0 0 NA 426980 TCGA-AB-3002 AML28 2 15628354 15628354 A G SNP DDX1 NM_004939.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-21155 NULL 0.024 - - - no_errors tier3 965 5 0.52 300 230 43.4 1 0 0 426980 TCGA-AB-3002 AML28 2 15674817 15674817 A G SNP DDX1 NM_004939.1 human genbank 54_36p 1 reviewed splice_site c.1018-2 e15-2 0.994 - - - no_errors tier1 143 0 75 60 44.44 3 100 426980 TCGA-AB-3002 AML28 2 18760057 18760057 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 21961328 21961328 C T SNP ENSG00000222621 ENST00000410689 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-38042 NULL 0 - - - no_errors tier3 722 5 0.69 491 382 43.76 0 0 NA 426980 TCGA-AB-3002 AML28 2 22019866 22019866 T A SNP ENSG00000222621 ENST00000410689 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*20200 NULL 0 - - - no_errors tier3 261 3 1.14 104 94 47.47 0 0 NA 426980 TCGA-AB-3002 AML28 2 22214628 22214628 G A SNP - - - - - - - - - - - - - - - tier3 556 5 0.89 409 247 37.6 0 0 NA 426980 TCGA-AB-3002 AML28 2 24234854 24234854 G A SNP C2orf84 ENST00000407625 human ensembl 54_36p 1 known intronic c.687-3026 e7-3026 0.001 - - - no_errors tier3 425 8 1.85 221 130 37.04 2 1 33.33 426980 TCGA-AB-3002 AML28 2 31964830 31964830 C T SNP MEMO1 NM_015955.1 human genbank 54_36p -1 validated intronic c.581-2795 e7-2795 0.019 - - - no_errors tier3 282 3 1.05 83 52 38.24 1 7 87.5 426980 TCGA-AB-3002 AML28 2 35393942 35393942 G C SNP - - - - - - - - - - - - - - - tier3 628 10 1.57 293 294 49.92 0 0 NA 426980 TCGA-AB-3002 AML28 2 35447877 35447877 G A SNP - - - - - - - - - - - - - - - tier3 567 7 1.21 247 157 38.77 0 0 NA 426980 TCGA-AB-3002 AML28 2 39866687 39866687 A C SNP THUMPD2 NM_025264.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-6894 NULL 0.006 - - - no_errors tier3 891 12 1.33 517 396 43.37 0 0 NA 426980 TCGA-AB-3002 AML28 2 41983085 41983085 A C SNP ENSG00000207218 ENST00000384489 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45069 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 43412218 43412218 C G SNP THADA NM_001083953.1 human genbank 54_36p -1 validated intronic c.4344-11035 e30-11035 0.001 - - - no_errors tier2 1138 13 1.13 643 564 46.65 3 1 25 426980 TCGA-AB-3002 AML28 2 45349654 45349654 C G SNP ENSG00000205054 ENST00000378479 human ensembl 54_36p -1 known 5_prime_flanking_region c.-78029 NULL 0.008 - - - no_errors tier3 371 2 0.54 260 244 48.22 0 0 NA 426980 TCGA-AB-3002 AML28 2 50855382 50855382 C T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.832+147129 e4+147129 0 - - - no_errors tier3 640 3 0.47 369 60 13.95 0 0 NA 426980 TCGA-AB-3002 AML28 2 51590347 51590347 T C SNP ENSG00000220872 ENST00000405610 human ensembl 54_36p 1 known 5_prime_flanking_region c.-1353 NULL 0.001 - - - no_coding_region:pseudogene tier3 631 5 0.79 326 264 44.59 0 0 NA 426980 TCGA-AB-3002 AML28 2 52337923 52337923 G A SNP ENSG00000202195 ENST00000365325 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-40714 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 53366757 53366757 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 57473570 57473570 T G SNP - - - - - - - - - - - - - - - tier3 355 2 0.56 170 150 46.73 0 0 NA 426980 TCGA-AB-3002 AML28 2 59919013 59919013 G A SNP LOC100133826 XM_001719055.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-7102 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 625 5 0.79 382 322 45.74 0 0 NA 426980 TCGA-AB-3002 AML28 2 73389479 73389479 G A SNP EGR4 NM_001965.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-15526 NULL 0 - - - no_errors tier2 967 7 0.72 707 587 45.36 0 0 NA 426980 TCGA-AB-3002 AML28 2 77814007 77814007 G A SNP - - - - - - - - - - - - - - - tier3 639 11 1.69 255 204 44.35 0 0 NA 426980 TCGA-AB-3002 AML28 2 79379094 79379094 C T SNP LOC100132577 XM_001726289.1 human genbank 54_36p 1 model intronic c.1+5183 e0+5183 0.001 - - - no_errors tier3 730 2 0.27 482 348 41.93 0 0 NA 426980 TCGA-AB-3002 AML28 2 95091162 95091162 C T SNP LOC100131662 XM_001716469.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-36285 NULL 0.001 - - - no_errors tier3 856 9 1.04 585 409 41.06 0 0 NA 426980 TCGA-AB-3002 AML28 2 95145242 95145242 T C SNP MRPS5 NM_031902.3 human genbank 54_36p -1 reviewed intronic c.140-567 e3-567 0.003 - - - no_errors tier3 324 0 0 161 101 38.55 0 0 0 426980 TCGA-AB-3002 AML28 2 100847570 100847570 A G SNP NPAS2 NM_002518.3 human genbank 54_36p 1 reviewed intronic c.1-40057 e1-40057 0.001 - - - no_errors tier3 405 4 0.98 379 312 45.09 0 0 NA 426980 TCGA-AB-3002 AML28 2 103280182 103280182 C T SNP - - - - - - - - - - - - - - - tier3 437 7 1.57 194 153 44.09 0 0 NA 426980 TCGA-AB-3002 AML28 2 104101578 104101578 C G SNP LOC728838 XM_001128590.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*24719 NULL 0 - - - no_errors tier3 687 4 0.58 362 283 43.81 0 0 NA 426980 TCGA-AB-3002 AML28 2 114769762 114769762 G A SNP ENSG00000208615 ENST00000385880 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14540 NULL 0 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 115512252 115512252 T A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.61-271033 e2-271033 0.002 - - - no_errors tier3 110 3 2.65 39 33 45.83 0 0 NA 426980 TCGA-AB-3002 AML28 2 116413903 116413903 A G SNP - - - - - - - - - - - - - - - tier3 478 3 0.62 158 109 40.82 0 0 NA 426980 TCGA-AB-3002 AML28 2 117169781 117169781 C T SNP - - - - - - - - - - - - - - - tier3 195 0 0 98 67 40.61 0 0 NA 426980 TCGA-AB-3002 AML28 2 117243344 117243344 T A SNP - - - - - - - - - - - - - - - tier3 274 1 0.36 136 97 41.63 0 0 NA 426980 TCGA-AB-3002 AML28 2 117285122 117285122 C T SNP - - - - - - - - - - - - - - - tier3 160 1 0.62 16 14 46.67 0 0 NA 426980 TCGA-AB-3002 AML28 2 118858220 118858220 G A SNP - - - - - - - - - - - - - - - tier2 869 11 1.25 614 460 42.83 0 0 NA 426980 TCGA-AB-3002 AML28 2 118907970 118907970 C T SNP - - - - - - - - - - - - - - - tier3 340 4 1.16 246 178 40.18 0 0 NA 426980 TCGA-AB-3002 AML28 2 121245170 121245170 G A SNP GLI2 NM_005270.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26197 NULL 0.003 - - - no_errors tier3 1264 10 0.78 367 309 45.64 0 0 NA 426980 TCGA-AB-3002 AML28 2 125456109 125456109 T C SNP ENSG00000206726 ENST00000383999 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7157 NULL 0.068 - - - no_errors tier3 697 8 1.13 195 167 46.13 0 0 NA 426980 TCGA-AB-3002 AML28 2 130861607 130861607 C A SNP CCDC115 NM_032357.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-45439 NULL 0.001 - - - no_errors tier3 465 6 1.27 213 184 46.23 0 0 NA 426980 TCGA-AB-3002 AML28 2 135984521 135984521 G A SNP ZRANB3 NM_032143.2 human genbank 54_36p -1 provisional intronic c.1-5985 e1-5985 0.618 - - - no_errors tier3 536 6 1.11 312 269 46.22 0 0 0 426980 TCGA-AB-3002 AML28 2 137572784 137572784 C T SNP THSD7B NM_001080427.1 human genbank 54_36p 1 provisional intronic c.1106+3623 e3+3623 0 - - - no_errors tier3 348 3 0.85 324 263 44.8 0 0 NA 426980 TCGA-AB-3002 AML28 2 137663285 137663285 C T SNP THSD7B NM_001080427.1 human genbank 54_36p 1 provisional intronic c.1630+18307 e6+18307 0.002 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 137781520 137781520 C T SNP THSD7B NM_001080427.1 human genbank 54_36p 1 provisional intronic c.2407+31454 e11+31454 0.001 - - - no_errors tier3 370 0 0 522 370 41.43 0 0 NA 426980 TCGA-AB-3002 AML28 2 142683503 142683503 T C SNP - - - - - - - - - - - - - - - tier3 408 5 1.2 282 205 42.09 0 0 NA 426980 TCGA-AB-3002 AML28 2 143270836 143270836 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 150797796 150797796 G C SNP - - - - - - - - - - - - - - - tier3 881 6 0.68 495 479 49.18 0 0 NA 426980 TCGA-AB-3002 AML28 2 153951142 153951142 T C SNP LOC391453 XM_001717379.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*15369 NULL 0 - - - no_errors tier3 530 7 1.3 303 244 44.2 0 0 NA 426980 TCGA-AB-3002 AML28 2 154172284 154172284 T G SNP - - - - - - - - - - - - - - - tier2 281 5 1.74 113 114 50.22 0 0 NA 426980 TCGA-AB-3002 AML28 2 163820542 163820542 C T SNP ENSG00000200902 ENST00000364032 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-33209 NULL 0.003 - - - no_errors tier3 599 3 0.5 284 240 45.8 0 0 NA 426980 TCGA-AB-3002 AML28 2 164530487 164530487 C T SNP - - - - - - - - - - - - - - - tier3 907 5 0.55 528 302 36.39 0 0 NA 426980 TCGA-AB-3002 AML28 2 165928971 165928971 G A SNP SCN2A NM_001040142.1 human genbank 54_36p 1 reviewed intronic c.3400-928 e17-928 0.945 - - - no_errors tier2 589 7 1.17 392 322 45.1 0 0 NA 426980 TCGA-AB-3002 AML28 2 172605263 172605263 T A SNP MAP1D NM_199227.1 human genbank 54_36p 1 validated intronic c.41-29209 e2-29209 0.997 - - - no_errors tier2 483 8 1.63 154 138 47.26 0 0 0 426980 TCGA-AB-3002 AML28 2 176491050 176491051 - T INS KIAA1715 NM_030650.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*11891 NULL 0.002:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 183982209 183982209 G A SNP - - - - - - - - - - - - - - - tier3 401 4 0.99 191 161 45.74 0 0 NA 426980 TCGA-AB-3002 AML28 2 185544371 185544371 T G SNP ZNF804A NM_194250.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*32373 NULL 0 - - - no_errors tier3 237 1 0.42 63 49 43.75 0 0 NA 426980 TCGA-AB-3002 AML28 2 189386034 189386034 T C SNP DIRC1 NM_052952.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-78142 NULL 0.002 - - - no_errors tier2 439 0 0 337 247 42.22 0 0 NA 426980 TCGA-AB-3002 AML28 2 196389158 196389158 C T SNP DNAH7 NM_018897.2 human genbank 54_36p -1 validated intronic c.9761+439 e51+439 0.015 - - - no_errors tier3 211 0 0 48 20 29.41 0 0 NA 426980 TCGA-AB-3002 AML28 2 196910181 196910181 G A SNP HECW2 NM_020760.1 human genbank 54_36p -1 provisional intronic c.401-2694 e3-2694 0.007 - - - no_errors tier3 310 4 1.27 147 115 43.73 0 0 NA 426980 TCGA-AB-3002 AML28 2 210309605 210309605 C T SNP C2orf21 NM_182587.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-35437 NULL 0.074 - - - no_errors tier3 621 2 0.32 394 279 41.39 0 0 NA 426980 TCGA-AB-3002 AML28 2 212678019 212678019 G A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.234+19703 e2+19703 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 215281284 215281284 C T SNP BARD1 NM_000465.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*20361 NULL 0.001 - - - no_errors tier2 499 3 0.6 504 347 40.73 0 0 NA 426980 TCGA-AB-3002 AML28 2 215847666 215847666 C T SNP ATIC NM_004044.5 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37445 NULL 0 - - - no_errors tier3 492 5 1 186 173 48.19 0 0 NA 426980 TCGA-AB-3002 AML28 2 217491643 217491643 G T SNP - - - - - - - - - - - - - - - tier3 996 10 0.99 423 333 43.99 0 0 NA 426980 TCGA-AB-3002 AML28 2 219997497 219997497 C T SNP DES NM_001927.3 human genbank 54_36p 1 reviewed intronic c.1288+711 e7+711 0.069 - - - no_errors tier3 620 4 0.64 191 158 45.27 0 0 0 426980 TCGA-AB-3002 AML28 2 224034377 224034377 G A SNP - - - - - - - - - - - - - - - tier3 918 11 1.18 311 186 37.42 0 0 NA 426980 TCGA-AB-3002 AML28 2 229682363 229682363 T C SNP PID1 NM_017933.1 human genbank 54_36p -1 validated intronic c.270+46415 e2+46415 0.524 - - - no_errors tier2 327 2 0.61 304 228 42.78 0 0 NA 426980 TCGA-AB-3002 AML28 2 233837397 233837397 C T SNP ATG16L1 NM_030803.3 human genbank 54_36p 1 validated silent c.336 p.D112 1 "superfamily_WD40 repeat-like,HMMPfam_ATG16" "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_ATG16,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 519 9 1.7 133 116 46.59 29 6 17.14 426980 TCGA-AB-3002 AML28 2 234415280 234415280 G A SNP HJURP NM_018410.3 human genbank 54_36p -1 validated silent c.885 p.S295 0 NULL NULL - no_errors tier1 486 4 0.82 335 271 44.65 15 9 37.5 426980 TCGA-AB-3002 AML28 2 234881052 234881052 T G SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 2 235085997 235085997 G T SNP ARL4C NM_005737.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-16028 NULL 0 - - - no_errors tier3 482 9 1.83 263 178 40.27 0 0 NA 426980 TCGA-AB-3002 AML28 2 239854071 239854071 T A SNP HDAC4 NM_006037.3 human genbank 54_36p -1 reviewed intronic c.23-30774 e2-30774 0.025 - - - no_errors tier3 1 0 0 NA NA NA 1 0 0 426980 TCGA-AB-3002 AML28 3 262560 262560 G C SNP CHL1 NM_006614.2 human genbank 54_36p 1 reviewed intronic c.1+1185 e0+1185 0.003 - - - no_errors tier3 403 0 0 241 67 21.75 0 0 NA 426980 TCGA-AB-3002 AML28 3 3039744 3039744 G T SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.1487-3042 e12-3042 0.999 - - - no_errors tier2 411 1 0.24 177 120 40.4 0 0 NA 426980 TCGA-AB-3002 AML28 3 6235039 6235039 G A SNP - - - - - - - - - - - - - - - tier3 268 2 0.74 168 132 43.85 0 0 NA 426980 TCGA-AB-3002 AML28 3 8239084 8239084 C - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 3 14810375 14810375 A G SNP FGD5 NM_152536.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25931 NULL 0 - - - no_errors tier3 526 2 0.38 240 186 43.56 0 0 NA 426980 TCGA-AB-3002 AML28 3 22266290 22266290 T G SNP - - - - - - - - - - - - - - - tier3 255 2 0.78 121 70 36.65 0 0 NA 426980 TCGA-AB-3002 AML28 3 26130020 26130020 G A SNP - - - - - - - - - - - - - - - tier3 861 10 1.15 642 518 44.66 0 0 0 426980 TCGA-AB-3002 AML28 3 26421838 26421838 C A SNP - - - - - - - - - - - - - - - tier2 681 1 0.15 467 79 14.44 0 0 NA 426980 TCGA-AB-3002 AML28 3 26492879 26492879 G A SNP - - - - - - - - - - - - - - - tier3 203 2 0.97 65 48 42.48 0 0 NA 426980 TCGA-AB-3002 AML28 3 42451811 42451811 T A SNP LYZL4 NM_144634.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-28064 NULL 0.008 - - - no_errors tier2 377 3 0.79 141 128 47.58 0 0 NA 426980 TCGA-AB-3002 AML28 3 45063478 45063478 G A SNP CDCP1 NM_022842.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*38656 NULL 0.005 - - - no_errors tier3 558 5 0.89 92 74 44.31 0 0 NA 426980 TCGA-AB-3002 AML28 3 48451865 48451865 G T SNP CCDC51 NM_024661.3 human genbank 54_36p -1 validated intronic c.1-315 e1-315 0 - - - no_errors tier2 609 1 0.16 172 112 39.44 1 0 0 426980 TCGA-AB-3002 AML28 3 61788317 61788320 TCTA - DEL PTPRG NM_002841.3 human genbank 54_36p 1 reviewed intronic c.190+78621_190+78618 e2+78621 0.000:0.000:0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 3 63494420 63494420 G A SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated intronic c.150-22839 e3-22839 0 - - - no_errors tier3 751 5 0.66 495 336 40.43 0 0 NA 426980 TCGA-AB-3002 AML28 3 64963656 64963656 T C SNP - - - - - - - - - - - - - - - tier3 155 1 0.64 44 54 55.1 0 0 NA 426980 TCGA-AB-3002 AML28 3 65861094 65861094 G A SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.313+137617 e1+137617 0 - - - no_errors tier3 766 4 0.52 623 483 43.67 0 0 NA 426980 TCGA-AB-3002 AML28 3 74634133 74634133 A C SNP CNTN3 NM_020872.1 human genbank 54_36p -1 validated intronic c.56-2507 e2-2507 0.001 - - - no_errors tier3 211 1 0.47 108 95 46.57 0 0 NA 426980 TCGA-AB-3002 AML28 3 76207102 76207102 G A SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.109+137659 e1+137659 0.003 - - - no_stop_codon:overly_large_intron tier3 337 0 0 276 222 44.58 0 0 NA 426980 TCGA-AB-3002 AML28 3 77104007 77104007 C G SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known intronic c.110-125848 e2-125848 0.018 - - - no_stop_codon:overly_large_intron tier3 199 3 1.49 86 79 47.88 0 0 NA 426980 TCGA-AB-3002 AML28 3 77340936 77340936 T C SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.388+110755 e2+110755 0.003 - - - no_errors tier3 158 1 0.63 48 43 47.25 0 0 NA 426980 TCGA-AB-3002 AML28 3 79101379 79101379 T C SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.173-30612 e3-30612 0.034 - - - no_errors tier3 341 2 0.58 184 136 42.37 0 0 NA 426980 TCGA-AB-3002 AML28 3 79270545 79270545 A G SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-13166 e2-13166 0.033 - - - no_errors tier3 101 1 0.98 29 43 59.72 0 0 NA 426980 TCGA-AB-3002 AML28 3 79386961 79386961 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-129582 e2-129582 0 - - - no_errors tier3 556 2 0.36 426 308 41.96 0 0 NA 426980 TCGA-AB-3002 AML28 3 79742487 79742487 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20736 NULL 0.074 - - - no_errors tier2 364 4 1.08 279 203 42.12 0 0 NA 426980 TCGA-AB-3002 AML28 3 80681007 80681007 A C SNP - - - - - - - - - - - - - - - tier3 571 9 1.55 353 291 45.19 0 0 NA 426980 TCGA-AB-3002 AML28 3 81690458 81690458 C T SNP GBE1 NM_000158.3 human genbank 54_36p -1 reviewed intronic c.1618+19308 e12+19308 0.002 - - - no_errors tier3 314 2 0.63 152 140 47.95 1 0 0 426980 TCGA-AB-3002 AML28 3 85130818 85130818 G C SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+39309 e1+39309 0 - - - no_errors tier2 306 2 0.65 125 83 39.9 0 0 NA 426980 TCGA-AB-3002 AML28 3 86508462 86508462 C G SNP ENSG00000222934 ENST00000411002 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*14152 NULL 0.007 - - - no_errors tier3 785 7 0.88 418 272 39.36 0 0 NA 426980 TCGA-AB-3002 AML28 3 96034176 96034176 G A SNP - - - - - - - - - - - - - - - tier3 372 3 0.8 181 128 41.29 0 0 NA 426980 TCGA-AB-3002 AML28 3 96785074 96785074 G A SNP - - - - - - - - - - - - - - - tier3 242 1 0.41 118 58 32.95 0 0 NA 426980 TCGA-AB-3002 AML28 3 96825543 96825543 A C SNP - - - - - - - - - - - - - - - tier3 260 4 1.52 108 119 52.42 0 0 NA 426980 TCGA-AB-3002 AML28 3 97423737 97423737 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 3 104548908 104548908 G A SNP - - - - - - - - - - - - - - - tier3 381 3 0.78 176 129 42.3 0 0 NA 426980 TCGA-AB-3002 AML28 3 108073672 108073672 C A SNP ENSG00000211412 ENST00000388677 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-26464 NULL 0.013 - - - pseudogene tier3 440 5 1.12 199 180 47.49 0 0 NA 426980 TCGA-AB-3002 AML28 3 110361937 110361937 G A SNP MORC1 NM_014429.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42341 NULL 0.012 - - - no_errors tier2 513 1 0.19 129 118 47.77 0 0 NA 426980 TCGA-AB-3002 AML28 3 111975407 111975407 C T SNP ENSG00000201426 ENST00000364556 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46749 NULL 0 - - - no_errors tier3 392 6 1.51 233 163 41.06 0 0 NA 426980 TCGA-AB-3002 AML28 3 116601690 116601690 G A SNP - - - - - - - - - - - - - - - tier2 385 3 0.77 215 163 43.12 0 0 NA 426980 TCGA-AB-3002 AML28 3 117888511 117888511 C T SNP BZW1L1 ENST00000359893 human ensembl 54_36p -1 known 5_prime_flanking_region c.-40569 NULL 0.005 - - - no_coding_region:pseudogene tier3 431 6 1.37 210 176 45.6 0 0 NA 426980 TCGA-AB-3002 AML28 3 118569453 118569453 C T SNP - - - - - - - - - - - - - - - tier2 226 0 0 148 118 44.36 0 0 NA 426980 TCGA-AB-3002 AML28 3 124283786 124283786 C T SNP PDIA5 NM_006810.2 human genbank 54_36p 1 provisional intronic c.43-6919 e2-6919 0.011 - - - no_errors tier3 713 5 0.69 581 460 44.15 1 0 0 426980 TCGA-AB-3002 AML28 3 128201638 128201638 G A SNP PLXNA1 NM_032242.2 human genbank 54_36p 1 validated intronic c.1309-3225 e3-3225 0.009 - - - no_errors tier3 51 0 0 17 12 41.38 0 0 0 426980 TCGA-AB-3002 AML28 3 128213011 128213011 C T SNP PLXNA1 NM_032242.2 human genbank 54_36p 1 validated intronic c.2044-480 e9-480 0.003 - - - no_errors tier3 306 2 0.65 65 55 45.45 0 1 100 426980 TCGA-AB-3002 AML28 3 132386205 132386205 A G SNP NEK11 NM_024800.1 human genbank 54_36p 1 reviewed intronic c.1399+13784 e12+13784 0.002 - - - no_errors tier3 241 2 0.82 84 75 47.17 0 0 0 426980 TCGA-AB-3002 AML28 3 148403134 148403134 G A SNP - - - - - - - - - - - - - - - tier3 355 4 1.11 123 71 36.6 0 0 NA 426980 TCGA-AB-3002 AML28 3 148730059 148730059 C G SNP FLJ30375 XM_001725628.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*19985 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 3 153189049 153189049 G T SNP - - - - - - - - - - - - - - - tier3 381 0 0 247 166 40.19 0 0 NA 426980 TCGA-AB-3002 AML28 3 153463724 153463724 T C SNP MBNL1 NM_207293.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36949 NULL 0 - - - no_errors tier3 663 3 0.45 129 132 50.57 2 2 50 426980 TCGA-AB-3002 AML28 3 153491359 153491359 T A SNP MBNL1 NM_021038.3 human genbank 54_36p 1 validated intronic c.1-8525 e1-8525 0.001 - - - no_errors tier3 378 5 1.31 330 224 40.43 1 2 66.67 426980 TCGA-AB-3002 AML28 3 153678808 153678808 A T SNP MBNL1 NM_207293.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*19002 NULL 0.006 - - - no_errors tier3 278 4 1.41 168 110 39.57 0 0 NA 426980 TCGA-AB-3002 AML28 3 165792039 165792039 C T SNP - - - - - - - - - - - - - - - tier3 728 5 0.68 384 315 45.06 0 0 NA 426980 TCGA-AB-3002 AML28 3 166025067 166025067 T C SNP - - - - - - - - - - - - - - - tier2 234 1 0.43 120 21 14.89 0 0 NA 426980 TCGA-AB-3002 AML28 3 168161221 168161221 C T SNP - - - - - - - - - - - - - - - tier2 335 1 0.3 113 72 38.92 0 0 NA 426980 TCGA-AB-3002 AML28 3 168374413 168374413 G A SNP - - - - - - - - - - - - - - - tier3 211 1 0.47 132 35 20.96 0 0 NA 426980 TCGA-AB-3002 AML28 3 174114325 174114325 G A SNP SPATA16 NM_031955.4 human genbank 54_36p -1 validated intronic c.1504-97 e9-97 1 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 3 175409328 175409328 G A SNP NLGN1 NM_014932.2 human genbank 54_36p 1 reviewed intronic c.647-66471 e3-66471 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 3 176132596 176132596 G A SNP NAALADL2 NM_207015.2 human genbank 54_36p 1 validated intronic c.43+72662 e1+72662 0.908 - - - no_errors tier3 350 6 1.69 316 200 38.76 0 0 NA 426980 TCGA-AB-3002 AML28 3 188452065 188452065 C T SNP MASP1 NM_139125.1 human genbank 54_36p -1 reviewed intronic c.1011+51 e7+51 0.001 - - - no_errors tier2 841 5 0.59 320 249 43.68 0 0 NA 426980 TCGA-AB-3002 AML28 3 192957721 192957721 G A SNP - - - - - - - - - - - - - - - tier2 387 1 0.26 298 216 42.02 0 0 NA 426980 TCGA-AB-3002 AML28 3 197927554 197927554 C G SNP PIGX NM_017861.2 human genbank 54_36p 1 validated intronic c.1-572 e1-572 0 - - - no_errors tier3 334 3 0.89 124 82 39.81 0 0 0 426980 TCGA-AB-3002 AML28 3 198619945 198619945 C T SNP - - - - - - - - - - - - - - - tier3 607 3 0.49 327 283 46.32 0 0 NA 426980 TCGA-AB-3002 AML28 4 1877350 1877350 C T SNP WHSC1 NM_001042424.2 human genbank 54_36p 1 reviewed intronic c.760+1447 e2+1447 0.002 - - - no_errors tier2 867 15 1.7 511 354 40.83 0 4 100 426980 TCGA-AB-3002 AML28 4 12642388 12642388 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 17783989 17783989 C T SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 18912208 18912208 G T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 20642343 20642343 C T SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.101-180955 e2-180955 0.002 - - - no_errors tier2 342 6 1.72 183 149 44.88 0 0 NA 426980 TCGA-AB-3002 AML28 4 22759171 22759171 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 23099928 23099928 G A SNP - - - - - - - - - - - - - - - tier3 385 2 0.51 196 171 46.59 1 0 0 426980 TCGA-AB-3002 AML28 4 23343723 23343723 C T SNP - - - - - - - - - - - - - - - tier2 397 3 0.75 560 439 43.77 0 0 NA 426980 TCGA-AB-3002 AML28 4 23465614 23465614 T C SNP PPARGC1A NM_013261.3 human genbank 54_36p -1 reviewed intronic c.235-23142 e3-23142 0.002 - - - no_errors tier3 225 1 0.44 134 143 51.62 0 0 NA 426980 TCGA-AB-3002 AML28 4 24719341 24719341 C T SNP SEPSECS NM_153825.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*15310 NULL 0 - - - no_errors tier3 1088 8 0.73 523 466 46.83 0 0 NA 426980 TCGA-AB-3002 AML28 4 25787928 25787928 C A SNP LOC389230 XM_943516.3 human genbank 54_36p 1 model 3_prime_flanking_region c.*49513 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 763 3 0.39 394 300 43.23 0 0 NA 426980 TCGA-AB-3002 AML28 4 29251450 29251450 C A SNP - - - - - - - - - - - - - - - tier3 388 1 0.26 208 116 35.8 0 0 NA 426980 TCGA-AB-3002 AML28 4 29705492 29705492 C T SNP - - - - - - - - - - - - - - - tier3 660 9 1.34 257 178 40.83 0 0 NA 426980 TCGA-AB-3002 AML28 4 29990099 29990099 C T SNP - - - - - - - - - - - - - - - tier3 339 1 0.29 66 48 42.11 0 0 NA 426980 TCGA-AB-3002 AML28 4 30058524 30058524 A T SNP - - - - - - - - - - - - - - - tier3 302 3 0.98 126 126 50 0 0 NA 426980 TCGA-AB-3002 AML28 4 31370390 31370390 A C SNP - - - - - - - - - - - - - - - tier2 159 2 1.24 36 31 46.27 0 0 NA 426980 TCGA-AB-3002 AML28 4 31779477 31779477 G C SNP LOC100130644 XM_001717608.1 human genbank 54_36p -1 model intronic c.1219-3646 e8-3646 0.004 - - - pseudogene:no_stop_codon tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 32281806 32281806 G C SNP - - - - - - - - - - - - - - - tier3 562 5 0.88 257 202 44.01 0 0 NA 426980 TCGA-AB-3002 AML28 4 33004111 33004111 A G SNP - - - - - - - - - - - - - - - tier3 226 2 0.88 89 92 50.83 0 0 NA 426980 TCGA-AB-3002 AML28 4 34925832 34925832 T A SNP - - - - - - - - - - - - - - - tier3 210 6 2.78 71 57 44.53 0 0 NA 426980 TCGA-AB-3002 AML28 4 58848996 58848996 G A SNP - - - - - - - - - - - - - - - tier3 308 2 0.65 87 116 57.14 0 0 NA 426980 TCGA-AB-3002 AML28 4 59326070 59326070 G T SNP - - - - - - - - - - - - - - - tier3 285 3 1.04 148 126 45.99 0 0 NA 426980 TCGA-AB-3002 AML28 4 59788820 59788820 C T SNP - - - - - - - - - - - - - - - tier3 448 7 1.54 124 119 48.77 0 0 NA 426980 TCGA-AB-3002 AML28 4 61451246 61451246 G T SNP - - - - - - - - - - - - - - - tier3 348 4 1.14 217 142 39.44 0 0 NA 426980 TCGA-AB-3002 AML28 4 61457317 61457317 C T SNP - - - - - - - - - - - - - - - tier3 407 3 0.73 259 191 42.44 0 0 NA 426980 TCGA-AB-3002 AML28 4 65237776 65237776 A G SNP - - - - - - - - - - - - - - - tier3 227 1 0.44 138 111 44.58 0 0 NA 426980 TCGA-AB-3002 AML28 4 66830014 66830014 C G SNP MIRN1269 ENST00000408636 human ensembl 54_36p 1 known 3_prime_flanking_region c.*4773 NULL 0.012 - - - no_errors tier3 392 1 0.25 104 57 35.4 0 0 NA 426980 TCGA-AB-3002 AML28 4 70035031 70035031 C T SNP UGT2B11 ENST00000305206 human ensembl 54_36p -1 known intronic c.1590+65609 e6+65609 0.004 - - - no_errors tier3 376 2 0.53 255 232 47.64 0 0 NA 426980 TCGA-AB-3002 AML28 4 71031857 71031857 T C SNP C4orf40 NM_214711.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22825 NULL 0 - - - no_errors tier3 148 5 3.27 86 94 52.22 0 0 NA 426980 TCGA-AB-3002 AML28 4 76113412 76113412 C A SNP DKFZP564O0823 NM_015393.2 human genbank 54_36p 1 validated intronic c.43+35808 e1+35808 0.034 - - - no_errors tier3 380 1 0.26 412 346 45.65 0 0 0 426980 TCGA-AB-3002 AML28 4 86249628 86249628 A C SNP ENSG00000201901 ENST00000365031 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*8628 NULL 0.095 - - - no_errors tier3 230 3 1.29 110 68 38.2 0 0 NA 426980 TCGA-AB-3002 AML28 4 92575664 92575664 T C SNP - - - - - - - - - - - - - - - tier3 207 1 0.48 107 73 40.56 0 0 0 426980 TCGA-AB-3002 AML28 4 99611966 99611966 T G SNP ENSG00000203420 ENST00000366239 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-27876 NULL 0.001 - - - no_coding_region:pseudogene tier3 376 2 0.53 207 161 43.75 3 3 50 426980 TCGA-AB-3002 AML28 4 103369618 103369618 G A SNP SLC39A8 NM_022154.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*33606 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 105253495 105253495 G A SNP - - - - - - - - - - - - - - - tier3 643 9 1.38 487 355 42.16 0 0 NA 426980 TCGA-AB-3002 AML28 4 107761470 107761470 T G SNP - - - - - - - - - - - - - - - tier3 454 5 1.09 168 132 43.85 0 0 NA 426980 TCGA-AB-3002 AML28 4 112311957 112311957 G A SNP - - - - - - - - - - - - - - - tier3 448 8 1.75 259 293 52.98 0 0 NA 426980 TCGA-AB-3002 AML28 4 112377379 112377379 G A SNP - - - - - - - - - - - - - - - tier3 462 3 0.65 225 150 40 0 0 NA 426980 TCGA-AB-3002 AML28 4 114555521 114555521 G T SNP ENSG00000206820 ENST00000384093 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-5407 NULL 0.05 - - - no_errors tier2 1078 5 0.46 543 403 42.56 0 0 NA 426980 TCGA-AB-3002 AML28 4 115824855 115824855 A G SNP UGT8 NM_003360.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*7962 NULL 0.007 - - - no_errors tier3 383 6 1.54 186 165 47.01 0 0 NA 426980 TCGA-AB-3002 AML28 4 116027622 116027622 G A SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.1537-16067 e6-16067 0.001 - - - no_errors tier3 402 3 0.74 359 294 45.02 0 0 NA 426980 TCGA-AB-3002 AML28 4 117029317 117029317 G A SNP - - - - - - - - - - - - - - - tier3 174 0 0 61 49 44.55 0 0 NA 426980 TCGA-AB-3002 AML28 4 126378916 126378916 C T SNP - - - - - - - - - - - - - - - tier3 299 4 1.32 128 74 36.63 0 0 NA 426980 TCGA-AB-3002 AML28 4 126390388 126390388 C G SNP - - - - - - - - - - - - - - - tier2 459 4 0.86 241 271 52.93 0 0 NA 426980 TCGA-AB-3002 AML28 4 128107864 128107864 C T SNP - - - - - - - - - - - - - - - tier3 683 4 0.58 227 172 42.89 0 0 NA 426980 TCGA-AB-3002 AML28 4 130405903 130405903 T G SNP - - - - - - - - - - - - - - - tier2 468 3 0.64 415 366 46.86 0 0 NA 426980 TCGA-AB-3002 AML28 4 131202373 131202373 G A SNP - - - - - - - - - - - - - - - tier3 506 6 1.17 239 175 42.27 0 0 NA 426980 TCGA-AB-3002 AML28 4 132134033 132134033 T A SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 132401736 132401736 G A SNP ENSG00000206782 ENST00000384055 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-12111 NULL 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 133674094 133674094 A C SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 4 134412099 134412099 G A SNP - - - - - - - - - - - - - - - tier2 164 0 0 126 103 44.59 0 0 NA 426980 TCGA-AB-3002 AML28 4 134645746 134645746 G A SNP - - - - - - - - - - - - - - - tier3 396 4 1 244 134 35.45 0 0 NA 426980 TCGA-AB-3002 AML28 4 137282440 137282440 G A SNP - - - - - - - - - - - - - - - tier3 71 0 0 26 23 46.94 0 0 NA 426980 TCGA-AB-3002 AML28 4 154497736 154497736 A T SNP MND1 NM_032117.2 human genbank 54_36p 1 validated intronic c.128-1340 e4-1340 0.27 - - - no_errors tier3 484 1 0.21 180 137 43.22 1 1 50 426980 TCGA-AB-3002 AML28 4 156877020 156877020 C T SNP GUCY1B3 NM_000857.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-22723 NULL 0.001 - - - no_errors tier3 348 6 1.69 275 189 40.73 11 4 26.67 426980 TCGA-AB-3002 AML28 4 167831999 167831999 A G SNP - - - - - - - - - - - - - - - tier2 230 1 0.43 119 98 44.95 0 0 NA 426980 TCGA-AB-3002 AML28 4 177146700 177146700 C A SNP GPM6A NM_005277.3 human genbank 54_36p -1 validated intronic c.1+13754 e0+13754 0.31 - - - no_errors tier3 633 7 1.09 454 341 42.89 0 0 NA 426980 TCGA-AB-3002 AML28 4 182792991 182792991 A C SNP - - - - - - - - - - - - - - - tier3 225 1 0.44 80 67 45.58 0 0 NA 426980 TCGA-AB-3002 AML28 4 184474803 184474803 G A SNP WWC2 NM_024949.5 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*927 NULL 0 - - - no_errors tier2 418 2 0.48 289 275 48.76 1 0 0 426980 TCGA-AB-3002 AML28 4 187184304 187184304 A G SNP TLR3 NM_003265.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-50464 NULL 0.002 - - - no_errors tier2 779 1 0.13 471 370 44 0 0 NA 426980 TCGA-AB-3002 AML28 4 187238379 187238379 C A SNP TLR3 NM_003265.2 human genbank 54_36p 1 reviewed intronic c.633+1200 e2+1200 0.035 - - - no_errors tier3 174 0 0 24 15 38.46 0 0 NA 426980 TCGA-AB-3002 AML28 4 188332814 188332814 C T SNP - - - - - - - - - - - - - - - tier3 476 3 0.62 319 243 43.16 0 0 NA 426980 TCGA-AB-3002 AML28 4 188720336 188720336 G A SNP - - - - - - - - - - - - - - - tier3 734 11 1.47 447 318 41.51 0 0 NA 426980 TCGA-AB-3002 AML28 5 1190263 1190263 T A SNP SLC12A7 NM_006598.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-25157 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 5 2494675 2494675 G A SNP - - - - - - - - - - - - - - - tier3 807 15 1.82 279 227 44.86 0 0 NA 426980 TCGA-AB-3002 AML28 5 4717258 4717258 G A SNP - - - - - - - - - - - - - - - tier3 618 3 0.48 312 224 41.79 0 0 NA 426980 TCGA-AB-3002 AML28 5 5067699 5067699 G A SNP ENSG00000215231 ENST00000399853 human ensembl 54_36p 1 known 5_prime_flanking_region c.-23935 NULL 0 - - - no_errors tier3 349 3 0.85 166 133 44.48 0 0 NA 426980 TCGA-AB-3002 AML28 5 6918384 6918384 T A SNP ENSG00000200243 ENST00000363373 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16809 NULL 0.155 - - - no_errors tier3 666 5 0.75 241 186 43.56 0 0 NA 426980 TCGA-AB-3002 AML28 5 7851544 7851544 C A SNP ADCY2 NM_020546.2 human genbank 54_36p 1 reviewed intronic c.2629-3787 e21-3787 0.003 - - - no_errors tier3 418 4 0.95 337 219 39.39 0 0 NA 426980 TCGA-AB-3002 AML28 5 7904871 7904871 C T SNP MTRR NM_024010.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17376 NULL 0.003 - - - no_errors tier3 213 2 0.93 151 118 43.87 0 0 NA 426980 TCGA-AB-3002 AML28 5 8283992 8283992 A - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 5 8621917 8621917 A T SNP LOC644010 XM_938374.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-44418 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 146 0 0 41 21 33.87 0 0 NA 426980 TCGA-AB-3002 AML28 5 12123636 12123636 A G SNP - - - - - - - - - - - - - - - tier3 394 2 0.51 352 333 48.61 0 0 NA 426980 TCGA-AB-3002 AML28 5 19051007 19051007 G T SNP - - - - - - - - - - - - - - - tier3 460 8 1.71 261 149 36.34 0 0 NA 426980 TCGA-AB-3002 AML28 5 23381427 23381427 T C SNP LOC391771 XR_038806.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-40419 NULL 0.911 - - - pseudogene tier2 488 8 1.61 233 171 42.33 0 0 NA 426980 TCGA-AB-3002 AML28 5 26672053 26672053 C T SNP - - - - - - - - - - - - - - - tier3 273 3 1.08 72 72 50 0 0 NA 426980 TCGA-AB-3002 AML28 5 27542961 27542961 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 5 39916942 39916942 C T SNP LOC100134241 XM_001717424.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*18002 NULL 0.04 - - - no_start_codon:pseudogene:no_stop_codon tier2 462 4 0.86 265 207 43.86 0 0 NA 426980 TCGA-AB-3002 AML28 5 43169431 43169431 A T SNP ZNF131 NM_003432.1 human genbank 54_36p 1 validated intronic c.227-5593 e3-5593 0 - - - no_errors tier3 1181 14 1.17 263 210 44.4 10 9 47.37 426980 TCGA-AB-3002 AML28 5 45672335 45672335 C T SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.849+8709 e2+8709 0.005 - - - no_errors tier3 415 1 0.24 335 206 38.08 0 0 NA 426980 TCGA-AB-3002 AML28 5 51522290 51522290 A T SNP - - - - - - - - - - - - - - - tier3 226 2 0.88 80 61 43.26 0 0 NA 426980 TCGA-AB-3002 AML28 5 52867999 52867999 C T SNP NDUFS4 NM_002495.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-24251 NULL 0.006 - - - no_errors tier3 1011 5 0.49 639 502 43.92 0 0 NA 426980 TCGA-AB-3002 AML28 5 65807411 65807411 A G SNP ENSG00000205619 ENST00000380914 human ensembl 54_36p 1 known intronic c.372+9311 e4+9311 0.008 - - - no_errors tier3 856 10 1.15 528 410 43.71 0 0 NA 426980 TCGA-AB-3002 AML28 5 73528567 73528567 T G SNP ENSG00000210914 ENST00000388179 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-21329 NULL 0 - - - pseudogene tier3 496 2 0.4 244 197 44.67 0 0 NA 426980 TCGA-AB-3002 AML28 5 73771482 73771482 T C SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 5 74136616 74136616 C T SNP FAM169A NM_015566.1 human genbank 54_36p -1 validated intronic c.799+121 e6+121 0.005 - - - no_errors tier3 526 2 0.38 230 185 44.58 1 0 0 426980 TCGA-AB-3002 AML28 5 77267867 77267867 A G SNP LOC728904 XM_001128764.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21352 NULL 1 - - - no_errors tier2 1563 17 1.08 611 467 43.32 0 0 NA 426980 TCGA-AB-3002 AML28 5 83283802 83283802 C T SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.1294-8659 e11-8659 0 - - - no_errors tier3 617 3 0.48 289 240 45.37 0 0 NA 426980 TCGA-AB-3002 AML28 5 87095961 87095961 G C SNP - - - - - - - - - - - - - - - tier3 384 0 0 140 116 45.14 0 0 NA 426980 TCGA-AB-3002 AML28 5 90039982 90039982 G T SNP GPR98 NM_032119.3 human genbank 54_36p 1 reviewed intronic c.8731-407 e39-407 0.001 - - - no_errors tier3 224 0 0 86 51 37.23 0 0 NA 426980 TCGA-AB-3002 AML28 5 90067397 90067397 G C SNP GPR98 NM_032119.3 human genbank 54_36p 1 reviewed intronic c.10549+6060 e50+6060 0.99 - - - no_errors tier2 206 1 0.48 103 91 46.91 0 0 NA 426980 TCGA-AB-3002 AML28 5 93059323 93059323 G A SNP FAM172A NM_032042.4 human genbank 54_36p -1 validated intronic c.1109-76732 e10-76732 0.001 - - - no_errors tier3 117 3 2.5 17 8 32 1 0 0 426980 TCGA-AB-3002 AML28 5 95272060 95272060 T C SNP ELL2 NM_012081.5 human genbank 54_36p -1 validated intronic c.481+3171 e4+3171 0 - - - no_errors tier3 NA NA NA NA NA NA 4 0 0 426980 TCGA-AB-3002 AML28 5 95502445 95502445 A G SNP LOC441097 XM_499010.1 human genbank 54_36p 1 model intronic c.189+29980 e3+29980 0.004 - - - no_errors tier3 481 5 1.03 345 257 42.69 0 0 NA 426980 TCGA-AB-3002 AML28 5 97334538 97334538 C A SNP - - - - - - - - - - - - - - - tier3 367 1 0.27 80 49 37.98 0 0 NA 426980 TCGA-AB-3002 AML28 5 98396322 98396322 T C SNP - - - - - - - - - - - - - - - tier3 855 4 0.47 599 459 43.26 0 0 NA 426980 TCGA-AB-3002 AML28 5 101210016 101210016 A T SNP - - - - - - - - - - - - - - - tier3 850 8 0.93 471 282 37.4 0 0 NA 426980 TCGA-AB-3002 AML28 5 104600196 104600196 C T SNP - - - - - - - - - - - - - - - tier2 230 1 0.43 51 39 43.33 0 0 NA 426980 TCGA-AB-3002 AML28 5 106172064 106172064 C T SNP - - - - - - - - - - - - - - - tier3 535 9 1.65 334 262 43.74 0 0 NA 426980 TCGA-AB-3002 AML28 5 106766017 106766017 G A SNP EFNA5 NM_001962.2 human genbank 54_36p -1 reviewed intronic c.419-14646 e3-14646 0.58 - - - no_errors tier3 571 5 0.87 501 379 43.07 0 0 NA 426980 TCGA-AB-3002 AML28 5 111269099 111269099 T G SNP - - - - - - - - - - - - - - - tier3 345 5 1.43 261 201 43.51 0 0 NA 426980 TCGA-AB-3002 AML28 5 118953335 118953335 T C SNP FAM170A NM_182761.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-40028 NULL 0 - - - no_errors tier3 504 5 0.98 267 266 49.91 0 0 NA 426980 TCGA-AB-3002 AML28 5 120450322 120450322 T C SNP - - - - - - - - - - - - - - - tier3 596 4 0.67 105 76 41.99 0 0 NA 426980 TCGA-AB-3002 AML28 5 120894390 120894390 A T SNP LOC391825 XR_016576.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*45052 NULL 0.003 - - - pseudogene tier2 238 1 0.42 192 151 44.02 0 0 NA 426980 TCGA-AB-3002 AML28 5 121905027 121905027 C T SNP - - - - - - - - - - - - - - - tier3 294 3 1.01 164 149 47.6 0 0 NA 426980 TCGA-AB-3002 AML28 5 127725400 127725400 G A SNP FBN2 NM_001999.3 human genbank 54_36p -1 reviewed silent c.2469 p.N823 0.992 "HMMSmart_SM00179,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" "PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_TB,superfamily_TB module/8-cys domain,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Growth factor receptor domain,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 859 5 0.58 674 500 42.59 2 0 426980 TCGA-AB-3002 AML28 5 127832888 127832888 G T SNP FBN2 NM_001999.3 human genbank 54_36p -1 reviewed intronic c.629-4375 e6-4375 0.043 - - - no_errors tier3 143 1 0.69 175 114 39.45 0 0 NA 426980 TCGA-AB-3002 AML28 5 128418437 128418437 A G SNP ISOC1 NM_016048.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-39922 NULL 0.007 - - - no_errors tier3 164 2 1.2 188 153 44.87 0 0 NA 426980 TCGA-AB-3002 AML28 5 133383451 133383451 G A SNP VDAC1 NM_003374.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-26849 NULL 0.062 - - - no_errors tier3 1717 11 0.64 669 508 43.12 0 0 NA 426980 TCGA-AB-3002 AML28 5 140243210 140243210 G A SNP PCDHA13 NM_018904.2 human genbank 54_36p 1 reviewed silent c.1173 p.P391 0 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 358 6 1.65 380 241 38.75 NA 426980 TCGA-AB-3002 AML28 5 140846278 140846278 C G SNP PCDHGC4 NM_018928.2 human genbank 54_36p 1 reviewed missense c.1354 p.P452A 0.999 "HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 627 5 0.79 571 363 38.87 12 13 52 426980 TCGA-AB-3002 AML28 5 147406379 147406379 C G SNP SPINK5 NM_006846.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17422 NULL 0 - - - no_errors tier3 379 7 1.81 160 127 44.25 0 0 NA 426980 TCGA-AB-3002 AML28 5 149649049 149649049 G T SNP CAMK2A NM_015981.3 human genbank 54_36p -1 reviewed intronic c.62+271 e1+271 0.001 - - - no_errors tier3 661 3 0.45 264 207 43.95 0 0 NA 426980 TCGA-AB-3002 AML28 5 152422952 152422952 C T SNP - - - - - - - - - - - - - - - tier2 419 7 1.64 286 254 47.04 0 0 NA 426980 TCGA-AB-3002 AML28 5 154221315 154221315 T C SNP CNOT8 NM_004779.4 human genbank 54_36p 1 provisional intronic c.1-1645 e1-1645 0.097 - - - no_errors tier3 1 0 0 NA NA NA 14 0 0 426980 TCGA-AB-3002 AML28 5 154835142 154835142 A G SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 5 155690400 155690400 G A SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.3+1233 e1+1233 0 - - - no_errors tier3 916 11 1.18 798 630 44.06 0 0 NA 426980 TCGA-AB-3002 AML28 5 157859403 157859403 G A SNP - - - - - - - - - - - - - - - tier2 580 7 1.19 265 208 43.97 0 0 NA 426980 TCGA-AB-3002 AML28 5 165198112 165198112 G A SNP - - - - - - - - - - - - - - - tier3 414 1 0.24 85 81 48.8 0 0 NA 426980 TCGA-AB-3002 AML28 5 176872959 176872959 C T SNP DDX41 NM_016222.2 human genbank 54_36p -1 reviewed splice_site c.1230+1 e11+1 1 - - - no_errors tier1 285 0 169 67 28.27 8 3 27.27 426980 TCGA-AB-3002 AML28 6 476579 476579 A G SNP EXOC2 NM_018303.4 human genbank 54_36p -1 reviewed intronic c.2380+890 e22+890 0.115 - - - no_errors tier3 474 4 0.84 201 147 42.24 1 5 83.33 426980 TCGA-AB-3002 AML28 6 492728 492728 C T SNP EXOC2 NM_018303.4 human genbank 54_36p -1 reviewed intronic c.2238+1447 e21+1447 0.001 - - - no_errors tier3 296 2 0.67 173 154 47.09 1 0 0 426980 TCGA-AB-3002 AML28 6 1343264 1343264 T C SNP FOXF2 NM_001452.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*3171 NULL 0.002 - - - no_errors tier3 149 1 0.67 9 21 70 0 0 NA 426980 TCGA-AB-3002 AML28 6 3174084 3174084 A - DEL TUBB2B NM_178012.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-1308 NULL 0.023 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 8223953 8223953 A T SNP - - - - - - - - - - - - - - - tier3 1329 11 0.82 538 396 42.4 0 0 NA 426980 TCGA-AB-3002 AML28 6 10480723 10480723 C T SNP LOC100130275 XM_001720213.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-42088 NULL 0.015 - - - no_errors tier3 577 4 0.69 130 98 42.98 0 0 NA 426980 TCGA-AB-3002 AML28 6 11556067 11556067 A G SNP LOC100131610 XM_001723558.1 human genbank 54_36p 1 model intronic c.540+58631 e1+58631 0.305 - - - no_start_codon:pseudogene:no_stop_codon tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 12712962 12712962 G A SNP LOC100133910 XM_001716430.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*25099 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 553 2 0.36 232 150 39.27 0 0 NA 426980 TCGA-AB-3002 AML28 6 13811863 13811863 A C SNP RANBP9 NM_005493.2 human genbank 54_36p -1 reviewed intronic c.572-6756 e2-6756 0 - - - no_errors tier3 669 6 0.89 281 216 43.46 2 4 66.67 426980 TCGA-AB-3002 AML28 6 15097734 15097734 G A SNP LOC728961 XM_001128918.2 human genbank 54_36p -1 model intronic c.173+7892 e2+7892 0.003 - - - no_errors tier3 981 14 1.41 299 204 40.56 0 0 NA 426980 TCGA-AB-3002 AML28 6 19459891 19459891 G A SNP ENSG00000218643 ENST00000403848 human ensembl 54_36p 1 known 3_prime_flanking_region c.*2618 NULL 0.001 - - - no_coding_region:pseudogene tier3 365 1 0.27 128 83 39.34 0 0 NA 426980 TCGA-AB-3002 AML28 6 20771810 20771810 G A SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated intronic c.371+14223 e3+14223 0 - - - no_errors tier3 394 5 1.25 397 291 42.3 0 2 100 426980 TCGA-AB-3002 AML28 6 31834161 31834161 G A SNP MSH5 NM_025259.3 human genbank 54_36p 1 reviewed intronic c.1194+112 e12+112 0 - - - no_errors tier3 321 1 0.31 177 138 43.81 3 1 25 426980 TCGA-AB-3002 AML28 6 44096637 44096637 A G SNP C6orf223 NM_153246.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*17796 NULL 0 - - - no_errors tier3 1226 6 0.49 320 299 48.3 0 0 NA 426980 TCGA-AB-3002 AML28 6 54282157 54282157 A T SNP TINAG NM_014464.3 human genbank 54_36p 1 validated intronic c.355+495 e1+495 0 - - - no_errors tier3 1068 11 1.02 651 518 44.31 0 0 NA 426980 TCGA-AB-3002 AML28 6 54919658 54919658 T - DEL FAM83B NM_001010872.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*4894 NULL 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 55539300 55539300 C T SNP HMGCLL1 NM_019036.1 human genbank 54_36p -1 validated intronic c.198+10535 e2+10535 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 57841439 57841439 C T SNP ENSG00000214566 ENST00000398589 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-45604 NULL 0.938 - - - no_coding_region:pseudogene tier3 336 6 1.75 421 339 44.61 0 0 NA 426980 TCGA-AB-3002 AML28 6 58021696 58021696 G T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 58720816 58720818 AGA - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 70346833 70346833 C A SNP - - - - - - - - - - - - - - - tier3 221 2 0.9 41 25 37.88 0 0 NA 426980 TCGA-AB-3002 AML28 6 70717771 70717771 A G SNP COL19A1 NM_001858.4 human genbank 54_36p 1 reviewed intronic c.937-8838 e9-8838 0 - - - no_errors tier3 186 4 2.11 46 43 48.31 0 0 NA 426980 TCGA-AB-3002 AML28 6 85368291 85368291 C T SNP - - - - - - - - - - - - - - - tier3 375 3 0.79 72 34 32.08 0 0 NA 426980 TCGA-AB-3002 AML28 6 87301445 87301445 G A SNP - - - - - - - - - - - - - - - tier3 578 1 0.17 209 145 40.96 0 0 NA 426980 TCGA-AB-3002 AML28 6 87483810 87483810 T A SNP ENSG00000218561 ENST00000407695 human ensembl 54_36p -1 known 3_prime_flanking_region c.*12335 NULL 0.001 - - - no_coding_region:pseudogene tier3 515 9 1.71 157 84 34.85 0 0 NA 426980 TCGA-AB-3002 AML28 6 89788729 89788729 A - DEL LOC100131124 XR_038480.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37337 NULL 0.009 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 93048600 93048600 T G SNP - - - - - - - - - - - - - - - tier3 342 2 0.58 73 45 38.14 0 0 NA 426980 TCGA-AB-3002 AML28 6 93341535 93341535 G A SNP - - - - - - - - - - - - - - - tier3 263 1 0.38 199 161 44.6 0 0 NA 426980 TCGA-AB-3002 AML28 6 93615117 93615117 C T SNP ENSG00000219387 ENST00000406040 human ensembl 54_36p -1 known 3_prime_flanking_region c.*39116 NULL 0 - - - no_coding_region:pseudogene tier3 843 8 0.94 430 331 43.5 1 0 0 426980 TCGA-AB-3002 AML28 6 94679810 94679810 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 94702338 94702338 T A SNP - - - - - - - - - - - - - - - tier3 442 2 0.45 108 77 41.4 0 0 NA 426980 TCGA-AB-3002 AML28 6 94982255 94982255 C T SNP - - - - - - - - - - - - - - - tier3 559 5 0.88 410 352 46.19 0 0 NA 426980 TCGA-AB-3002 AML28 6 98935123 98935123 A G SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 103079820 103079820 G A SNP LOC100132919 XM_001716737.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-30183 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 104504284 104504284 A C SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 6 117095855 117095855 C T SNP ZUFSP NM_145062.1 human genbank 54_36p -1 provisional intronic c.1+567 e0+567 0 - - - no_errors tier3 253 4 1.55 50 47 48.45 1 1 50 426980 TCGA-AB-3002 AML28 6 118632756 118632756 G A SNP SLC35F1 NM_001029858.3 human genbank 54_36p 1 validated intronic c.350-30609 e3-30609 0 - - - no_errors tier3 678 5 0.73 727 146 16.72 0 0 NA 426980 TCGA-AB-3002 AML28 6 120261348 120261348 A G SNP - - - - - - - - - - - - - - - tier3 600 4 0.66 464 348 42.86 0 0 NA 426980 TCGA-AB-3002 AML28 6 125783681 125783681 C T SNP - - - - - - - - - - - - - - - tier3 718 1 0.14 366 338 48.01 0 0 NA 426980 TCGA-AB-3002 AML28 6 129212144 129212144 T C SNP LAMA2 NM_000426.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33940 NULL 0 - - - no_errors tier3 465 6 1.27 218 182 45.5 0 0 NA 426980 TCGA-AB-3002 AML28 6 131347700 131347700 T G SNP EPB41L2 ENST00000337057 human ensembl 54_36p -1 known intronic c.1-28368 e1-28368 0.012 - - - no_errors tier3 515 22 4.1 260 227 46.52 0 2 100 426980 TCGA-AB-3002 AML28 6 140005900 140005900 G A SNP ENSG00000205695 ENST00000381279 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16858 NULL 0 - - - no_coding_region:pseudogene tier3 621 6 0.96 368 268 42.14 0 0 NA 426980 TCGA-AB-3002 AML28 6 141372185 141372185 A G SNP - - - - - - - - - - - - - - - tier2 374 4 1.06 114 83 42.13 0 0 NA 426980 TCGA-AB-3002 AML28 6 149337323 149337323 G A SNP UST NM_005715.2 human genbank 54_36p 1 validated intronic c.681+9931 e5+9931 0.006 - - - no_errors tier3 880 13 1.46 365 319 46.57 0 0 NA 426980 TCGA-AB-3002 AML28 6 159108034 159108034 T C SNP EZR NM_003379.1 human genbank 54_36p -1 reviewed missense c.1661 p.H554R 1 "superfamily_Moesin,HMMPfam_ERM" "superfamily_Moesin,HMMPfam_ERM,HMMPfam_FERM_N,HMMPfam_FERM_C,PatternScan_FERM_1,PatternScan_FERM_2,HMMPfam_FERM_M,superfamily_FERM_3-hlx,HMMSmart_B41,superfamily_SSF50729,superfamily_SSF54236" - no_errors tier1 687 5 0.72 558 443 44.21 72 58 44.62 426980 TCGA-AB-3002 AML28 6 160376110 160376110 C T SNP IGF2R NM_000876.2 human genbank 54_36p 1 reviewed intronic c.1315+566 e10+566 0.004 - - - no_errors tier3 664 2 0.3 385 280 42.11 0 0 0 426980 TCGA-AB-3002 AML28 6 165990044 165990044 G A SNP PDE10A NM_006661.1 human genbank 54_36p -1 validated intronic c.1+5381 e0+5381 0 - - - no_errors tier3 195 0 0 156 123 44.09 0 0 NA 426980 TCGA-AB-3002 AML28 7 1488902 1488902 G C SNP INTS1 NM_001080453.2 human genbank 54_36p -1 validated intronic c.3989-33 e28-33 0 - - - no_errors tier3 113 1 0.88 70 41 36.94 17 10 37.04 426980 TCGA-AB-3002 AML28 7 4033084 4033084 A G SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.2602+9574 e17+9574 0 - - - no_errors tier3 530 3 0.56 279 278 49.82 0 0 NA 426980 TCGA-AB-3002 AML28 7 4129053 4129053 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.3824-4486 e26-4486 0.001 - - - no_errors tier3 748 10 1.32 218 169 43.67 0 0 NA 426980 TCGA-AB-3002 AML28 7 6179392 6179392 A C SNP CYTH3 NM_004227.3 human genbank 54_36p -1 reviewed intronic c.449+417 e6+417 0.005 - - - no_errors tier3 292 0 0 186 160 46.24 5 1 16.67 426980 TCGA-AB-3002 AML28 7 13405534 13405534 T C SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 7 25018068 25018068 T A SNP OSBPL3 NM_015550.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-119452 NULL 0.809 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 7 30364283 30364283 G A SNP ZNRF2 NM_147128.3 human genbank 54_36p 1 validated intronic c.671+2309 e3+2309 0.009 - - - no_errors tier3 190 2 1.04 57 50 46.73 1 2 66.67 426980 TCGA-AB-3002 AML28 7 36118095 36118095 G A SNP EEPD1 NM_030636.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-42364 NULL 0.251 - - - no_errors tier3 432 4 0.92 295 260 46.85 0 0 NA 426980 TCGA-AB-3002 AML28 7 37373027 37373027 A T SNP ELMO1 NM_014800.1 human genbank 54_36p -1 reviewed intronic c.1-24135 e1-24135 0.002 - - - no_errors tier3 454 8 1.73 199 154 43.63 0 0 0 426980 TCGA-AB-3002 AML28 7 42112266 42112266 A G SNP GLI3 NM_000168.5 human genbank 54_36p -1 reviewed intronic c.368-29285 e3-29285 0 - - - no_errors tier3 609 15 2.4 494 427 46.31 0 0 NA 426980 TCGA-AB-3002 AML28 7 51341655 51341655 G A SNP COBL NM_015198.3 human genbank 54_36p -1 validated intronic c.41+10129 e1+10129 0.005 - - - no_errors tier3 352 3 0.85 111 128 53.56 0 0 NA 426980 TCGA-AB-3002 AML28 7 52033678 52033679 AA - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 7 57222145 57222145 G A SNP ZNF479 NM_033273.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-18172 NULL 0 - - - no_errors tier3 133 0 0 86 108 55.67 0 0 NA 426980 TCGA-AB-3002 AML28 7 62817336 62817336 A G SNP LOC730284 XR_037181.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 7 83555809 83555809 A G SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed intronic c.453+21913 e4+21913 0 - - - no_errors tier3 149 2 1.32 21 79 79 0 0 NA 426980 TCGA-AB-3002 AML28 7 86027626 86027626 G A SNP - - - - - - - - - - - - - - - tier3 493 4 0.8 373 262 41.26 0 0 NA 426980 TCGA-AB-3002 AML28 7 90612944 90612944 T C SNP PFTK1 NM_012395.2 human genbank 54_36p 1 validated intronic c.1356+27485 e13+27485 0.001 - - - no_errors tier3 1122 24 2.09 685 538 43.99 0 0 0 426980 TCGA-AB-3002 AML28 7 95042761 95042761 G A SNP ASB4 NM_016116.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*37754 NULL 0.114 - - - no_errors tier3 557 2 0.36 328 267 44.8 0 0 NA 426980 TCGA-AB-3002 AML28 7 101384020 101384020 C G SNP CUX1 NM_181552.2 human genbank 54_36p 1 reviewed intronic c.141+37795 e2+37795 0 - - - no_errors tier3 306 2 0.65 104 83 44.15 4 3 42.86 426980 TCGA-AB-3002 AML28 7 101609893 101609893 G A SNP CUX1 NM_181552.2 human genbank 54_36p 1 reviewed intronic c.1017+1236 e11+1236 0 - - - no_errors tier3 NA NA NA 1 0 0 5 0 0 426980 TCGA-AB-3002 AML28 7 101701575 101701575 C A SNP CUX1 NM_001913.2 human genbank 54_36p 1 reviewed intronic c.1256-1782 e15-1782 0.001 - - - no_errors tier3 NA NA NA NA NA NA 2 0 0 426980 TCGA-AB-3002 AML28 7 104071491 104071491 T G SNP LHFPL3 NM_199000.2 human genbank 54_36p 1 reviewed intronic c.446-92867 e2-92867 0 - - - no_errors tier3 490 3 0.61 284 216 43.11 0 0 NA 426980 TCGA-AB-3002 AML28 7 104521958 104521958 A G SNP MLL5 NM_018682.3 human genbank 54_36p 1 reviewed intronic c.1722+2961 e13+2961 0.001 - - - no_errors tier2 271 4 1.45 138 118 46.09 5 5 50 426980 TCGA-AB-3002 AML28 7 107318832 107318832 G A SNP DLD NM_000108.3 human genbank 54_36p 1 reviewed 5_prime_untranslated_region c.-100 NULL 0 - - - no_errors tier2 447 3 0.67 308 243 44.02 0 0 NA 426980 TCGA-AB-3002 AML28 7 111790453 111790453 G A SNP ZNF277 NM_021994.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*20433 NULL 0.002 - - - no_errors tier3 353 3 0.84 248 219 46.79 0 0 NA 426980 TCGA-AB-3002 AML28 7 113249295 113249295 A T SNP - - - - - - - - - - - - - - - tier3 36 1 2.7 3 5 62.5 0 0 NA 426980 TCGA-AB-3002 AML28 7 116559358 116559358 A T SNP ST7 NM_021908.3 human genbank 54_36p 1 reviewed intronic c.641+108 e6+108 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 426980 TCGA-AB-3002 AML28 7 123044780 123044780 G A SNP ASB15 NM_080928.3 human genbank 54_36p 1 validated intronic c.293-89 e4-89 0 - - - no_errors tier3 362 1 0.28 259 63 19.57 0 0 NA 426980 TCGA-AB-3002 AML28 7 124764287 124764287 C T SNP RPL31P39 ENST00000393325 human ensembl 54_36p -1 known 5_prime_flanking_region c.-36119 NULL 0 - - - no_coding_region:pseudogene tier3 668 4 0.59 322 214 39.93 0 0 NA 426980 TCGA-AB-3002 AML28 7 126570628 126570628 G T SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.511-36626 e2-36626 0.004 - - - no_errors tier3 652 6 0.91 321 265 45.14 0 0 NA 426980 TCGA-AB-3002 AML28 7 133740407 133740407 G C SNP ENSG00000221513 ENST00000408586 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-18016 NULL 0.317 - - - no_errors tier3 815 7 0.85 386 353 47.57 0 0 NA 426980 TCGA-AB-3002 AML28 7 134053260 134053260 C T SNP BPGM NM_001724.4 human genbank 54_36p 1 validated 3_prime_flanking_region c.*38937 NULL 0 - - - no_errors tier3 335 1 0.3 197 130 39.76 0 0 NA 426980 TCGA-AB-3002 AML28 7 135602031 135602031 C T SNP ENSG00000220982 ENST00000408055 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22209 NULL 0 - - - no_errors tier3 679 7 1.02 430 395 47.71 0 0 NA 426980 TCGA-AB-3002 AML28 7 137103410 137103410 C A SNP DGKI NM_004717.2 human genbank 54_36p -1 reviewed intronic c.402-78122 e2-78122 0.001 - - - no_errors tier2 725 4 0.55 446 376 45.69 0 0 NA 426980 TCGA-AB-3002 AML28 7 142295830 142295830 G A SNP TRPV6 NM_018646.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2447 NULL 0.009 - - - no_errors tier3 2502 43 1.69 392 317 44.71 0 1 100 426980 TCGA-AB-3002 AML28 7 147221246 147221246 G T SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2099-10344 e14-10344 0 - - - no_errors tier3 196 0 0 93 20 17.7 0 0 NA 426980 TCGA-AB-3002 AML28 7 155190566 155190566 C T SNP RBM33 NM_053043.2 human genbank 54_36p 1 validated intronic c.740-1749 e7-1749 0.01 - - - no_errors tier3 252 3 1.18 161 109 40.37 1 1 50 426980 TCGA-AB-3002 AML28 7 155941697 155941697 C T SNP - - - - - - - - - - - - - - - tier3 406 4 0.98 247 172 40.95 0 0 NA 426980 TCGA-AB-3002 AML28 7 156275264 156275264 G C SNP LMBR1 NM_022458.3 human genbank 54_36p -1 reviewed intronic c.423+6580 e5+6580 0 - - - no_errors tier2 144 0 0 110 56 33.73 0 2 100 426980 TCGA-AB-3002 AML28 7 157517592 157517592 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1723+49159 e11+49159 0 - - - no_errors tier3 188 3 1.57 121 108 47.16 0 1 100 426980 TCGA-AB-3002 AML28 7 157881758 157881758 A C SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.164-79373 e3-79373 0 - - - no_errors tier3 74 0 0 25 52 67.53 0 0 NA 426980 TCGA-AB-3002 AML28 7 158142951 158142951 G A SNP NCAPG2 NM_017760.5 human genbank 54_36p -1 validated intronic c.2061-793 e17-793 0.038 - - - no_errors tier3 NA NA NA NA NA NA 2 0 0 426980 TCGA-AB-3002 AML28 8 9643212 9643212 C G SNP TNKS NM_003747.2 human genbank 54_36p 1 validated intronic c.2832+80 e18+80 0.001 - - - no_errors tier2 448 3 0.67 181 130 41.8 2 0 0 426980 TCGA-AB-3002 AML28 8 10506675 10506675 G A SNP RP1L1 NM_178857.5 human genbank 54_36p -1 validated silent c.2343 p.S781 0.026 NULL "HMMPfam_DCX,HMMPfam_S-antigen,superfamily_SSF89837" - no_errors tier1 89 0 113 81 41.75 NA 426980 TCGA-AB-3002 AML28 8 15851312 15851312 G A SNP - - - - - - - - - - - - - - - tier3 476 1 0.21 294 194 39.75 0 0 NA 426980 TCGA-AB-3002 AML28 8 17462562 17462562 C T SNP SLC7A2 NM_003046.2 human genbank 54_36p 1 validated intronic c.1621+228 e9+228 0 - - - no_errors tier3 622 4 0.64 417 85 16.9 0 0 0 426980 TCGA-AB-3002 AML28 8 18259595 18259595 G A SNP NAT2 NM_000015.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-42199 NULL 0.001 - - - no_errors tier3 910 4 0.44 543 405 42.72 0 0 NA 426980 TCGA-AB-3002 AML28 8 18423549 18423549 C - DEL PSD3 NM_015310.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*13984 NULL 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 8 19134873 19134873 G A SNP LOC100128993 XM_001716686.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-48379 NULL 0.331 - - - no_errors tier3 506 5 0.98 178 107 37.54 0 0 NA 426980 TCGA-AB-3002 AML28 8 19797430 19797430 C T SNP LPL NM_000237.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-43802 NULL 0.005 - - - no_errors tier3 462 8 1.7 112 41 26.8 0 0 NA 426980 TCGA-AB-3002 AML28 8 23399978 23399978 G A SNP ENTPD4 NM_004901.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-36620 NULL 0.005 - - - no_errors tier3 363 2 0.55 152 93 37.8 0 0 NA 426980 TCGA-AB-3002 AML28 8 25223614 25223614 T C SNP DOCK5 NM_024940.6 human genbank 54_36p 1 validated intronic c.1193-226 e13-226 0.001 - - - no_errors tier3 344 3 0.86 156 145 48.17 0 0 0 426980 TCGA-AB-3002 AML28 8 26147194 26147195 - AT INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 8 37071774 37071774 C T SNP - - - - - - - - - - - - - - - tier3 712 4 0.56 355 256 41.63 0 0 NA 426980 TCGA-AB-3002 AML28 8 43485609 43485609 G C SNP ENSG00000221295 ENST00000408368 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-49359 NULL 0.068 - - - no_errors tier3 290 0 0 143 103 41.87 0 0 NA 426980 TCGA-AB-3002 AML28 8 52755739 52755739 T C SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.165-25866 e2-25866 0.001 - - - no_errors tier3 556 1 0.18 234 188 44.55 0 0 NA 426980 TCGA-AB-3002 AML28 8 55700208 55700208 G A SNP RP1 ENST00000220676 human ensembl 54_36p 1 known missense c.1213 p.A405T 0 NULL "HMMPfam_DCX,HMMSmart_DCX,superfamily_SSF89837" - no_errors tier1 331 2 0.6 175 141 44.62 NA 426980 TCGA-AB-3002 AML28 8 56048319 56048319 G A SNP - - - - - - - - - - - - - - - tier3 495 4 0.8 496 405 44.95 0 0 NA 426980 TCGA-AB-3002 AML28 8 57570082 57570082 G A SNP LOC389662 XR_016813.2 human genbank 54_36p -1 model intronic c.NULL NULL 0.004 - - - pseudogene tier3 353 4 1.11 151 104 40.47 0 0 NA 426980 TCGA-AB-3002 AML28 8 58670535 58670535 G A SNP LOC100130588 XM_001719422.1 human genbank 54_36p -1 model intronic c.127-960 e3-960 0 - - - no_errors tier3 410 2 0.49 261 178 40.55 0 0 NA 426980 TCGA-AB-3002 AML28 8 66169424 66169424 G T SNP - - - - - - - - - - - - - - - tier2 477 5 1.04 311 220 41.43 0 0 NA 426980 TCGA-AB-3002 AML28 8 72476284 72476284 G A SNP EYA1 NM_000503.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-46590 NULL 0.001 - - - no_errors tier3 694 2 0.29 363 84 18.71 0 0 NA 426980 TCGA-AB-3002 AML28 8 72546076 72546076 A T SNP ENSG00000221446 ENST00000408519 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*21479 NULL 0.005 - - - no_errors tier3 307 7 2.23 105 78 42.62 0 0 NA 426980 TCGA-AB-3002 AML28 8 73514564 73514564 G A SNP LOC100129527 XM_001715839.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*9849 NULL 0.004 - - - no_errors tier3 1 0 0 NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 8 75389062 75389062 G A SNP JPH1 NM_020647.2 human genbank 54_36p -1 reviewed intronic c.1139+589 e2+589 0 - - - no_errors tier3 402 2 0.49 145 127 46.69 0 0 NA 426980 TCGA-AB-3002 AML28 8 75738723 75738723 G A SNP FLJ39080 XM_499117.1 human genbank 54_36p 1 model intronic c.74-38446 e2-38446 0 - - - no_errors tier3 681 4 0.58 372 277 42.68 0 0 NA 426980 TCGA-AB-3002 AML28 8 76476615 76476615 C T SNP HNF4G ENST00000354370 human ensembl 54_36p 1 known 5_prime_flanking_region c.-142009 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 8 76851577 76851577 C - DEL ENSG00000221029 ENST00000408102 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9578 NULL 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 8 77816396 77816396 C G SNP ZFHX4 NM_024721.3 human genbank 54_36p 1 validated intronic c.3015+33558 e2+33558 0.001 - - - no_errors tier3 566 15 2.58 400 352 46.81 0 0 NA 426980 TCGA-AB-3002 AML28 8 85107492 85107492 C T SNP - - - - - - - - - - - - - - - tier2 211 2 0.94 172 113 39.65 0 0 NA 426980 TCGA-AB-3002 AML28 8 85843154 85843154 G A SNP RALYL NM_001100391.1 human genbank 54_36p 1 validated intronic c.296-6215 e3-6215 0 - - - no_errors tier3 755 8 1.05 778 576 42.51 0 0 NA 426980 TCGA-AB-3002 AML28 8 89286241 89286241 C T SNP MMP16 NM_005941.4 human genbank 54_36p -1 reviewed intronic c.133-7590 e2-7590 0.028 - - - no_errors tier3 456 6 1.3 355 293 45.15 0 0 NA 426980 TCGA-AB-3002 AML28 8 89616994 89616994 T C SNP - - - - - - - - - - - - - - - tier3 547 5 0.91 263 253 48.84 0 0 NA 426980 TCGA-AB-3002 AML28 8 93370813 93370813 C A SNP - - - - - - - - - - - - - - - tier2 274 2 0.72 117 104 47.06 0 0 NA 426980 TCGA-AB-3002 AML28 8 96685869 96685869 A G SNP ENSG00000202112 ENST00000365242 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*5246 NULL 0.013 - - - no_errors tier3 462 5 1.07 110 73 39.89 0 0 NA 426980 TCGA-AB-3002 AML28 8 99211320 99211320 A C SNP POP1 NM_015029.1 human genbank 54_36p 1 reviewed intronic c.487-62 e4-62 0 - - - no_errors tier3 415 3 0.72 194 169 46.56 0 0 0 426980 TCGA-AB-3002 AML28 8 112237114 112237114 C T SNP - - - - - - - - - - - - - - - tier2 96 0 0 19 13 40.62 0 0 NA 426980 TCGA-AB-3002 AML28 8 113969221 113969221 A C SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1634-28550 e11-28550 0.242 - - - no_errors tier3 309 1 0.32 146 144 49.66 0 0 NA 426980 TCGA-AB-3002 AML28 8 114061517 114061517 C A SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1031-3964 e7-3964 0.053 - - - no_errors tier3 34 0 0 5 1 16.67 0 0 NA 426980 TCGA-AB-3002 AML28 8 115392566 115392566 G A SNP - - - - - - - - - - - - - - - tier2 173 1 0.57 88 62 41.33 0 0 NA 426980 TCGA-AB-3002 AML28 8 118042077 118042077 C G SNP SLC30A8 ENST00000297345 human ensembl 54_36p 1 known intronic c.1+9538 e0+9538 0 - - - no_errors tier3 560 6 1.06 195 146 42.82 0 0 NA 426980 TCGA-AB-3002 AML28 8 122275659 122275659 T A SNP ENSG00000221644 ENST00000408717 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-7346 NULL 0.568 - - - no_errors tier2 210 1 0.47 149 129 46.4 0 0 NA 426980 TCGA-AB-3002 AML28 8 123028149 123028149 A T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 8 128036043 128036043 T C SNP - - - - - - - - - - - - - - - tier3 323 2 0.62 294 292 49.74 1 0 0 426980 TCGA-AB-3002 AML28 8 131174594 131174594 T C SNP ASAP1 NM_018482.2 human genbank 54_36p -1 validated intronic c.2402-1023 e24-1023 0.002 - - - no_errors tier3 705 11 1.54 301 290 49.07 2 3 60 426980 TCGA-AB-3002 AML28 8 132097125 132097125 A - DEL ADCY8 NM_001115.2 human genbank 54_36p -1 reviewed intronic c.960+23677 e1+23677 0.007 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 8 134943869 134943869 C G SNP - - - - - - - - - - - - - - - tier3 1851 151 7.52 787 601 43.24 0 0 NA 426980 TCGA-AB-3002 AML28 8 135796003 135796003 A G SNP ZFAT NM_020863.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-1715 NULL 0.001 - - - no_errors tier3 237 2 0.84 85 54 38.85 1 0 0 426980 TCGA-AB-3002 AML28 8 137034741 137034741 T C SNP - - - - - - - - - - - - - - - tier3 313 0 0 130 135 50.75 0 0 NA 426980 TCGA-AB-3002 AML28 8 137468026 137468026 A G SNP - - - - - - - - - - - - - - - tier3 68 1 1.45 20 16 44.44 0 0 NA 426980 TCGA-AB-3002 AML28 8 138290660 138290660 G A SNP - - - - - - - - - - - - - - - tier3 622 6 0.96 269 237 46.84 0 0 NA 426980 TCGA-AB-3002 AML28 8 140518544 140518544 C T SNP - - - - - - - - - - - - - - - tier3 551 6 1.08 241 202 45.5 0 0 NA 426980 TCGA-AB-3002 AML28 9 2900026 2900026 A G SNP ENSG00000215888 ENST00000401056 human ensembl 54_36p -1 known 5_prime_flanking_region c.-9222 NULL 0.368 - - - no_coding_region:pseudogene tier2 429 0 0 199 182 47.64 0 0 NA 426980 TCGA-AB-3002 AML28 9 4574855 4574855 C T SNP SLC1A1 NM_004170.4 human genbank 54_36p 1 validated intronic c.1329-457 e12-457 0 - - - no_errors tier3 437 3 0.68 441 340 43.37 0 0 NA 426980 TCGA-AB-3002 AML28 9 6574961 6574961 C T SNP GLDC NM_000170.2 human genbank 54_36p -1 validated intronic c.1850+2180 e15+2180 0.004 - - - no_errors tier3 346 2 0.57 247 198 44.49 1 0 0 426980 TCGA-AB-3002 AML28 9 7987216 7987216 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 9 11173362 11173362 G A SNP - - - - - - - - - - - - - - - tier3 390 8 2.01 152 105 40.86 0 0 NA 426980 TCGA-AB-3002 AML28 9 11413168 11413168 G T SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 9 12504476 12504476 G A SNP - - - - - - - - - - - - - - - tier3 459 2 0.43 310 252 44.76 0 0 NA 426980 TCGA-AB-3002 AML28 9 17216283 17216283 C T SNP CNTLN NM_017738.1 human genbank 54_36p 1 validated nonsense c.532 p.Q178* 1 superfamily_Prefoldin superfamily_Prefoldin - no_errors tier1 92 5 5.1 20 10 33.33 6 9 60 426980 TCGA-AB-3002 AML28 9 21738898 21738898 G A SNP ENSG00000210529 ENST00000387794 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*49375 NULL 0.052 - - - pseudogene tier3 152 0 0 32 12 27.27 0 0 NA 426980 TCGA-AB-3002 AML28 9 24735941 24735941 G A SNP - - - - - - - - - - - - - - - tier2 689 5 0.72 282 253 47.11 0 0 NA 426980 TCGA-AB-3002 AML28 9 24757662 24757662 C A SNP - - - - - - - - - - - - - - - tier3 465 2 0.43 263 217 45.21 0 0 NA 426980 TCGA-AB-3002 AML28 9 26298028 26298028 G C SNP - - - - - - - - - - - - - - - tier3 608 5 0.82 262 248 48.63 0 0 NA 426980 TCGA-AB-3002 AML28 9 27997115 27997115 C T SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1+5238 e0+5238 0 - - - no_errors tier3 765 4 0.52 449 332 42.46 0 0 NA 426980 TCGA-AB-3002 AML28 9 28164689 28164689 G A SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1+120517 e0+120517 0 - - - no_errors tier3 808 5 0.61 349 282 44.69 0 0 NA 426980 TCGA-AB-3002 AML28 9 28922586 28922586 G A SNP MIRN873 ENST00000401120 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43633 NULL 0.001 - - - no_errors tier3 606 4 0.66 214 159 42.63 0 0 NA 426980 TCGA-AB-3002 AML28 9 30807342 30807342 T C SNP ENSG00000221111 ENST00000408184 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-46145 NULL 0.01 - - - no_errors tier3 392 1 0.25 146 134 47.86 0 0 NA 426980 TCGA-AB-3002 AML28 9 30956521 30956521 C T SNP ENSG00000217724 ENST00000406166 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21562 NULL 0.003 - - - no_coding_region:pseudogene tier3 205 1 0.49 97 77 44.25 0 0 NA 426980 TCGA-AB-3002 AML28 9 31574972 31574972 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 9 33588933 33588933 T G SNP ANXA2P2 NR_003573.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25290 NULL 0 - - - pseudogene tier3 556 0 0 344 229 39.97 0 0 NA 426980 TCGA-AB-3002 AML28 9 73195718 73195718 G A SNP TRPM3 ENST00000357533 human ensembl 54_36p -1 known intronic c.183+55671 e1+55671 0 - - - no_errors tier3 571 7 1.21 239 196 45.06 0 0 NA 426980 TCGA-AB-3002 AML28 9 77399619 77399619 G A SNP - - - - - - - - - - - - - - - tier3 327 1 0.3 174 131 42.95 0 0 NA 426980 TCGA-AB-3002 AML28 9 78323275 78323275 A G SNP GCNT1 NM_001097633.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*14871 NULL 0 - - - no_errors tier3 219 2 0.9 71 49 40.83 2 1 33.33 426980 TCGA-AB-3002 AML28 9 81024926 81024926 C T SNP - - - - - - - - - - - - - - - tier3 301 4 1.31 155 115 42.44 0 0 NA 426980 TCGA-AB-3002 AML28 9 84985243 84985243 A G SNP - - - - - - - - - - - - - - - tier3 242 2 0.82 105 82 43.85 0 0 NA 426980 TCGA-AB-3002 AML28 9 87569444 87569444 C T SNP LOC100129901 XM_001716099.1 human genbank 54_36p 1 model missense c.128 p.A43V 0.997 NULL NULL - no_errors tier1 118 2 1.67 91 45 33.09 1 0 426980 TCGA-AB-3002 AML28 9 92449569 92449569 C T SNP DIRAS2 NM_017594.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-33640 NULL 0 - - - no_errors tier3 876 12 1.35 285 223 43.9 0 0 NA 426980 TCGA-AB-3002 AML28 9 97039394 97039394 C T SNP FANCC NM_000136.2 human genbank 54_36p -1 reviewed intronic c.345+3358 e3+3358 0.002 - - - no_errors tier3 776 6 0.77 776 539 40.9 2 0 0 426980 TCGA-AB-3002 AML28 9 105869891 105869891 A T SNP SMC2 NM_001042550.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-27596 NULL 0.015 - - - no_errors tier3 215 1 0.46 89 46 34.07 0 0 NA 426980 TCGA-AB-3002 AML28 9 108932860 108932860 G A SNP LOC100128086 XR_039419.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*12836 NULL 0.004 - - - pseudogene tier3 601 6 0.99 211 170 44.5 0 0 NA 426980 TCGA-AB-3002 AML28 9 116084387 116084387 G A SNP COL27A1 NM_032888.2 human genbank 54_36p 1 provisional missense c.3727 p.G1243R 1 HMMPfam_Collagen "HMMPfam_COLFI,HMMSmart_SM00038,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases" - no_errors tier1 123 2 1.6 82 60 42.25 NA 426980 TCGA-AB-3002 AML28 9 120306397 120306397 A T SNP - - - - - - - - - - - - - - - tier2 278 1 0.36 168 141 45.63 0 0 NA 426980 TCGA-AB-3002 AML28 9 120330151 120330151 A T SNP - - - - - - - - - - - - - - - tier3 416 2 0.48 252 208 45.22 0 0 NA 426980 TCGA-AB-3002 AML28 9 121505224 121505224 C T SNP - - - - - - - - - - - - - - - tier3 985 5 0.5 702 509 42 0 0 NA 426980 TCGA-AB-3002 AML28 9 121657474 121657474 C T SNP ENSG00000222745 ENST00000410813 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29572 NULL 0 - - - no_errors tier3 2524 39 1.52 1067 798 42.72 0 0 NA 426980 TCGA-AB-3002 AML28 9 123859764 123859764 A G SNP TTLL11 NM_194252.1 human genbank 54_36p -1 validated intronic c.733-18296 e2-18296 0.001 - - - no_errors tier3 421 8 1.86 210 214 50.47 0 0 0 426980 TCGA-AB-3002 AML28 9 124312959 124312959 C T SNP OR1J2 NM_054107.1 human genbank 54_36p 1 provisional missense c.58 p.R20W 0.002 superfamily_Family A G protein-coupled receptor-like "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 891 8 0.89 608 449 42.4 NA 426980 TCGA-AB-3002 AML28 9 125059195 125059195 C T SNP STRBP NM_018387.3 human genbank 54_36p -1 validated intronic c.1+11341 e0+11341 0.001 - - - no_errors tier3 637 11 1.7 232 168 42 2 3 60 426980 TCGA-AB-3002 AML28 9 135505247 135505247 C T SNP DBH NM_000787.3 human genbank 54_36p 1 reviewed intronic c.1192-1330 e7-1330 0 - - - no_errors tier3 221 2 0.9 101 80 44.2 4 2 33.33 426980 TCGA-AB-3002 AML28 10 5825694 5825694 A C SNP C10orf18 NM_017782.3 human genbank 54_36p 1 validated intronic c.2757+1199 e11+1199 0.003 - - - no_errors tier3 287 2 0.69 115 101 46.76 0 2 100 426980 TCGA-AB-3002 AML28 10 6072229 6072229 T C SNP IL15RA NM_002189.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12768 NULL 0.001 - - - no_errors tier3 444 8 1.77 145 161 52.61 0 0 NA 426980 TCGA-AB-3002 AML28 10 6189881 6189881 G A SNP RBM17 NM_032905.1 human genbank 54_36p 1 reviewed intronic c.506-774 e5-774 0.001 - - - no_errors tier3 467 1 0.21 210 86 29.05 10 13 56.52 426980 TCGA-AB-3002 AML28 10 7974199 7974199 G A SNP TAF3 NM_031923.2 human genbank 54_36p 1 provisional intronic c.409+67670 e2+67670 0.048 - - - no_errors tier3 410 5 1.2 197 152 43.55 0 0 0 426980 TCGA-AB-3002 AML28 10 14197973 14197973 C T SNP FRMD4A NM_018027.3 human genbank 54_36p -1 validated intronic c.45+214090 e1+214090 0 - - - no_errors tier3 896 2 0.22 426 304 41.59 0 0 NA 426980 TCGA-AB-3002 AML28 10 16571520 16571520 T - DEL PTER NM_001001484.1 human genbank 54_36p 1 validated intronic c.698+2898 e2+2898 0.153 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 21774153 21774153 C G SNP ENSG00000199222 ENST00000362352 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36498 NULL 0.996 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 24053538 24053538 T A SNP KIAA1217 NM_001098500.1 human genbank 54_36p 1 validated intronic c.1+29369 e0+29369 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 35053174 35053174 A G SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional intronic c.121-27821 e2-27821 0 - - - no_errors tier2 432 3 0.69 188 187 49.87 0 0 0 426980 TCGA-AB-3002 AML28 10 36520796 36520796 C A SNP - - - - - - - - - - - - - - - tier3 789 14 1.74 452 441 49.38 0 0 NA 426980 TCGA-AB-3002 AML28 10 37158144 37158144 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 37641146 37641146 C T SNP LOC646360 XM_933553.1 human genbank 54_36p 1 model intronic c.51-2166 e2-2166 0 - - - no_errors tier2 537 4 0.74 254 169 39.95 0 0 NA 426980 TCGA-AB-3002 AML28 10 49813619 49813619 C T SNP WDFY4 ENST00000325239 human ensembl 54_36p 1 known intronic c.3129-6238 e18-6238 0 - - - no_errors tier3 389 2 0.51 144 106 42.4 0 2 100 426980 TCGA-AB-3002 AML28 10 52992328 52992328 C A SNP PRKG1 NM_006258.1 human genbank 54_36p 1 validated intronic c.592+94726 e3+94726 0.451 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 56438960 56438961 TT - DEL PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1-111695_111696 e1-111694 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 58352080 58352080 C T SNP - - - - - - - - - - - - - - - tier3 382 1 0.26 125 105 45.65 0 0 NA 426980 TCGA-AB-3002 AML28 10 58951851 58951851 C T SNP ENSG00000218583 ENST00000403728 human ensembl 54_36p 1 known 3_prime_flanking_region c.*8660 NULL 0 - - - no_coding_region:pseudogene tier3 295 3 1 299 206 40.71 0 0 NA 426980 TCGA-AB-3002 AML28 10 63067047 63067047 A G SNP C10orf107 NM_173554.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-43960 NULL 0.002 - - - no_errors tier3 187 1 0.53 43 57 57 0 0 NA 426980 TCGA-AB-3002 AML28 10 65525766 65525766 C T SNP - - - - - - - - - - - - - - - tier3 380 3 0.78 103 71 40.8 0 0 NA 426980 TCGA-AB-3002 AML28 10 65586533 65586533 T - DEL LOC100129267 XR_037245.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*13103 NULL 0 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 79512024 79512024 G A SNP ENSG00000220250 ENST00000404396 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12633 NULL 0.993 - - - no_coding_region:pseudogene tier2 1364 11 0.8 553 437 44.14 0 0 0 426980 TCGA-AB-3002 AML28 10 79693537 79693537 C T SNP - - - - - - - - - - - - - - - tier3 574 8 1.37 312 236 43.07 1 1 50 426980 TCGA-AB-3002 AML28 10 81829774 81829774 C T SNP C10orf57 NM_025125.2 human genbank 54_36p 1 predicted intronic c.87+1252 e1+1252 0 - - - no_errors tier2 927 5 0.54 326 294 47.42 0 2 100 426980 TCGA-AB-3002 AML28 10 84233189 84233189 T C SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.953+124585 e2+124585 0 - - - no_errors tier3 620 5 0.8 573 470 45.02 0 0 NA 426980 TCGA-AB-3002 AML28 10 84773201 84773201 C G SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*37860 NULL 0.001 - - - no_errors tier3 751 1 0.13 342 55 13.82 0 0 NA 426980 TCGA-AB-3002 AML28 10 87275037 87275037 A - DEL ENSG00000223064 ENST00000411132 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-12079 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 89666645 89666645 T C SNP PTEN NM_000314.4 human genbank 54_36p 1 reviewed intronic c.165-8605 e3-8605 0.006 - - - no_errors tier3 996 8 0.8 405 335 45.27 11 8 42.11 426980 TCGA-AB-3002 AML28 10 90135755 90135755 C G SNP C10orf59 NM_001031709.1 human genbank 54_36p -1 provisional intronic c.527-23293 e5-23293 0.754 - - - no_errors tier3 388 4 1.02 239 165 40.84 0 0 NA 426980 TCGA-AB-3002 AML28 10 91687622 91687622 C T SNP LOC119358 XM_061427.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40832 NULL 0.002 - - - no_errors tier3 309 2 0.64 172 89 34.1 1 0 0 426980 TCGA-AB-3002 AML28 10 97380898 97380898 T C SNP ALDH18A1 NM_002860.1 human genbank 54_36p -1 reviewed intronic c.808+1808 e6+1808 0.001 - - - no_errors tier3 584 5 0.85 172 103 37.32 3 3 50 426980 TCGA-AB-3002 AML28 10 100679446 100679446 A C SNP HPSE2 NM_021828.3 human genbank 54_36p -1 validated intronic c.611-185643 e4-185643 0.019 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 106329053 106329053 G A SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 106427870 106427870 C T SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.627+36168 e1+36168 0.018 - - - no_errors tier3 552 5 0.9 342 276 44.66 0 0 NA 426980 TCGA-AB-3002 AML28 10 106961580 106961580 C A SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.2375+582 e17+582 0 - - - no_errors tier3 619 9 1.43 172 138 44.52 0 0 NA 426980 TCGA-AB-3002 AML28 10 107464815 107464815 A G SNP ENSG00000218440 ENST00000402674 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29202 NULL 0.004 - - - no_coding_region:pseudogene tier3 511 8 1.54 554 470 45.81 0 0 NA 426980 TCGA-AB-3002 AML28 10 112425052 112425052 G A SNP ENSG00000203869 ENST00000369521 human ensembl 54_36p 1 known intronic c.191+30659 e1+30659 0.001 - - - no_stop_codon tier3 654 4 0.61 335 270 44.63 0 0 NA 426980 TCGA-AB-3002 AML28 10 113939543 113939543 C - DEL GPAM NM_020918.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-8011 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 119569098 119569098 C A SNP - - - - - - - - - - - - - - - tier3 706 7 0.98 342 287 45.56 0 0 NA 426980 TCGA-AB-3002 AML28 10 120068920 120068920 T C SNP C10orf84 NM_022063.1 human genbank 54_36p -1 validated intronic c.543+6736 e5+6736 0 - - - no_errors tier3 224 3 1.32 38 45 54.22 4 1 20 426980 TCGA-AB-3002 AML28 10 122869500 122869500 G A SNP RPL19P16 ENST00000403175 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13020 NULL 0.018 - - - no_coding_region:pseudogene tier3 520 4 0.76 402 303 42.92 0 0 NA 426980 TCGA-AB-3002 AML28 10 129477518 129477518 A T SNP FOXI2 NM_207426.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*50299 NULL 0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 131267265 131267265 G A SNP MGMT NM_002412.3 human genbank 54_36p 1 validated intronic c.125+42634 e1+42634 0.001 - - - no_errors tier3 346 5 1.42 156 133 45.7 1 0 0 426980 TCGA-AB-3002 AML28 10 131606443 131606443 G A SNP EBF3 NM_001005463.1 human genbank 54_36p -1 validated intronic c.554+39069 e6+39069 0.001 - - - no_errors tier3 219 1 0.45 114 100 46.73 0 0 NA 426980 TCGA-AB-3002 AML28 10 133030953 133030953 G A SNP TCERG1L NM_174937.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31065 NULL 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 133123730 133123730 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 10 134689001 134689001 C T SNP GPR123 ENST00000368577 human ensembl 54_36p 1 known 5_prime_flanking_region c.-45422 NULL 0 - - - no_errors tier3 68 3 4.17 38 30 44.12 0 0 NA 426980 TCGA-AB-3002 AML28 11 9755975 9755975 C T SNP - - - - - - - - - - - - - - - tier2 560 11 1.92 349 246 41.34 4 0 0 426980 TCGA-AB-3002 AML28 11 11195136 11195136 G A SNP - - - - - - - - - - - - - - - tier2 1454 11 0.75 1068 880 45.13 0 0 NA 426980 TCGA-AB-3002 AML28 11 23229336 23229336 G A SNP - - - - - - - - - - - - - - - tier3 179 3 1.65 60 38 38.78 0 0 NA 426980 TCGA-AB-3002 AML28 11 25378975 25378975 G A SNP - - - - - - - - - - - - - - - tier2 585 7 1.18 201 158 44.01 0 0 NA 426980 TCGA-AB-3002 AML28 11 25798017 25798017 C A SNP - - - - - - - - - - - - - - - tier3 207 2 0.96 28 19 40.43 0 0 NA 426980 TCGA-AB-3002 AML28 11 26915201 26915201 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 11 27181250 27181250 T A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 11 29982645 29982645 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 11 35240206 35240206 A G SNP - - - - - - - - - - - - - - - tier2 588 2 0.34 275 203 42.47 0 3 100 426980 TCGA-AB-3002 AML28 11 36946532 36946532 G A SNP - - - - - - - - - - - - - - - tier3 416 4 0.95 320 218 40.52 0 0 NA 426980 TCGA-AB-3002 AML28 11 39838693 39838696 TATT - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 11 40908778 40908778 C A SNP - - - - - - - - - - - - - - - tier3 278 1 0.36 210 155 42.47 0 0 NA 426980 TCGA-AB-3002 AML28 11 41590836 41590836 C T SNP - - - - - - - - - - - - - - - tier3 725 2 0.27 577 434 42.8 0 0 NA 426980 TCGA-AB-3002 AML28 11 42335523 42335523 G A SNP - - - - - - - - - - - - - - - tier3 548 5 0.9 276 244 46.83 0 0 NA 426980 TCGA-AB-3002 AML28 11 42653124 42653124 C T SNP - - - - - - - - - - - - - - - tier3 721 4 0.55 203 142 41.16 0 0 NA 426980 TCGA-AB-3002 AML28 11 44434800 44434800 A T SNP - - - - - - - - - - - - - - - tier2 465 3 0.64 71 66 48.18 0 0 NA 426980 TCGA-AB-3002 AML28 11 45926741 45926741 C T SNP - - - - - - - - - - - - - - - tier3 415 2 0.48 385 285 42.47 5 6 54.55 426980 TCGA-AB-3002 AML28 11 54809368 54809368 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 11 56001745 56001745 T A SNP - - - - - - - - - - - - - - - tier3 513 11 2.1 162 181 52.77 0 0 NA 426980 TCGA-AB-3002 AML28 11 58285661 58285661 C G SNP - - - - - - - - - - - - - - - tier3 519 4 0.76 325 275 45.83 0 0 NA 426980 TCGA-AB-3002 AML28 11 61231163 61231163 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 11 64708652 64708652 A G SNP - - - - - - - - - - - - - - - tier2 265 4 1.49 177 152 46.2 0 2 100 426980 TCGA-AB-3002 AML28 11 71927795 71927795 C A SNP - - - - - - - - - - - - - - - tier3 660 10 1.49 866 578 40.03 0 0 NA 426980 TCGA-AB-3002 AML28 11 72603052 72603052 G A SNP - - - - - - - - - - - - - - - tier2 391 7 1.76 174 130 42.76 0 0 NA 426980 TCGA-AB-3002 AML28 11 72623244 72623244 G T SNP P2RY2 NM_002564.2 human genbank 54_36p 1 reviewed missense c.392 p.R131L 1 "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 798 3 0.37 278 242 46.54 5 6 54.55 426980 TCGA-AB-3002 AML28 11 75643493 75643493 A G SNP - - - - - - - - - - - - - - - tier3 542 4 0.73 324 221 40.55 0 0 NA 426980 TCGA-AB-3002 AML28 11 81152507 81152507 C T SNP - - - - - - - - - - - - - - - tier3 280 2 0.7 222 167 42.93 0 0 NA 426980 TCGA-AB-3002 AML28 11 81336777 81336777 A G SNP - - - - - - - - - - - - - - - tier3 395 5 1.25 187 134 41.74 0 0 NA 426980 TCGA-AB-3002 AML28 11 84939643 84939643 C A SNP - - - - - - - - - - - - - - - tier3 318 3 0.93 275 155 36.05 1 0 0 426980 TCGA-AB-3002 AML28 11 90823611 90823611 A T SNP - - - - - - - - - - - - - - - tier3 180 5 2.7 47 46 49.46 0 0 NA 426980 TCGA-AB-3002 AML28 11 93400566 93400566 C T SNP - - - - - - - - - - - - - - - tier3 765 12 1.54 592 455 43.46 0 0 NA 426980 TCGA-AB-3002 AML28 11 94446918 94446918 G A SNP - - - - - - - - - - - - - - - tier3 1045 7 0.67 387 317 45.03 0 0 NA 426980 TCGA-AB-3002 AML28 11 95840778 95840778 A G SNP - - - - - - - - - - - - - - - tier3 941 12 1.26 592 537 47.56 0 0 NA 426980 TCGA-AB-3002 AML28 11 98865252 98865252 C T SNP - - - - - - - - - - - - - - - tier3 330 6 1.78 228 169 42.57 0 0 NA 426980 TCGA-AB-3002 AML28 11 101052879 101052879 A G SNP - - - - - - - - - - - - - - - tier3 266 4 1.48 213 211 49.65 0 0 NA 426980 TCGA-AB-3002 AML28 11 105019563 105019563 T C SNP GRIA4 NM_000829.3 human genbank 54_36p 1 reviewed intronic c.247+31192 e2+31192 0.002 - - - no_errors tier3 246 0 0 133 120 47.43 0 0 NA 426980 TCGA-AB-3002 AML28 11 107076075 107076075 C G SNP SLN NM_003063.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*7696 NULL 0.004 - - - no_errors tier3 643 5 0.77 281 214 42.97 0 0 NA 426980 TCGA-AB-3002 AML28 11 111880324 111880324 C T SNP ENSG00000213233 ENST00000393025 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42090 NULL 0.002 - - - no_coding_region:pseudogene tier3 538 5 0.92 324 291 47.32 0 0 NA 426980 TCGA-AB-3002 AML28 11 112163120 112163120 C T SNP - - - - - - - - - - - - - - - tier2 327 6 1.8 266 190 41.67 0 0 NA 426980 TCGA-AB-3002 AML28 11 112700960 112700960 A T SNP TTC12 NM_017868.3 human genbank 54_36p 1 validated intronic c.322+346 e4+346 0 - - - no_errors tier3 505 7 1.37 367 320 46.58 0 0 NA 426980 TCGA-AB-3002 AML28 11 112788535 112788535 G A SNP DRD2 NM_000795.3 human genbank 54_36p -1 reviewed missense c.1091 p.S364F 1 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 698 11 1.55 339 282 45.41 NA 426980 TCGA-AB-3002 AML28 11 113654890 113654890 G A SNP NNMT NM_006169.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17599 NULL 0.002 - - - no_errors tier3 921 12 1.28 663 449 40.38 0 0 NA 426980 TCGA-AB-3002 AML28 11 114673288 114673288 G A SNP CADM1 NM_014333.1 human genbank 54_36p -1 validated intronic c.125-56938 e2-56938 1 - - - no_errors tier2 356 0 0 250 208 45.32 0 0 NA 426980 TCGA-AB-3002 AML28 11 115268684 115268684 C T SNP LOC728842 XM_001128599.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-30881 NULL 1 - - - no_errors tier2 2321 19 0.81 663 455 40.62 0 0 NA 426980 TCGA-AB-3002 AML28 11 126198932 126198932 G T SNP KIRREL3 NM_032531.2 human genbank 54_36p -1 provisional intronic c.55+176629 e1+176629 0.002 - - - no_errors tier3 438 1 0.23 541 112 17.15 0 0 NA 426980 TCGA-AB-3002 AML28 11 131387313 131387313 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.167+100561 e2+100561 0.847 - - - no_errors tier2 443 4 0.89 255 246 49.1 0 0 NA 426980 TCGA-AB-3002 AML28 11 132379291 132379291 A G SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.62-61176 e2-61176 0 - - - no_errors tier3 911 17 1.83 456 374 45.01 0 0 NA 426980 TCGA-AB-3002 AML28 11 132852036 132852036 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+55333 e1+55333 0 - - - no_errors tier3 668 8 1.18 404 320 44.08 0 0 NA 426980 TCGA-AB-3002 AML28 11 132950129 132950129 T A SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42700 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 11 133896437 133896437 C A SNP - - - - - - - - - - - - - - - tier3 413 2 0.48 124 141 53.21 0 0 NA 426980 TCGA-AB-3002 AML28 11 134163837 134163837 G A SNP - - - - - - - - - - - - - - - tier3 516 1 0.19 316 242 43.37 0 0 NA 426980 TCGA-AB-3002 AML28 12 6107212 6107213 - A INS VWF NM_000552.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4589 NULL 0.001:0.012 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 12 11544130 11544130 C A SNP ENSG00000221128 ENST00000408201 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*41994 NULL 0 - - - no_errors tier3 602 4 0.66 307 216 41.3 0 0 0 426980 TCGA-AB-3002 AML28 12 17634611 17634611 G A SNP - - - - - - - - - - - - - - - tier3 217 3 1.36 101 53 34.42 0 0 NA 426980 TCGA-AB-3002 AML28 12 22501031 22501031 A G SNP KIAA0528 NM_014802.1 human genbank 54_36p -1 predicted intronic c.2724+141 e22+141 0.006 - - - no_errors tier3 172 1 0.58 37 37 50 1 2 66.67 426980 TCGA-AB-3002 AML28 12 38252047 38252047 C T SNP ABCD2 NM_005164.3 human genbank 54_36p -1 reviewed intronic c.2003+1738 e9+1738 0 - - - no_errors tier3 237 5 2.06 101 83 45.11 0 0 NA 426980 TCGA-AB-3002 AML28 12 39750696 39750696 T C SNP CNTN1 NM_001843.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*592 NULL 1 - - - no_errors tier3 135 0 0 54 40 42.55 0 0 NA 426980 TCGA-AB-3002 AML28 12 40738362 40738362 T C SNP ENSG00000222884 ENST00000410952 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21468 NULL 0.023 - - - no_errors tier3 232 4 1.69 83 67 44.67 0 0 NA 426980 TCGA-AB-3002 AML28 12 45726711 45726711 T G SNP FAM113B ENST00000321382 human ensembl 54_36p 1 known 5_prime_flanking_region c.-188403 NULL 0.001 - - - no_errors tier3 346 5 1.42 296 213 41.85 0 0 NA 426980 TCGA-AB-3002 AML28 12 49922439 49922439 A G SNP DAZAP2 NM_014764.1 human genbank 54_36p 1 reviewed missense c.437 p.N146S 1 NULL NULL - no_errors tier1 1029 5 0.48 505 419 45.35 202 152 42.94 426980 TCGA-AB-3002 AML28 12 52469557 52469558 - A INS ENSG00000223213 ENST00000411281 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1797 NULL 0.000:0.016 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 12 52630115 52630115 G A SNP HOXC10 NM_017409.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35196 NULL 0.351 - - - no_errors tier2 206 2 0.96 63 52 45.22 0 0 NA 426980 TCGA-AB-3002 AML28 12 60459060 60459060 T A SNP FAM19A2 NM_178539.3 human genbank 54_36p -1 reviewed intronic c.107-23988 e2-23988 0.001 - - - no_errors tier3 630 13 2.02 415 313 42.99 0 0 NA 426980 TCGA-AB-3002 AML28 12 61776966 61776966 C T SNP AVPR1A NM_000706.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*50440 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 12 65872532 65872532 G A SNP - - - - - - - - - - - - - - - tier2 850 8 0.93 454 393 46.4 0 0 NA 426980 TCGA-AB-3002 AML28 12 67318219 67318219 G T SNP RAP1B NM_001010942.1 human genbank 54_36p 1 validated intronic c.1-10527 e1-10527 0.014 - - - no_errors tier3 357 4 1.11 89 41 31.54 19 18 48.65 426980 TCGA-AB-3002 AML28 12 69743439 69743439 T C SNP - - - - - - - - - - - - - - - tier3 423 3 0.7 188 146 43.71 0 0 NA 426980 TCGA-AB-3002 AML28 12 70646308 70646308 T A SNP TPH2 NM_173353.3 human genbank 54_36p 1 reviewed intronic c.609-6258 e6-6258 0.036 - - - no_errors tier3 392 11 2.72 108 106 49.53 0 0 NA 426980 TCGA-AB-3002 AML28 12 72126530 72126530 G A SNP - - - - - - - - - - - - - - - tier3 314 5 1.57 38 31 44.93 0 0 NA 426980 TCGA-AB-3002 AML28 12 72620513 72620513 T C SNP ENSG00000215944 ENST00000401125 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*40514 NULL 0.017 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 12 76312842 76312842 A G SNP - - - - - - - - - - - - - - - tier3 397 7 1.73 136 109 44.49 0 0 NA 426980 TCGA-AB-3002 AML28 12 76334367 76334367 T C SNP - - - - - - - - - - - - - - - tier3 325 2 0.61 307 242 44.08 0 0 NA 426980 TCGA-AB-3002 AML28 12 78733687 78733687 A T SNP PPP1R12A NM_002480.1 human genbank 54_36p -1 reviewed intronic c.1239+1618 e9+1618 0.059 - - - no_errors tier3 462 1 0.22 114 81 41.54 5 4 44.44 426980 TCGA-AB-3002 AML28 12 82184702 82184702 G C SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 12 82288736 82288736 G C SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 12 84100790 84100790 C T SNP LRRIQ1 NM_001079910.1 human genbank 54_36p 1 validated intronic c.4822+22167 e23+22167 0.9 - - - no_errors tier2 264 1 0.38 146 147 50.17 0 0 NA 426980 TCGA-AB-3002 AML28 12 85649382 85649382 A T SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1-4233 e1-4233 0.001 - - - no_errors tier3 218 1 0.46 88 62 41.33 0 0 NA 426980 TCGA-AB-3002 AML28 12 89300122 89300122 T A SNP - - - - - - - - - - - - - - - tier3 575 2 0.35 326 293 47.33 0 0 NA 426980 TCGA-AB-3002 AML28 12 103709935 103709935 C T SNP SLC41A2 NM_032148.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*13125 NULL 0.002 - - - no_errors tier3 527 3 0.56 417 335 44.55 0 0 NA 426980 TCGA-AB-3002 AML28 12 103754970 103754970 C A SNP SLC41A2 NM_032148.3 human genbank 54_36p -1 validated intronic c.1287+7410 e9+7410 0.03 - - - no_errors tier3 370 3 0.8 278 226 44.84 0 0 0 426980 TCGA-AB-3002 AML28 12 113791667 113791667 G A SNP - - - - - - - - - - - - - - - tier3 660 3 0.45 462 324 41.17 0 0 NA 426980 TCGA-AB-3002 AML28 12 115524734 115524734 G C SNP MAP1LC3B2 NM_001085481.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*26226 NULL 0.998 - - - no_errors tier3 1276 25 1.92 484 392 44.7 0 0 NA 426980 TCGA-AB-3002 AML28 12 117878438 117878438 C T SNP KIAA1853 NM_194286.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25633 NULL 0 - - - no_errors tier3 1460 1 0.07 939 185 16.46 0 0 NA 426980 TCGA-AB-3002 AML28 12 117977733 117977733 C T SNP KIAA1853 NM_194286.2 human genbank 54_36p 1 validated intronic c.132-46691 e2-46691 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 12 118090574 118090574 G A SNP HSPB8 NM_014365.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-10927 NULL 0.001 - - - no_errors tier3 1252 16 1.26 444 395 47.08 0 0 NA 426980 TCGA-AB-3002 AML28 12 118985298 118985298 T C SNP CCDC64 NM_207311.2 human genbank 54_36p 1 validated intronic c.762+1285 e3+1285 0.006 - - - no_errors tier3 516 3 0.58 250 225 47.37 2 0 0 426980 TCGA-AB-3002 AML28 12 125587394 125587394 A T SNP ENSG00000209315 ENST00000386580 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46754 NULL 0 - - - pseudogene tier3 516 2 0.39 313 211 40.27 0 0 NA 426980 TCGA-AB-3002 AML28 12 127744443 127744443 G A SNP TMEM132C ENST00000315208 human ensembl 54_36p 1 known nonsense c.414 p.W138* 1 NULL NULL - no_errors tier1 523 4 0.76 352 237 40.24 NA 426980 TCGA-AB-3002 AML28 13 20933001 20933001 G C SNP ZDHHC20 NM_153251.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-1691 NULL 0.001 - - - no_errors tier3 463 6 1.27 230 200 46.51 0 0 NA 426980 TCGA-AB-3002 AML28 13 22408757 22408757 C T SNP LOC646201 XR_016396.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-38096 NULL 0 - - - pseudogene tier3 283 3 1.05 138 75 35.05 0 0 NA 426980 TCGA-AB-3002 AML28 13 26223165 26223165 G A SNP GPR12 NM_005288.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*7795 NULL 0.001 - - - no_errors tier3 232 3 1.28 103 95 47.98 0 0 NA 426980 TCGA-AB-3002 AML28 13 26668487 26668487 G A SNP USP12 NM_182488.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-24711 NULL 0.001 - - - no_errors tier3 905 14 1.52 287 212 42.4 0 0 NA 426980 TCGA-AB-3002 AML28 13 27190634 27190634 T C SNP ENSG00000220042 ENST00000404181 human ensembl 54_36p -1 known 5_prime_flanking_region c.-21293 NULL 0.001 - - - no_coding_region:pseudogene tier3 530 5 0.93 404 319 44.12 0 0 NA 426980 TCGA-AB-3002 AML28 13 31988250 31988250 T C SNP N4BP2L2 NM_033111.2 human genbank 54_36p -1 validated intronic c.410+1744 e5+1744 0.025 - - - no_errors tier3 269 1 0.37 151 112 42.59 6 3 33.33 426980 TCGA-AB-3002 AML28 13 35326695 35326695 G A SNP DCLK1 NM_004734.3 human genbank 54_36p -1 validated missense c.976 p.R326C 0.998 NULL "HMMSmart_S_TKc,HMMPfam_DCX,HMMSmart_DCX,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,superfamily_SSF89837" - no_errors tier1 NA NA NA NA NA NA 2 0 426980 TCGA-AB-3002 AML28 13 36859103 36859103 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 13 37195144 37195144 T A SNP TRPC4 NM_016179.1 human genbank 54_36p -1 validated intronic c.897+22930 e2+22930 0.026 - - - no_errors tier3 279 8 2.79 259 206 44.21 0 0 NA 426980 TCGA-AB-3002 AML28 13 39334932 39334932 A G SNP ENSG00000212553 ENST00000391251 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-5568 NULL 0.005 - - - no_errors tier3 875 9 1.02 603 438 42.07 0 0 NA 426980 TCGA-AB-3002 AML28 13 41995685 41995685 C T SNP TNFSF11 NM_033012.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-57577 NULL 0.002 - - - no_errors tier3 496 0 0 368 348 48.54 0 0 NA 426980 TCGA-AB-3002 AML28 13 45021967 45021967 C T SNP uc001val.1 ENST00000298738 human ensembl 54_36p -1 known intronic c.1646+62 e11+62 0.001 - - - no_errors tier3 811 5 0.61 502 414 45.2 0 0 NA 426980 TCGA-AB-3002 AML28 13 46200945 46200945 G A SNP LRCH1 NM_015116.1 human genbank 54_36p 1 provisional intronic c.1765-38 e17-38 0.018 - - - no_errors tier3 477 4 0.83 365 280 43.41 4 4 50 426980 TCGA-AB-3002 AML28 13 48940144 48940146 TTC - DEL SETDB2 NM_031915.1 human genbank 54_36p 1 provisional intronic c.341+47_341+45 e5+47 0.001:0.002:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 13 51283947 51283947 C T SNP DHRS12 NM_001031719.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-12151 NULL 0.059 - - - no_errors tier3 422 5 1.16 199 135 40.3 0 0 NA 426980 TCGA-AB-3002 AML28 13 52485031 52485031 A G SNP OLFM4 NM_006418.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15942 NULL 0 - - - no_errors tier3 616 5 0.81 352 339 48.99 0 0 NA 426980 TCGA-AB-3002 AML28 13 53087241 53087241 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 13 54281740 54281740 T A SNP - - - - - - - - - - - - - - - tier3 652 5 0.76 182 143 44 0 0 NA 426980 TCGA-AB-3002 AML28 13 56387864 56387864 A G SNP ENSG00000201665 ENST00000364795 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30127 NULL 0 - - - no_errors tier3 325 3 0.91 171 114 40 0 0 NA 426980 TCGA-AB-3002 AML28 13 56609499 56609499 C T SNP PRR20 NM_198441.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3941 NULL 0.004 - - - no_errors tier3 449 3 0.66 226 48 17.52 0 0 NA 426980 TCGA-AB-3002 AML28 13 56856089 56856089 T A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 13 60085869 60085869 C T SNP TDRD3 NM_030794.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*46093 NULL 0 - - - no_errors tier2 585 7 1.18 338 300 46.95 0 0 NA 426980 TCGA-AB-3002 AML28 13 64007406 64007406 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 13 65644339 65644339 G A SNP - - - - - - - - - - - - - - - tier2 187 1 0.53 151 103 40.55 0 0 NA 426980 TCGA-AB-3002 AML28 13 67847605 67847605 G A SNP ENSG00000216655 ENST00000406978 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43859 NULL 0.014 - - - no_coding_region:pseudogene tier3 642 10 1.53 354 347 49.36 0 0 NA 426980 TCGA-AB-3002 AML28 13 69610861 69610861 A G SNP ATXN8OS NR_002717.2 human genbank 54_36p 1 reviewed intronic c.NULL NULL 0.005 - - - no_errors tier3 173 0 0 67 63 48.46 0 0 NA 426980 TCGA-AB-3002 AML28 13 71648612 71648613 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 13 72336490 72336490 G A SNP PIBF1 NM_006346.2 human genbank 54_36p 1 validated intronic c.1322+10196 e9+10196 0 - - - no_errors tier3 329 5 1.5 415 331 44.37 0 0 0 426980 TCGA-AB-3002 AML28 13 73191726 73191726 C T SNP KLF12 NM_007249.4 human genbank 54_36p -1 validated intronic c.870-4063 e6-4063 0.001 - - - no_errors tier3 204 0 0 69 82 54.3 0 0 0 426980 TCGA-AB-3002 AML28 13 73478334 73478334 T C SNP KLF12 NM_007249.4 human genbank 54_36p -1 validated intronic c.1-11143 e1-11143 0.001 - - - no_errors tier3 507 6 1.17 424 399 48.42 1 2 66.67 426980 TCGA-AB-3002 AML28 13 81894222 81894222 C T SNP - - - - - - - - - - - - - - - tier3 172 1 0.58 25 9 26.47 0 0 NA 426980 TCGA-AB-3002 AML28 13 88659359 88659359 C T SNP ENSG00000216336 ENST00000402795 human ensembl 54_36p -1 known 3_prime_flanking_region c.*39714 NULL 0 - - - no_coding_region:pseudogene tier3 246 5 1.99 78 63 44.68 0 0 NA 426980 TCGA-AB-3002 AML28 13 90922867 90922867 T G SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.325+23690 e2+23690 0.002 - - - no_errors tier3 211 3 1.4 26 23 46.94 0 0 NA 426980 TCGA-AB-3002 AML28 13 91524582 91524582 G A SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1402-70502 e7-70502 0.001 - - - no_errors tier3 393 6 1.5 266 158 37.18 0 0 NA 426980 TCGA-AB-3002 AML28 13 92660004 92660004 C G SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-17707 NULL 0.076 - - - no_errors tier3 341 3 0.87 140 130 48.15 0 0 NA 426980 TCGA-AB-3002 AML28 13 98449678 98449678 A G SNP DOCK9 NM_015296.1 human genbank 54_36p -1 validated intronic c.130-43872 e2-43872 0.001 - - - no_errors tier3 466 3 0.64 312 233 42.75 0 0 NA 426980 TCGA-AB-3002 AML28 13 100669487 100669487 C T SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.1626+10258 e12+10258 0.002 - - - no_errors tier3 331 4 1.19 298 217 41.97 0 0 NA 426980 TCGA-AB-3002 AML28 13 106731186 106731186 G A SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.916-70082 e2-70082 0.001 - - - no_errors tier3 239 6 2.45 104 84 44.68 0 0 NA 426980 TCGA-AB-3002 AML28 13 107168273 107168273 T A SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.915+147758 e1+147758 0 - - - no_errors tier3 779 10 1.27 449 333 42.58 0 0 NA 426980 TCGA-AB-3002 AML28 13 107421580 107421580 T A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 14 26940065 26940065 A T SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model intronic c.202-78878 e3-78878 0.002 - - - no_errors tier3 696 7 1 415 333 44.46 0 0 NA 426980 TCGA-AB-3002 AML28 14 27025730 27025730 C A SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model intronic c.202-164543 e3-164543 0 - - - no_errors tier3 472 7 1.46 432 96 18.15 0 0 NA 426980 TCGA-AB-3002 AML28 14 27882666 27882666 C T SNP - - - - - - - - - - - - - - - tier3 875 8 0.9 489 368 42.94 0 0 NA 426980 TCGA-AB-3002 AML28 14 28018404 28018404 A T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 14 29564667 29564667 C T SNP - - - - - - - - - - - - - - - tier3 406 6 1.45 200 180 47.37 0 0 NA 426980 TCGA-AB-3002 AML28 14 37892347 37892347 A G SNP - - - - - - - - - - - - - - - tier3 430 3 0.69 298 254 46.01 0 0 NA 426980 TCGA-AB-3002 AML28 14 39052401 39052401 G A SNP - - - - - - - - - - - - - - - tier3 545 2 0.37 166 153 47.96 0 0 NA 426980 TCGA-AB-3002 AML28 14 39324126 39324126 G T SNP - - - - - - - - - - - - - - - tier3 299 0 0 212 194 47.78 0 0 NA 426980 TCGA-AB-3002 AML28 14 42340455 42340455 G A SNP - - - - - - - - - - - - - - - tier3 511 49 8.75 477 415 46.52 0 0 NA 426980 TCGA-AB-3002 AML28 14 43332212 43332212 A G SNP - - - - - - - - - - - - - - - tier2 317 0 0 107 128 54.47 0 0 NA 426980 TCGA-AB-3002 AML28 14 51611289 51611289 C T SNP NID2 NM_007361.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5827 NULL 0 - - - no_errors tier3 707 4 0.56 246 221 47.22 0 0 NA 426980 TCGA-AB-3002 AML28 14 57443387 57443387 C T SNP - - - - - - - - - - - - - - - tier3 788 6 0.76 548 368 40.17 0 0 NA 426980 TCGA-AB-3002 AML28 14 57455787 57455787 A G SNP - - - - - - - - - - - - - - - tier3 701 5 0.71 296 212 41.73 0 0 NA 426980 TCGA-AB-3002 AML28 14 68077979 68077979 C A SNP RAD51L1 NM_133509.4 human genbank 54_36p 1 reviewed intronic c.1037-52976 e10-52976 0.04 - - - no_errors tier3 647 5 0.77 417 336 44.5 0 0 0 426980 TCGA-AB-3002 AML28 14 69464698 69464698 G T SNP SMOC1 NM_001034852.1 human genbank 54_36p 1 validated intronic c.100-23910 e2-23910 0.446 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 426980 TCGA-AB-3002 AML28 14 82080398 82080398 C A SNP - - - - - - - - - - - - - - - tier3 537 10 1.83 256 211 44.99 0 0 NA 426980 TCGA-AB-3002 AML28 14 82270165 82270165 A G SNP ENSG00000213346 ENST00000393582 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41013 NULL 0.001 - - - no_coding_region:pseudogene tier3 368 7 1.87 162 136 45.48 0 0 NA 426980 TCGA-AB-3002 AML28 14 83340615 83340615 C A SNP - - - - - - - - - - - - - - - tier3 646 2 0.31 164 116 41.43 0 0 NA 426980 TCGA-AB-3002 AML28 14 84412327 84412327 C T SNP - - - - - - - - - - - - - - - tier3 141 3 2.07 91 48 34.53 0 0 NA 426980 TCGA-AB-3002 AML28 14 84486691 84486691 T C SNP - - - - - - - - - - - - - - - tier3 628 14 2.18 370 352 48.69 0 0 NA 426980 TCGA-AB-3002 AML28 14 86134598 86134598 C A SNP - - - - - - - - - - - - - - - tier3 259 3 1.15 152 123 44.73 0 0 NA 426980 TCGA-AB-3002 AML28 14 88453068 88453068 A G SNP TTC8 NM_144596.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*39561 NULL 0.015 - - - no_errors tier3 1712 8 0.46 909 735 44.68 0 0 NA 426980 TCGA-AB-3002 AML28 14 89541452 89541452 G A SNP TDP1 NM_001008744.1 human genbank 54_36p 1 reviewed intronic c.1541+11872 e12+11872 0.001 - - - no_errors tier3 346 1 0.29 126 83 39.52 1 0 0 426980 TCGA-AB-3002 AML28 14 90229295 90229298 TGGC - DEL TTC7B NM_001010854.1 human genbank 54_36p -1 provisional intronic c.777+2299_777+2296 e6+2299 0.091:0.083:0.066:0.117 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 14 93157337 93157337 G A SNP KIAA1409 NM_020818.3 human genbank 54_36p 1 validated intronic c.3857-383 e27-383 0.974 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 14 94649887 94649887 C G SNP DICER1 NM_030621.3 human genbank 54_36p -1 reviewed intronic c.1908-573 e11-573 0.002 - - - no_errors tier3 572 0 0 488 352 41.81 0 1 100 426980 TCGA-AB-3002 AML28 14 98408503 98408503 A G SNP - - - - - - - - - - - - - - - tier3 1000 14 1.38 566 542 48.87 0 0 NA 426980 TCGA-AB-3002 AML28 14 104264418 104264422 CTGGT - DEL ADSSL1 NM_152328.3 human genbank 54_36p 1 validated intronic c.192+2574_192+2570 e1+2574 0.000:0.000:0.000:0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 14 104906418 104906418 G A SNP PACS2 NM_001100913.1 human genbank 54_36p 1 validated intronic c.741+497 e7+497 0.047 - - - no_errors tier2 NA NA NA NA NA NA 1 1 50 426980 TCGA-AB-3002 AML28 15 24514103 24514103 G A SNP GABRB3 NM_000814.4 human genbank 54_36p -1 reviewed intronic c.240+54539 e3+54539 0.007 - - - no_errors tier3 892 22 2.41 981 701 41.63 0 0 NA 426980 TCGA-AB-3002 AML28 15 35169607 35169607 T A SNP MEIS2 NM_170675.2 human genbank 54_36p -1 reviewed intronic c.639+3467 e6+3467 0.056 - - - no_errors tier3 229 0 0 15 17 51.52 0 0 NA 426980 TCGA-AB-3002 AML28 15 39166414 39166414 T C SNP INO80 NM_017553.1 human genbank 54_36p -1 validated intronic c.658+638 e5+638 0.003 - - - no_errors tier3 NA NA NA NA NA NA 7 0 0 426980 TCGA-AB-3002 AML28 15 46164943 46164943 T C SNP SLC24A5 NM_205850.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35591 NULL 0.005 - - - no_errors tier3 1083 9 0.82 724 542 42.81 0 0 NA 426980 TCGA-AB-3002 AML28 15 49315348 49315348 G A SNP CYP19A1 NM_000103.3 human genbank 54_36p -1 reviewed intronic c.296+1000 e2+1000 0.002 - - - no_errors tier3 421 8 1.86 204 210 50.6 0 0 NA 426980 TCGA-AB-3002 AML28 15 51906137 51906137 C T SNP - - - - - - - - - - - - - - - tier3 274 4 1.44 77 65 45.77 0 0 NA 426980 TCGA-AB-3002 AML28 15 55462340 55462340 A G SNP CGNL1 NM_032866.3 human genbank 54_36p 1 validated intronic c.1+6283 e0+6283 0.004 - - - no_errors tier2 662 3 0.45 128 72 35.82 0 0 NA 426980 TCGA-AB-3002 AML28 15 56211412 56211412 C A SNP AQP9 NM_020980.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-6645 NULL 0 - - - no_errors tier3 344 3 0.86 251 176 41.22 0 0 NA 426980 TCGA-AB-3002 AML28 15 61140600 61140600 G A SNP TPM1 NM_000366.5 human genbank 54_36p 1 reviewed intronic c.639+75 e6+75 0.059 - - - no_errors tier3 652 1 0.15 611 136 18.21 1 0 0 426980 TCGA-AB-3002 AML28 15 62677332 62677332 G A SNP ZNF609 NM_015042.1 human genbank 54_36p 1 provisional intronic c.748-24747 e2-24747 0.003 - - - no_errors tier3 499 6 1.19 174 124 41.47 3 1 25 426980 TCGA-AB-3002 AML28 15 64498952 64498956 ATTTT - DEL MAP2K1 NM_002755.3 human genbank 54_36p 1 reviewed intronic c.81-15467_81-15463 e2-15463 0.000:0.001:0.001:0.001:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 15 65312917 65312917 C T SNP FLJ11506 NM_024666.3 human genbank 54_36p -1 validated intronic c.452-1628 e5-1628 0.002 - - - no_errors tier3 780 8 1.01 366 330 47.35 0 0 0 426980 TCGA-AB-3002 AML28 15 81513464 81513464 C T SNP BTBD1 NM_025238.1 human genbank 54_36p -1 reviewed intronic c.558+2681 e2+2681 0 - - - no_errors tier3 196 4 1.99 52 22 29.73 4 1 20 426980 TCGA-AB-3002 AML28 15 88432938 88432938 C A SNP IDH2 NM_002168.2 human genbank 54_36p -1 reviewed missense c.419 p.R140L 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 393 4 1.01 173 134 43.65 155 138 47.1 426980 TCGA-AB-3002 AML28 15 93527184 93527184 A G SNP - - - - - - - - - - - - - - - tier3 154 1 0.65 16 14 46.67 0 0 NA 426980 TCGA-AB-3002 AML28 15 94349247 94349247 G A SNP - - - - - - - - - - - - - - - tier3 344 5 1.42 120 70 36.84 0 0 NA 426980 TCGA-AB-3002 AML28 15 94782752 94782752 C T SNP ENSG00000222617 ENST00000410685 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48068 NULL 0.118 - - - no_errors tier2 362 5 1.36 259 202 43.72 0 0 NA 426980 TCGA-AB-3002 AML28 15 97308324 97308324 C T SNP IGF1R NM_000875.3 human genbank 54_36p 1 reviewed intronic c.3588-1002 e20-1002 0 - - - no_errors tier3 362 4 1.09 188 137 42.15 0 0 0 426980 TCGA-AB-3002 AML28 16 3347262 3347262 A C SNP ZNF174 NM_003450.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44744 NULL 0.01 - - - no_errors tier3 994 16 1.58 314 284 47.49 0 0 NA 426980 TCGA-AB-3002 AML28 16 6495209 6495209 T C SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-149396 e1-149396 0.999 - - - no_errors tier3 715 6 0.83 261 198 43.14 0 0 NA 426980 TCGA-AB-3002 AML28 16 6654431 6654431 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+9779 e0+9779 0 - - - no_errors tier3 1214 10 0.82 835 620 42.58 0 0 NA 426980 TCGA-AB-3002 AML28 16 10721523 10721523 G A SNP NUBP1 NM_002484.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-23699 NULL 0.997 - - - no_errors tier3 116 1 0.85 51 33 39.29 0 0 NA 426980 TCGA-AB-3002 AML28 16 19190727 19190727 G A SNP uc002dga.2 ENST00000399195 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13948 NULL 0.042 - - - no_errors tier2 1174 9 0.76 514 391 43.16 0 0 NA 426980 TCGA-AB-3002 AML28 16 22640933 22640933 C T SNP - - - - - - - - - - - - - - - tier3 1 0 0 NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 16 23026044 23026044 C G SNP USP31 NM_020718.3 human genbank 54_36p -1 validated intronic c.772-735 e3-735 0.002 - - - no_errors tier3 533 11 2.02 635 506 44.31 0 1 100 426980 TCGA-AB-3002 AML28 16 24173849 24173849 G A SNP CACNG3 NM_006539.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1728 NULL 0 - - - no_errors tier2 561 5 0.88 173 131 42.95 0 0 NA 426980 TCGA-AB-3002 AML28 16 26547638 26547638 G T SNP ENSG00000221481 ENST00000408554 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18062 NULL 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 16 30758901 30758901 C T SNP LOC100129191 XM_001725676.1 human genbank 54_36p -1 model intronic c.10+618 e1+618 0.114 - - - no_errors tier3 NA NA NA NA NA NA 3 0 0 426980 TCGA-AB-3002 AML28 16 31290499 31290499 C T SNP ITGAX NM_000887.3 human genbank 54_36p 1 reviewed missense c.2053 p.R685C 1 "HMMPfam_Integrin_alpha2,superfamily_SSF69179" "HMMPfam_VWA,HMMSmart_VWA,HMMPfam_Integrin_alpha,HMMPfam_FG-GAP,HMMSmart_Int_alpha,HMMPfam_Integrin_alpha2,PatternScan_INTEGRIN_ALPHA,superfamily_SSF53300,superfamily_SSF69179,superfamily_SSF69318" - no_errors tier1 952 28 2.85 283 236 45.3 16 25 60.98 426980 TCGA-AB-3002 AML28 16 32090319 32090319 G A SNP HERC2P4 NR_002827.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-18944 NULL 1 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 16 47728294 47728294 C A SNP - - - - - - - - - - - - - - - tier3 521 4 0.76 229 191 45.48 0 0 NA 426980 TCGA-AB-3002 AML28 16 50053507 50053507 G A SNP - - - - - - - - - - - - - - - tier3 1237 17 1.36 677 525 43.64 0 0 NA 426980 TCGA-AB-3002 AML28 16 51061458 51061458 G A SNP TOX3 NM_001080430.1 human genbank 54_36p -1 provisional intronic c.88-1471 e2-1471 0.001 - - - no_errors tier2 722 3 0.41 278 222 44.22 0 0 NA 426980 TCGA-AB-3002 AML28 16 51097779 51097779 C T SNP TOX3 NM_001080430.1 human genbank 54_36p -1 provisional intronic c.88-37792 e2-37792 0 - - - no_errors tier3 559 5 0.89 372 263 41.42 0 0 NA 426980 TCGA-AB-3002 AML28 16 52416962 52416962 G T SNP FTO NM_001080432.1 human genbank 54_36p 1 provisional intronic c.124-315 e3-315 0 - - - no_errors tier3 445 2 0.45 153 107 41 0 0 0 426980 TCGA-AB-3002 AML28 16 54645012 54645012 C T SNP - - - - - - - - - - - - - - - tier3 597 4 0.66 417 345 45.22 0 0 NA 426980 TCGA-AB-3002 AML28 16 56639569 56639569 C T SNP ZNF319 NM_020807.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-49899 NULL 0 - - - no_errors tier3 285 4 1.37 62 40 39.22 0 0 NA 426980 TCGA-AB-3002 AML28 16 60206305 60206305 C T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*38708 NULL 0.004 - - - no_errors tier2 335 2 0.59 177 136 43.17 0 0 NA 426980 TCGA-AB-3002 AML28 16 60215077 60215077 A T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*29936 NULL 0.082 - - - no_errors tier3 588 1 0.17 286 231 44.68 0 0 NA 426980 TCGA-AB-3002 AML28 16 61457580 61457580 T A SNP ENSG00000223123 ENST00000411191 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-40127 NULL 0.001 - - - no_errors tier3 233 2 0.85 87 81 48.21 0 0 NA 426980 TCGA-AB-3002 AML28 16 63398942 63398942 C T SNP - - - - - - - - - - - - - - - tier3 131 1 0.76 60 60 50 0 0 NA 426980 TCGA-AB-3002 AML28 16 70613693 70613693 C T SNP DHODH NM_001361.3 human genbank 54_36p 1 reviewed intronic c.706-69 e6-69 0.001 - - - no_errors tier3 NA NA NA NA NA NA 1 0 0 426980 TCGA-AB-3002 AML28 16 75360773 75360773 T G SNP - - - - - - - - - - - - - - - tier3 676 7 1.02 504 397 44.06 0 0 NA 426980 TCGA-AB-3002 AML28 16 75496799 75496799 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 16 76093122 76093122 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 16 80961258 80961258 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 16 84568369 84568369 G A SNP - - - - - - - - - - - - - - - tier3 327 7 2.1 214 148 40.66 0 0 NA 426980 TCGA-AB-3002 AML28 16 84779125 84779125 C T SNP - - - - - - - - - - - - - - - tier3 891 19 2.09 580 517 46.96 0 0 NA 426980 TCGA-AB-3002 AML28 16 84887353 84887353 G A SNP ENSG00000199949 ENST00000363079 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20723 NULL 0.051 - - - no_errors tier3 301 0 0 136 109 44.49 0 0 NA 426980 TCGA-AB-3002 AML28 16 88525341 88525341 C T SNP TUBB3 NM_006086.2 human genbank 54_36p 1 validated intronic c.58-1139 e2-1139 0.001 - - - no_errors tier3 NA NA NA NA NA NA 1 0 0 426980 TCGA-AB-3002 AML28 17 1405588 1405588 G A SNP PITPNA NM_006224.3 human genbank 54_36p -1 validated intronic c.52-2395 e3-2395 0 - - - no_errors tier2 562 8 1.4 276 215 43.79 18 9 32.14 426980 TCGA-AB-3002 AML28 17 3989565 3989565 C T SNP ZZEF1 NM_015113.3 human genbank 54_36p -1 validated intronic c.354+3020 e1+3020 0.012 - - - no_errors tier3 681 14 2.01 304 219 41.87 5 2 28.57 426980 TCGA-AB-3002 AML28 17 6183218 6183218 G T SNP - - - - - - - - - - - - - - - tier3 674 7 1.03 350 262 42.81 0 0 NA 426980 TCGA-AB-3002 AML28 17 7334949 7334949 T - DEL POLR2A NM_000937.3 human genbank 54_36p 1 provisional intronic c.94-5035 e2-5035 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 10874727 10874727 C T SNP ENSG00000221701 ENST00000408774 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23103 NULL 0 - - - no_errors tier2 NA NA NA 1 0 0 0 0 NA 426980 TCGA-AB-3002 AML28 17 10930752 10930752 G A SNP ENSG00000221701 ENST00000408774 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*32775 NULL 0.024 - - - no_errors tier3 640 11 1.68 366 241 39.7 0 0 NA 426980 TCGA-AB-3002 AML28 17 11228967 11228967 C T SNP uc002gna.2 ENST00000409168 human ensembl 54_36p 1 known intronic c.895+5416 e3+5416 0.001 - - - no_errors tier3 444 5 1.11 222 213 48.97 0 0 NA 426980 TCGA-AB-3002 AML28 17 12827463 12827463 G T SNP RICH2 NM_014859.4 human genbank 54_36p 1 validated intronic c.1940-1110 e20-1110 0.009 - - - no_errors tier3 540 1 0.18 174 114 39.58 0 0 NA 426980 TCGA-AB-3002 AML28 17 17336440 17336440 C T SNP MED9 NM_018019.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*906 NULL 0 - - - no_errors tier3 353 0 0 158 133 45.7 7 6 46.15 426980 TCGA-AB-3002 AML28 17 27591454 27591454 G T SNP RHBDL3 NM_138328.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25868 NULL 0.011 - - - no_errors tier3 180 8 4.19 77 46 37.1 0 0 NA 426980 TCGA-AB-3002 AML28 17 27701282 27701282 C A SNP MIRN632 ENST00000385193 human ensembl 54_36p 1 known rna NULL NULL 0.749 - - - no_errors tier1 NA NA NA NA NA NA 15 0 426980 TCGA-AB-3002 AML28 17 29083093 29083093 A G SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.555+424017 e1+424017 0 - - - overly_large_intron tier3 806 0 0 350 264 43 0 0 NA 426980 TCGA-AB-3002 AML28 17 34007774 34007774 C T SNP SNIP NM_025248.2 human genbank 54_36p -1 validated intronic c.22+7689 e1+7689 0.011 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 35242270 35242271 - TA INS IKZF3 NM_012481.3 human genbank 54_36p -1 reviewed intronic c.8-341_8-340 e2-340 0.010:0.008 - - - no_errors tier4 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 39474680 39474683 TTTG - DEL LSM12 NM_152344.3 human genbank 54_36p -1 validated intronic c.259-1533_259-1530 e3-1530 0.003:0.000:0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 44439434 44439434 T C SNP IGF2BP1 NM_006546.3 human genbank 54_36p 1 reviewed intronic c.236+7904 e2+7904 0 - - - no_errors tier3 560 1 0.18 245 164 40 0 0 NA 426980 TCGA-AB-3002 AML28 17 48725946 48725946 C T SNP - - - - - - - - - - - - - - - tier3 549 4 0.72 134 109 44.86 0 0 NA 426980 TCGA-AB-3002 AML28 17 53499170 53499170 G C SNP DYNLL2 NM_080677.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20281 NULL 0 - - - no_errors tier3 809 2 0.25 260 178 40.45 0 0 NA 426980 TCGA-AB-3002 AML28 17 53763621 53763621 C G SNP MIRN142 ENST00000384835 human ensembl 54_36p -1 known rna NULL NULL 1 - - - no_errors tier1 1707 17 0.98 169 138 44.95 29 4 11.76 426980 TCGA-AB-3002 AML28 17 53763624 53763624 T C SNP MIRN142 ENST00000384835 human ensembl 54_36p -1 known rna NULL NULL 1 - - - no_errors tier1 1692 14 0.82 181 121 40.07 5 25 83.33 426980 TCGA-AB-3002 AML28 17 55959266 55959266 G A SNP APPBP2 NM_006380.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-1192 NULL 0.024 - - - no_errors tier2 608 7 1.13 227 133 36.94 0 0 NA 426980 TCGA-AB-3002 AML28 17 57103456 57103456 C A SNP BRIP1 NM_032043.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*11983 NULL 0.061 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 58109959 58109959 G A SNP MRC2 NM_006039.3 human genbank 54_36p 1 validated intronic c.2195+220 e13+220 0.003 - - - no_errors tier3 555 8 1.42 189 183 49.19 2 1 33.33 426980 TCGA-AB-3002 AML28 17 67169186 67169187 - T INS LOC124685 XR_040247.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*40014 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 67336579 67336579 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 68135164 68135164 G A SNP SLC39A11 NM_139177.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*20154 NULL 1 - - - no_errors tier2 376 3 0.79 119 89 42.58 67 0 0 426980 TCGA-AB-3002 AML28 17 69391987 69391987 C T SNP - - - - - - - - - - - - - - - tier3 512 9 1.73 204 143 41.21 0 0 NA 426980 TCGA-AB-3002 AML28 17 75712847 75712847 G A SNP GAA NM_000152.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*5122 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 75761724 75761724 G A SNP CARD14 NM_024110.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8109 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 17 78537248 78537248 C A SNP B3GNTL1 NM_001009905.1 human genbank 54_36p -1 validated intronic c.504+19032 e6+19032 0 - - - no_errors tier3 824 11 1.31 281 243 46.29 3 1 25 426980 TCGA-AB-3002 AML28 18 3244246 3244246 T G SNP MYL12A NM_006471.2 human genbank 54_36p 1 provisional intronic c.343+198 e2+198 0.087 - - - no_errors tier3 364 4 1.09 103 135 56.72 0 0 0 426980 TCGA-AB-3002 AML28 18 5752087 5752087 C A SNP LOC645355 XR_042016.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.02 - - - no_errors tier3 1621 30 1.82 617 428 40.96 0 0 NA 426980 TCGA-AB-3002 AML28 18 8081041 8081041 T A SNP PTPRM NM_001105244.1 human genbank 54_36p 1 reviewed intronic c.1856+2192 e11+2192 0.002 - - - no_errors tier3 525 9 1.69 332 257 43.63 0 0 NA 426980 TCGA-AB-3002 AML28 18 11523657 11523657 C T SNP LOC729589 XM_001130715.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*26886 NULL 0 - - - no_errors tier2 660 13 1.93 338 238 41.25 0 0 NA 426980 TCGA-AB-3002 AML28 18 21636245 21636245 C T SNP ENSG00000222577 ENST00000410645 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*15953 NULL 0.013 - - - no_errors tier3 405 6 1.45 193 131 40.43 0 0 NA 426980 TCGA-AB-3002 AML28 18 23266563 23266563 G C SNP FLJ45994 XR_040238.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 18 25819633 25819633 A G SNP - - - - - - - - - - - - - - - tier3 578 2 0.34 312 256 45.07 0 0 NA 426980 TCGA-AB-3002 AML28 18 26755043 26755043 C T SNP - - - - - - - - - - - - - - - tier3 460 2 0.43 361 276 43.26 0 0 NA 426980 TCGA-AB-3002 AML28 18 29671467 29671467 T A SNP NOL4 NM_003787.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*15337 NULL 0 - - - no_errors tier3 551 3 0.54 210 100 32.15 0 0 NA 426980 TCGA-AB-3002 AML28 18 35741493 35741493 C T SNP - - - - - - - - - - - - - - - tier3 483 2 0.41 261 187 41.74 0 0 NA 426980 TCGA-AB-3002 AML28 18 36665237 36665237 C A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 18 44444522 44444522 C T SNP KIAA0427 NM_014772.1 human genbank 54_36p 1 validated intronic c.327-294 e4-294 0.001 - - - no_errors tier2 2754 34 1.22 1425 1131 44.21 0 0 0 426980 TCGA-AB-3002 AML28 18 48158679 48158679 A - DEL DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.91+37433 e1+37433 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 18 48597561 48597561 T G SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.412+64819 e2+64819 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 18 51856664 51856664 C T SNP ENSG00000206129 ENST00000382897 human ensembl 54_36p -1 known intronic c.344-9495 e4-9495 0.998 - - - no_errors tier2 632 3 0.47 310 277 47.19 0 0 NA 426980 TCGA-AB-3002 AML28 18 52300165 52300165 C G SNP - - - - - - - - - - - - - - - tier2 961 9 0.93 511 420 45.11 0 0 NA 426980 TCGA-AB-3002 AML28 18 52601661 52601661 A T SNP WDR7 NM_015285.2 human genbank 54_36p 1 reviewed intronic c.3190+1776 e18+1776 0.055 - - - no_errors tier3 258 2 0.77 102 75 42.37 1 0 0 426980 TCGA-AB-3002 AML28 18 53076425 53076425 C T SNP ENSG00000202240 ENST00000365370 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*26406 NULL 0.001 - - - no_errors tier3 380 2 0.52 248 135 35.25 0 0 NA 426980 TCGA-AB-3002 AML28 18 65731094 65731094 T A SNP CD226 NM_006566.2 human genbank 54_36p -1 reviewed intronic c.383-16833 e3-16833 0.001 - - - no_errors tier3 1 0 0 NA NA NA 0 1 100 426980 TCGA-AB-3002 AML28 18 68062568 68062568 C A SNP - - - - - - - - - - - - - - - tier3 318 2 0.62 100 86 46.24 0 0 NA 426980 TCGA-AB-3002 AML28 18 68910507 68910507 G A SNP - - - - - - - - - - - - - - - tier3 337 1 0.3 148 100 40.32 0 0 NA 426980 TCGA-AB-3002 AML28 18 71709126 71709126 G A SNP - - - - - - - - - - - - - - - tier3 468 7 1.47 433 408 48.46 0 0 NA 426980 TCGA-AB-3002 AML28 18 71875808 71875808 G A SNP - - - - - - - - - - - - - - - tier3 681 5 0.73 215 181 45.71 0 0 NA 426980 TCGA-AB-3002 AML28 18 74063167 74063167 G A SNP - - - - - - - - - - - - - - - tier3 443 4 0.89 326 281 46.29 0 0 NA 426980 TCGA-AB-3002 AML28 19 8512789 8512789 C T SNP MYO1F NM_012335.2 human genbank 54_36p -1 provisional splice_site c.1610+1 e15+1 1 - - - no_errors tier1 197 2 1.01 41 31 43.06 18 11 36.67 426980 TCGA-AB-3002 AML28 19 8878800 8878800 C T SNP MUC16 NM_024690.2 human genbank 54_36p -1 validated intronic c.37806-282 e26-282 0.001 - - - no_errors tier3 2527 11 0.43 759 632 45.3 0 0 0 426980 TCGA-AB-3002 AML28 19 12640297 12640297 T C SNP MORG1 NM_001099737.1 human genbank 54_36p 1 validated intronic c.1-25 e1-25 0 - - - no_errors tier2 914 17 1.83 379 273 41.87 8 3 27.27 426980 TCGA-AB-3002 AML28 19 12722617 12722617 G A SNP BEST2 NM_017682.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1790 NULL 0.001 - - - no_errors tier3 768 4 0.52 310 287 48.07 0 1 100 426980 TCGA-AB-3002 AML28 19 32989705 32989705 G A SNP LOC100131141 XR_036861.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*693 NULL 0 - - - pseudogene tier3 NA NA NA NA NA NA 2 0 0 426980 TCGA-AB-3002 AML28 19 33202551 33202551 C T SNP - - - - - - - - - - - - - - - tier3 544 3 0.55 356 243 40.43 0 0 NA 426980 TCGA-AB-3002 AML28 19 34054026 34054026 G A SNP - - - - - - - - - - - - - - - tier2 389 8 2.01 171 179 51 0 0 NA 426980 TCGA-AB-3002 AML28 19 34208171 34208171 A T SNP ENSG00000209834 ENST00000387099 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23668 NULL 0 - - - pseudogene tier3 370 1 0.27 156 102 39.53 0 0 NA 426980 TCGA-AB-3002 AML28 19 41696897 41696897 A G SNP ZNF260 NM_001012756.1 human genbank 54_36p -1 validated missense c.1084 p.C362R 0.744 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 NA NA NA NA NA NA 8 0 426980 TCGA-AB-3002 AML28 19 42899759 42899759 T C SNP ZNF607 NM_032689.3 human genbank 54_36p -1 provisional intronic c.1+2251 e0+2251 0.017 - - - no_errors tier3 432 4 0.92 239 138 36.51 1 0 0 426980 TCGA-AB-3002 AML28 19 45027351 45027351 A G SNP FBL NM_001436.3 human genbank 54_36p -1 reviewed intronic c.10+1420 e1+1420 0.003 - - - no_errors tier3 1070 8 0.74 257 199 43.54 1 0 0 426980 TCGA-AB-3002 AML28 19 50958451 50958451 C T SNP LOC388553 XM_373809.1 human genbank 54_36p 1 model silent c.1554 p.T518 0.395 "HMMPfam_HMG_box,HMMSmart_SM00398,superfamily_HMG-box" "HMMPfam_HMG_box,HMMSmart_SM00398,HMMPfam_HLH,superfamily_HMG-box" - no_errors tier1 251 3 1.18 91 89 49.44 NA 426980 TCGA-AB-3002 AML28 19 60109826 60109826 C T SNP NCR1 NM_004829.1 human genbank 54_36p 1 validated silent c.204 p.A68 0 "HMMSmart_SM00409,superfamily_Immunoglobulin" "HMMSmart_SM00409,superfamily_Immunoglobulin" - no_errors tier1 NA NA NA NA NA NA 1 0 426980 TCGA-AB-3002 AML28 20 2709619 2709619 C T SNP RPL19P1 ENST00000404504 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*2709619 NULL 1 - - - no_coding_region:pseudogene tier2 1017 7 0.68 381 323 45.82 1 0 0 426980 TCGA-AB-3002 AML28 20 7450754 7450754 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 20 15271349 15271349 A G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.541-88701 e7-88701 0.011 - - - no_errors tier3 280 3 1.06 129 88 40.55 0 0 NA 426980 TCGA-AB-3002 AML28 20 15545992 15545992 G A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.645+117500 e8+117500 0.007 - - - no_errors tier2 576 5 0.86 139 132 48.71 0 0 NA 426980 TCGA-AB-3002 AML28 20 17900146 17900146 T A SNP C20orf72 NM_052865.2 human genbank 54_36p 1 predicted intronic c.511+1133 e1+1133 0.005 - - - no_errors tier3 NA NA NA NA NA NA 8 0 0 426980 TCGA-AB-3002 AML28 20 20853777 20853777 G C SNP - - - - - - - - - - - - - - - tier2 541 8 1.46 518 377 42.12 0 0 NA 426980 TCGA-AB-3002 AML28 20 22014823 22014823 A T SNP - - - - - - - - - - - - - - - tier3 163 0 0 84 66 44 0 0 NA 426980 TCGA-AB-3002 AML28 20 37620741 37620741 T A SNP - - - - - - - - - - - - - - - tier3 292 3 1.02 213 146 40.67 0 0 NA 426980 TCGA-AB-3002 AML28 20 37764465 37764465 G T SNP - - - - - - - - - - - - - - - tier3 688 4 0.58 414 277 40.09 0 0 NA 426980 TCGA-AB-3002 AML28 20 40268312 40268312 A T SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.2400-6870 e17-6870 0.483 - - - no_errors tier3 576 8 1.37 640 495 43.61 0 0 NA 426980 TCGA-AB-3002 AML28 20 42143829 42143829 C G SNP JPH2 NM_020433.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*33021 NULL 0 - - - no_errors tier3 527 1 0.19 372 285 43.31 0 0 NA 426980 TCGA-AB-3002 AML28 20 49730834 49730834 C T SNP ATP9A NM_006045.1 human genbank 54_36p -1 validated intronic c.800-4680 e10-4680 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 426980 TCGA-AB-3002 AML28 20 52026411 52026411 G A SNP BCAS1 NM_003657.2 human genbank 54_36p -1 reviewed intronic c.1141-1035 e7-1035 0 - - - no_errors tier2 460 4 0.86 275 219 44.33 0 0 NA 426980 TCGA-AB-3002 AML28 20 53475223 53475223 G T SNP - - - - - - - - - - - - - - - tier3 384 3 0.78 111 72 39.34 0 0 NA 426980 TCGA-AB-3002 AML28 20 61515246 61515246 C T SNP KCNQ2 NM_172107.4 human genbank 54_36p -1 reviewed splice_site c.1763+1 e15+1 1 - - - no_errors tier1 NA NA NA NA NA NA NA 426980 TCGA-AB-3002 AML28 21 14058883 14058883 C T SNP LOC441957 XR_016199.1 human genbank 54_36p 1 model rna NULL NULL 0.375 - - - pseudogene tier1 NA NA NA NA NA NA NA 426980 TCGA-AB-3002 AML28 21 21894381 21894381 G A SNP ENSG00000198434 ENST00000358086 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*34263 NULL 0.005 - - - no_coding_region:pseudogene tier3 222 4 1.77 87 60 40.82 0 0 NA 426980 TCGA-AB-3002 AML28 21 26930860 26930860 A G SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 21 27215461 27215461 C T SNP ADAMTS5 NM_007038.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*2782 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 1 0 0 426980 TCGA-AB-3002 AML28 21 30506811 30506811 G A SNP CLDN17 NM_012131.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-46005 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 21 36612009 36612009 A - DEL MORC3 NM_015358.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2424 NULL 0.043 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 21 40928109 40928109 G C SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.508+58497 e3+58497 0.001 - - - no_errors tier3 931 11 1.17 417 301 41.86 0 0 NA 426980 TCGA-AB-3002 AML28 21 41098119 41098119 G A SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.43+42296 e1+42296 0 - - - no_errors tier3 1145 14 1.21 702 582 45.26 0 0 NA 426980 TCGA-AB-3002 AML28 21 43023406 43023406 G A SNP PDE9A NM_002606.1 human genbank 54_36p 1 reviewed intronic c.263-1543 e5-1543 0 - - - no_errors tier3 592 11 1.82 246 195 44.22 0 0 NA 426980 TCGA-AB-3002 AML28 21 44100552 44100552 C T SNP MYL6P ENST00000401479 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-44100552 NULL 1 - - - no_coding_region:pseudogene tier2 187 0 0 89 78 46.71 0 0 NA 426980 TCGA-AB-3002 AML28 21 44111210 44111210 G A SNP AGPAT3 NM_020132.1 human genbank 54_36p 1 reviewed intronic c.1+1556 e0+1556 0.006 - - - no_errors tier3 127 1 0.78 107 117 52.23 2 0 0 426980 TCGA-AB-3002 AML28 21 44766031 44766031 G T SNP C21orf29 NM_144991.2 human genbank 54_36p -1 provisional intronic c.1566+163 e9+163 0 - - - no_errors tier3 142 1 0.7 138 86 38.22 0 0 NA 426980 TCGA-AB-3002 AML28 22 16635285 16635285 C T SNP BID NM_197966.2 human genbank 54_36p -1 reviewed intronic c.80+1091 e1+1091 0 - - - no_errors tier3 306 3 0.97 117 76 39.38 25 17 40.48 426980 TCGA-AB-3002 AML28 22 18266604 18266604 C G SNP TXNRD2 ENST00000400516 human ensembl 54_36p -1 known intronic c.663-13 e9-13 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 426980 TCGA-AB-3002 AML28 22 24107592 24107592 T - DEL LRP5L ENST00000402785 human ensembl 54_36p -1 known intronic c.1-15 e1-15 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 22 46314184 46314184 G T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 426980 TCGA-AB-3002 AML28 22 46343957 46343957 G A SNP - - - - - - - - - - - - - - - tier3 1352 4 0.29 1244 940 43 0 0 NA 775109 TCGA-AB-3005 AML39 Y 12051635 12051635 G A SNP LOC100128190 XR_037566.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-49331 NULL 0 - - - pseudogene tier3 232 0 0 37 133 77.78 0 0 NA 775109 TCGA-AB-3005 AML39 X 70110807 70110807 G A SNP SLC7A3 NM_001048164.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44235 NULL 0 - - - no_errors tier3 1151 2 0.17 50 266 84.18 0 0 NA 775109 TCGA-AB-3005 AML39 X 81164120 81164120 G A SNP ENSG00000206826 ENST00000384099 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-20688 NULL 0.02 - - - no_errors tier3 824 1 0.12 49 252 83.72 0 0 NA 775109 TCGA-AB-3005 AML39 X 87511725 87511725 T C SNP - - - - - - - - - - - - - - - tier3 432 1 0.23 19 60 75.95 0 0 NA 775109 TCGA-AB-3005 AML39 X 105065038 105065038 T C SNP NRK ENST00000243300 human ensembl 54_36p 1 known missense c.3448 p.S1150P 0.982 NULL "HMMPfam_CNH,HMMSmart_SM00036,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_p53-like transcription factors,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase" - no_errors tier1 776 1 0.13 425 65 13.24 NA 775109 TCGA-AB-3005 AML39 X 129873983 129873983 C T SNP ENOX2 NM_182314.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-203037 NULL 0.016 - - - no_errors tier3 1096 1 0.09 147 652 81.5 0 0 NA 775109 TCGA-AB-3005 AML39 1 3690478 3690478 G A SNP LRRC47 NM_020710.2 human genbank 54_36p -1 validated silent c.1252 p.L418 0.603 HMMPfam_B3_4 "HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMPfam_B3_4,superfamily_SSF52047" - no_errors tier1 345 0 59 68 53.12 22 18 40 775109 TCGA-AB-3005 AML39 1 7332017 7332017 G T SNP CAMTA1 NM_015215.1 human genbank 54_36p 1 validated intronic c.438+99744 e5+99744 0.011 - - - no_errors tier3 1215 1 0.08 339 257 43.05 0 0 NA 775109 TCGA-AB-3005 AML39 1 7452771 7452771 A G SNP CAMTA1 NM_015215.1 human genbank 54_36p 1 validated intronic c.510+2223 e6+2223 0 - - - no_errors tier3 645 2 0.3 205 182 46.91 0 0 NA 775109 TCGA-AB-3005 AML39 1 14457196 14457196 C T SNP - - - - - - - - - - - - - - - tier3 1392 3 0.21 129 124 49.01 0 0 NA 775109 TCGA-AB-3005 AML39 1 16814288 16814288 C G SNP NBPF1 ENST00000287968 human ensembl 54_36p -1 known 5_prime_flanking_region c.-37819 NULL 0 - - - no_errors tier3 1326 1 0.08 216 27 11.11 0 0 0 775109 TCGA-AB-3005 AML39 1 16817148 16817148 C A SNP NBPF1 ENST00000287968 human ensembl 54_36p -1 known 5_prime_flanking_region c.-40679 NULL 0 - - - no_errors tier3 1612 1 0.06 217 34 13.55 2 1 33.33 775109 TCGA-AB-3005 AML39 1 35916696 35916696 G A SNP PSMB2 NM_002794.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37076 NULL 0.346 - - - no_errors tier3 3886 3 0.08 231 171 42.54 0 0 NA 775109 TCGA-AB-3005 AML39 1 75713102 75713102 C T SNP SLC44A5 NM_152697.1 human genbank 54_36p -1 validated intronic c.13+66606 e1+66606 0.267 - - - no_errors tier3 1111 0 0 47 11 18.97 0 0 NA 775109 TCGA-AB-3005 AML39 1 79339774 79339774 C T SNP LOC729779 XR_016024.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-45395 NULL 0.003 - - - pseudogene tier3 1139 0 0 67 46 40.71 0 0 NA 775109 TCGA-AB-3005 AML39 1 100047192 100047192 A G SNP AGL NM_000028.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-41995 NULL 0 - - - no_errors tier3 1703 0 0 360 278 43.57 0 0 NA 775109 TCGA-AB-3005 AML39 1 106633215 106633215 G T SNP - - - - - - - - - - - - - - - tier3 1198 1 0.08 81 29 26.36 0 0 NA 775109 TCGA-AB-3005 AML39 1 143713851 143713851 A G SNP PDE4DIP NM_022359.2 human genbank 54_36p -1 validated intronic c.442-7793 e4-7793 0.002 - - - no_errors tier3 5270 3 0.06 1158 191 14.15 5 0 0 775109 TCGA-AB-3005 AML39 1 143984723 143984723 C T SNP NOTCH2NL NM_203458.3 human genbank 54_36p 1 validated nonsense c.220 p.R74* 0.852 "HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,superfamily_EGF/Laminin" "PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 5403 5 0.09 3924 650 14.2 66 15 18.52 775109 TCGA-AB-3005 AML39 1 144008077 144008077 A C SNP NBPF10 XM_001722184.3 human genbank 54_36p 1 model intronic c.493+149 e3+149 0.002 - - - no_errors tier3 562 1 0.18 282 54 16.07 13 0 0 775109 TCGA-AB-3005 AML39 1 161689105 161689105 T C SNP ENSG00000218131 ENST00000401780 human ensembl 54_36p -1 known 5_prime_flanking_region c.-29527 NULL 0 - - - no_coding_region:pseudogene tier3 1545 0 0 167 113 40.36 0 0 NA 775109 TCGA-AB-3005 AML39 1 193034283 193034283 T C SNP - - - - - - - - - - - - - - - tier3 1026 0 0 111 74 40 0 0 NA 775109 TCGA-AB-3005 AML39 1 195672744 195672744 A T SNP CRB1 NM_201253.1 human genbank 54_36p 1 reviewed intronic c.3749+1379 e9+1379 0.002 - - - no_errors tier3 1515 0 0 145 105 42 0 0 NA 775109 TCGA-AB-3005 AML39 1 196776363 196776363 G A SNP ATP6V1G3 NM_133262.2 human genbank 54_36p -1 reviewed missense c.41 p.A14V 1 HMMPfam_V-ATPase_G HMMPfam_V-ATPase_G - no_errors tier1 1583 2 0.13 603 380 38.62 NA 775109 TCGA-AB-3005 AML39 1 200777298 200777298 T C SNP PPP1R12B NM_032105.2 human genbank 54_36p 1 reviewed intronic c.2491-17330 e19-17330 0 - - - no_errors tier3 1655 1 0.06 484 318 39.65 2 1 33.33 775109 TCGA-AB-3005 AML39 1 212632685 212632685 A C SNP PTPN14 NM_005401.3 human genbank 54_36p -1 reviewed intronic c.929+976 e9+976 0.105 - - - no_errors tier3 2328 0 0 595 356 37.36 0 0 NA 775109 TCGA-AB-3005 AML39 1 213237965 213237965 C T SNP KCNK2 NM_001017424.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-7923 NULL 0.001 - - - no_errors tier3 1917 2 0.1 504 349 40.91 0 0 NA 775109 TCGA-AB-3005 AML39 1 215971473 215971473 G T SNP SPATA17 NM_138796.2 human genbank 54_36p 1 provisional intronic c.396-10467 e6-10467 0 - - - no_errors tier3 1076 1 0.09 165 69 29.49 0 0 NA 775109 TCGA-AB-3005 AML39 1 223735022 223735022 G A SNP ENAH NM_001008493.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*17078 NULL 0.001 - - - no_errors tier3 1599 3 0.19 305 256 45.63 0 0 NA 775109 TCGA-AB-3005 AML39 1 228507464 228507464 A C SNP GALNT2 NM_004481.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*25637 NULL 0 - - - no_errors tier3 888 0 0 62 56 47.46 0 0 NA 775109 TCGA-AB-3005 AML39 1 232985274 232985274 C T SNP LOC100130249 XM_001722882.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23052 NULL 0.002 - - - no_errors tier3 3323 5 0.15 1102 173 13.54 10 1 9.09 775109 TCGA-AB-3005 AML39 1 240544878 240544878 C G SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.51-26423 e2-26423 0.015 - - - no_errors tier3 1313 2 0.15 333 194 36.81 0 0 NA 775109 TCGA-AB-3005 AML39 1 242599351 242599351 G A SNP C1orf100 NM_001012970.1 human genbank 54_36p 1 predicted intronic c.56+4670 e1+4670 0.172 - - - no_errors tier3 3739 4 0.11 1174 103 8.07 0 0 NA 775109 TCGA-AB-3005 AML39 2 873813 873813 C G SNP LOC200493 XM_115715.5 human genbank 54_36p -1 model missense c.458 p.W153S 0.011 NULL NULL - no_start_codon:pseudogene:no_stop_codon tier1 2319 0 409 304 42.46 NA 775109 TCGA-AB-3005 AML39 2 2406542 2406542 A T SNP - - - - - - - - - - - - - - - tier3 1177 1 0.08 199 110 35.6 0 0 NA 775109 TCGA-AB-3005 AML39 2 17277320 17277320 G C SNP - - - - - - - - - - - - - - - tier3 1383 0 0 133 80 37.56 0 0 NA 775109 TCGA-AB-3005 AML39 2 19736164 19736164 G T SNP - - - - - - - - - - - - - - - tier3 1447 4 0.28 301 264 46.73 0 0 NA 775109 TCGA-AB-3005 AML39 2 20983971 20983971 T C SNP - - - - - - - - - - - - - - - tier3 1701 5 0.29 318 199 38.49 0 0 NA 775109 TCGA-AB-3005 AML39 2 23580870 23580870 G A SNP KLHL29 XM_001717454.1 human genbank 54_36p 1 model intronic c.765+28828 e4+28828 0.005 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 510 0 0 74 57 43.51 0 0 NA 775109 TCGA-AB-3005 AML39 2 26657790 26657790 A C SNP CIB4 NM_001029881.1 human genbank 54_36p -1 provisional intronic c.528-25 e7-25 0.004 - - - no_errors tier3 1184 3 0.25 288 221 43.25 0 0 NA 775109 TCGA-AB-3005 AML39 2 34580527 34580527 G A SNP - - - - - - - - - - - - - - - tier3 729 1 0.14 163 69 29.74 0 0 NA 775109 TCGA-AB-3005 AML39 2 51936713 51936713 G A SNP - - - - - - - - - - - - - - - tier3 2290 4 0.17 524 370 41.39 0 0 NA 775109 TCGA-AB-3005 AML39 2 77018858 77018858 C T SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1555-189308 e3-189308 0 - - - no_errors tier3 1273 1 0.08 159 78 32.91 0 0 NA 775109 TCGA-AB-3005 AML39 2 91186585 91186585 A C SNP ENSG00000219041 ENST00000405516 human ensembl 54_36p 1 known intronic c.301-132391 e2-132391 0.004 - - - no_start_codon:no_stop_codon tier3 4223 1 0.02 1648 328 16.58 7 1 12.5 775109 TCGA-AB-3005 AML39 2 91196508 91196508 C A SNP ENSG00000219041 ENST00000405516 human ensembl 54_36p 1 known intronic c.301-122468 e2-122468 0.006 - - - no_start_codon:no_stop_codon tier3 2472 6 0.24 482 117 19.5 3 1 25 775109 TCGA-AB-3005 AML39 2 133766779 133766779 G A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.143+10300 e2+10300 0.002 - - - no_errors tier3 1802 1 0.06 184 98 34.63 0 0 NA 775109 TCGA-AB-3005 AML39 2 137746730 137746730 T C SNP THSD7B NM_001080427.1 human genbank 54_36p 1 provisional intronic c.2303+28 e10+28 0.006 - - - no_errors tier3 2580 0 0 272 156 36.36 0 0 0 775109 TCGA-AB-3005 AML39 2 139994837 139994837 G C SNP ENSG00000206901 ENST00000384174 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*9242 NULL 0.002 - - - no_errors tier3 2549 1 0.04 1151 770 40.04 0 0 NA 775109 TCGA-AB-3005 AML39 2 140536319 140536319 C T SNP - - - - - - - - - - - - - - - tier3 2204 1 0.05 578 379 39.52 0 0 NA 775109 TCGA-AB-3005 AML39 2 140574890 140574890 C T SNP - - - - - - - - - - - - - - - tier3 1411 3 0.21 272 214 43.94 0 0 NA 775109 TCGA-AB-3005 AML39 2 140653997 140653997 C T SNP ENSG00000208282 ENST00000385547 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-40478 NULL 0 - - - pseudogene tier3 2930 5 0.17 508 391 43.44 0 0 NA 775109 TCGA-AB-3005 AML39 2 142777574 142777574 G T SNP - - - - - - - - - - - - - - - tier3 1499 0 0 239 163 40.55 0 0 NA 775109 TCGA-AB-3005 AML39 2 143133016 143133016 C T SNP - - - - - - - - - - - - - - - tier3 1476 2 0.13 340 251 42.4 0 0 NA 775109 TCGA-AB-3005 AML39 2 147157175 147157175 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 2 147676874 147676874 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 2 159325432 159325432 G A SNP DAPL1 NM_001017920.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-34699 NULL 0.001 - - - no_errors tier3 2613 2 0.08 389 210 35.06 0 0 NA 775109 TCGA-AB-3005 AML39 2 174034475 174034475 G A SNP LOC100130171 XR_038684.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-29232 NULL 0.083 - - - pseudogene tier3 1052 0 0 167 123 42.27 0 0 NA 775109 TCGA-AB-3005 AML39 2 175922949 175922949 G T SNP ENSG00000221347 ENST00000408420 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*19503 NULL 0.017 - - - no_errors tier3 3148 1 0.03 922 554 37.53 0 0 NA 775109 TCGA-AB-3005 AML39 2 178340894 178340894 C T SNP PDE11A NM_016953.1 human genbank 54_36p -1 reviewed intronic c.1788+1403 e10+1403 0 - - - no_errors tier3 1946 0 0 805 492 37.88 0 0 NA 775109 TCGA-AB-3005 AML39 2 180611491 180611491 T C SNP CWC22 NM_020943.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-45178 NULL 0 - - - no_errors tier3 1771 1 0.06 461 346 42.82 0 0 NA 775109 TCGA-AB-3005 AML39 2 188030875 188030875 T C SNP CALCRL NM_005795.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-72308 NULL 0.266 - - - no_errors tier3 696 2 0.29 44 30 40.54 0 0 NA 775109 TCGA-AB-3005 AML39 2 193867512 193867512 G A SNP LOC645314 XR_017462.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16940 NULL 0.759 - - - no_errors tier3 1995 2 0.1 559 205 26.8 0 0 NA 775109 TCGA-AB-3005 AML39 2 195166876 195166876 C T SNP - - - - - - - - - - - - - - - tier3 780 0 0 76 38 33.33 0 0 NA 775109 TCGA-AB-3005 AML39 2 203898237 203898237 C T SNP ABI2 NM_005759.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3246 NULL 0.01 - - - no_errors tier3 729 0 0 30 18 37.5 3 0 0 775109 TCGA-AB-3005 AML39 2 208277330 208277330 C T SNP CCNYL1 NM_152523.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-7746 NULL 0 - - - no_errors tier3 1357 1 0.07 217 127 36.92 0 0 NA 775109 TCGA-AB-3005 AML39 2 211910208 211910208 G A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*46377 NULL 0 - - - no_errors tier3 1592 0 0 336 253 42.95 0 0 NA 775109 TCGA-AB-3005 AML39 2 222291377 222291377 A G SNP - - - - - - - - - - - - - - - tier3 2051 2 0.1 308 187 37.78 0 0 NA 775109 TCGA-AB-3005 AML39 2 234488437 234488437 G A SNP TRPM8 NM_024080.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-11485 NULL 0.009 - - - no_errors tier3 3225 2 0.06 1051 670 38.93 0 0 NA 775109 TCGA-AB-3005 AML39 2 240630916 240630916 G A SNP LOC643905 NM_001080835.1 human genbank 54_36p -1 predicted missense c.157 p.R53W 0.003 NULL NULL - no_errors tier1 4899 3 0.06 4376 670 13.27 NA 775109 TCGA-AB-3005 AML39 2 240820276 240820276 G A SNP ENSG00000221412 ENST00000408485 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*29529 NULL 0.004 - - - no_errors tier3 923 1 0.11 324 288 47.06 0 0 NA 775109 TCGA-AB-3005 AML39 3 1923749 1923749 T C SNP ENSG00000214073 ENST00000397467 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*937 NULL 0.001 - - - no_coding_region:pseudogene tier3 1165 2 0.17 171 120 41.24 0 0 NA 775109 TCGA-AB-3005 AML39 3 6662946 6662946 C A SNP - - - - - - - - - - - - - - - tier3 1036 3 0.29 397 253 38.92 0 0 NA 775109 TCGA-AB-3005 AML39 3 18355515 18355515 C T SNP SATB1 NM_002971.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*10151 NULL 0.001 - - - no_errors tier3 1036 1 0.1 147 99 40.24 0 0 NA 775109 TCGA-AB-3005 AML39 3 20667564 20667564 G A SNP - - - - - - - - - - - - - - - tier3 1701 2 0.12 469 308 39.59 0 0 NA 775109 TCGA-AB-3005 AML39 3 22777775 22777775 C T SNP - - - - - - - - - - - - - - - tier3 1721 0 0 440 354 44.58 0 0 NA 775109 TCGA-AB-3005 AML39 3 25053481 25053481 T C SNP ENSG00000210001 ENST00000387266 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16539 NULL 0.61 - - - pseudogene tier3 1628 1 0.06 276 186 40.26 0 0 NA 775109 TCGA-AB-3005 AML39 3 25360976 25360976 T C SNP RARB ENST00000404969 human ensembl 54_36p 1 known intronic c.179-116712 e2-116712 0.006 - - - no_errors tier3 2594 5 0.19 562 257 31.38 0 0 NA 775109 TCGA-AB-3005 AML39 3 40758421 40758421 C T SNP LOC729505 XM_001130480.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-31367 NULL 0 - - - no_errors tier3 3734 2 0.05 1124 801 41.59 0 0 NA 775109 TCGA-AB-3005 AML39 3 43143007 43143007 C T SNP C3orf39 NM_032806.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-45080 NULL 0 - - - no_errors tier3 2049 0 0 237 154 39.29 0 0 NA 775109 TCGA-AB-3005 AML39 3 43800615 43800615 C G SNP - - - - - - - - - - - - - - - tier3 4115 2 0.05 1239 824 39.9 0 0 NA 775109 TCGA-AB-3005 AML39 3 46001045 46001045 C T SNP FYCO1 NM_024513.2 human genbank 54_36p -1 validated intronic c.55+307 e1+307 0.001 - - - no_errors tier3 1590 1 0.06 209 116 35.69 0 0 0 775109 TCGA-AB-3005 AML39 3 48669475 48669475 C T SNP CELSR3 NM_001407.2 human genbank 54_36p -1 reviewed silent c.4059 p.Q1353 1 NULL "PatternScan_ASX_HYDROXYL,HMMPfam_GPS,HMMSmart_SM00303,HMMPfam_7tm_2,HMMSmart_SM00282,HMMPfam_HRM,HMMSmart_SM00008,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Cadherin-like,PatternScan_G_PROTEIN_RECEP_F2_2,superfamily_EGF/Laminin" - no_errors tier1 819 1 0.12 162 148 47.59 7 1 12.5 775109 TCGA-AB-3005 AML39 3 58959970 58959970 C A SNP C3orf67 NM_198463.2 human genbank 54_36p -1 predicted intronic c.1+40353 e0+40353 0.007 - - - no_errors tier3 1170 0 0 486 345 41.52 0 0 NA 775109 TCGA-AB-3005 AML39 3 63420383 63420383 G T SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated intronic c.24+16198 e1+16198 0.001 - - - no_errors tier3 1600 1 0.06 173 84 32.56 0 0 NA 775109 TCGA-AB-3005 AML39 3 63475305 63475305 T A SNP SYNPR NM_144642.1 human genbank 54_36p 1 validated intronic c.149+33633 e2+33633 0.003 - - - no_errors tier3 2902 4 0.14 704 454 39.17 0 0 NA 775109 TCGA-AB-3005 AML39 3 74519543 74519543 G A SNP CNTN3 NM_020872.1 human genbank 54_36p -1 validated intronic c.455-16303 e5-16303 0.002 - - - no_errors tier3 1872 4 0.21 284 226 44.31 0 0 NA 775109 TCGA-AB-3005 AML39 3 76005480 76005480 G A SNP - - - - - - - - - - - - - - - tier3 1809 3 0.17 138 78 35.94 0 0 NA 775109 TCGA-AB-3005 AML39 3 77979483 77979483 T A SNP ENSG00000206891 ENST00000384164 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35798 NULL 0.001 - - - no_errors tier3 675 0 0 40 5 11.11 0 0 NA 775109 TCGA-AB-3005 AML39 3 79385322 79385322 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-127943 e2-127943 0.002 - - - no_errors tier3 3918 4 0.1 1314 987 42.89 0 0 NA 775109 TCGA-AB-3005 AML39 3 79455501 79455501 A T SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.89-198122 e2-198122 0.006 - - - no_errors tier3 1230 2 0.16 147 99 40.08 0 0 NA 775109 TCGA-AB-3005 AML39 3 97979991 97979991 T A SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-36167 NULL 0.003 - - - no_errors tier3 293 0 0 49 27 35.53 0 0 NA 775109 TCGA-AB-3005 AML39 3 111280555 111280555 A G SNP - - - - - - - - - - - - - - - tier3 382 0 0 37 23 38.33 0 0 NA 775109 TCGA-AB-3005 AML39 3 113218508 113218508 C A SNP TMPRSS7 NM_001042575.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30851 NULL 0.001 - - - no_errors tier3 1348 0 0 104 67 39.18 0 0 NA 775109 TCGA-AB-3005 AML39 3 116699367 116699367 C A SNP - - - - - - - - - - - - - - - tier3 1155 2 0.17 260 155 37.26 0 0 NA 775109 TCGA-AB-3005 AML39 3 119884065 119884065 A T SNP - - - - - - - - - - - - - - - tier3 2340 3 0.13 560 352 38.6 0 0 NA 775109 TCGA-AB-3005 AML39 3 120198964 120198964 C T SNP IGSF11 NM_001015887.1 human genbank 54_36p -1 validated intronic c.52+37104 e1+37104 0.002 - - - no_errors tier3 1615 1 0.06 475 345 42.07 0 0 NA 775109 TCGA-AB-3005 AML39 3 124595332 124595332 G A SNP ADCY5 NM_183357.1 human genbank 54_36p -1 validated intronic c.1135-41214 e2-41214 0.001 - - - no_errors tier3 186 1 0.53 71 65 47.79 0 0 NA 775109 TCGA-AB-3005 AML39 3 136829444 136829444 C T SNP - - - - - - - - - - - - - - - tier3 985 0 0 85 44 34.11 0 0 NA 775109 TCGA-AB-3005 AML39 3 148154409 148154409 G T SNP ENSG00000207156 ENST00000384427 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*42675 NULL 0.012 - - - no_errors tier3 2479 3 0.12 752 507 40.27 0 0 NA 775109 TCGA-AB-3005 AML39 3 149545145 149545145 T C SNP - - - - - - - - - - - - - - - tier3 1555 3 0.19 387 230 37.28 0 0 NA 775109 TCGA-AB-3005 AML39 3 158324472 158324472 G A SNP ENSG00000201778 ENST00000364908 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29559 NULL 0.004 - - - no_errors tier3 1235 0 0 295 164 35.73 0 0 NA 775109 TCGA-AB-3005 AML39 3 175623256 175623256 C T SNP LOC647212 XM_934517.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-8063 NULL 0.003 - - - no_errors tier3 1615 3 0.18 202 177 46.7 0 0 NA 775109 TCGA-AB-3005 AML39 3 186391986 186391986 A G SNP EHHADH NM_001966.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*722 NULL 0.001 - - - no_errors tier3 1013 1 0.1 99 53 34.87 3 1 25 775109 TCGA-AB-3005 AML39 4 4255332 4255332 G A SNP OTOP1 NM_177998.1 human genbank 54_36p -1 provisional intronic c.600-126 e4-126 0.001 - - - no_errors tier3 1143 1 0.09 227 146 39.14 0 0 NA 775109 TCGA-AB-3005 AML39 4 6332981 6332981 T A SNP WFS1 NM_006005.1 human genbank 54_36p 1 reviewed intronic c.232+2666 e1+2666 0.008 - - - no_errors tier3 282 0 0 59 44 42.72 0 0 NA 775109 TCGA-AB-3005 AML39 4 19053054 19053054 C T SNP - - - - - - - - - - - - - - - tier3 1619 2 0.12 130 115 46.75 0 0 NA 775109 TCGA-AB-3005 AML39 4 21721434 21721434 C T SNP - - - - - - - - - - - - - - - tier3 1091 1 0.09 281 169 37.56 0 0 NA 775109 TCGA-AB-3005 AML39 4 23205128 23205128 C T SNP - - - - - - - - - - - - - - - tier3 1780 4 0.22 489 346 41.39 0 0 NA 775109 TCGA-AB-3005 AML39 4 23862178 23862178 G A SNP - - - - - - - - - - - - - - - tier3 1985 1 0.05 453 321 41.42 0 0 NA 775109 TCGA-AB-3005 AML39 4 28391927 28391927 G A SNP ENSG00000215250 ENST00000399874 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*42088 NULL 0 - - - no_coding_region:pseudogene tier3 1322 3 0.23 122 72 37.11 0 0 NA 775109 TCGA-AB-3005 AML39 4 44329196 44329196 C A SNP YIPF7 NM_182592.2 human genbank 54_36p -1 validated intronic c.351-2872 e4-2872 0 - - - no_errors tier3 1026 3 0.29 144 105 42.17 0 0 NA 775109 TCGA-AB-3005 AML39 4 54373772 54373772 G A SNP - - - - - - - - - - - - - - - tier3 2201 1 0.05 352 213 37.63 0 0 NA 775109 TCGA-AB-3005 AML39 4 56195408 56195408 A G SNP NMU NM_006681.2 human genbank 54_36p -1 validated intronic c.112+1597 e1+1597 0.001 - - - no_errors tier3 1679 2 0.12 126 94 42.73 0 0 NA 775109 TCGA-AB-3005 AML39 4 56398406 56398406 A G SNP EXOC1 NM_001024924.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20841 NULL 0.018 - - - no_errors tier3 543 0 0 41 31 43.06 0 0 NA 775109 TCGA-AB-3005 AML39 4 63706662 63706662 C T SNP LOC728709 XM_001128250.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*15019 NULL 0 - - - no_errors tier3 863 0 0 59 40 40.4 0 0 NA 775109 TCGA-AB-3005 AML39 4 64569151 64569151 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 4 64678278 64678278 A C SNP - - - - - - - - - - - - - - - tier3 404 0 0 34 25 42.37 0 0 NA 775109 TCGA-AB-3005 AML39 4 66436605 66436605 T A SNP - - - - - - - - - - - - - - - tier3 552 1 0.18 26 15 36.59 0 0 NA 775109 TCGA-AB-3005 AML39 4 71248986 71248986 C G SNP PROL1 NM_021225.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-50606 NULL 0.064 - - - no_errors tier3 1537 2 0.13 85 47 35.61 0 0 NA 775109 TCGA-AB-3005 AML39 4 75096738 75096738 A - DEL PPBP NM_002704.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24054 NULL 0.031 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 4 76715114 76715114 C A SNP CDKL2 NM_003948.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*10953 NULL 0.006 - - - no_errors tier3 3355 7 0.21 412 270 39.59 0 0 NA 775109 TCGA-AB-3005 AML39 4 93424142 93424142 C A SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20689 NULL 0.007 - - - no_errors tier3 2418 4 0.16 784 536 40.61 0 0 NA 775109 TCGA-AB-3005 AML39 4 101136133 101136133 C T SNP H2AFZ NM_002106.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-45783 NULL 0 - - - no_errors tier3 1085 0 0 344 218 38.72 0 0 NA 775109 TCGA-AB-3005 AML39 4 105657284 105657284 C T SNP CXXC4 NM_025212.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-25383 NULL 0.001 - - - no_errors tier3 2253 1 0.04 156 60 27.78 0 0 NA 775109 TCGA-AB-3005 AML39 4 116093870 116093870 C T SNP NDST4 NM_022569.1 human genbank 54_36p -1 provisional intronic c.1222-15762 e4-15762 0.001 - - - no_errors tier3 1154 1 0.09 131 66 33.5 0 0 NA 775109 TCGA-AB-3005 AML39 4 117170222 117170222 C T SNP - - - - - - - - - - - - - - - tier3 719 1 0.14 35 17 32.69 0 0 NA 775109 TCGA-AB-3005 AML39 4 122442005 122442005 T C SNP QRFPR NM_198179.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*27914 NULL 0.003 - - - no_errors tier3 813 2 0.24 334 213 38.94 0 0 NA 775109 TCGA-AB-3005 AML39 4 126989777 126989777 T C SNP - - - - - - - - - - - - - - - tier3 1157 1 0.09 104 77 42.31 0 0 NA 775109 TCGA-AB-3005 AML39 4 127692200 127692200 T C SNP - - - - - - - - - - - - - - - tier3 1446 1 0.07 226 194 46.19 0 0 NA 775109 TCGA-AB-3005 AML39 4 130553027 130553027 C T SNP - - - - - - - - - - - - - - - tier3 876 1 0.11 95 79 45.4 0 0 NA 775109 TCGA-AB-3005 AML39 4 134561160 134561160 G T SNP - - - - - - - - - - - - - - - tier3 770 0 0 42 10 19.23 0 0 NA 775109 TCGA-AB-3005 AML39 4 139238318 139238318 C T SNP - - - - - - - - - - - - - - - tier3 1291 0 0 213 147 40.83 0 0 NA 775109 TCGA-AB-3005 AML39 4 143055682 143055682 C T SNP - - - - - - - - - - - - - - - tier3 648 0 0 123 98 44.34 0 0 NA 775109 TCGA-AB-3005 AML39 4 148176991 148176991 C T SNP - - - - - - - - - - - - - - - tier3 787 2 0.25 158 137 46.44 0 0 NA 775109 TCGA-AB-3005 AML39 4 148463817 148463817 G A SNP MIRN548G ENST00000408442 human ensembl 54_36p -1 known 3_prime_flanking_region c.*21414 NULL 0 - - - no_errors tier3 1217 2 0.16 340 270 44.26 0 0 NA 775109 TCGA-AB-3005 AML39 4 149839878 149839878 G T SNP - - - - - - - - - - - - - - - tier3 971 2 0.21 82 36 30.51 0 0 NA 775109 TCGA-AB-3005 AML39 4 149983206 149983206 T C SNP - - - - - - - - - - - - - - - tier3 2781 4 0.14 663 458 40.82 0 0 NA 775109 TCGA-AB-3005 AML39 4 164246389 164246389 A T SNP LOC729971 XM_001131925.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-3037 NULL 0.006 - - - no_errors tier3 1420 1 0.07 153 109 41.44 0 1 100 775109 TCGA-AB-3005 AML39 4 166072387 166072387 C A SNP C4orf39 NM_153027.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-25238 NULL 0 - - - no_errors tier3 1442 1 0.07 265 153 36.6 0 0 NA 775109 TCGA-AB-3005 AML39 4 179502549 179502549 C G SNP - - - - - - - - - - - - - - - tier3 1089 1 0.09 246 148 37.56 0 0 NA 775109 TCGA-AB-3005 AML39 4 187810783 187810783 T - DEL FAT1 NM_005245.3 human genbank 54_36p -1 reviewed intronic c.3580+10664 e2+10664 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 4 190369930 190369930 C A SNP - - - - - - - - - - - - - - - tier3 1838 1 0.05 431 261 37.72 0 0 NA 775109 TCGA-AB-3005 AML39 4 190816023 190816023 G A SNP - - - - - - - - - - - - - - - tier3 1624 1 0.06 459 91 16.55 0 0 NA 775109 TCGA-AB-3005 AML39 4 190848626 190848626 G A SNP ENSG00000202215 ENST00000365345 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*19061 NULL 0.009 - - - no_errors tier3 3139 2 0.06 1094 182 14.25 0 0 NA 775109 TCGA-AB-3005 AML39 4 190869432 190869432 A T SNP ENSG00000202215 ENST00000365345 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1570 NULL 0.001 - - - no_errors tier3 2432 1 0.04 450 54 10.71 0 0 NA 775109 TCGA-AB-3005 AML39 4 190876450 190876450 C T SNP ENSG00000202215 ENST00000365345 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-8588 NULL 0.003 - - - no_errors tier3 2966 0 0 1896 322 14.5 0 0 NA 775109 TCGA-AB-3005 AML39 5 15073818 15073818 C T SNP LOC402198 XM_001716525.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*15934 NULL 0 - - - no_errors tier3 1888 1 0.05 162 76 31.93 0 0 NA 775109 TCGA-AB-3005 AML39 5 15260853 15260853 C T SNP - - - - - - - - - - - - - - - tier3 1752 0 0 424 293 40.86 0 0 NA 775109 TCGA-AB-3005 AML39 5 15659880 15659880 T G SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.38-9212 e2-9212 0 - - - no_errors tier3 1674 0 0 414 264 38.82 0 0 NA 775109 TCGA-AB-3005 AML39 5 18196933 18196933 G C SNP - - - - - - - - - - - - - - - tier3 639 1 0.16 26 16 38.1 0 0 NA 775109 TCGA-AB-3005 AML39 5 22860478 22860478 A T SNP CDH12 NM_004061.3 human genbank 54_36p -1 reviewed intronic c.1+28446 e0+28446 0.002 - - - no_errors tier3 630 0 0 41 31 43.06 0 0 NA 775109 TCGA-AB-3005 AML39 5 26844764 26844764 C T SNP - - - - - - - - - - - - - - - tier3 533 1 0.19 148 116 43.77 0 0 NA 775109 TCGA-AB-3005 AML39 5 27381389 27381390 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 5 33830745 33830745 A T SNP ADAMTS12 NM_030955.2 human genbank 54_36p -1 reviewed intronic c.490-43335 e3-43335 0 - - - no_errors tier3 1191 0 0 264 214 44.77 0 0 NA 775109 TCGA-AB-3005 AML39 5 35867468 35867468 G T SNP IL7R NM_002185.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25369 NULL 0.012 - - - no_errors tier3 1476 2 0.14 552 324 36.99 0 0 NA 775109 TCGA-AB-3005 AML39 5 50370642 50370642 C T SNP ENSG00000207060 ENST00000384332 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*16302 NULL 0.001 - - - no_errors tier3 1202 1 0.08 324 238 42.35 0 0 NA 775109 TCGA-AB-3005 AML39 5 59751121 59751122 - T INS LOC653198 XR_039820.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-46823 NULL 0.004:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 5 64484471 64484471 G T SNP ADAMTS6 NM_197941.2 human genbank 54_36p -1 reviewed intronic c.3245-943 e24-943 0.511 - - - no_errors tier3 1362 0 0 197 125 38.82 0 0 NA 775109 TCGA-AB-3005 AML39 5 71245048 71245048 G A SNP - - - - - - - - - - - - - - - tier3 1623 2 0.12 126 30 19.23 0 0 NA 775109 TCGA-AB-3005 AML39 5 91307134 91307134 C T SNP - - - - - - - - - - - - - - - tier3 1030 0 0 124 75 37.5 0 0 NA 775109 TCGA-AB-3005 AML39 5 92110376 92110376 A C SNP ENSG00000221810 ENST00000408883 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31400 NULL 0.001 - - - no_errors tier3 975 0 0 124 93 42.86 0 0 NA 775109 TCGA-AB-3005 AML39 5 99076463 99076463 G A SNP - - - - - - - - - - - - - - - tier3 1005 2 0.2 163 95 36.82 0 0 NA 775109 TCGA-AB-3005 AML39 5 101950479 101950479 C A SNP - - - - - - - - - - - - - - - tier3 2612 2 0.08 660 365 35.58 0 0 NA 775109 TCGA-AB-3005 AML39 5 110936416 110936416 C T SNP ENSG00000221310 ENST00000408383 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*16839 NULL 0.31 - - - no_errors tier3 1668 1 0.06 460 339 42.38 0 0 NA 775109 TCGA-AB-3005 AML39 5 115238092 115238092 A G SNP AP3S1 NM_001284.2 human genbank 54_36p 1 validated intronic c.273+4368 e3+4368 0.012 - - - no_errors tier3 1199 0 0 174 131 42.95 0 0 0 775109 TCGA-AB-3005 AML39 5 117167427 117167427 G A SNP ENSG00000182152 ENST00000329863 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-24813 NULL 0.006 - - - no_coding_region:pseudogene tier3 1570 0 0 431 261 37.72 0 0 NA 775109 TCGA-AB-3005 AML39 5 120437428 120437428 C A SNP ENSG00000208998 ENST00000386263 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*42578 NULL 0.004 - - - pseudogene tier3 1095 6 0.54 278 159 36.22 0 0 NA 775109 TCGA-AB-3005 AML39 5 125227897 125227897 G T SNP - - - - - - - - - - - - - - - tier3 561 0 0 55 15 21.43 0 0 NA 775109 TCGA-AB-3005 AML39 5 126366224 126366224 A T SNP MARCH3 NM_178450.3 human genbank 54_36p -1 validated intronic c.1+27717 e0+27717 0 - - - no_errors tier3 1188 0 0 413 203 32.95 0 1 100 775109 TCGA-AB-3005 AML39 5 133857928 133857928 C T SNP PHF15 NM_015288.4 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-41519 NULL 0.131 - - - no_errors tier3 818 0 0 148 101 40.56 0 0 NA 775109 TCGA-AB-3005 AML39 5 134414290 134414290 A G SNP PITX1 NM_002653.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-16820 NULL 0 - - - no_errors tier3 875 3 0.34 99 101 50.5 0 0 NA 775109 TCGA-AB-3005 AML39 5 135952367 135952367 G A SNP - - - - - - - - - - - - - - - tier3 2871 1 0.03 483 322 40 0 0 NA 775109 TCGA-AB-3005 AML39 5 140704389 140704389 G A SNP PCDHGA3 NM_018916.3 human genbank 54_36p 1 reviewed missense c.605 p.R202H 0.968 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 1100 3 0.27 276 100 26.6 NA 775109 TCGA-AB-3005 AML39 5 142471377 142471377 A G SNP ARHGAP26 NM_015071.1 human genbank 54_36p 1 validated intronic c.1539-9369 e18-9369 0 - - - no_errors tier3 1484 1 0.07 308 144 31.86 0 0 0 775109 TCGA-AB-3005 AML39 5 143035351 143035351 G A SNP - - - - - - - - - - - - - - - tier3 1525 3 0.2 313 216 40.83 0 0 NA 775109 TCGA-AB-3005 AML39 5 155903796 155903796 T C SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed intronic c.294+35506 e3+35506 0 - - - no_errors tier3 2122 4 0.19 514 380 42.36 0 0 NA 775109 TCGA-AB-3005 AML39 5 168311461 168311461 T C SNP SLIT3 NM_003062.2 human genbank 54_36p -1 validated intronic c.414-68542 e5-68542 0.009 - - - no_errors tier3 1810 3 0.17 399 349 46.6 0 0 NA 775109 TCGA-AB-3005 AML39 5 172781622 172781622 C T SNP - - - - - - - - - - - - - - - tier3 1361 0 0 269 168 38.44 0 0 NA 775109 TCGA-AB-3005 AML39 5 175309806 175309806 C G SNP THOC3 NM_032361.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*9772 NULL 0.026 - - - no_errors tier3 1758 0 0 548 407 42.62 1 1 50 775109 TCGA-AB-3005 AML39 5 180643301 180643301 G A SNP GNB2L1 NM_006098.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-39895 NULL 0 - - - no_errors tier3 300 0 0 115 68 37.16 0 0 NA 775109 TCGA-AB-3005 AML39 6 318785 318785 G A SNP LOC730077 XM_001132307.2 human genbank 54_36p 1 model intronic c.173+70597 e1+70597 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 597 0 0 629 198 23.94 0 0 NA 775109 TCGA-AB-3005 AML39 6 1684374 1684374 T - DEL GMDS NM_001500.2 human genbank 54_36p -1 validated intronic c.890+3327 e8+3327 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 6 3655656 3655656 C A SNP LOC100129626 XM_001718834.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16348 NULL 0 - - - no_errors tier3 2003 2 0.1 474 328 40.9 0 0 NA 775109 TCGA-AB-3005 AML39 6 5938968 5938968 C T SNP NRN1 NM_016588.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*5240 NULL 0 - - - no_errors tier3 1702 1 0.06 372 205 35.41 0 0 NA 775109 TCGA-AB-3005 AML39 6 9766989 9766989 G A SNP OFCC1 ENST00000336327 human ensembl 54_36p -1 known 3_prime_flanking_region c.*48992 NULL 0.001 - - - no_start_codon:no_stop_codon tier3 1379 0 0 186 121 39.41 0 0 NA 775109 TCGA-AB-3005 AML39 6 12370270 12370270 G A SNP EDN1 NM_001955.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28579 NULL 0.017 - - - no_errors tier3 1619 1 0.06 305 214 41.23 0 0 NA 775109 TCGA-AB-3005 AML39 6 15593474 15593474 T A SNP JARID2 NM_004973.2 human genbank 54_36p 1 reviewed intronic c.671-2043 e6-2043 0.004 - - - no_errors tier3 1011 0 0 161 83 34.02 0 0 0 775109 TCGA-AB-3005 AML39 6 36033664 36033664 C T SNP SLC26A8 NM_052961.2 human genbank 54_36p -1 reviewed intronic c.1863+1551 e15+1551 0.001 - - - no_errors tier3 3498 2 0.06 559 358 38.83 0 1 100 775109 TCGA-AB-3005 AML39 6 41173998 41173998 A C SNP NFYA NM_002505.4 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*871 NULL 0.007 - - - no_errors tier3 839 0 0 135 111 45.12 24 22 47.83 775109 TCGA-AB-3005 AML39 6 41729194 41729194 C A SNP MDFI NM_005586.3 human genbank 54_36p 1 reviewed missense c.644 p.P215H 1 NULL PatternScan_TNFR_NGFR_1 - no_errors tier1 1362 3 0.22 297 198 40 NA 775109 TCGA-AB-3005 AML39 6 50216224 50216224 T C SNP - - - - - - - - - - - - - - - tier3 806 0 0 76 62 44.93 0 0 NA 775109 TCGA-AB-3005 AML39 6 53944430 53944430 C T SNP C6orf142 NM_138569.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-47356 NULL 0.009 - - - no_errors tier3 1776 1 0.06 485 308 38.74 0 0 NA 775109 TCGA-AB-3005 AML39 6 64163319 64163319 G T SNP ENSG00000218274 ENST00000403446 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-64163319 NULL 0 - - - no_coding_region:pseudogene tier3 555 0 0 114 79 40.93 0 0 NA 775109 TCGA-AB-3005 AML39 6 70995199 70995199 G A SNP COL9A1 NM_001851.4 human genbank 54_36p -1 reviewed intronic c.2504-2766 e37-2766 0 - - - no_errors tier3 1083 1 0.09 125 79 38.73 0 0 NA 775109 TCGA-AB-3005 AML39 6 80270335 80270335 T A SNP LCA5 NM_181714.1 human genbank 54_36p -1 validated intronic c.720+9313 e2+9313 0.025 - - - no_errors tier3 429 0 0 19 18 48.65 0 0 NA 775109 TCGA-AB-3005 AML39 6 94696694 94696694 G A SNP - - - - - - - - - - - - - - - tier3 1339 4 0.3 100 47 31.97 0 0 NA 775109 TCGA-AB-3005 AML39 6 96285684 96285684 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 6 96404171 96404171 A C SNP - - - - - - - - - - - - - - - tier3 1413 0 0 363 247 40.49 0 0 NA 775109 TCGA-AB-3005 AML39 6 96489926 96489926 A T SNP KRT18P50 XM_001716480.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-26194 NULL 0.092 - - - pseudogene tier3 965 2 0.21 139 96 40.85 0 0 NA 775109 TCGA-AB-3005 AML39 6 100342819 100342819 G A SNP - - - - - - - - - - - - - - - tier3 3533 0 0 949 699 42.42 0 0 NA 775109 TCGA-AB-3005 AML39 6 102618564 102618564 C T SNP GRIK2 NM_175768.3 human genbank 54_36p 1 reviewed missense c.2597 p.P866L 1 NULL "HMMPfam_Lig_chan,HMMSmart_PBPe,HMMPfam_ANF_receptor,HMMPfam_Lig_chan-Glu_bd,superfamily_SSF53822,superfamily_SSF53850" - no_errors tier1 1077 1 0.09 88 66 42.58 NA 775109 TCGA-AB-3005 AML39 6 110056868 110056868 T C SNP AKD2 ENST00000341338 human ensembl 54_36p -1 known intronic c.1254+3951 e11+3951 0.016 - - - no_errors tier3 392 2 0.51 16 20 55.56 0 0 0 775109 TCGA-AB-3005 AML39 6 117616945 117616945 C T SNP - - - - - - - - - - - - - - - tier3 1579 2 0.13 198 150 42.98 0 0 NA 775109 TCGA-AB-3005 AML39 6 121417978 121417978 G A SNP C6orf170 NM_152730.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*25638 NULL 0.005 - - - no_errors tier3 1377 2 0.14 206 110 34.81 0 0 NA 775109 TCGA-AB-3005 AML39 6 129277416 129277416 G A SNP LAMA2 NM_000426.3 human genbank 54_36p 1 reviewed intronic c.112+31221 e1+31221 0.001 - - - no_errors tier3 1382 0 0 133 53 28.49 0 0 NA 775109 TCGA-AB-3005 AML39 6 141300846 141300846 T A SNP ENSG00000216548 ENST00000407538 human ensembl 54_36p -1 known 5_prime_flanking_region c.-15105 NULL 0.011 - - - no_coding_region:pseudogene tier3 764 0 0 85 59 40.97 0 0 NA 775109 TCGA-AB-3005 AML39 6 145276663 145276663 T C SNP - - - - - - - - - - - - - - - tier3 1817 2 0.11 257 204 44.25 0 0 NA 775109 TCGA-AB-3005 AML39 6 159573533 159573533 C T SNP FNDC1 NM_032532.2 human genbank 54_36p 1 validated missense c.1999 p.R667W 0.002 NULL "HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like" - no_errors tier1 277 1 0.36 103 124 53.91 NA 775109 TCGA-AB-3005 AML39 7 2522704 2522704 A C SNP LFNG ENST00000402506 human ensembl 54_36p 1 known intronic c.219+3216 e2+3216 0.001 - - - no_errors tier3 102 1 0.97 33 19 36.54 0 0 NA 775109 TCGA-AB-3005 AML39 7 13750731 13750731 A G SNP - - - - - - - - - - - - - - - tier3 1721 2 0.12 284 205 41.92 0 0 NA 775109 TCGA-AB-3005 AML39 7 24185191 24185191 G A SNP ENSG00000210318 ENST00000387583 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46253 NULL 0 - - - pseudogene tier3 1290 4 0.31 459 307 40.08 0 0 NA 775109 TCGA-AB-3005 AML39 7 25010413 25010413 A C SNP OSBPL3 NM_015550.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-111797 NULL 0.001 - - - no_errors tier3 1125 2 0.18 374 199 34.73 0 0 NA 775109 TCGA-AB-3005 AML39 7 32096993 32096993 G A SNP PDE1C ENST00000284920 human ensembl 54_36p -1 known intronic c.309-38537 e4-38537 0 - - - no_errors tier3 1227 0 0 399 233 36.87 0 0 NA 775109 TCGA-AB-3005 AML39 7 36696544 36696544 C G SNP AOAH NM_001637.2 human genbank 54_36p -1 reviewed intronic c.128-3620 e2-3620 0.001 - - - no_errors tier3 2003 1 0.05 1170 759 39.25 0 4 100 775109 TCGA-AB-3005 AML39 7 67363121 67363121 C T SNP - - - - - - - - - - - - - - - tier3 1709 2 0.12 315 238 42.96 0 0 NA 775109 TCGA-AB-3005 AML39 7 69442401 69442401 A T SNP AUTS2 NM_015570.1 human genbank 54_36p 1 validated intronic c.661-96273 e5-96273 0.018 - - - no_errors tier3 1150 1 0.09 76 62 44.93 0 0 0 775109 TCGA-AB-3005 AML39 7 77487021 77487021 C T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed silent c.3915 p.Q1305 1 NULL "HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_Guanylate_kin,HMMSmart_SM00072,PatternScan_GUANYLATE_KINASE_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 286 0 57 65 53.28 NA 775109 TCGA-AB-3005 AML39 7 79103793 79103793 G A SNP ENSG00000200786 ENST00000363916 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-17568 NULL 0 - - - no_errors tier3 1121 3 0.27 108 110 50.46 0 0 NA 775109 TCGA-AB-3005 AML39 7 84203127 84203127 C T SNP - - - - - - - - - - - - - - - tier3 1880 0 0 450 281 38.44 0 0 NA 775109 TCGA-AB-3005 AML39 7 86324984 86324984 G C SNP GRM3 NM_000840.2 human genbank 54_36p 1 reviewed intronic c.2567-6550 e5-6550 0.344 - - - no_errors tier3 1455 1 0.07 281 184 39.57 0 0 NA 775109 TCGA-AB-3005 AML39 7 87927640 87927640 C G SNP ENSG00000207094 ENST00000384366 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-11158 NULL 0.005 - - - no_errors tier3 792 2 0.25 36 26 41.94 0 0 NA 775109 TCGA-AB-3005 AML39 7 93246257 93246257 T C SNP - - - - - - - - - - - - - - - tier3 1051 2 0.19 56 49 46.67 0 0 NA 775109 TCGA-AB-3005 AML39 7 100577190 100577190 G A SNP AP1S1 NM_001283.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-7326 NULL 0.015 - - - no_errors tier3 5173 0 0 534 403 43.01 0 0 NA 775109 TCGA-AB-3005 AML39 7 108553515 108553515 C T SNP - - - - - - - - - - - - - - - tier3 957 0 0 52 60 53.57 0 0 NA 775109 TCGA-AB-3005 AML39 7 111261573 111261573 G A SNP DOCK4 NM_014705.3 human genbank 54_36p -1 reviewed intronic c.2835+307 e26+307 0.001 - - - no_errors tier3 1776 0 0 355 185 34.26 0 0 NA 775109 TCGA-AB-3005 AML39 7 127472372 127472372 A G SNP SND1 NM_014390.2 human genbank 54_36p 1 validated intronic c.1780-29418 e17-29418 0 - - - no_errors tier3 1628 4 0.24 182 82 30.94 0 2 100 775109 TCGA-AB-3005 AML39 7 130188736 130188736 A G SNP LOC646329 XM_935369.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*29174 NULL 0 - - - no_errors tier3 841 0 0 103 85 45.21 0 0 NA 775109 TCGA-AB-3005 AML39 7 133168685 133168685 A G SNP EXOC4 NM_021807.1 human genbank 54_36p 1 reviewed intronic c.1734+15848 e11+15848 0.005 - - - no_errors tier3 1332 0 0 95 56 37.09 0 0 0 775109 TCGA-AB-3005 AML39 7 135517611 135517611 C T SNP - - - - - - - - - - - - - - - tier3 2970 1 0.03 1059 774 42.23 0 0 NA 775109 TCGA-AB-3005 AML39 7 136138739 136138739 G A SNP - - - - - - - - - - - - - - - tier3 934 0 0 108 67 38.29 0 0 NA 775109 TCGA-AB-3005 AML39 7 136291918 136291918 T A SNP CHRM2 NM_000739.2 human genbank 54_36p 1 reviewed intronic c.1-35556 e1-35556 0 - - - no_errors tier3 1120 1 0.09 93 76 44.97 0 0 NA 775109 TCGA-AB-3005 AML39 7 139952949 139952949 G A SNP DENND2A ENST00000403375 human ensembl 54_36p -1 known intronic c.1-874 e1-874 0 - - - no_errors tier3 1228 1 0.08 304 200 39.68 0 0 NA 775109 TCGA-AB-3005 AML39 7 150984289 150984289 T C SNP PRKAG2 NM_016203.1 human genbank 54_36p -1 reviewed intronic c.684+19150 e4+19150 0.072 - - - no_errors tier3 984 2 0.2 120 87 41.83 0 4 100 775109 TCGA-AB-3005 AML39 7 153044400 153044400 C G SNP LOC100130228 XM_001721136.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-8186 NULL 0 - - - no_errors tier3 1895 1 0.05 712 487 40.58 1 0 0 775109 TCGA-AB-3005 AML39 7 157270334 157270334 T A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1789-101944 e13-101944 0.1 - - - no_errors tier3 211 0 0 19 17 47.22 0 0 NA 775109 TCGA-AB-3005 AML39 8 2782940 2782940 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*574 NULL 0.002 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 965 0 0 252 150 37.31 0 0 NA 775109 TCGA-AB-3005 AML39 8 4803871 4803871 G T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+35391 e1+35391 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 801 0 0 61 32 34.41 0 0 NA 775109 TCGA-AB-3005 AML39 8 13210637 13210637 G A SNP DLC1 NM_182643.3 human genbank 54_36p -1 reviewed intronic c.1315-3455 e4-3455 0.002 - - - no_errors tier3 1234 0 0 321 200 38.39 0 0 NA 775109 TCGA-AB-3005 AML39 8 15640557 15640557 C G SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed intronic c.863-4861 e8-4861 0 - - - no_errors tier3 1147 0 0 156 89 36.33 0 0 NA 775109 TCGA-AB-3005 AML39 8 18758348 18758348 C T SNP PSD3 NM_015310.3 human genbank 54_36p -1 validated intronic c.1634+11116 e4+11116 0.008 - - - no_errors tier3 1192 0 0 199 81 28.93 0 0 NA 775109 TCGA-AB-3005 AML39 8 35334852 35334852 C T SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.103+121905 e1+121905 0 - - - no_errors tier3 1368 0 0 370 254 40.71 0 0 NA 775109 TCGA-AB-3005 AML39 8 36074299 36074299 G T SNP - - - - - - - - - - - - - - - tier3 2417 4 0.16 471 250 34.67 0 0 NA 775109 TCGA-AB-3005 AML39 8 40114404 40114404 C G SNP C8orf4 NM_020130.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15805 NULL 0 - - - no_errors tier3 1344 0 0 153 125 44.96 0 0 NA 775109 TCGA-AB-3005 AML39 8 101033452 101033452 G A SNP RGS22 NM_015668.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*10391 NULL 0 - - - no_errors tier3 1407 0 0 253 164 39.33 0 0 NA 775109 TCGA-AB-3005 AML39 8 107786936 107786936 C G SNP OXR1 NM_181354.2 human genbank 54_36p 1 validated intronic c.597-850 e6-850 0 - - - no_errors tier3 1216 0 0 148 85 36.48 0 1 100 775109 TCGA-AB-3005 AML39 8 115374731 115374731 G A SNP - - - - - - - - - - - - - - - tier3 880 2 0.23 82 53 39.26 0 0 NA 775109 TCGA-AB-3005 AML39 8 115461555 115461555 T C SNP - - - - - - - - - - - - - - - tier3 819 0 0 115 62 35.03 0 0 NA 775109 TCGA-AB-3005 AML39 8 124343881 124343881 T C SNP ZHX1 NM_001017926.1 human genbank 54_36p -1 reviewed intronic c.1+4813 e0+4813 0.01 - - - no_errors tier3 706 1 0.14 34 29 46.03 1 0 0 775109 TCGA-AB-3005 AML39 8 129283473 129283473 C A SNP ENSG00000201782 ENST00000364912 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-18459 NULL 0 - - - no_errors tier3 1411 0 0 355 210 37.1 0 0 NA 775109 TCGA-AB-3005 AML39 8 137165753 137165753 T C SNP - - - - - - - - - - - - - - - tier3 2187 2 0.09 543 302 35.74 0 0 NA 775109 TCGA-AB-3005 AML39 8 141364876 141364876 C T SNP TRAPPC9 NM_031466.4 human genbank 54_36p -1 provisional intronic c.2276-1574 e14-1574 0 - - - no_errors tier3 810 1 0.12 383 261 40.53 0 1 100 775109 TCGA-AB-3005 AML39 8 143549639 143549639 C T SNP BAI1 NM_001702.2 human genbank 54_36p 1 reviewed intronic c.785-4198 e2-4198 0.001 - - - no_errors tier3 554 1 0.18 59 34 36.56 0 0 NA 775109 TCGA-AB-3005 AML39 9 4807274 4807274 A G SNP RCL1 NM_005772.3 human genbank 54_36p 1 validated intronic c.137-6274 e2-6274 0.029 - - - no_errors tier3 714 0 0 34 15 30.61 0 0 0 775109 TCGA-AB-3005 AML39 9 7004610 7004610 G A SNP JMJD2C NM_015061.2 human genbank 54_36p 1 reviewed intronic c.2182+609 e13+609 0.003 - - - no_errors tier3 2076 2 0.1 283 185 39.53 0 3 100 775109 TCGA-AB-3005 AML39 9 24936148 24936148 G A SNP ENSG00000223088 ENST00000411156 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*40415 NULL 0.002 - - - no_errors tier3 1756 1 0.06 601 378 38.57 0 0 NA 775109 TCGA-AB-3005 AML39 9 29708792 29708792 A T SNP - - - - - - - - - - - - - - - tier3 1557 1 0.06 525 390 42.62 0 0 NA 775109 TCGA-AB-3005 AML39 9 30515952 30515952 T G SNP ENSG00000219252 ENST00000404726 human ensembl 54_36p -1 known 3_prime_flanking_region c.*32933 NULL 0 - - - no_coding_region:pseudogene tier3 1665 0 0 235 167 41.54 0 0 NA 775109 TCGA-AB-3005 AML39 9 72868139 72868139 G A SNP TRPM3 NM_001007471.1 human genbank 54_36p -1 reviewed intronic c.177+57775 e1+57775 0.001 - - - no_errors tier3 1793 1 0.06 358 238 39.8 0 0 NA 775109 TCGA-AB-3005 AML39 9 88365156 88365156 C T SNP - - - - - - - - - - - - - - - tier3 1393 2 0.14 360 201 35.83 0 0 NA 775109 TCGA-AB-3005 AML39 9 104663916 104663916 T G SNP - - - - - - - - - - - - - - - tier3 1396 0 0 253 131 34.11 0 0 NA 775109 TCGA-AB-3005 AML39 9 115341418 115341418 C T SNP RGS3 NM_144488.3 human genbank 54_36p 1 reviewed intronic c.2037+2399 e19+2399 0 - - - no_errors tier3 790 0 0 240 107 30.84 0 0 0 775109 TCGA-AB-3005 AML39 9 118009794 118009794 G T SNP PAPPA NM_002581.3 human genbank 54_36p 1 reviewed intronic c.1624+93 e3+93 0 - - - no_errors tier3 3909 6 0.15 655 379 36.65 0 0 NA 775109 TCGA-AB-3005 AML39 9 131252517 131252517 G A SNP LOC100128077 XM_001726459.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40064 NULL 0.002 - - - no_errors tier3 515 0 0 30 22 42.31 0 0 NA 775109 TCGA-AB-3005 AML39 10 13566271 13566271 C T SNP BEND7 NM_152751.1 human genbank 54_36p -1 validated intronic c.682-3141 e4-3141 0.001 - - - no_errors tier3 1474 1 0.07 450 313 41.02 0 0 0 775109 TCGA-AB-3005 AML39 10 16949454 16949454 T C SNP CUBN NM_001081.3 human genbank 54_36p -1 reviewed intronic c.9454+2187 e59+2187 0 - - - no_errors tier3 1926 0 0 240 216 47.37 0 0 0 775109 TCGA-AB-3005 AML39 10 24792809 24792809 C A SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated intronic c.847-9354 e6-9354 0.001 - - - no_errors tier3 2814 0 0 675 540 44.44 0 0 NA 775109 TCGA-AB-3005 AML39 10 25379908 25379908 T C SNP C10orf63 NM_145010.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-35037 NULL 0.136 - - - no_errors tier3 3980 4 0.1 232 186 44.39 0 0 NA 775109 TCGA-AB-3005 AML39 10 25738850 25738850 A T SNP GPR158 NM_020752.2 human genbank 54_36p 1 validated intronic c.1112-2335 e4-2335 0.001 - - - no_errors tier3 730 0 0 43 30 41.1 0 0 NA 775109 TCGA-AB-3005 AML39 10 34440220 34440220 G T SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional missense c.3954 p.D1318E 1 NULL "HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like" - no_errors tier1 581 0 169 130 43.48 NA 775109 TCGA-AB-3005 AML39 10 37835395 37835395 T C SNP ENSG00000217958 ENST00000401863 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16550 NULL 0.012 - - - no_coding_region:pseudogene tier3 393 0 0 27 29 51.79 0 0 NA 775109 TCGA-AB-3005 AML39 10 44239427 44239427 G T SNP CXCL12 NM_001033886.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-38968 NULL 0.002 - - - no_errors tier3 1516 1 0.07 405 257 38.82 0 0 NA 775109 TCGA-AB-3005 AML39 10 44582426 44582426 C T SNP ENSG00000220202 ENST00000407900 human ensembl 54_36p 1 known 5_prime_flanking_region c.-39471 NULL 0 - - - no_coding_region:pseudogene tier3 718 1 0.14 191 158 45.14 0 0 NA 775109 TCGA-AB-3005 AML39 10 47153386 47153386 G C SNP ANTXRL ENST00000354871 human ensembl 54_36p 1 known intronic c.1329+479 e15+479 0.004 - - - no_errors tier3 723 5 0.69 132 159 54.64 0 0 NA 775109 TCGA-AB-3005 AML39 10 50520714 50520714 G A SNP CHAT NM_020549.1 human genbank 54_36p 1 reviewed intronic c.1112-3843 e8-3843 0.001 - - - no_errors tier3 1665 1 0.06 483 398 45.18 0 0 NA 775109 TCGA-AB-3005 AML39 10 55078588 55078588 A T SNP - - - - - - - - - - - - - - - tier3 1176 0 0 266 193 42.05 0 0 NA 775109 TCGA-AB-3005 AML39 10 56376448 56376448 G A SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1-49182 e1-49182 0 - - - no_errors tier3 1271 1 0.08 79 65 45.14 0 0 NA 775109 TCGA-AB-3005 AML39 10 84367446 84367446 C A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.954-120867 e3-120867 0.002 - - - no_errors tier3 1624 1 0.06 327 261 44.39 0 0 NA 775109 TCGA-AB-3005 AML39 10 84943118 84943118 C T SNP - - - - - - - - - - - - - - - tier3 1380 0 0 361 261 41.96 0 0 NA 775109 TCGA-AB-3005 AML39 10 86260930 86260930 T C SNP KIAA1128 NM_018999.2 human genbank 54_36p 1 validated intronic c.2411-2255 e10-2255 0.007 - - - no_errors tier3 772 0 0 56 60 51.28 0 0 0 775109 TCGA-AB-3005 AML39 10 95174274 95174274 C T SNP MYOF NM_013451.3 human genbank 54_36p -1 reviewed intronic c.433+1544 e5+1544 0 - - - no_errors tier3 1932 2 0.1 544 348 38.93 1 0 0 775109 TCGA-AB-3005 AML39 10 95532661 95532661 C G SNP LGI1 NM_005097.2 human genbank 54_36p 1 reviewed intronic c.431+5297 e4+5297 0.015 - - - no_errors tier3 1908 0 0 423 244 36.58 0 0 NA 775109 TCGA-AB-3005 AML39 10 101026984 101026984 A T SNP HPSE2 NM_021828.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41435 NULL 0.006 - - - no_errors tier3 1253 0 0 144 87 37.66 0 0 NA 775109 TCGA-AB-3005 AML39 10 107807938 107807938 G A SNP - - - - - - - - - - - - - - - tier3 1033 0 0 205 114 35.74 0 0 NA 775109 TCGA-AB-3005 AML39 10 117415426 117415426 T C SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.3796-61322 e27-61322 0.018 - - - no_errors tier3 1266 2 0.16 393 219 35.78 0 0 NA 775109 TCGA-AB-3005 AML39 10 124603684 124603684 T A SNP FAM24B NM_152644.2 human genbank 54_36p -1 validated intronic c.1+1467 e0+1467 0.001 - - - no_errors tier3 2015 0 0 239 139 36.77 0 0 0 775109 TCGA-AB-3005 AML39 10 125431554 125431554 A C SNP GPR26 NM_153442.3 human genbank 54_36p 1 validated intronic c.783-5881 e3-5881 0.004 - - - no_errors tier3 887 0 0 212 126 37.28 0 0 NA 775109 TCGA-AB-3005 AML39 10 126722902 126722902 T C SNP CTBP2 NM_001083914.1 human genbank 54_36p -1 reviewed intronic c.1-5188 e1-5188 0 - - - no_errors tier3 1479 2 0.13 538 105 16.3 0 0 0 775109 TCGA-AB-3005 AML39 10 133236050 133236050 C T SNP - - - - - - - - - - - - - - - tier3 681 1 0.15 150 127 45.85 0 0 NA 775109 TCGA-AB-3005 AML39 11 2713012 2713012 G T SNP KCNQ1 NM_000218.2 human genbank 54_36p 1 reviewed intronic c.1515-33638 e12-33638 0 - - - no_errors tier3 512 0 0 107 81 43.09 1 0 0 775109 TCGA-AB-3005 AML39 11 5511344 5511344 T C SNP HBG2 ENST00000380259 human ensembl 54_36p -1 known intronic c.1+57287 e0+57287 0 - - - no_errors tier3 1715 2 0.12 402 286 41.57 0 0 NA 775109 TCGA-AB-3005 AML39 11 8765028 8765028 T C SNP ST5 NM_005418.3 human genbank 54_36p -1 reviewed intronic c.1+24342 e0+24342 0.01 - - - no_errors tier3 4398 5 0.11 1000 614 38.02 0 0 NA 775109 TCGA-AB-3005 AML39 11 29816880 29816880 C T SNP - - - - - - - - - - - - - - - tier3 2386 1 0.04 309 183 37.2 0 0 NA 775109 TCGA-AB-3005 AML39 11 31000981 31000981 G A SNP uc001msu.1 ENST00000342355 human ensembl 54_36p -1 known intronic c.1448+41611 e12+41611 0.002 - - - no_errors tier3 2553 1 0.04 598 386 39.19 0 0 NA 775109 TCGA-AB-3005 AML39 11 51269215 51269215 T C SNP OR4A5 NM_001005272.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-244 NULL 0 - - - no_errors tier3 830 0 0 157 127 44.56 0 0 NA 775109 TCGA-AB-3005 AML39 11 59667847 59667847 C T SNP MS4A6A NM_152852.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*28360 NULL 0.009 - - - no_errors tier3 1989 1 0.05 687 464 40.28 0 0 NA 775109 TCGA-AB-3005 AML39 11 68460886 68460886 C T SNP IGHMBP2 NM_002180.2 human genbank 54_36p 1 reviewed nonsense c.2362 p.R788* 0 NULL "HMMSmart_SM00154,HMMPfam_R3H,HMMSmart_SM00393,HMMSmart_SM00382,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_R3H domain" - no_errors tier1 470 0 109 98 47.34 7 3 30 775109 TCGA-AB-3005 AML39 11 70047461 70047461 C T SNP SHANK2 NM_012309.1 human genbank 54_36p -1 reviewed intronic c.298-20777 e3-20777 0.007 - - - no_errors tier3 897 0 0 218 186 46.04 0 0 NA 775109 TCGA-AB-3005 AML39 11 76453357 76453357 T C SNP CAPN5 NM_004055.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20224 NULL 0 - - - no_errors tier3 1677 5 0.3 344 180 34.35 0 0 NA 775109 TCGA-AB-3005 AML39 11 79700731 79700731 T C SNP - - - - - - - - - - - - - - - tier3 1374 2 0.15 345 302 46.6 0 0 NA 775109 TCGA-AB-3005 AML39 11 80508408 80508408 T C SNP - - - - - - - - - - - - - - - tier3 1421 1 0.07 175 192 52.32 0 0 NA 775109 TCGA-AB-3005 AML39 11 95820497 95820497 G A SNP ENSG00000200411 ENST00000363541 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*26887 NULL 0.001 - - - no_errors tier3 2723 1 0.04 480 323 40.22 0 0 NA 775109 TCGA-AB-3005 AML39 11 112428582 112428583 - A INS NCAM1 NM_181351.5 human genbank 54_36p 1 validated intronic c.53+90986_53+90985 e1+90986 0.012:0.018 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 11 115721286 115721286 C G SNP ENSG00000211210 ENST00000388475 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*24915 NULL 0.001 - - - pseudogene tier3 3062 1 0.03 583 462 44.21 0 0 NA 775109 TCGA-AB-3005 AML39 11 119522785 119522785 G A SNP TRIM29 NM_012101.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-8836 NULL 0 - - - no_errors tier3 1010 3 0.29 349 273 43.89 0 0 NA 775109 TCGA-AB-3005 AML39 11 131710683 131710683 G A SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*433 NULL 0 - - - no_errors tier3 1244 1 0.08 465 315 40.38 0 0 NA 775109 TCGA-AB-3005 AML39 11 132554548 132554548 G A SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.62-236433 e2-236433 0 - - - no_errors tier3 846 1 0.12 279 174 38.41 0 0 NA 775109 TCGA-AB-3005 AML39 12 1664111 1664111 T C SNP ADIPOR2 NM_024551.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-69660 NULL 0.255 - - - no_errors tier3 1459 2 0.14 95 64 40.25 0 0 NA 775109 TCGA-AB-3005 AML39 12 5326141 5326141 C T SNP LOC100133418 XM_001714459.1 human genbank 54_36p -1 model intronic c.444+4957 e2+4957 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 2877 0 0 800 573 41.73 0 0 NA 775109 TCGA-AB-3005 AML39 12 21935916 21935916 C T SNP ABCC9 NM_005691.2 human genbank 54_36p -1 reviewed intronic c.1802+2317 e12+2317 0.105 - - - no_errors tier3 1191 0 0 221 151 40.59 0 0 NA 775109 TCGA-AB-3005 AML39 12 42455273 42455273 A C SNP IRAK4 NM_016123.2 human genbank 54_36p 1 reviewed intronic c.716+1174 e5+1174 0.002 - - - no_errors tier3 1748 2 0.11 151 116 43.45 1 1 50 775109 TCGA-AB-3005 AML39 12 43042630 43042630 A - DEL TMEM117 NM_032256.1 human genbank 54_36p 1 provisional intronic c.769-14015 e6-14015 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 12 48457155 48457155 C T SNP TMBIM6 ENST00000395006 human ensembl 54_36p 1 known intronic c.691-3414 e9-3414 0.001 - - - no_stop_codon tier3 3498 5 0.14 1056 648 38.03 0 0 NA 775109 TCGA-AB-3005 AML39 12 52486167 52486167 G C SNP ENSG00000223213 ENST00000411281 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*14750 NULL 0.003 - - - no_errors tier3 4623 4 0.09 1218 788 39.24 0 0 NA 775109 TCGA-AB-3005 AML39 12 52588242 52588242 C T SNP HOXC13 NM_017410.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30716 NULL 0.002 - - - no_errors tier3 2307 1 0.04 332 212 38.9 0 0 NA 775109 TCGA-AB-3005 AML39 12 61451910 61451910 T G SNP PPM1H NM_020700.1 human genbank 54_36p -1 validated intronic c.869+16363 e4+16363 0.001 - - - no_errors tier3 2901 129 4.25 425 335 44.08 0 0 0 775109 TCGA-AB-3005 AML39 12 77318750 77318750 C G SNP - - - - - - - - - - - - - - - tier3 1443 0 0 202 117 36.56 0 0 NA 775109 TCGA-AB-3005 AML39 12 79509594 79509594 T C SNP - - - - - - - - - - - - - - - tier3 693 1 0.14 50 43 46.24 0 0 NA 775109 TCGA-AB-3005 AML39 12 83487571 83487571 G A SNP - - - - - - - - - - - - - - - tier3 2024 3 0.15 480 361 42.93 0 0 NA 775109 TCGA-AB-3005 AML39 12 84362539 84362539 G A SNP - - - - - - - - - - - - - - - tier3 1930 1 0.05 227 162 41.65 0 0 NA 775109 TCGA-AB-3005 AML39 12 96352606 96352606 A T SNP - - - - - - - - - - - - - - - tier3 1771 0 0 420 302 41.83 0 0 NA 775109 TCGA-AB-3005 AML39 12 98279873 98279873 G A SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.1756+37667 e12+37667 0 - - - no_errors tier3 1701 1 0.06 195 102 34.34 0 0 NA 775109 TCGA-AB-3005 AML39 12 105793958 105793958 A G SNP RIC8B NM_018157.2 human genbank 54_36p 1 validated intronic c.1452-9854 e9-9854 0.001 - - - no_errors tier3 1178 0 0 100 45 31.03 1 1 50 775109 TCGA-AB-3005 AML39 12 107541809 107541809 T G SNP SELPLG ENST00000228463 human ensembl 54_36p -1 known missense c.404 p.Q135P 0 NULL NULL - no_errors tier1 5024 15 0.3 1323 340 20.35 80 6 6.98 775109 TCGA-AB-3005 AML39 12 110233174 110233174 C T SNP CUX2 NM_015267.2 human genbank 54_36p 1 validated intronic c.1900+305 e15+305 0.012 - - - no_errors tier3 798 1 0.12 82 46 35.94 0 1 100 775109 TCGA-AB-3005 AML39 13 21154662 21154662 G T SNP FGF9 NM_002010.2 human genbank 54_36p 1 reviewed intronic c.381+1378 e2+1378 0.001 - - - no_errors tier3 744 0 0 54 23 29.87 0 0 NA 775109 TCGA-AB-3005 AML39 13 23035467 23035467 A G SNP TNFRSF19 NM_018647.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26856 NULL 0 - - - no_errors tier3 1866 1 0.05 259 158 37.89 0 0 NA 775109 TCGA-AB-3005 AML39 13 24904456 24904456 G T SNP ATP8A2 NM_016529.4 human genbank 54_36p 1 validated intronic c.77-36659 e2-36659 0.001 - - - no_errors tier3 2620 1 0.04 637 395 38.28 0 0 NA 775109 TCGA-AB-3005 AML39 13 38266793 38266794 - T INS FREM2 NM_207361.4 human genbank 54_36p 1 reviewed intronic c.6019+9848_6019+9847 e6+9848 0.001:0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 13 47112444 47112444 C G SNP - - - - - - - - - - - - - - - tier3 2881 2 0.07 420 277 39.74 0 0 NA 775109 TCGA-AB-3005 AML39 13 55845540 55845540 C A SNP - - - - - - - - - - - - - - - tier3 828 2 0.24 217 151 41.03 0 0 NA 775109 TCGA-AB-3005 AML39 13 60238237 60238237 A G SNP ENSG00000206854 ENST00000384127 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23458 NULL 0.002 - - - no_errors tier3 1706 2 0.12 649 471 41.98 0 0 NA 775109 TCGA-AB-3005 AML39 13 61691772 61691772 G A SNP - - - - - - - - - - - - - - - tier3 1030 0 0 251 171 40.52 0 0 NA 775109 TCGA-AB-3005 AML39 13 73876318 73876318 C G SNP LOC647283 XM_934682.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-22143 NULL 0.003 - - - no_errors tier3 921 1 0.11 295 226 43.38 0 0 NA 775109 TCGA-AB-3005 AML39 13 74828310 74828310 C T SNP TBC1D4 NM_014832.2 human genbank 54_36p -1 validated missense c.1249 p.V417I 1 "HMMPfam_PID,HMMSmart_SM00462,superfamily_PH domain-like" "HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p,HMMPfam_PID,HMMSmart_SM00462,superfamily_PH domain-like" - no_errors tier1 3311 2 0.06 604 345 36.35 1 100 775109 TCGA-AB-3005 AML39 13 85491365 85491365 T G SNP ENSG00000216694 ENST00000401781 human ensembl 54_36p 1 known 3_prime_flanking_region c.*49696 NULL 0.001 - - - no_coding_region:pseudogene tier3 250 0 0 13 23 63.89 0 0 NA 775109 TCGA-AB-3005 AML39 13 86490997 86490997 T C SNP - - - - - - - - - - - - - - - tier3 980 0 0 102 63 38.18 0 0 NA 775109 TCGA-AB-3005 AML39 13 92283848 92283848 A T SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1562-32688 e8-32688 0.002 - - - no_errors tier3 1156 1 0.09 203 174 46.15 0 0 NA 775109 TCGA-AB-3005 AML39 13 96028346 96028346 G A SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.708-254399 e2-254399 0.999 - - - no_errors tier3 1413 0 0 632 351 35.71 0 0 NA 775109 TCGA-AB-3005 AML39 13 97425085 97425085 C G SNP IPO5 NM_002271.4 human genbank 54_36p 1 reviewed intronic c.51-1863 e2-1863 0 - - - no_errors tier3 604 1 0.17 31 32 50.79 0 0 NA 775109 TCGA-AB-3005 AML39 13 101348986 101348986 G T SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.209-23339 e2-23339 0.008 - - - no_errors tier3 690 1 0.14 37 8 17.78 0 0 NA 775109 TCGA-AB-3005 AML39 13 113606057 113606057 G A SNP FAM70B NM_182614.2 human genbank 54_36p -1 provisional missense c.698 p.P233L 0.868 NULL NULL - no_errors tier1 219 0 73 78 51.66 0 775109 TCGA-AB-3005 AML39 14 25958474 25958474 C G SNP LOC100134404 XM_001722988.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37955 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1229 0 0 232 147 38.68 0 0 NA 775109 TCGA-AB-3005 AML39 14 27265215 27265215 A C SNP - - - - - - - - - - - - - - - tier3 1834 1 0.05 299 186 38.35 0 0 NA 775109 TCGA-AB-3005 AML39 14 27466637 27466637 C T SNP - - - - - - - - - - - - - - - tier3 1670 0 0 502 336 40.1 0 0 NA 775109 TCGA-AB-3005 AML39 14 28183754 28183754 G C SNP - - - - - - - - - - - - - - - tier3 1717 1 0.06 219 170 43.7 0 0 NA 775109 TCGA-AB-3005 AML39 14 38144823 38144823 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 14 61154061 61154061 G T SNP FLJ22447 XM_378462.1 human genbank 54_36p 1 model intronic c.25-33372 e2-33372 0 - - - no_errors tier3 2887 2 0.07 779 569 42.21 0 0 NA 775109 TCGA-AB-3005 AML39 14 73157695 73157695 A - DEL DNAL1 NM_031427.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37683 NULL 0.003 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 14 77788266 77788266 T C SNP NRXN3 ENST00000330071 human ensembl 54_36p 1 known intronic c.719+2060 e2+2060 0 - - - no_errors tier3 902 0 0 27 20 42.55 0 0 NA 775109 TCGA-AB-3005 AML39 14 88703920 88703920 A C SNP FOXN3 NM_001085471.1 human genbank 54_36p -1 reviewed intronic c.918-4854 e6-4854 0.001 - - - no_errors tier3 2152 1 0.05 389 300 43.54 0 0 0 775109 TCGA-AB-3005 AML39 14 91947527 91947527 G A SNP SLC24A4 NM_153646.2 human genbank 54_36p 1 validated intronic c.191-22482 e3-22482 0.001 - - - no_errors tier3 2120 3 0.14 334 199 37.13 0 0 NA 775109 TCGA-AB-3005 AML39 14 105329019 105329019 C T SNP IGHG3 ENST00000390550 human ensembl 54_36p -1 known 5_prime_flanking_region c.-20232 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1774 2 0.11 552 325 36.97 0 0 0 775109 TCGA-AB-3005 AML39 15 18819123 18819124 CT - DEL LOC100132980 XM_001723267.1 human genbank 54_36p 1 model intronic c.170-5018_170-5017 e3-5017 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 15 24386477 24386477 C G SNP GABRB3 NM_000814.4 human genbank 54_36p -1 reviewed intronic c.462-6823 e5-6823 0 - - - no_errors tier3 977 0 0 350 130 27.08 0 0 NA 775109 TCGA-AB-3005 AML39 15 34638258 34638258 A C SNP ENSG00000210354 ENST00000387619 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*11037 NULL 0 - - - pseudogene tier3 687 0 0 99 75 43.1 0 0 NA 775109 TCGA-AB-3005 AML39 15 34891710 34891710 A T SNP ENSG00000178351 ENST00000322237 human ensembl 54_36p -1 known intronic c.147+4960 e1+4960 0 - - - no_start_codon tier3 882 1 0.11 230 142 38.17 0 0 NA 775109 TCGA-AB-3005 AML39 15 35348234 35348234 A G SNP - - - - - - - - - - - - - - - tier3 926 0 0 83 82 49.7 0 0 NA 775109 TCGA-AB-3005 AML39 15 38360542 38360542 T A SNP C15orf56 NM_001039905.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-28161 NULL 0.001 - - - no_errors tier3 643 1 0.15 44 33 42.86 1 2 66.67 775109 TCGA-AB-3005 AML39 15 64028708 64028708 G A SNP MEGF11 NM_032445.2 human genbank 54_36p -1 validated intronic c.1062+8231 e7+8231 0 - - - no_errors tier3 2256 4 0.18 383 254 39.87 0 0 NA 775109 TCGA-AB-3005 AML39 15 74306505 74306505 A G SNP ETFA NM_000126.3 human genbank 54_36p -1 reviewed intronic c.883-1180 e11-1180 0.012 - - - no_errors tier3 486 2 0.41 38 14 26.92 1 0 0 775109 TCGA-AB-3005 AML39 15 78654698 78654698 C A SNP ARNT2 NM_014862.3 human genbank 54_36p 1 reviewed intronic c.1513+192 e14+192 0.001 - - - no_errors tier3 982 1 0.1 100 92 47.92 0 0 NA 775109 TCGA-AB-3005 AML39 15 93179661 93179661 A T SNP LOC440311 XR_016779.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-19893 NULL 0.001 - - - pseudogene tier3 1315 0 0 472 298 38.7 0 0 NA 775109 TCGA-AB-3005 AML39 15 95801003 95801003 C G SNP ENSG00000208887 ENST00000386152 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*15400 NULL 0.006 - - - pseudogene tier3 1728 2 0.12 519 289 35.77 0 0 NA 775109 TCGA-AB-3005 AML39 15 98967499 98967499 C T SNP ASB7 NM_198243.3 human genbank 54_36p 1 reviewed 5_prime_untranslated_region c.-2446 NULL 0.97 - - - no_errors tier3 1076 0 0 237 154 39.19 5 7 58.33 775109 TCGA-AB-3005 AML39 16 3357715 3357715 G A SNP ENSG00000209508 ENST00000386773 human ensembl 54_36p 1 novel rna NULL NULL 0.998 - - - pseudogene tier1 856 0 219 129 36.96 1 0 775109 TCGA-AB-3005 AML39 16 6179666 6179666 A G SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-127331 e1-127331 0 - - - no_errors tier3 3129 0 0 843 595 41.38 0 0 NA 775109 TCGA-AB-3005 AML39 16 14288927 14288927 G A SNP LOC100129781 XM_001717065.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-5585 NULL 0.056 - - - no_errors tier3 567 0 0 87 61 41.22 0 0 NA 775109 TCGA-AB-3005 AML39 16 14496384 14496384 T C SNP PARN NM_002582.1 human genbank 54_36p -1 reviewed intronic c.1481-12199 e22-12199 0.004 - - - no_errors tier3 1708 2 0.12 523 384 42.34 0 0 0 775109 TCGA-AB-3005 AML39 16 17778319 17778319 C T SNP - - - - - - - - - - - - - - - tier3 1597 0 0 688 442 39.12 0 0 NA 775109 TCGA-AB-3005 AML39 16 33444820 33444820 G A SNP LOC401847 XM_001718104.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-32365 NULL 0 - - - no_errors tier3 3178 5 0.16 1329 143 9.71 0 0 NA 775109 TCGA-AB-3005 AML39 16 34897102 34897102 C T SNP ENSG00000213541 ENST00000394840 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2053 NULL 0.001 - - - no_coding_region:pseudogene tier3 1129 2 0.18 70 38 35.19 0 0 NA 775109 TCGA-AB-3005 AML39 16 51435286 51435286 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 775109 TCGA-AB-3005 AML39 16 67612386 67612386 A C SNP TMCO7 NM_024562.1 human genbank 54_36p 1 validated intronic c.2843-1846 e16-1846 0.002 - - - no_errors tier3 2325 1 0.04 1105 511 31.58 0 0 0 775109 TCGA-AB-3005 AML39 16 69496276 69496276 C G SNP HYDIN NM_032821.2 human genbank 54_36p -1 validated intronic c.8514-808 e50-808 0.001 - - - no_errors tier3 6903 5 0.07 2307 559 19.49 0 0 NA 775109 TCGA-AB-3005 AML39 16 77399782 77399782 G A SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1056+375632 e8+375632 0.001 - - - no_errors tier3 2163 0 0 349 195 35.71 1 1 50 775109 TCGA-AB-3005 AML39 16 84281120 84281120 G A SNP GINS2 NM_016095.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-1115 NULL 0.122 - - - no_errors tier3 866 0 0 25 31 55.36 1 0 0 775109 TCGA-AB-3005 AML39 16 86971190 86971190 C A SNP - - - - - - - - - - - - - - - tier3 442 0 0 117 76 39.38 0 0 NA 775109 TCGA-AB-3005 AML39 17 4783930 4783930 G C SNP SLC25A11 NM_003562.3 human genbank 54_36p -1 provisional silent c.21 p.A7 0.997 NULL "superfamily_Mitochondrial carrier,HMMPfam_Mito_carr" - no_errors tier1 264 2 0.75 22 16 42.11 25 16 39.02 775109 TCGA-AB-3005 AML39 17 29235914 29235914 C T SNP ACCN1 NM_001094.4 human genbank 54_36p -1 reviewed intronic c.555+271196 e1+271196 0.117 - - - overly_large_intron tier3 331 0 0 57 22 27.85 0 0 NA 775109 TCGA-AB-3005 AML39 17 33033071 33033071 G A SNP AP1GBP1 NM_007247.3 human genbank 54_36p -1 reviewed intronic c.118+1452 e2+1452 0.299 - - - no_errors tier3 1556 1 0.06 209 129 38.17 0 0 0 775109 TCGA-AB-3005 AML39 17 40174745 40174745 G A SNP DBF4B NM_145663.2 human genbank 54_36p 1 validated intronic c.830+399 e10+399 0.005 - - - no_errors tier3 1682 0 0 207 179 46.37 1 0 0 775109 TCGA-AB-3005 AML39 17 44899218 44899218 G A SNP NGFR NM_002507.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28561 NULL 0.001 - - - no_errors tier3 1798 1 0.06 224 160 41.56 0 0 NA 775109 TCGA-AB-3005 AML39 17 51724714 51724714 A G SNP ANKFN1 NM_153228.2 human genbank 54_36p 1 validated intronic c.63-33867 e3-33867 0.001 - - - no_errors tier3 1473 2 0.14 321 200 38.39 0 0 NA 775109 TCGA-AB-3005 AML39 17 66643704 66643704 G A SNP - - - - - - - - - - - - - - - tier3 2400 4 0.17 782 567 41.97 0 0 NA 775109 TCGA-AB-3005 AML39 17 67018604 67018604 T G SNP LOC124685 XR_040247.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 1074 0 0 121 135 52.73 0 0 NA 775109 TCGA-AB-3005 AML39 17 69749945 69749945 G C SNP TTYH2 NM_032646.5 human genbank 54_36p 1 reviewed intronic c.636-1163 e5-1163 0.001 - - - no_errors tier3 849 0 0 181 106 36.68 0 0 0 775109 TCGA-AB-3005 AML39 17 72480852 72480852 A T SNP MGAT5B NM_198955.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*24337 NULL 0.018 - - - no_errors tier3 1167 0 0 206 130 38.69 0 0 NA 775109 TCGA-AB-3005 AML39 17 73462109 73462109 T G SNP - - - - - - - - - - - - - - - tier3 963 6 0.62 150 69 31.51 0 0 NA 775109 TCGA-AB-3005 AML39 17 74120008 74120008 C T SNP DNAH17 ENST00000300671 human ensembl 54_36p -1 known 5_prime_flanking_region c.-37274 NULL 0.001 - - - no_errors tier3 1049 0 0 123 79 38.92 0 0 NA 775109 TCGA-AB-3005 AML39 17 74161796 74161796 C T SNP LOC284120 XM_001721080.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23999 NULL 0 - - - no_errors tier3 1667 0 0 346 256 42.31 0 0 NA 775109 TCGA-AB-3005 AML39 17 74715219 74715219 C T SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1+28224 e0+28224 0.001 - - - no_errors tier3 533 0 0 92 47 33.81 0 0 NA 775109 TCGA-AB-3005 AML39 18 13204589 13204589 C T SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-173133 NULL 0 - - - no_errors tier3 312 0 0 39 28 41.79 0 0 NA 775109 TCGA-AB-3005 AML39 18 17975555 17975555 C T SNP GATA6 NM_005257.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29549 NULL 0.113 - - - no_errors tier3 2529 0 0 385 200 34.19 0 0 NA 775109 TCGA-AB-3005 AML39 18 25920124 25920124 C T SNP - - - - - - - - - - - - - - - tier3 757 1 0.13 112 49 30.43 0 0 NA 775109 TCGA-AB-3005 AML39 18 27198337 27198337 G A SNP LOC100131915 XM_001714713.1 human genbank 54_36p -1 model intronic c.194-9923 e3-9923 0 - - - no_errors tier3 1642 1 0.06 206 165 44.47 0 0 NA 775109 TCGA-AB-3005 AML39 18 35781793 35781793 G A SNP - - - - - - - - - - - - - - - tier3 1326 0 0 389 315 44.74 0 0 NA 775109 TCGA-AB-3005 AML39 18 35905854 35905854 A T SNP - - - - - - - - - - - - - - - tier3 1366 0 0 316 252 44.37 0 0 NA 775109 TCGA-AB-3005 AML39 18 36586556 36586556 A G SNP - - - - - - - - - - - - - - - tier3 2171 2 0.09 671 524 43.85 0 0 NA 775109 TCGA-AB-3005 AML39 18 38173477 38173477 C T SNP LOC284260 XM_001720683.1 human genbank 54_36p 1 model intronic c.1+113407 e0+113407 0 - - - no_errors tier3 1662 3 0.18 203 136 40.12 0 0 NA 775109 TCGA-AB-3005 AML39 18 47222729 47222729 G T SNP LOC729051 XR_042043.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 2469 1 0.04 490 356 42.08 0 0 NA 775109 TCGA-AB-3005 AML39 18 65332575 65332575 C T SNP DOK6 NM_152721.4 human genbank 54_36p 1 validated intronic c.67-50128 e2-50128 0 - - - no_errors tier3 1462 2 0.14 175 105 37.37 0 0 NA 775109 TCGA-AB-3005 AML39 18 69853668 69853668 T A SNP FBXO15 NM_152676.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*38008 NULL 0.009 - - - no_errors tier3 2358 1 0.04 572 369 39.17 0 0 NA 775109 TCGA-AB-3005 AML39 19 2493094 2493094 C T SNP GNG7 NM_052847.2 human genbank 54_36p -1 validated intronic c.1+13053 e0+13053 0.006 - - - no_errors tier3 364 0 0 42 43 50.59 1 0 0 775109 TCGA-AB-3005 AML39 19 5865448 5865448 C G SNP CAPS NM_004058.3 human genbank 54_36p 1 validated missense c.31 p.L11V 1 superfamily_SSF47473 "HMMSmart_EFh,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_SSF47473" - no_errors tier1 255 2 0.77 72 35 32.71 8 5 38.46 775109 TCGA-AB-3005 AML39 19 12181269 12181269 A G SNP LOC730651 XM_001719635.1 human genbank 54_36p 1 model 3_prime_untranslated_region c.*232 NULL 0.826 - - - no_errors tier3 1557 3 0.19 116 97 45.54 1 0 0 775109 TCGA-AB-3005 AML39 19 12802344 12802344 C T SNP RTBDN NM_031429.1 human genbank 54_36p -1 provisional intronic c.79-533 e3-533 0.013 - - - no_errors tier3 1186 2 0.17 135 126 48.09 0 0 NA 775109 TCGA-AB-3005 AML39 19 13246956 13246956 G A SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known intronic c.3992+708 e24+708 0.672 - - - no_errors tier3 3182 2 0.06 549 346 38.66 0 1 100 775109 TCGA-AB-3005 AML39 19 18422476 18422476 C T SNP ELL NM_006532.2 human genbank 54_36p -1 validated missense c.1276 p.G426S 0.27 NULL "HMMPfam_Occludin_ELL,HMMPfam_ELL" - no_errors tier1 90 0 20 21 51.22 7 2 22.22 775109 TCGA-AB-3005 AML39 19 45054508 45054508 G A SNP FCGBP NM_003890.2 human genbank 54_36p -1 validated intronic c.15352+50 e32+50 0.001 - - - no_errors tier3 602 1 0.17 80 91 53.22 0 0 NA 775109 TCGA-AB-3005 AML39 20 15252307 15252307 T C SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.540+93600 e6+93600 0 - - - no_errors tier3 1486 2 0.13 290 248 46.1 0 0 NA 775109 TCGA-AB-3005 AML39 20 21709691 21709691 G A SNP SLC25A6P1 ENST00000402848 human ensembl 54_36p -1 known 5_prime_flanking_region c.-37976 NULL 0.009 - - - no_coding_region:pseudogene tier3 1141 1 0.09 184 103 35.89 0 0 NA 775109 TCGA-AB-3005 AML39 20 31153474 31153474 G A SNP C20orf186 NM_182519.2 human genbank 54_36p 1 validated intronic c.1521-965 e12-965 0.004 - - - no_errors tier3 1433 4 0.28 138 128 48.12 0 0 NA 775109 TCGA-AB-3005 AML39 21 26704608 26704608 T C SNP ENSG00000197934 ENST00000357401 human ensembl 54_36p 1 known intronic c.1+4290 e0+4290 0.191 - - - no_errors tier3 2376 2 0.08 246 214 46.52 0 0 NA 775109 TCGA-AB-3005 AML39 21 32128423 32128423 C T SNP HUNK NM_014586.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-39436 NULL 0.017 - - - no_errors tier3 1785 2 0.11 686 495 41.91 0 0 NA 775109 TCGA-AB-3005 AML39 21 33846477 33846477 A G SNP SON NM_138927.1 human genbank 54_36p 1 reviewed missense c.3070 p.M1024V 1 NULL "HMMPfam_G-patch,HMMSmart_SM00443,HMMPfam_dsrm,superfamily_dsRNA-binding domain-like" - no_errors tier1 1197 2 0.17 315 238 43.04 149 136 47.72 775109 TCGA-AB-3005 AML39 22 22782117 22782117 G A SNP CABIN1 NM_012295.2 human genbank 54_36p 1 reviewed intronic c.1093+495 e8+495 0.005 - - - no_errors tier3 791 0 0 20 25 55.56 0 0 0 775109 TCGA-AB-3005 AML39 22 28975814 28975814 C T SNP LIF NM_002309.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3130 NULL 0 - - - no_errors tier3 819 1 0.12 127 85 40.09 0 0 NA 775109 TCGA-AB-3005 AML39 22 36539478 36539478 C T SNP GCAT NM_014291.2 human genbank 54_36p 1 reviewed silent c.492 p.D164 0.999 "HMMPfam_Aminotran_1_2,superfamily_PyrdxlP-dep_Trfase_major" "PatternScan_AA_TRANSFER_CLASS_2,HMMPfam_Aminotran_1_2,superfamily_PyrdxlP-dep_Trfase_major" - no_errors tier1 779 0 180 117 39.39 10 7 41.18 775109 TCGA-AB-3005 AML39 22 39229178 39229178 A G SNP MKL1 NM_020831.3 human genbank 54_36p -1 validated intronic c.1-39942 e1-39942 0 - - - no_errors tier3 764 1 0.13 219 135 38.14 7 8 50 808642 TCGA-AB-3006 AML06 X 11489342 11489342 A C SNP ARHGAP6 NM_013427.2 human genbank 54_36p -1 reviewed intronic c.588+102940 e1+102940 0.001 - - - no_errors tier3 32 3 8.57 41 80 66.12 0 0 NA 808642 TCGA-AB-3006 AML06 Y 17559277 17559277 C T SNP - - - - - - - - - - - - - - - tier3 99 5 4.81 48 150 75.38 0 0 NA 808642 TCGA-AB-3006 AML06 X 30184532 30184532 G A SNP NR0B1 NM_000475.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*48085 NULL 0 - - - no_errors tier3 240 10 4 60 264 81.23 0 0 NA 808642 TCGA-AB-3006 AML06 X 32717873 32717873 T C SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.649+19658 e7+19658 0 - - - no_errors tier3 51 5 8.93 41 177 81.19 0 0 NA 808642 TCGA-AB-3006 AML06 X 36469499 36469499 C A SNP ENSG00000221729 ENST00000408802 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-35892 NULL 0 - - - no_errors tier3 200 7 3.37 84 365 81.29 0 0 NA 808642 TCGA-AB-3006 AML06 X 38087548 38087548 A T SNP RPGR NM_001034853.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15984 NULL 1 - - - no_errors tier3 339 9 2.59 40 202 83.47 0 0 NA 808642 TCGA-AB-3006 AML06 X 67234812 67234812 G A SNP OPHN1 NM_002547.2 human genbank 54_36p -1 reviewed intronic c.1527-1216 e18-1216 0.792 - - - no_errors tier3 293 25 7.76 50 251 83.11 0 0 0 808642 TCGA-AB-3006 AML06 X 104989128 104989128 G A SNP NRK ENST00000243300 human ensembl 54_36p 1 known intronic c.124-21720 e3-21720 0.001 - - - no_errors tier3 116 7 5.69 49 252 83.72 0 0 NA 808642 TCGA-AB-3006 AML06 X 121049354 121049354 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 X 137493665 137493665 C T SNP FGF13 NM_004114.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*49012 NULL 0.006 - - - no_errors tier3 127 8 5.93 73 267 78.53 0 0 NA 808642 TCGA-AB-3006 AML06 X 138839090 138839090 C T SNP ATP11C ENST00000370557 human ensembl 54_36p -1 known intronic c.27+2751 e1+2751 0.732 - - - no_errors tier3 89 4 4.3 39 186 82.67 0 2 100 808642 TCGA-AB-3006 AML06 X 143238227 143238227 C T SNP ENSG00000220358 ENST00000404051 human ensembl 54_36p -1 known 5_prime_flanking_region c.-18336 NULL 0.949 - - - no_coding_region:pseudogene tier3 129 8 5.84 48 158 76.7 0 0 NA 808642 TCGA-AB-3006 AML06 X 145786478 145786478 C T SNP - - - - - - - - - - - - - - - tier3 35 0 0 13 40 75.47 0 0 NA 808642 TCGA-AB-3006 AML06 X 153344975 153344975 C T SNP PLXNA3 NM_017514.3 human genbank 54_36p 1 validated silent c.1365 p.P455 0.183 "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema" "HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema,HMMPfam_PSI,HMMPfam_TIG,HMMSmart_IPT,HMMSmart_PSI,superfamily_Rho_GAP,HMMPfam_Plexin_cytopl,superfamily_Ig_E-set,superfamily_Plexin-like_fold" - no_errors tier1 93 3 3.12 23 92 80 NA 808642 TCGA-AB-3006 AML06 1 1153156 1153156 G - DEL SDF4 NM_016176.3 human genbank 54_36p -1 validated intronic c.326+555 e1+555 0.699 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 1 32529472 32529472 G A SNP HDAC1 NM_004964.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-886 NULL 0.007 - - - no_errors tier3 265 4 1.49 192 75 28.09 0 0 NA 808642 TCGA-AB-3006 AML06 1 34653922 34653922 A T SNP - - - - - - - - - - - - - - - tier3 442 15 3.28 295 157 34.66 0 0 NA 808642 TCGA-AB-3006 AML06 1 36768042 36768042 G T SNP CSF3R NM_156039.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-50358 NULL 0 - - - no_errors tier2 182 16 8.08 187 137 42.28 0 0 NA 808642 TCGA-AB-3006 AML06 1 37218104 37218104 G A SNP GRIK3 NM_000831.3 human genbank 54_36p -1 reviewed intronic c.115+54078 e1+54078 0 - - - no_errors tier3 435 8 1.81 253 194 43.4 0 0 NA 808642 TCGA-AB-3006 AML06 1 40551300 40551301 - TA INS COL9A2 NM_001852.3 human genbank 54_36p -1 reviewed intronic c.250-258_250-257 e5-257 0.003:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 1 45134787 45134787 C T SNP EIF2B3 NM_020365.2 human genbank 54_36p -1 validated intronic c.656+827 e5+827 0.494 - - - no_errors tier2 258 11 4.09 271 160 37.04 5 3 37.5 808642 TCGA-AB-3006 AML06 1 51594519 51594519 C T SNP EPS15 NM_001981.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*441 NULL 0.95 - - - no_errors tier3 126 4 3.08 103 63 37.95 44 47 51.65 808642 TCGA-AB-3006 AML06 1 53405895 53405895 C T SNP CPT2 NM_000098.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29309 NULL 0.012 - - - no_errors tier3 204 4 1.92 274 187 40.48 0 0 NA 808642 TCGA-AB-3006 AML06 1 57168735 57168735 G A SNP C8B NM_000066.2 human genbank 54_36p -1 reviewed intronic c.1622-916 e12-916 0 - - - no_errors tier3 553 17 2.98 361 233 39.23 0 0 NA 808642 TCGA-AB-3006 AML06 1 60103607 60103607 G A SNP HOOK1 NM_015888.4 human genbank 54_36p 1 reviewed intronic c.1744+102 e18+102 0 - - - no_errors tier3 40 0 0 114 51 30.91 0 0 0 808642 TCGA-AB-3006 AML06 1 60106954 60106954 C T SNP HOOK1 NM_015888.4 human genbank 54_36p 1 reviewed intronic c.1947+343 e20+343 0 - - - no_errors tier3 36 1 2.7 124 80 39.22 0 0 NA 808642 TCGA-AB-3006 AML06 1 60256845 60256845 G A SNP C1orf87 NM_152377.1 human genbank 54_36p -1 predicted intronic c.1127+6816 e7+6816 0 - - - no_errors tier3 145 4 2.68 134 78 36.79 0 0 NA 808642 TCGA-AB-3006 AML06 1 79344356 79344356 A G SNP LOC729779 XR_016024.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-49977 NULL 0 - - - pseudogene tier3 155 10 6.06 76 62 44.93 0 0 NA 808642 TCGA-AB-3006 AML06 1 80678005 80678005 C T SNP ENSG00000218288 ENST00000405969 human ensembl 54_36p -1 known 3_prime_flanking_region c.*24575 NULL 0.195 - - - no_coding_region:pseudogene tier3 132 0 0 201 119 37.07 0 0 NA 808642 TCGA-AB-3006 AML06 1 90899883 90899883 T A SNP ENSG00000199666 ENST00000362796 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*3775 NULL 0.995 - - - no_errors tier2 260 3 1.14 269 156 36.71 0 0 NA 808642 TCGA-AB-3006 AML06 1 94215813 94215813 C T SNP ENSG00000216267 ENST00000405337 human ensembl 54_36p -1 known 5_prime_flanking_region c.-42425 NULL 0 - - - no_coding_region:pseudogene tier3 289 14 4.62 334 224 40 0 0 NA 808642 TCGA-AB-3006 AML06 1 105212840 105212840 C T SNP - - - - - - - - - - - - - - - tier3 72 0 0 93 47 33.57 0 0 NA 808642 TCGA-AB-3006 AML06 1 106028770 106028770 G T SNP ENSG00000218199 ENST00000405367 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13414 NULL 0 - - - no_coding_region:pseudogene tier3 51 0 0 108 65 37.57 0 0 NA 808642 TCGA-AB-3006 AML06 1 110321053 110321053 T A SNP AHCYL1 NM_006621.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-8145 NULL 0.005 - - - no_errors tier2 336 15 4.26 320 179 35.87 0 0 NA 808642 TCGA-AB-3006 AML06 1 112495858 112495858 C T SNP ENSG00000209265 ENST00000386530 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-43812 NULL 0.001 - - - pseudogene tier3 167 15 8.24 60 247 80.46 0 0 NA 808642 TCGA-AB-3006 AML06 1 116561642 116561642 A G SNP ENSG00000209230 ENST00000386495 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9547 NULL 0.902 - - - pseudogene tier3 215 7 3.15 229 150 39.47 0 0 NA 808642 TCGA-AB-3006 AML06 1 119019800 119019800 G A SNP ENSG00000219711 ENST00000401940 human ensembl 54_36p 1 known 5_prime_flanking_region c.-37345 NULL 0.001 - - - no_coding_region:pseudogene tier2 186 7 3.57 366 250 40.52 0 0 NA 808642 TCGA-AB-3006 AML06 1 149526479 149526479 C G SNP ZNF687 NM_020832.1 human genbank 54_36p 1 provisional missense c.1088 p.A363G 0.478 NULL "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 235 10 4.08 231 175 43.1 31 35 53.03 808642 TCGA-AB-3006 AML06 1 160992176 160992176 G A SNP DDR2 NM_001014796.1 human genbank 54_36p 1 reviewed missense c.664 p.G222R 0.972 NULL "HMMPfam_F5_F8_type_C,HMMSmart_FA58C,PatternScan_FA58C_1,PatternScan_FA58C_2,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_II,PatternScan_PROTEIN_KINASE_TYR,superfamily_Gal_bind_like,superfamily_Kinase_like" - no_errors tier1 283 5 1.74 198 112 36.13 NA 808642 TCGA-AB-3006 AML06 1 161741143 161741143 C T SNP ENSG00000200327 ENST00000363457 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36124 NULL 0.997 - - - no_errors tier2 215 8 3.59 111 70 38.67 0 0 NA 808642 TCGA-AB-3006 AML06 1 162324935 162324935 C T SNP - - - - - - - - - - - - - - - tier3 117 0 0 122 30 19.74 0 0 NA 808642 TCGA-AB-3006 AML06 1 162418232 162418232 G A SNP - - - - - - - - - - - - - - - tier3 156 3 1.89 213 164 43.5 0 0 NA 808642 TCGA-AB-3006 AML06 1 163746669 163746669 C G SNP LRRC52 NM_001005214.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-33489 NULL 0 - - - no_errors tier3 269 10 3.58 338 227 40.18 0 0 NA 808642 TCGA-AB-3006 AML06 1 165905467 165905467 G T SNP LOC100128751 XM_001726094.1 human genbank 54_36p 1 model 5_prime_untranslated_region c.-702 NULL 0 - - - no_errors tier3 167 3 1.75 392 248 38.75 3 5 62.5 808642 TCGA-AB-3006 AML06 1 175305459 175305459 G C SNP ASTN1 NM_004319.1 human genbank 54_36p -1 validated intronic c.284-8435 e2-8435 1 - - - no_errors tier2 696 22 3.06 376 249 39.59 0 0 NA 808642 TCGA-AB-3006 AML06 1 177946387 177946387 A G SNP FAM163A NM_173509.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-102469 NULL 0.005 - - - no_errors tier2 61 0 0 59 39 39.8 0 0 NA 808642 TCGA-AB-3006 AML06 1 181292583 181292583 G A SNP LAMC1 NM_002293.3 human genbank 54_36p 1 reviewed intronic c.418+32691 e1+32691 0.005 - - - no_errors tier3 289 4 1.37 200 109 35.28 0 0 NA 808642 TCGA-AB-3006 AML06 1 182858186 182858186 A G SNP C1orf21 NM_030806.3 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*2873 NULL 0.015 - - - no_errors tier3 242 2 0.82 393 246 38.5 0 2 100 808642 TCGA-AB-3006 AML06 1 187973137 187973137 G A SNP - - - - - - - - - - - - - - - tier3 72 1 1.37 122 58 32.22 0 0 NA 808642 TCGA-AB-3006 AML06 1 195274038 195274038 T A SNP F13B NM_001994.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*1093 NULL 0.002 - - - no_errors tier3 108 0 0 180 109 37.72 0 0 NA 808642 TCGA-AB-3006 AML06 1 197302579 197302579 C T SNP - - - - - - - - - - - - - - - tier3 222 7 3.06 385 204 34.63 0 0 NA 808642 TCGA-AB-3006 AML06 1 205324854 205324854 C T SNP C4BPA NM_000715.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28140 NULL 0 - - - no_errors tier2 157 2 1.25 209 169 44.71 0 0 NA 808642 TCGA-AB-3006 AML06 1 211968328 211968328 C A SNP - - - - - - - - - - - - - - - tier3 281 15 5.05 323 219 40.33 0 0 NA 808642 TCGA-AB-3006 AML06 1 213526295 213526295 T C SNP KCNK2 NM_001017425.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*51184 NULL 0 - - - no_errors tier3 362 9 2.43 300 178 37.24 0 0 NA 808642 TCGA-AB-3006 AML06 1 214452940 214452940 G C SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.3157+4412 e14+4412 0 - - - no_errors tier2 621 5 0.8 344 224 39.37 0 0 NA 808642 TCGA-AB-3006 AML06 1 215466069 215466069 C T SNP - - - - - - - - - - - - - - - tier3 155 1 0.64 323 202 38.4 0 0 NA 808642 TCGA-AB-3006 AML06 1 221780241 221780241 G A SNP LOC653428 XM_927368.3 human genbank 54_36p -1 model 3_prime_flanking_region c.*25117 NULL 0 - - - no_errors tier3 237 8 3.24 381 230 37.58 0 0 NA 808642 TCGA-AB-3006 AML06 1 223628001 223628001 C T SNP ENSG00000185842 ENST00000327794 human ensembl 54_36p 1 known intronic c.1734-1012 e14-1012 0 - - - no_errors tier3 117 5 4.1 288 122 29.76 1 1 50 808642 TCGA-AB-3006 AML06 1 236403411 236403411 T C SNP - - - - - - - - - - - - - - - tier3 297 6 1.97 313 200 38.99 0 0 NA 808642 TCGA-AB-3006 AML06 1 237337962 237337962 A T SNP - - - - - - - - - - - - - - - tier3 99 2 1.98 76 55 41.98 0 0 NA 808642 TCGA-AB-3006 AML06 1 240551993 240551993 A C SNP PLD5 NM_152666.1 human genbank 54_36p -1 provisional intronic c.50+26031 e1+26031 0.003 - - - no_errors tier3 108 2 1.82 211 112 34.57 0 0 NA 808642 TCGA-AB-3006 AML06 1 243681834 243681834 C T SNP KIF26B NM_018012.3 human genbank 54_36p 1 provisional intronic c.1166+32164 e4+32164 0.003 - - - no_errors tier3 42 0 0 197 139 41.37 0 0 NA 808642 TCGA-AB-3006 AML06 2 3621069 3621069 C A SNP COLEC11 NM_024027.3 human genbank 54_36p 1 validated intronic c.1+436 e0+436 0.001 - - - no_errors tier2 165 5 2.91 205 114 35.74 0 0 NA 808642 TCGA-AB-3006 AML06 2 3662529 3662529 G A SNP COLEC11 NM_024027.3 human genbank 54_36p 1 validated intronic c.203-469 e3-469 0.004 - - - no_errors tier3 206 7 3.27 246 215 46.44 0 0 NA 808642 TCGA-AB-3006 AML06 2 3667866 3667866 C T SNP COLEC11 NM_024027.3 human genbank 54_36p 1 validated intronic c.329-1043 e5-1043 0.001 - - - no_errors tier3 529 19 3.47 250 191 43.31 0 0 NA 808642 TCGA-AB-3006 AML06 2 7429472 7429472 C T SNP ENSG00000213774 ENST00000396295 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-46799 NULL 0 - - - no_coding_region:pseudogene tier2 385 15 3.74 449 304 40.37 0 0 NA 808642 TCGA-AB-3006 AML06 2 7553775 7553775 C G SNP - - - - - - - - - - - - - - - tier3 169 6 3.43 180 122 40.13 0 0 NA 808642 TCGA-AB-3006 AML06 2 12240716 12240716 T C SNP - - - - - - - - - - - - - - - tier3 175 0 0 168 84 33.33 0 0 NA 808642 TCGA-AB-3006 AML06 2 13130115 13130115 C T SNP - - - - - - - - - - - - - - - tier3 132 0 0 273 160 36.95 0 0 NA 808642 TCGA-AB-3006 AML06 2 16701981 16701981 G - DEL FAM49A NM_030797.2 human genbank 54_36p -1 provisional intronic c.1+8548 e0+8548 0.957 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 2 19455897 19455897 C T SNP OSR1 NM_145260.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-38850 NULL 0.003 - - - no_errors tier3 85 2 2.3 162 110 40.44 0 0 NA 808642 TCGA-AB-3006 AML06 2 21091435 21091435 C G SNP APOB NM_000384.2 human genbank 54_36p -1 reviewed intronic c.3696+15 e23+15 0.001 - - - no_errors tier3 317 3 0.94 333 202 37.76 0 0 NA 808642 TCGA-AB-3006 AML06 2 26179882 26179882 T A SNP RAB10 NM_016131.3 human genbank 54_36p 1 provisional intronic c.188+4787 e2+4787 0.05 - - - no_errors tier2 52 0 0 59 46 43.81 2 3 60 808642 TCGA-AB-3006 AML06 2 30899121 30899121 C T SNP CAPN13 NM_144575.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-35426 NULL 0 - - - no_errors tier2 119 2 1.65 170 105 38.04 0 0 NA 808642 TCGA-AB-3006 AML06 2 33092887 33092887 C T SNP LTBP1 NM_206943.2 human genbank 54_36p 1 reviewed intronic c.566-6593 e3-6593 0 - - - no_errors tier3 199 6 2.93 259 124 32.29 0 0 0 808642 TCGA-AB-3006 AML06 2 37967151 37967151 T C SNP FAM82A1 ENST00000354545 human ensembl 54_36p 1 known 5_prime_flanking_region c.-42774 NULL 0.004 - - - no_errors tier2 410 5 1.2 275 188 40.6 0 0 NA 808642 TCGA-AB-3006 AML06 2 41998962 41998962 G A SNP LOC400950 XM_376049.4 human genbank 54_36p -1 model 3_prime_flanking_region c.*20285 NULL 0 - - - no_errors tier3 484 37 7.09 820 483 37.07 0 0 NA 808642 TCGA-AB-3006 AML06 2 50486963 50486963 A T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.3364+59121 e16+59121 0 - - - no_errors tier3 100 0 0 133 77 36.67 0 0 NA 808642 TCGA-AB-3006 AML06 2 56473662 56473662 C T SNP CCDC85A NM_001080433.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*8668 NULL 0.004 - - - no_errors tier2 193 5 2.53 280 218 43.78 0 0 NA 808642 TCGA-AB-3006 AML06 2 64027831 64027831 G T SNP VPS54 NM_016516.1 human genbank 54_36p -1 reviewed intronic c.1245+190 e8+190 0 - - - no_errors tier2 195 3 1.52 271 116 29.82 2 0 0 808642 TCGA-AB-3006 AML06 2 64862183 64862183 T C SNP ENSG00000223130 ENST00000411198 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-35833 NULL 0.655 - - - no_errors tier3 257 3 1.15 238 154 39.19 0 0 NA 808642 TCGA-AB-3006 AML06 2 68404270 68404270 G A SNP CNRIP1 NM_015463.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-4234 NULL 0.001 - - - no_errors tier3 251 8 3.09 375 189 33.51 0 0 NA 808642 TCGA-AB-3006 AML06 2 69705329 69705329 T C SNP AAK1 NM_014911.3 human genbank 54_36p -1 reviewed intronic c.163+18185 e1+18185 0.002 - - - no_errors tier2 633 45 6.64 366 201 35.33 1 0 0 808642 TCGA-AB-3006 AML06 2 77541753 77541753 C T SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+57199 e2+57199 0 - - - no_errors tier3 34 0 0 50 24 32.43 0 0 NA 808642 TCGA-AB-3006 AML06 2 83104853 83104853 T C SNP - - - - - - - - - - - - - - - tier3 203 3 1.46 157 139 46.96 0 0 NA 808642 TCGA-AB-3006 AML06 2 84975652 84975652 C G SNP TMSB10 NM_021103.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-11001 NULL 0.006 - - - no_errors tier3 171 6 3.39 191 128 40.13 0 0 NA 808642 TCGA-AB-3006 AML06 2 85482483 85482483 C G SNP CAPG NM_001747.2 human genbank 54_36p -1 reviewed silent c.132 p.S44 0.472 "HMMSmart_SM00262,HMMPfam_Gelsolin,superfamily_Actin depolymerizing proteins" "HMMSmart_SM00262,HMMPfam_Gelsolin,superfamily_Actin depolymerizing proteins" - no_errors tier1 246 13 5.02 171 114 40 3 12 80 808642 TCGA-AB-3006 AML06 2 88860263 88860263 T C SNP RPIA NM_144563.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*29553 NULL 0 - - - no_errors tier3 100 0 0 59 44 42.72 0 0 0 808642 TCGA-AB-3006 AML06 2 95241945 95241945 T - DEL LOC344065 XM_292895.1 human genbank 54_36p 1 model intronic c.301+188 e4+188 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 2 102418486 102418486 G A SNP IL18RAP NM_003853.2 human genbank 54_36p 1 reviewed intronic c.580-1618 e4-1618 0 - - - no_errors tier3 343 8 2.27 225 132 36.97 0 0 0 808642 TCGA-AB-3006 AML06 2 104740060 104740060 C T SNP LOC284998 XM_498907.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-2830 NULL 1 - - - no_errors tier3 185 1 0.54 204 133 39.47 0 0 NA 808642 TCGA-AB-3006 AML06 2 108283798 108283798 C T SNP SULT1C2 NM_176825.3 human genbank 54_36p 1 reviewed missense c.383 p.P128L 0.728 "HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 334 13 3.74 290 178 38.03 3 4 57.14 808642 TCGA-AB-3006 AML06 2 115587144 115587144 G A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.61-196141 e2-196141 0 - - - no_errors tier2 265 3 1.12 275 156 36.19 0 0 NA 808642 TCGA-AB-3006 AML06 2 117201412 117201412 G A SNP - - - - - - - - - - - - - - - tier2 464 9 1.9 317 210 39.85 0 0 NA 808642 TCGA-AB-3006 AML06 2 119288509 119288509 G A SNP EN1 NM_001426.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*28475 NULL 0 - - - no_errors tier3 410 6 1.44 420 255 37.78 0 0 NA 808642 TCGA-AB-3006 AML06 2 120985068 120985068 G A SNP - - - - - - - - - - - - - - - tier3 308 6 1.91 265 162 37.85 0 0 NA 808642 TCGA-AB-3006 AML06 2 129069768 129069768 G A SNP - - - - - - - - - - - - - - - tier3 204 1 0.48 299 229 43.37 0 0 NA 808642 TCGA-AB-3006 AML06 2 129169084 129169084 C T SNP - - - - - - - - - - - - - - - tier3 136 4 2.86 184 84 31.34 0 0 NA 808642 TCGA-AB-3006 AML06 2 149731554 149731554 A T SNP LYPD6B NM_177964.3 human genbank 54_36p 1 provisional intronic c.77+5959 e2+5959 0 - - - no_errors tier3 593 12 1.98 578 329 36.27 0 0 NA 808642 TCGA-AB-3006 AML06 2 153069673 153069673 T C SNP FMNL2 NM_052905.3 human genbank 54_36p 1 reviewed intronic c.118-17030 e2-17030 0.01 - - - no_errors tier3 101 1 0.98 336 190 36.12 0 0 NA 808642 TCGA-AB-3006 AML06 2 160787903 160787903 A G SNP ITGB6 NM_000888.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-23083 NULL 0.001 - - - no_errors tier3 204 6 2.84 253 160 38.65 0 0 NA 808642 TCGA-AB-3006 AML06 2 164215772 164215772 C A SNP FIGN NM_018086.2 human genbank 54_36p -1 validated intronic c.26-39210 e2-39210 0.001 - - - no_errors tier2 352 6 1.67 330 209 38.7 0 0 NA 808642 TCGA-AB-3006 AML06 2 167199918 167199918 G A SNP - - - - - - - - - - - - - - - tier3 68 1 1.45 66 22 25 0 0 NA 808642 TCGA-AB-3006 AML06 2 168641292 168641292 G C SNP STK39 NM_013233.2 human genbank 54_36p -1 reviewed intronic c.1090-1305 e11-1305 0 - - - no_errors tier3 169 0 0 207 159 43.44 2 0 0 808642 TCGA-AB-3006 AML06 2 169168164 169168164 G A SNP LASS6 NM_203463.1 human genbank 54_36p 1 validated intronic c.408-27577 e4-27577 0.001 - - - no_errors tier3 250 9 3.47 260 162 38.39 5 4 44.44 808642 TCGA-AB-3006 AML06 2 175242225 175242225 T G SNP WIPF1 NM_001077269.1 human genbank 54_36p -1 reviewed intronic c.1+13523 e0+13523 0.004 - - - no_errors tier3 129 4 3.01 154 111 41.89 0 0 NA 808642 TCGA-AB-3006 AML06 2 180619115 180619115 G A SNP CWC22 NM_020943.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-52802 NULL 0.005 - - - no_errors tier2 202 4 1.94 262 127 32.56 0 0 NA 808642 TCGA-AB-3006 AML06 2 200018989 200018989 A G SNP SATB2 NM_015265.2 human genbank 54_36p -1 validated intronic c.169+9848 e1+9848 0.001 - - - no_errors tier3 39 0 0 65 36 35.64 0 0 NA 808642 TCGA-AB-3006 AML06 2 200615238 200615238 G A SNP - - - - - - - - - - - - - - - tier3 206 4 1.9 228 188 45.19 0 0 NA 808642 TCGA-AB-3006 AML06 2 204386862 204386862 A G SNP ENSG00000211573 ENST00000390147 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49097 NULL 0.001 - - - no_errors tier3 261 7 2.61 347 214 38.01 0 0 NA 808642 TCGA-AB-3006 AML06 2 214953741 214953741 G A SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1721-29368 e16-29368 0 - - - no_errors tier3 332 14 4.05 320 241 42.81 0 0 NA 808642 TCGA-AB-3006 AML06 2 219874632 219874632 G A SNP PTPRN NM_002846.2 human genbank 54_36p -1 reviewed missense c.1048 p.R350C 0.966 NULL "HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II" - no_errors tier1 274 13 4.53 355 258 42.09 NA 808642 TCGA-AB-3006 AML06 2 221062476 221062476 C T SNP ENSG00000222096 ENST00000410164 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12419 NULL 0.001 - - - no_errors tier3 380 11 2.81 344 173 33.46 0 0 NA 808642 TCGA-AB-3006 AML06 2 227631117 227631117 G A SNP COL4A4 NM_000092.4 human genbank 54_36p -1 reviewed intronic c.2384-557 e28-557 0.053 - - - no_errors tier3 135 1 0.73 313 91 22.52 0 0 NA 808642 TCGA-AB-3006 AML06 2 239163224 239163224 G A SNP - - - - - - - - - - - - - - - tier3 240 10 3.97 311 204 39.61 0 0 NA 808642 TCGA-AB-3006 AML06 3 978351 978351 A G SNP LOC100134121 XM_001714675.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-22116 NULL 0.032 - - - no_start_codon:pseudogene:no_stop_codon tier3 81 6 6.9 159 188 54.18 0 0 NA 808642 TCGA-AB-3006 AML06 3 2807244 2807244 T C SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.359-28926 e4-28926 1 - - - no_errors tier2 150 4 2.58 339 267 44.06 0 0 NA 808642 TCGA-AB-3006 AML06 3 3018366 3018366 G A SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.1486+13210 e11+13210 0.014 - - - no_errors tier2 164 5 2.96 392 239 37.88 0 0 NA 808642 TCGA-AB-3006 AML06 3 3705861 3705861 G T SNP ENSG00000223036 ENST00000411104 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*42599 NULL 0.007 - - - no_errors tier3 242 3 1.22 308 144 31.79 0 0 NA 808642 TCGA-AB-3006 AML06 3 6681886 6681886 A G SNP - - - - - - - - - - - - - - - tier2 403 3 0.73 240 121 33.43 1 0 0 808642 TCGA-AB-3006 AML06 3 8145220 8145220 C T SNP - - - - - - - - - - - - - - - tier3 166 6 3.49 173 114 39.72 0 0 NA 808642 TCGA-AB-3006 AML06 3 10972882 10972882 G A SNP SLC6A1 NM_003042.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-61016 NULL 0 - - - no_errors tier3 553 33 5.63 175 108 38.16 0 0 NA 808642 TCGA-AB-3006 AML06 3 20138520 20138520 C T SNP KAT2B NM_003884.4 human genbank 54_36p 1 reviewed intronic c.1277-644 e9-644 0 - - - no_errors tier3 106 1 0.91 130 80 37.91 0 0 0 808642 TCGA-AB-3006 AML06 3 21137075 21137075 C T SNP ENSG00000221659 ENST00000408732 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17684 NULL 0.004 - - - no_errors tier3 206 1 0.48 382 165 30.16 0 0 NA 808642 TCGA-AB-3006 AML06 3 21304464 21304464 G A SNP - - - - - - - - - - - - - - - tier3 398 1 0.25 292 156 34.74 0 0 NA 808642 TCGA-AB-3006 AML06 3 23033802 23033802 C A SNP - - - - - - - - - - - - - - - tier3 261 5 1.88 308 150 32.75 0 0 NA 808642 TCGA-AB-3006 AML06 3 31904001 31904001 C T SNP OSBPL10 NM_017784.3 human genbank 54_36p -1 reviewed intronic c.282-7675 e2-7675 0.001 - - - no_errors tier2 321 16 4.75 273 143 34.29 1 0 0 808642 TCGA-AB-3006 AML06 3 35000355 35000355 G A SNP - - - - - - - - - - - - - - - tier3 111 2 1.77 192 104 35.02 0 0 NA 808642 TCGA-AB-3006 AML06 3 35756101 35756101 C T SNP ARPP-21 NM_016300.1 human genbank 54_36p 1 validated intronic c.1905+28 e15+28 0 - - - no_errors tier3 241 9 3.6 222 105 32.11 0 0 0 808642 TCGA-AB-3006 AML06 3 35915714 35915714 T A SNP - - - - - - - - - - - - - - - tier3 226 4 1.74 262 213 44.84 0 0 NA 808642 TCGA-AB-3006 AML06 3 40252507 40252507 A - DEL MYRIP NM_015460.2 human genbank 54_36p 1 validated intronic c.2100+1959 e11+1959 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 3 41679966 41679966 T A SNP ULK4 NM_017886.2 human genbank 54_36p -1 validated intronic c.3071+136 e29+136 0 - - - no_errors tier3 105 1 0.94 328 187 36.24 0 0 0 808642 TCGA-AB-3006 AML06 3 53488484 53488484 G T SNP CACNA1D NM_000720.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-15750 NULL 0 - - - no_errors tier2 187 2 1.06 186 88 32.12 0 0 NA 808642 TCGA-AB-3006 AML06 3 54503459 54503459 A T SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.382-9100 e5-9100 0.006 - - - no_errors tier3 304 7 2.25 417 289 40.82 0 0 NA 808642 TCGA-AB-3006 AML06 3 64662538 64662538 G C SNP LOC730057 XM_001132251.1 human genbank 54_36p 1 model intronic c.129+7990 e2+7990 0.008 - - - no_errors tier3 50 3 5.66 136 85 38.46 0 0 NA 808642 TCGA-AB-3006 AML06 3 65757836 65757836 T A SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.314-175033 e2-175033 0.015 - - - no_errors tier3 155 3 1.9 304 238 43.83 0 0 NA 808642 TCGA-AB-3006 AML06 3 65843347 65843347 C T SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.313+155364 e1+155364 0.001 - - - no_errors tier3 402 2 0.5 248 102 29.14 0 0 NA 808642 TCGA-AB-3006 AML06 3 78335507 78335507 C T SNP ENSG00000222574 ENST00000410642 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*41674 NULL 0.003 - - - no_errors tier3 317 4 1.24 318 191 37.52 0 0 NA 808642 TCGA-AB-3006 AML06 3 80607516 80607516 G A SNP - - - - - - - - - - - - - - - tier3 73 0 0 105 62 37.13 0 0 NA 808642 TCGA-AB-3006 AML06 3 85613724 85613724 T C SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.62-320163 e2-320163 0.622 - - - no_errors tier3 74 0 0 131 67 33.84 0 0 NA 808642 TCGA-AB-3006 AML06 3 86051462 86051462 C G SNP CADM2 NM_153184.2 human genbank 54_36p 1 validated intronic c.679+7079 e5+7079 0.002 - - - no_errors tier3 289 9 3.02 282 118 29.5 0 0 NA 808642 TCGA-AB-3006 AML06 3 86058469 86058469 G A SNP CADM2 NM_153184.2 human genbank 54_36p 1 validated intronic c.680-9138 e6-9138 0.001 - - - no_errors tier3 43 0 0 86 48 35.82 0 0 NA 808642 TCGA-AB-3006 AML06 3 86423753 86423753 G A SNP - - - - - - - - - - - - - - - tier3 42 0 0 76 51 40.16 0 0 NA 808642 TCGA-AB-3006 AML06 3 96030752 96030752 G A SNP - - - - - - - - - - - - - - - tier3 57 0 0 81 35 30.17 0 0 NA 808642 TCGA-AB-3006 AML06 3 97197799 97197799 A G SNP - - - - - - - - - - - - - - - tier3 52 0 0 90 53 37.06 0 0 NA 808642 TCGA-AB-3006 AML06 3 97257940 97257940 A G SNP ENSG00000222633 ENST00000410701 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13180 NULL 0.009 - - - no_errors tier3 106 2 1.85 78 64 45.07 0 0 NA 808642 TCGA-AB-3006 AML06 3 97367005 97367006 - A INS ENSG00000221477 ENST00000408550 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*1346 NULL 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 3 100612750 100612750 T A SNP - - - - - - - - - - - - - - - tier3 758 16 2.07 400 280 41.18 0 0 NA 808642 TCGA-AB-3006 AML06 3 108327054 108327054 G A SNP LOC344595 XM_001128525.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-5001 NULL 0.03 - - - no_errors tier3 36 0 0 63 43 40.57 0 0 NA 808642 TCGA-AB-3006 AML06 3 114391074 114391074 G T SNP BOC NM_033254.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-60266 NULL 0.002 - - - no_errors tier3 95 4 4.04 236 115 32.76 0 0 NA 808642 TCGA-AB-3006 AML06 3 117756043 117756043 C T SNP ENSG00000209192 ENST00000386457 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*28104 NULL 0 - - - pseudogene tier3 60 1 1.64 88 41 31.78 0 0 NA 808642 TCGA-AB-3006 AML06 3 120024737 120024737 T G SNP - - - - - - - - - - - - - - - tier3 482 7 1.43 220 164 42.71 0 0 NA 808642 TCGA-AB-3006 AML06 3 124548251 124548251 C T SNP ADCY5 NM_183357.1 human genbank 54_36p -1 validated intronic c.1406+1068 e3+1068 0 - - - no_errors tier3 539 21 3.74 246 106 30.03 0 0 NA 808642 TCGA-AB-3006 AML06 3 135315176 135315176 G A SNP RYK NM_001005861.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*44511 NULL 0.948 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier2 50 1 1.96 102 75 42.37 0 0 NA 808642 TCGA-AB-3006 AML06 3 138121111 138121111 C T SNP NCK1 NM_006153.3 human genbank 54_36p 1 reviewed intronic c.1-8405 e1-8405 0 - - - no_errors tier3 60 0 0 133 50 27.32 1 0 0 808642 TCGA-AB-3006 AML06 3 138976765 138976765 T A SNP SOX14 NM_004189.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*9726 NULL 0.001 - - - no_errors tier3 299 6 1.94 337 249 42.49 0 0 NA 808642 TCGA-AB-3006 AML06 3 140191897 140191897 C T SNP FOXL2 NM_023067.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-43643 NULL 0.028 - - - no_errors tier3 516 8 1.52 540 385 41.49 0 0 NA 808642 TCGA-AB-3006 AML06 3 140309657 140309657 C T SNP - - - - - - - - - - - - - - - tier3 127 9 6.62 93 65 40.88 0 0 NA 808642 TCGA-AB-3006 AML06 3 141702004 141702004 A T SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.1345-31852 e9-31852 0 - - - no_errors tier3 163 5 2.98 320 236 42.37 0 0 NA 808642 TCGA-AB-3006 AML06 3 143986570 143986570 T C SNP TRPC1 NM_003304.4 human genbank 54_36p 1 validated missense c.1193 p.I398T 1 NULL "HMMSmart_SM00248,superfamily_Ankyrin repeat,HMMPfam_Ion_trans,HMMPfam_TRP_2" - no_errors tier1 91 0 80 57 41.61 NA 808642 TCGA-AB-3006 AML06 3 144162096 144162096 C T SNP SR140 NM_001080415.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-41065 NULL 0.047 - - - no_errors tier3 240 4 1.64 192 187 49.34 0 0 NA 808642 TCGA-AB-3006 AML06 3 149213089 149213089 C T SNP - - - - - - - - - - - - - - - tier3 247 2 0.8 324 148 31.36 0 0 NA 808642 TCGA-AB-3006 AML06 3 149341582 149341582 C T SNP ENSG00000205412 ENST00000379950 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*25234 NULL 0 - - - no_coding_region:pseudogene tier3 62 1 1.59 166 97 36.88 0 0 NA 808642 TCGA-AB-3006 AML06 3 153843886 153843886 A T SNP - - - - - - - - - - - - - - - tier3 57 1 1.72 76 67 46.85 0 0 NA 808642 TCGA-AB-3006 AML06 3 161885302 161885302 C T SNP ENSG00000207084 ENST00000384356 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-12109 NULL 0.001 - - - no_errors tier3 429 6 1.38 369 247 40.03 0 0 NA 808642 TCGA-AB-3006 AML06 3 165695098 165695098 G A SNP - - - - - - - - - - - - - - - tier2 135 0 0 236 120 33.71 0 0 NA 808642 TCGA-AB-3006 AML06 3 170307181 170307181 C T SNP EVI1 NM_001105077.2 human genbank 54_36p -1 validated intronic c.2232+1227 e9+1227 0 - - - no_errors tier3 258 4 1.53 181 78 30.12 0 0 NA 808642 TCGA-AB-3006 AML06 3 170354151 170354151 T C SNP MDS1 NM_004991.2 human genbank 54_36p -1 validated intronic c.376-3914 e3-3914 0.091 - - - no_errors tier3 111 1 0.89 176 141 44.48 0 0 NA 808642 TCGA-AB-3006 AML06 3 177873408 177873408 G A SNP - - - - - - - - - - - - - - - tier3 133 1 0.75 143 104 42.11 0 0 NA 808642 TCGA-AB-3006 AML06 3 181767850 181767850 A T SNP TTC14 NM_133462.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-34894 NULL 0.029 - - - no_errors tier3 87 2 2.25 239 136 35.88 0 0 NA 808642 TCGA-AB-3006 AML06 3 183005032 183005032 A C SNP ENSG00000222173 ENST00000410241 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8851 NULL 0.026 - - - no_errors tier3 237 6 2.47 225 176 43.89 0 0 NA 808642 TCGA-AB-3006 AML06 3 186432567 186432567 A G SNP EHHADH NM_001966.2 human genbank 54_36p -1 validated intronic c.352-2542 e4-2542 0.043 - - - no_errors tier2 42 0 0 164 75 31.38 0 0 0 808642 TCGA-AB-3006 AML06 3 187332305 187332305 T - DEL ETV5 NM_004454.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-25954 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 3 191272134 191272134 T C SNP LEPREL1 NM_018192.1 human genbank 54_36p -1 validated intronic c.480+48601 e1+48601 0 - - - no_errors tier2 115 3 2.54 210 120 36.25 0 0 NA 808642 TCGA-AB-3006 AML06 3 192398365 192398365 A T SNP OSTN NM_198184.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-14651 NULL 0.999 - - - no_errors tier2 154 4 2.53 231 140 37.74 0 0 NA 808642 TCGA-AB-3006 AML06 3 192954231 192954231 C T SNP - - - - - - - - - - - - - - - tier3 234 0 0 169 121 41.72 0 0 NA 808642 TCGA-AB-3006 AML06 3 196604547 196604547 C T SNP ACAP2 NM_012287.4 human genbank 54_36p -1 validated intronic c.54-10382 e2-10382 0.001 - - - no_errors tier3 38 0 0 123 67 35.26 0 10 100 808642 TCGA-AB-3006 AML06 4 2629193 2629193 T A SNP C4orf8 NM_003704.3 human genbank 54_36p 1 validated intronic c.439-135 e4-135 0 - - - no_errors tier3 119 1 0.83 217 140 39.22 6 2 25 808642 TCGA-AB-3006 AML06 4 7552325 7552325 C T SNP SORCS2 NM_020777.2 human genbank 54_36p 1 reviewed intronic c.99-31832 e3-31832 0.006 - - - no_errors tier3 262 6 2.23 157 99 38.67 0 0 NA 808642 TCGA-AB-3006 AML06 4 10026156 10026156 C A SNP ZNF518B NM_053042.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*27670 NULL 0.017 - - - no_errors tier2 230 5 2.13 188 111 37.12 0 0 NA 808642 TCGA-AB-3006 AML06 4 11738060 11738060 T C SNP - - - - - - - - - - - - - - - tier2 139 7 4.79 202 160 44.08 0 0 NA 808642 TCGA-AB-3006 AML06 4 12620770 12620770 C T SNP - - - - - - - - - - - - - - - tier3 162 6 3.57 379 209 35.54 0 0 NA 808642 TCGA-AB-3006 AML06 4 17970555 17970555 T G SNP - - - - - - - - - - - - - - - tier2 150 8 5.06 298 203 40.52 0 0 NA 808642 TCGA-AB-3006 AML06 4 23583628 23583628 C A SNP - - - - - - - - - - - - - - - tier3 267 7 2.55 271 170 38.55 0 0 NA 808642 TCGA-AB-3006 AML06 4 24286511 24286511 G A SNP - - - - - - - - - - - - - - - tier3 192 3 1.54 194 91 31.93 0 0 NA 808642 TCGA-AB-3006 AML06 4 26844331 26844331 T C SNP FLJ45721 XR_041600.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-25527 NULL 0.001 - - - no_errors tier3 168 6 3.43 395 273 40.87 0 0 NA 808642 TCGA-AB-3006 AML06 4 29488936 29488936 T C SNP - - - - - - - - - - - - - - - tier3 84 2 2.33 170 49 22.27 0 0 NA 808642 TCGA-AB-3006 AML06 4 29765586 29765586 G T SNP - - - - - - - - - - - - - - - tier2 108 2 1.82 99 61 38.12 0 0 NA 808642 TCGA-AB-3006 AML06 4 32756581 32756581 A C SNP - - - - - - - - - - - - - - - tier3 290 6 2.02 270 164 37.7 0 0 NA 808642 TCGA-AB-3006 AML06 4 32769743 32769743 C A SNP - - - - - - - - - - - - - - - tier3 198 1 0.5 285 117 28.96 0 0 NA 808642 TCGA-AB-3006 AML06 4 40132487 40132487 C T SNP RBM47 NM_001098634.1 human genbank 54_36p -1 validated intronic c.1330+728 e2+728 0 - - - no_errors tier2 198 6 2.94 237 115 32.49 0 0 0 808642 TCGA-AB-3006 AML06 4 42122884 42122884 C T SNP ATP8A1 NM_006095.1 human genbank 54_36p -1 reviewed intronic c.3124-2405 e34-2405 0 - - - no_errors tier3 66 0 0 199 88 30.66 0 0 0 808642 TCGA-AB-3006 AML06 4 44117166 44117166 G A SNP KCTD8 NM_198353.2 human genbank 54_36p -1 validated intronic c.961+27171 e1+27171 0.003 - - - no_errors tier3 216 1 0.46 273 123 30.98 0 0 NA 808642 TCGA-AB-3006 AML06 4 47201637 47201637 C T SNP ATP10D NM_020453.3 human genbank 54_36p 1 validated intronic c.1-7641 e1-7641 0 - - - no_errors tier3 54 0 0 113 64 36.16 0 0 0 808642 TCGA-AB-3006 AML06 4 58580826 58580826 G A SNP - - - - - - - - - - - - - - - tier3 194 7 3.48 222 177 44.36 0 0 NA 808642 TCGA-AB-3006 AML06 4 58763286 58763286 G A SNP - - - - - - - - - - - - - - - tier3 107 1 0.93 135 61 31.12 0 0 NA 808642 TCGA-AB-3006 AML06 4 60465103 60465103 C T SNP - - - - - - - - - - - - - - - tier3 102 2 1.92 148 97 39.59 0 0 NA 808642 TCGA-AB-3006 AML06 4 70035524 70035524 A G SNP UGT2B11 ENST00000305206 human ensembl 54_36p -1 known intronic c.1590+65116 e6+65116 0.002 - - - no_errors tier3 82 2 2.35 110 94 45.85 0 0 NA 808642 TCGA-AB-3006 AML06 4 70294823 70294823 G A SNP ENSG00000215111 ENST00000359915 human ensembl 54_36p 1 known intronic c.148-1178 e2-1178 0 - - - no_start_codon:no_stop_codon tier3 123 2 1.6 160 93 36.76 2 0 0 808642 TCGA-AB-3006 AML06 4 71146311 71146311 G A SNP CSN3 NM_005212.2 human genbank 54_36p 1 validated intronic c.54+1132 e1+1132 0 - - - no_errors tier3 118 4 3.28 241 143 37.24 0 0 NA 808642 TCGA-AB-3006 AML06 4 80096082 80096082 T C SNP PAQR3 NM_001040202.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16680 NULL 0 - - - no_errors tier3 97 0 0 184 112 37.84 0 0 NA 808642 TCGA-AB-3006 AML06 4 81632721 81632721 G A SNP C4orf22 NM_152770.1 human genbank 54_36p 1 predicted intronic c.243-90550 e3-90550 0.001 - - - no_errors tier2 86 1 1.14 173 82 32.16 0 0 NA 808642 TCGA-AB-3006 AML06 4 86947076 86947076 G A SNP ARHGAP24 NM_001025616.2 human genbank 54_36p 1 validated intronic c.268+84927 e2+84927 0.002 - - - no_errors tier3 83 0 0 250 95 27.54 1 0 0 808642 TCGA-AB-3006 AML06 4 90680448 90680448 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 4 93656882 93656882 G C SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.89-73423 e2-73423 0.011 - - - no_errors tier2 274 5 1.79 295 211 41.62 0 0 NA 808642 TCGA-AB-3006 AML06 4 94623208 94623208 A G SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.1859-7605 e12-7605 0.001 - - - no_errors tier3 336 15 4.26 492 344 41.15 0 0 NA 808642 TCGA-AB-3006 AML06 4 95941490 95941490 T C SNP BMPR1B NM_001203.2 human genbank 54_36p 1 reviewed intronic c.1+43248 e0+43248 0.033 - - - no_errors tier3 137 5 3.52 150 81 35.06 0 0 NA 808642 TCGA-AB-3006 AML06 4 97318703 97318703 G C SNP ENSG00000201744 ENST00000364874 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26126 NULL 0 - - - no_errors tier3 86 4 4.44 127 71 35.68 0 0 NA 808642 TCGA-AB-3006 AML06 4 106413341 106413341 C T SNP TET2 ENST00000265149 human ensembl 54_36p 1 known nonsense c.760 p.R254* 0.839 NULL NULL - no_start_codon tier1 191 6 3.03 249 158 38.82 38 25 39.68 808642 TCGA-AB-3006 AML06 4 110272158 110272158 C T SNP COL25A1 NM_198721.2 human genbank 54_36p -1 validated intronic c.368-81374 e3-81374 0 - - - no_errors tier2 137 5 3.52 184 115 38.46 0 0 NA 808642 TCGA-AB-3006 AML06 4 115770916 115770916 G A SNP UGT8 NM_003360.1 human genbank 54_36p 1 validated intronic c.822+6609 e1+6609 0.007 - - - no_errors tier3 58 0 0 82 55 40.15 0 0 NA 808642 TCGA-AB-3006 AML06 4 118225696 118225696 A T SNP TRAM1L1 NM_152402.2 human genbank 54_36p -1 validated missense c.302 p.V101E 1 HMMPfam_TRAM1 "HMMPfam_TRAM_LAG1_CLN8,HMMSmart_TLC,HMMPfam_TRAM1" - no_errors tier1 113 2 1.74 187 136 42.11 NA 808642 TCGA-AB-3006 AML06 4 122333879 122333879 T A SNP TNIP3 NM_024873.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-29149 NULL 0.003 - - - no_errors tier3 140 3 2.1 159 101 38.85 0 0 NA 808642 TCGA-AB-3006 AML06 4 126246864 126246864 G A SNP - - - - - - - - - - - - - - - tier3 79 3 3.66 122 80 39.6 0 0 NA 808642 TCGA-AB-3006 AML06 4 134170116 134170116 C T SNP - - - - - - - - - - - - - - - tier3 45 0 0 173 65 27.31 0 0 NA 808642 TCGA-AB-3006 AML06 4 135506951 135506951 A T SNP - - - - - - - - - - - - - - - tier3 318 9 2.75 372 229 38.04 0 0 NA 808642 TCGA-AB-3006 AML06 4 137759086 137759086 G A SNP - - - - - - - - - - - - - - - tier3 77 0 0 40 25 38.46 0 0 NA 808642 TCGA-AB-3006 AML06 4 138955785 138955785 G A SNP - - - - - - - - - - - - - - - tier3 189 2 1.05 283 138 32.78 0 0 NA 808642 TCGA-AB-3006 AML06 4 141590831 141590831 C G SNP LOC152586 XM_001725473.1 human genbank 54_36p -1 model intronic c.492+1183 e4+1183 0 - - - no_errors tier2 72 2 2.67 150 53 26.11 0 0 NA 808642 TCGA-AB-3006 AML06 4 142749840 142749840 G A SNP IL15 NM_000585.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-110228 NULL 0 - - - no_errors tier3 262 6 2.24 175 105 37.5 0 0 NA 808642 TCGA-AB-3006 AML06 4 144678733 144678734 - T INS SMARCA5 NM_003601.2 human genbank 54_36p 1 reviewed intronic c.1496-460_1496-459 e12-459 0.006:0.013 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 4 146539827 146539827 G A SNP - - - - - - - - - - - - - - - tier3 282 12 4.08 275 176 38.94 0 0 NA 808642 TCGA-AB-3006 AML06 4 153008912 153008912 C T SNP - - - - - - - - - - - - - - - tier3 128 3 2.29 95 51 34.93 0 0 NA 808642 TCGA-AB-3006 AML06 4 158935702 158935702 T C SNP ENSG00000200521 ENST00000363651 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26987 NULL 0 - - - no_errors tier3 54 0 0 191 148 43.66 0 0 NA 808642 TCGA-AB-3006 AML06 4 167850115 167850115 C A SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*42532 NULL 0 - - - no_errors tier3 87 3 3.33 119 57 32.39 0 0 NA 808642 TCGA-AB-3006 AML06 4 174732344 174732344 C T SNP HAND2 NM_021973.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-45329 NULL 0 - - - no_errors tier3 95 5 4.95 193 89 31.56 0 0 NA 808642 TCGA-AB-3006 AML06 4 178387203 178387203 T A SNP ENSG00000222859 ENST00000410927 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47357 NULL 0.001 - - - no_errors tier3 134 1 0.74 242 122 33.52 0 0 NA 808642 TCGA-AB-3006 AML06 4 180169383 180169383 G T SNP - - - - - - - - - - - - - - - tier3 149 3 1.97 144 122 45.86 0 0 NA 808642 TCGA-AB-3006 AML06 4 189184626 189184626 C T SNP ENSG00000203361 ENST00000366186 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-36781 NULL 0.001 - - - no_coding_region:pseudogene tier3 825 9 1.08 301 168 35.82 0 0 NA 808642 TCGA-AB-3006 AML06 5 1536814 1536814 C T SNP LPCAT1 NM_024830.3 human genbank 54_36p -1 validated intronic c.668-213 e6-213 0.002 - - - no_errors tier2 61 0 0 98 52 34.67 2 0 0 808642 TCGA-AB-3006 AML06 5 3356056 3356056 C T SNP - - - - - - - - - - - - - - - tier3 104 2 1.89 160 26 13.98 0 0 NA 808642 TCGA-AB-3006 AML06 5 8961491 8961491 G T SNP - - - - - - - - - - - - - - - tier2 156 5 3.09 218 128 36.89 0 0 NA 808642 TCGA-AB-3006 AML06 5 12219717 12219717 A G SNP - - - - - - - - - - - - - - - tier3 201 0 0 281 139 33.02 0 0 NA 808642 TCGA-AB-3006 AML06 5 12254593 12254594 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 5 25947663 25947663 G A SNP LOC100133558 XM_001716419.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*9705 NULL 0.026 - - - no_start_codon:pseudogene:no_stop_codon tier3 136 0 0 118 54 31.4 0 0 0 808642 TCGA-AB-3006 AML06 5 25963154 25963154 C T SNP LOC100133558 XM_001716419.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-5601 NULL 0.011 - - - no_start_codon:pseudogene:no_stop_codon tier3 199 4 1.97 270 188 41.05 0 0 NA 808642 TCGA-AB-3006 AML06 5 26593991 26593991 C T SNP - - - - - - - - - - - - - - - tier3 65 2 2.99 152 92 37.7 0 0 NA 808642 TCGA-AB-3006 AML06 5 29082614 29082614 C T SNP - - - - - - - - - - - - - - - tier3 60 0 0 174 90 34.09 0 0 NA 808642 TCGA-AB-3006 AML06 5 29385295 29385295 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 5 35062019 35062019 A C SNP AGXT2 NM_031900.2 human genbank 54_36p -1 reviewed intronic c.870+253 e8+253 0 - - - no_errors tier2 87 2 2.25 106 34 24.29 0 0 NA 808642 TCGA-AB-3006 AML06 5 37591457 37591457 G C SNP WDR70 NM_018034.2 human genbank 54_36p 1 provisional intronic c.917+39008 e9+39008 0.033 - - - no_errors tier3 229 6 2.55 171 93 34.96 1 0 0 808642 TCGA-AB-3006 AML06 5 38770130 38770130 C T SNP - - - - - - - - - - - - - - - tier3 240 5 2.04 209 158 43.05 0 0 NA 808642 TCGA-AB-3006 AML06 5 42236640 42236640 G A SNP - - - - - - - - - - - - - - - tier3 150 2 1.32 169 97 36.47 0 0 NA 808642 TCGA-AB-3006 AML06 5 45323465 45323465 T A SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.1618+15993 e6+15993 0 - - - no_errors tier3 140 0 0 165 87 34.52 0 0 NA 808642 TCGA-AB-3006 AML06 5 45323468 45323468 G T SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated intronic c.1618+15990 e6+15990 0 - - - no_errors tier3 139 0 0 162 82 33.61 0 0 NA 808642 TCGA-AB-3006 AML06 5 51364393 51364393 A T SNP - - - - - - - - - - - - - - - tier3 179 4 2.17 187 135 41.93 0 0 NA 808642 TCGA-AB-3006 AML06 5 56173211 56173211 C G SNP MAP3K1 NM_005921.1 human genbank 54_36p 1 validated intronic c.483-14973 e2-14973 0.001 - - - no_errors tier3 129 0 0 215 180 45.57 1 4 80 808642 TCGA-AB-3006 AML06 5 56260413 56260413 G C SNP MIER3 NM_152622.3 human genbank 54_36p -1 validated missense c.859 p.R287G 1 "HMMSmart_SANT,superfamily_Homeodomain_like,HMMPfam_Myb_DNA-binding" "HMMPfam_ELM2,HMMSmart_SANT,superfamily_Homeodomain_like,HMMPfam_Myb_DNA-binding,PatternScan_EF_HAND_1" - no_errors tier1 258 7 2.64 182 87 32.34 13 12 48 808642 TCGA-AB-3006 AML06 5 57137549 57137549 G A SNP - - - - - - - - - - - - - - - tier3 267 5 1.84 270 184 40.35 0 0 NA 808642 TCGA-AB-3006 AML06 5 58546056 58546056 A G SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.647+1304 e2+1304 0.001 - - - no_errors tier3 165 1 0.6 143 87 37.83 0 0 0 808642 TCGA-AB-3006 AML06 5 62780802 62780802 G A SNP - - - - - - - - - - - - - - - tier2 76 1 1.3 185 94 33.69 0 0 NA 808642 TCGA-AB-3006 AML06 5 62799496 62799496 C A SNP - - - - - - - - - - - - - - - tier3 40 1 2.44 150 55 26.83 0 0 NA 808642 TCGA-AB-3006 AML06 5 68834280 68834280 G A SNP OCLN NM_002538.2 human genbank 54_36p 1 reviewed intronic c.1-1480 e1-1480 0.063 - - - no_errors tier2 255 7 2.67 210 148 41.34 4 4 50 808642 TCGA-AB-3006 AML06 5 71527714 71527714 T C SNP MAP1B NM_005909.3 human genbank 54_36p 1 validated missense c.2776 p.F926L 1 NULL "HMMPfam_MAP1B_neuraxin,PatternScan_MAP1B_NEURAXIN" - no_errors tier1 464 17 3.52 471 349 42.41 NA 808642 TCGA-AB-3006 AML06 5 79928924 79928924 G A SNP ANKRD34B NM_001004441.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-37330 NULL 0 - - - no_errors tier3 102 1 0.97 115 71 38.17 0 1 100 808642 TCGA-AB-3006 AML06 5 87866292 87866293 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 5 88001791 88001791 A T SNP MIRN9-2 ENST00000384838 human ensembl 54_36p -1 known 5_prime_flanking_region c.-3278 NULL 1 - - - no_errors tier3 191 2 1.04 199 99 33.22 0 0 NA 808642 TCGA-AB-3006 AML06 5 88854676 88854676 G A SNP - - - - - - - - - - - - - - - tier3 112 2 1.75 211 77 26.74 0 0 NA 808642 TCGA-AB-3006 AML06 5 89903861 89903861 G A SNP GPR98 NM_032119.3 human genbank 54_36p 1 reviewed intronic c.22+13371 e1+13371 0.003 - - - no_errors tier2 478 5 1.04 266 177 39.95 0 0 NA 808642 TCGA-AB-3006 AML06 5 92225600 92225600 G A SNP LOC391810 XM_001723772.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*26024 NULL 0 - - - pseudogene tier3 81 1 1.22 278 140 33.49 0 0 NA 808642 TCGA-AB-3006 AML06 5 98186454 98186454 C T SNP FLJ35946 XM_931448.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-50196 NULL 0 - - - no_errors tier3 57 0 0 248 128 34.04 0 0 NA 808642 TCGA-AB-3006 AML06 5 100179353 100179353 T C SNP ST8SIA4 NM_005668.4 human genbank 54_36p -1 reviewed intronic c.798-3621 e5-3621 0.004 - - - no_errors tier3 97 3 3 201 139 40.88 2 1 33.33 808642 TCGA-AB-3006 AML06 5 100400870 100400870 C T SNP ENSG00000203447 ENST00000366265 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*30862 NULL 0.067 - - - no_coding_region:pseudogene tier2 131 7 5.07 294 178 37.71 0 0 NA 808642 TCGA-AB-3006 AML06 5 104131347 104131347 T C SNP ENSG00000209193 ENST00000386458 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*12541 NULL 0.004 - - - pseudogene tier2 59 5 7.81 142 104 42.11 0 0 NA 808642 TCGA-AB-3006 AML06 5 105779164 105779164 C T SNP - - - - - - - - - - - - - - - tier3 170 0 0 189 120 38.71 1 0 0 808642 TCGA-AB-3006 AML06 5 110766837 110766837 C - DEL CAMK4 NM_001744.3 human genbank 54_36p 1 reviewed intronic c.459+8458 e5+8458 0.038 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 5 111858643 111858643 C T SNP - - - - - - - - - - - - - - - tier3 254 3 1.17 398 132 24.86 0 0 NA 808642 TCGA-AB-3006 AML06 5 119983764 119983764 G A SNP PRR16 NM_016644.1 human genbank 54_36p 1 provisional intronic c.91-65784 e2-65784 0.003 - - - no_errors tier3 98 1 1.01 277 102 26.91 0 0 NA 808642 TCGA-AB-3006 AML06 5 124708078 124708078 C T SNP ENSG00000222107 ENST00000410175 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*6338 NULL 0 - - - no_errors tier3 476 16 3.25 249 151 37.75 0 0 NA 808642 TCGA-AB-3006 AML06 5 127014257 127014257 G A SNP CTXN3 NM_001048252.2 human genbank 54_36p 1 validated intronic c.1+1278 e0+1278 0.001 - - - no_errors tier3 77 2 2.53 80 64 44.44 0 0 NA 808642 TCGA-AB-3006 AML06 5 131830453 131830453 C T SNP uc003kwy.1 ENST00000378953 human ensembl 54_36p 1 known intronic c.89-8805 e3-8805 0.74 - - - no_errors tier2 239 5 2.05 175 103 37.05 7 10 58.82 808642 TCGA-AB-3006 AML06 5 138485732 138485732 C T SNP SIL1 NM_001037633.1 human genbank 54_36p -1 reviewed intronic c.106-971 e2-971 0.022 - - - no_errors tier3 139 4 2.8 137 88 38.94 1 0 0 808642 TCGA-AB-3006 AML06 5 140168251 140168251 C T SNP PCDHA4 NM_018907.2 human genbank 54_36p 1 reviewed missense c.1295 p.S432L 0.781 "HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like" "HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like" - no_errors tier1 44 0 127 101 44.1 NA 808642 TCGA-AB-3006 AML06 5 140320536 140320536 G A SNP PCDHAC1 NM_018898.3 human genbank 54_36p 1 reviewed intronic c.2434-18182 e2-18182 0.971 - - - no_errors tier2 65 0 0 119 33 21.71 0 0 NA 808642 TCGA-AB-3006 AML06 5 143808359 143808359 T C SNP KCTD16 NM_020768.3 human genbank 54_36p 1 validated intronic c.833-25057 e2-25057 0.981 - - - no_errors tier3 356 7 1.91 285 158 35.67 0 1 100 808642 TCGA-AB-3006 AML06 5 155290202 155290202 A T SNP - - - - - - - - - - - - - - - tier3 116 3 2.52 174 99 36 0 0 NA 808642 TCGA-AB-3006 AML06 5 155581903 155581903 A T SNP - - - - - - - - - - - - - - - tier3 117 3 2.5 155 80 34.04 0 0 NA 808642 TCGA-AB-3006 AML06 5 158322406 158322406 G A SNP EBF1 NM_024007.3 human genbank 54_36p -1 validated intronic c.554+110576 e6+110576 0.003 - - - no_errors tier3 110 2 1.77 238 146 38.02 1 0 0 808642 TCGA-AB-3006 AML06 5 167014960 167014960 G A SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.503-220609 e3-220609 0 - - - no_errors tier3 215 1 0.46 259 128 33.07 0 0 NA 808642 TCGA-AB-3006 AML06 5 168788528 168788528 G A SNP - - - - - - - - - - - - - - - tier3 249 7 2.73 361 164 31.24 0 0 NA 808642 TCGA-AB-3006 AML06 5 174736238 174736238 A G SNP - - - - - - - - - - - - - - - tier3 342 5 1.44 373 306 45.07 0 0 NA 808642 TCGA-AB-3006 AML06 5 179985356 179985356 G T SNP FLT4 NM_182925.4 human genbank 54_36p -1 reviewed intronic c.1421+119 e10+119 0.001 - - - no_errors tier3 101 3 2.86 35 15 30 0 0 NA 808642 TCGA-AB-3006 AML06 6 6118412 6118412 C T SNP F13A1 NM_000129.3 human genbank 54_36p -1 reviewed intronic c.1747+1400 e11+1400 0.001 - - - no_errors tier3 410 11 2.61 154 91 37.14 0 0 0 808642 TCGA-AB-3006 AML06 6 7804728 7804728 A G SNP BMP6 NM_001718.4 human genbank 54_36p 1 reviewed intronic c.858-1955 e3-1955 0 - - - no_errors tier3 210 4 1.87 242 127 34.42 0 0 0 808642 TCGA-AB-3006 AML06 6 8399961 8399961 G A SNP SLC35B3 NM_015948.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20342 NULL 0 - - - no_errors tier3 63 2 3.08 169 100 37.17 0 0 NA 808642 TCGA-AB-3006 AML06 6 9950405 9950405 G A SNP OFCC1 ENST00000316020 human ensembl 54_36p -1 known intronic c.831+330 e7+330 0.628 - - - no_errors tier2 403 12 2.89 295 179 37.76 0 0 NA 808642 TCGA-AB-3006 AML06 6 12826516 12826516 C T SNP PHACTR1 NM_030948.1 human genbank 54_36p 1 validated intronic c.1-401 e1-401 0 - - - no_errors tier3 242 2 0.82 280 253 47.47 0 0 NA 808642 TCGA-AB-3006 AML06 6 20965517 20965517 G A SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated intronic c.742+11129 e7+11129 0 - - - no_errors tier3 105 2 1.87 129 78 37.68 5 0 0 808642 TCGA-AB-3006 AML06 6 22698699 22698699 T A SNP HDGFL1 NM_138574.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*20160 NULL 0.874 - - - no_errors tier3 152 0 0 318 214 40.23 0 0 NA 808642 TCGA-AB-3006 AML06 6 24222734 24222734 T C SNP NRSN1 NM_080723.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-19801 NULL 0.011 - - - no_errors tier3 413 13 3.05 303 180 37.27 0 0 NA 808642 TCGA-AB-3006 AML06 6 26392943 26392943 T C SNP HIST1H4H ENST00000289352 human ensembl 54_36p -1 known intronic c.312+298 e1+298 0.018 - - - no_errors tier3 157 2 1.26 112 87 43.72 1 0 0 808642 TCGA-AB-3006 AML06 6 27746398 27746398 G A SNP ENSG00000216676 ENST00000404273 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17815 NULL 0 - - - no_coding_region:pseudogene tier3 330 2 0.6 264 192 42.11 0 0 NA 808642 TCGA-AB-3006 AML06 6 32303468 32303468 G A SNP NOTCH4 NM_004557.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3785 NULL 0 - - - no_errors tier3 633 5 0.78 281 183 39.44 0 0 NA 808642 TCGA-AB-3006 AML06 6 34107218 34107218 C T SNP GRM4 NM_000841.1 human genbank 54_36p -1 reviewed intronic c.2443-3097 e9-3097 0.001 - - - no_errors tier3 456 18 3.8 286 186 39.41 0 0 NA 808642 TCGA-AB-3006 AML06 6 39478050 39478050 C T SNP KIF6 NM_145027.4 human genbank 54_36p -1 validated intronic c.1811-16624 e16-16624 0.005 - - - no_errors tier3 243 0 0 509 345 40.4 0 0 NA 808642 TCGA-AB-3006 AML06 6 50178979 50178979 G A SNP - - - - - - - - - - - - - - - tier2 82 4 4.65 87 38 30.4 0 0 NA 808642 TCGA-AB-3006 AML06 6 50753425 50753425 C T SNP TFAP2D NM_172238.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36303 NULL 0.001 - - - no_errors tier2 67 1 1.47 204 132 39.29 0 0 NA 808642 TCGA-AB-3006 AML06 6 54808634 54808634 G A SNP FAM83B NM_001010872.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-34370 NULL 0.001 - - - no_errors tier3 296 4 1.33 344 232 40.21 0 0 NA 808642 TCGA-AB-3006 AML06 6 55272041 55272041 G A SNP GFRAL NM_207410.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28271 NULL 0 - - - no_errors tier3 149 0 0 139 83 37.39 0 0 NA 808642 TCGA-AB-3006 AML06 6 63798017 63798017 T A SNP - - - - - - - - - - - - - - - tier3 182 2 1.09 297 190 39.01 0 0 NA 808642 TCGA-AB-3006 AML06 6 66886924 66886924 C T SNP ENSG00000218890 ENST00000402902 human ensembl 54_36p -1 known 5_prime_flanking_region c.-25401 NULL 0 - - - no_coding_region:pseudogene tier3 261 0 0 241 160 39.8 0 0 NA 808642 TCGA-AB-3006 AML06 6 69028697 69028697 C A SNP - - - - - - - - - - - - - - - tier3 85 2 2.3 125 84 40.19 0 0 NA 808642 TCGA-AB-3006 AML06 6 69966525 69966525 G A SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.2481-33378 e16-33378 0 - - - no_errors tier3 128 4 3.03 191 71 27.1 0 0 NA 808642 TCGA-AB-3006 AML06 6 78086707 78086707 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 6 85235056 85235056 G A SNP ENSG00000214465 ENST00000398372 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-37818 NULL 0 - - - no_coding_region:pseudogene tier3 161 7 4.17 257 185 41.86 0 0 NA 808642 TCGA-AB-3006 AML06 6 87360512 87360512 T A SNP - - - - - - - - - - - - - - - tier3 57 0 0 61 38 38.38 0 0 NA 808642 TCGA-AB-3006 AML06 6 91934026 91934026 C G SNP - - - - - - - - - - - - - - - tier3 123 1 0.8 111 67 37.64 0 0 NA 808642 TCGA-AB-3006 AML06 6 94835086 94835086 C T SNP - - - - - - - - - - - - - - - tier3 80 3 3.61 175 89 33.71 0 0 NA 808642 TCGA-AB-3006 AML06 6 95010561 95010562 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 6 95209409 95209409 T G SNP ENSG00000216853 ENST00000404146 human ensembl 54_36p -1 known 3_prime_flanking_region c.*3770 NULL 0.997 - - - no_coding_region:pseudogene tier2 100 2 1.94 85 51 37.5 0 0 NA 808642 TCGA-AB-3006 AML06 6 95438154 95438154 G A SNP - - - - - - - - - - - - - - - tier3 48 1 2.04 131 57 30.32 0 0 NA 808642 TCGA-AB-3006 AML06 6 95632039 95632039 C T SNP - - - - - - - - - - - - - - - tier3 57 1 1.72 133 78 36.97 0 0 NA 808642 TCGA-AB-3006 AML06 6 98422418 98422418 C A SNP - - - - - - - - - - - - - - - tier3 45 2 4.26 105 46 30.26 0 0 NA 808642 TCGA-AB-3006 AML06 6 98906003 98906003 G T SNP - - - - - - - - - - - - - - - tier3 102 1 0.97 290 188 39.33 0 0 NA 808642 TCGA-AB-3006 AML06 6 102231393 102231393 A T SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.723+21 e4+21 0 - - - no_errors tier3 114 2 1.72 145 86 37.23 0 0 NA 808642 TCGA-AB-3006 AML06 6 102906844 102906844 G A SNP - - - - - - - - - - - - - - - tier3 55 1 1.79 51 34 40 0 0 NA 808642 TCGA-AB-3006 AML06 6 107504293 107504293 G A SNP BEND3 NM_001080450.1 human genbank 54_36p -1 provisional intronic c.241-5446 e3-5446 0.004 - - - no_errors tier2 501 23 4.38 348 221 38.84 0 0 NA 808642 TCGA-AB-3006 AML06 6 120095719 120095719 C T SNP LOC728727 XM_001128292.2 human genbank 54_36p 1 model intronic c.226-110192 e4-110192 0.003 - - - no_errors tier3 269 4 1.47 260 162 38.39 0 0 NA 808642 TCGA-AB-3006 AML06 6 121756243 121756243 C G SNP GJA1 NM_000165.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-53450 NULL 0.001 - - - no_errors tier2 257 3 1.15 189 90 32.26 0 0 NA 808642 TCGA-AB-3006 AML06 6 154403628 154403628 G A SNP OPRM1 NM_001008505.3 human genbank 54_36p 1 validated intronic c.290+966 e1+966 0 - - - no_errors tier2 188 1 0.53 245 182 42.42 0 0 NA 808642 TCGA-AB-3006 AML06 6 160390608 160390608 C T SNP IGF2R NM_000876.2 human genbank 54_36p 1 reviewed intronic c.2515-887 e19-887 0.037 - - - no_errors tier3 152 1 0.65 201 125 38.34 0 0 0 808642 TCGA-AB-3006 AML06 6 169028086 169028086 C A SNP - - - - - - - - - - - - - - - tier2 65 4 5.8 138 106 43.44 0 0 NA 808642 TCGA-AB-3006 AML06 6 169508346 169508346 G A SNP - - - - - - - - - - - - - - - tier3 404 6 1.46 373 285 43.31 0 0 NA 808642 TCGA-AB-3006 AML06 7 1355418 1355418 G A SNP LOC100134171 XM_001714238.1 human genbank 54_36p 1 model intronic c.171+402 e2+402 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 100 1 0.99 99 67 40.36 0 0 NA 808642 TCGA-AB-3006 AML06 7 6279729 6279729 C T SNP LOC100130749 XM_001720821.1 human genbank 54_36p 1 model intronic c.23-6479 e2-6479 0.984 - - - no_start_codon:pseudogene:no_stop_codon tier2 118 4 3.28 171 96 35.82 0 0 NA 808642 TCGA-AB-3006 AML06 7 10647924 10647924 A G SNP - - - - - - - - - - - - - - - tier3 192 3 1.54 389 196 33.5 0 0 NA 808642 TCGA-AB-3006 AML06 7 15430845 15430845 A T SNP TMEM195 NM_001004320.1 human genbank 54_36p -1 provisional intronic c.514-6042 e5-6042 0 - - - no_errors tier3 163 1 0.61 233 157 40.15 0 0 NA 808642 TCGA-AB-3006 AML06 7 21569818 21569818 C T SNP DNAH11 ENST00000328843 human ensembl 54_36p 1 known intronic c.983-511 e6-511 0.022 - - - no_errors tier3 130 1 0.76 176 93 34.57 0 0 NA 808642 TCGA-AB-3006 AML06 7 31460877 31460877 G A SNP - - - - - - - - - - - - - - - tier3 675 15 2.17 262 200 43.29 0 0 NA 808642 TCGA-AB-3006 AML06 7 37057624 37057625 - TC INS ELMO1 NM_014800.1 human genbank 54_36p -1 reviewed intronic c.1301-38060_1301-38059 e15-38059 0.054:0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 7 38421610 38421610 C T SNP AMPH NM_001635.2 human genbank 54_36p -1 reviewed intronic c.1398+2340 e17+2340 0 - - - no_errors tier3 232 6 2.51 149 96 39.18 0 1 100 808642 TCGA-AB-3006 AML06 7 38506703 38506703 G C SNP AMPH NM_001635.2 human genbank 54_36p -1 reviewed intronic c.205+3072 e3+3072 0.001 - - - no_errors tier3 325 12 3.56 313 244 43.81 0 0 NA 808642 TCGA-AB-3006 AML06 7 40126672 40126672 G T SNP C7orf10 NM_024728.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-14452 NULL 0.001 - - - no_errors tier3 272 12 4.23 156 93 37.35 2 3 60 808642 TCGA-AB-3006 AML06 7 42044722 42044722 C T SNP GLI3 NM_000168.5 human genbank 54_36p -1 reviewed intronic c.1028+1440 e6+1440 0 - - - no_errors tier3 347 5 1.42 368 272 42.5 0 0 NA 808642 TCGA-AB-3006 AML06 7 46541741 46541741 G A SNP - - - - - - - - - - - - - - - tier2 333 3 0.89 277 171 38.17 0 0 NA 808642 TCGA-AB-3006 AML06 7 47318071 47318071 G A SNP TNS3 NM_022748.10 human genbank 54_36p -1 validated intronic c.2651-6945 e16-6945 0 - - - no_errors tier3 140 2 1.41 163 97 37.31 1 5 83.33 808642 TCGA-AB-3006 AML06 7 49711251 49711251 T A SNP - - - - - - - - - - - - - - - tier3 271 5 1.81 207 113 35.09 0 0 NA 808642 TCGA-AB-3006 AML06 7 52359793 52359793 A G SNP - - - - - - - - - - - - - - - tier3 70 3 4.11 74 64 46.38 0 0 NA 808642 TCGA-AB-3006 AML06 7 54635559 54635559 T A SNP ENSG00000200471 ENST00000363601 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20653 NULL 0 - - - no_errors tier3 245 4 1.6 257 158 38.07 0 0 NA 808642 TCGA-AB-3006 AML06 7 54926083 54926083 C T SNP ENSG00000218586 ENST00000407916 human ensembl 54_36p 1 known 5_prime_flanking_region c.-42557 NULL 0.001 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 37 0 0 103 46 30.87 0 0 NA 808642 TCGA-AB-3006 AML06 7 55140889 55140889 A G SNP EGFR NM_005228.3 human genbank 54_36p 1 reviewed intronic c.89-36584 e2-36584 0.001 - - - no_errors tier3 317 2 0.62 279 189 40.3 0 0 NA 808642 TCGA-AB-3006 AML06 7 56386840 56386840 G A SNP LOC442676 XM_001718425.1 human genbank 54_36p 1 model intronic c.359+172 e3+172 0 - - - no_errors tier3 169 8 4.52 39 27 40.91 0 0 NA 808642 TCGA-AB-3006 AML06 7 62323540 62323540 C T SNP ENSG00000199231 ENST00000362361 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-49708 NULL 0 - - - no_errors tier3 78 0 0 109 79 42.02 0 0 NA 808642 TCGA-AB-3006 AML06 7 63102699 63102700 TT - DEL LOC100129126 XM_001715328.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16567 NULL 0.699:0.649 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 7 75856803 75856803 G T SNP SRCRB4D NM_080744.1 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*509 NULL 0.711 - - - no_errors tier3 196 6 2.97 229 130 36.11 0 0 NA 808642 TCGA-AB-3006 AML06 7 76924977 76924977 G T SNP PION NM_017439.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41403 NULL 0.008 - - - no_errors tier3 38 1 2.56 129 80 38.28 0 0 NA 808642 TCGA-AB-3006 AML06 7 82243205 82243205 A G SNP PCLO NM_033026.2 human genbank 54_36p -1 validated intronic c.15008-14460 e23-14460 0 - - - no_errors tier3 89 4 4.3 91 56 38.1 0 0 NA 808642 TCGA-AB-3006 AML06 7 84489910 84489910 T C SNP SEMA3D NM_152754.2 human genbank 54_36p -1 validated intronic c.1192-45 e11-45 0.003 - - - no_errors tier3 88 2 2.22 140 65 31.55 0 0 NA 808642 TCGA-AB-3006 AML06 7 84909986 84909986 C T SNP - - - - - - - - - - - - - - - tier3 31 1 3.12 59 48 44.86 0 0 NA 808642 TCGA-AB-3006 AML06 7 87652010 87652011 - A INS ADAM22 NM_021723.2 human genbank 54_36p 1 reviewed intronic c.2576+2735_2576+2734 e29+2735 0.003:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 7 90167840 90167840 A C SNP PFTK1 ENST00000380050 human ensembl 54_36p 1 known intronic c.124-25977 e3-25977 0.982 - - - no_errors tier3 443 6 1.34 438 316 41.85 2 0 0 808642 TCGA-AB-3006 AML06 7 98203384 98203384 G A SNP ENSG00000207204 ENST00000384475 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*26893 NULL 0.002 - - - no_errors tier3 332 6 1.77 171 86 33.33 0 0 NA 808642 TCGA-AB-3006 AML06 7 99012619 99012619 C T SNP C7orf38 NM_145111.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-28653 NULL 0.001 - - - no_errors tier3 91 0 0 141 58 28.86 0 0 NA 808642 TCGA-AB-3006 AML06 7 99818871 99818871 C T SNP PILRA NM_013439.2 human genbank 54_36p 1 reviewed intronic c.455-6576 e3-6576 0.022 - - - no_errors tier3 470 25 5.05 268 165 38.02 2 0 0 808642 TCGA-AB-3006 AML06 7 100654983 100654983 C T SNP PLOD3 NM_001084.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-7708 NULL 0.001 - - - no_errors tier3 266 2 0.75 152 109 41.76 2 2 50 808642 TCGA-AB-3006 AML06 7 106675748 106675748 T A SNP COG5 NM_006348.2 human genbank 54_36p -1 validated intronic c.1946+329 e17+329 0 - - - no_errors tier3 112 6 5.08 168 87 34.12 1 2 66.67 808642 TCGA-AB-3006 AML06 7 113569991 113569991 G A SNP ENSG00000208668 ENST00000385933 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*704 NULL 0.005 - - - pseudogene tier2 175 7 3.85 264 164 38.32 0 0 NA 808642 TCGA-AB-3006 AML06 7 114341853 114341853 G T SNP MDFIC ENST00000393486 human ensembl 54_36p 1 known 5_prime_flanking_region c.-8472 NULL 0 - - - no_errors tier3 266 5 1.85 180 98 35.25 0 0 NA 808642 TCGA-AB-3006 AML06 7 119230183 119230183 G A SNP - - - - - - - - - - - - - - - tier3 116 2 1.69 132 88 40 0 0 NA 808642 TCGA-AB-3006 AML06 7 125960487 125960487 G A SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed missense c.2185 p.R729W 0.995 HMMPfam_7tm_3 "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_Periplasmic binding protein-like I" - no_errors tier1 378 3 0.79 187 129 40.69 NA 808642 TCGA-AB-3006 AML06 7 126753327 126753327 C T SNP ZNF800 NM_176814.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*45777 NULL 0.001 - - - no_errors tier3 235 6 2.48 368 220 37.41 0 0 NA 808642 TCGA-AB-3006 AML06 7 127196294 127196294 T C SNP SND1 NM_014390.2 human genbank 54_36p 1 validated intronic c.1153-38480 e11-38480 0 - - - no_errors tier3 108 3 2.7 200 114 36.31 2 1 33.33 808642 TCGA-AB-3006 AML06 7 130965734 130965734 C G SNP LOC647030 XR_017470.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*31440 NULL 0.01 - - - no_errors tier3 1189 22 1.82 587 391 39.98 0 0 NA 808642 TCGA-AB-3006 AML06 7 131000873 131000873 G A SNP LOC647030 XR_017470.2 human genbank 54_36p -1 model intronic c.NULL NULL 1 - - - no_errors tier2 556 5 0.89 269 235 46.44 0 0 NA 808642 TCGA-AB-3006 AML06 7 132648668 132648668 C A SNP EXOC4 NM_021807.1 human genbank 54_36p 1 reviewed intronic c.657-3910 e5-3910 0.025 - - - no_errors tier3 81 2 2.41 274 112 29.02 0 1 100 808642 TCGA-AB-3006 AML06 7 136384858 136384858 C T SNP LOC100128744 XM_001718911.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24143 NULL 0.002 - - - no_errors tier3 137 3 2.14 180 115 38.98 0 0 NA 808642 TCGA-AB-3006 AML06 7 142135190 142135190 T A SNP PRSS1 NM_002769.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1720 NULL 0 - - - no_errors tier3 240 3 1.23 420 263 38.45 1 0 0 808642 TCGA-AB-3006 AML06 7 151335302 151335302 C T SNP GALNTL5 NM_145292.2 human genbank 54_36p 1 provisional intronic c.909-543 e6-543 0.001 - - - no_errors tier3 55 0 0 152 86 35.83 0 0 NA 808642 TCGA-AB-3006 AML06 7 158056491 158056491 G A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.112+16520 e1+16520 0 - - - no_errors tier3 99 3 2.91 112 66 37.08 0 0 NA 808642 TCGA-AB-3006 AML06 8 4085208 4085208 T G SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.415+179675 e3+179675 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 142 0 0 222 122 35.47 0 0 NA 808642 TCGA-AB-3006 AML06 8 10105650 10105650 T C SNP MSRA NM_012331.1 human genbank 54_36p 1 reviewed intronic c.211+2829 e2+2829 0 - - - no_errors tier3 227 8 3.4 245 185 43.02 0 1 100 808642 TCGA-AB-3006 AML06 8 13082195 13082195 C T SNP DLC1 NM_182643.3 human genbank 54_36p -1 reviewed intronic c.1349-64658 e5-64658 0.004 - - - no_errors tier3 91 0 0 319 179 35.94 0 0 NA 808642 TCGA-AB-3006 AML06 8 15393817 15393817 C G SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48494 NULL 0.18 - - - no_errors tier3 172 4 2.27 226 144 38.92 0 0 NA 808642 TCGA-AB-3006 AML06 8 17352953 17352953 C T SNP MTMR7 NM_004686.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37781 NULL 0 - - - no_errors tier3 222 1 0.45 169 85 33.46 0 0 NA 808642 TCGA-AB-3006 AML06 8 19859747 19859747 G A SNP LPL NM_000237.2 human genbank 54_36p 1 reviewed intronic c.1019-1304 e7-1304 0.001 - - - no_errors tier3 138 7 4.83 240 156 39.39 0 0 NA 808642 TCGA-AB-3006 AML06 8 20262191 20262191 G A SNP LOC100133494 XM_001717636.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-36519 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 592 10 1.66 420 265 38.69 0 0 NA 808642 TCGA-AB-3006 AML06 8 32426045 32426045 G A SNP NRG1 NM_013962.2 human genbank 54_36p 1 reviewed intronic c.746-146843 e2-146843 0.018 - - - overly_large_intron tier3 186 3 1.59 129 84 39.44 0 0 NA 808642 TCGA-AB-3006 AML06 8 35241341 35241341 C G SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.103+28394 e1+28394 0.009 - - - no_errors tier3 102 0 0 174 90 33.96 0 0 NA 808642 TCGA-AB-3006 AML06 8 40145952 40145952 C T SNP C8orf4 NM_020130.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*15423 NULL 0.005 - - - no_errors tier3 650 18 2.69 298 183 38.05 0 0 NA 808642 TCGA-AB-3006 AML06 8 41704059 41704059 C T SNP ANK1 NM_020476.3 human genbank 54_36p -1 reviewed intronic c.328-36 e5-36 0.001 - - - no_errors tier3 193 4 2.03 194 128 39.75 1 0 0 808642 TCGA-AB-3006 AML06 8 49212010 49212010 C T SNP - - - - - - - - - - - - - - - tier3 245 6 2.39 152 92 37.4 0 0 NA 808642 TCGA-AB-3006 AML06 8 50931644 50931644 T A SNP LOC100127998 XM_001714676.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-49242 NULL 0.016 - - - no_errors tier2 79 0 0 246 152 38.19 0 0 NA 808642 TCGA-AB-3006 AML06 8 54198077 54198077 C T SNP - - - - - - - - - - - - - - - tier3 67 5 6.94 225 140 38.36 0 0 NA 808642 TCGA-AB-3006 AML06 8 59743452 59743452 C T SNP NSMAF NM_003580.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-8708 NULL 0.002 - - - no_errors tier3 279 8 2.79 161 113 41.24 0 0 NA 808642 TCGA-AB-3006 AML06 8 61104817 61104817 C A SNP - - - - - - - - - - - - - - - tier2 138 3 2.13 218 163 42.67 0 0 NA 808642 TCGA-AB-3006 AML06 8 63746560 63746560 A T SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.274-75485 e4-75485 0.001 - - - no_errors tier2 308 7 2.22 171 131 43.38 0 0 NA 808642 TCGA-AB-3006 AML06 8 67271674 67271674 G A SNP CRH NM_000756.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-19408 NULL 0.978 - - - no_errors tier3 634 17 2.61 356 225 38.53 0 0 NA 808642 TCGA-AB-3006 AML06 8 77601896 77601896 A T SNP - - - - - - - - - - - - - - - tier3 80 1 1.23 105 63 37.5 0 0 NA 808642 TCGA-AB-3006 AML06 8 83310798 83310798 C T SNP - - - - - - - - - - - - - - - tier3 92 1 1.08 173 89 33.97 0 0 NA 808642 TCGA-AB-3006 AML06 8 88967031 88967031 A C SNP WDR21C NM_152418.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11716 NULL 0.007 - - - no_errors tier3 111 2 1.77 81 45 35.71 0 0 NA 808642 TCGA-AB-3006 AML06 8 97592926 97592926 C T SNP SDC2 NM_002998.3 human genbank 54_36p 1 reviewed intronic c.60+17191 e1+17191 0 - - - no_errors tier3 80 1 1.23 111 104 48.15 0 0 NA 808642 TCGA-AB-3006 AML06 8 113011533 113011533 C T SNP - - - - - - - - - - - - - - - tier3 169 4 2.29 239 125 34.15 0 0 NA 808642 TCGA-AB-3006 AML06 8 117960354 117960354 C T SNP RAD21 NM_006265.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-12205 NULL 0.004 - - - no_errors tier2 241 4 1.63 175 98 35.9 0 0 NA 808642 TCGA-AB-3006 AML06 8 124877290 124877290 G C SNP FAM91A1 NM_144963.2 human genbank 54_36p 1 validated intronic c.1412-2221 e16-2221 0.988 - - - no_errors tier2 117 1 0.85 159 55 25.58 1 3 75 808642 TCGA-AB-3006 AML06 8 129464935 129464935 G A SNP - - - - - - - - - - - - - - - tier3 373 12 3.11 270 200 42.55 0 0 NA 808642 TCGA-AB-3006 AML06 8 131078637 131078637 T C SNP FAM49B ENST00000401979 human ensembl 54_36p -1 known intronic c.1+19161 e0+19161 0 - - - no_errors tier3 715 7 0.97 206 152 42.46 4 2 33.33 808642 TCGA-AB-3006 AML06 8 131948490 131948490 G A SNP ADCY8 NM_001115.2 human genbank 54_36p -1 reviewed intronic c.2210+784 e9+784 0.012 - - - no_errors tier3 99 3 2.88 167 121 42.01 0 0 NA 808642 TCGA-AB-3006 AML06 8 137362486 137362486 G A SNP - - - - - - - - - - - - - - - tier2 235 3 1.26 352 237 40.24 0 0 NA 808642 TCGA-AB-3006 AML06 8 138459902 138459902 C G SNP - - - - - - - - - - - - - - - tier3 277 7 2.46 359 212 37.06 0 0 NA 808642 TCGA-AB-3006 AML06 8 144000544 144000544 G A SNP CYP11B1 NM_000497.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42313 NULL 0.002 - - - no_errors tier2 355 14 3.79 113 71 38.59 0 0 NA 808642 TCGA-AB-3006 AML06 9 1876931 1876931 C T SNP - - - - - - - - - - - - - - - tier3 103 4 3.74 201 112 35.78 0 0 NA 808642 TCGA-AB-3006 AML06 9 7293209 7293209 C G SNP LOC100134424 XR_038546.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-18268 NULL 0.039 - - - pseudogene tier3 558 5 0.88 551 373 40.32 0 0 NA 808642 TCGA-AB-3006 AML06 9 11826399 11826399 A G SNP - - - - - - - - - - - - - - - tier2 581 3 0.51 422 250 37.2 0 0 NA 808642 TCGA-AB-3006 AML06 9 21678379 21678379 T A SNP ENSG00000220090 ENST00000404053 human ensembl 54_36p 1 known 5_prime_flanking_region c.-6796 NULL 0 - - - no_coding_region:pseudogene tier3 646 13 1.97 365 250 40.65 0 0 NA 808642 TCGA-AB-3006 AML06 9 22588959 22588959 T A SNP - - - - - - - - - - - - - - - tier3 42 1 2.33 101 49 32.67 0 0 NA 808642 TCGA-AB-3006 AML06 9 28406976 28406976 C A SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional intronic c.1-44110 e1-44110 0.001 - - - no_errors tier3 52 0 0 163 42 20.49 0 0 NA 808642 TCGA-AB-3006 AML06 9 38526982 38526982 A G SNP ENSG00000220217 ENST00000402014 human ensembl 54_36p -1 known 5_prime_flanking_region c.-31503 NULL 0.029 - - - no_coding_region:pseudogene tier3 94 1 1.05 96 59 38.06 0 0 NA 808642 TCGA-AB-3006 AML06 9 75351311 75351311 C T SNP - - - - - - - - - - - - - - - tier2 91 3 3.19 215 119 35.63 0 0 NA 808642 TCGA-AB-3006 AML06 9 75962216 75962216 G A SNP - - - - - - - - - - - - - - - tier3 226 9 3.83 263 170 39.26 0 0 NA 808642 TCGA-AB-3006 AML06 9 77208923 77208923 G A SNP ENSG00000220707 ENST00000404903 human ensembl 54_36p -1 known 5_prime_flanking_region c.-1195 NULL 0 - - - no_coding_region:pseudogene tier3 52 1 1.89 63 38 37.62 0 0 NA 808642 TCGA-AB-3006 AML06 9 79699968 79699968 C A SNP GNAQ NM_002072.2 human genbank 54_36p -1 provisional intronic c.321+26929 e2+26929 0 - - - no_errors tier2 201 1 0.5 372 290 43.74 6 10 62.5 808642 TCGA-AB-3006 AML06 9 82184654 82184654 G A SNP ENSG00000218777 ENST00000404193 human ensembl 54_36p -1 known 5_prime_flanking_region c.-19581 NULL 0.015 - - - no_coding_region:pseudogene tier3 278 5 1.77 252 155 38.08 0 0 NA 808642 TCGA-AB-3006 AML06 9 88363077 88363077 G A SNP - - - - - - - - - - - - - - - tier3 110 7 5.98 244 176 41.9 0 0 NA 808642 TCGA-AB-3006 AML06 9 97557065 97557065 T G SNP ENSG00000175611 ENST00000375268 human ensembl 54_36p -1 known 3_prime_flanking_region c.*120213 NULL 0.001 - - - no_start_codon tier3 52 0 0 88 37 29.6 0 0 NA 808642 TCGA-AB-3006 AML06 9 100086058 100086058 A T SNP TBC1D2 NM_018421.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-28414 NULL 0.001 - - - no_errors tier3 195 8 3.94 307 210 40.54 0 0 NA 808642 TCGA-AB-3006 AML06 9 103804926 103804926 T A SNP - - - - - - - - - - - - - - - tier3 266 5 1.85 346 181 34.35 0 0 NA 808642 TCGA-AB-3006 AML06 9 111077696 111077696 G C SNP EPB41L4B NM_019114.2 human genbank 54_36p -1 validated intronic c.411+4222 e2+4222 0 - - - no_errors tier2 161 4 2.42 212 134 38.73 0 0 NA 808642 TCGA-AB-3006 AML06 9 111131893 111131893 G A SNP EPB41L4B NM_019114.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9346 NULL 0.005 - - - no_errors tier3 1092 20 1.8 241 140 36.75 0 0 NA 808642 TCGA-AB-3006 AML06 9 115781231 115781231 A G SNP ZNF618 NM_133374.2 human genbank 54_36p 1 validated intronic c.78-9191 e3-9191 0 - - - no_errors tier3 221 1 0.45 194 112 36.6 0 0 0 808642 TCGA-AB-3006 AML06 9 116505893 116505893 G A SNP LOC100129633 XM_001718491.1 human genbank 54_36p -1 model intronic c.505-7561 e4-7561 0 - - - no_errors tier3 320 8 2.44 314 164 34.24 1 0 0 808642 TCGA-AB-3006 AML06 9 119697659 119697659 G A SNP LOC100129489 XM_001725742.1 human genbank 54_36p -1 model intronic c.1+1623 e0+1623 0.004 - - - no_errors tier3 173 2 1.14 184 120 39.34 0 0 NA 808642 TCGA-AB-3006 AML06 9 119734927 119734927 C T SNP LOC100129489 XM_001725742.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-57819 NULL 0.001 - - - no_errors tier3 126 6 4.55 266 233 46.6 0 0 NA 808642 TCGA-AB-3006 AML06 9 121829251 121829251 T G SNP - - - - - - - - - - - - - - - tier3 406 13 3.1 536 354 39.78 0 0 NA 808642 TCGA-AB-3006 AML06 9 124475830 124475830 C T SNP OR1L3 NM_001005234.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1400 NULL 0 - - - no_errors tier3 207 5 2.34 712 188 20.89 0 0 NA 808642 TCGA-AB-3006 AML06 9 132430372 132430372 G A SNP FUBP3 NM_003934.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-14517 NULL 0.272 - - - no_errors tier3 307 4 1.29 164 73 30.8 0 0 NA 808642 TCGA-AB-3006 AML06 10 10827633 10827633 C T SNP ENSG00000220885 ENST00000402557 human ensembl 54_36p -1 known 3_prime_flanking_region c.*30559 NULL 0.004 - - - no_coding_region:pseudogene tier3 109 1 0.91 109 76 41.08 0 0 NA 808642 TCGA-AB-3006 AML06 10 19652526 19652526 A G SNP - - - - - - - - - - - - - - - tier3 56 1 1.75 130 47 26.55 0 0 NA 808642 TCGA-AB-3006 AML06 10 26222992 26222992 G A SNP MYO3A NM_017433.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-58054 NULL 0 - - - no_errors tier3 337 7 2.03 355 171 32.51 0 0 NA 808642 TCGA-AB-3006 AML06 10 26720331 26720331 G A SNP APBB1IP NM_019043.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-100931 NULL 0.017 - - - no_errors tier2 139 0 0 331 207 38.48 0 0 NA 808642 TCGA-AB-3006 AML06 10 27219179 27219179 G A SNP ABI1 NM_005470.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29381 NULL 0 - - - no_errors tier3 124 4 3.12 147 88 37.45 0 0 NA 808642 TCGA-AB-3006 AML06 10 28723581 28723581 G A SNP ENSG00000218641 ENST00000407154 human ensembl 54_36p 1 known 5_prime_flanking_region c.-41555 NULL 0 - - - no_coding_region:pseudogene tier3 112 6 5.08 147 83 35.93 0 0 NA 808642 TCGA-AB-3006 AML06 10 43432541 43432541 C G SNP ZNF485 NM_145312.3 human genbank 54_36p 1 validated missense c.927 p.H309Q 0.995 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMSmart_KRAB,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 165 0 143 100 41.15 6 9 60 808642 TCGA-AB-3006 AML06 10 52502160 52502160 A G SNP PRKG1 NM_001098512.1 human genbank 54_36p 1 validated intronic c.266+80750 e1+80750 0.982 - - - no_errors tier3 117 4 3.31 85 65 43.33 0 0 NA 808642 TCGA-AB-3006 AML06 10 54966884 54966884 C T SNP - - - - - - - - - - - - - - - tier3 85 2 2.27 315 162 33.96 0 0 NA 808642 TCGA-AB-3006 AML06 10 56962162 56962162 G A SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+95229 e0+95229 0 - - - no_errors tier2 67 0 0 138 67 32.68 0 0 NA 808642 TCGA-AB-3006 AML06 10 59190495 59190495 C T SNP - - - - - - - - - - - - - - - tier3 52 2 3.7 97 57 37.01 0 0 NA 808642 TCGA-AB-3006 AML06 10 59296518 59296518 G C SNP - - - - - - - - - - - - - - - tier3 142 3 2.07 297 110 27.03 0 0 NA 808642 TCGA-AB-3006 AML06 10 60721124 60721124 T G SNP FAM13C NM_198215.2 human genbank 54_36p -1 validated intronic c.508-7911 e6-7911 0.001 - - - no_errors tier3 142 1 0.7 217 157 41.98 0 0 0 808642 TCGA-AB-3006 AML06 10 61262158 61262158 T C SNP CCDC6 NM_005436.3 human genbank 54_36p -1 validated intronic c.582+131 e3+131 0.001 - - - no_errors tier3 99 0 0 279 165 37.16 2 1 33.33 808642 TCGA-AB-3006 AML06 10 73431560 73431560 G C SNP CHST3 NM_004273.4 human genbank 54_36p 1 reviewed intronic c.1-3940 e1-3940 0 - - - no_errors tier3 328 4 1.2 120 77 39.09 0 0 NA 808642 TCGA-AB-3006 AML06 10 78705079 78705079 T C SNP KCNMA1 NM_001014797.1 human genbank 54_36p -1 reviewed intronic c.541-24059 e3-24059 0 - - - no_errors tier3 128 5 3.73 193 111 36.51 0 0 NA 808642 TCGA-AB-3006 AML06 10 85738059 85738059 A T SNP ENSG00000200789 ENST00000363919 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-15009 NULL 0.017 - - - no_errors tier3 195 3 1.52 198 131 39.82 0 0 NA 808642 TCGA-AB-3006 AML06 10 92478039 92478039 G C SNP ENSG00000197911 ENST00000356117 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31458 NULL 0.978 - - - no_coding_region:pseudogene tier3 212 2 0.93 210 126 37.5 0 0 NA 808642 TCGA-AB-3006 AML06 10 99330725 99330725 T C SNP ANKRD2 NM_020349.1 human genbank 54_36p 1 validated intronic c.636+25 e5+25 0.03 - - - no_errors tier3 553 15 2.63 247 135 35.06 0 0 NA 808642 TCGA-AB-3006 AML06 10 106906213 106906213 G A SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.1483-673 e10-673 0.118 - - - no_errors tier2 226 1 0.44 250 137 35.4 0 0 NA 808642 TCGA-AB-3006 AML06 10 113627387 113627387 C T SNP - - - - - - - - - - - - - - - tier3 97 0 0 167 85 33.73 0 0 NA 808642 TCGA-AB-3006 AML06 10 116282637 116282637 C T SNP ABLIM1 NM_002313.1 human genbank 54_36p -1 reviewed intronic c.894+12117 e6+12117 0 - - - no_errors tier2 397 10 2.46 233 147 38.68 0 0 NA 808642 TCGA-AB-3006 AML06 10 118482813 118482813 A G SNP HSPA12A NM_025015.2 human genbank 54_36p -1 validated intronic c.40+9118 e1+9118 0.005 - - - no_errors tier3 303 7 2.26 241 178 42.48 0 0 NA 808642 TCGA-AB-3006 AML06 10 123971437 123971437 C G SNP TACC2 NM_206862.2 human genbank 54_36p 1 reviewed intronic c.7547-2794 e11-2794 0 - - - no_errors tier3 256 5 1.92 174 111 38.81 0 0 NA 808642 TCGA-AB-3006 AML06 10 129697963 129697963 A G SNP PTPRE NM_006504.4 human genbank 54_36p 1 reviewed intronic c.1+27413 e0+27413 0.002 - - - no_errors tier3 174 5 2.79 224 140 38.46 0 0 NA 808642 TCGA-AB-3006 AML06 10 132621905 132621905 A G SNP - - - - - - - - - - - - - - - tier3 173 2 1.14 260 159 37.95 0 0 NA 808642 TCGA-AB-3006 AML06 11 3351357 3351357 C T SNP ZNF195 NM_007152.1 human genbank 54_36p -1 validated intronic c.4-1848 e2-1848 0.008 - - - no_errors tier3 207 3 1.43 222 162 42.08 2 1 33.33 808642 TCGA-AB-3006 AML06 11 4424395 4424395 A T SNP OR52K1 NM_001005171.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-42312 NULL 0.004 - - - no_errors tier3 122 2 1.61 325 160 32.99 0 0 NA 808642 TCGA-AB-3006 AML06 11 15985893 15985893 G A SNP SOX6 NM_033326.1 human genbank 54_36p -1 reviewed intronic c.1732+7171 e12+7171 0.005 - - - no_errors tier3 346 0 0 517 276 34.8 2 0 0 808642 TCGA-AB-3006 AML06 11 24103794 24103794 G A SNP - - - - - - - - - - - - - - - tier3 125 1 0.79 213 149 41.16 0 0 NA 808642 TCGA-AB-3006 AML06 11 24112388 24112388 G A SNP - - - - - - - - - - - - - - - tier3 108 5 4.42 137 66 32.51 0 0 NA 808642 TCGA-AB-3006 AML06 11 26377209 26377209 C T SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated intronic c.47-42832 e2-42832 0.002 - - - no_errors tier3 270 2 0.73 366 209 36.35 0 0 NA 808642 TCGA-AB-3006 AML06 11 27865686 27865686 C T SNP ENSG00000176668 ENST00000314102 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*2439 NULL 0 - - - no_coding_region:pseudogene tier3 422 9 2.09 479 290 37.66 0 0 NA 808642 TCGA-AB-3006 AML06 11 28706669 28706669 G A SNP - - - - - - - - - - - - - - - tier3 129 0 0 315 150 32.26 0 0 NA 808642 TCGA-AB-3006 AML06 11 31758302 31758302 A G SNP ELP4 NM_019040.3 human genbank 54_36p 1 reviewed intronic c.1144-3215 e10-3215 0 - - - no_errors tier3 142 2 1.39 247 140 35.99 2 1 33.33 808642 TCGA-AB-3006 AML06 11 42371204 42371204 G A SNP - - - - - - - - - - - - - - - tier2 173 4 2.26 284 182 39.06 0 0 NA 808642 TCGA-AB-3006 AML06 11 51250972 51250972 T C SNP OR4A5 NM_001005272.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*17052 NULL 0 - - - no_errors tier3 76 1 1.3 161 102 38.78 0 0 NA 808642 TCGA-AB-3006 AML06 11 54890879 54890879 G A SNP OR4A15 NM_001005275.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1057 NULL 0 - - - no_errors tier3 107 4 3.57 140 62 30.69 0 0 NA 808642 TCGA-AB-3006 AML06 11 56802356 56802356 G A SNP APLNR NM_005161.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-41302 NULL 0.005 - - - no_errors tier2 405 7 1.7 169 132 43.85 0 0 NA 808642 TCGA-AB-3006 AML06 11 57063540 57063540 C G SNP TIMM10 NM_012456.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-9302 NULL 0.017 - - - no_errors tier2 497 6 1.19 306 189 38.1 1 1 50 808642 TCGA-AB-3006 AML06 11 66924341 66924342 - T INS PPP1CA NM_001008709.1 human genbank 54_36p -1 reviewed intronic c.451+394_451+393 e3+394 0.003:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 11 67825627 67825627 T A SNP LRP5 NM_002335.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-11132 NULL 0.026 - - - no_errors tier3 1187 31 2.55 380 327 46.25 0 0 NA 808642 TCGA-AB-3006 AML06 11 67956410 67956410 G T SNP LRP5 NM_002335.2 human genbank 54_36p 1 validated intronic c.3764-1236 e18-1236 0.001 - - - no_errors tier3 128 5 3.76 187 113 37.67 1 4 80 808642 TCGA-AB-3006 AML06 11 70879760 70879760 C T SNP NADSYN1 NM_018161.4 human genbank 54_36p 1 validated intronic c.1694+90 e17+90 0 - - - no_errors tier3 464 19 3.93 197 144 42.23 1 1 50 808642 TCGA-AB-3006 AML06 11 72000733 72000733 A G SNP PDE2A NM_002599.1 human genbank 54_36p -1 validated intronic c.145-3290 e3-3290 0 - - - no_errors tier3 1490 39 2.55 214 110 33.95 0 0 NA 808642 TCGA-AB-3006 AML06 11 74646108 74646108 C T SNP ARRB1 NM_004041.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*8747 NULL 0.001 - - - no_errors tier3 208 2 0.95 110 85 43.59 3 3 50 808642 TCGA-AB-3006 AML06 11 79788542 79788542 G A SNP - - - - - - - - - - - - - - - tier3 239 2 0.83 398 219 35.49 0 0 NA 808642 TCGA-AB-3006 AML06 11 80362433 80362433 C T SNP - - - - - - - - - - - - - - - tier3 396 11 2.7 403 285 41.36 0 0 NA 808642 TCGA-AB-3006 AML06 11 87799043 87799043 C T SNP - - - - - - - - - - - - - - - tier3 167 2 1.18 382 168 30.55 1 2 66.67 808642 TCGA-AB-3006 AML06 11 91091065 91091065 C T SNP - - - - - - - - - - - - - - - tier3 235 1 0.42 161 101 38.55 0 0 NA 808642 TCGA-AB-3006 AML06 11 93029483 93029483 T C SNP KIAA1731 ENST00000344196 human ensembl 54_36p 1 known 5_prime_flanking_region c.-45833 NULL 0.002 - - - no_errors tier3 252 3 1.18 161 113 41.24 0 0 NA 808642 TCGA-AB-3006 AML06 11 99843629 99843629 G T SNP - - - - - - - - - - - - - - - tier2 213 5 2.28 161 87 35.08 0 0 NA 808642 TCGA-AB-3006 AML06 11 101529023 101529023 T - DEL YAP1 NM_006106.1 human genbank 54_36p 1 reviewed intronic c.573-9374 e3-9374 0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 11 103109193 103109193 A G SNP - - - - - - - - - - - - - - - tier3 130 0 0 149 103 40.87 0 0 NA 808642 TCGA-AB-3006 AML06 11 104411178 104411178 C A SNP CASP5 NM_004347.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-26302 NULL 0 - - - no_errors tier3 113 0 0 193 112 36.72 1 0 0 808642 TCGA-AB-3006 AML06 11 105699157 105699157 C T SNP - - - - - - - - - - - - - - - tier3 246 3 1.2 239 119 33.24 0 0 NA 808642 TCGA-AB-3006 AML06 11 117869938 117869938 T C SNP MLL NM_005933.2 human genbank 54_36p 1 validated intronic c.5170-275 e17-275 0.005 - - - no_errors tier3 192 7 3.52 293 208 41.52 2 0 0 808642 TCGA-AB-3006 AML06 11 120468238 120468238 G - DEL TECTA NM_005422.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-10347 NULL 0.014 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 11 121260124 121260124 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 11 122602636 122602636 G A SNP ASAM NM_024769.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-31778 NULL 0.001 - - - no_errors tier2 180 4 2.17 281 178 38.78 0 0 NA 808642 TCGA-AB-3006 AML06 11 130489324 130489324 C T SNP ENSG00000221516 ENST00000408589 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2204 NULL 0.002 - - - no_errors tier3 204 12 5.48 365 194 34.64 0 0 NA 808642 TCGA-AB-3006 AML06 11 132620291 132620291 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+287078 e1+287078 0 - - - no_errors tier3 225 3 1.32 179 122 40.53 0 0 NA 808642 TCGA-AB-3006 AML06 11 132906289 132906289 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+1080 e1+1080 0.876 - - - no_errors tier3 392 24 5.77 323 211 39.51 0 0 NA 808642 TCGA-AB-3006 AML06 12 744136 744136 A T SNP WNK1 NM_018979.2 human genbank 54_36p 1 validated intronic c.759+10385 e1+10385 0 - - - no_errors tier3 263 5 1.87 150 115 43.4 4 4 50 808642 TCGA-AB-3006 AML06 12 3931422 3931422 G A SNP - - - - - - - - - - - - - - - tier3 184 7 3.65 226 158 41.15 0 0 NA 808642 TCGA-AB-3006 AML06 12 3949838 3949838 T G SNP - - - - - - - - - - - - - - - tier3 87 0 0 46 21 31.34 0 0 NA 808642 TCGA-AB-3006 AML06 12 15518072 15518072 A G SNP PTPRO NM_030667.2 human genbank 54_36p 1 reviewed intronic c.76-10103 e2-10103 0.005 - - - no_errors tier3 61 4 6.15 114 68 37.36 0 0 NA 808642 TCGA-AB-3006 AML06 12 16621521 16621521 G A SNP LMO3 NM_001001395.1 human genbank 54_36p -1 validated intronic c.207-16782 e2-16782 0.01 - - - no_errors tier3 58 0 0 145 97 40.08 0 0 NA 808642 TCGA-AB-3006 AML06 12 17260926 17260926 C T SNP - - - - - - - - - - - - - - - tier2 244 6 2.4 274 138 33.41 0 0 NA 808642 TCGA-AB-3006 AML06 12 17549587 17549587 C T SNP - - - - - - - - - - - - - - - tier2 170 7 3.95 177 105 37.23 0 0 NA 808642 TCGA-AB-3006 AML06 12 19996280 19996280 G A SNP ENSG00000221679 ENST00000408752 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20786 NULL 0.152 - - - no_errors tier3 157 5 3.09 205 111 35.13 0 0 NA 808642 TCGA-AB-3006 AML06 12 22091207 22091207 T G SNP CMAS NM_018686.3 human genbank 54_36p 1 reviewed intronic c.260+443 e1+443 0 - - - no_errors tier3 209 4 1.88 216 130 37.57 2 2 50 808642 TCGA-AB-3006 AML06 12 30232663 30232663 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 12 33811811 33811811 G T SNP - - - - - - - - - - - - - - - tier3 359 4 1.1 337 213 38.66 0 0 NA 808642 TCGA-AB-3006 AML06 12 37494882 37494882 A G SNP CPNE8 NM_153634.2 human genbank 54_36p -1 reviewed intronic c.407+14566 e6+14566 0.012 - - - no_errors tier3 85 3 3.41 221 123 35.76 1 4 80 808642 TCGA-AB-3006 AML06 12 39133268 39133268 C T SNP MUC19 XM_497341.1 human genbank 54_36p 1 model intronic c.3307+2483 e29+2483 0.004 - - - no_errors tier3 54 0 0 71 42 37.17 0 0 NA 808642 TCGA-AB-3006 AML06 12 39233938 39233938 G A SNP MUC19 ENST00000380816 human ensembl 54_36p 1 known intronic c.991+3135 e19+3135 0.19 - - - no_start_codon tier2 210 4 1.87 182 91 33.33 0 0 0 808642 TCGA-AB-3006 AML06 12 43333465 43333465 G T SNP NELL2 NM_006159.1 human genbank 54_36p -1 reviewed intronic c.1444+12069 e13+12069 0.001 - - - no_errors tier3 113 2 1.74 268 140 34.31 1 0 0 808642 TCGA-AB-3006 AML06 12 50110925 50110925 G - DEL SLC4A8 NM_001039960.1 human genbank 54_36p 1 validated intronic c.48+5839 e1+5839 0.057 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 12 51708259 51708259 G A SNP EIF4B NM_001417.4 human genbank 54_36p 1 validated intronic c.979+20 e8+20 0 - - - no_errors tier3 164 3 1.8 143 71 33.18 3 6 60 808642 TCGA-AB-3006 AML06 12 56312117 56312117 G A SNP B4GALNT1 NM_001478.3 human genbank 54_36p -1 reviewed silent c.66 p.L22 0.988 NULL "HMMPfam_Glycos_transf_2,superfamily_SSF53448" - no_errors tier1 216 4 1.82 118 84 41.58 NA 808642 TCGA-AB-3006 AML06 12 57576541 57576541 A T SNP LRIG3 NM_153377.1 human genbank 54_36p -1 provisional intronic c.384-5696 e4-5696 0.001 - - - no_errors tier3 205 2 0.97 281 166 37.14 0 0 NA 808642 TCGA-AB-3006 AML06 12 60054166 60054166 C A SNP - - - - - - - - - - - - - - - tier3 308 15 4.62 199 93 31.85 0 0 NA 808642 TCGA-AB-3006 AML06 12 60925421 60925421 A G SNP USP15 NM_006313.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-15042 NULL 0.004 - - - no_errors tier3 56 2 3.45 198 133 40.06 2 1 33.33 808642 TCGA-AB-3006 AML06 12 65624658 65624658 G A SNP - - - - - - - - - - - - - - - tier3 284 4 1.39 152 114 42.54 0 0 NA 808642 TCGA-AB-3006 AML06 12 70889300 70889300 G A SNP - - - - - - - - - - - - - - - tier2 307 7 2.23 209 170 44.85 0 0 NA 808642 TCGA-AB-3006 AML06 12 77756495 77756495 T - DEL LOC100129021 XM_001714516.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-25625 NULL 0.024 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 12 82209590 82209590 C A SNP - - - - - - - - - - - - - - - tier3 110 4 3.51 237 130 35.33 0 0 NA 808642 TCGA-AB-3006 AML06 12 84107467 84107467 T G SNP LRRIQ1 NM_001079910.1 human genbank 54_36p 1 validated intronic c.4822+28844 e23+28844 0.032 - - - no_errors tier3 45 0 0 125 82 39.61 0 0 NA 808642 TCGA-AB-3006 AML06 12 84622910 84622910 C T SNP - - - - - - - - - - - - - - - tier3 105 1 0.94 233 165 41.46 0 0 NA 808642 TCGA-AB-3006 AML06 12 88734818 88734818 C T SNP - - - - - - - - - - - - - - - tier3 153 2 1.29 264 133 33.5 0 0 NA 808642 TCGA-AB-3006 AML06 12 92420500 92420500 T C SNP MRPL42 NM_014050.2 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*1372 NULL 0.001 - - - no_errors tier3 39 2 4.88 61 70 53.44 7 9 56.25 808642 TCGA-AB-3006 AML06 12 94339928 94339928 G A SNP ENSG00000222544 ENST00000410612 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*16716 NULL 0.054 - - - no_errors tier3 355 11 3 132 79 37.44 0 0 NA 808642 TCGA-AB-3006 AML06 12 94451003 94451003 A G SNP USP44 NM_001042403.1 human genbank 54_36p -1 validated silent c.1161 p.T387 0.997 "HMMPfam_UCH,superfamily_Cysteine proteinases" "HMMPfam_UCH,HMMPfam_zf-UBP,HMMSmart_SM00290,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_Cysteine proteinases" - no_errors tier1 172 5 2.82 258 158 37.98 12 9 42.86 808642 TCGA-AB-3006 AML06 12 96997823 96997823 G A SNP - - - - - - - - - - - - - - - tier3 96 2 2.04 106 50 32.05 0 0 NA 808642 TCGA-AB-3006 AML06 12 103414788 103414788 T C SNP CHST11 NM_018413.4 human genbank 54_36p 1 provisional intronic c.118+39351 e1+39351 0.003 - - - no_errors tier3 171 4 2.29 192 117 37.74 9 10 52.63 808642 TCGA-AB-3006 AML06 12 117570323 117570323 G A SNP - - - - - - - - - - - - - - - tier2 206 5 2.37 344 226 39.58 0 0 NA 808642 TCGA-AB-3006 AML06 12 118157373 118157373 G A SNP HSPB8 NM_014365.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*41327 NULL 0 - - - no_errors tier3 614 10 1.6 335 190 36.12 0 0 NA 808642 TCGA-AB-3006 AML06 12 120739645 120739645 C T SNP RHOF NM_019034.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23723 NULL 0 - - - no_errors tier2 143 0 0 100 66 39.76 3 1 25 808642 TCGA-AB-3006 AML06 12 126521531 126521531 G A SNP - - - - - - - - - - - - - - - tier3 154 7 4.35 206 96 31.79 0 0 NA 808642 TCGA-AB-3006 AML06 12 128219095 128219095 G A SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.1443+40923 e5+40923 0.005 - - - no_errors tier3 190 5 2.56 248 175 41.37 0 0 NA 808642 TCGA-AB-3006 AML06 13 22142638 22142638 G T SNP ENSG00000218515 ENST00000405171 human ensembl 54_36p -1 known 3_prime_flanking_region c.*25524 NULL 0 - - - no_coding_region:pseudogene tier3 209 2 0.95 215 93 30.19 0 0 NA 808642 TCGA-AB-3006 AML06 13 25241635 25241635 G A SNP ATP8A2 NM_016529.4 human genbank 54_36p 1 validated intronic c.2568+268 e26+268 0.015 - - - no_errors tier3 290 11 3.65 299 210 41.18 0 0 NA 808642 TCGA-AB-3006 AML06 13 25990078 25990078 G - DEL WASF3 NM_006646.5 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-124330 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 13 26000531 26000531 A G SNP WASF3 NM_006646.5 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-113877 NULL 0 - - - no_errors tier2 148 11 6.88 108 75 40.98 0 0 NA 808642 TCGA-AB-3006 AML06 13 26207492 26207492 G A SNP WASF3 NM_006646.5 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*49510 NULL 0 - - - no_errors tier2 74 2 2.56 59 31 33.7 0 0 NA 808642 TCGA-AB-3006 AML06 13 27506262 27506263 - TCATATTCTCTGAAATCAACGTAGAAGTACTCA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1793 p.598in_frame_insDEYFYVDFREY 0.821 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 808642 TCGA-AB-3006 AML06 13 28337785 28337785 G A SNP - - - - - - - - - - - - - - - tier2 278 11 3.81 295 195 39.8 0 0 0 808642 TCGA-AB-3006 AML06 13 36763022 36763022 C T SNP - - - - - - - - - - - - - - - tier3 195 4 2 147 89 37.55 0 0 NA 808642 TCGA-AB-3006 AML06 13 43660176 43660176 G A SNP ENSG00000139656 ENST00000267129 human ensembl 54_36p -1 known 5_prime_flanking_region c.-27185 NULL 0.002 - - - no_errors tier3 214 7 3.17 293 200 40.49 0 0 NA 808642 TCGA-AB-3006 AML06 13 44329687 44329687 T - DEL LOC144817 XR_040343.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-47921 NULL 0.01 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 13 44390167 44390167 G C SNP NUFIP1 NM_012345.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*23174 NULL 0.739 - - - no_errors tier2 216 12 5.26 267 191 41.7 0 0 NA 808642 TCGA-AB-3006 AML06 13 53328785 53328785 C T SNP - - - - - - - - - - - - - - - tier3 75 0 0 48 38 44.19 0 0 NA 808642 TCGA-AB-3006 AML06 13 53918172 53918172 G A SNP LOC100128485 XM_001717043.1 human genbank 54_36p 1 model intronic c.457+4693 e1+4693 0.005 - - - no_errors tier2 181 3 1.63 167 113 40.36 0 0 NA 808642 TCGA-AB-3006 AML06 13 55244124 55244124 G A SNP - - - - - - - - - - - - - - - tier3 107 3 2.73 136 91 40.09 0 0 NA 808642 TCGA-AB-3006 AML06 13 55550363 55550363 T - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 13 57768383 57768383 C T SNP - - - - - - - - - - - - - - - tier3 108 2 1.82 92 61 39.87 0 0 NA 808642 TCGA-AB-3006 AML06 13 58488598 58488598 G A SNP ENSG00000219286 ENST00000402266 human ensembl 54_36p -1 known 5_prime_flanking_region c.-5857 NULL 0 - - - no_coding_region:pseudogene tier3 467 15 3.11 323 196 37.76 0 0 NA 808642 TCGA-AB-3006 AML06 13 63108769 63108769 T C SNP - - - - - - - - - - - - - - - tier2 188 2 1.05 275 178 39.29 0 0 NA 808642 TCGA-AB-3006 AML06 13 68605244 68605244 A G SNP ENSG00000216426 ENST00000401939 human ensembl 54_36p -1 known 5_prime_flanking_region c.-31055 NULL 0 - - - no_coding_region:pseudogene tier3 86 1 1.15 134 67 33.33 0 0 NA 808642 TCGA-AB-3006 AML06 13 75311199 75311199 C T SNP LMO7 NM_005358.5 human genbank 54_36p 1 reviewed intronic c.2605+866 e19+866 0 - - - no_errors tier3 83 1 1.19 166 91 35.41 1 0 0 808642 TCGA-AB-3006 AML06 13 83163831 83163831 G A SNP - - - - - - - - - - - - - - - tier3 723 8 1.09 356 200 35.97 0 0 NA 808642 TCGA-AB-3006 AML06 13 83184557 83184557 C T SNP - - - - - - - - - - - - - - - tier3 42 1 2.33 168 115 40.64 0 0 NA 808642 TCGA-AB-3006 AML06 13 89746893 89746893 C T SNP - - - - - - - - - - - - - - - tier2 61 0 0 196 86 30.5 0 0 NA 808642 TCGA-AB-3006 AML06 13 91850572 91850572 T G SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1561+255329 e7+255329 0 - - - no_errors tier3 160 2 1.23 215 96 30.87 0 0 NA 808642 TCGA-AB-3006 AML06 13 95890173 95890173 C T SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+348349 e1+348349 0.002 - - - no_errors tier3 128 4 3.03 137 101 42.26 0 0 NA 808642 TCGA-AB-3006 AML06 13 100748375 100748375 C A SNP NALCN NM_052867.2 human genbank 54_36p -1 validated intronic c.800-5657 e7-5657 0.001 - - - no_errors tier3 182 1 0.55 360 199 35.6 0 0 NA 808642 TCGA-AB-3006 AML06 13 103179938 103179938 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 13 107303898 107303898 G C SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.915+12133 e1+12133 0.001 - - - no_errors tier3 49 2 3.92 100 57 36.31 0 0 NA 808642 TCGA-AB-3006 AML06 13 108977528 108977528 G T SNP - - - - - - - - - - - - - - - tier3 299 5 1.64 498 302 37.75 0 0 NA 808642 TCGA-AB-3006 AML06 13 110881180 110881180 C T SNP - - - - - - - - - - - - - - - tier3 774 8 1.02 145 112 43.41 0 0 NA 808642 TCGA-AB-3006 AML06 14 27354779 27354779 G T SNP - - - - - - - - - - - - - - - tier3 80 2 2.44 70 37 34.58 0 0 NA 808642 TCGA-AB-3006 AML06 14 29878553 29878553 T C SNP - - - - - - - - - - - - - - - tier3 105 4 3.67 171 142 45.37 0 0 NA 808642 TCGA-AB-3006 AML06 14 30238304 30238304 C G SNP SCFD1 NM_016106.2 human genbank 54_36p 1 validated intronic c.1340-841 e16-841 0.002 - - - no_errors tier2 117 9 7.09 167 87 34.12 1 2 66.67 808642 TCGA-AB-3006 AML06 14 32073069 32073069 A T SNP AKAP6 NM_004274.4 human genbank 54_36p 1 reviewed intronic c.325-1442 e2-1442 0 - - - no_errors tier2 59 0 0 149 91 37.92 0 0 NA 808642 TCGA-AB-3006 AML06 14 32872033 32872033 C A SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.347-34110 e4-34110 0 - - - no_errors tier3 227 5 2.16 330 190 36.54 0 0 NA 808642 TCGA-AB-3006 AML06 14 35544827 35544827 G T SNP - - - - - - - - - - - - - - - tier3 156 6 3.7 201 133 39.82 0 0 NA 808642 TCGA-AB-3006 AML06 14 37745629 37745629 A T SNP SSTR1 NM_001049.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2717 NULL 0.001 - - - no_errors tier3 66 1 1.49 104 68 39.53 0 0 NA 808642 TCGA-AB-3006 AML06 14 40287302 40287302 C T SNP - - - - - - - - - - - - - - - tier3 54 0 0 186 72 27.8 0 0 NA 808642 TCGA-AB-3006 AML06 14 41945126 41945126 G T SNP - - - - - - - - - - - - - - - tier3 277 5 1.77 484 283 36.85 0 0 NA 808642 TCGA-AB-3006 AML06 14 45988916 45988916 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 14 71566044 71566044 C T SNP RGS6 NM_004296.4 human genbank 54_36p 1 validated intronic c.84+64699 e1+64699 0.001 - - - no_errors tier2 123 3 2.38 503 296 37 0 0 NA 808642 TCGA-AB-3006 AML06 14 71966978 71966978 T C SNP RGS6 NM_004296.4 human genbank 54_36p 1 validated intronic c.185-24011 e3-24011 0.005 - - - no_errors tier3 307 23 6.97 444 283 38.93 0 0 NA 808642 TCGA-AB-3006 AML06 14 74789254 74789254 G A SNP LOC730011 XM_001132072.2 human genbank 54_36p -1 model intronic c.91-13609 e2-13609 0.001 - - - no_errors tier3 419 10 2.33 367 241 39.57 0 0 NA 808642 TCGA-AB-3006 AML06 14 77968111 77968111 T A SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.1+28137 e0+28137 0 - - - no_errors tier3 153 6 3.77 147 129 46.74 0 0 NA 808642 TCGA-AB-3006 AML06 14 78625973 78625973 C T SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2143+101736 e10+101736 0.001 - - - no_errors tier3 175 1 0.57 238 149 38.5 0 0 NA 808642 TCGA-AB-3006 AML06 14 79740682 79740682 C T SNP DIO2 ENST00000388841 human ensembl 54_36p -1 known intronic c.223-1298 e2-1298 0.995 - - - no_errors tier2 166 3 1.76 255 117 31.37 0 0 NA 808642 TCGA-AB-3006 AML06 14 79844394 79844394 G A SNP - - - - - - - - - - - - - - - tier3 423 8 1.86 813 510 38.52 0 0 NA 808642 TCGA-AB-3006 AML06 14 80341316 80341316 C G SNP C14orf145 NM_152446.3 human genbank 54_36p -1 validated intronic c.1210-12109 e12-12109 0.003 - - - no_errors tier3 76 2 2.56 149 89 37.39 0 0 0 808642 TCGA-AB-3006 AML06 14 80517439 80517439 G A SNP TSHR NM_000369.2 human genbank 54_36p 1 reviewed intronic c.170+25492 e1+25492 0.029 - - - no_errors tier3 258 7 2.64 224 110 32.93 0 0 NA 808642 TCGA-AB-3006 AML06 14 84580895 84580895 G T SNP - - - - - - - - - - - - - - - tier3 141 6 4.08 137 106 43.62 0 0 NA 808642 TCGA-AB-3006 AML06 14 91508264 91508264 G A SNP TRIP11 NM_004239.2 human genbank 54_36p -1 validated intronic c.5719+550 e20+550 0.001 - - - no_errors tier3 259 1 0.38 367 251 40.61 3 2 40 808642 TCGA-AB-3006 AML06 14 91848948 91848948 G A SNP SLC24A4 NM_153646.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-11031 NULL 0 - - - no_errors tier3 115 0 0 103 68 39.77 0 0 NA 808642 TCGA-AB-3006 AML06 14 94785069 94785069 G T SNP CLMN NM_024734.3 human genbank 54_36p -1 validated intronic c.83-18846 e2-18846 0.001 - - - no_errors tier3 45 1 2.17 61 20 24.69 0 0 0 808642 TCGA-AB-3006 AML06 14 98142330 98142330 C T SNP - - - - - - - - - - - - - - - tier3 368 7 1.86 255 138 35.11 0 0 NA 808642 TCGA-AB-3006 AML06 15 22894517 22894517 A T SNP SNORD116-26 NR_003340.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-1221 NULL 0.001 - - - no_errors tier3 30 1 3.23 160 84 34.43 0 0 0 808642 TCGA-AB-3006 AML06 15 24061031 24061031 G C SNP - - - - - - - - - - - - - - - tier3 123 2 1.6 278 136 32.85 0 0 NA 808642 TCGA-AB-3006 AML06 15 25331818 25331819 - A INS GABRG3 ENST00000333743 human ensembl 54_36p 1 known intronic c.575-67573_575-67572 e6-67572 0.007:0.011 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 15 25521202 25521202 C T SNP - - - - - - - - - - - - - - - tier3 258 4 1.53 268 147 35.34 0 0 NA 808642 TCGA-AB-3006 AML06 15 25735188 25735188 C T SNP OCA2 NM_000275.2 human genbank 54_36p -1 reviewed intronic c.2432+28512 e22+28512 0 - - - no_errors tier2 171 6 3.39 344 210 37.91 0 0 NA 808642 TCGA-AB-3006 AML06 15 27236705 27236705 G T SNP uc010azk.1 ENST00000261275 human ensembl 54_36p -1 known intronic c.121-5369 e2-5369 0.007 - - - no_start_codon tier3 773 21 2.64 260 168 39.25 0 0 NA 808642 TCGA-AB-3006 AML06 15 33453412 33453412 G A SNP ATPBD4 NM_080650.1 human genbank 54_36p -1 validated intronic c.663-311 e8-311 0.891 - - - no_errors tier2 152 4 2.55 281 167 37.28 0 0 0 808642 TCGA-AB-3006 AML06 15 39291012 39291012 A G SNP EXD1 NM_152596.2 human genbank 54_36p -1 provisional intronic c.274-1935 e5-1935 0 - - - no_errors tier3 85 0 0 92 44 32.35 0 0 NA 808642 TCGA-AB-3006 AML06 15 56076020 56076020 G A SNP ALDH1A2 NM_003888.2 human genbank 54_36p -1 reviewed intronic c.494-1391 e5-1391 0.003 - - - no_errors tier2 53 1 1.85 70 47 39.83 0 0 NA 808642 TCGA-AB-3006 AML06 15 56242803 56242803 G A SNP AQP9 NM_020980.3 human genbank 54_36p 1 reviewed intronic c.112-3361 e2-3361 0.015 - - - no_errors tier3 270 5 1.82 303 173 36.34 0 0 NA 808642 TCGA-AB-3006 AML06 15 57314807 57314807 A G SNP MYO1E NM_004998.2 human genbank 54_36p -1 validated intronic c.420+1269 e5+1269 0.003 - - - no_errors tier3 271 7 2.51 179 102 35.92 0 0 NA 808642 TCGA-AB-3006 AML06 15 57957734 57957734 C T SNP ENSG00000220585 ENST00000404391 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4748 NULL 0.349 - - - no_coding_region:pseudogene tier2 356 10 2.73 235 161 40.66 0 0 NA 808642 TCGA-AB-3006 AML06 15 76172361 76172361 G A SNP SH2D7 NM_001101404.1 human genbank 54_36p 1 provisional intronic c.176+204 e1+204 0 - - - no_errors tier3 78 1 1.27 89 54 37.5 0 0 NA 808642 TCGA-AB-3006 AML06 15 86350888 86350888 G A SNP NTRK3 NM_001012338.1 human genbank 54_36p -1 reviewed intronic c.1585+26204 e12+26204 0.001 - - - no_errors tier3 365 8 2.14 400 290 42.03 0 0 NA 808642 TCGA-AB-3006 AML06 15 91647188 91647188 A - DEL ENSG00000212063 ENST00000390774 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16632 NULL 0.008 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 15 93086235 93086235 A G SNP - - - - - - - - - - - - - - - tier3 517 16 2.99 423 233 35.52 0 0 NA 808642 TCGA-AB-3006 AML06 15 93825799 93825799 G A SNP - - - - - - - - - - - - - - - tier3 457 17 3.58 189 170 47.35 0 0 NA 808642 TCGA-AB-3006 AML06 15 94211359 94211359 T C SNP - - - - - - - - - - - - - - - tier3 284 7 2.41 269 166 37.99 0 0 NA 808642 TCGA-AB-3006 AML06 15 95580830 95580830 C G SNP - - - - - - - - - - - - - - - tier2 148 0 0 244 130 34.76 0 0 NA 808642 TCGA-AB-3006 AML06 16 3526995 3526995 G A SNP CLUAP1 NM_024793.1 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*723 NULL 0.001 - - - no_errors tier3 289 7 2.36 258 152 36.89 7 7 50 808642 TCGA-AB-3006 AML06 16 5778715 5778715 C T SNP ENSG00000221257 ENST00000408330 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27925 NULL 0.347 - - - no_errors tier3 919 11 1.18 411 265 39.2 0 0 NA 808642 TCGA-AB-3006 AML06 16 8075275 8075275 G A SNP - - - - - - - - - - - - - - - tier3 451 7 1.53 438 230 34.43 0 0 NA 808642 TCGA-AB-3006 AML06 16 8524068 8524068 A T SNP LOC283953 XM_208930.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*35708 NULL 0.895 - - - no_errors tier3 426 8 1.83 348 261 42.86 0 0 NA 808642 TCGA-AB-3006 AML06 16 13143727 13143727 G A SNP - - - - - - - - - - - - - - - tier3 365 10 2.67 183 117 38.87 0 0 NA 808642 TCGA-AB-3006 AML06 16 16578539 16578539 T C SNP - - - - - - - - - - - - - - - tier3 341 3 0.87 131 91 40.99 0 0 NA 808642 TCGA-AB-3006 AML06 16 22305030 22305030 T A SNP LOC100129767 XR_039365.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - pseudogene tier2 91 2 2.15 130 72 35.64 0 2 100 808642 TCGA-AB-3006 AML06 16 25244557 25244557 C T SNP - - - - - - - - - - - - - - - tier3 111 4 3.48 248 172 40.86 0 0 NA 808642 TCGA-AB-3006 AML06 16 25624926 25624926 A T SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.734+12953 e1+12953 0.005 - - - no_errors tier2 149 3 1.97 179 121 40.33 0 0 NA 808642 TCGA-AB-3006 AML06 16 26375941 26375941 G A SNP - - - - - - - - - - - - - - - tier3 392 8 2 395 273 40.87 0 0 NA 808642 TCGA-AB-3006 AML06 16 31002400 31002400 C T SNP POL3S NM_001039503.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*212 NULL 0.001 - - - no_errors tier3 96 2 2.04 138 79 36.41 2 1 33.33 808642 TCGA-AB-3006 AML06 16 45359372 45359372 T C SNP MYLK3 NM_182493.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19766 NULL 0.033 - - - no_errors tier3 416 5 1.19 269 176 39.55 0 0 NA 808642 TCGA-AB-3006 AML06 16 53166563 53166563 G A SNP - - - - - - - - - - - - - - - tier3 111 1 0.88 222 73 24.66 0 0 NA 808642 TCGA-AB-3006 AML06 16 53166569 53166569 G A SNP - - - - - - - - - - - - - - - tier3 119 1 0.83 232 84 26.58 0 0 NA 808642 TCGA-AB-3006 AML06 16 54488470 54488470 C T SNP CES7 NM_145024.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-21836 NULL 0.003 - - - no_errors tier3 64 5 7.25 115 74 38.95 0 0 NA 808642 TCGA-AB-3006 AML06 16 63185635 63185635 G A SNP - - - - - - - - - - - - - - - tier3 377 2 0.53 211 161 43.05 0 0 NA 808642 TCGA-AB-3006 AML06 16 64436439 64436439 T G SNP - - - - - - - - - - - - - - - tier3 429 10 2.28 372 234 38.61 0 0 NA 808642 TCGA-AB-3006 AML06 16 72257964 72257964 C T SNP - - - - - - - - - - - - - - - tier3 458 8 1.72 394 259 39.66 0 0 NA 808642 TCGA-AB-3006 AML06 16 76171086 76171086 C A SNP - - - - - - - - - - - - - - - tier3 165 3 1.79 235 124 34.44 1 0 0 808642 TCGA-AB-3006 AML06 16 78462975 78462975 C T SNP - - - - - - - - - - - - - - - tier2 272 11 3.89 271 188 40.96 0 0 NA 808642 TCGA-AB-3006 AML06 16 78954067 78954067 G A SNP LOC729847 XM_001131495.1 human genbank 54_36p -1 model intronic c.191+129901 e1+129901 0.998 - - - no_errors tier2 461 23 4.75 472 261 35.56 0 0 NA 808642 TCGA-AB-3006 AML06 16 82328319 82328319 C T SNP CDH13 NM_001257.3 human genbank 54_36p 1 reviewed intronic c.1539-10895 e11-10895 0 - - - no_errors tier2 280 5 1.75 335 208 38.24 0 0 NA 808642 TCGA-AB-3006 AML06 16 82840211 82840211 C T SNP KCNG4 NM_172347.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11619 NULL 0.016 - - - no_errors tier3 262 8 2.96 211 97 31.49 0 0 NA 808642 TCGA-AB-3006 AML06 16 86217920 86217920 C T SNP JPH3 NM_020655.2 human genbank 54_36p 1 reviewed intronic c.383-17445 e2-17445 0.004 - - - no_errors tier3 75 1 1.32 213 187 46.75 0 0 NA 808642 TCGA-AB-3006 AML06 17 2978464 2978464 C A SNP OR1G1 NM_003555.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-869 NULL 0 - - - no_errors tier3 390 2 0.51 593 355 37.41 0 0 NA 808642 TCGA-AB-3006 AML06 17 10461401 10461401 G A SNP LOC100134147 XM_001716952.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-19760 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier2 175 8 4.37 215 144 39.89 0 0 NA 808642 TCGA-AB-3006 AML06 17 11440734 11440734 G A SNP DNAH9 NM_001372.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1807 NULL 0 - - - no_errors tier2 181 10 5.18 293 161 35.46 0 0 NA 808642 TCGA-AB-3006 AML06 17 16658715 16658715 G A SNP ENSG00000205310 ENST00000379570 human ensembl 54_36p 1 known 5_prime_flanking_region c.-39259 NULL 0 - - - no_coding_region:pseudogene tier3 124 4 3.12 271 90 24.79 0 0 NA 808642 TCGA-AB-3006 AML06 17 28196464 28196464 A G SNP MYO1D NM_015194.1 human genbank 54_36p -1 provisional intronic c.95+31445 e1+31445 0.013 - - - no_errors tier3 108 1 0.92 291 190 39.5 0 0 NA 808642 TCGA-AB-3006 AML06 17 32482279 32482279 C A SNP AATF NM_012138.3 human genbank 54_36p 1 reviewed intronic c.1620-5735 e12-5735 0 - - - no_errors tier3 632 11 1.71 341 179 34.42 2 4 66.67 808642 TCGA-AB-3006 AML06 17 44805251 44805251 C T SNP ZNF652 NM_014897.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-55165 NULL 0 - - - no_errors tier3 594 20 3.26 500 347 40.82 0 0 NA 808642 TCGA-AB-3006 AML06 17 46022948 46022948 T C SNP CACNA1G NM_018896.3 human genbank 54_36p 1 validated missense c.2419 p.Y807H 1 "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" "HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels" - no_errors tier1 383 1 0.26 425 297 41.02 NA 808642 TCGA-AB-3006 AML06 17 47089732 47089732 G T SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.466-3636 e5-3636 0 - - - no_errors tier3 326 7 2.1 306 191 38.43 0 0 NA 808642 TCGA-AB-3006 AML06 17 51945357 51945357 C T SNP ANKFN1 NM_153228.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*30450 NULL 0.005 - - - no_errors tier3 72 6 7.69 192 94 32.87 0 0 NA 808642 TCGA-AB-3006 AML06 17 66149855 66149856 - T INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 17 70323709 70323710 AG - DEL TMEM104 NM_017728.3 human genbank 54_36p 1 validated intronic c.637-3775_637-3774 e8-3774 0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 17 71003592 71003592 A G SNP KIAA0195 NM_014738.4 human genbank 54_36p 1 validated intronic c.2945-50 e22-50 0 - - - no_errors tier3 359 16 4.23 171 113 39.65 1 0 0 808642 TCGA-AB-3006 AML06 18 572504 572504 G A SNP CLUL1 NM_014410.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-35497 NULL 0.001 - - - no_errors tier3 121 2 1.63 339 170 33.4 0 0 NA 808642 TCGA-AB-3006 AML06 18 5483331 5483331 C T SNP EPB41L3 NM_012307.2 human genbank 54_36p -1 provisional intronic c.1-4138 e1-4138 0 - - - no_errors tier3 94 0 0 184 75 28.96 0 0 NA 808642 TCGA-AB-3006 AML06 18 6703012 6703012 G C SNP - - - - - - - - - - - - - - - tier3 226 1 0.44 310 128 29.22 0 0 NA 808642 TCGA-AB-3006 AML06 18 17223689 17223689 T C SNP KIAA1772 ENST00000400483 human ensembl 54_36p 1 known intronic c.355+5327 e2+5327 0.039 - - - no_stop_codon tier3 89 1 1.11 140 122 46.56 0 0 NA 808642 TCGA-AB-3006 AML06 18 20776458 20776458 C T SNP - - - - - - - - - - - - - - - tier2 196 5 2.49 224 141 38.63 0 0 NA 808642 TCGA-AB-3006 AML06 18 28745702 28745702 C T SNP C18orf34 NM_001105528.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*26271 NULL 0.957 - - - no_errors tier2 76 1 1.27 244 129 34.58 0 0 NA 808642 TCGA-AB-3006 AML06 18 33211183 33211183 G A SNP BRUNOL4 NM_020180.1 human genbank 54_36p -1 reviewed intronic c.370-55341 e3-55341 0.003 - - - no_errors tier2 492 16 3.14 503 375 42.71 0 0 NA 808642 TCGA-AB-3006 AML06 18 36776142 36776142 C T SNP - - - - - - - - - - - - - - - tier3 94 1 1.05 134 98 42.24 0 0 NA 808642 TCGA-AB-3006 AML06 18 36985821 36985821 T A SNP - - - - - - - - - - - - - - - tier2 219 10 4.37 302 184 37.7 0 0 NA 808642 TCGA-AB-3006 AML06 18 37800780 37800781 - A INS PIK3C3 NM_002647.2 human genbank 54_36p 1 validated intronic c.402-3509_402-3508 e4-3508 0.082:0.072 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 18 38888090 38888090 C A SNP RIT2 NM_002930.2 human genbank 54_36p -1 provisional intronic c.104-20260 e2-20260 0 - - - no_errors tier3 403 11 2.65 281 184 39.57 0 0 NA 808642 TCGA-AB-3006 AML06 18 39939576 39939576 T G SNP ENSG00000202060 ENST00000365190 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33912 NULL 0 - - - no_errors tier3 301 11 3.51 174 124 41.47 0 0 NA 808642 TCGA-AB-3006 AML06 18 40298227 40298227 C A SNP - - - - - - - - - - - - - - - tier3 136 3 2.16 74 44 37.29 0 0 NA 808642 TCGA-AB-3006 AML06 18 53151688 53151688 C T SNP ST8SIA3 NM_015879.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-19388 NULL 0 - - - no_errors tier2 501 17 3.28 467 278 37.32 0 0 NA 808642 TCGA-AB-3006 AML06 18 54447723 54447723 G T SNP MALT1 NM_006785.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-42133 NULL 0 - - - no_errors tier3 269 17 5.9 173 116 39.86 0 0 NA 808642 TCGA-AB-3006 AML06 18 58807640 58807640 C T SNP PHLPP NM_194449.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*9996 NULL 0.078 - - - no_errors tier3 262 6 2.24 265 158 37.26 0 0 NA 808642 TCGA-AB-3006 AML06 18 62880655 62880655 G A SNP - - - - - - - - - - - - - - - tier3 98 1 1.01 123 64 34.22 0 0 NA 808642 TCGA-AB-3006 AML06 18 63150448 63150448 G A SNP - - - - - - - - - - - - - - - tier3 80 5 5.88 192 110 36.42 0 0 NA 808642 TCGA-AB-3006 AML06 18 68222062 68222062 G T SNP - - - - - - - - - - - - - - - tier3 110 1 0.9 148 78 34.51 0 0 NA 808642 TCGA-AB-3006 AML06 18 70108255 70108255 T A SNP CYB5A NM_148923.2 human genbank 54_36p -1 validated intronic c.129+1707 e1+1707 0 - - - no_errors tier3 163 1 0.61 444 275 38.25 0 1 100 808642 TCGA-AB-3006 AML06 18 71995250 71995250 G A SNP - - - - - - - - - - - - - - - tier3 276 4 1.43 314 194 38.19 0 0 NA 808642 TCGA-AB-3006 AML06 18 74511884 74511884 G A SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*29123 NULL 0.058 - - - no_errors tier3 124 2 1.59 250 157 38.57 0 0 NA 808642 TCGA-AB-3006 AML06 18 75114470 75114470 T A SNP ATP9B NM_198531.3 human genbank 54_36p 1 validated silent c.1209 p.G403 0.999 HMMPfam_E1-E2_ATPase "HMMPfam_Hydrolase,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N" - no_errors tier1 75 3 3.85 168 118 41.11 21 21 50 808642 TCGA-AB-3006 AML06 19 3963909 3963909 G T SNP PIAS4 NM_015897.2 human genbank 54_36p 1 provisional intronic c.28-12 e2-12 0.35 - - - no_errors tier3 137 2 1.43 149 94 38.68 0 1 100 808642 TCGA-AB-3006 AML06 19 4261404 4261404 G A SNP FSD1 NM_024333.1 human genbank 54_36p 1 provisional intronic c.369-68 e6-68 0.003 - - - no_errors tier3 220 12 5.15 92 52 35.86 0 0 0 808642 TCGA-AB-3006 AML06 19 9757924 9757924 C T SNP ZNF846 NM_001077624.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-21298 NULL 0 - - - no_errors tier2 135 3 2.16 65 53 44.92 0 0 NA 808642 TCGA-AB-3006 AML06 19 19487967 19487967 T C SNP NDUFA13 NM_015965.5 human genbank 54_36p 1 validated missense c.169 p.S57P 0 NULL HMMPfam_GRIM-19 - no_errors tier1 250 5 1.96 186 138 42.59 2 3 60 808642 TCGA-AB-3006 AML06 19 23253863 23253863 C T SNP LOC100132815 XM_001726889.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-16745 NULL 0 - - - no_errors tier3 131 0 0 83 18 17.82 0 0 0 808642 TCGA-AB-3006 AML06 19 33479137 33479137 C T SNP LOC727780 XM_001125708.1 human genbank 54_36p -1 model intronic c.62-1856 e3-1856 0.084 - - - no_errors tier3 461 7 1.5 157 97 38.04 0 0 NA 808642 TCGA-AB-3006 AML06 19 34806470 34806470 A G SNP PLEKHF1 NM_024310.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-50117 NULL 0.028 - - - no_errors tier3 186 6 3.11 182 97 34.77 0 0 NA 808642 TCGA-AB-3006 AML06 19 36473673 36473673 C T SNP TSHZ3 NM_020856.2 human genbank 54_36p -1 validated intronic c.41-11175 e2-11175 0.994 - - - no_errors tier3 732 8 1.08 626 343 35.36 0 0 NA 808642 TCGA-AB-3006 AML06 19 40236527 40236527 C T SNP HPN NM_002151.1 human genbank 54_36p 1 provisional intronic c.160+4267 e3+4267 0.007 - - - no_errors tier3 160 13 7.47 136 88 39.29 0 0 NA 808642 TCGA-AB-3006 AML06 19 48503272 48503272 G A SNP PSG9 NM_002784.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-37849 NULL 0.003 - - - no_errors tier2 282 5 1.74 163 87 34.8 0 0 0 808642 TCGA-AB-3006 AML06 19 56166368 56166368 T A SNP KLK5 NM_001077491.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-18643 NULL 0.001 - - - no_errors tier3 518 28 5.11 68 47 40.87 0 0 NA 808642 TCGA-AB-3006 AML06 20 5789850 5789850 A T SNP C20orf196 NM_152504.2 human genbank 54_36p 1 predicted intronic c.179-1820 e2-1820 0.003 - - - no_errors tier3 240 1 0.41 307 188 37.98 3 1 25 808642 TCGA-AB-3006 AML06 20 7593831 7593831 G A SNP ENSG00000223193 ENST00000411261 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31333 NULL 0.135 - - - no_errors tier2 265 1 0.38 360 230 38.98 0 0 NA 808642 TCGA-AB-3006 AML06 20 8156095 8156095 A G SNP PLCB1 NM_015192.2 human genbank 54_36p 1 reviewed intronic c.177+77077 e2+77077 0.003 - - - no_errors tier3 665 28 4.01 520 410 43.94 8 10 55.56 808642 TCGA-AB-3006 AML06 20 10680808 10680808 T C SNP - - - - - - - - - - - - - - - tier2 139 2 1.42 141 103 42.21 0 0 NA 808642 TCGA-AB-3006 AML06 20 15252779 15252779 G T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.540+94072 e6+94072 0 - - - no_errors tier2 110 3 2.65 195 83 29.86 0 0 NA 808642 TCGA-AB-3006 AML06 20 18148252 18148252 A T SNP ENSG00000217970 ENST00000403467 human ensembl 54_36p 1 known 5_prime_flanking_region c.-505 NULL 0.031 - - - no_coding_region:pseudogene tier3 199 3 1.49 126 70 35.71 0 0 NA 808642 TCGA-AB-3006 AML06 20 22432260 22432260 A G SNP - - - - - - - - - - - - - - - tier3 242 6 2.42 280 181 39.26 0 0 NA 808642 TCGA-AB-3006 AML06 20 35258590 35258590 A G SNP RPN2 NM_002951.1 human genbank 54_36p 1 reviewed intronic c.208-1624 e3-1624 0.003 - - - no_errors tier2 134 1 0.74 246 169 40.72 1 1 50 808642 TCGA-AB-3006 AML06 20 44822117 44822117 A G SNP LOC100127904 XM_001722183.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-8002 NULL 0 - - - no_errors tier3 206 4 1.9 124 78 38.61 0 0 NA 808642 TCGA-AB-3006 AML06 20 44970575 44970575 G A SNP EYA2 NM_005244.3 human genbank 54_36p 1 reviewed intronic c.1+13542 e0+13542 0.008 - - - no_errors tier3 521 8 1.51 158 123 43.77 0 0 NA 808642 TCGA-AB-3006 AML06 20 48106060 48106060 C T SNP TMEM189-UBE2V1 NM_199203.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*26652 NULL 0 - - - no_errors tier3 258 3 1.15 229 130 36.01 0 0 NA 808642 TCGA-AB-3006 AML06 20 52700780 52700780 T A SNP DOK5 NM_018431.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*355 NULL 0.922 - - - no_errors tier2 124 1 0.8 145 97 40.08 0 0 NA 808642 TCGA-AB-3006 AML06 20 55949677 55949677 G T SNP ENSG00000221451 ENST00000408524 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-34803 NULL 0.001 - - - no_errors tier3 339 6 1.73 337 211 38.43 0 0 NA 808642 TCGA-AB-3006 AML06 20 56592439 56592439 G A SNP ENSG00000221174 ENST00000408247 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21107 NULL 0.296 - - - no_errors tier3 953 23 2.35 778 534 40.49 0 0 NA 808642 TCGA-AB-3006 AML06 20 56637260 56637260 C T SNP STX16 NM_001001433.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23209 NULL 0 - - - no_errors tier3 278 4 1.42 166 114 40.71 0 0 NA 808642 TCGA-AB-3006 AML06 21 21080154 21080154 G A SNP ENSG00000215351 ENST00000400115 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*42162 NULL 0 - - - no_coding_region:pseudogene tier3 280 0 0 199 96 32.54 0 0 NA 808642 TCGA-AB-3006 AML06 21 23224346 23224346 C A SNP ENSG00000219889 ENST00000401698 human ensembl 54_36p 1 known 3_prime_flanking_region c.*46154 NULL 0.045 - - - no_coding_region:pseudogene tier3 126 1 0.79 159 92 36.65 0 0 NA 808642 TCGA-AB-3006 AML06 21 24338377 24338377 C T SNP - - - - - - - - - - - - - - - tier3 55 0 0 96 42 30.43 0 0 NA 808642 TCGA-AB-3006 AML06 21 30106721 30106721 C T SNP GRIK1 NM_000830.3 human genbank 54_36p -1 reviewed intronic c.119-118468 e2-118468 0.009 - - - no_errors tier3 188 3 1.57 344 184 34.72 0 0 NA 808642 TCGA-AB-3006 AML06 21 38197153 38197153 T A SNP KCNJ6 NM_002240.2 human genbank 54_36p -1 reviewed intronic c.1+12904 e0+12904 0.002 - - - no_errors tier3 347 6 1.7 294 187 38.88 0 0 NA 808642 TCGA-AB-3006 AML06 21 40526628 40526628 T - DEL DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.2356+43266 e11+43266 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 808642 TCGA-AB-3006 AML06 21 42654150 42654150 C T SNP TFF3 NM_003226.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-45447 NULL 0 - - - no_errors tier3 294 3 1 200 131 39.58 0 0 NA 808642 TCGA-AB-3006 AML06 22 25627014 25627014 T A SNP LOC100130624 XR_038453.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13470 NULL 0.001 - - - pseudogene tier3 377 14 3.58 423 267 38.7 0 0 NA 808642 TCGA-AB-3006 AML06 22 25865166 25865166 C G SNP - - - - - - - - - - - - - - - tier3 357 7 1.92 423 353 45.43 0 0 NA 808642 TCGA-AB-3006 AML06 22 26960702 26960702 C T SNP TTC28 ENST00000397906 human ensembl 54_36p -1 known intronic c.933+61484 e5+61484 0.001 - - - no_errors tier3 195 2 1.02 214 101 32.06 1 0 0 808642 TCGA-AB-3006 AML06 22 30997572 30997572 G A SNP SLC5A4 NM_014227.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16256 NULL 1 - - - no_errors tier2 84 0 0 232 181 43.72 0 0 0 808642 TCGA-AB-3006 AML06 22 48468151 48468151 G C SNP C22orf34 ENST00000405854 human ensembl 54_36p -1 known 5_prime_flanking_region c.-61605 NULL 0.69 - - - no_errors tier3 40 0 0 73 53 42.06 0 0 NA 943309 TCGA-AB-3007 AML51 X 9782308 9782308 G A SNP SHROOM2 NM_001649.2 human genbank 54_36p 1 reviewed intronic c.166-19384 e2-19384 0.003 - - - no_errors tier3 379 11 2.81 68 223 76.63 0 0 NA 943309 TCGA-AB-3007 AML51 X 10150879 10150879 C T SNP CLCN4 NM_001830.3 human genbank 54_36p 1 reviewed intronic c.2192+1962 e10+1962 0 - - - no_errors tier3 803 5 0.62 240 638 72.5 0 0 0 943309 TCGA-AB-3007 AML51 Y 22776219 22776219 T A SNP RBMY1F NM_152585.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-39715 NULL 0 - - - no_errors tier3 265 3 1.12 159 618 79.54 0 0 NA 943309 TCGA-AB-3007 AML51 X 26356488 26356489 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 X 38381211 38381211 C T SNP TSPAN7 NM_004615.3 human genbank 54_36p 1 reviewed intronic c.82-29108 e2-29108 0 - - - no_errors tier3 397 11 2.69 122 298 70.95 0 0 NA 943309 TCGA-AB-3007 AML51 X 47887175 47887175 C T SNP ENSG00000218182 ENST00000402220 human ensembl 54_36p 1 known 5_prime_flanking_region c.-13564 NULL 0.026 - - - no_coding_region:pseudogene tier3 559 1 0.18 153 434 73.94 0 0 NA 943309 TCGA-AB-3007 AML51 X 49317075 49317075 C A SNP ENSG00000220450 ENST00000407777 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-49317075 NULL 1 - - - no_coding_region:pseudogene tier2 258 0 0 169 202 54.3 0 0 NA 943309 TCGA-AB-3007 AML51 X 54717882 54717882 C A SNP ENSG00000215197 ENST00000399757 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*2086 NULL 0 - - - no_coding_region:pseudogene tier3 136 1 0.73 28 74 72.55 0 0 NA 943309 TCGA-AB-3007 AML51 X 103477328 103477328 G A SNP - - - - - - - - - - - - - - - tier3 179 1 0.56 91 193 67.96 0 0 NA 943309 TCGA-AB-3007 AML51 X 122200276 122200277 - T INS GRIA3 NM_000828.4 human genbank 54_36p 1 reviewed intronic c.269-14559_269-14558 e3-14558 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 X 140275049 140275049 G T SNP ENSG00000220346 ENST00000407507 human ensembl 54_36p 1 known 5_prime_flanking_region c.-27604 NULL 0.027 - - - no_coding_region:pseudogene tier3 375 3 0.79 126 327 72.19 0 0 NA 943309 TCGA-AB-3007 AML51 X 141354530 141354530 T A SNP ENSG00000201000 ENST00000364130 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*27907 NULL 0.057 - - - no_errors tier3 154 0 0 95 361 79.17 0 0 NA 943309 TCGA-AB-3007 AML51 1 12710596 12710596 G A SNP AADACL3 NM_001103170.1 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*2046 NULL 0 - - - no_errors tier3 1736 6 0.34 1065 584 35.29 0 0 NA 943309 TCGA-AB-3007 AML51 1 19718380 19718380 A G SNP CAPZB NM_004930.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33861 NULL 0 - - - no_errors tier3 2609 7 0.27 551 322 36.84 0 0 NA 943309 TCGA-AB-3007 AML51 1 35396937 35396937 G A SNP ENSG00000201868 ENST00000364998 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-37220 NULL 0.007 - - - no_errors tier3 161 0 0 144 29 16.76 0 0 0 943309 TCGA-AB-3007 AML51 1 44095185 44095185 C T SNP ST3GAL3 NM_174963.2 human genbank 54_36p 1 reviewed intronic c.509+18615 e5+18615 0.001 - - - no_errors tier3 451 1 0.22 283 113 28.54 3 0 0 943309 TCGA-AB-3007 AML51 1 53378438 53378438 C T SNP SLC1A7 NM_006671.4 human genbank 54_36p -1 validated intronic c.135+2137 e1+2137 0.995 - - - no_errors tier3 476 0 0 475 278 36.87 0 0 NA 943309 TCGA-AB-3007 AML51 1 71790070 71790070 C T SNP NEGR1 NM_173808.2 human genbank 54_36p -1 validated intronic c.940+41018 e6+41018 0 - - - no_errors tier3 174 0 0 343 210 37.84 0 0 NA 943309 TCGA-AB-3007 AML51 1 75664213 75664213 C T SNP SLC44A5 NM_152697.1 human genbank 54_36p -1 validated intronic c.14-29319 e2-29319 0.006 - - - no_errors tier3 329 1 0.3 503 276 35.34 0 0 NA 943309 TCGA-AB-3007 AML51 1 77303757 77303757 G A SNP LOC256483 XM_173015.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-2442 NULL 0.818 - - - no_errors tier3 433 2 0.46 349 230 39.72 0 0 NA 943309 TCGA-AB-3007 AML51 1 80027856 80027856 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 1 83092986 83092987 TC - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 1 91479611 91479611 A G SNP ENSG00000206817 ENST00000384090 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20159 NULL 0.022 - - - no_errors tier3 320 0 0 285 183 39.1 0 0 NA 943309 TCGA-AB-3007 AML51 1 93619373 93619373 G A SNP LOC100131564 XM_001719527.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-34715 NULL 0.03 - - - no_errors tier3 931 0 0 761 390 33.85 0 2 100 943309 TCGA-AB-3007 AML51 1 94367384 94367384 C T SNP ABCA4 NM_000350.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-8195 NULL 0.002 - - - no_errors tier3 464 1 0.22 528 252 32.31 0 0 NA 943309 TCGA-AB-3007 AML51 1 96322609 96322609 T C SNP - - - - - - - - - - - - - - - tier3 815 4 0.49 1317 715 35.15 0 0 NA 943309 TCGA-AB-3007 AML51 1 99172007 99172007 G A SNP PAP2D NM_001037317.2 human genbank 54_36p -1 reviewed intronic c.622-11805 e4-11805 0 - - - no_errors tier3 799 1 0.12 353 226 39.03 0 0 NA 943309 TCGA-AB-3007 AML51 1 104826307 104826307 C A SNP - - - - - - - - - - - - - - - tier2 322 0 0 367 100 21.41 0 0 NA 943309 TCGA-AB-3007 AML51 1 105057097 105057097 C T SNP - - - - - - - - - - - - - - - tier3 125 0 0 165 82 33.2 0 0 NA 943309 TCGA-AB-3007 AML51 1 105320311 105320311 C A SNP - - - - - - - - - - - - - - - tier3 59 0 0 62 21 25.3 0 0 NA 943309 TCGA-AB-3007 AML51 1 107132717 107132717 G A SNP ENSG00000209237 ENST00000386502 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-15829 NULL 0.001 - - - pseudogene tier3 168 0 0 182 110 37.67 0 0 NA 943309 TCGA-AB-3007 AML51 1 107204854 107204854 G T SNP - - - - - - - - - - - - - - - tier3 153 0 0 226 153 40.37 0 0 NA 943309 TCGA-AB-3007 AML51 1 109126705 109126705 A T SNP STXBP3 NM_007269.2 human genbank 54_36p 1 validated intronic c.905+43 e10+43 0.006 - - - no_errors tier3 295 3 1.01 369 199 35.04 1 1 50 943309 TCGA-AB-3007 AML51 1 112629891 112629891 G C SNP - - - - - - - - - - - - - - - tier3 839 7 0.83 562 260 31.59 0 0 NA 943309 TCGA-AB-3007 AML51 1 114192657 114192657 T C SNP PTPN22 NM_015967.3 human genbank 54_36p -1 reviewed intronic c.915+28 e11+28 0 - - - no_errors tier3 513 5 0.96 513 304 37.21 5 4 44.44 943309 TCGA-AB-3007 AML51 1 115100002 115100002 T C SNP CSDE1 NM_001007553.1 human genbank 54_36p -1 validated intronic c.1+2067 e0+2067 0.026 - - - no_errors tier2 288 0 0 224 91 28.89 7 6 46.15 943309 TCGA-AB-3007 AML51 1 116040376 116040376 G A SNP VANGL1 NM_138959.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*4853 NULL 0.001 - - - no_errors tier3 464 5 1.07 225 138 38.02 1 2 66.67 943309 TCGA-AB-3007 AML51 1 151723022 151723022 C G SNP S100A7 NM_002963.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24909 NULL 0.006 - - - no_errors tier3 922 7 0.75 442 224 33.63 0 0 NA 943309 TCGA-AB-3007 AML51 1 155841933 155841933 G T SNP FCRL4 NM_031282.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-7575 NULL 0.026 - - - no_errors tier3 888 2 0.22 397 262 39.76 0 0 NA 943309 TCGA-AB-3007 AML51 1 162100076 162100076 T C SNP - - - - - - - - - - - - - - - tier3 782 0 0 572 221 27.83 0 0 NA 943309 TCGA-AB-3007 AML51 1 167187797 167187797 G C SNP LOC391132 XR_017287.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*12941 NULL 0.228 - - - pseudogene tier3 1738 8 0.46 900 476 34.59 0 0 NA 943309 TCGA-AB-3007 AML51 1 168590326 168590326 C T SNP ENSG00000217933 ENST00000403539 human ensembl 54_36p -1 known 3_prime_flanking_region c.*14662 NULL 0.015 - - - no_coding_region:pseudogene tier3 770 4 0.52 619 345 35.79 0 0 NA 943309 TCGA-AB-3007 AML51 1 169363441 169363441 G C SNP FMO6P ENST00000236166 human ensembl 54_36p 1 known 5_prime_flanking_region c.-10534 NULL 0.037 - - - no_errors tier3 763 2 0.26 558 343 38.07 0 0 NA 943309 TCGA-AB-3007 AML51 1 170215814 170215814 C T SNP DNM3 NM_015569.1 human genbank 54_36p 1 validated intronic c.236-7605 e3-7605 0.004 - - - no_errors tier3 894 2 0.22 960 511 34.71 0 0 NA 943309 TCGA-AB-3007 AML51 1 176017032 176017032 A T SNP - - - - - - - - - - - - - - - tier3 3476 4 0.11 1172 693 37.12 0 0 NA 943309 TCGA-AB-3007 AML51 1 183914337 183914337 G A SNP ENSG00000201596 ENST00000364726 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-44400 NULL 0 - - - no_errors tier2 589 3 0.51 425 208 32.81 0 0 NA 943309 TCGA-AB-3007 AML51 1 187203099 187203099 C T SNP - - - - - - - - - - - - - - - tier3 508 0 0 221 109 33.03 0 0 NA 943309 TCGA-AB-3007 AML51 1 188270204 188270204 T C SNP ENSG00000217253 ENST00000404055 human ensembl 54_36p -1 known 5_prime_flanking_region c.-41354 NULL 0.008 - - - no_coding_region:pseudogene tier3 638 9 1.39 427 247 36.65 0 0 NA 943309 TCGA-AB-3007 AML51 1 191778642 191778642 G A SNP - - - - - - - - - - - - - - - tier3 703 3 0.42 459 238 34.15 0 0 NA 943309 TCGA-AB-3007 AML51 1 192531268 192531268 T C SNP - - - - - - - - - - - - - - - tier3 605 3 0.49 353 198 35.93 0 0 NA 943309 TCGA-AB-3007 AML51 1 194242770 194242770 C G SNP - - - - - - - - - - - - - - - tier3 274 0 0 567 271 32.34 0 0 NA 943309 TCGA-AB-3007 AML51 1 211713591 211713591 G A SNP LOC643330 XM_926662.2 human genbank 54_36p -1 model intronic c.63+1551 e1+1551 0.001 - - - no_errors tier2 378 2 0.52 328 202 38.11 0 0 NA 943309 TCGA-AB-3007 AML51 1 212169286 212169286 C T SNP - - - - - - - - - - - - - - - tier3 1391 7 0.5 805 297 26.93 0 0 NA 943309 TCGA-AB-3007 AML51 1 214090498 214090498 G A SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.8846-4500 e44-4500 0 - - - no_errors tier3 833 3 0.36 395 185 31.9 0 0 NA 943309 TCGA-AB-3007 AML51 1 214409211 214409211 C A SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.4627+6006 e20+6006 0.007 - - - no_errors tier3 300 0 0 292 128 30.48 0 0 NA 943309 TCGA-AB-3007 AML51 1 238760346 238760347 - A INS GREM2 NM_022469.3 human genbank 54_36p -1 reviewed intronic c.1-36948_36949 e1-36947 0.001:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 4573670 4573670 A T SNP ENSG00000216435 ENST00000402611 human ensembl 54_36p -1 known 5_prime_flanking_region c.-33149 NULL 0.002 - - - no_coding_region:pseudogene tier3 408 0 0 448 219 32.74 0 0 NA 943309 TCGA-AB-3007 AML51 2 13526887 13526887 C A SNP - - - - - - - - - - - - - - - tier3 135 0 0 409 162 28.37 0 0 NA 943309 TCGA-AB-3007 AML51 2 20099263 20099263 G T SNP LAPTM4A NM_014713.4 human genbank 54_36p -1 reviewed intronic c.433-959 e5-959 0 - - - no_errors tier3 816 6 0.73 527 276 34.29 4 2 33.33 943309 TCGA-AB-3007 AML51 2 24948160 24948160 G T SNP ADCY3 NM_004036.3 human genbank 54_36p -1 reviewed intronic c.825+783 e2+783 0.01 - - - no_errors tier2 516 1 0.19 881 564 39 2 2 50 943309 TCGA-AB-3007 AML51 2 29727762 29727762 C G SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.952+43458 e3+43458 0 - - - no_errors tier2 492 4 0.81 839 403 32.42 0 0 NA 943309 TCGA-AB-3007 AML51 2 29896192 29896192 G T SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.667+100171 e1+100171 0 - - - no_errors tier2 891 3 0.34 479 275 36.47 0 0 NA 943309 TCGA-AB-3007 AML51 2 33843450 33843450 C T SNP MYADML ENST00000322472 human ensembl 54_36p -1 known 5_prime_flanking_region c.-37104 NULL 0 - - - no_errors tier3 340 5 1.45 522 193 26.99 0 0 NA 943309 TCGA-AB-3007 AML51 2 34479787 34479787 A C SNP ENSG00000212025 ENST00000390736 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2448 NULL 0.001 - - - no_errors tier3 870 1 0.11 551 298 35.1 0 0 NA 943309 TCGA-AB-3007 AML51 2 34984066 34984066 G A SNP - - - - - - - - - - - - - - - tier3 69 0 0 85 33 27.97 0 0 NA 943309 TCGA-AB-3007 AML51 2 41076550 41076550 G C SNP LOC285176 XM_001725319.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-48059 NULL 0.004 - - - no_start_codon:pseudogene:no_stop_codon tier3 746 1 0.13 567 150 20.92 0 0 NA 943309 TCGA-AB-3007 AML51 2 50722515 50722515 C T SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.833-18258 e5-18258 0.009 - - - no_errors tier3 509 1 0.2 558 294 34.51 0 0 NA 943309 TCGA-AB-3007 AML51 2 52012498 52012498 A G SNP ENSG00000220786 ENST00000404352 human ensembl 54_36p -1 known 5_prime_flanking_region c.-4494 NULL 0.018 - - - no_coding_region:pseudogene tier3 483 0 0 341 135 28.36 0 0 NA 943309 TCGA-AB-3007 AML51 2 52426037 52426037 T C SNP ENSG00000202195 ENST00000365325 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47299 NULL 0 - - - no_errors tier3 1015 0 0 869 345 28.4 0 0 NA 943309 TCGA-AB-3007 AML51 2 56610291 56610291 C T SNP - - - - - - - - - - - - - - - tier3 542 3 0.55 537 265 33 0 0 NA 943309 TCGA-AB-3007 AML51 2 60184705 60184705 T C SNP - - - - - - - - - - - - - - - tier2 765 1 0.13 334 178 34.7 0 0 NA 943309 TCGA-AB-3007 AML51 2 73208611 73208612 - A INS RAB11FIP5 NM_015470.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-15198 NULL 0.017:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 74458845 74458845 G A SNP DCTN1 NM_004082.1 human genbank 54_36p -1 reviewed silent c.69 p.S23 0.99 superfamily_Cap-Gly domain "HMMPfam_CAP_GLY,PatternScan_CAP_GLY_1,superfamily_Spectrin repeat,superfamily_Cap-Gly domain" - no_errors tier1 949 1 0.11 646 362 35.84 14 10 41.67 943309 TCGA-AB-3007 AML51 2 79754235 79754235 T - DEL CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.102+21943 e1+21943 0.015 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 81725493 81725493 G A SNP - - - - - - - - - - - - - - - tier3 632 3 0.47 341 153 30.97 0 0 NA 943309 TCGA-AB-3007 AML51 2 82383398 82383398 A T SNP ENSG00000201311 ENST00000364441 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*4304 NULL 0.001 - - - no_errors tier3 256 1 0.39 196 115 36.98 0 0 NA 943309 TCGA-AB-3007 AML51 2 89284321 89284321 C T SNP IGKV2-24 ENST00000390257 human ensembl 54_36p -1 known 5_prime_flanking_region c.-26592 NULL 0.505 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 472 3 0.63 295 184 38.33 0 0 0 943309 TCGA-AB-3007 AML51 2 111470293 111470293 G C SNP ACOXL NM_001105516.2 human genbank 54_36p 1 validated intronic c.1371+241 e14+241 0.002 - - - no_errors tier3 606 0 0 484 294 37.79 0 0 NA 943309 TCGA-AB-3007 AML51 2 111470294 111470294 C T SNP ACOXL NM_001105516.2 human genbank 54_36p 1 validated intronic c.1371+242 e14+242 0.003 - - - no_errors tier3 605 0 0 478 296 38.19 0 0 NA 943309 TCGA-AB-3007 AML51 2 114657982 114657982 C T SNP - - - - - - - - - - - - - - - tier3 326 2 0.61 306 218 41.52 0 0 NA 943309 TCGA-AB-3007 AML51 2 117433292 117433292 G T SNP - - - - - - - - - - - - - - - tier3 776 0 0 825 247 23.02 0 0 NA 943309 TCGA-AB-3007 AML51 2 119049618 119049618 G A SNP - - - - - - - - - - - - - - - tier3 506 2 0.39 272 118 30.26 0 0 NA 943309 TCGA-AB-3007 AML51 2 139804184 139804184 T A SNP - - - - - - - - - - - - - - - tier3 242 2 0.82 218 136 38.42 0 0 NA 943309 TCGA-AB-3007 AML51 2 141070526 141070526 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.7194+2144 e43+2144 0.005 - - - no_errors tier2 249 0 0 305 180 37.11 0 0 NA 943309 TCGA-AB-3007 AML51 2 142210166 142210166 A C SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.205+74152 e2+74152 0.007 - - - no_errors tier3 1163 2 0.17 717 336 31.91 0 0 NA 943309 TCGA-AB-3007 AML51 2 145605768 145605769 - A INS LOC730124 XM_001132529.1 human genbank 54_36p 1 model intronic c.127-40267_127-40266 e2-40266 0.016:0.056 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 146224568 146224568 C T SNP - - - - - - - - - - - - - - - tier3 1026 0 0 440 201 31.36 0 0 NA 943309 TCGA-AB-3007 AML51 2 147375023 147375023 G T SNP - - - - - - - - - - - - - - - tier3 386 1 0.26 229 103 31.02 0 0 NA 943309 TCGA-AB-3007 AML51 2 149771120 149771120 G A SNP LYPD6B NM_177964.3 human genbank 54_36p 1 provisional intronic c.229+956 e3+956 0.001 - - - no_errors tier3 284 2 0.7 292 168 36.52 0 0 NA 943309 TCGA-AB-3007 AML51 2 153990372 153990373 - A INS LOC642635 XR_016188.2 human genbank 54_36p -1 model intronic c.NULL NULL 0.087:0.083 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 154744952 154744953 - T INS GALNT13 NM_052917.2 human genbank 54_36p 1 validated intronic c.311+39688_311+39687 e2+39688 0.000:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 160994167 160994168 - A INS RBMS1 NM_016836.4 human genbank 54_36p -1 reviewed intronic c.76-62020_76-62019 e2-62019 0.004:0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 162748292 162748292 C G SNP FAP NM_004460.2 human genbank 54_36p -1 reviewed intronic c.1815-68 e21-68 1 - - - no_errors tier2 201 0 0 339 163 32.47 0 0 NA 943309 TCGA-AB-3007 AML51 2 164023672 164023672 A C SNP - - - - - - - - - - - - - - - tier3 148 0 0 288 187 39.37 0 0 NA 943309 TCGA-AB-3007 AML51 2 168602812 168602812 T C SNP STK39 NM_013233.2 human genbank 54_36p -1 reviewed intronic c.1377-20961 e15-20961 0.009 - - - no_errors tier2 411 0 0 322 198 38 0 0 0 943309 TCGA-AB-3007 AML51 2 179327344 179327344 G A SNP TTN NM_133379.3 human genbank 54_36p -1 reviewed intronic c.10304-1192 e44-1192 0 - - - no_errors tier2 220 0 0 238 120 33.52 0 0 NA 943309 TCGA-AB-3007 AML51 2 181541517 181541517 G T SNP UBE2E3 NM_006357.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13498 NULL 0 - - - no_errors tier3 408 0 0 322 126 28.12 0 0 NA 943309 TCGA-AB-3007 AML51 2 188658692 188658692 C A SNP - - - - - - - - - - - - - - - tier3 760 1 0.13 517 290 35.85 0 0 NA 943309 TCGA-AB-3007 AML51 2 188897317 188897317 G C SNP GULP1 NM_016315.2 human genbank 54_36p 1 validated intronic c.1+31233 e0+31233 0.984 - - - no_errors tier3 431 2 0.46 292 138 32.02 0 0 NA 943309 TCGA-AB-3007 AML51 2 192156551 192156551 G A SNP - - - - - - - - - - - - - - - tier3 466 1 0.21 445 185 29.37 0 0 NA 943309 TCGA-AB-3007 AML51 2 199419190 199419190 T A SNP - - - - - - - - - - - - - - - tier3 224 1 0.44 446 189 29.76 0 0 NA 943309 TCGA-AB-3007 AML51 2 211602964 211602964 T C SNP - - - - - - - - - - - - - - - tier3 177 0 0 189 92 32.74 0 0 NA 943309 TCGA-AB-3007 AML51 2 211611481 211611482 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 2 212828126 212828126 G A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.83-130253 e2-130253 0 - - - no_errors tier3 458 0 0 514 262 33.76 0 0 NA 943309 TCGA-AB-3007 AML51 2 214138743 214138743 C G SNP SPAG16 NM_024532.1 human genbank 54_36p 1 validated intronic c.1070+75684 e10+75684 0 - - - no_errors tier3 716 0 0 658 213 24.43 0 0 NA 943309 TCGA-AB-3007 AML51 2 216673162 216673162 C T SNP TMEM169 NM_138390.1 human genbank 54_36p 1 validated silent c.546 p.Y182 0.998 NULL NULL - no_errors tier1 2880 4 0.14 1169 629 34.91 NA 943309 TCGA-AB-3007 AML51 2 220342252 220342252 C T SNP - - - - - - - - - - - - - - - tier3 652 2 0.31 343 185 35.04 0 0 NA 943309 TCGA-AB-3007 AML51 2 221712382 221712382 T A SNP - - - - - - - - - - - - - - - tier3 140 0 0 191 127 39.94 0 0 NA 943309 TCGA-AB-3007 AML51 2 224002541 224002541 C T SNP ENSG00000221064 ENST00000408137 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-28170 NULL 0.433 - - - no_errors tier3 251 0 0 176 53 23.14 0 0 NA 943309 TCGA-AB-3007 AML51 2 225206248 225206248 G T SNP CUL3 NM_003590.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-48278 NULL 0.02 - - - no_errors tier3 1199 2 0.17 341 146 29.92 0 0 NA 943309 TCGA-AB-3007 AML51 2 227140528 227140528 T A SNP ENSG00000208062 ENST00000385327 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23660 NULL 0.002 - - - pseudogene tier3 862 2 0.23 482 273 36.11 0 0 NA 943309 TCGA-AB-3007 AML51 2 229153366 229153366 G A SNP - - - - - - - - - - - - - - - tier3 183 2 1.08 280 140 33.33 0 0 NA 943309 TCGA-AB-3007 AML51 2 238598582 238598582 C A SNP UBE2F NM_080678.1 human genbank 54_36p 1 provisional intronic c.283-140 e5-140 0.001 - - - no_errors tier3 850 0 0 575 375 39.43 1 0 0 943309 TCGA-AB-3007 AML51 2 239418551 239418551 T A SNP ENSG00000201897 ENST00000365027 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*42174 NULL 0.004 - - - no_errors tier3 155 2 1.27 176 118 40.14 0 0 NA 943309 TCGA-AB-3007 AML51 3 506356 506356 G A SNP - - - - - - - - - - - - - - - tier2 116 1 0.85 146 46 23.96 0 0 NA 943309 TCGA-AB-3007 AML51 3 5312035 5312035 C A SNP ENSG00000222517 ENST00000410585 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42127 NULL 0.001 - - - no_errors tier3 632 1 0.16 300 190 38.7 0 0 NA 943309 TCGA-AB-3007 AML51 3 6374866 6374866 G A SNP - - - - - - - - - - - - - - - tier3 733 1 0.14 278 140 33.49 0 0 NA 943309 TCGA-AB-3007 AML51 3 14917481 14917481 A G SNP FGD5 NM_152536.3 human genbank 54_36p 1 validated intronic c.2483-33 e9-33 0 - - - no_errors tier3 918 6 0.65 573 331 36.62 0 0 NA 943309 TCGA-AB-3007 AML51 3 21879557 21879557 A C SNP ENSG00000221384 ENST00000408457 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33224 NULL 0.001 - - - no_errors tier3 169 0 0 352 202 36.4 0 0 NA 943309 TCGA-AB-3007 AML51 3 29353014 29353014 T A SNP RBMS3 NM_001003793.1 human genbank 54_36p 1 reviewed intronic c.75+54763 e1+54763 0 - - - no_errors tier3 379 0 0 356 203 36.31 0 0 NA 943309 TCGA-AB-3007 AML51 3 32850269 32850269 A G SNP TRIM71 NM_001039111.1 human genbank 54_36p 1 provisional intronic c.852+14841 e1+14841 0.705 - - - no_errors tier3 518 0 0 317 175 35.57 0 0 0 943309 TCGA-AB-3007 AML51 3 38083054 38083054 C A SNP DLEC1 NM_007337.2 human genbank 54_36p 1 reviewed intronic c.1173+2640 e6+2640 0 - - - no_errors tier3 294 0 0 104 62 37.35 0 0 NA 943309 TCGA-AB-3007 AML51 3 55882306 55882306 G A SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2564+15151 e13+15151 0.003 - - - no_errors tier3 881 0 0 550 312 36.19 0 0 NA 943309 TCGA-AB-3007 AML51 3 60293780 60293780 T A SNP FHIT NM_002012.2 human genbank 54_36p -1 reviewed intronic c.103+203853 e1+203853 1 - - - no_errors tier2 427 3 0.7 402 236 36.99 0 0 NA 943309 TCGA-AB-3007 AML51 3 65115385 65115385 G A SNP - - - - - - - - - - - - - - - tier3 720 5 0.69 459 210 31.34 0 0 NA 943309 TCGA-AB-3007 AML51 3 65954387 65954387 G C SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.313+44324 e1+44324 0 - - - no_errors tier3 1612 3 0.19 1114 694 38.36 0 0 NA 943309 TCGA-AB-3007 AML51 3 67360037 67360037 C T SNP - - - - - - - - - - - - - - - tier2 2626 2 0.08 517 267 34.01 0 0 NA 943309 TCGA-AB-3007 AML51 3 74970995 74970995 G C SNP - - - - - - - - - - - - - - - tier3 128 0 0 182 53 22.46 0 0 NA 943309 TCGA-AB-3007 AML51 3 77552125 77552125 G T SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.389-57130 e3-57130 0.453 - - - no_errors tier2 386 1 0.26 434 127 22.64 0 0 NA 943309 TCGA-AB-3007 AML51 3 77552151 77552151 A G SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.389-57104 e3-57104 0.006 - - - no_errors tier3 432 1 0.23 464 141 23.31 0 0 NA 943309 TCGA-AB-3007 AML51 3 84394437 84394437 G T SNP ENSG00000221380 ENST00000408453 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*27516 NULL 0.013 - - - no_errors tier3 126 0 0 180 57 23.95 0 0 NA 943309 TCGA-AB-3007 AML51 3 95990281 95990281 G T SNP - - - - - - - - - - - - - - - tier3 97 0 0 97 65 40.12 0 0 NA 943309 TCGA-AB-3007 AML51 3 96706245 96706245 C G SNP - - - - - - - - - - - - - - - tier2 108 1 0.92 225 82 26.71 0 0 NA 943309 TCGA-AB-3007 AML51 3 97648616 97648616 C T SNP ENSG00000216136 ENST00000401317 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13672 NULL 0 - - - no_errors tier3 236 0 0 242 96 28.24 0 0 NA 943309 TCGA-AB-3007 AML51 3 106139286 106139286 T C SNP - - - - - - - - - - - - - - - tier3 420 1 0.24 346 170 32.95 0 0 NA 943309 TCGA-AB-3007 AML51 3 108979837 108979837 A G SNP BBX NM_020235.1 human genbank 54_36p 1 validated intronic c.2055-71 e10-71 0.028 - - - no_errors tier3 242 0 0 342 204 37.36 0 1 100 943309 TCGA-AB-3007 AML51 3 111914052 111914052 A G SNP ENSG00000201426 ENST00000364556 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-14506 NULL 0.031 - - - no_errors tier2 336 0 0 292 157 34.89 0 0 NA 943309 TCGA-AB-3007 AML51 3 120670921 120670921 T C SNP KTELC1 NM_152305.2 human genbank 54_36p 1 validated intronic c.85+278 e1+278 0.008 - - - no_errors tier2 435 0 0 262 116 30.61 3 5 62.5 943309 TCGA-AB-3007 AML51 3 125370358 125370358 G A SNP KALRN NM_001024660.2 human genbank 54_36p 1 reviewed intronic c.68-59169 e2-59169 0.031 - - - no_errors tier3 866 0 0 433 213 32.97 0 0 NA 943309 TCGA-AB-3007 AML51 3 132914151 132914151 G A SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.360+10829 e2+10829 0.001 - - - no_errors tier3 115 1 0.86 169 110 39.43 0 0 NA 943309 TCGA-AB-3007 AML51 3 135485162 135485162 T C SNP RYK NM_001005861.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-32976 NULL 0.001 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 795 3 0.38 699 402 36.51 0 0 NA 943309 TCGA-AB-3007 AML51 3 138843672 138843672 C T SNP - - - - - - - - - - - - - - - tier3 545 0 0 688 433 38.59 0 0 NA 943309 TCGA-AB-3007 AML51 3 139641475 139641475 G A SNP FAM62C NM_031913.3 human genbank 54_36p 1 validated intronic c.327+4818 e1+4818 0 - - - no_errors tier2 735 8 1.08 391 199 33.73 0 0 NA 943309 TCGA-AB-3007 AML51 3 146907344 146907344 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 3 160484085 160484085 C T SNP SCHIP1 NM_014575.2 human genbank 54_36p 1 provisional intronic c.63+9719 e1+9719 0 - - - no_errors tier3 68 0 0 130 60 31.41 0 0 NA 943309 TCGA-AB-3007 AML51 3 162539119 162539119 G A SNP LOC646085 XR_017630.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-8112 NULL 0.008 - - - pseudogene tier3 101 0 0 170 68 28.57 0 0 NA 943309 TCGA-AB-3007 AML51 3 168310273 168310273 T C SNP LOC131055 XM_067176.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*43466 NULL 0.007 - - - no_errors tier3 80 0 0 105 55 34.38 0 0 NA 943309 TCGA-AB-3007 AML51 3 174368001 174368002 - A INS SPATA16 NM_031955.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49786 NULL 0.024:0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 3 178534951 178534951 A G SNP - - - - - - - - - - - - - - - tier3 773 1 0.13 414 202 32.79 0 0 NA 943309 TCGA-AB-3007 AML51 3 183314774 183314774 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 8609024 8609024 C T SNP CPZ NM_001014447.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36437 NULL 0 - - - no_errors tier3 552 0 0 243 201 45.27 0 0 NA 943309 TCGA-AB-3007 AML51 4 11306847 11306847 C G SNP LOC644753 XM_932350.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-49402 NULL 0 - - - no_errors tier3 224 4 1.75 370 189 33.81 0 0 NA 943309 TCGA-AB-3007 AML51 4 11443125 11443125 C T SNP - - - - - - - - - - - - - - - tier3 646 1 0.15 482 149 23.58 0 0 NA 943309 TCGA-AB-3007 AML51 4 11655080 11655081 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 12280642 12280642 A G SNP - - - - - - - - - - - - - - - tier3 619 2 0.32 284 282 49.82 0 0 NA 943309 TCGA-AB-3007 AML51 4 12992822 12992822 G T SNP RAB28 NM_001017979.1 human genbank 54_36p -1 provisional intronic c.392-506 e5-506 0 - - - no_errors tier3 180 0 0 413 220 34.76 2 3 60 943309 TCGA-AB-3007 AML51 4 14078605 14078605 T A SNP - - - - - - - - - - - - - - - tier3 464 0 0 693 354 33.81 0 0 NA 943309 TCGA-AB-3007 AML51 4 20089293 20089293 C T SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.468-2144 e6-2144 1 - - - no_errors tier2 424 1 0.24 364 213 36.85 0 0 NA 943309 TCGA-AB-3007 AML51 4 23315826 23315827 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 23984368 23984368 G A SNP ENSG00000222262 ENST00000410330 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*47529 NULL 0.001 - - - no_errors tier3 683 3 0.44 269 145 35.02 0 0 NA 943309 TCGA-AB-3007 AML51 4 27177158 27177158 C A SNP - - - - - - - - - - - - - - - tier3 174 2 1.14 407 222 35.24 0 0 NA 943309 TCGA-AB-3007 AML51 4 28273090 28273090 C T SNP ENSG00000210070 ENST00000387335 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48829 NULL 0 - - - pseudogene tier3 331 0 0 454 155 25.45 0 0 NA 943309 TCGA-AB-3007 AML51 4 28548635 28548635 C T SNP - - - - - - - - - - - - - - - tier3 252 0 0 406 172 29.76 0 0 NA 943309 TCGA-AB-3007 AML51 4 29897146 29897146 C T SNP - - - - - - - - - - - - - - - tier2 228 1 0.44 316 108 25.47 0 0 NA 943309 TCGA-AB-3007 AML51 4 30709458 30709458 A C SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3227-43735 e4-43735 0.003 - - - no_errors tier3 406 0 0 398 187 31.86 0 0 NA 943309 TCGA-AB-3007 AML51 4 31387809 31387809 G A SNP - - - - - - - - - - - - - - - tier3 362 0 0 216 116 34.94 0 0 NA 943309 TCGA-AB-3007 AML51 4 35278544 35278544 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 35690072 35690072 G T SNP - - - - - - - - - - - - - - - tier3 114 0 0 126 65 34.03 0 0 0 943309 TCGA-AB-3007 AML51 4 40782573 40782574 - A INS APBB2 NM_173075.4 human genbank 54_36p -1 validated intronic c.1+14839_14838 e0+14839 0.055:0.048 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 47080320 47080320 G T SNP GABRB1 NM_000812.3 human genbank 54_36p 1 reviewed intronic c.545-19772 e6-19772 0.004 - - - no_errors tier3 195 0 0 228 170 42.61 0 0 NA 943309 TCGA-AB-3007 AML51 4 59484186 59484186 T C SNP - - - - - - - - - - - - - - - tier2 246 3 1.2 388 125 24.37 0 0 NA 943309 TCGA-AB-3007 AML51 4 65149737 65149738 - A INS ENSG00000210689 ENST00000387954 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6142 NULL 0.001:0.001 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 65679821 65679821 G C SNP - - - - - - - - - - - - - - - tier3 193 0 0 218 87 28.52 0 0 NA 943309 TCGA-AB-3007 AML51 4 67356978 67356978 G A SNP - - - - - - - - - - - - - - - tier3 119 0 0 138 82 37.27 0 0 NA 943309 TCGA-AB-3007 AML51 4 73200755 73200756 TT - DEL NPFFR2 NM_004885.1 human genbank 54_36p 1 reviewed intronic c.300-12411_300-12410 e2-12410 0.071:0.070 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 87193166 87193167 - T INS MAPK10 NM_138982.2 human genbank 54_36p -1 reviewed intronic c.1110+11276_1110+11275 e9+11276 0.039:0.048 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 89273698 89273698 C T SNP ABCG2 NM_004827.2 human genbank 54_36p -1 reviewed intronic c.204-887 e2-887 0.003 - - - no_errors tier2 592 8 1.33 463 254 35.43 0 0 0 943309 TCGA-AB-3007 AML51 4 89876252 89876252 G C SNP FAM13A NM_014883.1 human genbank 54_36p -1 validated intronic c.2646+1394 e21+1394 0.007 - - - no_errors tier3 253 1 0.39 350 146 29.44 2 1 33.33 943309 TCGA-AB-3007 AML51 4 93041572 93041572 C A SNP - - - - - - - - - - - - - - - tier3 292 0 0 341 182 34.8 0 0 NA 943309 TCGA-AB-3007 AML51 4 93943397 93943397 A G SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.244+212937 e2+212937 0 - - - no_errors tier3 273 0 0 253 140 35.53 0 0 NA 943309 TCGA-AB-3007 AML51 4 94614658 94614658 T C SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.1859-16155 e12-16155 0.001 - - - no_errors tier2 64 0 0 82 44 34.92 0 0 NA 943309 TCGA-AB-3007 AML51 4 95873956 95873956 T C SNP BMPR1B NM_001203.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-370643 NULL 0 - - - no_errors tier3 602 2 0.33 487 302 38.28 0 0 NA 943309 TCGA-AB-3007 AML51 4 97505419 97505419 A T SNP ENSG00000201640 ENST00000364770 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16207 NULL 0 - - - no_errors tier2 263 0 0 336 204 37.78 0 0 NA 943309 TCGA-AB-3007 AML51 4 98336378 98336378 G C SNP - - - - - - - - - - - - - - - tier2 60 0 0 48 23 32.39 0 0 NA 943309 TCGA-AB-3007 AML51 4 106021684 106021684 T G SNP - - - - - - - - - - - - - - - tier3 886 3 0.34 862 290 25.15 0 0 NA 943309 TCGA-AB-3007 AML51 4 107372033 107372033 G A SNP TBCKL NM_033115.2 human genbank 54_36p -1 provisional intronic c.1501+302 e15+302 0 - - - no_errors tier3 392 1 0.25 268 117 30.39 1 0 0 943309 TCGA-AB-3007 AML51 4 111272073 111272073 C T SNP ELOVL6 NM_024090.1 human genbank 54_36p -1 validated intronic c.90-25840 e2-25840 0 - - - no_errors tier3 344 1 0.29 269 145 35.02 0 0 NA 943309 TCGA-AB-3007 AML51 4 111779758 111779758 G A SNP PITX2 ENST00000354925 human ensembl 54_36p -1 known intronic c.1-999 e1-999 0.006 - - - no_errors tier3 629 2 0.32 346 185 34.84 0 0 NA 943309 TCGA-AB-3007 AML51 4 126067245 126067245 A G SNP - - - - - - - - - - - - - - - tier3 143 1 0.69 173 96 35.69 0 0 NA 943309 TCGA-AB-3007 AML51 4 126073440 126073440 C T SNP - - - - - - - - - - - - - - - tier3 500 0 0 341 187 35.42 0 0 NA 943309 TCGA-AB-3007 AML51 4 128424975 128424976 - G INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 134395820 134395820 C G SNP - - - - - - - - - - - - - - - tier3 325 0 0 205 83 28.82 0 0 NA 943309 TCGA-AB-3007 AML51 4 134924499 134924499 C A SNP ENSG00000209005 ENST00000386270 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-4949 NULL 0.006 - - - pseudogene tier2 394 2 0.51 354 135 27.61 0 0 NA 943309 TCGA-AB-3007 AML51 4 136463934 136463934 T C SNP ENSG00000207188 ENST00000384459 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-7811 NULL 0.348 - - - no_errors tier2 475 0 0 510 201 28.27 0 0 NA 943309 TCGA-AB-3007 AML51 4 136596414 136596414 C A SNP - - - - - - - - - - - - - - - tier2 113 0 0 190 69 26.54 0 0 NA 943309 TCGA-AB-3007 AML51 4 136605462 136605462 C G SNP - - - - - - - - - - - - - - - tier3 94 0 0 235 56 19.18 0 0 NA 943309 TCGA-AB-3007 AML51 4 136812991 136812991 C T SNP - - - - - - - - - - - - - - - tier3 674 0 0 425 198 31.78 0 0 NA 943309 TCGA-AB-3007 AML51 4 136946019 136946019 T C SNP - - - - - - - - - - - - - - - tier3 519 1 0.19 490 271 35.52 0 0 NA 943309 TCGA-AB-3007 AML51 4 137600506 137600506 C G SNP - - - - - - - - - - - - - - - tier3 184 0 0 275 180 39.56 0 0 NA 943309 TCGA-AB-3007 AML51 4 137606701 137606701 G T SNP - - - - - - - - - - - - - - - tier3 292 2 0.68 341 161 32.07 0 0 NA 943309 TCGA-AB-3007 AML51 4 137788710 137788710 G A SNP - - - - - - - - - - - - - - - tier3 387 2 0.51 301 152 33.55 0 0 NA 943309 TCGA-AB-3007 AML51 4 142037485 142037485 C A SNP RNF150 NM_020724.1 human genbank 54_36p -1 validated intronic c.1198+14263 e6+14263 0.003 - - - no_errors tier3 747 1 0.13 441 175 28.41 0 0 NA 943309 TCGA-AB-3007 AML51 4 144997100 144997100 G A SNP GYPE NM_002102.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*20258 NULL 0 - - - no_errors tier3 189 1 0.52 211 84 28.47 2 1 33.33 943309 TCGA-AB-3007 AML51 4 159951169 159951169 T G SNP FNIP2 NM_020840.1 human genbank 54_36p 1 validated intronic c.108-15349 e2-15349 0 - - - no_errors tier2 699 3 0.43 577 295 33.83 0 0 NA 943309 TCGA-AB-3007 AML51 4 160362256 160362256 C T SNP RAPGEF2 NM_014247.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46502 NULL 0.002 - - - no_errors tier2 607 2 0.33 633 349 35.5 2 0 0 943309 TCGA-AB-3007 AML51 4 160992825 160992825 T C SNP - - - - - - - - - - - - - - - tier3 277 0 0 404 240 37.27 0 0 NA 943309 TCGA-AB-3007 AML51 4 162063059 162063059 C G SNP - - - - - - - - - - - - - - - tier3 285 0 0 377 34 8.25 0 0 NA 943309 TCGA-AB-3007 AML51 4 162133154 162133154 G A SNP ENSG00000221362 ENST00000408435 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*11325 NULL 0 - - - no_errors tier3 178 0 0 198 100 33.56 0 0 NA 943309 TCGA-AB-3007 AML51 4 162323234 162323234 C A SNP - - - - - - - - - - - - - - - tier3 313 2 0.63 314 164 34.31 0 0 NA 943309 TCGA-AB-3007 AML51 4 163978158 163978158 A T SNP - - - - - - - - - - - - - - - tier3 262 0 0 389 209 34.89 0 0 NA 943309 TCGA-AB-3007 AML51 4 167164136 167164136 G T SNP TLL1 NM_012464.3 human genbank 54_36p 1 reviewed intronic c.1043-1782 e9-1782 0.005 - - - no_errors tier3 329 2 0.6 171 102 37.36 0 0 NA 943309 TCGA-AB-3007 AML51 4 169049563 169049563 G A SNP ENSG00000221576 ENST00000408649 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13232 NULL 0.011 - - - no_errors tier3 308 4 1.28 175 104 37.14 0 0 NA 943309 TCGA-AB-3007 AML51 4 170903793 170903793 A C SNP C4orf27 NM_017867.2 human genbank 54_36p -1 validated intronic c.497+2677 e4+2677 0.002 - - - no_errors tier3 40 0 0 208 90 30.2 1 0 0 943309 TCGA-AB-3007 AML51 4 179534267 179534267 T C SNP ENSG00000201727 ENST00000364857 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-30576 NULL 0 - - - no_errors tier3 81 0 0 155 72 31.72 0 0 NA 943309 TCGA-AB-3007 AML51 4 180024066 180024067 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 4 180283856 180283856 A T SNP - - - - - - - - - - - - - - - tier3 91 0 0 142 63 30.73 0 0 NA 943309 TCGA-AB-3007 AML51 4 182216527 182216527 C T SNP LOC728081 XM_001127776.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*6071 NULL 0 - - - no_errors tier3 289 0 0 256 86 25.15 0 0 NA 943309 TCGA-AB-3007 AML51 4 188141921 188141921 C T SNP - - - - - - - - - - - - - - - tier3 1052 2 0.19 817 434 34.69 0 0 NA 943309 TCGA-AB-3007 AML51 5 4299067 4299067 C T SNP - - - - - - - - - - - - - - - tier3 649 1 0.15 426 219 33.95 0 0 NA 943309 TCGA-AB-3007 AML51 5 4585857 4585857 G A SNP - - - - - - - - - - - - - - - tier2 528 1 0.19 584 172 22.75 0 0 NA 943309 TCGA-AB-3007 AML51 5 5156373 5156373 C T SNP ADAMTS16 NM_139056.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-37208 NULL 0.074 - - - no_errors tier2 991 12 1.2 713 276 27.85 0 0 NA 943309 TCGA-AB-3007 AML51 5 5636201 5636201 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 5 6547105 6547105 G A SNP uc003jdp.2 ENST00000399816 human ensembl 54_36p 1 known 3_prime_flanking_region c.*2643 NULL 0 - - - no_start_codon tier3 675 2 0.3 484 189 28.08 0 0 NA 943309 TCGA-AB-3007 AML51 5 7243959 7243959 G A SNP - - - - - - - - - - - - - - - tier3 389 1 0.26 499 251 33.47 0 0 NA 943309 TCGA-AB-3007 AML51 5 8963646 8963646 G A SNP - - - - - - - - - - - - - - - tier3 511 4 0.78 434 224 34.04 0 0 NA 943309 TCGA-AB-3007 AML51 5 10252430 10252430 G T SNP ENSG00000196193 ENST00000358163 human ensembl 54_36p 1 known 5_prime_flanking_region c.-2191 NULL 0 - - - no_coding_region:pseudogene tier3 588 0 0 414 280 40.35 1 0 0 943309 TCGA-AB-3007 AML51 5 14640104 14640104 G A SNP FAM105A NM_019018.2 human genbank 54_36p 1 validated intronic c.64+5037 e1+5037 0.004 - - - no_errors tier3 657 0 0 326 195 37.36 3 2 40 943309 TCGA-AB-3007 AML51 5 16010592 16010592 G T SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*20297 NULL 0 - - - no_errors tier3 734 0 0 424 152 26.39 0 0 NA 943309 TCGA-AB-3007 AML51 5 17688319 17688319 G A SNP LOC391769 XM_373079.1 human genbank 54_36p -1 model silent c.78 p.A26 0.986 superfamily_Histone-fold "HMMSmart_SM00428,PatternScan_HISTONE_H3_2,HMMPfam_Histone,superfamily_Histone-fold" - no_errors tier1 197 0 221 161 41.82 NA 943309 TCGA-AB-3007 AML51 5 19157433 19157433 T C SNP - - - - - - - - - - - - - - - tier3 478 3 0.62 562 325 36.6 0 0 NA 943309 TCGA-AB-3007 AML51 5 24101393 24101393 G T SNP - - - - - - - - - - - - - - - tier3 189 0 0 208 101 32.69 0 0 NA 943309 TCGA-AB-3007 AML51 5 30214355 30214355 G A SNP - - - - - - - - - - - - - - - tier3 322 0 0 359 180 33.4 0 0 NA 943309 TCGA-AB-3007 AML51 5 30621040 30621040 C T SNP - - - - - - - - - - - - - - - tier3 327 1 0.3 523 256 32.86 0 0 NA 943309 TCGA-AB-3007 AML51 5 32963305 32963305 C T SNP LOC340113 XM_379324.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21644 NULL 0.995 - - - no_errors tier2 664 0 0 615 168 21.43 0 0 NA 943309 TCGA-AB-3007 AML51 5 35244667 35244667 T C SNP PRLR NM_000949.4 human genbank 54_36p -1 validated intronic c.1+21460 e0+21460 0.023 - - - no_errors tier3 241 1 0.41 177 126 41.58 0 0 NA 943309 TCGA-AB-3007 AML51 5 38068222 38068222 A G SNP - - - - - - - - - - - - - - - tier3 645 1 0.15 348 206 37.12 0 0 NA 943309 TCGA-AB-3007 AML51 5 45177928 45177928 G A SNP - - - - - - - - - - - - - - - tier3 735 1 0.14 551 226 29.05 0 0 NA 943309 TCGA-AB-3007 AML51 5 45755655 45755655 T A SNP HCN1 NM_021072.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23703 NULL 0.001 - - - no_errors tier3 240 2 0.83 113 81 41.75 0 0 NA 943309 TCGA-AB-3007 AML51 5 53560068 53560068 G A SNP ARL15 NM_019087.2 human genbank 54_36p -1 validated intronic c.49-56553 e2-56553 0.007 - - - no_errors tier3 193 0 0 326 149 31.37 0 0 0 943309 TCGA-AB-3007 AML51 5 58867573 58867573 G T SNP PDE4D NM_001104631.1 human genbank 54_36p -1 validated intronic c.456-320022 e2-320022 0.002 - - - no_errors tier2 522 1 0.19 553 311 36 2 0 0 943309 TCGA-AB-3007 AML51 5 62957456 62957456 G A SNP - - - - - - - - - - - - - - - tier3 1531 1 0.07 616 379 38.09 0 0 NA 943309 TCGA-AB-3007 AML51 5 72190122 72190122 A G SNP TNPO1 NM_002270.3 human genbank 54_36p 1 reviewed intronic c.355+2616 e4+2616 0.002 - - - no_errors tier3 143 1 0.69 128 51 28.49 3 0 0 943309 TCGA-AB-3007 AML51 5 89279561 89279561 C T SNP LOC729011 XM_001132729.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*9996 NULL 0 - - - no_errors tier3 959 2 0.21 590 177 23.08 0 0 NA 943309 TCGA-AB-3007 AML51 5 92045180 92045180 G A SNP ENSG00000221810 ENST00000408883 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*33715 NULL 0 - - - no_errors tier3 495 3 0.6 341 178 34.3 0 0 NA 943309 TCGA-AB-3007 AML51 5 92547942 92547942 G A SNP - - - - - - - - - - - - - - - tier2 634 3 0.47 333 143 30.04 0 0 NA 943309 TCGA-AB-3007 AML51 5 99866531 99866531 A G SNP FAM174A NM_198507.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-32603 NULL 0.017 - - - no_errors tier3 782 1 0.13 441 262 37.11 0 0 NA 943309 TCGA-AB-3007 AML51 5 104804496 104804496 A T SNP - - - - - - - - - - - - - - - tier3 644 0 0 479 162 25.27 0 0 NA 943309 TCGA-AB-3007 AML51 5 113050697 113050697 C T SNP - - - - - - - - - - - - - - - tier3 690 3 0.43 487 274 36.01 0 0 NA 943309 TCGA-AB-3007 AML51 5 116635767 116635767 C T SNP - - - - - - - - - - - - - - - tier3 177 0 0 438 204 31.78 0 0 NA 943309 TCGA-AB-3007 AML51 5 119044124 119044124 G T SNP FAM170A NM_182761.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*45496 NULL 0.539 - - - no_errors tier3 549 0 0 643 345 34.85 7 0 0 943309 TCGA-AB-3007 AML51 5 121267247 121267248 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 5 147038423 147038423 C T SNP JAKMIP2 NM_014790.3 human genbank 54_36p -1 provisional intronic c.1-6713 e1-6713 0 - - - no_errors tier3 197 0 0 202 91 30.95 0 0 NA 943309 TCGA-AB-3007 AML51 5 165119067 165119067 C T SNP ENSG00000213403 ENST00000393907 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*23316 NULL 0.011 - - - no_coding_region:pseudogene tier2 540 6 1.1 334 141 29.68 0 0 NA 943309 TCGA-AB-3007 AML51 5 175225838 175225838 G T SNP CPLX2 NM_006650.1 human genbank 54_36p 1 reviewed intronic c.1-12423 e1-12423 0.001 - - - no_errors tier3 1847 1 0.05 671 473 41.24 0 0 NA 943309 TCGA-AB-3007 AML51 6 864681 864681 G A SNP LOC730031 XM_001132155.2 human genbank 54_36p 1 model intronic c.742+1792 e5+1792 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 1326 6 0.45 392 246 38.56 0 0 NA 943309 TCGA-AB-3007 AML51 6 6578300 6578300 G A SNP LY86 NM_004271.3 human genbank 54_36p 1 validated intronic c.352+6647 e3+6647 0 - - - no_errors tier3 564 4 0.7 899 322 26.31 1 0 0 943309 TCGA-AB-3007 AML51 6 7146253 7146253 C G SNP RREB1 NM_001003699.2 human genbank 54_36p 1 validated intronic c.426-9783 e4-9783 0.14 - - - no_errors tier3 1283 3 0.23 629 385 37.97 5 5 50 943309 TCGA-AB-3007 AML51 6 16331130 16331130 C T SNP GMPR NM_006877.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-15774 NULL 0.001 - - - no_errors tier3 707 5 0.7 326 196 37.55 0 0 NA 943309 TCGA-AB-3007 AML51 6 20103995 20103995 C G SNP ENSG00000177246 ENST00000320470 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46964 NULL 0 - - - no_coding_region:pseudogene tier3 1589 2 0.13 858 470 35.36 0 0 NA 943309 TCGA-AB-3007 AML51 6 23833322 23833322 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 6 28736550 28736550 T C SNP LOC646160 XM_929122.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-27199 NULL 0 - - - no_errors tier3 240 3 1.23 214 134 38.51 0 0 NA 943309 TCGA-AB-3007 AML51 6 46247774 46247774 A G SNP ENPP5 NM_021572.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-3816 NULL 0 - - - no_errors tier3 254 0 0 203 95 31.88 0 0 NA 943309 TCGA-AB-3007 AML51 6 50270492 50270492 G T SNP - - - - - - - - - - - - - - - tier3 445 1 0.22 428 181 29.72 0 0 NA 943309 TCGA-AB-3007 AML51 6 50667291 50667291 C G SNP - - - - - - - - - - - - - - - tier2 258 0 0 186 106 36.3 0 0 NA 943309 TCGA-AB-3007 AML51 6 57813040 57813040 C T SNP ENSG00000214566 ENST00000398589 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-17205 NULL 0.987 - - - no_coding_region:pseudogene tier2 795 1 0.13 678 364 34.9 0 0 NA 943309 TCGA-AB-3007 AML51 6 62456518 62456518 A G SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.953-7594 e9-7594 0.002 - - - no_errors tier3 362 0 0 659 198 23.1 0 0 NA 943309 TCGA-AB-3007 AML51 6 68599313 68599313 C T SNP - - - - - - - - - - - - - - - tier3 429 2 0.46 302 157 34.2 0 0 NA 943309 TCGA-AB-3007 AML51 6 70047919 70047919 T C SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.2814+42080 e18+42080 0.001 - - - no_errors tier3 390 0 0 451 248 35.48 0 0 NA 943309 TCGA-AB-3007 AML51 6 70079156 70079156 G T SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.2815-12329 e19-12329 0 - - - no_errors tier3 261 2 0.76 293 102 25.76 0 0 NA 943309 TCGA-AB-3007 AML51 6 75860167 75860168 - T INS COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed intronic c.8649+1376_8649+1375 e59+1376 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 6 86578395 86578395 G A SNP ENSG00000200427 ENST00000363557 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-34203 NULL 0.068 - - - no_errors tier3 982 5 0.51 491 239 32.69 0 2 100 943309 TCGA-AB-3007 AML51 6 89297441 89297441 C T SNP - - - - - - - - - - - - - - - tier3 1333 3 0.22 639 351 35.45 0 0 NA 943309 TCGA-AB-3007 AML51 6 93704943 93704943 G A SNP ENSG00000219387 ENST00000406040 human ensembl 54_36p -1 known 5_prime_flanking_region c.-49923 NULL 0 - - - no_coding_region:pseudogene tier3 575 1 0.17 402 233 36.69 0 0 NA 943309 TCGA-AB-3007 AML51 6 98204739 98204739 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 6 99041139 99041139 T G SNP - - - - - - - - - - - - - - - tier2 244 0 0 848 444 34.37 0 0 NA 943309 TCGA-AB-3007 AML51 6 102631663 102631663 C A SNP ENSG00000218536 ENST00000405705 human ensembl 54_36p 1 known 5_prime_flanking_region c.-1777 NULL 0.007 - - - no_coding_region:pseudogene tier3 129 1 0.77 201 121 37.58 0 0 NA 943309 TCGA-AB-3007 AML51 6 104888486 104888486 C A SNP - - - - - - - - - - - - - - - tier3 1156 5 0.43 548 327 37.37 0 0 NA 943309 TCGA-AB-3007 AML51 6 115886015 115886015 G A SNP - - - - - - - - - - - - - - - tier3 429 0 0 442 204 31.53 0 0 NA 943309 TCGA-AB-3007 AML51 6 116371739 116371739 C T SNP FRK NM_002031.2 human genbank 54_36p -1 reviewed intronic c.1140+361 e6+361 0.002 - - - no_errors tier3 809 3 0.37 360 179 33.21 0 0 NA 943309 TCGA-AB-3007 AML51 6 119620534 119620534 A C SNP MAN1A1 NM_005907.2 human genbank 54_36p -1 reviewed intronic c.898-9316 e5-9316 0.002 - - - no_errors tier3 761 0 0 456 232 33.72 4 4 50 943309 TCGA-AB-3007 AML51 6 123403816 123403816 T C SNP RLBP1L2 NM_001010852.2 human genbank 54_36p 1 provisional intronic c.565-7650 e3-7650 0 - - - no_errors tier3 297 3 1 392 218 35.74 0 0 NA 943309 TCGA-AB-3007 AML51 6 123955807 123955807 T A SNP TRDN NM_006073.2 human genbank 54_36p -1 validated intronic c.23-21831 e2-21831 0.194 - - - no_errors tier3 84 0 0 414 116 21.89 0 0 NA 943309 TCGA-AB-3007 AML51 6 128119837 128119837 A - DEL C6orf190 NM_001010923.1 human genbank 54_36p -1 validated intronic c.1759-37176 e5-37176 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 6 131744585 131744585 G A SNP - - - - - - - - - - - - - - - tier2 419 0 0 418 185 30.68 0 0 NA 943309 TCGA-AB-3007 AML51 6 133342060 133342060 T C SNP ENSG00000213122 ENST00000392387 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*18342 NULL 0.002 - - - no_coding_region:pseudogene tier3 150 0 0 288 157 35.28 0 0 NA 943309 TCGA-AB-3007 AML51 6 136230460 136230460 A T SNP PDE7B NM_018945.3 human genbank 54_36p 1 validated intronic c.21+15610 e1+15610 0.002 - - - no_errors tier3 254 1 0.39 255 83 24.34 0 0 NA 943309 TCGA-AB-3007 AML51 6 136421825 136421825 A G SNP PDE7B NM_018945.3 human genbank 54_36p 1 validated intronic c.83-49737 e3-49737 0.117 - - - no_errors tier3 475 3 0.63 353 207 36.96 0 0 NA 943309 TCGA-AB-3007 AML51 6 143882560 143882560 A G SNP FUCA2 NM_032020.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-8096 NULL 0 - - - no_errors tier3 2067 6 0.29 955 539 36.08 5 4 44.44 943309 TCGA-AB-3007 AML51 6 145309993 145309993 G A SNP - - - - - - - - - - - - - - - tier3 349 0 0 379 129 25.39 0 0 NA 943309 TCGA-AB-3007 AML51 6 145779822 145779822 G A SNP ENSG00000201119 ENST00000364249 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46245 NULL 0 - - - no_errors tier3 575 6 1.03 490 285 36.77 0 0 NA 943309 TCGA-AB-3007 AML51 6 148444096 148444096 G A SNP - - - - - - - - - - - - - - - tier2 768 1 0.13 472 185 28.16 0 0 NA 943309 TCGA-AB-3007 AML51 6 150746383 150746383 G A SNP IYD NM_203395.1 human genbank 54_36p 1 validated intronic c.179-5798 e2-5798 0 - - - no_errors tier3 240 0 0 397 261 39.61 0 0 NA 943309 TCGA-AB-3007 AML51 6 152280279 152280279 C T SNP ESR1 NM_000125.3 human genbank 54_36p 1 reviewed intronic c.761-26722 e4-26722 0.875 - - - no_errors tier2 363 0 0 473 232 32.91 0 0 NA 943309 TCGA-AB-3007 AML51 6 164105030 164105030 C T SNP - - - - - - - - - - - - - - - tier2 561 0 0 324 174 34.94 0 0 NA 943309 TCGA-AB-3007 AML51 6 167674657 167674657 G A SNP TTLL2 NM_031949.4 human genbank 54_36p 1 validated missense c.1279 p.A427T 0 NULL "HMMPfam_TTL,superfamily_Glutathione synthetase ATP-binding domain-like" - no_errors tier1 1012 2 0.2 331 188 36.08 2 0 943309 TCGA-AB-3007 AML51 6 169716567 169716567 T A SNP WDR27 NM_182552.3 human genbank 54_36p -1 validated intronic c.2523+8290 e23+8290 0.002 - - - no_errors tier3 1057 0 0 889 560 38.59 1 2 66.67 943309 TCGA-AB-3007 AML51 7 9440306 9440306 T A SNP - - - - - - - - - - - - - - - tier2 802 10 1.23 586 351 37.42 0 0 NA 943309 TCGA-AB-3007 AML51 7 10146739 10146739 A - DEL LOC340268 XR_041608.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*17648 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 7 12279567 12279567 A T SNP LOC100134661 XR_039175.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-3032 NULL 0 - - - pseudogene tier3 144 1 0.69 269 97 26.5 0 0 NA 943309 TCGA-AB-3007 AML51 7 14485541 14485542 - T INS DGKB NM_004080.2 human genbank 54_36p -1 reviewed intronic c.1774-1167_1774-1166 e20-1166 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 7 22511837 22511837 C T SNP MGC87042 XM_001723244.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-1235 NULL 0 - - - no_errors tier3 206 0 0 287 118 29.14 0 0 NA 943309 TCGA-AB-3007 AML51 7 34005984 34005984 C T SNP BMPER NM_133468.3 human genbank 54_36p 1 validated intronic c.576+25063 e6+25063 0.002 - - - no_errors tier3 344 0 0 313 191 37.9 0 0 NA 943309 TCGA-AB-3007 AML51 7 34426685 34426685 C T SNP ENSG00000197085 ENST00000357959 human ensembl 54_36p -1 known intronic c.189-2876 e4-2876 0 - - - no_errors tier3 614 4 0.65 368 210 36.27 0 0 NA 943309 TCGA-AB-3007 AML51 7 38832358 38832358 C G SNP VPS41 NM_014396.3 human genbank 54_36p -1 reviewed intronic c.321+4021 e5+4021 0.011 - - - no_errors tier3 347 2 0.57 302 190 38.62 1 0 0 943309 TCGA-AB-3007 AML51 7 39493267 39493267 G A SNP LOC100134792 XM_001726652.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-24793 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier2 447 1 0.22 611 211 25.67 0 0 NA 943309 TCGA-AB-3007 AML51 7 40865968 40865968 G A SNP C7orf10 NM_024728.1 human genbank 54_36p 1 predicted intronic c.1142-472 e15-472 0.001 - - - no_errors tier3 1647 3 0.18 992 651 39.62 0 0 NA 943309 TCGA-AB-3007 AML51 7 43240043 43240043 A G SNP HECW1 NM_015052.3 human genbank 54_36p 1 validated intronic c.1-9956 e1-9956 0.001 - - - no_errors tier3 1376 3 0.22 790 317 28.64 0 0 NA 943309 TCGA-AB-3007 AML51 7 45372457 45372457 A T SNP - - - - - - - - - - - - - - - tier3 234 1 0.43 572 250 30.41 0 0 NA 943309 TCGA-AB-3007 AML51 7 46462848 46462848 G A SNP - - - - - - - - - - - - - - - tier3 107 2 1.83 134 55 29.1 0 0 NA 943309 TCGA-AB-3007 AML51 7 49081991 49081991 G C SNP LOC100134710 XR_038112.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-27984 NULL 0 - - - pseudogene tier3 268 2 0.74 265 133 33.42 0 0 NA 943309 TCGA-AB-3007 AML51 7 53108413 53108413 G - DEL DKFZp564N2472 NM_182595.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*36664 NULL 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 7 53600760 53600760 A G SNP - - - - - - - - - - - - - - - tier3 799 1 0.12 826 467 36.12 0 0 NA 943309 TCGA-AB-3007 AML51 7 56728826 56728826 A G SNP LOC730382 XM_001714509.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-2494 NULL 0.017 - - - no_errors tier3 253 0 0 277 150 35.13 0 0 0 943309 TCGA-AB-3007 AML51 7 62097231 62097231 T G SNP LOC100128613 XM_001715200.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*45587 NULL 0 - - - no_errors tier3 171 2 1.16 670 344 33.89 0 0 NA 943309 TCGA-AB-3007 AML51 7 62137617 62137617 G T SNP ENSG00000207443 ENST00000384712 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-28235 NULL 0.019 - - - no_errors tier3 1823 3 0.16 968 602 38.3 0 0 NA 943309 TCGA-AB-3007 AML51 7 70548922 70548922 C T SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.962+24895 e5+24895 0.006 - - - no_errors tier3 475 4 0.84 224 113 33.53 0 0 NA 943309 TCGA-AB-3007 AML51 7 78942636 78942636 A - DEL MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-22064 NULL 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 7 81654963 81654963 G C SNP CACNA2D1 NM_000722.2 human genbank 54_36p -1 reviewed intronic c.295-17102 e4-17102 0.003 - - - no_errors tier2 249 0 0 172 129 42.86 0 0 NA 943309 TCGA-AB-3007 AML51 7 82099546 82099546 A G SNP ENSG00000213530 ENST00000394740 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41473 NULL 0.001 - - - no_coding_region:pseudogene tier3 212 2 0.93 552 186 25.17 0 0 NA 943309 TCGA-AB-3007 AML51 7 83606230 83606230 A C SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed intronic c.113-4027 e2-4027 0 - - - no_errors tier2 383 2 0.52 317 183 36.53 0 0 NA 943309 TCGA-AB-3007 AML51 7 85089371 85089371 A G SNP - - - - - - - - - - - - - - - tier3 602 5 0.82 673 232 25.64 0 0 NA 943309 TCGA-AB-3007 AML51 7 87916334 87916334 C G SNP ENSG00000207094 ENST00000384366 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*9 NULL 0.001 - - - no_errors tier3 781 0 0 386 207 34.85 0 0 NA 943309 TCGA-AB-3007 AML51 7 99139664 99139665 - T INS CYP3A7 ENST00000292414 human ensembl 54_36p -1 known intronic c.1497+1409_1497+1408 e13+1409 0.004:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 7 110593045 110593045 C G SNP IMMP2L NM_032549.2 human genbank 54_36p -1 provisional intronic c.240-202188 e3-202188 0.049 - - - no_errors tier3 894 0 0 457 373 44.94 0 0 NA 943309 TCGA-AB-3007 AML51 7 112540694 112540694 T A SNP GPR85 NM_018970.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-28682 NULL 0 - - - no_errors tier3 670 1 0.15 133 186 58.13 0 0 NA 943309 TCGA-AB-3007 AML51 7 117431081 117431081 C T SNP - - - - - - - - - - - - - - - tier3 780 5 0.64 227 404 63.92 0 0 NA 943309 TCGA-AB-3007 AML51 7 124835397 124835397 T A SNP - - - - - - - - - - - - - - - tier3 647 1 0.15 142 270 65.53 0 0 NA 943309 TCGA-AB-3007 AML51 7 132267180 132267180 C A SNP CHCHD3 NM_017812.2 human genbank 54_36p -1 provisional intronic c.369+43289 e4+43289 0.999 - - - no_errors tier2 539 6 1.1 110 186 62.84 0 0 NA 943309 TCGA-AB-3007 AML51 8 6137899 6137899 T A SNP LOC100134356 XM_001716700.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-35661 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 619 7 1.12 567 222 28.14 0 0 NA 943309 TCGA-AB-3007 AML51 8 10913950 10913950 T A SNP XKR6 NM_173683.3 human genbank 54_36p -1 provisional intronic c.765-94200 e2-94200 0 - - - no_errors tier3 544 0 0 663 181 21.34 0 0 NA 943309 TCGA-AB-3007 AML51 8 10913951 10913951 C T SNP XKR6 NM_173683.3 human genbank 54_36p -1 provisional intronic c.765-94201 e2-94201 0 - - - no_errors tier3 547 0 0 662 181 21.42 0 0 NA 943309 TCGA-AB-3007 AML51 8 14074827 14074827 G - DEL SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.425-8245 e5-8245 0.019 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 8 15011911 15011911 C T SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.39+127554 e1+127554 0.001 - - - no_errors tier3 261 0 0 308 298 49.17 0 0 NA 943309 TCGA-AB-3007 AML51 8 15730590 15730590 C G SNP - - - - - - - - - - - - - - - tier3 1172 4 0.34 1328 408 23.48 0 0 NA 943309 TCGA-AB-3007 AML51 8 18092990 18092990 A C SNP NAT1 NM_000662.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-30847 NULL 0.012 - - - no_errors tier2 541 0 0 495 161 24.51 0 0 NA 943309 TCGA-AB-3007 AML51 8 18424305 18424305 G A SNP PSD3 NM_015310.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*13228 NULL 0.001 - - - no_errors tier3 497 4 0.8 1510 532 26.05 0 0 NA 943309 TCGA-AB-3007 AML51 8 21301960 21301960 G A SNP - - - - - - - - - - - - - - - tier3 558 0 0 756 273 26.53 0 0 NA 943309 TCGA-AB-3007 AML51 8 24459706 24459706 G A SNP LOC100133599 XM_001715698.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-19710 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 339 1 0.29 748 199 21.01 1 0 0 943309 TCGA-AB-3007 AML51 8 27158338 27158338 G A SNP STMN4 NM_030795.2 human genbank 54_36p -1 provisional intronic c.1-1103 e1-1103 0 - - - no_errors tier2 491 1 0.2 482 166 25.58 0 0 NA 943309 TCGA-AB-3007 AML51 8 30060452 30060452 T A SNP LEPROTL1 NM_015344.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-12119 NULL 0.002 - - - no_errors tier2 291 2 0.68 304 420 58.01 0 2 100 943309 TCGA-AB-3007 AML51 8 35771724 35771724 G A SNP UNC5D NM_080872.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*4101 NULL 1 - - - no_errors tier2 290 0 0 339 123 26.62 0 0 NA 943309 TCGA-AB-3007 AML51 8 40129835 40129835 C T SNP C8orf4 NM_020130.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-374 NULL 0 - - - no_errors tier2 675 7 1.03 417 172 29.2 0 0 NA 943309 TCGA-AB-3007 AML51 8 40955961 40955961 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 8 49552909 49552909 G A SNP ENSG00000210974 ENST00000388239 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14321 NULL 0.035 - - - pseudogene tier3 524 0 0 1071 405 27.4 0 0 NA 943309 TCGA-AB-3007 AML51 8 50142894 50142894 C A SNP C8orf22 NM_001007176.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-5049 NULL 0 - - - no_errors tier3 273 0 0 830 279 25.16 0 0 NA 943309 TCGA-AB-3007 AML51 8 55028718 55028718 C A SNP RGS20 NM_170587.3 human genbank 54_36p 1 validated intronic c.744-471 e5-471 0.757 - - - no_errors tier3 281 1 0.35 575 115 16.64 0 0 NA 943309 TCGA-AB-3007 AML51 8 56657060 56657060 A T SNP - - - - - - - - - - - - - - - tier3 838 1 0.12 1335 318 19.23 0 0 NA 943309 TCGA-AB-3007 AML51 8 63472123 63472123 T G SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.54+147883 e1+147883 0.007 - - - no_errors tier3 113 0 0 157 181 53.55 0 0 NA 943309 TCGA-AB-3007 AML51 8 64794384 64794384 T C SNP - - - - - - - - - - - - - - - tier3 154 0 0 209 227 52.06 0 0 NA 943309 TCGA-AB-3007 AML51 8 72851826 72851826 C T SNP ENSG00000200191 ENST00000363321 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*38457 NULL 0.011 - - - no_errors tier3 807 5 0.62 646 684 51.43 0 0 NA 943309 TCGA-AB-3007 AML51 8 75890412 75890412 A T SNP PI15 NM_015886.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-9628 NULL 0.001 - - - no_errors tier3 1040 2 0.19 788 228 22.44 0 0 NA 943309 TCGA-AB-3007 AML51 8 76595121 76595121 T C SNP HNF4G ENST00000354370 human ensembl 54_36p 1 known intronic c.1-23480 e1-23480 0 - - - no_errors tier3 52 0 0 56 75 57.25 0 0 NA 943309 TCGA-AB-3007 AML51 8 77479693 77479693 T G SNP - - - - - - - - - - - - - - - tier2 498 6 1.19 343 483 58.47 0 0 NA 943309 TCGA-AB-3007 AML51 8 80222597 80222597 T C SNP - - - - - - - - - - - - - - - tier3 436 2 0.46 458 460 50.11 0 0 NA 943309 TCGA-AB-3007 AML51 8 80981645 80981645 C A SNP MRPS28 NM_014018.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*12125 NULL 0.001 - - - no_errors tier3 459 7 1.5 417 467 52.65 0 0 NA 943309 TCGA-AB-3007 AML51 8 87697149 87697149 C T SNP CNGB3 NM_019098.3 human genbank 54_36p -1 validated intronic c.1579-4134 e14-4134 0.002 - - - no_errors tier2 446 1 0.22 518 137 20.82 0 0 NA 943309 TCGA-AB-3007 AML51 8 93816047 93816047 A G SNP FLJ46284 XR_041984.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 189 1 0.53 290 296 50.51 0 0 NA 943309 TCGA-AB-3007 AML51 8 96265925 96265925 G A SNP PLEKHF2 NM_024613.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*29727 NULL 0.007 - - - no_errors tier3 675 0 0 492 431 46.65 0 0 NA 943309 TCGA-AB-3007 AML51 8 96320366 96320366 C T SNP C8orf37 NM_177965.2 human genbank 54_36p -1 predicted 3_prime_flanking_region c.*8655 NULL 0 - - - no_errors tier3 301 3 0.99 447 179 28.59 0 0 NA 943309 TCGA-AB-3007 AML51 8 102213650 102213650 C T SNP ENSG00000202360 ENST00000365490 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-5713 NULL 0.001 - - - no_errors tier3 989 4 0.4 584 636 52.05 0 0 NA 943309 TCGA-AB-3007 AML51 8 106912565 106912565 G A SNP ZFPM2 NM_012082.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*27623 NULL 0.066 - - - no_errors tier3 400 0 0 656 224 25.43 0 0 NA 943309 TCGA-AB-3007 AML51 8 107230683 107230683 G A SNP - - - - - - - - - - - - - - - tier3 276 0 0 435 181 29.34 0 0 NA 943309 TCGA-AB-3007 AML51 8 110056518 110056518 T C SNP - - - - - - - - - - - - - - - tier3 1938 14 0.72 1697 665 28.15 0 0 NA 943309 TCGA-AB-3007 AML51 8 110953464 110953464 G C SNP ENSG00000222729 ENST00000410797 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*1779 NULL 0.004 - - - no_errors tier3 218 0 0 626 109 14.81 0 0 NA 943309 TCGA-AB-3007 AML51 8 112280599 112280599 A G SNP - - - - - - - - - - - - - - - tier3 334 0 0 538 141 20.74 0 0 NA 943309 TCGA-AB-3007 AML51 8 113448873 113448873 T G SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.6136+12884 e38+12884 0.021 - - - no_errors tier3 841 1 0.12 1124 230 16.97 0 0 NA 943309 TCGA-AB-3007 AML51 8 114170948 114170948 A C SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.917+9213 e5+9213 0 - - - no_errors tier3 179 0 0 375 101 21.22 0 0 NA 943309 TCGA-AB-3007 AML51 8 115146072 115146072 C A SNP - - - - - - - - - - - - - - - tier3 845 3 0.35 473 560 54.21 0 0 NA 943309 TCGA-AB-3007 AML51 8 115268534 115268534 C A SNP - - - - - - - - - - - - - - - tier3 84 0 0 259 49 15.86 0 0 NA 943309 TCGA-AB-3007 AML51 8 115580587 115580587 C T SNP - - - - - - - - - - - - - - - tier3 365 1 0.27 388 380 49.48 0 0 NA 943309 TCGA-AB-3007 AML51 8 116020176 116020176 T C SNP - - - - - - - - - - - - - - - tier3 360 1 0.28 522 195 27.2 0 0 NA 943309 TCGA-AB-3007 AML51 8 117280871 117280871 G A SNP - - - - - - - - - - - - - - - tier3 322 1 0.31 412 114 21.63 0 0 NA 943309 TCGA-AB-3007 AML51 8 130439904 130439904 G T SNP - - - - - - - - - - - - - - - tier3 232 2 0.85 429 79 15.55 5 1 16.67 943309 TCGA-AB-3007 AML51 8 135537159 135537159 A C SNP ZFAT NM_020863.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*22748 NULL 0.003 - - - no_errors tier3 796 1 0.13 880 316 26.4 0 0 NA 943309 TCGA-AB-3007 AML51 8 138739390 138739390 C G SNP - - - - - - - - - - - - - - - tier3 550 3 0.54 560 714 56 0 0 NA 943309 TCGA-AB-3007 AML51 9 981278 981278 G A SNP DMRT3 NM_021240.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*273 NULL 0 - - - no_errors tier2 220 0 0 116 64 35.56 0 0 NA 943309 TCGA-AB-3007 AML51 9 1207473 1207473 C T SNP - - - - - - - - - - - - - - - tier3 247 1 0.4 360 171 32.2 0 0 NA 943309 TCGA-AB-3007 AML51 9 5206481 5206482 - T INS INSL6 NM_007179.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-30879 NULL 0.019:0.075 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 9 8735319 8735319 C T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-11373 e1-11373 0.008 - - - no_errors tier3 963 6 0.62 527 327 38.29 0 0 NA 943309 TCGA-AB-3007 AML51 9 11511022 11511022 A T SNP - - - - - - - - - - - - - - - tier3 75 0 0 131 51 28.02 0 0 NA 943309 TCGA-AB-3007 AML51 9 12446011 12446011 A C SNP - - - - - - - - - - - - - - - tier3 743 0 0 803 301 27.26 0 0 NA 943309 TCGA-AB-3007 AML51 9 16625208 16625208 C A SNP BNC2 NM_017637.5 human genbank 54_36p -1 validated intronic c.331-52125 e4-52125 0.574 - - - no_errors tier2 114 0 0 205 87 29.79 0 0 NA 943309 TCGA-AB-3007 AML51 9 19961641 19961641 G A SNP - - - - - - - - - - - - - - - tier3 446 0 0 456 269 37.05 0 0 NA 943309 TCGA-AB-3007 AML51 9 22117547 22117547 G T SNP LOC729983 XM_001718065.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-26811 NULL 0.001 - - - no_errors tier3 662 4 0.6 364 216 37.18 0 0 NA 943309 TCGA-AB-3007 AML51 9 25494132 25494132 A T SNP - - - - - - - - - - - - - - - tier3 613 2 0.33 771 266 25.63 0 0 NA 943309 TCGA-AB-3007 AML51 9 25790975 25790975 T A SNP - - - - - - - - - - - - - - - tier3 385 1 0.26 292 101 25.7 0 0 NA 943309 TCGA-AB-3007 AML51 9 27472616 27472616 A G SNP MOBKL2B NM_024761.3 human genbank 54_36p -1 reviewed intronic c.1-26870 e1-26870 0 - - - no_errors tier3 1309 6 0.45 632 316 33.3 2 0 0 943309 TCGA-AB-3007 AML51 9 33893737 33893737 T G SNP UBE2R2 NM_017811.3 human genbank 54_36p 1 reviewed intronic c.362+3468 e3+3468 0.01 - - - no_errors tier3 393 1 0.25 260 153 37.05 5 4 44.44 943309 TCGA-AB-3007 AML51 9 33954434 33954434 A T SNP UBAP2 NM_018449.2 human genbank 54_36p -1 reviewed intronic c.680-645 e8-645 0.032 - - - no_errors tier3 229 0 0 329 194 37.09 3 4 57.14 943309 TCGA-AB-3007 AML51 9 35980364 35980364 G A SNP RECK NM_021111.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46632 NULL 0.001 - - - no_errors tier3 680 1 0.15 490 265 35.1 0 0 NA 943309 TCGA-AB-3007 AML51 9 38337346 38337346 C T SNP ALDH1B1 NM_000692.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-48400 NULL 0.001 - - - no_errors tier2 244 0 0 180 105 36.84 0 0 NA 943309 TCGA-AB-3007 AML51 9 74544381 74544382 - T INS TMC1 NM_138691.2 human genbank 54_36p 1 reviewed intronic c.363-474_363-473 e5-473 0.008:0.035 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 9 74890748 74890748 A T SNP LOC100132782 XM_001715620.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-34712 NULL 0.544 - - - no_errors tier3 117 0 0 143 88 38.1 0 0 NA 943309 TCGA-AB-3007 AML51 9 79600262 79600262 A C SNP GNAQ NM_002072.2 human genbank 54_36p -1 provisional intronic c.606-934 e5-934 0 - - - no_errors tier3 195 1 0.51 264 158 37.44 3 4 57.14 943309 TCGA-AB-3007 AML51 9 86314561 86314561 C T SNP - - - - - - - - - - - - - - - tier3 679 0 0 486 282 36.67 0 0 NA 943309 TCGA-AB-3007 AML51 9 86773067 86773067 C T SNP NTRK2 NM_006180.1 human genbank 54_36p 1 reviewed intronic c.2172+12815 e16+12815 0.005 - - - no_errors tier3 523 3 0.57 476 266 35.85 0 0 NA 943309 TCGA-AB-3007 AML51 9 87207042 87207042 G A SNP - - - - - - - - - - - - - - - tier2 650 0 0 485 297 37.98 0 0 NA 943309 TCGA-AB-3007 AML51 9 88353135 88353135 T A SNP - - - - - - - - - - - - - - - tier3 416 0 0 509 297 36.85 0 0 NA 943309 TCGA-AB-3007 AML51 9 88419667 88419667 C T SNP - - - - - - - - - - - - - - - tier3 318 1 0.31 425 247 36.7 0 0 NA 943309 TCGA-AB-3007 AML51 9 90460220 90460220 G A SNP LOC286238 NM_001100111.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-3458 NULL 0.008 - - - no_errors tier3 852 3 0.35 373 212 36.24 0 0 NA 943309 TCGA-AB-3007 AML51 9 97264757 97264757 G T SNP PTCH1 NM_000264.3 human genbank 54_36p -1 reviewed intronic c.2561-656 e16-656 0 - - - no_errors tier3 615 4 0.65 386 191 33.1 2 1 33.33 943309 TCGA-AB-3007 AML51 9 97272381 97272381 G A SNP PTCH1 NM_000264.3 human genbank 54_36p -1 reviewed intronic c.1729-347 e13-347 0 - - - no_errors tier3 788 1 0.13 383 185 32.57 2 2 50 943309 TCGA-AB-3007 AML51 9 98234715 98234715 G A SNP HABP4 NM_014282.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-17668 NULL 0.001 - - - no_errors tier3 695 0 0 289 123 29.85 0 0 NA 943309 TCGA-AB-3007 AML51 9 99420289 99420289 C T SNP C9orf97 NM_139246.4 human genbank 54_36p -1 validated intronic c.483-309 e3-309 0 - - - no_errors tier3 597 5 0.83 447 218 32.73 0 0 0 943309 TCGA-AB-3007 AML51 9 99440443 99440443 A G SNP NCBP1 NM_002486.4 human genbank 54_36p 1 reviewed intronic c.35-2454 e2-2454 0.001 - - - no_errors tier3 600 3 0.5 414 175 29.71 1 3 75 943309 TCGA-AB-3007 AML51 9 104717368 104717368 T A SNP ENSG00000216733 ENST00000404477 human ensembl 54_36p 1 known 5_prime_flanking_region c.-7353 NULL 0.004 - - - no_coding_region:pseudogene tier2 788 2 0.25 385 195 33.62 0 0 NA 943309 TCGA-AB-3007 AML51 9 117734966 117734966 C T SNP C9orf27 ENST00000374014 human ensembl 54_36p -1 known 5_prime_flanking_region c.-28225 NULL 0 - - - no_start_codon tier3 1514 14 0.92 1639 1007 38.06 0 0 NA 943309 TCGA-AB-3007 AML51 9 117926194 117926194 T C SNP PAPPA NM_002581.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30079 NULL 0.003 - - - no_errors tier3 1271 10 0.78 830 455 35.38 0 0 NA 943309 TCGA-AB-3007 AML51 9 118013630 118013630 G T SNP PAPPA NM_002581.3 human genbank 54_36p 1 reviewed intronic c.1625-109 e4-109 0 - - - no_errors tier3 919 5 0.54 560 323 36.58 0 0 NA 943309 TCGA-AB-3007 AML51 9 131301058 131301058 C T SNP ENSG00000204054 ENST00000372489 human ensembl 54_36p 1 known intronic c.603+7014 e1+7014 0.021 - - - no_errors tier3 5593 20 0.36 1957 1159 37.17 0 1 100 943309 TCGA-AB-3007 AML51 9 134456666 134456666 G T SNP DDX31 NM_022779.7 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*3408 NULL 1 - - - no_errors tier2 104 1 0.95 170 58 25.44 0 0 NA 943309 TCGA-AB-3007 AML51 9 135483924 135483924 C A SNP DBH NM_000787.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-7391 NULL 0 - - - no_errors tier3 506 2 0.39 217 159 42.29 0 0 NA 943309 TCGA-AB-3007 AML51 10 610936 610936 G C SNP DIP2C NM_014974.2 human genbank 54_36p -1 reviewed intronic c.86-88466 e2-88466 0.004 - - - no_errors tier2 413 2 0.48 291 207 41.57 0 0 NA 943309 TCGA-AB-3007 AML51 10 19834175 19834175 A G SNP C10orf112 ENST00000377265 human ensembl 54_36p 1 known intronic c.160+6594 e1+6594 0.078 - - - no_start_codon:no_stop_codon tier3 438 2 0.45 486 293 37.61 1 0 0 943309 TCGA-AB-3007 AML51 10 22153407 22153407 T C SNP DNAJC1 NM_022365.3 human genbank 54_36p -1 provisional intronic c.979-18373 e9-18373 0.005 - - - no_errors tier3 545 1 0.18 453 246 35.19 1 1 50 943309 TCGA-AB-3007 AML51 10 36675621 36675621 A G SNP - - - - - - - - - - - - - - - tier3 654 0 0 400 199 33.17 0 0 NA 943309 TCGA-AB-3007 AML51 10 43696930 43696930 G A SNP C10orf136 XM_926383.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*31776 NULL 0 - - - no_errors tier2 1092 0 0 849 525 38.15 0 0 NA 943309 TCGA-AB-3007 AML51 10 49223304 49223304 C A SNP MAPK8 ENST00000374189 human ensembl 54_36p 1 known intronic c.1+38434 e0+38434 0.203 - - - no_errors tier3 1901 0 0 1253 345 21.59 8 4 33.33 943309 TCGA-AB-3007 AML51 10 50387833 50387833 A C SNP ERCC6 NM_000124.2 human genbank 54_36p -1 reviewed intronic c.1398-3769 e5-3769 0.001 - - - no_errors tier3 429 1 0.23 306 94 23.5 2 0 0 943309 TCGA-AB-3007 AML51 10 54123806 54123806 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 10 58167588 58167588 C G SNP - - - - - - - - - - - - - - - tier3 273 0 0 149 74 33.18 0 0 NA 943309 TCGA-AB-3007 AML51 10 58289979 58289979 T C SNP - - - - - - - - - - - - - - - tier3 95 0 0 111 54 32.73 0 0 NA 943309 TCGA-AB-3007 AML51 10 58625106 58625106 T A SNP - - - - - - - - - - - - - - - tier3 435 2 0.46 589 189 24.26 0 0 NA 943309 TCGA-AB-3007 AML51 10 74525803 74525803 A C SNP P4HA1 NM_000917.3 human genbank 54_36p -1 reviewed intronic c.1+727 e0+727 0 - - - no_errors tier2 330 1 0.3 221 143 39.29 3 0 0 943309 TCGA-AB-3007 AML51 10 78029273 78029273 A G SNP C10orf11 NM_032024.3 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*42221 NULL 0.002 - - - no_errors tier3 1142 7 0.61 617 294 32.27 1 0 0 943309 TCGA-AB-3007 AML51 10 84834434 84834434 T A SNP ENSG00000200774 ENST00000363904 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16631 NULL 0.002 - - - no_errors tier3 156 0 0 190 89 31.9 0 0 NA 943309 TCGA-AB-3007 AML51 10 84853463 84853464 - T INS ENSG00000200774 ENST00000363904 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-35660 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 10 87373919 87373919 A G SNP GRID1 NM_017551.2 human genbank 54_36p -1 reviewed intronic c.2194-4149 e14-4149 0.002 - - - no_errors tier3 692 3 0.43 329 139 29.7 0 0 0 943309 TCGA-AB-3007 AML51 10 88677223 88677223 G A SNP SNCG NM_003087.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-31212 NULL 0.076 - - - no_errors tier3 359 0 0 213 124 36.8 0 4 100 943309 TCGA-AB-3007 AML51 10 91806220 91806220 T A SNP - - - - - - - - - - - - - - - tier3 354 3 0.84 303 167 35.53 0 0 NA 943309 TCGA-AB-3007 AML51 10 92140636 92140636 G A SNP - - - - - - - - - - - - - - - tier3 291 0 0 271 109 28.68 0 0 NA 943309 TCGA-AB-3007 AML51 10 94280732 94280732 T C SNP IDE NM_004969.2 human genbank 54_36p -1 validated intronic c.661+753 e4+753 0.05 - - - no_errors tier3 111 0 0 104 68 39.53 1 0 0 943309 TCGA-AB-3007 AML51 10 97794773 97794773 A C SNP CCNJ NM_019084.1 human genbank 54_36p 1 validated intronic c.69+564 e1+564 0.006 - - - no_errors tier2 276 2 0.72 435 214 32.97 7 3 30 943309 TCGA-AB-3007 AML51 10 106460041 106460041 T G SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.627+68339 e1+68339 0 - - - no_errors tier3 1046 1 0.1 827 364 30.51 0 0 NA 943309 TCGA-AB-3007 AML51 10 107249724 107249724 C T SNP ENSG00000207068 ENST00000384340 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-34683 NULL 0.003 - - - no_errors tier3 120 0 0 186 108 36.73 0 0 NA 943309 TCGA-AB-3007 AML51 10 107798634 107798634 T G SNP - - - - - - - - - - - - - - - tier3 637 0 0 822 396 32.49 0 0 NA 943309 TCGA-AB-3007 AML51 10 108194047 108194047 A T SNP - - - - - - - - - - - - - - - tier3 914 2 0.22 807 401 33.2 0 0 NA 943309 TCGA-AB-3007 AML51 10 111811466 111811466 T C SNP ADD3 NM_016824.2 human genbank 54_36p 1 reviewed intronic c.1-38907 e1-38907 0.185 - - - no_errors tier3 389 1 0.26 581 324 35.72 2 0 0 943309 TCGA-AB-3007 AML51 10 114586483 114586483 A G SNP ENSG00000203854 ENST00000369398 human ensembl 54_36p 1 known 5_prime_flanking_region c.-17895 NULL 0 - - - no_errors tier3 327 0 0 148 119 44.57 4 3 42.86 943309 TCGA-AB-3007 AML51 10 117911357 117911357 C A SNP GFRA1 NM_005264.1 human genbank 54_36p -1 reviewed intronic c.434-36299 e5-36299 0 - - - no_errors tier3 343 1 0.29 704 290 29.12 0 0 NA 943309 TCGA-AB-3007 AML51 10 120961762 120961762 C T SNP GRK5 NM_005308.2 human genbank 54_36p 1 reviewed intronic c.52+4291 e1+4291 0.238 - - - no_errors tier3 461 3 0.65 303 141 31.76 1 0 0 943309 TCGA-AB-3007 AML51 10 121169052 121169052 G A SNP GRK5 NM_005308.2 human genbank 54_36p 1 reviewed intronic c.340-3616 e5-3616 0.002 - - - no_errors tier3 311 0 0 375 192 33.86 0 0 0 943309 TCGA-AB-3007 AML51 10 125406201 125406201 A G SNP GPR26 NM_153442.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-9713 NULL 0 - - - no_errors tier3 318 0 0 213 145 40.5 0 0 NA 943309 TCGA-AB-3007 AML51 10 127698635 127698635 G A SNP ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed intronic c.2539-251 e22-251 0.005 - - - no_errors tier3 239 0 0 247 137 35.68 0 0 NA 943309 TCGA-AB-3007 AML51 10 128099236 128099236 G A SNP ADAM12 NM_003474.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-32532 NULL 0 - - - no_errors tier3 672 0 0 474 303 39 0 0 NA 943309 TCGA-AB-3007 AML51 10 129135284 129135284 C T SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.5549-364 e52-364 0 - - - no_errors tier3 546 2 0.36 350 252 41.72 0 0 NA 943309 TCGA-AB-3007 AML51 10 130618255 130618255 A G SNP LOC728327 XR_041016.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*13730 NULL 0.706 - - - no_errors tier3 138 0 0 184 149 44.74 0 0 NA 943309 TCGA-AB-3007 AML51 10 133076742 133076742 C T SNP - - - - - - - - - - - - - - - tier3 1002 2 0.2 959 556 36.68 0 0 NA 943309 TCGA-AB-3007 AML51 11 20970750 20970750 C T SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1300+32068 e12+32068 0 - - - no_errors tier3 599 0 0 409 222 35.18 0 0 NA 943309 TCGA-AB-3007 AML51 11 21692010 21692010 C A SNP - - - - - - - - - - - - - - - tier3 688 3 0.43 443 224 33.53 0 0 NA 943309 TCGA-AB-3007 AML51 11 21926436 21926436 C T SNP - - - - - - - - - - - - - - - tier3 404 3 0.74 279 155 35.71 0 0 NA 943309 TCGA-AB-3007 AML51 11 23856813 23856813 A T SNP ENSG00000209584 ENST00000386849 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*28813 NULL 0 - - - pseudogene tier3 492 0 0 264 108 29.03 0 0 NA 943309 TCGA-AB-3007 AML51 11 36036225 36036225 G A SNP LDLRAD3 NM_174902.2 human genbank 54_36p 1 provisional intronic c.193+21850 e2+21850 0.002 - - - no_errors tier3 555 1 0.18 778 413 34.68 0 0 NA 943309 TCGA-AB-3007 AML51 11 37878507 37878507 C T SNP LOC100130668 XM_001724391.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-46390 NULL 0.011 - - - no_start_codon:pseudogene:no_stop_codon tier3 323 1 0.31 307 94 23.44 0 0 NA 943309 TCGA-AB-3007 AML51 11 39283863 39283863 T C SNP ENSG00000201591 ENST00000364721 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*44524 NULL 0.001 - - - no_errors tier2 245 1 0.41 367 235 39.04 0 0 NA 943309 TCGA-AB-3007 AML51 11 40518780 40518780 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 11 40761353 40761353 T A SNP ENSG00000221357 ENST00000408430 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*23622 NULL 0.005 - - - no_errors tier3 272 1 0.36 235 106 31.09 0 0 NA 943309 TCGA-AB-3007 AML51 11 42244245 42244245 C T SNP LOC387761 XM_373495.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-12117 NULL 0.002 - - - no_errors tier3 287 2 0.69 271 112 29.24 0 0 NA 943309 TCGA-AB-3007 AML51 11 45248744 45248744 T G SNP SYT13 NM_020826.2 human genbank 54_36p -1 validated intronic c.184-14726 e2-14726 0.002 - - - no_errors tier3 278 0 0 163 78 32.37 0 0 NA 943309 TCGA-AB-3007 AML51 11 59316265 59316265 G T SNP STX3 NM_004177.3 human genbank 54_36p 1 provisional splice_site c.466+1 e6+1 1 - - - no_errors tier1 1497 0 683 387 36.13 3 100 943309 TCGA-AB-3007 AML51 11 69529187 69529187 G A SNP LOC100127946 XM_001717040.1 human genbank 54_36p 1 model intronic c.59-10242 e2-10242 0 - - - no_errors tier3 1430 3 0.21 843 440 34.24 0 0 NA 943309 TCGA-AB-3007 AML51 11 79246590 79246590 T C SNP - - - - - - - - - - - - - - - tier3 808 0 0 338 222 39.57 0 0 NA 943309 TCGA-AB-3007 AML51 11 79556672 79556672 A C SNP - - - - - - - - - - - - - - - tier3 849 1 0.12 930 433 31.77 0 0 NA 943309 TCGA-AB-3007 AML51 11 83678834 83678834 G T SNP DLG2 NM_001364.1 human genbank 54_36p -1 reviewed intronic c.205-38852 e3-38852 0.004 - - - no_errors tier3 506 1 0.2 362 103 22.15 0 0 NA 943309 TCGA-AB-3007 AML51 11 97148014 97148014 C A SNP - - - - - - - - - - - - - - - tier3 138 0 0 259 128 33.07 0 0 NA 943309 TCGA-AB-3007 AML51 11 99519965 99519965 T C SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1581-47103 e12-47103 0.4 - - - no_errors tier3 241 1 0.41 652 339 34.21 0 0 NA 943309 TCGA-AB-3007 AML51 11 103317372 103317372 A T SNP PDGFD NM_025208.4 human genbank 54_36p -1 reviewed intronic c.772+2018 e5+2018 0 - - - no_errors tier2 664 5 0.75 564 332 37.01 1 0 0 943309 TCGA-AB-3007 AML51 11 105119454 105119454 G A SNP GRIA4 NM_000829.3 human genbank 54_36p 1 reviewed intronic c.248-9463 e3-9463 0 - - - no_errors tier2 570 0 0 641 277 30.17 0 0 NA 943309 TCGA-AB-3007 AML51 11 105848947 105848947 C T SNP - - - - - - - - - - - - - - - tier3 388 1 0.26 535 228 29.88 0 0 NA 943309 TCGA-AB-3007 AML51 11 109229732 109229732 C T SNP - - - - - - - - - - - - - - - tier3 145 0 0 300 111 27.01 0 0 NA 943309 TCGA-AB-3007 AML51 11 112963540 112963540 C T SNP ENSG00000211178 ENST00000388443 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-25252 NULL 0.001 - - - pseudogene tier3 813 1 0.12 636 224 26.05 0 0 NA 943309 TCGA-AB-3007 AML51 11 114510549 114510549 C T SNP CADM1 NM_014333.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*41855 NULL 0.001 - - - no_errors tier3 1228 5 0.41 540 260 32.5 0 0 NA 943309 TCGA-AB-3007 AML51 11 125932668 125932668 G A SNP KIRREL3 NM_032531.2 human genbank 54_36p -1 provisional intronic c.133+5272 e2+5272 0.006 - - - no_errors tier3 1381 2 0.14 1013 276 21.41 0 0 NA 943309 TCGA-AB-3007 AML51 11 131088745 131088745 T C SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.83-197923 e2-197923 0 - - - no_errors tier3 253 0 0 1056 342 24.46 0 0 NA 943309 TCGA-AB-3007 AML51 11 132296820 132296820 G A SNP OPCML NM_002545.1 human genbank 54_36p -1 reviewed intronic c.167+21211 e1+21211 0.19 - - - no_errors tier3 622 0 0 379 152 28.63 0 0 NA 943309 TCGA-AB-3007 AML51 11 132359960 132359960 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.62-41845 e2-41845 0 - - - no_errors tier3 1462 9 0.61 883 323 26.78 0 0 NA 943309 TCGA-AB-3007 AML51 11 133852551 133852551 G A SNP ENSG00000216049 ENST00000401230 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-26608 NULL 0 - - - no_errors tier3 1612 3 0.19 906 385 29.82 0 0 NA 943309 TCGA-AB-3007 AML51 11 133917099 133917099 T C SNP - - - - - - - - - - - - - - - tier3 279 0 0 525 424 44.68 0 0 NA 943309 TCGA-AB-3007 AML51 12 5906031 5906031 G T SNP ANO2 NM_020373.2 human genbank 54_36p -1 validated intronic c.11-3800 e2-3800 0.063 - - - no_errors tier3 589 2 0.34 242 97 28.61 0 0 NA 943309 TCGA-AB-3007 AML51 12 32489154 32489154 A G SNP ENSG00000207176 ENST00000384447 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48806 NULL 0.002 - - - no_errors tier3 180 0 0 203 104 33.88 0 0 NA 943309 TCGA-AB-3007 AML51 12 41661288 41661288 G A SNP - - - - - - - - - - - - - - - tier3 506 1 0.2 540 291 35.02 0 0 NA 943309 TCGA-AB-3007 AML51 12 49876972 49876972 A C SNP POU6F1 ENST00000389243 human ensembl 54_36p -1 known missense c.759 p.S253R 1 NULL "HMMPfam_Pou,HMMSmart_SM00352,PatternScan_POU_1,PatternScan_POU_2,HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like,superfamily_lambda repressor-like DNA-binding domains" - no_errors tier1 369 2 0.54 296 159 34.87 2 0 943309 TCGA-AB-3007 AML51 12 51317484 51317484 C T SNP KRT73 NM_175068.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-18909 NULL 0.001 - - - no_errors tier3 476 2 0.42 396 170 29.98 0 0 NA 943309 TCGA-AB-3007 AML51 12 53728941 53728941 A G SNP NEUROD4 NM_021191.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*21455 NULL 0.015 - - - no_errors tier3 506 0 0 458 217 32.1 0 0 NA 943309 TCGA-AB-3007 AML51 12 65843480 65843480 A G SNP - - - - - - - - - - - - - - - tier3 144 0 0 373 152 28.95 0 0 NA 943309 TCGA-AB-3007 AML51 12 68897035 68897035 A T SNP CNOT2 NM_014515.4 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-61239 NULL 0.004 - - - no_errors tier3 462 2 0.43 350 197 36.01 3 1 25 943309 TCGA-AB-3007 AML51 12 69700437 69700437 G A SNP - - - - - - - - - - - - - - - tier3 294 2 0.68 194 93 32.29 0 0 NA 943309 TCGA-AB-3007 AML51 12 70425726 70425726 G A SNP RAB21 NM_014999.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-9451 NULL 0.043 - - - no_errors tier2 1054 0 0 565 251 30.76 0 0 NA 943309 TCGA-AB-3007 AML51 12 70633034 70633034 G A SNP TPH2 NM_173353.3 human genbank 54_36p 1 reviewed intronic c.608+3332 e5+3332 0.002 - - - no_errors tier3 910 3 0.33 600 230 27.71 0 0 NA 943309 TCGA-AB-3007 AML51 12 72022462 72022462 C G SNP - - - - - - - - - - - - - - - tier3 68 0 0 177 58 24.58 0 0 NA 943309 TCGA-AB-3007 AML51 12 72496900 72496900 C T SNP - - - - - - - - - - - - - - - tier3 136 0 0 116 76 39.58 0 0 NA 943309 TCGA-AB-3007 AML51 12 74647006 74647006 C T SNP LOC100131830 XM_001718976.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-47075 NULL 0 - - - no_errors tier3 286 0 0 306 129 29.66 0 0 NA 943309 TCGA-AB-3007 AML51 12 75519614 75519614 C G SNP LOC441642 XM_001714198.1 human genbank 54_36p 1 model intronic c.549+1263 e3+1263 0.001 - - - pseudogene tier3 1459 5 0.34 721 326 31.14 0 0 NA 943309 TCGA-AB-3007 AML51 12 84052438 84052438 A G SNP LRRIQ1 NM_001079910.1 human genbank 54_36p 1 validated intronic c.4210-3321 e18-3321 0.005 - - - no_errors tier3 206 0 0 370 180 32.73 0 0 NA 943309 TCGA-AB-3007 AML51 12 84087133 84087133 A G SNP LRRIQ1 NM_001079910.1 human genbank 54_36p 1 validated intronic c.4822+8510 e23+8510 0.002 - - - no_errors tier3 398 2 0.5 324 167 34.01 0 0 NA 943309 TCGA-AB-3007 AML51 12 85326950 85326950 C G SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+26115 e0+26115 0 - - - no_errors tier3 308 0 0 210 114 35.19 0 0 NA 943309 TCGA-AB-3007 AML51 12 85640312 85640312 C T SNP MGAT4C NM_013244.3 human genbank 54_36p -1 validated intronic c.1+4805 e0+4805 0 - - - no_errors tier2 622 0 0 457 280 37.99 0 0 NA 943309 TCGA-AB-3007 AML51 12 85961873 85961873 C T SNP - - - - - - - - - - - - - - - tier3 341 0 0 489 297 37.79 0 0 NA 943309 TCGA-AB-3007 AML51 12 109457884 109457884 A T SNP PPTC7 NM_139283.1 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*1341 NULL 0.997 - - - no_errors tier2 137 2 1.43 261 108 29.27 13 8 38.1 943309 TCGA-AB-3007 AML51 12 117463094 117463094 C T SNP - - - - - - - - - - - - - - - tier3 1791 5 0.28 823 504 37.98 0 0 NA 943309 TCGA-AB-3007 AML51 12 126477953 126477953 C G SNP - - - - - - - - - - - - - - - tier3 597 2 0.33 662 269 28.89 0 0 NA 943309 TCGA-AB-3007 AML51 13 19765004 19765004 T C SNP - - - - - - - - - - - - - - - tier2 293 0 0 310 152 32.9 0 0 NA 943309 TCGA-AB-3007 AML51 13 21967537 21967537 A T SNP - - - - - - - - - - - - - - - tier3 1809 5 0.28 757 284 27.28 0 0 NA 943309 TCGA-AB-3007 AML51 13 22738872 22738872 T C SNP SGCG NM_000231.2 human genbank 54_36p 1 reviewed intronic c.386-12626 e4-12626 0 - - - no_errors tier3 356 2 0.56 370 255 40.67 0 0 NA 943309 TCGA-AB-3007 AML51 13 27506255 27506256 - ATCATATTCATATTCTCTGAA INS FLT3 NM_004119.2 human genbank 54_36p -1 reviewed in_frame_ins c.1801_1800 p.600in_frame_insFREYEYD 1.000:0.998 superfamily_Kinase_like "HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726" - no_errors tier1 NA NA NA NA NA NA NA 943309 TCGA-AB-3007 AML51 13 29365912 29365912 A G SNP UBL3 NM_007106.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-44237 NULL 0.002 - - - no_errors tier3 214 0 0 228 107 31.94 0 0 NA 943309 TCGA-AB-3007 AML51 13 34071805 34071805 G A SNP ENSG00000220002 ENST00000407757 human ensembl 54_36p -1 known 5_prime_flanking_region c.-25002 NULL 0.016 - - - no_coding_region:pseudogene tier3 781 0 0 966 482 33.22 0 0 NA 943309 TCGA-AB-3007 AML51 13 36324204 36324204 T C SNP SMAD9 NM_005905.1 human genbank 54_36p -1 validated intronic c.1149+1352 e4+1352 0.007 - - - no_errors tier3 264 0 0 202 122 37.65 0 0 NA 943309 TCGA-AB-3007 AML51 13 37718936 37718936 G A SNP - - - - - - - - - - - - - - - tier3 267 0 0 682 227 24.86 0 0 NA 943309 TCGA-AB-3007 AML51 13 38862832 38862832 T C SNP LHFP NM_005780.2 human genbank 54_36p -1 reviewed intronic c.386-12169 e2-12169 0 - - - no_errors tier3 1011 0 0 417 286 40.62 0 0 0 943309 TCGA-AB-3007 AML51 13 52764295 52764295 G A SNP ENSG00000223329 ENST00000411397 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33789 NULL 0.986 - - - no_errors tier2 449 1 0.22 240 139 36.58 0 0 NA 943309 TCGA-AB-3007 AML51 13 54231007 54231007 C T SNP - - - - - - - - - - - - - - - tier3 85 0 0 139 89 39.04 0 0 NA 943309 TCGA-AB-3007 AML51 13 54779631 54779631 C A SNP - - - - - - - - - - - - - - - tier3 85 0 0 155 71 31.28 0 0 NA 943309 TCGA-AB-3007 AML51 13 56223380 56223380 C A SNP - - - - - - - - - - - - - - - tier3 288 2 0.69 355 148 29.37 0 0 0 943309 TCGA-AB-3007 AML51 13 57335924 57335924 T C SNP ENSG00000209790 ENST00000387055 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*20627 NULL 0.995 - - - pseudogene tier3 283 0 0 334 129 27.86 0 0 NA 943309 TCGA-AB-3007 AML51 13 62225789 62225789 C T SNP - - - - - - - - - - - - - - - tier3 150 1 0.66 169 70 29.29 0 0 NA 943309 TCGA-AB-3007 AML51 13 62485173 62485173 G C SNP - - - - - - - - - - - - - - - tier3 612 3 0.49 275 170 38.2 0 0 NA 943309 TCGA-AB-3007 AML51 13 66711941 66711941 C A SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11368 NULL 0.001 - - - no_errors tier3 291 1 0.34 194 90 31.69 0 0 NA 943309 TCGA-AB-3007 AML51 13 67023555 67023555 T A SNP - - - - - - - - - - - - - - - tier3 134 0 0 234 112 32.37 0 0 NA 943309 TCGA-AB-3007 AML51 13 68205284 68205284 T C SNP ENSG00000209895 ENST00000387160 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-39072 NULL 0.114 - - - pseudogene tier3 483 1 0.21 270 149 35.48 0 0 NA 943309 TCGA-AB-3007 AML51 13 74758360 74758360 G C SNP TBC1D4 NM_014832.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*569 NULL 0.003 - - - no_errors tier3 936 2 0.21 802 475 37.14 6 1 14.29 943309 TCGA-AB-3007 AML51 13 84658876 84658876 G T SNP - - - - - - - - - - - - - - - tier3 370 1 0.27 224 156 41.05 0 0 NA 943309 TCGA-AB-3007 AML51 13 86338564 86338564 C T SNP - - - - - - - - - - - - - - - tier3 419 0 0 511 247 32.5 0 0 NA 943309 TCGA-AB-3007 AML51 13 89434453 89434453 C G SNP ENSG00000215418 ENST00000400284 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-7641 NULL 0 - - - no_coding_region:pseudogene tier3 40 0 0 54 25 31.65 0 0 NA 943309 TCGA-AB-3007 AML51 13 89824305 89824305 C A SNP - - - - - - - - - - - - - - - tier3 186 0 0 219 82 27.24 0 0 NA 943309 TCGA-AB-3007 AML51 13 92849442 92849442 C T SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.161-146075 e2-146075 0 - - - no_errors tier3 852 3 0.35 339 188 35.67 0 0 NA 943309 TCGA-AB-3007 AML51 13 95834608 95834608 T A SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.707+292784 e1+292784 0.007 - - - no_errors tier3 559 0 0 397 183 31.55 0 0 NA 943309 TCGA-AB-3007 AML51 13 99071383 99071383 C T SNP CLYBL NM_206808.1 human genbank 54_36p 1 validated intronic c.62+14371 e1+14371 0.001 - - - no_errors tier3 570 1 0.17 599 261 30.31 6 3 33.33 943309 TCGA-AB-3007 AML51 13 100064420 100064420 G C SNP TMTC4 NM_032813.1 human genbank 54_36p -1 validated intronic c.1951+151 e15+151 0.005 - - - no_errors tier3 226 0 0 263 124 31.96 0 0 0 943309 TCGA-AB-3007 AML51 13 101542890 101542890 T C SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.209-217243 e2-217243 0 - - - no_errors tier3 266 0 0 307 123 28.6 0 0 NA 943309 TCGA-AB-3007 AML51 13 104993679 104993679 T C SNP - - - - - - - - - - - - - - - tier3 406 1 0.25 415 189 31.24 0 0 NA 943309 TCGA-AB-3007 AML51 13 105356121 105356121 C T SNP - - - - - - - - - - - - - - - tier3 268 0 0 334 146 30.35 0 0 NA 943309 TCGA-AB-3007 AML51 13 106847991 106847991 T - DEL FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.916-186887 e2-186887 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 13 106883760 106883760 G T SNP FAM155A NM_001080396.1 human genbank 54_36p -1 provisional intronic c.916-222656 e2-222656 0.001 - - - no_errors tier3 237 0 0 207 104 33.44 0 0 NA 943309 TCGA-AB-3007 AML51 13 108316841 108316841 T A SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.1359+250 e11+250 0.019 - - - no_errors tier3 100 1 0.99 111 48 30.19 0 0 NA 943309 TCGA-AB-3007 AML51 14 22780828 22780828 C T SNP LOC100131781 XM_001716883.1 human genbank 54_36p 1 model intronic c.100+1334 e1+1334 0.001 - - - no_errors tier3 583 0 0 384 164 29.93 0 0 NA 943309 TCGA-AB-3007 AML51 14 25225430 25225430 A G SNP - - - - - - - - - - - - - - - tier3 202 0 0 245 114 31.75 0 0 NA 943309 TCGA-AB-3007 AML51 14 27326249 27326249 G A SNP - - - - - - - - - - - - - - - tier3 656 0 0 731 263 26.46 0 0 NA 943309 TCGA-AB-3007 AML51 14 29264102 29264102 T C SNP PRKD1 NM_002742.2 human genbank 54_36p -1 validated intronic c.403+391 e2+391 0.008 - - - no_errors tier3 1029 2 0.19 755 423 35.85 0 0 NA 943309 TCGA-AB-3007 AML51 14 29329313 29329313 A - DEL PRKD1 NM_002742.2 human genbank 54_36p -1 validated intronic c.265-64682 e2-64682 0.084 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 14 33322255 33322255 T C SNP NPAS3 NM_173159.2 human genbank 54_36p 1 validated intronic c.1114+4726 e9+4726 0 - - - no_errors tier3 278 1 0.36 129 100 43.67 0 0 NA 943309 TCGA-AB-3007 AML51 14 39250939 39250939 G A SNP - - - - - - - - - - - - - - - tier3 512 1 0.19 276 174 38.67 0 0 NA 943309 TCGA-AB-3007 AML51 14 43791413 43791413 C T SNP - - - - - - - - - - - - - - - tier2 548 4 0.72 585 283 32.57 0 0 NA 943309 TCGA-AB-3007 AML51 14 43941822 43941822 T A SNP LOC729165 XM_001133158.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*41930 NULL 0.998 - - - no_errors tier2 319 1 0.31 246 117 32.23 0 0 NA 943309 TCGA-AB-3007 AML51 14 46631541 46631541 T A SNP MDGA2 NM_182830.1 human genbank 54_36p -1 validated intronic c.301+4266 e2+4266 0 - - - no_errors tier2 264 0 0 529 230 30.26 0 0 NA 943309 TCGA-AB-3007 AML51 14 46631564 46631564 C T SNP MDGA2 NM_182830.1 human genbank 54_36p -1 validated intronic c.301+4243 e2+4243 0.04 - - - no_errors tier2 271 0 0 565 234 29.29 0 0 NA 943309 TCGA-AB-3007 AML51 14 47616497 47616497 A G SNP - - - - - - - - - - - - - - - tier3 256 0 0 363 181 32.61 0 0 NA 943309 TCGA-AB-3007 AML51 14 52576512 52576513 - A INS DDHD1 NM_030637.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*6724 NULL 0.002:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 14 59280328 59280328 C T SNP RTN1 NM_021136.2 human genbank 54_36p -1 reviewed intronic c.1015+1851 e2+1851 0.005 - - - no_errors tier3 938 0 0 803 434 35.06 0 0 0 943309 TCGA-AB-3007 AML51 14 68055430 68055430 T A SNP RAD51L1 NM_133509.4 human genbank 54_36p 1 reviewed intronic c.1036+50710 e9+50710 0.051 - - - no_errors tier2 599 1 0.17 429 286 40 0 0 NA 943309 TCGA-AB-3007 AML51 14 73375424 73375424 G A SNP ZNF410 NM_021188.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-53208 NULL 0.066 - - - no_errors tier3 605 2 0.33 435 249 36.4 0 0 NA 943309 TCGA-AB-3007 AML51 14 83195914 83195914 T C SNP - - - - - - - - - - - - - - - tier3 287 0 0 318 158 33.19 0 0 NA 943309 TCGA-AB-3007 AML51 14 83197858 83197858 A T SNP - - - - - - - - - - - - - - - tier3 260 0 0 493 276 35.89 0 0 NA 943309 TCGA-AB-3007 AML51 14 91263077 91263077 A G SNP CATSPERB NM_024764.2 human genbank 54_36p -1 validated intronic c.80-1812 e2-1812 0.003 - - - no_errors tier2 618 2 0.32 653 358 35.41 0 0 NA 943309 TCGA-AB-3007 AML51 14 93127225 93127225 C A SNP KIAA1409 NM_020818.3 human genbank 54_36p 1 validated intronic c.2502-2554 e20-2554 0.006 - - - no_errors tier3 1008 12 1.18 983 355 26.53 0 0 NA 943309 TCGA-AB-3007 AML51 14 105901313 105901313 C T SNP ENSG00000211954 ENST00000390614 human ensembl 54_36p -1 known 5_prime_flanking_region c.-24624 NULL 0.006 - - - no_stop_codon:bad_bp_length_for_coding_region tier3 292 2 0.68 159 95 37.4 0 0 0 943309 TCGA-AB-3007 AML51 15 19127067 19127067 T C SNP LOC401805 XR_017148.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-33100 NULL 0 - - - pseudogene tier3 77 0 0 217 52 19.33 0 0 NA 943309 TCGA-AB-3007 AML51 15 22232411 22232411 G C SNP - - - - - - - - - - - - - - - tier3 463 0 0 369 206 35.76 0 0 NA 943309 TCGA-AB-3007 AML51 15 22364029 22364029 G T SNP - - - - - - - - - - - - - - - tier3 395 0 0 176 96 35.16 0 0 NA 943309 TCGA-AB-3007 AML51 15 22614450 22614450 T A SNP SNRPN NM_022805.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-156244 NULL 0.003 - - - no_errors tier3 572 2 0.35 333 180 35.02 0 0 NA 943309 TCGA-AB-3007 AML51 15 24191038 24191038 G A SNP - - - - - - - - - - - - - - - tier3 361 1 0.28 497 279 35.95 0 0 NA 943309 TCGA-AB-3007 AML51 15 33727013 33727013 C T SNP - - - - - - - - - - - - - - - tier3 750 0 0 480 242 33.52 0 0 NA 943309 TCGA-AB-3007 AML51 15 34068709 34068709 T A SNP - - - - - - - - - - - - - - - tier3 415 0 0 435 250 36.5 0 0 NA 943309 TCGA-AB-3007 AML51 15 37649977 37649977 A G SNP THBS1 NM_003246.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11374 NULL 0.001 - - - no_errors tier3 155 0 0 90 79 46.75 0 0 NA 943309 TCGA-AB-3007 AML51 15 39937252 39937252 G A SNP SPTBN5 NM_016642.2 human genbank 54_36p -1 validated intronic c.8227-52 e49-52 0 - - - no_errors tier3 117 0 0 136 104 43.33 0 0 NA 943309 TCGA-AB-3007 AML51 15 43888940 43888940 C T SNP - - - - - - - - - - - - - - - tier2 298 3 1 342 186 35.23 0 0 NA 943309 TCGA-AB-3007 AML51 15 46326467 46326467 G A SNP SLC12A1 NM_000338.2 human genbank 54_36p 1 validated missense c.1522 p.A508T 0.998 HMMPfam_AA_permease "HMMPfam_AA_permease,HMMPfam_AA_permease_N" - no_errors tier1 1545 3 0.19 1033 326 23.88 NA 943309 TCGA-AB-3007 AML51 15 56461462 56461462 C T SNP LIPC ENST00000356113 human ensembl 54_36p 1 known 5_prime_flanking_region c.-50062 NULL 0.05 - - - no_errors tier3 800 6 0.74 542 290 34.81 0 0 NA 943309 TCGA-AB-3007 AML51 15 59811765 59811765 T A SNP - - - - - - - - - - - - - - - tier3 273 1 0.36 273 160 36.95 0 0 NA 943309 TCGA-AB-3007 AML51 15 69244719 69244719 G A SNP THSD4 NM_024817.2 human genbank 54_36p 1 provisional intronic c.99+10394 e2+10394 1 - - - no_errors tier2 152 2 1.3 126 78 38.24 20 0 0 943309 TCGA-AB-3007 AML51 15 75732987 75732987 C T SNP LINGO1 NM_032808.5 human genbank 54_36p -1 validated 5_prime_flanking_region c.-21275 NULL 0.051 - - - no_errors tier2 876 2 0.23 567 177 23.73 0 0 NA 943309 TCGA-AB-3007 AML51 15 85600113 85600113 C A SNP - - - - - - - - - - - - - - - tier3 354 0 0 428 237 35.59 0 0 NA 943309 TCGA-AB-3007 AML51 15 85846913 85846913 G A SNP ENSG00000207150 ENST00000384421 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-28389 NULL 0 - - - no_errors tier3 148 0 0 176 61 25.74 0 0 NA 943309 TCGA-AB-3007 AML51 15 86166582 86166582 G T SNP NTRK3 ENST00000394480 human ensembl 54_36p -1 known 3_prime_flanking_region c.*54588 NULL 0 - - - no_errors tier3 310 0 0 379 180 32.2 0 0 NA 943309 TCGA-AB-3007 AML51 15 99706510 99706510 G C SNP PCSK6 ENST00000348070 human ensembl 54_36p -1 known intronic c.1856-16751 e15-16751 0 - - - no_errors tier3 762 3 0.39 555 314 36.13 0 0 NA 943309 TCGA-AB-3007 AML51 16 6775044 6775044 C - DEL A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+130392 e0+130392 0.174 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 16 6784195 6784195 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+139543 e0+139543 0 - - - no_errors tier3 1891 5 0.26 574 364 38.76 0 0 NA 943309 TCGA-AB-3007 AML51 16 8407391 8407391 G T SNP - - - - - - - - - - - - - - - tier3 921 0 0 653 358 35.38 0 0 NA 943309 TCGA-AB-3007 AML51 16 14088443 14088443 A G SNP MKL2 NM_014048.3 human genbank 54_36p 1 validated intronic c.1+7731 e0+7731 0.002 - - - no_errors tier3 480 2 0.41 267 106 28.42 0 0 0 943309 TCGA-AB-3007 AML51 16 54467430 54467430 G A SNP CES1 NM_001025195.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42962 NULL 0.014 - - - no_errors tier3 269 1 0.37 316 89 21.98 0 0 NA 943309 TCGA-AB-3007 AML51 16 58865208 58865208 T A SNP - - - - - - - - - - - - - - - tier2 188 0 0 123 85 40.87 0 0 NA 943309 TCGA-AB-3007 AML51 16 59018958 59018958 C T SNP - - - - - - - - - - - - - - - tier3 468 0 0 465 259 35.72 0 0 NA 943309 TCGA-AB-3007 AML51 16 59137091 59137091 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 16 59964260 59964260 T C SNP - - - - - - - - - - - - - - - tier3 68 0 0 35 35 50 0 0 NA 943309 TCGA-AB-3007 AML51 16 60108817 60108817 C T SNP - - - - - - - - - - - - - - - tier3 642 0 0 629 223 26.14 0 0 NA 943309 TCGA-AB-3007 AML51 16 60156267 60156267 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 16 60309509 60309509 C T SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.1537-4146 e9-4146 0 - - - no_errors tier3 627 1 0.16 707 361 33.74 0 0 NA 943309 TCGA-AB-3007 AML51 16 61987917 61987917 T C SNP LOC390735 XM_001129659.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-45363 NULL 0.001 - - - pseudogene tier3 1227 0 0 941 390 29.3 0 0 NA 943309 TCGA-AB-3007 AML51 16 62220483 62220483 A G SNP - - - - - - - - - - - - - - - tier2 637 1 0.16 378 199 34.49 0 0 NA 943309 TCGA-AB-3007 AML51 16 66964650 66964650 C A SNP SMPD3 NM_018667.3 human genbank 54_36p -1 validated intronic c.1-859 e1-859 0.014 - - - no_errors tier2 390 0 0 404 257 38.82 0 0 NA 943309 TCGA-AB-3007 AML51 16 67575648 67575648 C A SNP TMCO7 NM_024562.1 human genbank 54_36p 1 validated intronic c.2842+10076 e15+10076 0.145 - - - no_errors tier3 1372 0 0 635 380 37.44 1 0 0 943309 TCGA-AB-3007 AML51 16 72499039 72499039 C T SNP LOC441506 XR_017565.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*32914 NULL 0 - - - pseudogene tier3 650 1 0.15 667 216 24.43 0 0 NA 943309 TCGA-AB-3007 AML51 16 75695614 75695614 C T SNP - - - - - - - - - - - - - - - tier3 96 0 0 122 73 37.44 0 0 NA 943309 TCGA-AB-3007 AML51 16 77029329 77029329 G A SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1056+5179 e8+5179 0.018 - - - no_errors tier3 625 4 0.64 322 152 32.07 1 2 66.67 943309 TCGA-AB-3007 AML51 16 77395260 77395260 T C SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.1056+371110 e8+371110 0 - - - no_errors tier3 771 5 0.64 614 313 33.76 4 3 42.86 943309 TCGA-AB-3007 AML51 16 80890205 80890205 T A SNP - - - - - - - - - - - - - - - tier3 56 0 0 77 58 42.96 0 0 NA 943309 TCGA-AB-3007 AML51 16 83111382 83111382 C T SNP KIAA1609 NM_020947.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-22189 NULL 0 - - - no_errors tier3 497 1 0.2 365 184 33.45 0 0 NA 943309 TCGA-AB-3007 AML51 17 12037397 12037397 C T SNP MAP2K4 NM_003010.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*52095 NULL 0 - - - no_errors tier3 2007 10 0.5 862 405 31.94 0 0 NA 943309 TCGA-AB-3007 AML51 17 12134191 12134191 C T SNP - - - - - - - - - - - - - - - tier2 523 0 0 558 345 38.21 0 0 NA 943309 TCGA-AB-3007 AML51 17 12580894 12580894 T A SNP MYOCD NM_153604.1 human genbank 54_36p 1 provisional intronic c.591+516 e6+516 0 - - - no_errors tier3 1245 3 0.24 438 288 39.67 0 0 NA 943309 TCGA-AB-3007 AML51 17 16428512 16428512 T C SNP ZNF287 NM_020653.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16763 NULL 0 - - - no_errors tier2 933 4 0.43 663 290 30.33 0 0 NA 943309 TCGA-AB-3007 AML51 17 35414283 35414283 G T SNP CSF3 NM_000759.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-10971 NULL 0.046 - - - no_errors tier3 866 0 0 375 159 29.78 0 0 NA 943309 TCGA-AB-3007 AML51 17 38316527 38316527 T G SNP G6PC NM_000151.2 human genbank 54_36p 1 reviewed missense c.632 p.L211R 0.741 NULL "HMMPfam_PAP2,HMMSmart_acidPPc,superfamily_AcPase_VanPerase" - no_errors tier1 1467 0 1322 792 37.43 NA 943309 TCGA-AB-3007 AML51 17 42731151 42731151 C T SNP ITGB3 NM_000212.2 human genbank 54_36p 1 reviewed intronic c.1691-522 e11-522 0.003 - - - no_errors tier2 982 6 0.61 579 341 37.07 0 0 NA 943309 TCGA-AB-3007 AML51 17 44143238 44143238 A C SNP LOC100132903 XM_001726558.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-12828 NULL 0.003 - - - no_errors tier3 587 1 0.17 410 253 38.16 0 0 NA 943309 TCGA-AB-3007 AML51 17 44934922 44934922 C T SNP NGFR NM_002507.2 human genbank 54_36p 1 reviewed intronic c.208+357 e2+357 0.85 - - - no_errors tier2 984 0 0 986 511 34.02 0 0 NA 943309 TCGA-AB-3007 AML51 17 46490930 46490930 G C SNP SPAG9 NM_003971.2 human genbank 54_36p -1 reviewed intronic c.425-2088 e3-2088 0.148 - - - no_errors tier3 295 0 0 312 171 35.33 0 0 0 943309 TCGA-AB-3007 AML51 17 46729095 46729096 - C INS UTP18 NM_016001.2 human genbank 54_36p 1 validated intronic c.1647-230_1647-229 e13-229 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 17 48295946 48295946 T C SNP - - - - - - - - - - - - - - - tier3 308 1 0.32 208 127 37.91 0 0 NA 943309 TCGA-AB-3007 AML51 17 49369930 49369930 A T SNP - - - - - - - - - - - - - - - tier3 369 1 0.27 229 110 32.45 0 0 NA 943309 TCGA-AB-3007 AML51 17 53700141 53700141 C T SNP LPO NM_006151.1 human genbank 54_36p 1 validated splice_region c.1932-6 e12-6 0.867 - - - no_errors tier3 180 0 0 158 80 33.33 413 472 53.33 943309 TCGA-AB-3007 AML51 17 61131193 61131193 C A SNP CCDC46 NM_145036.2 human genbank 54_36p -1 validated intronic c.2608-15395 e23-15395 0.001 - - - no_errors tier3 649 1 0.15 446 236 34.55 0 0 NA 943309 TCGA-AB-3007 AML51 17 64920813 64920813 T C SNP MAP2K6 NM_002758.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1908 NULL 0 - - - no_errors tier3 625 1 0.16 538 264 32.8 0 0 NA 943309 TCGA-AB-3007 AML51 17 66527100 66527100 C T SNP ENSG00000211252 ENST00000388517 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12283 NULL 0 - - - pseudogene tier3 1341 13 0.96 816 586 41.74 0 0 NA 943309 TCGA-AB-3007 AML51 17 70830137 70830137 C T SNP GRB2 NM_002086.4 human genbank 54_36p -1 reviewed intronic c.300-634 e4-634 0 - - - no_errors tier3 412 0 0 233 101 30.24 13 4 23.53 943309 TCGA-AB-3007 AML51 17 73880390 73880390 G C SNP SOCS3 NM_003955.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-13619 NULL 0.002 - - - no_errors tier3 519 0 0 256 101 28.21 0 0 NA 943309 TCGA-AB-3007 AML51 18 3033451 3033451 T G SNP LPIN2 NM_014646.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-82613 NULL 0.001 - - - no_errors tier3 718 2 0.28 466 269 36.55 0 0 NA 943309 TCGA-AB-3007 AML51 18 3403095 3403095 G A SNP TGIF1 NM_174886.2 human genbank 54_36p 1 reviewed intronic c.1+843 e0+843 0.079 - - - no_errors tier3 199 0 0 209 129 38.17 0 0 NA 943309 TCGA-AB-3007 AML51 18 6201289 6201289 A G SNP L3MBTL4 NM_173464.3 human genbank 54_36p -1 validated intronic c.981+1859 e10+1859 0.001 - - - no_errors tier3 629 4 0.63 793 459 36.66 0 0 NA 943309 TCGA-AB-3007 AML51 18 20935933 20935933 C G SNP ZNF521 NM_015461.2 human genbank 54_36p -1 validated intronic c.3659-9890 e5-9890 1 - - - no_errors tier2 641 0 0 589 148 20.05 0 0 NA 943309 TCGA-AB-3007 AML51 18 21508408 21508408 C T SNP - - - - - - - - - - - - - - - tier2 821 0 0 659 378 36.45 0 0 NA 943309 TCGA-AB-3007 AML51 18 25658130 25658130 T C SNP LOC100132664 XM_001714672.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*39121 NULL 0.001 - - - no_errors tier3 606 8 1.3 336 155 31.57 0 0 NA 943309 TCGA-AB-3007 AML51 18 25882333 25882333 T A SNP - - - - - - - - - - - - - - - tier3 147 0 0 265 117 30.63 0 0 NA 943309 TCGA-AB-3007 AML51 18 36104427 36104427 G A SNP - - - - - - - - - - - - - - - tier3 939 4 0.42 673 405 37.53 0 0 NA 943309 TCGA-AB-3007 AML51 18 39960530 39960531 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 18 43436333 43436333 C T SNP ENSG00000184125 ENST00000328279 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*25112 NULL 0 - - - no_coding_region:pseudogene tier3 1015 2 0.2 490 280 36.27 0 0 NA 943309 TCGA-AB-3007 AML51 18 52218379 52218379 A G SNP - - - - - - - - - - - - - - - tier3 440 4 0.9 492 281 36.3 0 0 NA 943309 TCGA-AB-3007 AML51 18 52634730 52634731 - T INS WDR7 NM_015285.2 human genbank 54_36p 1 reviewed intronic c.3304+357_3304+356 e19+357 0.018:0.040 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 18 56494536 56494536 C T SNP ENSG00000214345 ENST00000398159 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*11953 NULL 0 - - - no_coding_region:pseudogene tier3 147 0 0 153 65 29.82 0 0 NA 943309 TCGA-AB-3007 AML51 18 68083028 68083028 G T SNP - - - - - - - - - - - - - - - tier3 436 2 0.46 391 210 34.94 0 0 NA 943309 TCGA-AB-3007 AML51 18 69467167 69467168 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 18 71856366 71856366 G A SNP - - - - - - - - - - - - - - - tier3 460 0 0 318 182 35.9 0 0 NA 943309 TCGA-AB-3007 AML51 18 74966931 74966931 G A SNP ATP9B NM_198531.3 human genbank 54_36p 1 validated intronic c.294-4412 e3-4412 0.001 - - - no_errors tier3 289 0 0 315 123 28.02 0 1 100 943309 TCGA-AB-3007 AML51 19 11172227 11172227 C T SNP DOCK6 NM_020812.2 human genbank 54_36p -1 validated intronic c.5940-82 e47-82 0 - - - no_errors tier3 1114 6 0.53 521 277 34.5 0 1 100 943309 TCGA-AB-3007 AML51 19 11875824 11875824 C G SNP ZNF69 NM_021915.2 human genbank 54_36p 1 validated intronic c.209+44 e3+44 0.028 - - - no_errors tier3 97 0 0 112 75 40.11 1 0 0 943309 TCGA-AB-3007 AML51 19 33395704 33395704 G C SNP - - - - - - - - - - - - - - - tier3 1645 9 0.54 1212 623 33.93 0 0 NA 943309 TCGA-AB-3007 AML51 19 34516118 34516118 G T SNP - - - - - - - - - - - - - - - tier3 580 1 0.17 292 190 39.42 0 0 NA 943309 TCGA-AB-3007 AML51 19 34788656 34788656 C A SNP POP4 ENST00000392279 human ensembl 54_36p 1 known intronic c.4+2661 e1+2661 0.001 - - - no_start_codon tier2 379 1 0.26 344 190 35.58 0 0 NA 943309 TCGA-AB-3007 AML51 19 37240059 37240059 C T SNP - - - - - - - - - - - - - - - tier2 1115 1 0.09 1159 496 29.95 0 0 NA 943309 TCGA-AB-3007 AML51 19 43651119 43651119 T - DEL RYR1 NM_000540.2 human genbank 54_36p 1 reviewed intronic c.3382-327 e26-327 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 19 44891563 44891563 T A SNP LGALS14 NM_203471.2 human genbank 54_36p 1 reviewed intronic c.391-114 e4-114 0 - - - no_errors tier3 394 1 0.25 797 408 33.8 0 0 NA 943309 TCGA-AB-3007 AML51 19 50325132 50325132 C T SNP LOC284352 XM_001723010.1 human genbank 54_36p 1 model intronic c.203-8480 e2-8480 0.003 - - - no_errors tier3 588 0 0 283 169 37.39 3 2 40 943309 TCGA-AB-3007 AML51 19 62361657 62361657 G A SNP DUXA NM_001012729.1 human genbank 54_36p -1 validated splice_region c.293-4 e4-4 0.004 - - - no_errors tier2 422 0 0 247 145 36.9 0 0 NA 943309 TCGA-AB-3007 AML51 20 922945 922945 C T SNP RSPO4 NM_001029871.2 human genbank 54_36p -1 validated intronic c.79+7784 e1+7784 0 - - - no_errors tier2 944 1 0.11 653 358 35.38 0 0 NA 943309 TCGA-AB-3007 AML51 20 7073257 7073257 C G SNP - - - - - - - - - - - - - - - tier3 404 0 0 463 238 33.95 0 0 NA 943309 TCGA-AB-3007 AML51 20 11626375 11626375 T G SNP LOC728573 XR_042057.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10375 NULL 0.001 - - - no_errors tier3 450 2 0.44 292 164 35.96 0 0 NA 943309 TCGA-AB-3007 AML51 20 14699559 14699559 G A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.418+85954 e5+85954 0.033 - - - no_errors tier3 736 1 0.14 315 187 37.25 0 0 NA 943309 TCGA-AB-3007 AML51 20 14804082 14804082 T A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.418+190477 e5+190477 0 - - - no_errors tier3 647 0 0 526 148 21.96 0 0 NA 943309 TCGA-AB-3007 AML51 20 15898050 15898050 T C SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.985+1775 e13+1775 0 - - - no_errors tier3 408 4 0.97 326 150 31.51 0 0 0 943309 TCGA-AB-3007 AML51 20 31071042 31071042 C T SNP BPIL1 NM_025227.1 human genbank 54_36p 1 reviewed splice_region c.910-5 e10-5 0.015 - - - no_errors tier3 960 1 0.1 601 403 40.06 0 0 NA 943309 TCGA-AB-3007 AML51 20 40531936 40531936 C T SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.1450+2384 e8+2384 0 - - - no_errors tier3 833 8 0.95 814 447 35.45 0 0 NA 943309 TCGA-AB-3007 AML51 20 43323943 43323943 G A SNP RBPJL NM_014276.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45034 NULL 0.001 - - - no_errors tier2 582 0 0 680 357 34.43 0 0 NA 943309 TCGA-AB-3007 AML51 20 45134975 45134975 C T SNP EYA2 NM_172113.3 human genbank 54_36p 1 reviewed intronic c.498+677 e6+677 0 - - - no_errors tier3 109 0 0 143 43 23.12 0 0 NA 943309 TCGA-AB-3007 AML51 20 55105173 55105173 C T SNP - - - - - - - - - - - - - - - tier3 373 2 0.53 159 124 43.82 0 0 NA 943309 TCGA-AB-3007 AML51 20 55928591 55928591 C G SNP LOC100129869 XM_001723509.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*38552 NULL 0.001 - - - no_errors tier3 775 0 0 633 368 36.73 0 0 NA 943309 TCGA-AB-3007 AML51 20 58993621 58993621 C T SNP - - - - - - - - - - - - - - - tier2 188 2 1.04 56 178 75.74 0 0 NA 943309 TCGA-AB-3007 AML51 20 59287458 59287458 G A SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.169+24070 e2+24070 0.001 - - - no_errors tier3 256 0 0 108 76 41.3 0 0 NA 943309 TCGA-AB-3007 AML51 21 13597681 13597681 G A SNP LOC100129305 XM_001714760.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-10953 NULL 0.004 - - - no_errors tier3 138 0 0 178 55 23.61 0 0 NA 943309 TCGA-AB-3007 AML51 21 17637237 17637237 A G SNP - - - - - - - - - - - - - - - tier3 257 1 0.39 340 186 35.36 0 0 NA 943309 TCGA-AB-3007 AML51 21 21837198 21837199 - T INS NCAM2 ENST00000400546 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*5049 NULL 0.000:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 21 24229438 24229439 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 943309 TCGA-AB-3007 AML51 21 24367381 24367381 C A SNP - - - - - - - - - - - - - - - tier3 582 4 0.68 697 309 30.72 0 0 NA 943309 TCGA-AB-3007 AML51 21 25019826 25019826 C T SNP - - - - - - - - - - - - - - - tier2 1108 1 0.09 563 340 37.61 0 0 NA 943309 TCGA-AB-3007 AML51 22 16402686 16402686 G A SNP CECR2 ENST00000400585 human ensembl 54_36p 1 known missense c.2788 p.D930N 0.021 NULL "HMMPfam_Bromodomain,HMMSmart_BROMO,superfamily_Bromodomain,PatternScan_BROMODOMAIN_1" - no_errors tier1 356 2 0.56 352 181 33.96 NA 943309 TCGA-AB-3007 AML51 22 18099884 18099884 C T SNP TBX1 NM_080647.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-27283 NULL 0.374 - - - no_errors tier2 120 0 0 214 127 37.24 0 0 NA 943309 TCGA-AB-3007 AML51 22 22842779 22842779 G A SNP CABIN1 NM_012295.2 human genbank 54_36p 1 reviewed intronic c.4301-2555 e27-2555 0.158 - - - no_errors tier3 599 0 0 218 132 37.71 4 0 0 943309 TCGA-AB-3007 AML51 22 26281467 26281467 G A SNP - - - - - - - - - - - - - - - tier3 1396 4 0.29 234 128 35.36 0 0 NA 943309 TCGA-AB-3007 AML51 22 38398117 38398117 C T SNP CACNA1I NM_021096.1 human genbank 54_36p 1 reviewed intronic c.4540-33 e27-33 0 - - - no_errors tier3 606 0 0 228 134 37.02 0 0 0 943309 TCGA-AB-3007 AML51 22 42054067 42054067 T C SNP SCUBE1 NM_173050.2 human genbank 54_36p -1 validated intronic c.221-8052 e3-8052 0 - - - no_errors tier3 702 1 0.14 291 109 27.25 0 0 NA 943309 TCGA-AB-3007 AML51 22 45413658 45413658 C T SNP GRAMD4 NM_015124.2 human genbank 54_36p 1 validated intronic c.283+1137 e2+1137 0.984 - - - no_errors tier3 970 0 0 656 290 30.56 1 0 0 943309 TCGA-AB-3007 AML51 22 47039892 47039892 C T SNP - - - - - - - - - - - - - - - tier3 1049 1 0.09 332 200 37.45 0 0 NA 943309 TCGA-AB-3007 AML51 22 47992581 47992581 C T SNP ENSG00000217384 ENST00000407128 human ensembl 54_36p -1 known 3_prime_flanking_region c.*3257 NULL 0 - - - no_coding_region:pseudogene tier3 369 0 0 298 159 34.72 0 0 NA 849660 TCGA-AB-3008 AML05 X 6891953 6891953 G A SNP LOC392425 XM_001720545.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-25417 NULL 0.001 - - - pseudogene tier3 182 227 55.5 24 415 94.53 0 1 100 849660 TCGA-AB-3008 AML05 X 29477881 29477881 C T SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.704-118587 e5-118587 0 - - - no_errors tier2 103 38 26.95 178 228 56.16 0 0 NA 849660 TCGA-AB-3008 AML05 X 66832515 66832515 G T SNP AR NM_000044.2 human genbank 54_36p 1 reviewed intronic c.1885+9822 e3+9822 0.026 - - - no_errors tier2 238 536 69.25 19 364 95.04 0 0 NA 849660 TCGA-AB-3008 AML05 1 56095700 56095700 A G SNP - - - - - - - - - - - - - - - tier3 332 101 23.33 363 332 47.77 0 0 NA 849660 TCGA-AB-3008 AML05 1 80133903 80133903 G A SNP - - - - - - - - - - - - - - - tier3 261 90 25.35 484 480 49.64 0 0 NA 849660 TCGA-AB-3008 AML05 1 92196835 92196835 A T SNP BRDT NM_001726.3 human genbank 54_36p 1 validated intronic c.1-4028 e1-4028 0.061 - - - no_errors tier3 710 257 26.58 280 223 44.33 0 0 NA 849660 TCGA-AB-3008 AML05 1 99427958 99427958 A T SNP LOC100129620 XM_001726877.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*42989 NULL 0.021 - - - no_errors tier3 1023 193 15.86 397 391 49.49 0 0 NA 849660 TCGA-AB-3008 AML05 1 102254656 102254656 G A SNP OLFM3 NM_058170.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19696 NULL 0.002 - - - no_errors tier3 333 108 24.49 563 441 43.92 0 0 NA 849660 TCGA-AB-3008 AML05 1 156984589 156984589 T G SNP OR6K6 NM_001005184.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-6641 NULL 0.694 - - - no_errors tier3 913 242 20.93 856 715 45.45 0 0 NA 849660 TCGA-AB-3008 AML05 1 157865788 157865788 C T SNP APCS NM_001639.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*40666 NULL 0 - - - no_errors tier3 422 121 22.24 527 381 41.87 0 0 NA 849660 TCGA-AB-3008 AML05 1 161090872 161090872 G A SNP C1orf110 NM_178550.4 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*307 NULL 0 - - - no_errors tier3 1020 196 16.12 881 832 48.57 0 0 NA 849660 TCGA-AB-3008 AML05 1 175674914 175674914 A C SNP LOC400796 XM_001132413.2 human genbank 54_36p -1 model intronic c.198-45367 e3-45367 0.005 - - - no_errors tier2 859 270 23.89 523 436 45.42 0 0 NA 849660 TCGA-AB-3008 AML05 1 184361396 184361396 G A SNP HMCN1 NM_031935.2 human genbank 54_36p 1 reviewed silent c.12537 p.T4179 0.818 "HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin" "PatternScan_ASX_HYDROXYL,PatternScan_CECROPIN,HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMSmart_SM00179,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,HMMPfam_G2F,HMMSmart_SM00682,superfamily_GFP-like,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_I-set,HMMPfam_ig,PatternScan_EGF_CA,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_EGF/Laminin" - no_errors tier1 459 155 25.24 603 618 50.61 NA 849660 TCGA-AB-3008 AML05 1 201370120 201370120 T C SNP ADORA1 NM_000674.2 human genbank 54_36p 1 reviewed intronic c.341+5187 e1+5187 0.001 - - - no_errors tier3 381 80 17.24 326 269 45.06 0 0 NA 849660 TCGA-AB-3008 AML05 1 217193578 217193578 C G SNP LOC643717 XM_931762.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-3736 NULL 1 - - - no_errors tier2 731 158 17.77 563 463 45.13 0 0 NA 849660 TCGA-AB-3008 AML05 1 227977550 227977550 T A SNP - - - - - - - - - - - - - - - tier3 825 362 30.5 404 338 45.49 0 0 NA 849660 TCGA-AB-3008 AML05 1 239050308 239050308 C T SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.685-3970 e10-3970 0.004 - - - no_errors tier3 460 147 24.22 354 340 48.99 0 0 NA 849660 TCGA-AB-3008 AML05 2 18119212 18119212 G T SNP ENSG00000212455 ENST00000391153 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33732 NULL 0.001 - - - no_errors tier3 964 279 22.45 830 916 52.46 0 0 NA 849660 TCGA-AB-3008 AML05 2 30996007 30996007 C T SNP GALNT14 NM_024572.2 human genbank 54_36p -1 validated intronic c.1380+4482 e13+4482 0.109 - - - no_errors tier3 889 217 19.62 631 591 48.36 0 0 0 849660 TCGA-AB-3008 AML05 2 55841985 55841985 C T SNP - - - - - - - - - - - - - - - tier3 547 150 21.52 526 463 46.81 0 0 NA 849660 TCGA-AB-3008 AML05 2 58240469 58240469 T C SNP VRK2 NM_006296.1 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*137 NULL 0.006 - - - no_errors tier3 141 48 25.4 316 225 41.59 18 10 35.71 849660 TCGA-AB-3008 AML05 2 73962742 73962742 G T SNP ACTG2 NM_001615.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-19205 NULL 0.012 - - - no_errors tier3 513 177 25.65 272 254 48.29 0 0 NA 849660 TCGA-AB-3008 AML05 2 84354992 84354992 C A SNP uc010ffz.1 ENST00000331369 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16462 NULL 0 - - - no_errors tier3 1204 286 19.19 464 394 45.87 0 0 NA 849660 TCGA-AB-3008 AML05 2 102571251 102571251 C T SNP SLC9A2 NM_003048.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-31489 NULL 0 - - - no_errors tier2 487 110 18.43 453 330 41.98 0 0 NA 849660 TCGA-AB-3008 AML05 2 116690683 116690683 C A SNP - - - - - - - - - - - - - - - tier3 452 71 13.58 412 298 41.91 0 0 NA 849660 TCGA-AB-3008 AML05 2 133537266 133537266 G A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.341+66754 e4+66754 0.001 - - - no_errors tier3 863 309 26.37 626 547 46.59 0 0 NA 849660 TCGA-AB-3008 AML05 2 139680097 139680097 G A SNP - - - - - - - - - - - - - - - tier3 97 19 16.38 135 80 37.21 0 0 NA 849660 TCGA-AB-3008 AML05 2 140089816 140089816 C A SNP - - - - - - - - - - - - - - - tier2 610 282 31.61 481 458 48.78 0 0 NA 849660 TCGA-AB-3008 AML05 2 140140799 140140799 C T SNP - - - - - - - - - - - - - - - tier3 614 121 16.46 379 306 44.61 0 0 NA 849660 TCGA-AB-3008 AML05 2 142767411 142767411 T C SNP - - - - - - - - - - - - - - - tier3 580 168 22.43 602 508 45.72 0 0 NA 849660 TCGA-AB-3008 AML05 2 208604721 208604721 G T SNP PLEKHM3 NM_001080475.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-30113 NULL 0.995 - - - no_errors tier2 849 109 11.37 388 175 31.08 1 0 0 849660 TCGA-AB-3008 AML05 2 210859810 210859810 A G SNP MYL1 NM_079420.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*4205 NULL 0.002 - - - no_errors tier3 227 67 22.79 476 488 50.62 0 0 NA 849660 TCGA-AB-3008 AML05 2 211646789 211646789 A G SNP - - - - - - - - - - - - - - - tier3 372 107 22.34 191 184 49.07 0 0 NA 849660 TCGA-AB-3008 AML05 3 18811458 18811458 T A SNP - - - - - - - - - - - - - - - tier3 610 282 31.61 612 540 46.83 0 0 NA 849660 TCGA-AB-3008 AML05 3 19534019 19534019 G A SNP KCNH8 NM_144633.2 human genbank 54_36p 1 reviewed intronic c.2543-475 e15-475 0.001 - - - no_errors tier3 521 220 29.69 480 472 49.48 0 0 0 849660 TCGA-AB-3008 AML05 3 20139255 20139255 G A SNP KAT2B NM_003884.4 human genbank 54_36p 1 reviewed silent c.1368 p.E456 1 NULL "HMMPfam_Acetyltransf_1,HMMPfam_Bromodomain,HMMSmart_BROMO,superfamily_Bromodomain,HMMPfam_PCAF_N,superfamily_Acyl_CoA_acyltransferase,PatternScan_BROMODOMAIN_1" - no_errors tier1 981 271 21.65 503 385 43.26 39 18 31.58 849660 TCGA-AB-3008 AML05 3 20316499 20316499 T G SNP ENSG00000199577 ENST00000362707 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-30933 NULL 0 - - - no_errors tier2 489 157 24.3 498 350 41.27 0 0 NA 849660 TCGA-AB-3008 AML05 3 24398744 24398744 C T SNP THRB NM_000461.4 human genbank 54_36p -1 reviewed intronic c.1-44878 e1-44878 0 - - - no_errors tier3 767 349 31.27 446 430 49.09 0 0 NA 849660 TCGA-AB-3008 AML05 3 60283214 60283214 C A SNP FHIT NM_002012.2 human genbank 54_36p -1 reviewed intronic c.103+214419 e1+214419 0.005 - - - no_errors tier3 236 80 25.32 398 302 43.14 1 5 83.33 849660 TCGA-AB-3008 AML05 3 74640365 74640365 T C SNP CNTN3 NM_020872.1 human genbank 54_36p -1 validated intronic c.56-8739 e2-8739 0.002 - - - no_errors tier3 476 148 23.72 353 284 44.58 0 0 NA 849660 TCGA-AB-3008 AML05 3 77938743 77938743 C T SNP ENSG00000206891 ENST00000384164 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*4839 NULL 0.005 - - - no_errors tier3 336 109 24.49 343 230 40.14 0 0 NA 849660 TCGA-AB-3008 AML05 3 80366970 80366970 T C SNP - - - - - - - - - - - - - - - tier3 284 62 17.92 289 246 45.98 0 0 NA 849660 TCGA-AB-3008 AML05 3 111130713 111130713 G A SNP ENSG00000214380 ENST00000398237 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12236 NULL 0.007 - - - no_coding_region:pseudogene tier3 1088 437 28.66 729 572 43.97 0 1 100 849660 TCGA-AB-3008 AML05 3 168013588 168013588 G A SNP ENSG00000185790 ENST00000331839 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*1518 NULL 0.001 - - - no_coding_region:pseudogene tier3 606 273 31.02 418 369 46.89 0 0 NA 849660 TCGA-AB-3008 AML05 3 180043833 180043833 T - DEL KCNMB2 NM_005832.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*414 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 849660 TCGA-AB-3008 AML05 3 194471024 194471024 A C SNP HRASLS NM_020386.3 human genbank 54_36p 1 validated intronic c.406-63 e3-63 0 - - - no_errors tier3 236 64 21.33 297 242 44.9 0 0 NA 849660 TCGA-AB-3008 AML05 3 194861004 194861004 C T SNP OPA1 NM_130837.2 human genbank 54_36p 1 reviewed intronic c.2520+960 e25+960 0 - - - no_errors tier3 335 121 26.54 340 294 46.23 0 0 0 849660 TCGA-AB-3008 AML05 4 19289024 19289024 A C SNP - - - - - - - - - - - - - - - tier3 292 88 23.16 540 434 44.56 0 0 NA 849660 TCGA-AB-3008 AML05 4 21264713 21264713 C T SNP KCNIP4 NM_001035003.1 human genbank 54_36p -1 reviewed intronic c.88+43358 e1+43358 0 - - - no_errors tier3 401 171 29.84 402 355 46.83 0 0 NA 849660 TCGA-AB-3008 AML05 4 36948433 36948433 G T SNP ENSG00000215243 ENST00000389006 human ensembl 54_36p 1 known intronic c.1+25198 e0+25198 0 - - - no_start_codon:no_stop_codon tier2 668 307 31.49 541 471 46.54 0 0 NA 849660 TCGA-AB-3008 AML05 4 66057088 66057088 G T SNP EPHA5 NM_004439.5 human genbank 54_36p -1 reviewed intronic c.911-13232 e4-13232 0.003 - - - no_errors tier3 271 86 24.09 392 343 46.67 0 0 NA 849660 TCGA-AB-3008 AML05 4 79240297 79240297 G A SNP FRAS1 ENST00000380674 human ensembl 54_36p 1 known intronic c.108+34103 e2+34103 0.353 - - - no_errors tier3 602 155 20.48 399 312 43.88 0 0 NA 849660 TCGA-AB-3008 AML05 4 80866066 80866066 T C SNP - - - - - - - - - - - - - - - tier3 456 77 14.45 594 250 29.62 0 0 NA 849660 TCGA-AB-3008 AML05 4 100006134 100006134 C A SNP EIF4E NM_001968.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*15068 NULL 0.009 - - - no_errors tier3 849 315 27.06 592 607 50.58 0 0 NA 849660 TCGA-AB-3008 AML05 4 111816444 111816444 G A SNP PITX2 NM_153426.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42841 NULL 0.997 - - - no_errors tier3 889 390 30.47 747 642 46.22 0 0 NA 849660 TCGA-AB-3008 AML05 4 121990761 121990761 T G SNP PRDM5 NM_018699.2 human genbank 54_36p -1 reviewed intronic c.300+3262 e3+3262 1 - - - no_errors tier2 464 101 17.88 545 460 45.77 0 0 NA 849660 TCGA-AB-3008 AML05 4 123841786 123841786 T C SNP BBS12 NM_152618.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40712 NULL 0.953 - - - no_errors tier2 275 102 26.98 412 363 46.78 0 0 NA 849660 TCGA-AB-3008 AML05 4 125568121 125568121 C T SNP ENSG00000214796 ENST00000398989 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8231 NULL 0.001 - - - no_coding_region:pseudogene tier2 1435 536 27.17 763 701 47.85 0 0 NA 849660 TCGA-AB-3008 AML05 4 140362638 140362638 C A SNP ELF2 ENST00000394235 human ensembl 54_36p -1 known 5_prime_flanking_region c.-84333 NULL 0.003 - - - no_errors tier3 1284 258 16.72 384 350 47.68 1 0 0 849660 TCGA-AB-3008 AML05 4 178227151 178227151 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 849660 TCGA-AB-3008 AML05 4 181288573 181288573 C G SNP - - - - - - - - - - - - - - - tier3 350 67 16.07 386 152 28.25 0 0 NA 849660 TCGA-AB-3008 AML05 4 182731946 182731946 A T SNP - - - - - - - - - - - - - - - tier3 1038 195 15.82 681 304 30.86 0 0 NA 849660 TCGA-AB-3008 AML05 4 190657421 190657421 T A SNP HSP90AA4P ENST00000378770 human ensembl 54_36p 1 known 3_prime_flanking_region c.*24083 NULL 0.001 - - - no_start_codon tier2 220 38 14.73 516 431 45.51 0 0 NA 849660 TCGA-AB-3008 AML05 4 190657902 190657902 G A SNP HSP90AA4P ENST00000378770 human ensembl 54_36p 1 known 3_prime_flanking_region c.*24564 NULL 0 - - - no_start_codon tier3 399 89 18.24 649 573 46.81 0 0 NA 849660 TCGA-AB-3008 AML05 5 4912356 4912356 T C SNP - - - - - - - - - - - - - - - tier3 582 163 21.88 375 335 47.12 0 0 NA 849660 TCGA-AB-3008 AML05 5 11072645 11072645 C A SNP CTNND2 NM_001332.2 human genbank 54_36p -1 validated intronic c.3000-1475 e18-1475 0.002 - - - no_errors tier3 257 104 28.81 366 353 49.1 0 0 NA 849660 TCGA-AB-3008 AML05 5 29316448 29316448 G A SNP - - - - - - - - - - - - - - - tier3 622 214 25.6 434 333 43.42 0 0 NA 849660 TCGA-AB-3008 AML05 5 39589677 39589677 C A SNP - - - - - - - - - - - - - - - tier3 1017 269 20.92 696 539 43.57 0 0 NA 849660 TCGA-AB-3008 AML05 5 44835863 44835863 C T SNP MRPS30 NM_016640.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8959 NULL 0.069 - - - no_errors tier2 517 139 21.16 677 528 43.82 0 0 0 849660 TCGA-AB-3008 AML05 5 59300192 59300192 A G SNP PDE4D ENST00000309641 human ensembl 54_36p -1 known intronic c.230+19880 e1+19880 0.001 - - - no_start_codon tier3 506 195 27.82 446 376 45.74 0 0 NA 849660 TCGA-AB-3008 AML05 5 62732421 62732421 C T SNP - - - - - - - - - - - - - - - tier3 459 121 20.86 313 271 46.32 0 0 NA 849660 TCGA-AB-3008 AML05 5 86126672 86126672 G T SNP ENSG00000221694 ENST00000408767 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36720 NULL 0 - - - no_errors tier3 741 305 29.16 509 410 44.61 0 2 100 849660 TCGA-AB-3008 AML05 5 89713550 89713550 G A SNP LOC731157 XR_037460.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-28009 NULL 0.005 - - - pseudogene tier3 532 182 25.45 493 379 43.46 0 0 NA 849660 TCGA-AB-3008 AML05 5 105408071 105408071 C A SNP - - - - - - - - - - - - - - - tier3 410 135 24.77 263 237 47.4 0 0 NA 849660 TCGA-AB-3008 AML05 6 3164983 3164983 T C SNP LOC100131504 XM_001714394.1 human genbank 54_36p 1 model intronic c.231+244 e3+244 0.006 - - - no_errors tier3 254 91 26.38 186 121 39.29 0 0 0 849660 TCGA-AB-3008 AML05 6 33595679 33595679 C G SNP ENSG00000223251 ENST00000411319 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20770 NULL 0.106 - - - no_errors tier3 666 255 27.69 295 273 47.98 0 0 NA 849660 TCGA-AB-3008 AML05 6 71963594 71963594 A G SNP ENSG00000207180 ENST00000384451 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*14452 NULL 0.004 - - - no_errors tier3 379 131 25.69 427 380 47.03 0 0 NA 849660 TCGA-AB-3008 AML05 6 91630852 91630852 A C SNP - - - - - - - - - - - - - - - tier3 1184 534 31.03 592 516 46.4 0 0 NA 849660 TCGA-AB-3008 AML05 6 91767859 91767859 T C SNP - - - - - - - - - - - - - - - tier3 452 194 30.03 484 441 47.68 0 0 NA 849660 TCGA-AB-3008 AML05 6 102387680 102387680 T C SNP GRIK2 NM_021956.3 human genbank 54_36p 1 reviewed intronic c.1317+14629 e9+14629 0.003 - - - no_errors tier3 140 50 26.32 273 223 44.96 0 0 NA 849660 TCGA-AB-3008 AML05 6 114055692 114055692 C T SNP LOC728590 XM_001127860.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*45937 NULL 0 - - - pseudogene tier3 739 254 25.58 573 464 44.7 0 0 NA 849660 TCGA-AB-3008 AML05 6 126568052 126568052 A G SNP - - - - - - - - - - - - - - - tier3 558 101 15.33 343 136 28.39 0 0 NA 849660 TCGA-AB-3008 AML05 6 160756222 160756222 C T SNP SLC22A3 NM_021977.2 human genbank 54_36p 1 reviewed intronic c.975+4354 e5+4354 0 - - - no_errors tier3 449 83 15.57 394 302 43.33 0 0 0 849660 TCGA-AB-3008 AML05 7 11902406 11902406 C A SNP - - - - - - - - - - - - - - - tier3 325 82 20.15 396 244 38.12 0 0 NA 849660 TCGA-AB-3008 AML05 7 21579648 21579648 C A SNP DNAH11 ENST00000328843 human ensembl 54_36p 1 known intronic c.1593+1532 e8+1532 0.001 - - - no_errors tier3 361 122 25.26 286 338 54.08 0 0 NA 849660 TCGA-AB-3008 AML05 7 109819535 109819535 A T SNP - - - - - - - - - - - - - - - tier3 442 135 23.4 290 230 44.23 0 0 NA 849660 TCGA-AB-3008 AML05 7 113211129 113211129 G A SNP - - - - - - - - - - - - - - - tier3 497 162 24.58 291 230 44.15 0 0 NA 849660 TCGA-AB-3008 AML05 7 136247113 136247113 G T SNP CHRM2 NM_000739.2 human genbank 54_36p 1 reviewed intronic c.1+42408 e0+42408 0 - - - no_errors tier3 307 128 29.43 558 496 47.01 0 0 NA 849660 TCGA-AB-3008 AML05 7 144931147 144931147 C A SNP - - - - - - - - - - - - - - - tier3 861 331 27.77 547 498 47.56 0 0 NA 849660 TCGA-AB-3008 AML05 8 3891664 3891664 T A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.416-14635 e4-14635 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 393 130 24.86 471 413 46.72 0 0 NA 849660 TCGA-AB-3008 AML05 8 9914254 9914254 C T SNP MSRA NM_012331.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35183 NULL 0.219 - - - no_errors tier3 209 70 25.09 371 268 41.94 0 0 NA 849660 TCGA-AB-3008 AML05 8 35352234 35352234 C T SNP UNC5D ENST00000404895 human ensembl 54_36p 1 known intronic c.103+139287 e1+139287 0 - - - no_errors tier2 1060 150 12.4 483 192 28.4 0 0 NA 849660 TCGA-AB-3008 AML05 8 36941604 36941604 G A SNP KCNU1 NM_001031836.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*29008 NULL 0 - - - no_errors tier3 199 45 18.44 307 197 39.09 0 0 NA 849660 TCGA-AB-3008 AML05 8 39615383 39615383 A T SNP ADAM18 NM_014237.1 human genbank 54_36p 1 reviewed intronic c.909+161 e10+161 0 - - - no_errors tier3 183 30 14.08 272 235 46.35 0 0 NA 849660 TCGA-AB-3008 AML05 8 57620767 57620767 T A SNP LOC389662 XR_016813.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-5188 NULL 0 - - - pseudogene tier3 815 299 26.82 844 629 42.64 0 0 NA 849660 TCGA-AB-3008 AML05 8 64979381 64979381 C T SNP - - - - - - - - - - - - - - - tier2 424 67 13.65 534 191 26.34 0 0 NA 849660 TCGA-AB-3008 AML05 8 74155955 74155955 C T SNP C8orf84 NM_153225.3 human genbank 54_36p -1 validated missense c.247 p.D83N 0.085 "HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat" "HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,PatternScan_SMB_1" - no_errors tier1 729 289 28.39 350 373 51.52 NA 849660 TCGA-AB-3008 AML05 8 76165888 76165888 A C SNP - - - - - - - - - - - - - - - tier3 1209 443 26.8 776 616 44.22 0 0 NA 849660 TCGA-AB-3008 AML05 8 88487363 88487363 C G SNP CNBD1 NM_173538.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*23392 NULL 0 - - - no_errors tier3 527 185 25.98 574 519 47.44 0 0 NA 849660 TCGA-AB-3008 AML05 8 92516519 92516519 G A SNP SLC26A7 NM_134266.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*40841 NULL 0 - - - no_errors tier2 455 127 21.82 421 326 43.64 0 0 NA 849660 TCGA-AB-3008 AML05 8 93601303 93601303 C A SNP - - - - - - - - - - - - - - - tier3 613 192 23.85 522 426 44.94 0 0 NA 849660 TCGA-AB-3008 AML05 8 94555356 94555356 A G SNP LOC100129242 XM_001717187.1 human genbank 54_36p -1 model intronic c.279+21307 e3+21307 0 - - - no_errors tier3 887 173 16.32 1014 433 29.92 0 0 NA 849660 TCGA-AB-3008 AML05 8 97223753 97223753 G A SNP GDF6 NM_001001557.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*2214 NULL 0.999 - - - no_errors tier2 617 166 21.2 559 428 43.32 0 0 NA 849660 TCGA-AB-3008 AML05 8 105144078 105144078 C T SNP RIMS2 NM_001100117.1 human genbank 54_36p 1 validated intronic c.3334+48059 e19+48059 0 - - - no_errors tier2 279 71 20.29 403 304 43 0 0 NA 849660 TCGA-AB-3008 AML05 8 110686508 110686508 C - DEL GOLSYN NM_001099744.1 human genbank 54_36p -1 validated intronic c.427+13739 e3+13739 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 849660 TCGA-AB-3008 AML05 8 133512807 133512807 C T SNP KCNQ3 NM_004519.2 human genbank 54_36p -1 reviewed intronic c.386+48769 e1+48769 0 - - - no_errors tier3 925 146 13.63 481 460 48.78 0 0 NA 849660 TCGA-AB-3008 AML05 8 139051023 139051023 G A SNP FLJ45872 XR_040309.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.004 - - - no_errors tier3 653 134 17.03 624 525 45.69 0 0 NA 849660 TCGA-AB-3008 AML05 8 139304253 139304253 T G SNP FAM135B NM_015912.3 human genbank 54_36p -1 validated intronic c.669+20114 e6+20114 0.014 - - - no_errors tier3 1686 498 22.8 574 515 47.29 0 0 NA 849660 TCGA-AB-3008 AML05 9 13910113 13910113 T C SNP LOC100131263 XM_001724969.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-7923 NULL 0.008 - - - no_errors tier3 342 90 20.83 489 452 48.03 0 0 NA 849660 TCGA-AB-3008 AML05 9 71257710 71257710 C T SNP APBA1 NM_001163.3 human genbank 54_36p -1 reviewed intronic c.1789-673 e8-673 0.023 - - - no_errors tier2 435 161 27.01 358 333 48.19 8 6 42.86 849660 TCGA-AB-3008 AML05 9 84846074 84846074 T C SNP RASEF NM_152573.2 human genbank 54_36p -1 provisional intronic c.432-15418 e2-15418 0 - - - no_errors tier2 278 109 28.17 285 257 47.42 0 0 NA 849660 TCGA-AB-3008 AML05 9 104909054 104909054 A G SNP ENSG00000217435 ENST00000402842 human ensembl 54_36p 1 known 3_prime_flanking_region c.*41353 NULL 0.002 - - - no_coding_region:pseudogene tier3 299 92 23.47 298 235 44.01 0 0 NA 849660 TCGA-AB-3008 AML05 9 108315288 108315288 G A SNP - - - - - - - - - - - - - - - tier3 573 195 25.36 430 344 44.39 0 0 NA 849660 TCGA-AB-3008 AML05 9 119854464 119854464 A - DEL LOC389787 XM_001725747.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*30499 NULL 0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 849660 TCGA-AB-3008 AML05 10 8847991 8847991 A G SNP LOC100133979 XR_037040.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37874 NULL 0.007 - - - pseudogene tier3 532 104 16.35 364 313 46.23 0 0 NA 849660 TCGA-AB-3008 AML05 10 24792265 24792265 C T SNP KIAA1217 NM_019590.1 human genbank 54_36p 1 validated intronic c.847-9898 e6-9898 0 - - - no_errors tier3 616 172 21.83 447 496 52.49 0 1 100 849660 TCGA-AB-3008 AML05 10 29043373 29043373 G T SNP LOC729590 XM_001723003.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-32957 NULL 0 - - - no_errors tier3 1076 33 2.97 770 163 17.47 0 0 NA 849660 TCGA-AB-3008 AML05 10 37072369 37072369 A G SNP - - - - - - - - - - - - - - - tier3 474 114 19.32 198 168 45.78 0 0 NA 849660 TCGA-AB-3008 AML05 10 97210850 97210850 A C SNP SORBS1 NM_015385.1 human genbank 54_36p -1 validated intronic c.1-19923 e1-19923 0.009 - - - no_errors tier3 228 75 24.75 341 266 43.82 0 0 NA 849660 TCGA-AB-3008 AML05 10 116780395 116780395 G T SNP - - - - - - - - - - - - - - - tier3 1319 203 13.33 1218 541 30.72 0 0 NA 849660 TCGA-AB-3008 AML05 10 116780396 116780396 A G SNP - - - - - - - - - - - - - - - tier3 1310 204 13.47 1208 538 30.81 0 0 NA 849660 TCGA-AB-3008 AML05 11 8029285 8029285 T C SNP TUB NM_003320.4 human genbank 54_36p 1 reviewed intronic c.203+11470 e2+11470 0.002 - - - no_errors tier3 105 47 30.92 66 253 79.31 0 0 NA 849660 TCGA-AB-3008 AML05 11 38528432 38528432 T C SNP - - - - - - - - - - - - - - - tier3 472 29 5.79 405 72 15.06 0 0 NA 849660 TCGA-AB-3008 AML05 11 39660558 39660558 T G SNP - - - - - - - - - - - - - - - tier3 533 564 51.37 300 1003 76.98 0 0 NA 849660 TCGA-AB-3008 AML05 11 42466812 42466812 T A SNP - - - - - - - - - - - - - - - tier3 236 156 39.8 210 432 67.19 0 0 NA 849660 TCGA-AB-3008 AML05 11 99071067 99071067 A G SNP CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.56-124418 e2-124418 0.004 - - - no_errors tier2 439 198 31.03 422 379 47.32 0 0 NA 849660 TCGA-AB-3008 AML05 11 105633918 105633918 A G SNP - - - - - - - - - - - - - - - tier3 648 254 28.16 675 584 46.39 0 0 NA 849660 TCGA-AB-3008 AML05 11 108831908 108831908 G A SNP C11orf87 NM_207645.2 human genbank 54_36p 1 predicted 3_prime_flanking_region c.*31745 NULL 0 - - - no_errors tier3 702 145 17.12 411 244 37.25 0 0 NA 849660 TCGA-AB-3008 AML05 11 115369047 115369047 A C SNP - - - - - - - - - - - - - - - tier3 520 141 21.27 363 333 47.84 0 0 NA 849660 TCGA-AB-3008 AML05 11 131939785 131939785 G A SNP OPCML NM_002545.1 human genbank 54_36p -1 reviewed intronic c.401-35495 e3-35495 0.2 - - - no_errors tier3 822 246 22.97 378 306 44.74 0 0 NA 849660 TCGA-AB-3008 AML05 11 132853510 132853510 C T SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.61+53859 e1+53859 0 - - - no_errors tier3 1046 307 22.69 704 623 46.91 0 0 NA 849660 TCGA-AB-3008 AML05 12 40146011 40146011 G A SNP PDZRN4 NM_013377.3 human genbank 54_36p 1 validated intronic c.69+27929 e1+27929 0.002 - - - no_errors tier2 397 85 17.63 483 430 47.1 0 0 NA 849660 TCGA-AB-3008 AML05 12 52519096 52519096 C T SNP ENSG00000223213 ENST00000411281 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47679 NULL 1 - - - no_errors tier2 1157 542 31.83 922 925 49.97 0 0 NA 849660 TCGA-AB-3008 AML05 12 66550776 66550776 A G SNP - - - - - - - - - - - - - - - tier3 198 46 18.78 264 170 39.17 0 0 NA 849660 TCGA-AB-3008 AML05 12 82366119 82366119 C T SNP - - - - - - - - - - - - - - - tier3 292 65 18.21 318 307 49.12 0 0 NA 849660 TCGA-AB-3008 AML05 12 96060310 96060310 A C SNP - - - - - - - - - - - - - - - tier3 233 78 25.08 281 266 48.63 0 0 NA 849660 TCGA-AB-3008 AML05 12 113346885 113346885 C T SNP TBX5 NM_000192.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-20799 NULL 0 - - - no_errors tier3 781 133 14.55 457 353 43.58 0 0 NA 849660 TCGA-AB-3008 AML05 12 116634516 116634516 G A SNP KSR2 NM_173598.4 human genbank 54_36p -1 validated intronic c.624-44670 e3-44670 0.822 - - - no_errors tier3 992 190 16.07 377 367 49.33 0 0 NA 849660 TCGA-AB-3008 AML05 12 121567769 121567769 C G SNP RSRC2 NM_023012.4 human genbank 54_36p -1 validated missense c.560 p.R187T 1 NULL NULL - no_errors tier1 305 127 29.4 356 337 48.63 59 67 53.17 849660 TCGA-AB-3008 AML05 13 60100264 60100264 C T SNP LOC390407 XM_001723657.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*8757 NULL 0 - - - no_errors tier2 573 141 19.72 787 589 42.81 0 0 NA 849660 TCGA-AB-3008 AML05 13 69191870 69191870 G A SNP KLHL1 NM_020866.2 human genbank 54_36p -1 validated intronic c.1803-156 e9-156 0 - - - no_errors tier3 348 100 22.32 261 198 43.14 0 0 NA 849660 TCGA-AB-3008 AML05 13 71754607 71754607 T A SNP - - - - - - - - - - - - - - - tier3 257 91 26.15 635 637 50.08 0 0 NA 849660 TCGA-AB-3008 AML05 13 92788420 92788420 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.160+110550 e1+110550 0.003 - - - no_errors tier3 379 135 26.26 626 471 42.94 0 0 NA 849660 TCGA-AB-3008 AML05 14 26912679 26912679 G A SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model intronic c.202-51492 e3-51492 0 - - - no_errors tier2 367 59 13.85 362 291 44.56 0 0 NA 849660 TCGA-AB-3008 AML05 14 33784557 33784557 T C SNP - - - - - - - - - - - - - - - tier3 823 305 26.85 709 735 50.52 0 0 NA 849660 TCGA-AB-3008 AML05 14 41632847 41632847 T A SNP - - - - - - - - - - - - - - - tier3 318 116 26.73 532 446 45.56 0 0 NA 849660 TCGA-AB-3008 AML05 14 51104994 51104994 C T SNP FRMD6 NM_001042481.1 human genbank 54_36p 1 validated intronic c.1-1822 e1-1822 0.001 - - - no_errors tier3 362 103 22.15 561 399 41.52 0 0 NA 849660 TCGA-AB-3008 AML05 14 79250987 79250987 G A SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2805+16954 e13+16954 0.965 - - - no_errors tier3 701 280 28.54 604 481 44.29 0 0 NA 849660 TCGA-AB-3008 AML05 14 81312825 81312825 G T SNP - - - - - - - - - - - - - - - tier3 342 100 22.62 821 719 46.63 0 0 NA 849660 TCGA-AB-3008 AML05 14 85680817 85680817 C A SNP - - - - - - - - - - - - - - - tier3 514 85 14.19 527 513 49.33 1 1 50 849660 TCGA-AB-3008 AML05 14 95404007 95404007 G T SNP LOC730125 XM_001134301.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-9249 NULL 0 - - - no_errors tier2 757 206 21.37 332 310 48.29 0 0 NA 849660 TCGA-AB-3008 AML05 15 35244855 35244855 G C SNP - - - - - - - - - - - - - - - tier2 324 67 17.14 548 242 30.63 0 0 NA 849660 TCGA-AB-3008 AML05 15 48162738 48162738 T C SNP ATP8B4 NM_024837.2 human genbank 54_36p -1 validated intronic c.29-9064 e2-9064 0 - - - no_errors tier3 639 116 15.36 469 392 45.53 5 2 28.57 849660 TCGA-AB-3008 AML05 15 69327356 69327356 A G SNP THSD4 NM_024817.2 human genbank 54_36p 1 provisional intronic c.912+4867 e4+4867 0.016 - - - no_errors tier3 491 146 22.92 321 320 49.92 0 0 NA 849660 TCGA-AB-3008 AML05 15 69961428 69961428 C A SNP MYO9A NM_006901.2 human genbank 54_36p -1 validated intronic c.5399-1475 e28-1475 0.002 - - - no_errors tier3 309 83 21.17 478 413 46.35 4 1 16.67 849660 TCGA-AB-3008 AML05 15 99675579 99675579 T A SNP PCSK6 ENST00000348070 human ensembl 54_36p -1 known intronic c.2566+468 e20+468 0.002 - - - no_errors tier3 220 36 14.06 103 43 29.45 0 0 0 849660 TCGA-AB-3008 AML05 16 7667961 7667961 C T SNP A2BP1 NM_145891.1 human genbank 54_36p 1 reviewed intronic c.1058+1120 e11+1120 0.97 - - - no_errors tier3 563 171 23.3 358 299 45.51 0 0 NA 849660 TCGA-AB-3008 AML05 16 50218171 50218171 G T SNP ENSG00000212961 ENST00000406883 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19032 NULL 0 - - - no_coding_region:pseudogene tier3 821 364 30.69 579 518 47.22 0 0 NA 849660 TCGA-AB-3008 AML05 16 50438665 50438665 A G SNP - - - - - - - - - - - - - - - tier3 307 49 13.76 216 243 52.94 0 0 NA 849660 TCGA-AB-3008 AML05 16 55742030 55742030 G T SNP RSPRY1 NM_133368.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-54042 NULL 0.01 - - - no_errors tier3 1047 202 16.17 554 540 49.32 1 1 50 849660 TCGA-AB-3008 AML05 16 58372095 58372095 C G SNP LOC644649 XR_017144.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-25293 NULL 0.055 - - - pseudogene tier2 527 181 25.56 550 537 49.4 0 0 NA 849660 TCGA-AB-3008 AML05 16 65453097 65453097 C T SNP NAE1 NM_003905.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-30794 NULL 0 - - - no_errors tier3 1085 314 22.4 633 555 45.83 0 0 NA 849660 TCGA-AB-3008 AML05 16 85620737 85620737 C A SNP - - - - - - - - - - - - - - - tier3 469 69 12.83 671 271 28.77 0 0 NA 849660 TCGA-AB-3008 AML05 17 3264988 3264988 C T SNP OR1E1 NM_003553.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-16534 NULL 0 - - - no_errors tier3 331 77 18.87 472 383 44.74 0 0 NA 849660 TCGA-AB-3008 AML05 17 10192152 10192152 G A SNP MYH13 NM_003802.2 human genbank 54_36p -1 validated intronic c.1145-1312 e11-1312 0.001 - - - no_errors tier3 959 210 17.96 455 422 48.12 0 0 NA 849660 TCGA-AB-3008 AML05 17 41294463 41294463 C T SNP MAPT NM_016835.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-101077 NULL 0.05 - - - no_errors tier2 1289 503 28.05 355 307 46.37 0 0 NA 849660 TCGA-AB-3008 AML05 17 54419189 54419189 C T SNP TRIM37 NM_001005207.2 human genbank 54_36p -1 reviewed intronic c.2892-4125 e25-4125 0 - - - no_errors tier3 618 192 23.7 495 531 51.75 0 0 NA 849660 TCGA-AB-3008 AML05 18 4085199 4085199 G T SNP - - - - - - - - - - - - - - - tier3 395 105 21 359 289 44.46 0 0 NA 849660 TCGA-AB-3008 AML05 18 11099284 11099284 C T SNP - - - - - - - - - - - - - - - tier3 218 62 22.14 276 210 43.21 0 0 NA 849660 TCGA-AB-3008 AML05 18 12837997 12837997 G T SNP PTPN2 NM_002828.2 human genbank 54_36p -1 reviewed intronic c.161-11107 e3-11107 0.006 - - - no_errors tier3 380 127 25.05 435 329 43.06 1 0 0 849660 TCGA-AB-3008 AML05 18 13364156 13364156 C T SNP C18orf1 NM_181481.2 human genbank 54_36p 1 validated intronic c.1-13184 e1-13184 0.001 - - - no_errors tier3 168 41 19.62 475 356 42.84 0 4 100 849660 TCGA-AB-3008 AML05 18 36316952 36316952 C T SNP - - - - - - - - - - - - - - - tier3 473 109 18.73 448 405 47.48 0 0 NA 849660 TCGA-AB-3008 AML05 18 48132105 48132105 T A SNP DCC NM_005215.2 human genbank 54_36p 1 validated intronic c.91+10859 e1+10859 0.001 - - - no_errors tier3 357 105 22.73 274 243 47 0 0 NA 849660 TCGA-AB-3008 AML05 18 56820060 56820060 C T SNP - - - - - - - - - - - - - - - tier3 584 117 16.69 677 346 33.82 0 0 NA 849660 TCGA-AB-3008 AML05 18 74240386 74240386 C T SNP - - - - - - - - - - - - - - - tier2 179 60 25.1 221 157 41.53 0 0 NA 849660 TCGA-AB-3008 AML05 19 4984669 4984669 G A SNP JMJD2B NM_015015.2 human genbank 54_36p 1 validated intronic c.141+627 e1+627 0 - - - no_errors tier3 253 72 22.09 310 285 47.9 3 1 25 849660 TCGA-AB-3008 AML05 19 9963790 9963790 G A SNP COL5A3 NM_015719.3 human genbank 54_36p -1 reviewed intronic c.1849-66 e22-66 0.002 - - - no_errors tier3 4044 831 17.04 793 718 47.49 0 0 0 849660 TCGA-AB-3008 AML05 19 35384717 35384717 C A SNP - - - - - - - - - - - - - - - tier3 708 140 16.51 392 359 47.74 0 0 NA 849660 TCGA-AB-3008 AML05 19 38484248 38484249 - CAA INS CEBPA NM_004364.3 human genbank 54_36p -1 reviewed in_frame_ins c.913_912 p.304in_frame_insL 1.000:1.000 "HMMSmart_BRLZ,HMMPfam_bZIP_2" "HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 849660 TCGA-AB-3008 AML05 19 56786070 56786071 - CACCTG INS LOC100132800 XM_001724852.1 human genbank 54_36p 1 model in_frame_ins c.45_46 p.17in_frame_insHL 0.099:0.155 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA 849660 TCGA-AB-3008 AML05 20 22089016 22089016 C T SNP - - - - - - - - - - - - - - - tier3 405 158 28.06 509 485 48.79 0 0 NA 849660 TCGA-AB-3008 AML05 20 26148833 26148833 C A SNP LOC284801 XM_378973.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-11388 NULL 0.054 - - - no_errors tier3 860 98 10.23 2437 549 18.39 0 0 NA 849660 TCGA-AB-3008 AML05 20 44685599 44685599 C T SNP SLC13A3 NM_022829.1 human genbank 54_36p -1 reviewed intronic c.112-9828 e2-9828 0.016 - - - no_errors tier3 1883 682 26.58 1012 986 49.35 0 0 NA 849660 TCGA-AB-3008 AML05 20 53305636 53305636 C T SNP - - - - - - - - - - - - - - - tier3 653 242 27.01 350 301 46.24 0 0 NA 849660 TCGA-AB-3008 AML05 20 55833375 55833375 C T SNP - - - - - - - - - - - - - - - tier2 258 104 28.73 232 212 47.64 0 0 NA 849660 TCGA-AB-3008 AML05 21 10070257 10070257 C A SNP BAGE4 NM_181704.1 human genbank 54_36p -1 provisional intronic c.120-791 e3-791 0.098 - - - no_errors tier3 470 40 7.84 1263 210 14.25 0 0 0 849660 TCGA-AB-3008 AML05 21 26408220 26408220 A G SNP APP NM_000484.2 human genbank 54_36p -1 reviewed intronic c.58-1886 e2-1886 0.008 - - - no_errors tier3 543 186 25.51 441 401 47.57 0 0 0 849660 TCGA-AB-3008 AML05 22 22603109 22603109 C A SNP GSTT2 NM_000854.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-49280 NULL 0.473 - - - no_errors tier3 682 124 15.38 383 279 42.15 0 4 100 849660 TCGA-AB-3008 AML05 22 28593076 28593076 G T SNP MTMR3 NM_021090.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-103973 NULL 0.001 - - - no_errors tier3 661 142 17.68 225 154 40.53 0 0 NA 869586 TCGA-AB-3009 AML43 MT 3919 3919 G A SNP MT-ND1 ENST00000361390 human ensembl 54_36p 1 known silent c.612 p.E204 NULL "HMMPfam_NADHdh,PatternScan_COMPLEX1_ND1_2" "HMMPfam_NADHdh,PatternScan_COMPLEX1_ND1_1,PatternScan_COMPLEX1_ND1_2" - no_errors tier1 NA NA NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 X 508177 508177 G A SNP SHOX NM_000451.3 human genbank 54_36p 1 reviewed intronic c.1+2840 e0+2840 0.08 - - - no_errors tier3 215 1 0.46 55 45 45 0 0 NA 869586 TCGA-AB-3009 AML43 X 2427079 2427079 T C SNP ZBED1 NM_004729.3 human genbank 54_36p -1 validated intronic c.1+1779 e0+1779 0.001 - - - no_errors tier2 163 2 1.2 53 50 48.08 3 1 25 869586 TCGA-AB-3009 AML43 X 9952490 9952492 GGA - DEL WWC3 NM_015691.3 human genbank 54_36p 1 validated intronic c.1+8592_8594 e0+8592 0.000:0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 X 15274686 15274686 C G SNP FIGF NM_004469.2 human genbank 54_36p -1 reviewed intronic c.939-384 e7-384 0 - - - no_errors tier3 417 6 1.42 4 79 95.18 0 0 NA 869586 TCGA-AB-3009 AML43 Y 27050713 27050713 T C SNP ENSG00000215506 ENST00000328758 human ensembl 54_36p 1 novel intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 188 3 1.57 20 228 91.94 0 0 NA 869586 TCGA-AB-3009 AML43 X 27570931 27570931 C T SNP uc004dbv.1 ENST00000359110 human ensembl 54_36p 1 known 3_prime_flanking_region c.*9098 NULL 0.001 - - - no_coding_region:pseudogene tier2 398 4 0.99 35 290 89.23 0 0 NA 869586 TCGA-AB-3009 AML43 X 29548786 29548786 A G SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.704-47682 e5-47682 0.015 - - - no_errors tier2 83 0 0 2 31 93.94 0 0 NA 869586 TCGA-AB-3009 AML43 X 29962225 29962225 A G SNP ENSG00000218702 ENST00000407256 human ensembl 54_36p -1 known 5_prime_flanking_region c.-16306 NULL 0.003 - - - no_coding_region:pseudogene tier3 370 3 0.8 7 109 93.97 0 0 NA 869586 TCGA-AB-3009 AML43 X 40119720 40119720 G T SNP ENSG00000214045 ENST00000397351 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14794 NULL 0 - - - no_coding_region:pseudogene tier3 347 10 2.8 24 228 90.48 0 0 NA 869586 TCGA-AB-3009 AML43 X 79431528 79431528 G A SNP ENSG00000215104 ENST00000399581 human ensembl 54_36p -1 known intronic c.448+168 e6+168 0.041 - - - no_start_codon tier3 490 8 1.6 224 250 52.74 0 0 NA 869586 TCGA-AB-3009 AML43 X 82891773 82891773 C A SNP LOC648283 XR_038857.1 human genbank 54_36p -1 model splice_region c.NULL NULL 0.006 - - - pseudogene tier3 155 1 0.64 6 65 91.55 0 0 NA 869586 TCGA-AB-3009 AML43 X 91194846 91194846 C G SNP PCDH11X NM_032968.1 human genbank 54_36p 1 reviewed intronic c.3034-148184 e3-148184 0.275 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 X 91457678 91457678 A G SNP PCDH11X NM_032968.1 human genbank 54_36p 1 reviewed intronic c.3144+52880 e4+52880 0.01 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 X 92968362 92968362 A G SNP - - - - - - - - - - - - - - - tier3 99 7 6.6 2 85 97.7 0 0 NA 869586 TCGA-AB-3009 AML43 X 97645952 97645952 C T SNP - - - - - - - - - - - - - - - tier3 177 1 0.56 4 55 93.22 0 0 NA 869586 TCGA-AB-3009 AML43 X 110124130 110124130 G A SNP - - - - - - - - - - - - - - - tier3 1396 12 0.85 60 596 90.72 0 0 NA 869586 TCGA-AB-3009 AML43 X 112979355 112979355 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 X 113807806 113807806 C T SNP HTR2C NM_000868.2 human genbank 54_36p 1 reviewed intronic c.1+53211 e0+53211 0.001 - - - no_errors tier2 201 9 4.29 8 102 92.73 0 0 NA 869586 TCGA-AB-3009 AML43 X 131787031 131787031 C T SNP HS6ST2 ENST00000319809 human ensembl 54_36p -1 known intronic c.942-116828 e5-116828 0.002 - - - no_errors tier3 449 12 2.6 37 287 88.58 0 0 NA 869586 TCGA-AB-3009 AML43 X 132161919 132161919 C T SNP TFDP3 NM_016521.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*16817 NULL 0.086 - - - no_errors tier3 458 13 2.76 17 168 90.81 0 0 NA 869586 TCGA-AB-3009 AML43 X 133378890 133378890 G T SNP PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed missense c.860 p.G287V 1 "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger" "HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger" - no_errors tier1 301 1 0.33 15 176 92.15 37 100 869586 TCGA-AB-3009 AML43 X 144715326 144715326 G A SNP SLITRK2 ENST00000335565 human ensembl 54_36p 1 known intronic c.2151+1540 e1+1540 0.979 - - - no_stop_codon tier2 143 8 5.3 7 43 86 0 0 NA 869586 TCGA-AB-3009 AML43 X 145019083 145019083 C T SNP - - - - - - - - - - - - - - - tier3 209 4 1.88 11 74 87.06 0 0 NA 869586 TCGA-AB-3009 AML43 X 145600667 145600667 G A SNP - - - - - - - - - - - - - - - tier3 285 6 2.06 21 168 88.89 0 0 NA 869586 TCGA-AB-3009 AML43 X 151560017 151560017 C T SNP GABRQ NM_018558.1 human genbank 54_36p 1 reviewed intronic c.238+434 e2+434 0.002 - - - no_errors tier3 942 17 1.77 34 395 92.07 0 0 NA 869586 TCGA-AB-3009 AML43 1 3022471 3022471 C T SNP PRDM16 NM_022114.2 human genbank 54_36p 1 reviewed intronic c.37+46751 e1+46751 0 - - - no_errors tier3 290 0 0 91 61 40.13 0 0 NA 869586 TCGA-AB-3009 AML43 1 11747101 11747101 G A SNP CLCN6 NM_001286.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-41806 NULL 0 - - - no_errors tier3 2047 27 1.3 422 473 52.85 0 0 NA 869586 TCGA-AB-3009 AML43 1 12339316 12339316 T C SNP VPS13D NM_015378.2 human genbank 54_36p 1 reviewed intronic c.9998+148 e48+148 0.97 - - - no_errors tier3 294 3 1.01 124 81 39.51 0 4 100 869586 TCGA-AB-3009 AML43 1 14105605 14105605 C T SNP C1orf196 ENST00000401953 human ensembl 54_36p 1 known intronic c.121+12767 e1+12767 0 - - - no_stop_codon tier3 787 6 0.76 186 168 47.32 2 0 0 869586 TCGA-AB-3009 AML43 1 14341255 14341255 G A SNP C1orf196 ENST00000401953 human ensembl 54_36p 1 known intronic c.122-38262 e2-38262 0.265 - - - no_stop_codon tier3 1577 19 1.19 515 418 44.75 0 0 0 869586 TCGA-AB-3009 AML43 1 15456527 15456527 G A SNP FHAD1 ENST00000375999 human ensembl 54_36p 1 known intronic c.144+5567 e2+5567 0 - - - no_stop_codon tier3 1033 8 0.76 459 428 48.2 0 0 NA 869586 TCGA-AB-3009 AML43 1 17558566 17558566 G T SNP PADI4 NM_012387.2 human genbank 54_36p 1 reviewed intronic c.1758+76 e15+76 0.001 - - - no_errors tier3 456 2 0.44 146 144 49.66 0 1 100 869586 TCGA-AB-3009 AML43 1 17822004 17822004 C T SNP ARHGEF10L NM_018125.2 human genbank 54_36p 1 validated intronic c.1021-74 e11-74 0 - - - no_errors tier3 756 7 0.92 207 172 45.38 0 0 NA 869586 TCGA-AB-3009 AML43 1 20178272 20178272 C T SNP PLA2G2A NM_000300.2 human genbank 54_36p -1 provisional intronic c.1-313 e1-313 0 - - - no_errors tier3 1514 13 0.85 526 500 48.73 0 0 NA 869586 TCGA-AB-3009 AML43 1 22962664 22962664 G A SNP EPHB2 NM_004442.6 human genbank 54_36p 1 reviewed intronic c.62-17837 e2-17837 0 - - - no_errors tier3 486 0 0 140 108 43.55 0 0 NA 869586 TCGA-AB-3009 AML43 1 23051601 23051601 C T SNP EPHB2 NM_004442.6 human genbank 54_36p 1 reviewed intronic c.812-10516 e4-10516 0.97 - - - no_errors tier2 347 4 1.13 71 50 41.32 0 0 NA 869586 TCGA-AB-3009 AML43 1 25222394 25222394 T C SNP - - - - - - - - - - - - - - - tier3 510 13 2.49 142 125 46.82 0 0 NA 869586 TCGA-AB-3009 AML43 1 30047873 30047873 G A SNP - - - - - - - - - - - - - - - tier2 316 1 0.32 55 48 46.6 0 0 NA 869586 TCGA-AB-3009 AML43 1 30588269 30588269 G A SNP LOC100134154 XM_001726211.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*24263 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 327 0 0 166 83 33.33 0 0 NA 869586 TCGA-AB-3009 AML43 1 34170985 34170985 C T SNP CSMD2 NM_052896.3 human genbank 54_36p -1 validated intronic c.592+2963 e4+2963 0.002 - - - no_errors tier3 1020 6 0.58 402 302 42.9 0 0 NA 869586 TCGA-AB-3009 AML43 1 34646377 34646377 G A SNP - - - - - - - - - - - - - - - tier3 1287 21 1.6 400 321 44.52 0 0 NA 869586 TCGA-AB-3009 AML43 1 34803824 34803824 C A SNP - - - - - - - - - - - - - - - tier3 618 8 1.28 356 292 45.06 0 0 NA 869586 TCGA-AB-3009 AML43 1 35138238 35138238 G A SNP DLGAP3 NM_001080418.1 human genbank 54_36p -1 provisional intronic c.1313+18 e2+18 0.001 - - - no_errors tier3 813 7 0.85 367 340 47.95 0 0 NA 869586 TCGA-AB-3009 AML43 1 36853337 36853337 G A SNP ENSG00000220821 ENST00000404010 human ensembl 54_36p 1 known 5_prime_flanking_region c.-15186 NULL 0 - - - no_coding_region:pseudogene tier3 3341 41 1.21 507 414 44.95 0 0 NA 869586 TCGA-AB-3009 AML43 1 45149811 45149811 T C SNP EIF2B3 NM_020365.2 human genbank 54_36p -1 validated intronic c.567-14108 e5-14108 0.001 - - - no_errors tier3 1590 24 1.49 472 500 51.44 3 0 0 869586 TCGA-AB-3009 AML43 1 45858196 45858196 C T SNP NASP NM_172164.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*1796 NULL 0.014 - - - no_errors tier3 559 5 0.88 160 129 44.48 9 8 47.06 869586 TCGA-AB-3009 AML43 1 58484050 58484050 C T SNP DAB1 NM_021080.3 human genbank 54_36p -1 reviewed intronic c.1+4450 e0+4450 0 - - - no_errors tier3 1010 3 0.3 69 36 33.96 1 0 0 869586 TCGA-AB-3009 AML43 1 61049431 61049431 G A SNP - - - - - - - - - - - - - - - tier3 788 7 0.88 242 221 47.32 0 0 NA 869586 TCGA-AB-3009 AML43 1 64277040 64277040 C T SNP ROR1 NM_005012.1 human genbank 54_36p 1 validated intronic c.164-10911 e3-10911 0.018 - - - no_errors tier3 400 2 0.5 75 50 40 0 0 NA 869586 TCGA-AB-3009 AML43 1 73704484 73704485 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 75051626 75051626 C T SNP TYW3 NM_138467.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*49241 NULL 0.001 - - - no_errors tier3 721 11 1.5 168 144 46.15 0 0 NA 869586 TCGA-AB-3009 AML43 1 75400544 75400544 G A SNP ENSG00000206999 ENST00000384272 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20774 NULL 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 79586157 79586157 A T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 80505153 80505153 A T SNP ENSG00000218484 ENST00000402916 human ensembl 54_36p 1 known 5_prime_flanking_region c.-16472 NULL 0.169 - - - no_coding_region:pseudogene tier2 391 0 0 137 106 43.62 0 0 NA 869586 TCGA-AB-3009 AML43 1 80743777 80743777 C T SNP ENSG00000218288 ENST00000405969 human ensembl 54_36p -1 known 5_prime_flanking_region c.-40751 NULL 0 - - - no_coding_region:pseudogene tier3 294 0 0 165 24 12.7 0 0 NA 869586 TCGA-AB-3009 AML43 1 80882926 80882926 C T SNP - - - - - - - - - - - - - - - tier3 716 9 1.24 179 109 37.85 0 0 NA 869586 TCGA-AB-3009 AML43 1 81481229 81481229 C G SNP ENSG00000223026 ENST00000411094 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-8833 NULL 0.986 - - - no_errors tier2 371 3 0.8 113 118 51.08 0 0 NA 869586 TCGA-AB-3009 AML43 1 82154481 82154481 C T SNP LPHN2 NM_012302.2 human genbank 54_36p 1 reviewed intronic c.287+8978 e2+8978 0.001 - - - no_errors tier3 461 5 1.07 185 126 40.51 0 0 NA 869586 TCGA-AB-3009 AML43 1 82513492 82513492 G A SNP - - - - - - - - - - - - - - - tier3 1134 12 1.05 842 183 17.84 0 0 NA 869586 TCGA-AB-3009 AML43 1 82979893 82979893 G C SNP - - - - - - - - - - - - - - - tier2 609 9 1.45 261 185 41.48 0 0 NA 869586 TCGA-AB-3009 AML43 1 85563599 85563599 A G SNP DDAH1 NM_012137.1 human genbank 54_36p -1 reviewed intronic c.598-445 e5-445 0.003 - - - no_errors tier2 1621 17 1.04 457 356 43.79 0 0 NA 869586 TCGA-AB-3009 AML43 1 87704659 87704659 G T SNP ENSG00000199318 ENST00000362448 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13015 NULL 1 - - - no_errors tier2 336 5 1.47 91 55 37.41 0 0 NA 869586 TCGA-AB-3009 AML43 1 88418025 88418025 G A SNP - - - - - - - - - - - - - - - tier2 257 4 1.53 62 45 42.06 0 0 NA 869586 TCGA-AB-3009 AML43 1 89889861 89889861 A G SNP LRRC8C NM_032270.4 human genbank 54_36p 1 validated intronic c.1+18392 e0+18392 0.001 - - - no_errors tier3 264 3 1.12 107 68 38.86 9 8 47.06 869586 TCGA-AB-3009 AML43 1 89910422 89910422 C T SNP LRRC8C NM_032270.4 human genbank 54_36p 1 validated intronic c.1-14195 e1-14195 0 - - - no_errors tier2 2113 30 1.4 623 562 47.35 12 12 50 869586 TCGA-AB-3009 AML43 1 90007390 90007390 G A SNP ENSG00000211209 ENST00000388474 human ensembl 54_36p -1 known 5_prime_flanking_region c.-925 NULL 0 - - - pseudogene tier3 499 6 1.19 251 225 47.27 3 1 25 869586 TCGA-AB-3009 AML43 1 95852418 95852419 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 96796746 96796746 C T SNP ENSG00000211377 ENST00000388642 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24610 NULL 0.001 - - - pseudogene tier3 780 0 0 209 178 45.99 0 0 NA 869586 TCGA-AB-3009 AML43 1 98866988 98866992 CTTAT - DEL SNX7 NM_015976.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-56053 NULL 0.024:0.025:0.027:0.027:0.022 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 99260217 99260217 T A SNP LOC100129620 XM_001726877.1 human genbank 54_36p 1 model intronic c.9+17428 e1+17428 0 - - - no_errors tier2 536 3 0.56 139 101 42.08 0 0 NA 869586 TCGA-AB-3009 AML43 1 100625419 100625419 T A SNP CDC14A NM_033312.3 human genbank 54_36p 1 reviewed intronic c.217-3457 e4-3457 0.011 - - - no_errors tier3 306 0 0 92 63 40.65 0 0 0 869586 TCGA-AB-3009 AML43 1 101021626 101021626 A G SNP VCAM1 NM_001078.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*45199 NULL 0 - - - no_errors tier3 329 10 2.95 96 67 41.1 0 0 NA 869586 TCGA-AB-3009 AML43 1 104258517 104258517 G A SNP ENSG00000220951 ENST00000401965 human ensembl 54_36p 1 known 5_prime_flanking_region c.-12195 NULL 0.005 - - - no_coding_region:pseudogene tier3 889 19 2.09 240 237 49.58 0 0 NA 869586 TCGA-AB-3009 AML43 1 105515812 105515812 G A SNP - - - - - - - - - - - - - - - tier3 1068 18 1.66 364 262 41.79 0 0 NA 869586 TCGA-AB-3009 AML43 1 106131808 106131808 C T SNP - - - - - - - - - - - - - - - tier2 531 8 1.48 137 119 46.48 0 0 NA 869586 TCGA-AB-3009 AML43 1 106715566 106715566 C T SNP - - - - - - - - - - - - - - - tier2 361 5 1.36 133 137 50.74 0 0 NA 869586 TCGA-AB-3009 AML43 1 108308251 108308251 A G SNP VAV3 NM_006113.1 human genbank 54_36p -1 reviewed intronic c.204+560 e1+560 0.02 - - - no_errors tier2 366 5 1.34 174 120 40.54 1 1 50 869586 TCGA-AB-3009 AML43 1 108373360 108373360 G A SNP - - - - - - - - - - - - - - - tier3 1039 12 1.14 385 305 44.2 0 0 NA 869586 TCGA-AB-3009 AML43 1 109572363 109572363 G C SNP SARS NM_006513.2 human genbank 54_36p 1 reviewed intronic c.208-134 e3-134 0.001 - - - no_errors tier3 335 3 0.88 35 23 39.66 1 0 0 869586 TCGA-AB-3009 AML43 1 110820433 110820434 - AC INS CYMP NR_003599.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-4478 NULL 0.000:0.001 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 117611163 117611163 C T SNP ENSG00000223204 ENST00000411272 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-23510 NULL 0.09 - - - no_errors tier2 749 8 1.06 247 247 49.9 0 0 NA 869586 TCGA-AB-3009 AML43 1 118567276 118567276 C A SNP SPAG17 NM_206996.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-37973 NULL 0.018 - - - no_errors tier3 912 14 1.51 383 318 45.36 0 0 NA 869586 TCGA-AB-3009 AML43 1 148144145 148144145 G A SNP SV2A NM_014849.3 human genbank 54_36p -1 validated silent c.1956 p.I652 0.996 "HMMPfam_MFS_1,superfamily_MFS general substrate transporter" "PatternScan_SUGAR_TRANSPORT_2,HMMPfam_MFS_1,superfamily_MFS general substrate transporter" - no_errors tier1 4665 53 1.12 849 772 47.62 46 77 62.6 869586 TCGA-AB-3009 AML43 1 148398368 148398369 - G INS PLEKHO1 NM_016274.4 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*26 NULL 0.000:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 150571282 150571282 A C SNP LOC100128468 XM_001718271.1 human genbank 54_36p 1 model intronic c.462-401 e4-401 0 - - - no_errors tier2 1503 13 0.86 773 658 45.95 0 0 NA 869586 TCGA-AB-3009 AML43 1 155813811 155813811 A T SNP FCRL4 NM_031282.1 human genbank 54_36p -1 provisional intronic c.1429+1077 e10+1077 0.002 - - - no_errors tier3 643 5 0.77 155 106 40.61 0 0 NA 869586 TCGA-AB-3009 AML43 1 157408286 157408286 G A SNP CADM3 NM_021189.1 human genbank 54_36p 1 validated intronic c.88+19 e1+19 1 - - - no_errors tier2 167 5 2.91 55 60 52.17 0 0 NA 869586 TCGA-AB-3009 AML43 1 159331196 159331196 G T SNP USF1 NM_007122.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-51507 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 160240958 160240959 - A INS OLFML2B NM_015441.1 human genbank 54_36p -1 provisional intronic c.723+1752_723+1751 e4+1752 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 161173886 161173886 G A SNP ENSG00000219987 ENST00000405744 human ensembl 54_36p -1 known 3_prime_flanking_region c.*42079 NULL 0 - - - no_coding_region:pseudogene tier3 957 7 0.73 290 249 46.2 0 0 NA 869586 TCGA-AB-3009 AML43 1 168739155 168739155 C T SNP GORAB NM_152281.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-28759 NULL 0.009 - - - no_errors tier2 960 9 0.93 523 411 43.91 0 0 NA 869586 TCGA-AB-3009 AML43 1 169564687 169564688 - A INS FMO4 NM_002022.1 human genbank 54_36p 1 reviewed intronic c.485-2716_485-2715 e4-2715 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 175674904 175674904 T A SNP LOC400796 XM_001132413.2 human genbank 54_36p -1 model intronic c.198-45357 e3-45357 0.017 - - - no_errors tier2 1512 8 0.53 388 294 43.11 0 2 100 869586 TCGA-AB-3009 AML43 1 176375491 176375491 G A SNP RASAL2 NM_170692.2 human genbank 54_36p 1 reviewed intronic c.148+45039 e1+45039 0.038 - - - no_errors tier3 154 2 1.28 35 24 40.68 0 0 NA 869586 TCGA-AB-3009 AML43 1 177650817 177650817 C T SNP C1orf125 NM_144696.3 human genbank 54_36p 1 validated intronic c.1230+3793 e11+3793 0 - - - no_errors tier3 386 1 0.26 134 89 39.91 0 0 NA 869586 TCGA-AB-3009 AML43 1 181488479 181488479 C T SNP NMNAT2 NM_015039.2 human genbank 54_36p -1 reviewed missense c.844 p.G282S 0.996 superfamily_Nucleotidylyl transferase "HMMPfam_CTP_transf_2,superfamily_Nucleotidylyl transferase" - no_errors tier1 1606 7 0.43 741 577 43.78 NA 869586 TCGA-AB-3009 AML43 1 188037336 188037336 A G SNP - - - - - - - - - - - - - - - tier2 922 33 3.46 167 119 41.61 0 0 NA 869586 TCGA-AB-3009 AML43 1 188581276 188581276 C A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional intronic c.237-63773 e2-63773 0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 189330554 189330554 C T SNP - - - - - - - - - - - - - - - tier3 701 7 0.99 174 132 43.14 0 0 NA 869586 TCGA-AB-3009 AML43 1 191933988 191933988 C T SNP ENSG00000208231 ENST00000385496 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*34074 NULL 0.032 - - - pseudogene tier3 551 6 1.07 180 159 46.9 0 0 NA 869586 TCGA-AB-3009 AML43 1 192800989 192800989 G A SNP - - - - - - - - - - - - - - - tier3 418 7 1.65 177 155 46.69 0 0 NA 869586 TCGA-AB-3009 AML43 1 194464035 194464035 C T SNP KCNT2 NM_198503.2 human genbank 54_36p -1 validated missense c.3350 p.R1117Q 0.822 NULL "HMMPfam_BK_channel_a,HMMPfam_Ion_trans_2,superfamily_NAD(P)-binding Rossmann-fold domains,superfamily_Voltage-gated potassium channels" - no_errors tier1 385 3 0.77 148 116 43.94 NA 869586 TCGA-AB-3009 AML43 1 194688957 194688957 C T SNP KCNT2 NM_198503.2 human genbank 54_36p -1 validated intronic c.638+12089 e8+12089 0.001 - - - no_errors tier3 881 8 0.9 528 461 46.57 0 0 NA 869586 TCGA-AB-3009 AML43 1 195270064 195270064 G A SNP F13B NM_001994.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*5067 NULL 0.001 - - - no_errors tier3 768 5 0.65 199 126 38.77 0 0 NA 869586 TCGA-AB-3009 AML43 1 199884746 199884746 C T SNP NAV1 NM_020443.3 human genbank 54_36p 1 reviewed silent c.327 p.P109 0.689 NULL "HMMSmart_AAA,PatternScan_PPASE,superfamily_SSF52540" - no_errors tier1 317 1 0.31 120 93 43.66 1 2 66.67 869586 TCGA-AB-3009 AML43 1 208906360 208906360 G A SNP HHAT NM_018194.1 human genbank 54_36p 1 validated intronic c.1391-7893 e11-7893 0 - - - no_errors tier3 704 8 1.12 316 286 47.43 2 0 0 869586 TCGA-AB-3009 AML43 1 209213244 209213244 C T SNP KCNH1 NM_172362.3 human genbank 54_36p -1 reviewed intronic c.1032+45504 e6+45504 0.007 - - - no_errors tier3 1008 26 2.51 154 142 47.65 0 0 NA 869586 TCGA-AB-3009 AML43 1 210726833 210726833 C T SNP ENSG00000203259 ENST00000366090 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-22611 NULL 0.001 - - - no_coding_region:pseudogene tier2 1153 15 1.28 273 208 43.24 0 1 100 869586 TCGA-AB-3009 AML43 1 213434125 213434125 C T SNP KCNK2 NM_001017425.2 human genbank 54_36p 1 reviewed intronic c.824-794 e6-794 0 - - - no_errors tier3 123 1 0.79 54 38 41.3 0 0 NA 869586 TCGA-AB-3009 AML43 1 214374854 214374854 G A SNP USH2A NM_206933.5 human genbank 54_36p -1 reviewed intronic c.4628-37676 e21-37676 0 - - - no_errors tier3 866 9 1.03 332 333 50.08 0 0 NA 869586 TCGA-AB-3009 AML43 1 214889105 214889105 C T SNP ESRRG NM_001438.1 human genbank 54_36p -1 validated intronic c.589+1833 e3+1833 0.012 - - - no_errors tier3 645 10 1.52 241 120 33.24 0 0 NA 869586 TCGA-AB-3009 AML43 1 215154767 215154767 C A SNP ESRRG NM_206594.1 human genbank 54_36p -1 validated intronic c.1+24780 e0+24780 0.003 - - - no_errors tier2 2658 19 0.71 900 805 47.21 0 0 NA 869586 TCGA-AB-3009 AML43 1 215841463 215841463 C T SNP GPATCH2 NM_018040.2 human genbank 54_36p -1 provisional intronic c.1098+8823 e5+8823 0 - - - no_errors tier3 790 5 0.63 259 219 45.72 2 3 60 869586 TCGA-AB-3009 AML43 1 216163968 216163968 G A SNP - - - - - - - - - - - - - - - tier3 536 3 0.56 185 160 46.38 0 0 NA 869586 TCGA-AB-3009 AML43 1 216304035 216304035 G A SNP - - - - - - - - - - - - - - - tier2 843 3 0.35 292 322 52.44 0 0 NA 869586 TCGA-AB-3009 AML43 1 217256405 217256405 T C SNP - - - - - - - - - - - - - - - tier3 233 2 0.85 26 24 48 0 0 NA 869586 TCGA-AB-3009 AML43 1 221173612 221173612 G T SNP DISP1 NM_032890.2 human genbank 54_36p 1 reviewed intronic c.1+5077 e0+5077 0.001 - - - no_errors tier3 179 0 0 62 7 10.14 0 0 NA 869586 TCGA-AB-3009 AML43 1 221677366 221677367 - T INS C1orf65 NM_152610.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*42054 NULL 0.309:0.300 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 1 221705623 221705623 C T SNP - - - - - - - - - - - - - - - tier3 940 6 0.63 224 175 43.86 0 0 NA 869586 TCGA-AB-3009 AML43 1 225627629 225627629 C T SNP ENSG00000219921 ENST00000404641 human ensembl 54_36p -1 known 3_prime_flanking_region c.*37312 NULL 0 - - - no_coding_region:pseudogene tier3 1874 11 0.58 421 397 48.53 0 0 NA 869586 TCGA-AB-3009 AML43 1 229081409 229081409 C A SNP C1orf198 NM_032800.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-10528 NULL 0 - - - no_errors tier3 1054 19 1.77 254 203 44.42 0 0 NA 869586 TCGA-AB-3009 AML43 1 229494826 229494826 G A SNP C1orf124 NM_032018.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45927 NULL 0.107 - - - no_errors tier3 570 6 1.04 500 449 47.26 0 0 NA 869586 TCGA-AB-3009 AML43 1 230362104 230362104 C A SNP - - - - - - - - - - - - - - - tier2 1278 21 1.62 317 296 48.29 0 0 NA 869586 TCGA-AB-3009 AML43 1 231744754 231744754 A G SNP - - - - - - - - - - - - - - - tier3 2266 20 0.87 680 557 44.99 0 0 NA 869586 TCGA-AB-3009 AML43 1 233105368 233105368 C A SNP ENSG00000222571 ENST00000410639 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1188 NULL 0.027 - - - no_errors tier3 857 8 0.92 401 275 40.68 0 0 NA 869586 TCGA-AB-3009 AML43 1 236205132 236205132 A G SNP ENSG00000219264 ENST00000402955 human ensembl 54_36p -1 known 5_prime_flanking_region c.-23673 NULL 0.222 - - - no_coding_region:pseudogene tier2 1207 16 1.31 485 386 44.27 0 0 NA 869586 TCGA-AB-3009 AML43 1 236435727 236435727 C T SNP - - - - - - - - - - - - - - - tier3 173 3 1.7 33 21 38.89 0 0 NA 869586 TCGA-AB-3009 AML43 1 236647090 236647090 C T SNP - - - - - - - - - - - - - - - tier2 1077 16 1.46 263 224 45.81 0 0 NA 869586 TCGA-AB-3009 AML43 1 236849286 236849286 C T SNP - - - - - - - - - - - - - - - tier3 656 9 1.35 302 243 44.51 0 0 NA 869586 TCGA-AB-3009 AML43 1 237548643 237548643 G A SNP - - - - - - - - - - - - - - - tier3 787 2 0.25 225 164 42.16 0 0 NA 869586 TCGA-AB-3009 AML43 1 239381660 239381660 C A SNP RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.79-52975 e2-52975 0.008 - - - no_errors tier2 766 9 1.16 290 224 43.58 0 0 NA 869586 TCGA-AB-3009 AML43 2 118458 118458 G A SNP LOC647654 XR_037949.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-3719 NULL 0.002 - - - pseudogene tier3 714 16 2.19 195 227 53.79 0 0 NA 869586 TCGA-AB-3009 AML43 2 963422 963422 C T SNP SNTG2 ENST00000308624 human ensembl 54_36p 1 known intronic c.72+26668 e1+26668 0 - - - no_errors tier3 1969 19 0.95 496 397 44.41 0 0 NA 869586 TCGA-AB-3009 AML43 2 1684403 1684403 C T SNP PXDN NM_012293.1 human genbank 54_36p -1 validated intronic c.201-8490 e2-8490 0.329 - - - no_errors tier3 204 4 1.92 112 114 50.44 0 0 NA 869586 TCGA-AB-3009 AML43 2 2895021 2895021 C T SNP - - - - - - - - - - - - - - - tier2 762 12 1.55 185 146 44.11 0 0 NA 869586 TCGA-AB-3009 AML43 2 3703521 3703521 G A SNP ALLC NM_018436.3 human genbank 54_36p 1 validated intronic c.85-412 e3-412 0 - - - no_errors tier2 664 3 0.45 296 240 44.78 0 0 NA 869586 TCGA-AB-3009 AML43 2 4534542 4534542 G T SNP ENSG00000216435 ENST00000402611 human ensembl 54_36p -1 known 3_prime_flanking_region c.*5127 NULL 0.001 - - - no_coding_region:pseudogene tier3 1493 21 1.39 455 358 44.03 0 0 NA 869586 TCGA-AB-3009 AML43 2 4835095 4835095 G T SNP ENSG00000210527 ENST00000387792 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17371 NULL 0.002 - - - pseudogene tier3 262 5 1.87 114 73 39.04 0 0 NA 869586 TCGA-AB-3009 AML43 2 5486989 5486989 C T SNP - - - - - - - - - - - - - - - tier3 716 4 0.55 226 204 47.22 0 0 NA 869586 TCGA-AB-3009 AML43 2 5650617 5650617 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 7081077 7081077 A G SNP RNF144A NM_014746.3 human genbank 54_36p 1 reviewed intronic c.510-874 e5-874 0 - - - no_errors tier3 489 4 0.81 136 106 43.8 5 11 68.75 869586 TCGA-AB-3009 AML43 2 14371539 14371539 C T SNP ENSG00000222245 ENST00000410313 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-27214 NULL 0 - - - no_errors tier3 1478 20 1.34 517 402 43.74 0 0 NA 869586 TCGA-AB-3009 AML43 2 18529058 18529059 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 19391113 19391113 G A SNP OSR1 NM_145260.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*24404 NULL 0.038 - - - no_errors tier3 2133 23 1.07 495 428 46.37 2 0 0 869586 TCGA-AB-3009 AML43 2 21462746 21462746 T G SNP - - - - - - - - - - - - - - - tier3 629 4 0.63 192 152 44.19 0 0 NA 869586 TCGA-AB-3009 AML43 2 23233620 23233620 C A SNP - - - - - - - - - - - - - - - tier2 511 8 1.54 102 97 48.74 0 0 NA 869586 TCGA-AB-3009 AML43 2 28074844 28074845 - T INS BRE NM_004899.3 human genbank 54_36p 1 validated intronic c.300+10386_300+10385 e3+10386 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 28786413 28786419 TAATTAA - DEL PPP1CB NM_002709.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-42082 NULL 0.052:0.039:0.031:0.012:0.001:0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 34022984 34022984 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 34651077 34651077 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 35718525 35718525 G A SNP - - - - - - - - - - - - - - - tier3 640 4 0.62 196 156 44.32 0 0 NA 869586 TCGA-AB-3009 AML43 2 39034368 39034368 A T SNP ENSG00000214694 ENST00000409978 human ensembl 54_36p 1 known intronic c.1137+478 e10+478 0.035 - - - no_errors tier3 817 2 0.24 316 107 25.24 0 1 100 869586 TCGA-AB-3009 AML43 2 43770990 43770990 T - DEL PLEKHH2 NM_172069.3 human genbank 54_36p 1 validated intronic c.187-2167 e3-2167 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 44812014 44812014 C G SNP C2orf34 NM_024766.3 human genbank 54_36p 1 validated intronic c.624-12251 e8-12251 0.003 - - - no_errors tier3 1019 5 0.49 505 280 35.67 0 0 0 869586 TCGA-AB-3009 AML43 2 47676114 47676114 C A SNP KCNK12 NM_022055.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25140 NULL 0.009 - - - no_errors tier3 740 13 1.72 191 183 48.8 0 0 NA 869586 TCGA-AB-3009 AML43 2 49557457 49557457 G A SNP - - - - - - - - - - - - - - - tier3 368 4 1.08 32 13 28.89 0 0 NA 869586 TCGA-AB-3009 AML43 2 50905412 50905412 G C SNP NRXN1 NM_004801.1 human genbank 54_36p -1 reviewed intronic c.832+97099 e4+97099 0 - - - no_errors tier3 645 3 0.46 165 155 48.44 0 0 NA 869586 TCGA-AB-3009 AML43 2 52327615 52327615 C A SNP - - - - - - - - - - - - - - - tier2 594 10 1.65 86 84 49.41 0 0 NA 869586 TCGA-AB-3009 AML43 2 57449163 57449163 T C SNP - - - - - - - - - - - - - - - tier3 634 7 1.09 126 154 54.8 0 0 NA 869586 TCGA-AB-3009 AML43 2 59650870 59650870 T A SNP ENSG00000209293 ENST00000386558 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*33365 NULL 0 - - - pseudogene tier2 1396 8 0.57 194 148 43.27 0 0 NA 869586 TCGA-AB-3009 AML43 2 66396484 66396484 C A SNP ENSG00000221107 ENST00000408180 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-33362 NULL 0.994 - - - no_errors tier3 694 7 1 203 178 46.6 0 0 NA 869586 TCGA-AB-3009 AML43 2 67805940 67805940 G A SNP - - - - - - - - - - - - - - - tier3 1027 6 0.58 475 308 39.29 0 0 NA 869586 TCGA-AB-3009 AML43 2 68345908 68345908 C T SNP PPP3R1 NM_000945.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-13145 NULL 0.001 - - - no_errors tier3 1076 16 1.47 174 136 43.73 3 2 40 869586 TCGA-AB-3009 AML43 2 72405888 72405888 A G SNP EXOC6B NM_015189.1 human genbank 54_36p -1 validated intronic c.2196+9696 e20+9696 0.643 - - - no_errors tier3 985 12 1.2 438 378 46.32 0 0 NA 869586 TCGA-AB-3009 AML43 2 74498548 74498548 G A SNP DCTN1 NM_004082.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-37876 NULL 0.018 - - - no_errors tier3 316 8 2.46 178 112 38.36 0 0 NA 869586 TCGA-AB-3009 AML43 2 77783494 77783494 A G SNP ENSG00000208894 ENST00000386159 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*34323 NULL 0.003 - - - pseudogene tier3 419 2 0.48 44 46 51.11 0 0 NA 869586 TCGA-AB-3009 AML43 2 77922371 77922371 A T SNP - - - - - - - - - - - - - - - tier2 324 4 1.22 54 44 44.9 0 0 NA 869586 TCGA-AB-3009 AML43 2 79831845 79831845 C G SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.298+6629 e2+6629 0 - - - no_errors tier3 867 3 0.34 166 131 44.11 0 0 NA 869586 TCGA-AB-3009 AML43 2 80018562 80018562 C A SNP CTNNA2 NM_004389.2 human genbank 54_36p 1 validated intronic c.1059+28128 e6+28128 0.069 - - - no_errors tier3 504 5 0.98 200 111 35.69 0 0 NA 869586 TCGA-AB-3009 AML43 2 81196674 81196674 G T SNP - - - - - - - - - - - - - - - tier3 624 12 1.88 271 264 49.35 0 0 NA 869586 TCGA-AB-3009 AML43 2 82418827 82418827 A G SNP ENSG00000201311 ENST00000364441 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31024 NULL 0.01 - - - no_errors tier3 546 1 0.18 161 183 53.04 0 0 NA 869586 TCGA-AB-3009 AML43 2 82787207 82787207 C T SNP - - - - - - - - - - - - - - - tier3 963 5 0.52 371 292 44.04 0 0 NA 869586 TCGA-AB-3009 AML43 2 84327755 84327755 G A SNP uc010ffz.1 ENST00000331369 human ensembl 54_36p 1 known 5_prime_flanking_region c.-43699 NULL 0.011 - - - no_errors tier3 545 12 2.14 366 294 44.41 0 0 NA 869586 TCGA-AB-3009 AML43 2 88836257 88836261 GAGTT - DEL ENSG00000221686 ENST00000408759 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-11693 NULL 0.001:0.000:0.000:0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 94793322 94793322 C A SNP ANKRD20B NR_003366.2 human genbank 54_36p -1 validated intronic c.NULL NULL 0.996 - - - pseudogene tier3 301 0 0 116 101 46.54 0 0 NA 869586 TCGA-AB-3009 AML43 2 96121006 96121006 C T SNP ADRA2B NM_000682.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*23266 NULL 0.013 - - - no_errors tier2 829 6 0.72 262 205 43.9 0 0 NA 869586 TCGA-AB-3009 AML43 2 99819633 99819633 A G SNP AFF3 NM_001025108.1 human genbank 54_36p -1 reviewed intronic c.996+738 e6+738 0.978 - - - no_errors tier2 260 3 1.14 43 45 51.14 1 2 66.67 869586 TCGA-AB-3009 AML43 2 100951891 100951891 G A SNP NPAS2 NM_002518.3 human genbank 54_36p 1 reviewed intronic c.1055+569 e10+569 0 - - - no_errors tier3 433 5 1.14 128 91 41.55 0 0 NA 869586 TCGA-AB-3009 AML43 2 100974121 100974121 C T SNP NPAS2 NM_002518.3 human genbank 54_36p 1 reviewed intronic c.2111+355 e18+355 0 - - - no_errors tier2 695 7 1 188 176 48.35 0 0 NA 869586 TCGA-AB-3009 AML43 2 101352567 101352567 G A SNP CREG2 NM_153836.3 human genbank 54_36p -1 validated intronic c.611+13860 e2+13860 0.014 - - - no_errors tier3 2050 15 0.72 786 558 41.52 0 0 NA 869586 TCGA-AB-3009 AML43 2 101644202 101644202 A G SNP MAP4K4 NM_145686.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36773 NULL 0.005 - - - no_errors tier2 261 3 1.14 34 28 45.16 0 0 NA 869586 TCGA-AB-3009 AML43 2 102946459 102946459 C A SNP - - - - - - - - - - - - - - - tier3 759 9 1.17 249 243 49.39 0 0 NA 869586 TCGA-AB-3009 AML43 2 103732160 103732160 G T SNP - - - - - - - - - - - - - - - tier3 444 2 0.45 135 104 43.51 0 0 NA 869586 TCGA-AB-3009 AML43 2 105927416 105927416 C T SNP LOC100132455 XM_001721082.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*14708 NULL 0 - - - no_errors tier3 306 0 0 51 45 46.39 0 0 NA 869586 TCGA-AB-3009 AML43 2 108976530 108976530 G A SNP EDAR NM_022336.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-62628 NULL 0.001 - - - no_errors tier3 1396 32 2.24 332 269 44.76 0 0 NA 869586 TCGA-AB-3009 AML43 2 115898068 115898068 C T SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.272-75488 e4-75488 0 - - - no_errors tier3 863 6 0.69 303 243 44.51 0 0 NA 869586 TCGA-AB-3009 AML43 2 116417004 116417004 C T SNP - - - - - - - - - - - - - - - tier3 703 2 0.28 189 179 48.64 0 0 NA 869586 TCGA-AB-3009 AML43 2 116686644 116686644 G A SNP - - - - - - - - - - - - - - - tier3 480 3 0.62 163 156 48.9 0 0 NA 869586 TCGA-AB-3009 AML43 2 116976596 116976596 G T SNP - - - - - - - - - - - - - - - tier3 239 0 0 46 28 37.84 0 0 NA 869586 TCGA-AB-3009 AML43 2 118763902 118763902 G A SNP - - - - - - - - - - - - - - - tier3 1565 1 0.06 806 160 16.55 0 0 NA 869586 TCGA-AB-3009 AML43 2 125273710 125273710 T C SNP CNTNAP5 NM_130773.2 human genbank 54_36p 1 reviewed intronic c.3214+1343 e19+1343 0.005 - - - no_errors tier3 936 6 0.64 219 205 48.35 0 0 NA 869586 TCGA-AB-3009 AML43 2 131501602 131501602 C T SNP ARHGEF4 NM_015320.2 human genbank 54_36p 1 reviewed intronic c.428-386 e3-386 0 - - - no_errors tier3 613 9 1.44 132 121 47.83 0 0 NA 869586 TCGA-AB-3009 AML43 2 133304226 133304226 C A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.807+30309 e9+30309 0.002 - - - no_errors tier3 1059 11 1.03 423 269 38.87 0 0 NA 869586 TCGA-AB-3009 AML43 2 138462489 138462490 - G INS HNMT NM_006895.1 human genbank 54_36p 1 reviewed intronic c.191-12469_191-12468 e3-12468 0.062:0.079 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 141704189 141704189 C T SNP LRP1B NM_018557.2 human genbank 54_36p -1 validated intronic c.593-710 e6-710 0 - - - no_errors tier3 664 3 0.45 143 95 39.92 0 0 NA 869586 TCGA-AB-3009 AML43 2 144039224 144039225 - GGCGGCGACCCGCCG INS ARHGAP15 NM_018460.3 human genbank 54_36p 1 validated intronic c.1003+8700_1003+8699 e10+8700 0.559:0.568 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 147777631 147777631 T A SNP ENSG00000208251 ENST00000385516 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-20378 NULL 0.496 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 148426126 148426126 G A SNP ORC4L NM_002552.2 human genbank 54_36p -1 reviewed intronic c.588+286 e7+286 0 - - - no_errors tier3 156 0 0 44 27 38.03 2 3 60 869586 TCGA-AB-3009 AML43 2 151102056 151102056 A G SNP RND3 NM_005168.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49879 NULL 0.003 - - - no_errors tier3 356 4 1.11 51 35 40.7 0 0 NA 869586 TCGA-AB-3009 AML43 2 156266038 156266038 T C SNP - - - - - - - - - - - - - - - tier3 237 4 1.65 72 30 29.41 0 0 NA 869586 TCGA-AB-3009 AML43 2 157000487 157000487 C T SNP GPD2 NM_001083112.3 human genbank 54_36p 1 validated 5_prime_untranslated_region c.-40377 NULL 0.005 - - - no_errors tier2 185 3 1.6 89 53 37.06 3 0 0 869586 TCGA-AB-3009 AML43 2 157144907 157144907 A T SNP GPD2 NM_000408.3 human genbank 54_36p 1 validated intronic c.2058+361 e15+361 0.795 - - - no_errors tier3 NA NA NA NA NA NA 1 1 33.33 869586 TCGA-AB-3009 AML43 2 158726162 158726162 C T SNP UPP2 NM_173355.1 human genbank 54_36p 1 validated 3_prime_flanking_region c.*26514 NULL 0 - - - no_errors tier3 952 5 0.52 412 275 40.03 0 0 NA 869586 TCGA-AB-3009 AML43 2 169488496 169488496 G A SNP ABCB11 NM_003742.2 human genbank 54_36p -1 reviewed missense c.3848 p.A1283V 0.982 "HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_ABC_membrane,HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 758 11 1.43 244 214 46.72 NA 869586 TCGA-AB-3009 AML43 2 170014135 170014135 C T SNP BBS5 NM_152384.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30175 NULL 0.001 - - - no_errors tier3 963 5 0.52 357 281 44.04 0 0 NA 869586 TCGA-AB-3009 AML43 2 172895156 172895157 - CCCCAGAGA INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 174437766 174437766 G A SNP SP3 NM_003111.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*45149 NULL 0 - - - no_errors tier2 1644 22 1.32 727 558 43.42 0 0 NA 869586 TCGA-AB-3009 AML43 2 177304022 177304022 C T SNP LOC375295 XM_374020.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-40066 NULL 0 - - - no_errors tier3 665 5 0.75 256 188 42.34 0 0 NA 869586 TCGA-AB-3009 AML43 2 177922539 177922540 - GA INS ENSG00000213963 ENST00000397057 human ensembl 54_36p -1 known intronic c.1-10867_10868 e1-10866 1.000:0.997 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 178772824 178772824 A - DEL OSBPL6 NM_032523.2 human genbank 54_36p 1 reviewed intronic c.1+5177 e0+5177 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 178850982 178850982 C T SNP OSBPL6 NM_032523.2 human genbank 54_36p 1 reviewed intronic c.1-6918 e1-6918 0.001 - - - no_errors tier3 1300 17 1.29 357 302 45.83 0 0 NA 869586 TCGA-AB-3009 AML43 2 179181002 179181003 - GAC INS TTN ENST00000375038 human ensembl 54_36p -1 known in_frame_ins c.40703_40702 p.I13568in_frame_insSL 1.000:1.000 "HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_WD40 repeat-like,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_PPAK,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Protein kinase-like (PK-like),superfamily_WD40 repeat-like,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,HMMPfam_Pkinase,PatternScan_FGGY_KINASES_1,PatternScan_PEROXIDASE_1,superfamily_Immunoglobulin,superfamily_vWA-like,superfamily_Positive stranded ssRNA viruses" - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 2 183591905 183591905 G A SNP NCKAP1 NM_205842.3 human genbank 54_36p -1 validated intronic c.237+4874 e3+4874 0 - - - no_errors tier3 465 4 0.85 121 52 30.06 0 0 0 869586 TCGA-AB-3009 AML43 2 184617885 184617885 C T SNP - - - - - - - - - - - - - - - tier3 542 4 0.73 229 182 44.28 0 0 NA 869586 TCGA-AB-3009 AML43 2 185768090 185768090 A G SNP - - - - - - - - - - - - - - - tier3 835 8 0.95 119 89 42.79 0 0 NA 869586 TCGA-AB-3009 AML43 2 186405735 186405735 G A SNP FLJ44048 NM_207482.2 human genbank 54_36p 1 validated intronic c.4682-327 e7-327 0.055 - - - no_errors tier3 397 0 0 103 47 31.33 0 0 NA 869586 TCGA-AB-3009 AML43 2 188554119 188554119 G A SNP - - - - - - - - - - - - - - - tier3 139 1 0.71 27 15 35.71 0 0 NA 869586 TCGA-AB-3009 AML43 2 189640171 189640171 G A SNP COL5A2 NM_000393.3 human genbank 54_36p -1 reviewed intronic c.1402-418 e22-418 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 190632484 190632484 T C SNP MSTN NM_005259.2 human genbank 54_36p -1 reviewed intronic c.747+549 e2+549 0.007 - - - no_errors tier3 303 0 0 67 63 48.46 0 0 0 869586 TCGA-AB-3009 AML43 2 193034189 193034189 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 204365567 204365567 T C SNP ENSG00000211573 ENST00000390147 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27802 NULL 0.004 - - - no_errors tier3 768 13 1.66 258 195 42.86 0 0 NA 869586 TCGA-AB-3009 AML43 2 206131128 206131128 C A SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated intronic c.3074+4756 e21+4756 0 - - - no_errors tier3 1220 5 0.41 591 481 44.83 1 0 0 869586 TCGA-AB-3009 AML43 2 206152603 206152603 G A SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated intronic c.3074+26231 e21+26231 0.001 - - - no_errors tier2 731 7 0.95 237 250 51.33 0 0 NA 869586 TCGA-AB-3009 AML43 2 206976570 206976571 - T INS ADAM23 NM_003812.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-40266 NULL 0.009:0.011 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 208047027 208047028 - TT INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 209526236 209526236 C T SNP ENSG00000202164 ENST00000365294 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-32603 NULL 0.172 - - - no_errors tier3 715 3 0.42 186 145 43.41 0 0 NA 869586 TCGA-AB-3009 AML43 2 211114327 211114327 G A SNP CPS1 NM_001875.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15376 NULL 0.431 - - - no_errors tier2 704 10 1.4 360 282 43.93 0 0 NA 869586 TCGA-AB-3009 AML43 2 211283939 211283939 C T SNP CPS1 NM_001875.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*32985 NULL 0 - - - no_errors tier3 845 11 1.28 284 201 41.36 0 0 NA 869586 TCGA-AB-3009 AML43 2 222406435 222406435 G A SNP - - - - - - - - - - - - - - - tier2 716 5 0.69 475 121 20.27 0 0 NA 869586 TCGA-AB-3009 AML43 2 227762967 227762967 C T SNP COL4A3 NM_000091.3 human genbank 54_36p 1 reviewed intronic c.87+25194 e1+25194 0.004 - - - no_errors tier3 1131 12 1.05 301 238 43.99 0 0 NA 869586 TCGA-AB-3009 AML43 2 234326238 234326238 A T SNP UGT1A4 NM_007120.2 human genbank 54_36p 1 reviewed intronic c.868-14181 e2-14181 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 2 236198765 236198765 G A SNP AGAP1 NM_001037131.1 human genbank 54_36p 1 validated intronic c.164-83797 e2-83797 0 - - - no_errors tier2 957 15 1.54 230 194 45.75 0 0 NA 869586 TCGA-AB-3009 AML43 2 237129575 237129575 A G SNP ENSG00000213834 ENST00000396500 human ensembl 54_36p 1 known intronic c.77-12136 e2-12136 0.005 - - - no_start_codon:no_stop_codon tier3 645 3 0.46 281 224 44.36 0 0 0 869586 TCGA-AB-3009 AML43 2 239464461 239464461 G A SNP TWIST2 NM_057179.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32455 NULL 0 - - - no_coding_region tier3 704 3 0.42 151 129 46.07 0 0 NA 869586 TCGA-AB-3009 AML43 2 240260571 240260571 G A SNP ENSG00000213827 ENST00000396488 human ensembl 54_36p 1 known 5_prime_flanking_region c.-30708 NULL 0 - - - no_start_codon:no_stop_codon tier3 804 12 1.47 285 249 46.54 0 0 NA 869586 TCGA-AB-3009 AML43 3 1151817 1151817 G T SNP CNTN6 NM_014461.2 human genbank 54_36p 1 reviewed intronic c.1-12794 e1-12794 0.007 - - - no_errors tier2 696 5 0.71 227 260 53.39 0 0 NA 869586 TCGA-AB-3009 AML43 3 1501179 1501179 A T SNP - - - - - - - - - - - - - - - tier3 704 11 1.54 322 247 43.41 0 0 NA 869586 TCGA-AB-3009 AML43 3 2034970 2034970 G A SNP - - - - - - - - - - - - - - - tier3 791 3 0.38 453 77 14.53 0 0 NA 869586 TCGA-AB-3009 AML43 3 2078249 2078249 C T SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-509939 NULL 0 - - - no_errors tier3 658 13 1.93 127 99 43.81 0 0 NA 869586 TCGA-AB-3009 AML43 3 2244802 2244802 T A SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.1-111060 e1-111060 0.007 - - - no_errors tier2 88 0 0 2 6 75 0 0 NA 869586 TCGA-AB-3009 AML43 3 2984885 2984885 T G SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.1359-20144 e11-20144 0.924 - - - no_errors tier3 1300 19 1.44 375 342 47.7 0 0 NA 869586 TCGA-AB-3009 AML43 3 3679305 3679305 A G SNP ENSG00000223036 ENST00000411104 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*16043 NULL 0 - - - no_errors tier3 391 0 0 69 61 46.56 0 0 NA 869586 TCGA-AB-3009 AML43 3 5767652 5767652 A G SNP - - - - - - - - - - - - - - - tier3 1116 4 0.36 286 256 47.23 0 0 NA 869586 TCGA-AB-3009 AML43 3 8069738 8069738 G A SNP - - - - - - - - - - - - - - - tier3 858 13 1.49 178 152 46.06 0 0 NA 869586 TCGA-AB-3009 AML43 3 8111011 8111011 G A SNP - - - - - - - - - - - - - - - tier3 872 9 1.02 196 183 48.28 0 0 NA 869586 TCGA-AB-3009 AML43 3 9761731 9761731 T C SNP BRPF1 NM_001003694.1 human genbank 54_36p 1 reviewed missense c.2960 p.V987A 1 NULL "HMMPfam_PWWP,HMMSmart_PWWP,HMMPfam_Bromodomain,HMMSmart_BROMO,superfamily_Bromodomain,HMMSmart_PHD,PatternScan_ZINC_FINGER_C2H2_1,superfamily_FYVE_PHD_ZnF,HMMSmart_ZnF_C2H2,HMMPfam_EPL1,PatternScan_ZF_PHD_1,HMMPfam_PHD,superfamily_SSF63748" - no_errors tier1 1044 2 0.19 291 203 40.85 32 30 48.39 869586 TCGA-AB-3009 AML43 3 10155644 10155644 G A SNP IRAK2 NM_001570.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25995 NULL 0.015 - - - no_errors tier3 845 4 0.47 130 97 42.73 0 0 NA 869586 TCGA-AB-3009 AML43 3 10231291 10231291 A T SNP IRAK2 NM_001570.3 human genbank 54_36p 1 reviewed intronic c.788+1059 e6+1059 0.052 - - - no_errors tier3 812 13 1.57 36 38 51.35 3 0 0 869586 TCGA-AB-3009 AML43 3 10636309 10636309 C T SNP ATP2B2 ENST00000397077 human ensembl 54_36p -1 known intronic c.1+293 e0+293 0 - - - no_errors tier2 1224 12 0.97 200 164 45.05 0 0 NA 869586 TCGA-AB-3009 AML43 3 11182425 11182425 A G SNP HRH1 NM_001098212.3 human genbank 54_36p 1 reviewed intronic c.1+11185 e0+11185 0.001 - - - no_errors tier2 1278 23 1.77 270 180 40 0 0 NA 869586 TCGA-AB-3009 AML43 3 12178231 12178231 T C SNP SYN2 ENST00000341648 human ensembl 54_36p 1 known intronic c.630+123 e7+123 0 - - - no_errors tier3 1877 31 1.62 519 415 44.29 0 0 NA 869586 TCGA-AB-3009 AML43 3 21174762 21174763 - A INS ENSG00000221659 ENST00000408732 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19925 NULL 0.002:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 3 25507680 25507680 G A SNP RARB NM_000965.3 human genbank 54_36p 1 reviewed intronic c.307-9997 e3-9997 0 - - - no_errors tier3 695 7 1 166 182 52.15 0 0 NA 869586 TCGA-AB-3009 AML43 3 27052799 27052799 C A SNP - - - - - - - - - - - - - - - tier3 1427 20 1.38 558 518 48.14 0 0 NA 869586 TCGA-AB-3009 AML43 3 30365401 30365401 C T SNP ENSG00000199927 ENST00000363057 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-44370 NULL 0 - - - no_errors tier3 607 3 0.49 159 117 41.94 0 0 NA 869586 TCGA-AB-3009 AML43 3 36370530 36370530 G A SNP STAC NM_003149.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-26610 NULL 0.008 - - - no_errors tier3 978 11 1.11 396 276 41.07 0 0 NA 869586 TCGA-AB-3009 AML43 3 38544147 38544147 C T SNP EXOG ENST00000358249 human ensembl 54_36p 1 known intronic c.270+3707 e4+3707 0.001 - - - no_errors tier3 1604 9 0.56 634 503 44.24 9 8 47.06 869586 TCGA-AB-3009 AML43 3 41780881 41780881 T A SNP ULK4 NM_017886.2 human genbank 54_36p -1 validated intronic c.2194-9897 e21-9897 0.002 - - - no_errors tier3 264 2 0.75 94 63 40.13 0 1 100 869586 TCGA-AB-3009 AML43 3 45071520 45071520 T A SNP CDCP1 NM_022842.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*30614 NULL 0 - - - no_errors tier3 660 11 1.64 83 97 53.89 0 0 NA 869586 TCGA-AB-3009 AML43 3 50268699 50268699 G A SNP GNAI2 NM_002070.2 human genbank 54_36p 1 validated missense c.536 p.R179H 0.998 "HMMPfam_G-alpha,superfamily_Transducin (alpha subunit) insertion domain,HMMSmart_SM00275,superfamily_P-loop containing nucleoside triphosphate hydrolases" "HMMPfam_G-alpha,superfamily_Transducin (alpha subunit) insertion domain,HMMSmart_SM00275,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 481 3 0.62 172 44 20.28 510 213 29.46 869586 TCGA-AB-3009 AML43 3 51728562 51728562 T A SNP ENSG00000201595 ENST00000364725 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-24924 NULL 0.014 - - - no_errors tier2 1048 22 2.06 68 63 48.09 1 0 0 869586 TCGA-AB-3009 AML43 3 53895898 53895898 A G SNP uc003dhe.1 ENST00000231908 human ensembl 54_36p -1 known intronic c.194+20 e3+20 0 - - - no_errors tier3 318 0 0 63 53 45.69 0 0 0 869586 TCGA-AB-3009 AML43 3 55215807 55215807 A G SNP - - - - - - - - - - - - - - - tier3 710 12 1.66 222 202 47.64 0 0 NA 869586 TCGA-AB-3009 AML43 3 64994383 64994383 G C SNP - - - - - - - - - - - - - - - tier2 1428 6 0.42 324 280 46.36 0 0 NA 869586 TCGA-AB-3009 AML43 3 65900914 65900914 C T SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.313+97797 e1+97797 0.001 - - - no_errors tier3 1084 10 0.91 313 225 41.74 0 0 NA 869586 TCGA-AB-3009 AML43 3 76036604 76036604 G T SNP ROBO2 ENST00000403211 human ensembl 54_36p 1 known 5_prime_flanking_region c.-32731 NULL 0 - - - no_stop_codon:overly_large_intron tier3 169 0 0 45 15 25 0 0 NA 869586 TCGA-AB-3009 AML43 3 77331179 77331179 A C SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.388+100998 e2+100998 0.004 - - - no_errors tier2 794 22 2.69 370 259 41.18 0 0 NA 869586 TCGA-AB-3009 AML43 3 77729580 77729580 G T SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.2854+989 e19+989 0.003 - - - no_errors tier3 289 2 0.69 68 49 41.88 0 0 NA 869586 TCGA-AB-3009 AML43 3 77854450 77854450 G T SNP - - - - - - - - - - - - - - - tier3 804 10 1.23 321 303 48.4 0 0 NA 869586 TCGA-AB-3009 AML43 3 78065897 78065897 A G SNP - - - - - - - - - - - - - - - tier3 719 12 1.64 202 127 38.6 0 0 NA 869586 TCGA-AB-3009 AML43 3 78833219 78833219 G A SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.1046-12607 e8-12607 0.006 - - - no_errors tier3 732 10 1.35 215 185 46.25 0 0 NA 869586 TCGA-AB-3009 AML43 3 79042227 79042227 C T SNP ROBO1 NM_002941.1 human genbank 54_36p -1 reviewed intronic c.499+28214 e3+28214 0.001 - - - no_errors tier3 400 1 0.25 104 103 49.76 0 0 NA 869586 TCGA-AB-3009 AML43 3 79977138 79977138 G T SNP - - - - - - - - - - - - - - - tier3 415 1 0.24 72 26 26.53 0 0 NA 869586 TCGA-AB-3009 AML43 3 80089414 80089414 C A SNP - - - - - - - - - - - - - - - tier2 441 5 1.12 164 103 38.58 0 0 NA 869586 TCGA-AB-3009 AML43 3 80218392 80218392 C - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 3 80560540 80560540 T G SNP - - - - - - - - - - - - - - - tier3 764 9 1.16 138 144 50.7 0 0 NA 869586 TCGA-AB-3009 AML43 3 80989228 80989228 T A SNP - - - - - - - - - - - - - - - tier3 263 0 0 36 43 54.43 0 0 NA 869586 TCGA-AB-3009 AML43 3 82551753 82551753 G A SNP - - - - - - - - - - - - - - - tier3 437 4 0.91 83 62 42.76 0 0 NA 869586 TCGA-AB-3009 AML43 3 83059588 83059588 G A SNP - - - - - - - - - - - - - - - tier2 456 7 1.51 237 219 48.03 0 0 NA 869586 TCGA-AB-3009 AML43 3 85162026 85162026 C T SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+70517 e1+70517 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 3 88866317 88866317 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 3 89935385 89935385 G A SNP - - - - - - - - - - - - - - - tier3 467 2 0.43 80 79 49.69 0 0 NA 869586 TCGA-AB-3009 AML43 3 96666103 96666103 G A SNP - - - - - - - - - - - - - - - tier3 950 7 0.73 309 316 50.56 0 0 NA 869586 TCGA-AB-3009 AML43 3 96784077 96784077 T C SNP - - - - - - - - - - - - - - - tier2 592 3 0.5 145 104 41.6 0 0 NA 869586 TCGA-AB-3009 AML43 3 97215967 97215967 A G SNP - - - - - - - - - - - - - - - tier3 547 4 0.73 109 66 37.71 0 0 NA 869586 TCGA-AB-3009 AML43 3 97893567 97893567 G A SNP ENSG00000212031 ENST00000390742 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-25754 NULL 0.001 - - - no_errors tier3 707 8 1.12 171 48 21.92 0 0 NA 869586 TCGA-AB-3009 AML43 3 98446452 98446452 T A SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.1606+631 e5+631 0.013 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 3 98606525 98606525 G A SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.1607-159 e6-159 0 - - - no_errors tier3 434 3 0.68 190 147 43.62 0 0 NA 869586 TCGA-AB-3009 AML43 3 110985679 110985679 T A SNP - - - - - - - - - - - - - - - tier3 679 6 0.87 61 77 55.8 0 0 NA 869586 TCGA-AB-3009 AML43 3 111440867 111440867 A G SNP - - - - - - - - - - - - - - - tier3 647 16 2.4 169 161 48.79 0 0 NA 869586 TCGA-AB-3009 AML43 3 112622545 112622545 C T SNP - - - - - - - - - - - - - - - tier3 811 8 0.98 145 113 43.8 0 0 NA 869586 TCGA-AB-3009 AML43 3 114733815 114733816 - T INS ENSG00000214369 ENST00000379462 human ensembl 54_36p 1 known intronic c.9+14558_9+14557 e1+14558 0.003:0.044 - - - no_start_codon tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 3 115862709 115862709 G C SNP ZBTB20 NM_015642.3 human genbank 54_36p -1 provisional intronic c.1+32356 e0+32356 0.965 - - - no_errors tier3 1136 6 0.52 485 103 17.52 18 1 5.26 869586 TCGA-AB-3009 AML43 3 116000742 116000742 G C SNP ZBTB20 NM_015642.3 human genbank 54_36p -1 provisional intronic c.1+1896 e0+1896 0.001 - - - no_errors tier3 1608 17 1.05 616 600 49.34 3 1 25 869586 TCGA-AB-3009 AML43 3 117215291 117215291 A G SNP LSAMP NM_002338.2 human genbank 54_36p -1 reviewed intronic c.514+5761 e3+5761 0 - - - no_errors tier3 504 5 0.98 84 83 49.7 0 0 NA 869586 TCGA-AB-3009 AML43 3 117925746 117925746 C T SNP - - - - - - - - - - - - - - - tier3 1359 12 0.87 410 319 43.76 0 0 NA 869586 TCGA-AB-3009 AML43 3 118376358 118376358 A G SNP - - - - - - - - - - - - - - - tier3 441 6 1.34 70 65 48.15 0 0 NA 869586 TCGA-AB-3009 AML43 3 119101366 119101366 G A SNP - - - - - - - - - - - - - - - tier3 601 6 0.99 124 102 44.93 0 0 NA 869586 TCGA-AB-3009 AML43 3 125738237 125738237 G A SNP KALRN NM_001024660.2 human genbank 54_36p 1 reviewed intronic c.4930-26143 e34-26143 0 - - - no_errors tier3 491 4 0.81 87 64 42.38 0 0 NA 869586 TCGA-AB-3009 AML43 3 127261201 127261201 G A SNP SLC41A3 NM_001008485.1 human genbank 54_36p -1 validated intronic c.273+8279 e1+8279 0 - - - no_errors tier3 960 3 0.31 433 362 45.53 1 0 0 869586 TCGA-AB-3009 AML43 3 130212164 130212164 C T SNP CCDC48 XM_001130701.1 human genbank 54_36p 1 model intronic c.1352+6554 e5+6554 0.478 - - - no_errors tier3 446 4 0.89 204 62 23.22 0 0 NA 869586 TCGA-AB-3009 AML43 3 134126457 134126457 C T SNP - - - - - - - - - - - - - - - tier3 92 1 1.06 22 15 40.54 0 0 NA 869586 TCGA-AB-3009 AML43 3 141311794 141311794 C T SNP CLSTN2 NM_022131.2 human genbank 54_36p 1 validated intronic c.110-65689 e2-65689 0 - - - no_errors tier3 865 7 0.8 187 162 46.42 0 0 NA 869586 TCGA-AB-3009 AML43 3 142302687 142302688 - C INS SPSB4 NM_080862.1 human genbank 54_36p 1 provisional intronic c.694+34357_694+34356 e1+34357 0.001:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 3 149286574 149286574 G T SNP ENSG00000221457 ENST00000408530 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*5175 NULL 0.001 - - - no_errors tier3 174 2 1.14 16 3 15.79 0 0 NA 869586 TCGA-AB-3009 AML43 3 149292848 149292848 C A SNP ENSG00000221457 ENST00000408530 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*11449 NULL 0 - - - no_errors tier3 241 0 0 23 22 48.89 0 0 NA 869586 TCGA-AB-3009 AML43 3 158822306 158822306 G A SNP C3orf55 NM_001099777.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*43490 NULL 0 - - - no_errors tier3 1103 10 0.9 506 403 44.33 0 0 NA 869586 TCGA-AB-3009 AML43 3 159747211 159747211 C T SNP MLF1 NM_022443.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-24573 NULL 0.001 - - - no_errors tier3 957 2 0.21 271 196 41.97 5 2 28.57 869586 TCGA-AB-3009 AML43 3 164377776 164377776 G A SNP LOC647109 XM_930126.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*22459 NULL 0 - - - no_errors tier3 575 4 0.69 201 152 42.94 0 0 NA 869586 TCGA-AB-3009 AML43 3 164688095 164688095 T G SNP ENSG00000221205 ENST00000408278 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*28789 NULL 0 - - - no_errors tier3 302 2 0.66 36 27 42.86 0 0 NA 869586 TCGA-AB-3009 AML43 3 164995486 164995486 C T SNP - - - - - - - - - - - - - - - tier3 854 7 0.81 242 203 45.41 0 0 NA 869586 TCGA-AB-3009 AML43 3 167307898 167307898 G A SNP - - - - - - - - - - - - - - - tier3 662 9 1.34 134 113 45.75 0 0 NA 869586 TCGA-AB-3009 AML43 3 167420251 167420251 C T SNP ENSG00000208601 ENST00000385866 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13439 NULL 0 - - - pseudogene tier3 735 2 0.27 222 189 45.99 0 0 NA 869586 TCGA-AB-3009 AML43 3 167997880 167997880 T G SNP ENSG00000185790 ENST00000331839 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13759 NULL 0.001 - - - no_coding_region:pseudogene tier3 112 6 5.08 12 21 63.64 0 0 NA 869586 TCGA-AB-3009 AML43 3 170003465 170003465 C T SNP LOC253820 XM_001726233.1 human genbank 54_36p 1 model silent c.324 p.P108 0.015 "HMMSmart_SM00181,superfamily_EGF/Laminin" "PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMSmart_SM00181,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin" - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 3 170876894 170876894 C A SNP MDS1 NM_004991.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-13040 NULL 0.001 - - - no_errors tier3 713 2 0.28 296 202 40.56 0 0 NA 869586 TCGA-AB-3009 AML43 3 175311421 175311421 C A SNP NLGN1 NM_014932.2 human genbank 54_36p 1 reviewed intronic c.647-164378 e3-164378 0.243 - - - no_errors tier2 369 1 0.27 206 140 40.46 0 0 NA 869586 TCGA-AB-3009 AML43 3 177183210 177183210 C T SNP - - - - - - - - - - - - - - - tier3 336 1 0.3 132 88 39.46 0 0 NA 869586 TCGA-AB-3009 AML43 3 184874164 184874164 T C SNP KLHL24 NM_017644.3 human genbank 54_36p 1 validated intronic c.1602+1198 e5+1198 0.03 - - - no_errors tier3 1389 11 0.79 599 441 42.4 11 11 50 869586 TCGA-AB-3009 AML43 3 186144885 186144885 C T SNP VPS8 NM_001009921.2 human genbank 54_36p 1 validated intronic c.3035+4160 e35+4160 0.006 - - - no_errors tier3 1210 13 1.06 487 355 42.11 1 0 0 869586 TCGA-AB-3009 AML43 3 186776963 186776963 C T SNP LIPH NM_139248.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-24010 NULL 0.012 - - - no_errors tier3 169 4 2.3 13 11 45.83 0 0 NA 869586 TCGA-AB-3009 AML43 3 187943981 187943981 A T SNP KNG1 NM_000893.2 human genbank 54_36p 1 validated intronic c.1204-207 e11-207 0 - - - no_errors tier3 1267 17 1.32 255 144 36.09 0 0 NA 869586 TCGA-AB-3009 AML43 3 192086469 192086469 A T SNP LOC647309 XM_930379.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-22824 NULL 0.018 - - - no_errors tier3 393 3 0.76 107 111 50.92 0 0 NA 869586 TCGA-AB-3009 AML43 3 192511916 192511916 C T SNP UTS2D ENST00000340524 human ensembl 54_36p -1 known intronic c.1+4603 e0+4603 0.001 - - - no_errors tier3 1546 23 1.46 343 299 46.57 0 0 NA 869586 TCGA-AB-3009 AML43 3 192676992 192676992 C A SNP PYDC2 NM_001083308.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*15053 NULL 0.015 - - - no_errors tier3 722 10 1.37 189 114 37.62 0 0 NA 869586 TCGA-AB-3009 AML43 3 193463531 193463531 A G SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed intronic c.414+72313 e3+72313 0 - - - no_errors tier3 468 4 0.85 103 98 48.76 0 0 NA 869586 TCGA-AB-3009 AML43 3 195575023 195575023 C T SNP LRRC15 NM_130830.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11956 NULL 0 - - - no_errors tier3 244 0 0 53 24 31.17 0 0 NA 869586 TCGA-AB-3009 AML43 4 196944 196944 C T SNP ZNF732 ENST00000356347 human ensembl 54_36p 1 known intronic c.1+374 e0+374 0 - - - no_start_codon tier2 538 3 0.55 271 251 47.99 2 0 0 869586 TCGA-AB-3009 AML43 4 2044468 2044468 C T SNP POLN NM_181808.2 human genbank 54_36p -1 validated intronic c.2517+25 e23+25 0 - - - no_errors tier3 262 9 3.32 106 101 48.33 2 1 33.33 869586 TCGA-AB-3009 AML43 4 12084534 12084534 A G SNP - - - - - - - - - - - - - - - tier3 394 7 1.75 129 100 43.67 0 0 NA 869586 TCGA-AB-3009 AML43 4 12107182 12107182 C A SNP - - - - - - - - - - - - - - - tier3 684 5 0.72 174 176 50.29 0 0 NA 869586 TCGA-AB-3009 AML43 4 14954202 14954202 G T SNP C1QTNF7 NM_031911.1 human genbank 54_36p 1 validated intronic c.1+3273 e0+3273 0.004 - - - no_errors tier3 549 6 1.08 100 76 43.18 0 0 NA 869586 TCGA-AB-3009 AML43 4 18285640 18285640 C T SNP - - - - - - - - - - - - - - - tier3 2094 14 0.66 648 450 40.95 0 0 NA 869586 TCGA-AB-3009 AML43 4 18683902 18683902 C T SNP - - - - - - - - - - - - - - - tier3 1354 13 0.95 295 221 42.83 0 0 NA 869586 TCGA-AB-3009 AML43 4 18920367 18920367 G A SNP - - - - - - - - - - - - - - - tier2 1301 9 0.69 391 314 44.54 0 0 NA 869586 TCGA-AB-3009 AML43 4 19193052 19193052 C T SNP - - - - - - - - - - - - - - - tier3 476 6 1.24 199 132 39.76 0 0 NA 869586 TCGA-AB-3009 AML43 4 19864204 19864204 C T SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-333 NULL 0.606 - - - no_errors tier2 269 2 0.74 156 103 39.77 0 0 NA 869586 TCGA-AB-3009 AML43 4 19876182 19876182 G A SNP SLIT2 NM_004787.1 human genbank 54_36p 1 provisional intronic c.324-3349 e4-3349 0 - - - no_errors tier3 570 8 1.38 195 144 42.48 0 0 NA 869586 TCGA-AB-3009 AML43 4 20516603 20516603 C T SNP KCNIP4 NM_147183.1 human genbank 54_36p -1 reviewed intronic c.101-55215 e2-55215 0.003 - - - no_errors tier3 659 5 0.75 179 123 40.73 0 0 NA 869586 TCGA-AB-3009 AML43 4 21110916 21110916 G A SNP KCNIP4 NM_001035003.1 human genbank 54_36p -1 reviewed intronic c.88+197155 e1+197155 0 - - - no_errors tier3 701 6 0.85 182 82 31.06 0 0 NA 869586 TCGA-AB-3009 AML43 4 21119183 21119183 T G SNP KCNIP4 NM_001035003.1 human genbank 54_36p -1 reviewed intronic c.88+188888 e1+188888 0 - - - no_errors tier3 863 4 0.46 219 195 47.1 0 0 NA 869586 TCGA-AB-3009 AML43 4 21319658 21319658 C T SNP KCNIP4 NM_025221.1 human genbank 54_36p -1 reviewed intronic c.61+239634 e1+239634 0.001 - - - overly_large_intron tier3 472 0 0 60 9 13.04 0 0 NA 869586 TCGA-AB-3009 AML43 4 23632204 23632204 C A SNP - - - - - - - - - - - - - - - tier3 1140 6 0.52 510 432 45.86 0 0 NA 869586 TCGA-AB-3009 AML43 4 23750349 23750349 C T SNP - - - - - - - - - - - - - - - tier3 679 4 0.59 301 327 52.07 0 0 NA 869586 TCGA-AB-3009 AML43 4 27195937 27195937 G A SNP ENSG00000221807 ENST00000408880 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*49061 NULL 0.949 - - - no_errors tier2 503 9 1.75 145 122 45.69 0 0 NA 869586 TCGA-AB-3009 AML43 4 27578426 27578426 T A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 28561760 28561760 C G SNP - - - - - - - - - - - - - - - tier3 525 5 0.94 136 89 39.56 0 0 NA 869586 TCGA-AB-3009 AML43 4 28906848 28906848 C T SNP - - - - - - - - - - - - - - - tier3 668 16 2.34 199 145 42.15 0 0 NA 869586 TCGA-AB-3009 AML43 4 28960008 28960008 C T SNP - - - - - - - - - - - - - - - tier3 501 3 0.6 142 111 43.87 0 0 NA 869586 TCGA-AB-3009 AML43 4 29105232 29105232 C G SNP ENSG00000209052 ENST00000386317 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-16126 NULL 0.001 - - - pseudogene tier3 262 1 0.38 31 12 27.91 0 0 NA 869586 TCGA-AB-3009 AML43 4 29107730 29107731 - T INS ENSG00000209052 ENST00000386317 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-13628 NULL 0.000:0.001 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 30563192 30563192 A - DEL PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3226+32127 e3+32127 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 30653089 30653089 C T SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3227-100104 e4-100104 0 - - - no_errors tier3 545 7 1.26 104 82 44.09 0 0 NA 869586 TCGA-AB-3009 AML43 4 30712415 30712415 G T SNP PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3227-40778 e4-40778 0.018 - - - no_errors tier3 1101 3 0.27 258 178 40.83 0 0 NA 869586 TCGA-AB-3009 AML43 4 30729745 30729745 T - DEL PCDH7 NM_032457.2 human genbank 54_36p 1 reviewed intronic c.3227-23448 e4-23448 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 30764036 30764036 A C SNP LOC645716 XM_933075.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-17970 NULL 0 - - - no_errors tier3 1144 7 0.61 488 436 47.14 0 0 NA 869586 TCGA-AB-3009 AML43 4 31298402 31298402 A C SNP - - - - - - - - - - - - - - - tier3 941 2 0.21 469 330 41.2 0 0 NA 869586 TCGA-AB-3009 AML43 4 31827243 31827243 G A SNP LOC100130644 XM_001717608.1 human genbank 54_36p -1 model intronic c.676-19385 e5-19385 0.047 - - - pseudogene:no_stop_codon tier3 1144 5 0.43 163 114 41.16 1 0 0 869586 TCGA-AB-3009 AML43 4 32781093 32781093 A C SNP - - - - - - - - - - - - - - - tier3 607 5 0.82 143 117 45 0 0 NA 869586 TCGA-AB-3009 AML43 4 35250271 35250271 G A SNP - - - - - - - - - - - - - - - tier2 293 0 0 80 67 45.58 0 0 NA 869586 TCGA-AB-3009 AML43 4 35471130 35471130 A G SNP - - - - - - - - - - - - - - - tier3 802 3 0.37 210 188 47.24 0 0 NA 869586 TCGA-AB-3009 AML43 4 36530355 36530355 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 36730979 36730979 T C SNP - - - - - - - - - - - - - - - tier3 1208 8 0.66 449 374 45.44 0 0 NA 869586 TCGA-AB-3009 AML43 4 37062353 37062353 C T SNP ENSG00000215243 ENST00000389006 human ensembl 54_36p 1 known intronic c.57+27854 e1+27854 0 - - - no_start_codon:no_stop_codon tier3 695 7 1 253 200 44.15 0 0 NA 869586 TCGA-AB-3009 AML43 4 37856847 37856847 G T SNP TBC1D1 NM_015173.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*41496 NULL 0.041 - - - no_errors tier3 1013 9 0.88 298 244 45.02 0 0 NA 869586 TCGA-AB-3009 AML43 4 41866526 41866526 G A SNP BEND4 NM_207406.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-17609 NULL 0 - - - no_errors tier3 1887 27 1.41 568 529 48.18 0 0 NA 869586 TCGA-AB-3009 AML43 4 45360745 45360745 C A SNP - - - - - - - - - - - - - - - tier3 519 2 0.38 220 171 43.73 0 0 NA 869586 TCGA-AB-3009 AML43 4 53509282 53509282 G A SNP SCFD2 NM_152540.3 human genbank 54_36p -1 validated intronic c.1562-27488 e6-27488 0 - - - no_errors tier2 1310 13 0.98 546 428 43.9 2 0 0 869586 TCGA-AB-3009 AML43 4 56396856 56396856 G A SNP LOC100129077 XM_001713831.1 human genbank 54_36p -1 model intronic c.104+1153 e1+1153 0 - - - no_errors tier3 1006 12 1.18 131 134 50.57 0 0 NA 869586 TCGA-AB-3009 AML43 4 58046630 58046630 C T SNP ENSG00000210638 ENST00000387903 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*6563 NULL 0 - - - pseudogene tier3 1654 5 0.3 570 206 26.48 0 0 NA 869586 TCGA-AB-3009 AML43 4 59003521 59003521 C A SNP - - - - - - - - - - - - - - - tier3 181 0 0 31 7 18.42 0 0 NA 869586 TCGA-AB-3009 AML43 4 59753060 59753060 C T SNP - - - - - - - - - - - - - - - tier2 465 7 1.47 149 116 43.77 0 0 NA 869586 TCGA-AB-3009 AML43 4 63048485 63048485 C A SNP - - - - - - - - - - - - - - - tier3 438 1 0.23 70 26 27.08 0 0 NA 869586 TCGA-AB-3009 AML43 4 63365101 63365101 C T SNP LOC644556 XM_001719457.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-966 NULL 0.002 - - - no_errors tier2 NA NA NA NA NA NA 1 0 0 869586 TCGA-AB-3009 AML43 4 63845241 63845241 C G SNP - - - - - - - - - - - - - - - tier3 411 13 3.06 97 74 43.27 0 0 NA 869586 TCGA-AB-3009 AML43 4 65524263 65524263 G A SNP - - - - - - - - - - - - - - - tier3 551 5 0.9 222 164 42.49 0 0 NA 869586 TCGA-AB-3009 AML43 4 66607172 66607172 A - DEL ENSG00000210740 ENST00000388005 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-6523 NULL 0.001 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 66875415 66875415 G C SNP - - - - - - - - - - - - - - - tier3 311 7 2.2 100 61 37.89 0 0 NA 869586 TCGA-AB-3009 AML43 4 69928008 69928008 T C SNP UGT2B11 ENST00000305206 human ensembl 54_36p -1 known intronic c.1590-22951 e7-22951 0 - - - no_errors tier3 604 7 1.15 175 177 50.28 0 0 NA 869586 TCGA-AB-3009 AML43 4 70511151 70511151 A G SNP UGT2A1 NM_006798.2 human genbank 54_36p -1 validated intronic c.716-11450 e2-11450 0 - - - no_errors tier3 600 3 0.5 246 210 46.05 0 0 NA 869586 TCGA-AB-3009 AML43 4 71747205 71747205 C T SNP IGJ NM_144646.3 human genbank 54_36p -1 validated intronic c.65-409 e2-409 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 869586 TCGA-AB-3009 AML43 4 76450527 76450527 T - DEL LOC643100 XM_931316.1 human genbank 54_36p -1 model intronic c.171+20232 e2+20232 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 80251211 80251211 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 80339543 80339543 C T SNP - - - - - - - - - - - - - - - tier2 1275 6 0.47 460 339 42.43 1 2 66.67 869586 TCGA-AB-3009 AML43 4 80829340 80829340 T C SNP - - - - - - - - - - - - - - - tier3 199 3 1.49 23 30 56.6 0 0 NA 869586 TCGA-AB-3009 AML43 4 87781430 87781430 G A SNP PTPN13 NM_080685.2 human genbank 54_36p 1 reviewed intronic c.115+5882 e1+5882 0 - - - no_errors tier3 670 1 0.15 144 146 50.34 0 0 NA 869586 TCGA-AB-3009 AML43 4 94206628 94206628 C T SNP GRID2 NM_001510.2 human genbank 54_36p 1 validated intronic c.245-18541 e3-18541 0.018 - - - no_errors tier3 264 0 0 128 106 45.3 0 0 NA 869586 TCGA-AB-3009 AML43 4 95615408 95615408 T C SNP PDLIM5 NM_006457.2 human genbank 54_36p 1 reviewed intronic c.96+19850 e1+19850 0.023 - - - no_errors tier3 640 1 0.16 194 128 39.75 0 1 100 869586 TCGA-AB-3009 AML43 4 106092739 106092739 T - DEL LOC643675 XR_041865.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-21579 NULL 0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 116971210 116971210 C A SNP - - - - - - - - - - - - - - - tier3 41 1 2.38 30 26 46.43 0 0 NA 869586 TCGA-AB-3009 AML43 4 120921013 120921013 T G SNP - - - - - - - - - - - - - - - tier3 1259 13 1.02 377 244 39.29 0 0 NA 869586 TCGA-AB-3009 AML43 4 121285570 121285570 G A SNP LOC100128580 XM_001724885.1 human genbank 54_36p 1 model intronic c.317-5576 e3-5576 0 - - - no_errors tier3 780 12 1.52 280 245 46.67 0 0 NA 869586 TCGA-AB-3009 AML43 4 125600762 125600762 G A SNP ENSG00000214796 ENST00000398989 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-23037 NULL 0.197 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 126588250 126588250 C T SNP FAT4 NM_024582.4 human genbank 54_36p 1 validated intronic c.7445-816 e9-816 0 - - - no_errors tier3 267 2 0.74 46 48 51.06 0 0 NA 869586 TCGA-AB-3009 AML43 4 126893935 126893935 C T SNP - - - - - - - - - - - - - - - tier3 131 1 0.76 12 30 71.43 0 0 NA 869586 TCGA-AB-3009 AML43 4 127516900 127516900 C A SNP - - - - - - - - - - - - - - - tier2 781 12 1.51 286 227 44.25 0 0 NA 869586 TCGA-AB-3009 AML43 4 130454747 130454747 G A SNP - - - - - - - - - - - - - - - tier3 1207 6 0.49 336 380 53.07 0 0 NA 869586 TCGA-AB-3009 AML43 4 130541766 130541766 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 133038147 133038147 G A SNP LOC646187 XR_016991.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 416 7 1.65 170 142 45.51 0 0 NA 869586 TCGA-AB-3009 AML43 4 137108969 137108969 C A SNP ENSG00000207322 ENST00000384592 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*27565 NULL 0.001 - - - no_errors tier3 128 1 0.78 48 22 31.43 0 0 NA 869586 TCGA-AB-3009 AML43 4 137637510 137637510 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 142258827 142258827 G T SNP RNF150 NM_020724.1 human genbank 54_36p -1 validated intronic c.484+14102 e1+14102 0 - - - no_errors tier3 1408 9 0.64 505 415 45.11 0 0 NA 869586 TCGA-AB-3009 AML43 4 142853353 142853353 T A SNP IL15 NM_000585.3 human genbank 54_36p 1 reviewed intronic c.1-6616 e1-6616 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 152840379 152840380 - AC INS PET112L NM_004564.1 human genbank 54_36p -1 provisional intronic c.1197+1551_1197+1550 e9+1551 0.002:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 152868972 152868972 A G SNP PET112L NM_004564.1 human genbank 54_36p -1 provisional intronic c.328-8832 e3-8832 0.001 - - - no_errors tier3 583 0 0 129 125 49.21 1 0 0 869586 TCGA-AB-3009 AML43 4 154334476 154334476 C T SNP TRIM2 NM_015271.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-76512 NULL 0 - - - no_errors tier3 1282 15 1.15 308 301 49.43 0 0 NA 869586 TCGA-AB-3009 AML43 4 162690344 162690344 T C SNP FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.1016-7049 e8-7049 0.004 - - - no_errors tier3 880 17 1.89 295 300 50.42 0 0 NA 869586 TCGA-AB-3009 AML43 4 163264471 163264471 A - DEL FSTL5 NM_020116.1 human genbank 54_36p -1 validated intronic c.1-12457 e1-12457 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 166070056 166070056 C A SNP C4orf39 NM_153027.1 human genbank 54_36p 1 predicted 5_prime_flanking_region c.-27569 NULL 0.001 - - - no_errors tier3 712 6 0.83 128 117 47.76 0 0 NA 869586 TCGA-AB-3009 AML43 4 167015901 167015901 G T SNP TLL1 NM_012464.3 human genbank 54_36p 1 reviewed intronic c.169+1226 e1+1226 0 - - - no_errors tier2 821 7 0.85 312 205 39.58 0 0 NA 869586 TCGA-AB-3009 AML43 4 168415185 168415185 C T SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23286 NULL 0.002 - - - no_errors tier3 623 3 0.48 116 74 38.95 0 0 NA 869586 TCGA-AB-3009 AML43 4 168629207 168629207 C T SNP - - - - - - - - - - - - - - - tier3 608 0 0 126 46 26.74 0 0 NA 869586 TCGA-AB-3009 AML43 4 173920794 173920794 C T SNP GALNTL6 NM_001034845.2 human genbank 54_36p 1 validated intronic c.554-46293 e5-46293 0.102 - - - no_errors tier3 897 12 1.32 286 261 47.71 0 0 NA 869586 TCGA-AB-3009 AML43 4 174728239 174728239 C A SNP HAND2 NM_021973.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-41224 NULL 0 - - - no_errors tier3 823 13 1.55 196 188 48.96 0 0 NA 869586 TCGA-AB-3009 AML43 4 176729323 176729323 G T SNP - - - - - - - - - - - - - - - tier3 637 9 1.39 128 35 21.47 0 0 NA 869586 TCGA-AB-3009 AML43 4 179697612 179697612 T C SNP - - - - - - - - - - - - - - - tier3 1074 22 2.01 357 312 46.64 0 0 NA 869586 TCGA-AB-3009 AML43 4 182026988 182026988 C T SNP - - - - - - - - - - - - - - - tier3 199 0 0 64 53 45.3 0 0 NA 869586 TCGA-AB-3009 AML43 4 182229752 182229752 C T SNP LOC728081 XM_001127776.1 human genbank 54_36p -1 model intronic c.133-7125 e3-7125 0.001 - - - no_errors tier3 1016 19 1.83 211 128 37.76 0 0 NA 869586 TCGA-AB-3009 AML43 4 182348378 182348378 C G SNP LOC728081 XM_001127776.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-31151 NULL 0.989 - - - no_errors tier2 1175 14 1.17 155 130 45.45 0 0 NA 869586 TCGA-AB-3009 AML43 4 182597952 182597952 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 183462889 183462889 G A SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-19279 NULL 0 - - - no_errors tier3 1119 21 1.84 468 403 46.27 0 0 NA 869586 TCGA-AB-3009 AML43 4 183488821 183488821 C T SNP ODZ3 NM_001080477.1 human genbank 54_36p 1 provisional intronic c.232+6422 e1+6422 0 - - - no_errors tier2 1383 7 0.5 626 515 45.1 0 0 NA 869586 TCGA-AB-3009 AML43 4 183981898 183981899 - T INS ENSG00000221186 ENST00000408259 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2477 NULL 0.002:0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 186118876 186118876 C T SNP LOC728203 XM_001128664.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-28324 NULL 0.006 - - - no_errors tier3 380 4 1.04 169 41 19.52 0 0 NA 869586 TCGA-AB-3009 AML43 4 186649789 186649789 C T SNP CCDC110 NM_152775.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19958 NULL 0.406 - - - no_errors tier3 573 8 1.37 157 131 45.49 0 0 NA 869586 TCGA-AB-3009 AML43 4 187679838 187679838 T C SNP MTNR1A NM_005958.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*11999 NULL 0.01 - - - no_errors tier3 781 13 1.64 218 190 46.57 0 0 NA 869586 TCGA-AB-3009 AML43 4 187885961 187885961 G A SNP FAT1 NM_005245.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-17986 NULL 0 - - - no_errors tier3 536 12 2.19 190 130 40.5 0 0 NA 869586 TCGA-AB-3009 AML43 4 187925810 187925810 C T SNP FAT1 NM_005245.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-57835 NULL 0 - - - no_errors tier3 837 7 0.83 327 268 45.04 0 0 NA 869586 TCGA-AB-3009 AML43 4 188198245 188198245 T C SNP - - - - - - - - - - - - - - - tier3 1334 29 2.12 386 278 41.87 0 0 NA 869586 TCGA-AB-3009 AML43 4 188687167 188687168 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 4 189159937 189159937 G A SNP ZFP42 NM_174900.3 human genbank 54_36p 1 validated intronic c.1-924 e1-924 0.001 - - - no_errors tier3 667 9 1.33 254 222 46.64 0 0 NA 869586 TCGA-AB-3009 AML43 4 189400871 189400871 G A SNP - - - - - - - - - - - - - - - tier3 1140 10 0.87 209 247 54.05 0 0 NA 869586 TCGA-AB-3009 AML43 4 189441137 189441137 C T SNP - - - - - - - - - - - - - - - tier2 358 8 2.19 199 156 43.94 0 0 NA 869586 TCGA-AB-3009 AML43 5 1283613 1283613 C T SNP SLC6A18 NM_182632.2 human genbank 54_36p 1 validated intronic c.161-1721 e2-1721 0.004 - - - no_errors tier3 325 2 0.61 97 84 46.41 0 0 NA 869586 TCGA-AB-3009 AML43 5 1410892 1410892 G A SNP CLPTM1L NM_030782.3 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-12936 NULL 0.041 - - - no_errors tier3 373 6 1.58 158 125 44.17 0 0 NA 869586 TCGA-AB-3009 AML43 5 1482894 1482894 C A SNP SLC6A3 NM_001044.3 human genbank 54_36p -1 validated intronic c.653+2685 e3+2685 0.004 - - - no_errors tier3 599 9 1.48 87 114 56.72 0 0 NA 869586 TCGA-AB-3009 AML43 5 4347954 4347954 T - DEL ENSG00000221195 ENST00000408268 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*7935 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 5 5195032 5195032 A C SNP ADAMTS16 NM_139056.2 human genbank 54_36p 1 reviewed intronic c.175+1153 e2+1153 0.001 - - - no_errors tier3 145 0 0 53 39 42.39 0 0 NA 869586 TCGA-AB-3009 AML43 5 6011937 6011937 C T SNP LOC100133551 XM_001721670.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*25260 NULL 0.001 - - - no_start_codon:pseudogene tier3 875 6 0.68 176 74 29.6 0 0 NA 869586 TCGA-AB-3009 AML43 5 8136010 8136010 A G SNP - - - - - - - - - - - - - - - tier3 569 2 0.35 127 144 52.94 0 0 NA 869586 TCGA-AB-3009 AML43 5 8688495 8688495 C T SNP ENSG00000209923 ENST00000387188 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-16210 NULL 0 - - - pseudogene tier3 388 8 2.02 118 54 31.4 0 0 NA 869586 TCGA-AB-3009 AML43 5 9560797 9560797 G A SNP SEMA5A NM_003966.2 human genbank 54_36p -1 validated intronic c.1+37899 e0+37899 0 - - - no_errors tier3 790 6 0.75 400 347 46.45 0 0 NA 869586 TCGA-AB-3009 AML43 5 11221977 11221977 C T SNP CTNND2 NM_001332.2 human genbank 54_36p -1 validated intronic c.1976-9106 e12-9106 0 - - - no_errors tier3 1012 6 0.59 160 149 48.22 0 0 NA 869586 TCGA-AB-3009 AML43 5 15521544 15521544 T - DEL FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-32242 NULL 0.757 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 5 16072497 16072497 C A SNP MARCH11 NM_001102562.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*48083 NULL 0 - - - no_errors tier3 793 5 0.63 210 161 43.4 0 0 NA 869586 TCGA-AB-3009 AML43 5 19662222 19662222 C T SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed intronic c.644-13755 e4-13755 0 - - - no_errors tier3 503 7 1.37 252 180 41.57 0 0 NA 869586 TCGA-AB-3009 AML43 5 20266446 20266446 G A SNP - - - - - - - - - - - - - - - tier3 374 0 0 129 97 42.73 0 0 NA 869586 TCGA-AB-3009 AML43 5 20612321 20612321 T A SNP - - - - - - - - - - - - - - - tier3 275 0 0 38 35 47.95 0 0 NA 869586 TCGA-AB-3009 AML43 5 23016236 23016236 T G SNP - - - - - - - - - - - - - - - tier3 1186 21 1.74 287 251 46.65 0 0 NA 869586 TCGA-AB-3009 AML43 5 24634237 24634237 G C SNP CDH10 NM_006727.2 human genbank 54_36p -1 reviewed intronic c.1-4758 e1-4758 0 - - - no_errors tier3 471 1 0.21 91 73 44.51 0 0 NA 869586 TCGA-AB-3009 AML43 5 26191116 26191116 T C SNP - - - - - - - - - - - - - - - tier3 182 0 0 47 43 47.78 0 0 NA 869586 TCGA-AB-3009 AML43 5 27519527 27519527 C T SNP - - - - - - - - - - - - - - - tier3 470 7 1.47 247 198 44.49 31 0 0 869586 TCGA-AB-3009 AML43 5 28213116 28213116 G A SNP - - - - - - - - - - - - - - - tier3 627 8 1.25 117 71 37.77 0 0 NA 869586 TCGA-AB-3009 AML43 5 40075061 40075061 C T SNP - - - - - - - - - - - - - - - tier2 554 8 1.42 181 90 33.21 0 0 NA 869586 TCGA-AB-3009 AML43 5 41026023 41026023 C A SNP C7 NM_000587.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*8591 NULL 0 - - - no_errors tier3 1223 13 1.05 288 215 42.66 0 0 NA 869586 TCGA-AB-3009 AML43 5 41340785 41340785 C T SNP C6 ENST00000263413 human ensembl 54_36p -1 known 5_prime_flanking_region c.-101696 NULL 0 - - - no_errors tier3 1020 17 1.64 342 267 43.7 0 0 NA 869586 TCGA-AB-3009 AML43 5 45050802 45050803 - A INS ENSG00000222945 ENST00000411013 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*13553 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 5 50287607 50287607 G A SNP - - - - - - - - - - - - - - - tier3 789 7 0.88 206 204 49.76 0 0 NA 869586 TCGA-AB-3009 AML43 5 50319955 50319955 A T SNP - - - - - - - - - - - - - - - tier3 547 5 0.91 136 116 46.03 0 0 NA 869586 TCGA-AB-3009 AML43 5 52674933 52674933 G A SNP - - - - - - - - - - - - - - - tier3 1369 37 2.63 352 248 41.33 0 0 NA 869586 TCGA-AB-3009 AML43 5 58047178 58047178 A C SNP RAB3C NM_138453.2 human genbank 54_36p 1 provisional intronic c.253-10408 e3-10408 0.019 - - - no_errors tier3 659 4 0.6 143 132 48 0 0 NA 869586 TCGA-AB-3009 AML43 5 61925228 61925228 A T SNP IPO11 ENST00000409296 human ensembl 54_36p 1 known intronic c.2798+1973 e28+1973 0 - - - no_errors tier3 517 14 2.64 209 185 46.95 0 0 0 869586 TCGA-AB-3009 AML43 5 62828121 62828122 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 5 66228134 66228134 T A SNP MAST4 NM_015183.1 human genbank 54_36p 1 validated intronic c.40-3401 e2-3401 0.001 - - - no_errors tier3 427 3 0.7 121 83 40.69 0 0 NA 869586 TCGA-AB-3009 AML43 5 68754819 68754819 C T SNP MARVELD2 NM_001038603.1 human genbank 54_36p 1 provisional intronic c.1147-1365 e2-1365 0 - - - no_errors tier3 580 2 0.34 235 190 44.71 0 0 NA 869586 TCGA-AB-3009 AML43 5 73010150 73010150 G A SNP RGNEF NM_001080479.1 human genbank 54_36p 1 provisional intronic c.1-6272 e1-6272 0 - - - no_errors tier3 961 3 0.31 261 161 38.15 0 0 NA 869586 TCGA-AB-3009 AML43 5 81957081 81957081 T C SNP - - - - - - - - - - - - - - - tier3 761 6 0.78 426 375 46.7 0 0 NA 869586 TCGA-AB-3009 AML43 5 83095005 83095005 G A SNP HAPLN1 NM_001884.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-89907 NULL 0 - - - no_errors tier3 479 5 1.03 229 183 44.42 0 0 NA 869586 TCGA-AB-3009 AML43 5 83291845 83291845 C T SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.1293+2935 e10+2935 0 - - - no_errors tier3 261 4 1.51 47 15 24.19 1 0 0 869586 TCGA-AB-3009 AML43 5 84796281 84796281 C T SNP - - - - - - - - - - - - - - - tier2 750 1 0.13 279 256 47.85 0 0 NA 869586 TCGA-AB-3009 AML43 5 91259125 91259125 C T SNP - - - - - - - - - - - - - - - tier3 97 2 2.02 25 14 35.9 0 0 NA 869586 TCGA-AB-3009 AML43 5 99860373 99860373 G A SNP FAM174A NM_198507.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-38761 NULL 0.003 - - - no_errors tier3 379 4 1.04 180 168 48.28 0 0 NA 869586 TCGA-AB-3009 AML43 5 100265461 100265461 T A SNP ST8SIA4 NM_005668.4 human genbank 54_36p -1 reviewed intronic c.113+985 e1+985 0 - - - no_errors tier3 NA NA NA NA NA NA 1 0 0 869586 TCGA-AB-3009 AML43 5 104006486 104006486 G A SNP - - - - - - - - - - - - - - - tier3 202 3 1.46 52 46 46.94 0 0 NA 869586 TCGA-AB-3009 AML43 5 107201359 107201359 T C SNP FBXL17 NM_022824.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*23961 NULL 0.014 - - - no_errors tier3 1210 8 0.66 485 311 39.07 0 0 NA 869586 TCGA-AB-3009 AML43 5 116352856 116352856 C G SNP - - - - - - - - - - - - - - - tier3 1827 14 0.76 481 434 47.38 0 0 NA 869586 TCGA-AB-3009 AML43 5 117154709 117154709 T C SNP ENSG00000182152 ENST00000329863 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12095 NULL 0.016 - - - no_coding_region:pseudogene tier3 413 5 1.2 192 212 52.48 0 0 NA 869586 TCGA-AB-3009 AML43 5 117806828 117806828 C T SNP - - - - - - - - - - - - - - - tier3 676 2 0.29 127 120 48.58 0 0 NA 869586 TCGA-AB-3009 AML43 5 122462602 122462602 C T SNP PRDM6 ENST00000407847 human ensembl 54_36p 1 known intronic c.593-646 e2-646 0.001 - - - no_errors tier2 209 5 2.34 95 82 46.33 0 0 NA 869586 TCGA-AB-3009 AML43 5 123606437 123606437 T C SNP ENSG00000214750 ENST00000398908 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-21789 NULL 0.001 - - - no_coding_region:pseudogene tier3 1247 28 2.19 392 326 45.4 0 0 NA 869586 TCGA-AB-3009 AML43 5 124421179 124421179 C T SNP - - - - - - - - - - - - - - - tier3 265 2 0.74 68 45 39.82 0 0 NA 869586 TCGA-AB-3009 AML43 5 127001815 127001815 C T SNP CTXN3 NM_001048252.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-19298 NULL 0 - - - no_errors tier3 1851 26 1.39 642 498 43.68 0 0 NA 869586 TCGA-AB-3009 AML43 5 127934833 127934833 C T SNP FBN2 NM_001999.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33638 NULL 0 - - - no_errors tier2 688 7 1.01 269 205 43.25 0 0 NA 869586 TCGA-AB-3009 AML43 5 128331328 128331328 C A SNP SLC27A6 NM_001017372.1 human genbank 54_36p 1 reviewed intronic c.481+1118 e1+1118 0 - - - no_errors tier3 255 1 0.39 94 14 12.96 0 0 NA 869586 TCGA-AB-3009 AML43 5 129733200 129733201 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 5 133794553 133794553 A T SNP CDKN2AIPNL NM_080656.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-19109 NULL 0.061 - - - no_errors tier2 1432 12 0.83 187 91 32.73 0 0 NA 869586 TCGA-AB-3009 AML43 5 138778650 138778650 C G SNP DNAJC18 NM_152686.2 human genbank 54_36p -1 provisional intronic c.953-790 e8-790 0.002 - - - no_errors tier3 673 6 0.88 264 185 41.11 1 2 66.67 869586 TCGA-AB-3009 AML43 5 141578573 141578573 T A SNP - - - - - - - - - - - - - - - tier3 1200 1 0.08 377 117 23.68 0 0 NA 869586 TCGA-AB-3009 AML43 5 143554034 143554034 G T SNP KCTD16 NM_020768.3 human genbank 54_36p 1 validated intronic c.1-12111 e1-12111 0.002 - - - no_errors tier3 1335 5 0.37 473 162 25.43 0 0 NA 869586 TCGA-AB-3009 AML43 5 145689874 145689874 C T SNP POU4F3 NM_002700.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-8995 NULL 0.01 - - - no_errors tier3 2530 12 0.47 308 166 35.02 0 0 NA 869586 TCGA-AB-3009 AML43 5 149344538 149344539 - CCC INS SLC26A2 NM_000112.3 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*2969 NULL 0.004:0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 5 149761862 149761862 G A SNP CD74 NM_001025159.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*134 NULL 0.001 - - - no_errors tier3 978 6 0.61 275 201 42.23 1376 1065 43.63 869586 TCGA-AB-3009 AML43 5 151415323 151415323 G A SNP - - - - - - - - - - - - - - - tier3 1240 15 1.2 310 325 51.18 0 0 NA 869586 TCGA-AB-3009 AML43 5 156250002 156250002 G A SNP TIMD4 NM_138379.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*29044 NULL 0 - - - no_errors tier3 2204 32 1.43 451 429 48.75 0 0 NA 869586 TCGA-AB-3009 AML43 5 157119862 157119862 G A SNP ENSG00000206819 ENST00000384092 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-48822 NULL 0 - - - no_errors tier3 663 1 0.15 224 58 20.57 5 3 37.5 869586 TCGA-AB-3009 AML43 5 159213503 159213503 C T SNP - - - - - - - - - - - - - - - tier3 710 5 0.7 117 109 48.23 0 0 NA 869586 TCGA-AB-3009 AML43 5 163315359 163315359 C T SNP - - - - - - - - - - - - - - - tier2 638 0 0 246 167 40.44 0 0 NA 869586 TCGA-AB-3009 AML43 5 165252124 165252124 A G SNP - - - - - - - - - - - - - - - tier3 1376 18 1.29 584 562 49.04 0 0 NA 869586 TCGA-AB-3009 AML43 5 166441782 166441782 C T SNP - - - - - - - - - - - - - - - tier3 801 4 0.5 200 181 47.38 0 0 NA 869586 TCGA-AB-3009 AML43 5 166898714 166898714 A T SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.502+163658 e2+163658 0.639 - - - no_errors tier2 568 6 1.05 130 155 54.39 0 0 NA 869586 TCGA-AB-3009 AML43 5 167178479 167178479 C T SNP ODZ2 ENST00000388903 human ensembl 54_36p 1 known intronic c.503-57090 e3-57090 0.003 - - - no_errors tier3 1252 36 2.79 392 352 47.31 0 0 NA 869586 TCGA-AB-3009 AML43 5 171987112 171987112 G A SNP LOC100128482 XM_001715108.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37647 NULL 0.034 - - - no_errors tier3 1343 13 0.96 432 295 40.58 0 0 NA 869586 TCGA-AB-3009 AML43 5 172597106 172597106 C T SNP NKX2-5 NM_004387.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2414 NULL 0.078 - - - no_errors tier2 1354 16 1.17 217 239 52.41 0 0 NA 869586 TCGA-AB-3009 AML43 5 176460736 176460736 G A SNP NSD1 NM_022455.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33975 NULL 0 - - - no_errors tier3 326 2 0.61 100 82 44.81 0 0 NA 869586 TCGA-AB-3009 AML43 6 3979247 3979247 G A SNP PRPF4B NM_003913.4 human genbank 54_36p 1 reviewed intronic c.1238+1259 e2+1259 0.023 - - - no_errors tier3 293 6 2.01 47 22 31.88 0 0 0 869586 TCGA-AB-3009 AML43 6 4318625 4318625 A T SNP - - - - - - - - - - - - - - - tier3 2098 12 0.57 353 322 47.63 0 0 NA 869586 TCGA-AB-3009 AML43 6 15481562 15481562 C T SNP JARID2 NM_004973.2 human genbank 54_36p 1 reviewed intronic c.46-765 e2-765 0 - - - no_errors tier3 578 6 1.02 136 83 37.9 6 2 25 869586 TCGA-AB-3009 AML43 6 18123087 18123087 T C SNP KIF13A NM_022113.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-27414 NULL 0.006 - - - no_errors tier3 338 1 0.29 27 28 50.91 0 0 NA 869586 TCGA-AB-3009 AML43 6 19868483 19868483 C T SNP - - - - - - - - - - - - - - - tier3 841 9 1.05 201 191 48.72 0 0 NA 869586 TCGA-AB-3009 AML43 6 20536224 20536225 - CTCC INS E2F3 NM_001949.3 human genbank 54_36p 1 reviewed intronic c.393+25389_393+25388 e1+25389 0.005:0.004 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 24626589 24626589 A G SNP ALDH5A1 NM_170740.3 human genbank 54_36p 1 reviewed intronic c.910-2019 e7-2019 0.001 - - - no_errors tier2 829 14 1.66 182 179 49.58 0 0 0 869586 TCGA-AB-3009 AML43 6 30800185 30800185 T C SNP TUBB NM_178014.2 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*32 NULL 0.002 - - - no_errors tier3 1 0 0 1 0 0 482 192 28.4 869586 TCGA-AB-3009 AML43 6 33396275 33396275 G A SNP DAXX NM_001350.1 human genbank 54_36p -1 reviewed missense c.1111 p.R371W 1 HMMPfam_Daxx HMMPfam_Daxx - no_errors tier1 1578 27 1.68 303 199 39.64 19 24 55.81 869586 TCGA-AB-3009 AML43 6 33906603 33906603 C T SNP MLN NM_002418.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29685 NULL 0.006 - - - no_errors tier3 898 10 1.1 178 208 53.89 0 0 NA 869586 TCGA-AB-3009 AML43 6 39977212 39977212 C T SNP DAAM2 NM_015345.2 human genbank 54_36p 1 validated missense c.2965 p.R989C 1 HMMSmart_SM00498 "HMMSmart_SM00498,HMMPfam_Drf_FH3,HMMPfam_Drf_GBD,HMMPfam_FH2,superfamily_Formin homology 2 domain (FH2 domain)" - no_errors tier1 709 11 1.51 235 214 47.03 NA 869586 TCGA-AB-3009 AML43 6 40675531 40675531 C T SNP LRFN2 NM_020737.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-166701 NULL 0.001 - - - no_errors tier2 2491 24 0.95 576 569 49.69 0 0 NA 869586 TCGA-AB-3009 AML43 6 40865465 40865465 A C SNP - - - - - - - - - - - - - - - tier2 1576 11 0.69 430 392 47.69 0 0 NA 869586 TCGA-AB-3009 AML43 6 44351654 44351654 G A SNP TMEM151B ENST00000388811 human ensembl 54_36p 1 known silent c.1113 p.T371 0.977 NULL NULL - no_errors tier1 292 1 0.34 116 103 47.03 NA 869586 TCGA-AB-3009 AML43 6 45028492 45028492 C T SNP SUPT3H NM_181356.2 human genbank 54_36p -1 provisional intronic c.834+533 e9+533 0 - - - no_errors tier3 533 4 0.74 137 109 44.31 0 1 100 869586 TCGA-AB-3009 AML43 6 46963602 46963602 C T SNP GPR116 NM_001098518.1 human genbank 54_36p -1 validated intronic c.328+429 e3+429 0.001 - - - no_errors tier3 961 9 0.93 327 308 48.5 0 0 NA 869586 TCGA-AB-3009 AML43 6 51685200 51685200 T A SNP PKHD1 NM_138694.3 human genbank 54_36p -1 reviewed intronic c.10156+31942 e59+31942 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 53286741 53286742 - CCTGGTAGGCAA INS ELOVL5 NM_021814.3 human genbank 54_36p -1 provisional intronic c.1-18278_18279 e1-18277 0.002:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 62689159 62689159 T G SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.484-19924 e5-19924 0 - - - no_errors tier3 787 4 0.51 217 168 43.64 0 0 NA 869586 TCGA-AB-3009 AML43 6 65410114 65410114 G T SNP ENSG00000184936 ENST00000330816 human ensembl 54_36p -1 known 5_prime_flanking_region c.-26035 NULL 0 - - - no_stop_codon tier2 618 6 0.96 250 264 51.36 0 0 NA 869586 TCGA-AB-3009 AML43 6 65976834 65976834 C T SNP LOC727977 XM_001126270.2 human genbank 54_36p 1 model intronic c.33+82178 e1+82178 0.003 - - - no_errors tier3 787 3 0.38 266 265 49.91 0 0 NA 869586 TCGA-AB-3009 AML43 6 67396065 67396065 G A SNP - - - - - - - - - - - - - - - tier3 388 2 0.51 157 176 52.85 0 0 NA 869586 TCGA-AB-3009 AML43 6 68084645 68084645 G A SNP - - - - - - - - - - - - - - - tier3 205 0 0 58 35 37.63 0 0 NA 869586 TCGA-AB-3009 AML43 6 69877328 69877328 G A SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.2480+34677 e15+34677 0.002 - - - no_errors tier3 541 11 1.99 105 84 44.44 0 0 NA 869586 TCGA-AB-3009 AML43 6 72910224 72910224 C T SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated intronic c.472-35775 e5-35775 0.001 - - - no_errors tier3 750 2 0.27 408 68 14.26 0 0 NA 869586 TCGA-AB-3009 AML43 6 75454007 75454007 G A SNP - - - - - - - - - - - - - - - tier3 535 3 0.56 209 125 37.43 0 0 NA 869586 TCGA-AB-3009 AML43 6 75872009 75872009 T A SNP COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed intronic c.8179-281 e53-281 0 - - - no_errors tier3 418 5 1.18 196 131 40.06 0 0 NA 869586 TCGA-AB-3009 AML43 6 75917701 75917701 G A SNP COL12A1 NM_004370.5 human genbank 54_36p -1 reviewed silent c.4023 p.V1341 0.459 "HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like" "HMMPfam_VWA,HMMSmart_SM00327,HMMSmart_SM00210,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Collagen,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_vWA-like" - no_errors tier1 505 8 1.56 156 124 44.29 1 0 869586 TCGA-AB-3009 AML43 6 76192831 76192831 C T SNP FILIP1 NM_015687.2 human genbank 54_36p -1 validated intronic c.1-11417 e1-11417 0.005 - - - no_errors tier3 991 9 0.9 231 237 50.64 0 0 NA 869586 TCGA-AB-3009 AML43 6 76716833 76716833 A T SNP IMPG1 NM_001563.2 human genbank 54_36p -1 provisional intronic c.1824+166 e13+166 0.066 - - - no_errors tier3 428 6 1.38 153 105 40.7 0 0 NA 869586 TCGA-AB-3009 AML43 6 77534162 77534162 G T SNP - - - - - - - - - - - - - - - tier3 170 1 0.58 29 8 21.62 0 0 NA 869586 TCGA-AB-3009 AML43 6 78132876 78132876 C T SNP - - - - - - - - - - - - - - - tier3 368 3 0.81 90 60 40 0 0 NA 869586 TCGA-AB-3009 AML43 6 78733352 78733352 T A SNP ENSG00000214481 ENST00000398401 human ensembl 54_36p 1 known 3_prime_flanking_region c.*43576 NULL 0 - - - no_stop_codon tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 80356095 80356095 G A SNP C6orf152 ENST00000392961 human ensembl 54_36p -1 known intronic c.1-70574 e1-70574 0 - - - no_errors tier3 474 0 0 137 21 13.29 0 0 NA 869586 TCGA-AB-3009 AML43 6 80528802 80528802 A G SNP C6orf152 ENST00000392961 human ensembl 54_36p -1 known intronic c.1+36599 e0+36599 0.004 - - - no_errors tier3 816 7 0.85 174 171 49.57 0 0 NA 869586 TCGA-AB-3009 AML43 6 82333029 82333030 - T INS LOC100131508 XM_001720073.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-13773 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 82854081 82854081 G T SNP - - - - - - - - - - - - - - - tier2 1204 34 2.74 416 357 46.12 0 0 NA 869586 TCGA-AB-3009 AML43 6 84357966 84357967 - T INS SNAP91 NM_014841.2 human genbank 54_36p -1 validated intronic c.1931-235_1931-234 e21-234 0.002:0.051 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 87597030 87597030 G A SNP LOC643962 XR_041993.1 human genbank 54_36p -1 model rna NULL NULL 0.002 - - - no_errors tier1 153 2 1.29 11 12 52.17 NA 869586 TCGA-AB-3009 AML43 6 89948418 89948418 C T SNP GABRR1 NM_002042.3 human genbank 54_36p -1 reviewed missense c.856 p.A286T 1 "HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore" "HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore,HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like,PatternScan_NEUROTR_ION_CHANNEL" - no_errors tier1 919 14 1.5 370 316 46.06 1 100 869586 TCGA-AB-3009 AML43 6 91450832 91450832 C T SNP - - - - - - - - - - - - - - - tier3 1347 11 0.81 475 380 44.39 0 0 NA 869586 TCGA-AB-3009 AML43 6 92034634 92034634 T A SNP - - - - - - - - - - - - - - - tier3 92 0 0 11 7 38.89 0 0 NA 869586 TCGA-AB-3009 AML43 6 92083597 92083597 T C SNP - - - - - - - - - - - - - - - tier3 379 5 1.3 108 109 50 0 0 NA 869586 TCGA-AB-3009 AML43 6 94849356 94849356 C G SNP - - - - - - - - - - - - - - - tier3 212 1 0.47 44 31 41.33 0 0 NA 869586 TCGA-AB-3009 AML43 6 96935294 96935294 G A SNP - - - - - - - - - - - - - - - tier2 515 4 0.77 144 115 44.23 0 0 NA 869586 TCGA-AB-3009 AML43 6 97344287 97344287 C T SNP GPR63 NM_030784.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*8782 NULL 0 - - - no_errors tier3 801 15 1.84 563 505 47.24 2 0 0 869586 TCGA-AB-3009 AML43 6 98868269 98868269 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 103552654 103552655 - T INS ENSG00000217120 ENST00000407015 human ensembl 54_36p 1 known 5_prime_flanking_region c.-4428 NULL 0.000:0.001 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 104194545 104194545 C T SNP - - - - - - - - - - - - - - - tier3 394 6 1.5 140 101 41.91 0 0 NA 869586 TCGA-AB-3009 AML43 6 107361572 107361572 C T SNP MIRN587 ENST00000384845 human ensembl 54_36p 1 known 3_prime_flanking_region c.*22784 NULL 0.005 - - - no_errors tier3 1372 2 0.15 398 282 41.47 0 0 NA 869586 TCGA-AB-3009 AML43 6 107911572 107911572 A G SNP SOBP NM_018013.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-6942 NULL 0.001 - - - no_errors tier3 437 8 1.8 61 69 53.08 0 0 NA 869586 TCGA-AB-3009 AML43 6 108973472 108973472 C T SNP FOXO3 NM_001455.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15633 NULL 0.001 - - - no_errors tier2 425 2 0.47 175 90 33.83 0 0 NA 869586 TCGA-AB-3009 AML43 6 109236604 109236604 G A SNP ARMC2 NM_032131.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-45560 NULL 0 - - - no_errors tier3 1018 8 0.78 678 618 47.58 0 0 NA 869586 TCGA-AB-3009 AML43 6 114486344 114486344 C T SNP HS3ST5 NM_153612.3 human genbank 54_36p -1 validated intronic c.108-297 e2-297 0.985 - - - no_errors tier3 484 10 2.02 130 132 50.38 0 0 NA 869586 TCGA-AB-3009 AML43 6 116543169 116543169 G A SNP NT5DC1 NM_152729.2 human genbank 54_36p 1 validated intronic c.365-378 e5-378 0 - - - no_errors tier3 424 5 1.17 102 82 44.57 0 0 0 869586 TCGA-AB-3009 AML43 6 116546904 116546904 G A SNP COL10A1 NM_000493.3 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*1025 NULL 0.005 - - - no_errors tier2 333 5 1.47 69 50 42.02 0 0 NA 869586 TCGA-AB-3009 AML43 6 117234348 117234348 C A SNP GPRC6A NM_148963.2 human genbank 54_36p -1 validated missense c.1213 p.D405Y 0.004 "HMMPfam_ANF_receptor,superfamily_Periplasmic binding protein-like I" "HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_2,superfamily_Periplasmic binding protein-like I" - no_errors tier1 999 12 1.19 493 434 46.82 NA 869586 TCGA-AB-3009 AML43 6 119393476 119393476 T A SNP FAM184A NM_024581.1 human genbank 54_36p -1 validated intronic c.160-5799 e2-5799 0.526 - - - no_errors tier3 267 1 0.37 37 29 43.94 1 0 0 869586 TCGA-AB-3009 AML43 6 121696163 121696163 A T SNP C6orf170 NM_152730.4 human genbank 54_36p -1 validated intronic c.155+958 e1+958 0.001 - - - no_errors tier3 592 4 0.67 77 54 41.22 0 0 0 869586 TCGA-AB-3009 AML43 6 122089204 122089204 G T SNP ENSG00000219135 ENST00000406913 human ensembl 54_36p -1 known 5_prime_flanking_region c.-45900 NULL 0 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 124876095 124876095 C A SNP NKAIN2 NM_001040214.1 human genbank 54_36p 1 validated intronic c.274-144936 e4-144936 0.001 - - - no_errors tier3 277 0 0 60 17 22.08 0 0 NA 869586 TCGA-AB-3009 AML43 6 126252643 126252643 A G SNP NCOA7 NM_181782.1 human genbank 54_36p 1 validated missense c.1750 p.K584E 0.014 NULL "HMMSmart_SM00257,HMMPfam_GRAM,HMMPfam_TLD,HMMSmart_SM00584,HMMPfam_LysM,superfamily_LysM domain" - no_errors tier1 443 1 0.23 150 115 43.4 11 7 38.89 869586 TCGA-AB-3009 AML43 6 132760245 132760245 C T SNP MOXD1 NM_015529.2 human genbank 54_36p -1 validated intronic c.264+3750 e1+3750 0 - - - no_errors tier2 993 12 1.19 246 184 42.69 0 0 NA 869586 TCGA-AB-3009 AML43 6 143970701 143970701 T C SNP PHACTR2 NM_014721.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-439 NULL 0 - - - no_errors tier3 417 1 0.24 152 159 50.96 1 1 50 869586 TCGA-AB-3009 AML43 6 144327153 144327153 G T SNP PLAGL1 NM_001080951.1 human genbank 54_36p -1 reviewed intronic c.1+464 e0+464 0.004 - - - no_errors tier3 702 7 0.99 275 258 48.41 12 10 45.45 869586 TCGA-AB-3009 AML43 6 148349163 148349163 C A SNP - - - - - - - - - - - - - - - tier2 1287 22 1.68 384 312 44.83 0 0 NA 869586 TCGA-AB-3009 AML43 6 148695029 148695029 A - DEL SASH1 ENST00000367469 human ensembl 54_36p 1 known intronic c.22-57934 e2-57934 0.013 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 149503164 149503165 - GGTTCGCTTCTTTAAGGG INS LOC729200 XR_015835.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-27647 NULL 0.001:0.000 - - - pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 6 150400423 150400423 C T SNP RAET1L NM_130900.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-12123 NULL 0 - - - no_errors tier2 923 11 1.17 227 158 40.83 0 0 NA 869586 TCGA-AB-3009 AML43 6 153178125 153178125 C T SNP - - - - - - - - - - - - - - - tier3 532 4 0.74 287 193 40.21 0 0 NA 869586 TCGA-AB-3009 AML43 6 159876141 159876141 G T SNP LOC642738 XR_017625.2 human genbank 54_36p -1 model 5_prime_flanking_region c.-8546 NULL 0.001 - - - pseudogene tier3 1379 22 1.57 513 371 41.97 0 0 NA 869586 TCGA-AB-3009 AML43 6 160718533 160718533 C T SNP SLC22A3 NM_021977.2 human genbank 54_36p 1 reviewed intronic c.430-20468 e2-20468 0 - - - no_errors tier3 524 1 0.19 149 101 40.24 0 0 NA 869586 TCGA-AB-3009 AML43 6 161879231 161879231 G T SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.1083+10645 e9+10645 0 - - - no_errors tier3 944 11 1.15 477 422 46.89 0 0 NA 869586 TCGA-AB-3009 AML43 6 162006577 162006577 G A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.872-96139 e8-96139 0.006 - - - no_errors tier3 1289 10 0.77 352 301 46.02 0 0 NA 869586 TCGA-AB-3009 AML43 6 163316275 163316275 G T SNP PACRG NM_152410.1 human genbank 54_36p 1 reviewed intronic c.292-86897 e3-86897 0.106 - - - no_errors tier3 1205 1 0.08 498 303 37.78 0 0 NA 869586 TCGA-AB-3009 AML43 6 168215885 168215885 G A SNP FRMD1 NM_024919.1 human genbank 54_36p -1 validated intronic c.304+2889 e2+2889 0 - - - no_errors tier3 526 10 1.86 104 71 40.34 0 0 NA 869586 TCGA-AB-3009 AML43 6 168920610 168920610 G A SNP - - - - - - - - - - - - - - - tier3 792 20 2.45 180 179 49.86 0 0 NA 869586 TCGA-AB-3009 AML43 7 3872973 3872973 G A SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated intronic c.847+45232 e5+45232 0 - - - no_errors tier3 877 5 0.57 620 551 47.05 0 0 NA 869586 TCGA-AB-3009 AML43 7 5607312 5607312 T C SNP FSCN1 NM_003088.2 human genbank 54_36p 1 validated intronic c.833-2102 e2-2102 0.275 - - - no_errors tier3 962 2 0.21 163 167 50.61 2 2 50 869586 TCGA-AB-3009 AML43 7 9128829 9128829 T C SNP - - - - - - - - - - - - - - - tier2 428 8 1.83 127 93 42.27 0 0 NA 869586 TCGA-AB-3009 AML43 7 11758269 11758269 G A SNP THSD7A NM_015204.1 human genbank 54_36p -1 validated intronic c.190+79639 e1+79639 0 - - - no_errors tier3 981 6 0.61 306 237 43.65 0 0 NA 869586 TCGA-AB-3009 AML43 7 12126741 12126741 C T SNP - - - - - - - - - - - - - - - tier3 680 14 2.02 298 182 37.92 0 0 NA 869586 TCGA-AB-3009 AML43 7 12343039 12343039 G T SNP VWDE ENST00000275358 human ensembl 54_36p -1 known intronic c.2335+100 e15+100 0.483 - - - no_errors tier3 170 1 0.58 63 49 43.36 0 0 NA 869586 TCGA-AB-3009 AML43 7 12893363 12893363 G C SNP ENSG00000222974 ENST00000411042 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*10267 NULL 0 - - - no_errors tier3 168 0 0 15 23 60.53 0 0 NA 869586 TCGA-AB-3009 AML43 7 13310673 13310673 C A SNP - - - - - - - - - - - - - - - tier2 1006 6 0.59 248 200 44.64 0 0 NA 869586 TCGA-AB-3009 AML43 7 13982316 13982316 G A SNP ETV1 ENST00000405358 human ensembl 54_36p -1 known intronic c.277+1261 e4+1261 0 - - - no_errors tier3 975 12 1.21 287 255 47.05 0 0 NA 869586 TCGA-AB-3009 AML43 7 14027804 14027804 G T SNP ETV1 ENST00000405358 human ensembl 54_36p -1 known 5_prime_flanking_region c.-32888 NULL 0.143 - - - no_errors tier3 624 3 0.48 173 127 42.33 0 0 NA 869586 TCGA-AB-3009 AML43 7 16471580 16471580 A - DEL SOSTDC1 NM_015464.2 human genbank 54_36p -1 reviewed intronic c.205+34 e1+34 0.183 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 16612624 16612624 G A SNP ANKMY2 NM_020319.1 human genbank 54_36p -1 provisional intronic c.883-1625 e8-1625 0.008 - - - no_errors tier3 186 0 0 28 20 41.67 0 1 100 869586 TCGA-AB-3009 AML43 7 18985171 18985171 C A SNP HDAC9 NM_178425.1 human genbank 54_36p 1 reviewed intronic c.3170+3070 e24+3070 0.001 - - - no_errors tier3 1320 9 0.68 271 170 38.46 0 0 0 869586 TCGA-AB-3009 AML43 7 19896920 19896920 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 20705083 20705083 C T SNP ABCB5 NM_178559.4 human genbank 54_36p 1 validated intronic c.819+385 e5+385 0.286 - - - no_errors tier3 279 3 1.06 200 160 44.44 0 0 NA 869586 TCGA-AB-3009 AML43 7 21231709 21231709 A - DEL ENSG00000222573 ENST00000410641 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-9735 NULL 0.013 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 21530093 21530093 G T SNP DNAH11 ENST00000328843 human ensembl 54_36p 1 known 5_prime_flanking_region c.-19296 NULL 0.006 - - - no_errors tier3 624 22 3.4 111 45 28.66 0 0 NA 869586 TCGA-AB-3009 AML43 7 22567575 22567575 C T SNP ENSG00000179460 ENST00000325349 human ensembl 54_36p -1 novel intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier2 1101 6 0.54 453 340 42.88 0 0 NA 869586 TCGA-AB-3009 AML43 7 27582747 27582748 - A INS HIBADH NM_152740.2 human genbank 54_36p -1 validated intronic c.485-33504_485-33503 e5-33503 0.103:0.090 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 28538689 28538689 G A SNP CREB5 NM_182898.1 human genbank 54_36p 1 reviewed intronic c.291+24809 e4+24809 0.005 - - - no_errors tier2 691 7 1 251 216 46.15 0 0 NA 869586 TCGA-AB-3009 AML43 7 34480256 34480256 G A SNP ENSG00000197085 ENST00000357959 human ensembl 54_36p -1 known intronic c.189-56447 e4-56447 0 - - - no_errors tier3 512 6 1.16 99 121 55 0 0 NA 869586 TCGA-AB-3009 AML43 7 36496966 36496969 AATC - DEL LOC100134511 XM_001726584.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-44897 NULL 0.179:0.267:0.288:0.307 - - - no_start_codon:pseudogene:no_stop_codon tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 41365685 41365685 T A SNP - - - - - - - - - - - - - - - tier2 483 1 0.21 184 160 46.51 0 0 NA 869586 TCGA-AB-3009 AML43 7 45917575 45917575 G A SNP LOC100129619 XM_001718075.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-9442 NULL 0 - - - no_errors tier3 949 7 0.73 378 267 41.33 0 0 NA 869586 TCGA-AB-3009 AML43 7 46613062 46613062 T A SNP - - - - - - - - - - - - - - - tier2 605 2 0.33 476 378 44.26 0 0 NA 869586 TCGA-AB-3009 AML43 7 46999091 46999091 G A SNP LOC100132447 XM_001725581.1 human genbank 54_36p 1 model intronic c.120+20583 e2+20583 0.002 - - - no_errors tier3 1560 34 2.13 786 584 42.6 0 0 NA 869586 TCGA-AB-3009 AML43 7 48243583 48243583 C T SNP ABCA13 NM_152701.2 human genbank 54_36p 1 reviewed intronic c.601-578 e6-578 0 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 378 2 0.53 80 72 47.37 0 0 NA 869586 TCGA-AB-3009 AML43 7 48517246 48517246 G A SNP ABCA13 NM_152701.2 human genbank 54_36p 1 reviewed intronic c.13183+714 e47+714 0 - - - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1456 15 1.02 354 319 47.19 0 0 0 869586 TCGA-AB-3009 AML43 7 53945984 53945984 A T SNP LOC100134708 XM_001726848.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-37965 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 142 0 0 12 9 42.86 0 0 NA 869586 TCGA-AB-3009 AML43 7 62139096 62139096 G A SNP ENSG00000207443 ENST00000384712 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-29714 NULL 0 - - - no_errors tier3 1 0 0 NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 63209688 63209689 AG - DEL ENSG00000209045 ENST00000386310 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1330 NULL 1.000:0.999 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 64554301 64554301 G A SNP - - - - - - - - - - - - - - - tier2 809 17 2.06 200 129 39.09 0 0 0 869586 TCGA-AB-3009 AML43 7 67727257 67727257 T C SNP - - - - - - - - - - - - - - - tier2 1066 13 1.2 156 149 48.69 0 0 NA 869586 TCGA-AB-3009 AML43 7 69598443 69598444 - T INS AUTS2 NM_015570.1 human genbank 54_36p 1 validated intronic c.690+59740_690+59739 e5+59740 0.003:0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 70083513 70083513 G A SNP - - - - - - - - - - - - - - - tier2 1687 30 1.75 734 630 46.15 0 0 NA 869586 TCGA-AB-3009 AML43 7 75641728 75641728 G A SNP uc003uer.2 ENST00000388802 human ensembl 54_36p 1 known 5_prime_flanking_region c.-60593 NULL 0.033 - - - no_stop_codon tier3 494 6 1.2 107 70 39.55 0 0 NA 869586 TCGA-AB-3009 AML43 7 77964306 77964306 C T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.965+4524 e5+4524 0.004 - - - no_errors tier3 627 3 0.47 212 191 47.16 0 0 NA 869586 TCGA-AB-3009 AML43 7 79553451 79553451 C A SNP GNAI1 NM_002069.5 human genbank 54_36p 1 validated 5_prime_flanking_region c.-48962 NULL 0 - - - no_errors tier3 646 9 1.37 186 117 38.61 0 0 NA 869586 TCGA-AB-3009 AML43 7 79811760 79811760 C A SNP ENSG00000209130 ENST00000386395 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*26012 NULL 0 - - - pseudogene tier3 565 10 1.74 141 101 41.74 0 0 NA 869586 TCGA-AB-3009 AML43 7 82688262 82688262 C T SNP - - - - - - - - - - - - - - - tier3 797 12 1.48 240 145 37.66 0 0 NA 869586 TCGA-AB-3009 AML43 7 82707778 82707778 C T SNP - - - - - - - - - - - - - - - tier2 344 6 1.71 57 41 41.84 0 0 NA 869586 TCGA-AB-3009 AML43 7 83500850 83500850 C A SNP SEMA3A NM_006080.2 human genbank 54_36p -1 reviewed intronic c.667+12726 e6+12726 0 - - - no_errors tier3 537 6 1.1 168 121 41.87 0 0 NA 869586 TCGA-AB-3009 AML43 7 85736915 85736915 T C SNP - - - - - - - - - - - - - - - tier3 492 4 0.81 91 80 46.78 0 0 NA 869586 TCGA-AB-3009 AML43 7 85740139 85740139 T A SNP - - - - - - - - - - - - - - - tier3 814 2 0.25 187 140 42.81 0 0 NA 869586 TCGA-AB-3009 AML43 7 89409537 89409537 C A SNP - - - - - - - - - - - - - - - tier3 523 4 0.76 120 71 36.79 0 0 NA 869586 TCGA-AB-3009 AML43 7 90733681 90733681 G A SNP FZD1 NM_003505.1 human genbank 54_36p 1 reviewed missense c.1550 p.R517H 1 HMMPfam_Frizzled "superfamily_Frizzled cysteine-rich domain,HMMPfam_Frizzled,HMMPfam_Fz,HMMSmart_SM00063" - no_errors tier1 323 5 1.52 302 242 44.49 7 6 46.15 869586 TCGA-AB-3009 AML43 7 91075171 91075171 G A SNP - - - - - - - - - - - - - - - tier3 640 7 1.08 232 239 50.74 1 0 0 869586 TCGA-AB-3009 AML43 7 94408472 94408472 G A SNP PPP1R9A NM_017650.2 human genbank 54_36p 1 validated intronic c.1395+29716 e1+29716 0 - - - no_errors tier3 687 12 1.72 395 283 41.74 0 0 NA 869586 TCGA-AB-3009 AML43 7 95994573 95994573 G A SNP FLJ42280 XR_040255.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23802 NULL 0.366 - - - no_errors tier3 1194 13 1.08 372 311 45.53 0 0 NA 869586 TCGA-AB-3009 AML43 7 103196046 103196046 A - DEL RELN NM_005045.3 human genbank 54_36p -1 reviewed intronic c.544+8194 e4+8194 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 108836479 108836479 G A SNP - - - - - - - - - - - - - - - tier3 1343 15 1.1 546 436 44.4 0 0 NA 869586 TCGA-AB-3009 AML43 7 113957820 113957821 - A INS FOXP2 NM_148898.2 human genbank 54_36p 1 reviewed intronic c.169-4088_169-4087 e2-4087 0.932:0.138 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 117982213 117982213 A T SNP - - - - - - - - - - - - - - - tier3 498 4 0.8 134 20 12.99 0 0 NA 869586 TCGA-AB-3009 AML43 7 118021666 118021666 C T SNP - - - - - - - - - - - - - - - tier3 1262 10 0.79 433 354 44.98 0 0 NA 869586 TCGA-AB-3009 AML43 7 118788131 118788131 T G SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 119110412 119110412 G A SNP - - - - - - - - - - - - - - - tier3 175 1 0.57 26 8 23.53 0 0 NA 869586 TCGA-AB-3009 AML43 7 121048122 121048122 G C SNP ENSG00000221690 ENST00000408763 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-46078 NULL 0.001 - - - no_errors tier3 604 5 0.82 91 97 51.6 0 0 NA 869586 TCGA-AB-3009 AML43 7 121180499 121180499 G T SNP ENSG00000208616 ENST00000385881 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*16498 NULL 0 - - - pseudogene tier3 610 9 1.45 193 192 49.74 0 0 NA 869586 TCGA-AB-3009 AML43 7 121979809 121979809 G A SNP CADPS2 NM_017954.2 human genbank 54_36p -1 validated intronic c.1475+2031 e8+2031 0.002 - - - no_errors tier3 536 10 1.83 298 261 46.69 0 0 NA 869586 TCGA-AB-3009 AML43 7 124683407 124683407 C T SNP RPL31P39 ENST00000393325 human ensembl 54_36p -1 known 3_prime_flanking_region c.*44387 NULL 0 - - - no_coding_region:pseudogene tier3 1098 12 1.08 186 129 40.95 0 0 NA 869586 TCGA-AB-3009 AML43 7 124892606 124892606 A C SNP - - - - - - - - - - - - - - - tier3 372 2 0.53 112 118 51.3 0 0 NA 869586 TCGA-AB-3009 AML43 7 125413416 125413416 C A SNP - - - - - - - - - - - - - - - tier3 669 1 0.15 234 162 40.91 0 0 NA 869586 TCGA-AB-3009 AML43 7 126133132 126133132 G T SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.1357+64023 e6+64023 0.001 - - - no_errors tier3 147 3 2 11 24 68.57 0 0 NA 869586 TCGA-AB-3009 AML43 7 126677763 126677763 C A SNP GRM8 ENST00000339582 human ensembl 54_36p -1 known intronic c.1+2324 e0+2324 0 - - - no_errors tier3 489 7 1.41 178 164 47.95 0 0 NA 869586 TCGA-AB-3009 AML43 7 130050909 130050909 C T SNP TSGA13 NM_052933.2 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-30321 NULL 0.029 - - - no_errors tier3 582 9 1.52 163 141 46.38 0 0 NA 869586 TCGA-AB-3009 AML43 7 133834313 133834313 C T SNP AKR1B1 NM_001628.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-39959 NULL 0.002 - - - no_errors tier3 475 6 1.24 151 114 43.02 0 0 NA 869586 TCGA-AB-3009 AML43 7 135616675 135616675 G A SNP ENSG00000220982 ENST00000408055 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*36853 NULL 0.031 - - - no_errors tier3 801 4 0.5 203 147 42 0 0 NA 869586 TCGA-AB-3009 AML43 7 136953685 136953685 C A SNP DGKI NM_004717.2 human genbank 54_36p -1 reviewed intronic c.993+1425 e8+1425 0 - - - no_errors tier3 2016 20 0.98 755 524 40.97 0 0 NA 869586 TCGA-AB-3009 AML43 7 140813368 140813368 G A SNP LOC100131199 XM_001714428.1 human genbank 54_36p 1 model intronic c.338-3437 e3-3437 0.005 - - - no_errors tier3 1421 10 0.7 500 395 44.08 0 0 NA 869586 TCGA-AB-3009 AML43 7 143334961 143334961 A G SNP OR2A5 NM_012365.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-43467 NULL 0 - - - no_errors tier3 903 8 0.88 304 251 45.23 0 0 NA 869586 TCGA-AB-3009 AML43 7 145279476 145279476 G A SNP ENSG00000208307 ENST00000385572 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-45878 NULL 0.278 - - - pseudogene tier3 524 7 1.32 247 160 39.31 0 0 NA 869586 TCGA-AB-3009 AML43 7 145812969 145812969 G A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.98-289327 e2-289327 0 - - - no_errors tier3 413 3 0.72 47 26 35.62 0 0 NA 869586 TCGA-AB-3009 AML43 7 147045265 147045265 G A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2098+77934 e13+77934 0 - - - no_errors tier3 724 4 0.55 450 71 13.63 0 0 NA 869586 TCGA-AB-3009 AML43 7 147184461 147184461 C T SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2099-47129 e14-47129 0.001 - - - no_errors tier2 592 16 2.63 353 298 45.71 0 0 NA 869586 TCGA-AB-3009 AML43 7 147458830 147458830 T - DEL CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.2554+12517 e16+12517 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 7 150308416 150308416 G A SNP KCNH2 NM_000238.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-2482 NULL 0 - - - no_errors tier3 374 6 1.58 91 77 45.83 0 0 NA 869586 TCGA-AB-3009 AML43 7 150449000 150449000 C T SNP AGAP3 NM_031946.1 human genbank 54_36p 1 validated intronic c.1128+835 e8+835 0.017 - - - no_errors tier3 574 3 0.52 151 139 47.77 3 1 25 869586 TCGA-AB-3009 AML43 7 154050162 154050162 T A SNP DPP6 ENST00000252510 human ensembl 54_36p 1 known intronic c.628-10302 e6-10302 0 - - - no_errors tier3 1388 39 2.73 235 191 44.84 0 0 NA 869586 TCGA-AB-3009 AML43 7 155933309 155933309 G A SNP - - - - - - - - - - - - - - - tier3 1435 13 0.89 262 197 42.73 0 0 NA 869586 TCGA-AB-3009 AML43 7 156029939 156029939 C T SNP - - - - - - - - - - - - - - - tier3 998 8 0.79 237 252 51.43 0 0 NA 869586 TCGA-AB-3009 AML43 7 157401607 157401607 C T SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1724-17417 e12-17417 0 - - - no_errors tier3 394 11 2.72 125 114 47.7 0 1 100 869586 TCGA-AB-3009 AML43 7 157546337 157546337 G A SNP PTPRN2 NM_002847.3 human genbank 54_36p -1 reviewed intronic c.1723+20414 e11+20414 0 - - - no_errors tier3 113 1 0.88 41 33 44.59 1 0 0 869586 TCGA-AB-3009 AML43 8 1797828 1797828 G A SNP ARHGEF10 NM_014629.2 human genbank 54_36p 1 reviewed intronic c.481+2071 e3+2071 0.046 - - - no_errors tier2 271 4 1.45 96 75 43.35 0 0 0 869586 TCGA-AB-3009 AML43 8 2615106 2615106 C T SNP - - - - - - - - - - - - - - - tier3 997 27 2.63 376 250 39.94 0 4 100 869586 TCGA-AB-3009 AML43 8 3374021 3374021 C T SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.1348-35365 e12-35365 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 636 10 1.54 227 194 45.97 0 0 NA 869586 TCGA-AB-3009 AML43 8 3844133 3844133 A G SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.611-1093 e5-1093 0.016 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 502 8 1.57 165 212 56.23 0 0 NA 869586 TCGA-AB-3009 AML43 8 4514793 4514793 C G SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.86-32305 e2-32305 0.003 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 460 6 1.29 166 129 43.73 0 0 NA 869586 TCGA-AB-3009 AML43 8 4666132 4666132 G A SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+173130 e1+173130 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 1469 9 0.61 509 408 44.4 0 0 NA 869586 TCGA-AB-3009 AML43 8 5533819 5533819 C T SNP - - - - - - - - - - - - - - - tier3 601 7 1.15 215 191 47.04 0 0 NA 869586 TCGA-AB-3009 AML43 8 6563244 6563245 - CTGTCCTGTACCAT INS AGPAT5 NM_018361.3 human genbank 54_36p 1 reviewed intronic c.220-6555_220-6554 e2-6554 0.000:0.000 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 8 8483635 8483635 G A SNP ENSG00000222487 ENST00000410555 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-6060 NULL 0 - - - no_errors tier2 1053 15 1.4 236 207 46.73 0 0 NA 869586 TCGA-AB-3009 AML43 8 11035050 11035050 A - DEL XKR6 NM_173683.3 human genbank 54_36p -1 provisional intronic c.764+60445 e1+60445 0.051 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 8 14003678 14003678 G A SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.744+578 e7+578 0 - - - no_errors tier3 328 3 0.91 67 36 34.95 0 0 NA 869586 TCGA-AB-3009 AML43 8 15129878 15129878 C T SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.39+9587 e1+9587 0 - - - no_errors tier3 451 2 0.44 153 78 33.77 0 0 NA 869586 TCGA-AB-3009 AML43 8 15637985 15637985 G A SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed intronic c.862+5376 e7+5376 0 - - - no_errors tier3 1170 3 0.26 621 100 13.87 0 2 100 869586 TCGA-AB-3009 AML43 8 17926247 17926247 A C SNP PCM1 NM_006197.3 human genbank 54_36p 1 validated intronic c.5842-903 e35-903 0.003 - - - no_errors tier3 211 2 0.94 64 56 46.67 7 4 36.36 869586 TCGA-AB-3009 AML43 8 19365821 19365821 C T SNP CSGALNACT1 NM_018371.1 human genbank 54_36p -1 validated intronic c.635-5388 e2-5388 0 - - - no_errors tier3 1230 6 0.48 362 341 48.44 0 0 0 869586 TCGA-AB-3009 AML43 8 20096196 20096196 C T SNP LOC100133494 XM_001717636.1 human genbank 54_36p -1 model intronic c.154-3666 e3-3666 0.004 - - - no_start_codon:pseudogene:no_stop_codon tier3 247 1 0.4 88 73 45.34 0 0 NA 869586 TCGA-AB-3009 AML43 8 21547942 21547942 C T SNP GFRA2 ENST00000306793 human ensembl 54_36p -1 known 3_prime_flanking_region c.*47128 NULL 0.405 - - - no_errors tier2 1311 16 1.2 397 355 47.21 0 0 NA 869586 TCGA-AB-3009 AML43 8 22120146 22120146 C T SNP BMP1 NM_006129.2 human genbank 54_36p 1 reviewed intronic c.2234-166 e17-166 0 - - - no_errors tier3 1987 13 0.65 286 240 45.63 4 2 33.33 869586 TCGA-AB-3009 AML43 8 22640746 22640746 G A SNP PEBP4 NM_144962.2 human genbank 54_36p -1 validated intronic c.358-68 e4-68 0.02 - - - no_errors tier3 3509 25 0.71 682 600 46.8 0 0 NA 869586 TCGA-AB-3009 AML43 8 25061684 25061684 T C SNP DOCK5 NM_024940.6 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36657 NULL 0.034 - - - no_errors tier3 692 4 0.57 309 223 41.92 0 0 NA 869586 TCGA-AB-3009 AML43 8 30202324 30202324 C T SNP DCTN6 NM_006571.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*42093 NULL 0 - - - no_errors tier3 1112 14 1.24 166 143 46.28 0 0 NA 869586 TCGA-AB-3009 AML43 8 34617311 34617311 C T SNP - - - - - - - - - - - - - - - tier3 1543 23 1.47 430 326 43.06 0 0 NA 869586 TCGA-AB-3009 AML43 8 34710517 34710517 C T SNP - - - - - - - - - - - - - - - tier3 1769 19 1.06 560 397 41.44 0 0 NA 869586 TCGA-AB-3009 AML43 8 37792367 37792367 G A SNP GPR124 NM_032777.7 human genbank 54_36p 1 validated intronic c.317+724 e2+724 0 - - - no_errors tier3 NA NA NA NA NA NA 0 2 100 869586 TCGA-AB-3009 AML43 8 40901384 40901384 G A SNP ZMAT4 NM_024645.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-99032 NULL 0.001 - - - no_errors tier3 859 10 1.14 258 236 47.77 0 0 NA 869586 TCGA-AB-3009 AML43 8 49695481 49695481 G A SNP FLJ46365 XR_040286.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*28575 NULL 0 - - - no_errors tier2 1800 24 1.32 566 547 49.15 0 0 NA 869586 TCGA-AB-3009 AML43 8 49768959 49768959 G A SNP EFCAB1 NM_024593.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*30895 NULL 0 - - - no_errors tier3 415 6 1.43 159 103 39.31 0 0 NA 869586 TCGA-AB-3009 AML43 8 52769210 52769210 C T SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.165-39337 e2-39337 0.001 - - - no_errors tier2 1043 20 1.88 281 273 49.28 0 0 NA 869586 TCGA-AB-3009 AML43 8 52919557 52919557 T C SNP PCMTD1 NM_052937.2 human genbank 54_36p -1 validated intronic c.410+1217 e2+1217 0 - - - no_errors tier2 473 5 1.05 204 178 46.6 4 12 75 869586 TCGA-AB-3009 AML43 8 56380197 56380197 C T SNP XKR4 NM_052898.1 human genbank 54_36p 1 provisional intronic c.807-52595 e2-52595 0 - - - no_errors tier3 979 18 1.8 285 297 50.94 0 0 NA 869586 TCGA-AB-3009 AML43 8 56433852 56433852 G A SNP XKR4 NM_052898.1 human genbank 54_36p 1 provisional intronic c.1006+861 e2+861 0 - - - no_errors tier3 2070 10 0.48 591 442 42.79 0 0 NA 869586 TCGA-AB-3009 AML43 8 63723910 63723910 C A SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.273+59003 e3+59003 0.001 - - - no_errors tier3 832 18 2.12 353 317 47.24 0 0 NA 869586 TCGA-AB-3009 AML43 8 68686633 68686633 C T SNP CPA6 NM_020361.1 human genbank 54_36p -1 validated intronic c.192+12332 e2+12332 0 - - - no_errors tier2 923 15 1.6 231 240 50.85 1 3 75 869586 TCGA-AB-3009 AML43 8 69257911 69257911 C T SNP PREX2 NM_024870.2 human genbank 54_36p 1 validated intronic c.4347-8600 e36-8600 0 - - - no_errors tier3 1220 14 1.13 290 296 50.43 0 0 NA 869586 TCGA-AB-3009 AML43 8 72611511 72611511 C T SNP LOC100132809 XM_001715796.1 human genbank 54_36p -1 model intronic c.580-874 e3-874 0.001 - - - no_errors tier3 934 17 1.79 247 199 44.52 0 0 NA 869586 TCGA-AB-3009 AML43 8 76784885 76784885 A G SNP - - - - - - - - - - - - - - - tier3 665 8 1.19 317 297 48.37 0 0 NA 869586 TCGA-AB-3009 AML43 8 77920715 77920715 C A SNP ZFHX4 NM_024721.3 human genbank 54_36p 1 validated intronic c.3407-3101 e6-3101 0.011 - - - no_errors tier3 318 4 1.24 80 63 44.06 0 0 NA 869586 TCGA-AB-3009 AML43 8 79939985 79939985 G A SNP - - - - - - - - - - - - - - - tier3 437 7 1.57 89 56 38.62 0 0 NA 869586 TCGA-AB-3009 AML43 8 80274759 80274759 T G SNP - - - - - - - - - - - - - - - tier3 447 0 0 142 112 44.09 0 0 NA 869586 TCGA-AB-3009 AML43 8 82111729 82111729 G A SNP PAG1 NM_018440.3 human genbank 54_36p -1 reviewed intronic c.1-6850 e1-6850 0.155 - - - no_errors tier2 587 11 1.84 158 82 34.17 0 1 100 869586 TCGA-AB-3009 AML43 8 82285709 82285709 C T SNP LOC646463 XM_001716133.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-43210 NULL 0 - - - pseudogene tier3 502 6 1.18 255 209 45.04 0 0 NA 869586 TCGA-AB-3009 AML43 8 83837357 83837357 G A SNP - - - - - - - - - - - - - - - tier3 414 0 0 211 57 21.27 0 0 NA 869586 TCGA-AB-3009 AML43 8 89618273 89618273 G T SNP - - - - - - - - - - - - - - - tier3 2005 14 0.69 737 617 45.57 0 0 NA 869586 TCGA-AB-3009 AML43 8 91377089 91377089 G A SNP - - - - - - - - - - - - - - - tier3 338 1 0.29 57 39 40.62 0 0 NA 869586 TCGA-AB-3009 AML43 8 91615221 91615221 G A SNP ENSG00000199354 ENST00000362484 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22581 NULL 0 - - - no_errors tier3 858 8 0.92 313 261 45.47 0 0 NA 869586 TCGA-AB-3009 AML43 8 92065382 92065382 C T SNP LOC100127983 XM_001722571.1 human genbank 54_36p -1 model intronic c.1+1136 e0+1136 0.027 - - - no_errors tier3 293 2 0.67 93 61 39.61 0 0 NA 869586 TCGA-AB-3009 AML43 8 92594485 92594485 C T SNP ENSG00000209198 ENST00000386463 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48947 NULL 0.024 - - - pseudogene tier3 464 6 1.28 188 110 36.91 0 0 NA 869586 TCGA-AB-3009 AML43 8 96026248 96026248 A G SNP TP53INP1 NM_033285.1 human genbank 54_36p -1 validated intronic c.1-3753 e1-3753 0 - - - no_errors tier3 700 11 1.54 184 180 49.45 4 1 20 869586 TCGA-AB-3009 AML43 8 98358079 98358079 C A SNP TSPYL5 NM_033512.2 human genbank 54_36p -1 validated missense c.1170 p.E390D 0.998 HMMPfam_NAP HMMPfam_NAP - no_errors tier1 1485 11 0.74 406 347 46.08 NA 869586 TCGA-AB-3009 AML43 8 100274306 100274306 C A SNP VPS13B NM_017890.2 human genbank 54_36p 1 reviewed missense c.2360 p.T787N 1 NULL PatternScan_ZINC_PROTEASE - no_errors tier1 937 8 0.85 629 458 42.1 26 18 40.91 869586 TCGA-AB-3009 AML43 8 102195749 102195749 G A SNP ENSG00000202360 ENST00000365490 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23614 NULL 0 - - - no_errors tier3 563 3 0.53 132 103 43.83 0 0 NA 869586 TCGA-AB-3009 AML43 8 103718738 103718738 G A SNP KLF10 NM_005655.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*12798 NULL 0.589 - - - no_errors tier3 714 7 0.97 111 119 51.74 0 0 NA 869586 TCGA-AB-3009 AML43 8 104741189 104741189 G A SNP RIMS2 NM_001100117.1 human genbank 54_36p 1 validated intronic c.177-37301 e2-37301 0.998 - - - no_errors tier2 1192 10 0.83 585 511 46.58 0 0 NA 869586 TCGA-AB-3009 AML43 8 105436497 105436497 C T SNP TM7SF4 NM_030788.2 human genbank 54_36p 1 reviewed missense c.1246 p.R416C 0.698 HMMPfam_DC_STAMP HMMPfam_DC_STAMP - no_errors tier1 1265 5 0.39 294 284 49.05 NA 869586 TCGA-AB-3009 AML43 8 105440530 105440530 T C SNP DPYS NM_001385.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*22072 NULL 0.001 - - - no_errors tier3 1353 15 1.09 428 342 44.3 0 0 NA 869586 TCGA-AB-3009 AML43 8 108709296 108709296 T C SNP - - - - - - - - - - - - - - - tier3 381 4 1.04 76 79 50.97 0 0 NA 869586 TCGA-AB-3009 AML43 8 112102672 112102672 C T SNP - - - - - - - - - - - - - - - tier2 510 12 2.29 149 76 33.78 0 0 NA 869586 TCGA-AB-3009 AML43 8 112908937 112908937 T A SNP - - - - - - - - - - - - - - - tier3 166 3 1.78 21 24 53.33 0 0 NA 869586 TCGA-AB-3009 AML43 8 112908940 112908940 A T SNP - - - - - - - - - - - - - - - tier3 170 3 1.73 21 27 56.25 0 0 NA 869586 TCGA-AB-3009 AML43 8 113563112 113563112 G T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.5279-9000 e32-9000 0.003 - - - no_errors tier3 608 7 1.14 122 140 53.44 0 0 NA 869586 TCGA-AB-3009 AML43 8 113884103 113884103 C T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1860-2424 e13-2424 0.013 - - - no_errors tier3 214 2 0.92 46 33 41.77 0 0 NA 869586 TCGA-AB-3009 AML43 8 113952281 113952281 G T SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.1634-11610 e11-11610 0 - - - no_errors tier3 892 4 0.45 140 132 48.53 0 0 NA 869586 TCGA-AB-3009 AML43 8 114524003 114524003 C A SNP CSMD3 NM_198123.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-5744 NULL 0.662 - - - no_errors tier3 304 2 0.65 17 4 19.05 0 0 NA 869586 TCGA-AB-3009 AML43 8 116221163 116221163 G A SNP - - - - - - - - - - - - - - - tier3 658 4 0.6 131 107 44.96 0 0 NA 869586 TCGA-AB-3009 AML43 8 123401103 123401103 A T SNP - - - - - - - - - - - - - - - tier3 596 12 1.97 210 211 50 0 0 NA 869586 TCGA-AB-3009 AML43 8 126722699 126722699 C T SNP - - - - - - - - - - - - - - - tier3 1075 20 1.82 399 251 38.44 0 0 NA 869586 TCGA-AB-3009 AML43 8 129603854 129603854 C T SNP - - - - - - - - - - - - - - - tier3 1320 6 0.45 353 317 47.31 0 0 NA 869586 TCGA-AB-3009 AML43 8 132866073 132866073 G A SNP - - - - - - - - - - - - - - - tier3 432 6 1.37 76 121 61.11 0 1 100 869586 TCGA-AB-3009 AML43 8 133786740 133786740 C T SNP TMEM71 ENST00000395406 human ensembl 54_36p -1 known intronic c.873-7095 e9-7095 0.006 - - - no_stop_codon tier3 1497 27 1.77 610 379 38.32 8 0 0 869586 TCGA-AB-3009 AML43 8 136741543 136741543 G T SNP LOC100130092 XR_039545.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-34137 NULL 0.001 - - - pseudogene tier3 2297 28 1.2 640 495 43.61 0 0 NA 869586 TCGA-AB-3009 AML43 8 137945484 137945484 G A SNP - - - - - - - - - - - - - - - tier3 1313 16 1.2 502 422 45.67 0 0 NA 869586 TCGA-AB-3009 AML43 8 138136457 138136457 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 8 138808147 138808147 G A SNP - - - - - - - - - - - - - - - tier3 250 2 0.79 26 21 44.68 0 0 NA 869586 TCGA-AB-3009 AML43 8 139010667 139010667 T A SNP FLJ45872 XR_040309.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - no_errors tier3 1107 21 1.86 375 284 43.1 0 0 NA 869586 TCGA-AB-3009 AML43 8 141826006 141826006 T C SNP PTK2 NM_005607.3 human genbank 54_36p -1 reviewed intronic c.1584+35 e17+35 0 - - - no_errors tier3 312 2 0.64 125 126 50.2 0 0 NA 869586 TCGA-AB-3009 AML43 8 142691667 142691667 C T SNP - - - - - - - - - - - - - - - tier3 362 5 1.36 94 90 48.91 0 0 NA 869586 TCGA-AB-3009 AML43 8 143442253 143442253 C T SNP TSNARE1 NM_145003.2 human genbank 54_36p -1 validated intronic c.1-8222 e1-8222 0.001 - - - no_errors tier2 525 2 0.38 204 184 47.42 1 1 50 869586 TCGA-AB-3009 AML43 8 143622650 143622650 C T SNP BAI1 NM_001702.2 human genbank 54_36p 1 reviewed missense c.4625 p.T1542M 0.068 NULL "HMMPfam_GPS,HMMSmart_SM00303,HMMPfam_7tm_2,HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_HRM,HMMSmart_SM00008" - no_errors tier1 284 0 65 76 53.52 3 4 57.14 869586 TCGA-AB-3009 AML43 8 143691876 143691876 C G SNP ARC NM_015193.3 human genbank 54_36p -1 validated missense c.759 p.W253C 1 NULL NULL - no_errors tier1 434 1 0.23 215 137 38.81 2 100 869586 TCGA-AB-3009 AML43 8 145639466 145639466 G A SNP NFKBIL2 ENST00000409379 human ensembl 54_36p -1 known missense c.311 p.T104M 0.004 superfamily_TPR-like "HMMPfam_TPR_1,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,HMMSmart_SM00368,HMMSmart_SM00028,superfamily_TPR-like,superfamily_RNI-like" - no_errors tier1 170 0 88 55 38.46 19 16 45.71 869586 TCGA-AB-3009 AML43 9 2715979 2715979 G A SNP KCNV2 NM_133497.2 human genbank 54_36p 1 reviewed intronic c.1357-3467 e2-3467 0 - - - no_errors tier3 902 10 1.1 262 246 48.43 0 1 100 869586 TCGA-AB-3009 AML43 9 6228687 6228687 G A SNP IL33 NM_033439.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3008 NULL 0.001 - - - no_errors tier3 570 5 0.87 115 87 43.07 0 0 0 869586 TCGA-AB-3009 AML43 9 8780779 8780779 G T SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-56833 e1-56833 0 - - - no_errors tier3 332 6 1.76 108 88 44.67 0 0 NA 869586 TCGA-AB-3009 AML43 9 9326002 9326002 G A SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1+61447 e0+61447 0 - - - no_errors tier3 328 4 1.2 50 29 36.71 0 0 NA 869586 TCGA-AB-3009 AML43 9 9452332 9452332 G A SNP PTPRD NM_002839.1 human genbank 54_36p -1 reviewed intronic c.1-64850 e1-64850 0.999 - - - no_errors tier2 595 4 0.67 316 77 19.59 0 0 NA 869586 TCGA-AB-3009 AML43 9 11778521 11778521 C T SNP - - - - - - - - - - - - - - - tier3 668 7 1.03 341 276 44.73 0 0 NA 869586 TCGA-AB-3009 AML43 9 12372897 12372897 G C SNP - - - - - - - - - - - - - - - tier3 893 6 0.67 313 188 37.45 0 0 NA 869586 TCGA-AB-3009 AML43 9 12462110 12462110 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 20967939 20967939 T A SNP KIAA1797 NM_017794.3 human genbank 54_36p 1 validated intronic c.4262-399 e36-399 0.014 - - - no_errors tier3 1182 13 1.09 267 238 47.13 0 2 100 869586 TCGA-AB-3009 AML43 9 23653985 23653986 - A INS LOC402360 XR_017263.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-17910 NULL 0.226:0.202 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 23993511 23993511 G A SNP LOC286260 XM_001723591.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-0 NULL 0.998 - - - rna_with_coding_region tier2 456 3 0.65 266 235 46.91 0 0 NA 869586 TCGA-AB-3009 AML43 9 24788760 24788760 T C SNP - - - - - - - - - - - - - - - tier3 604 1 0.17 222 149 39.84 0 0 NA 869586 TCGA-AB-3009 AML43 9 25271855 25271855 A T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 25520654 25520654 G T SNP - - - - - - - - - - - - - - - tier3 377 0 0 88 10 10.2 0 0 NA 869586 TCGA-AB-3009 AML43 9 25733587 25733587 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 27496041 27496042 - A INS MOBKL2B NM_024761.3 human genbank 54_36p -1 reviewed intronic c.1+23511_23510 e0+23511 0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 30116649 30116649 C T SNP - - - - - - - - - - - - - - - tier3 875 12 1.35 271 257 48.49 0 0 NA 869586 TCGA-AB-3009 AML43 9 31824992 31824992 C T SNP - - - - - - - - - - - - - - - tier3 921 2 0.22 370 409 52.44 0 0 NA 869586 TCGA-AB-3009 AML43 9 34558623 34558623 G A SNP CNTFR NM_001842.3 human genbank 54_36p -1 reviewed intronic c.85+272 e1+272 0 - - - no_errors tier2 765 5 0.64 232 157 40.15 0 0 NA 869586 TCGA-AB-3009 AML43 9 37138478 37138478 T C SNP ZCCHC7 NM_032226.2 human genbank 54_36p 1 validated intronic c.610+21539 e1+21539 0 - - - no_errors tier3 115 0 0 35 36 50.7 3 5 62.5 869586 TCGA-AB-3009 AML43 9 39132812 39132812 C G SNP CNTNAP3 NM_033655.3 human genbank 54_36p -1 reviewed intronic c.1756+1425 e11+1425 0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 39160257 39160257 C T SNP CNTNAP3 NM_033655.3 human genbank 54_36p -1 reviewed intronic c.1333+1109 e8+1109 0 - - - no_errors tier3 324 8 2.4 167 162 49.09 0 0 NA 869586 TCGA-AB-3009 AML43 9 74858303 74858303 C T SNP ENSG00000220631 ENST00000407176 human ensembl 54_36p 1 known intronic c.NULL NULL 0 - - - no_coding_region:pseudogene tier3 414 5 1.19 183 165 47.14 0 0 NA 869586 TCGA-AB-3009 AML43 9 75453786 75453786 C T SNP ENSG00000219821 ENST00000402152 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*75453786 NULL 1 - - - no_coding_region:pseudogene tier2 736 4 0.54 332 263 44.2 0 0 NA 869586 TCGA-AB-3009 AML43 9 75857041 75857041 C T SNP - - - - - - - - - - - - - - - tier3 843 5 0.59 643 517 44.49 0 0 NA 869586 TCGA-AB-3009 AML43 9 77672764 77672764 A T SNP PCSK5 NM_006200.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23154 NULL 0 - - - no_errors tier3 594 2 0.34 186 139 42.77 0 0 NA 869586 TCGA-AB-3009 AML43 9 81202267 81202267 C A SNP CHCHD9 ENST00000338392 human ensembl 54_36p 1 known 3_prime_flanking_region c.*5773 NULL 0 - - - no_errors tier3 1059 11 1.03 359 269 42.83 0 0 NA 869586 TCGA-AB-3009 AML43 9 82369236 82369236 G A SNP ENSG00000218149 ENST00000405609 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-82369236 NULL 1 - - - no_coding_region:pseudogene tier2 618 2 0.32 301 236 43.95 0 0 NA 869586 TCGA-AB-3009 AML43 9 84069279 84069279 G A SNP - - - - - - - - - - - - - - - tier3 1137 13 1.13 432 374 46.4 0 0 NA 869586 TCGA-AB-3009 AML43 9 87310011 87310011 G A SNP AGTPBP1 NM_015239.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*41833 NULL 0.008 - - - no_errors tier3 1484 5 0.34 527 365 40.87 0 0 NA 869586 TCGA-AB-3009 AML43 9 90923638 90923638 C T SNP SHC3 NM_016848.4 human genbank 54_36p -1 validated intronic c.475-6277 e2-6277 0.001 - - - no_errors tier3 903 12 1.31 193 156 44.57 0 0 0 869586 TCGA-AB-3009 AML43 9 92997205 92997205 A G SNP LOC100128909 XM_001723661.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-32029 NULL 0.015 - - - no_errors tier2 604 7 1.14 252 247 49.4 0 1 100 869586 TCGA-AB-3009 AML43 9 95020233 95020233 C A SNP WNK2 NM_006648.3 human genbank 54_36p 1 reviewed intronic c.682-11566 e2-11566 0 - - - no_errors tier3 318 3 0.93 88 70 44.3 0 0 NA 869586 TCGA-AB-3009 AML43 9 95096259 95096259 G A SNP WNK2 NM_006648.3 human genbank 54_36p 1 reviewed intronic c.5708+983 e22+983 0.276 - - - no_errors tier3 157 2 1.26 89 74 45.4 0 0 NA 869586 TCGA-AB-3009 AML43 9 95486459 95486459 G A SNP PHF2 NM_005392.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*6680 NULL 0.008 - - - no_errors tier3 244 2 0.81 62 39 38.61 0 0 NA 869586 TCGA-AB-3009 AML43 9 97513272 97513272 G A SNP ENSG00000175611 ENST00000375268 human ensembl 54_36p -1 known 3_prime_flanking_region c.*164006 NULL 0 - - - no_start_codon tier2 951 7 0.73 264 224 45.81 0 0 NA 869586 TCGA-AB-3009 AML43 9 98437138 98437138 T C SNP CDC14B NM_033331.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-15657 NULL 0 - - - no_errors tier3 1240 15 1.19 175 123 41.28 0 0 NA 869586 TCGA-AB-3009 AML43 9 100051345 100051345 C T SNP TBC1D2 NM_018421.3 human genbank 54_36p -1 validated intronic c.511+2543 e2+2543 0.001 - - - no_errors tier3 1055 16 1.49 343 316 47.95 2 1 33.33 869586 TCGA-AB-3009 AML43 9 103136695 103136695 G A SNP ENSG00000220569 ENST00000406860 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-103136695 NULL 0.996 - - - no_coding_region:pseudogene tier3 588 9 1.51 233 195 45.56 0 0 NA 869586 TCGA-AB-3009 AML43 9 112429998 112429998 A G SNP SVEP1 NM_153366.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-48354 NULL 0.002 - - - no_errors tier3 485 3 0.61 205 186 47.57 0 0 NA 869586 TCGA-AB-3009 AML43 9 112540631 112540631 A G SNP MUSK NM_005592.2 human genbank 54_36p 1 validated intronic c.753+4155 e6+4155 0.019 - - - no_errors tier3 1242 18 1.43 448 384 46.1 0 0 NA 869586 TCGA-AB-3009 AML43 9 115637768 115637768 C T SNP ZNF618 NM_133374.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-40714 NULL 0.003 - - - no_errors tier3 707 5 0.7 238 149 38.5 0 0 NA 869586 TCGA-AB-3009 AML43 9 118895816 118895816 G A SNP ASTN2 NM_198187.3 human genbank 54_36p -1 validated intronic c.1276+2328 e5+2328 0 - - - no_errors tier3 1815 17 0.93 316 224 41.48 0 0 NA 869586 TCGA-AB-3009 AML43 9 120457959 120457959 T A SNP - - - - - - - - - - - - - - - tier3 2715 31 1.13 1007 932 48.07 0 0 NA 869586 TCGA-AB-3009 AML43 9 122962406 122962407 - T INS CEP110 NM_007018.4 human genbank 54_36p 1 reviewed splice_region_ins c.5089+5_5089+4 e30+5 1.000:1.000 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 124303704 124303705 - T INS OR1J1 NM_001004451.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-23678 NULL 0.120:0.061 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 9 125239975 125239975 C T SNP DENND1A NM_020946.1 human genbank 54_36p -1 validated intronic c.1488+2485 e19+2485 0 - - - no_errors tier3 678 7 1.02 182 112 38.1 4 1 20 869586 TCGA-AB-3009 AML43 9 130824292 130824292 G A SNP SH3GLB2 NM_020145.2 human genbank 54_36p -1 provisional intronic c.205+90 e2+90 0.314 - - - no_errors tier2 436 6 1.35 187 72 27.8 1 0 0 869586 TCGA-AB-3009 AML43 9 133152891 133152891 C T SNP FAM78A NM_033387.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11504 NULL 0 - - - no_errors tier3 341 8 2.29 114 97 45.97 0 0 NA 869586 TCGA-AB-3009 AML43 9 134657601 134657601 T C SNP C9orf98 NM_152572.2 human genbank 54_36p -1 validated intronic c.1121+241 e11+241 0.001 - - - no_errors tier3 1075 34 3.07 298 248 45.42 1 0 0 869586 TCGA-AB-3009 AML43 9 135068561 135068561 G A SNP GBGT1 NM_021996.4 human genbank 54_36p -1 validated 5_prime_flanking_region c.-40941 NULL 0.001 - - - no_errors tier2 2044 25 1.21 609 493 44.74 0 0 NA 869586 TCGA-AB-3009 AML43 9 135249598 135249598 C T SNP C9orf96 NM_153710.3 human genbank 54_36p 1 validated intronic c.702+241 e8+241 0.001 - - - no_errors tier3 295 3 1.01 52 35 40.23 0 0 NA 869586 TCGA-AB-3009 AML43 10 617405 617405 T A SNP DIP2C NM_014974.2 human genbank 54_36p -1 reviewed intronic c.86-94935 e2-94935 0.009 - - - no_errors tier3 123 3 2.38 9 16 64 0 0 NA 869586 TCGA-AB-3009 AML43 10 1709805 1709805 A G SNP ADARB2 NM_018702.2 human genbank 54_36p -1 reviewed intronic c.100+59440 e1+59440 0 - - - no_errors tier3 1144 22 1.89 284 273 49.01 0 0 NA 869586 TCGA-AB-3009 AML43 10 2534120 2534120 C T SNP LOC727878 XM_001126639.1 human genbank 54_36p -1 model missense c.20 p.R7Q 0 NULL NULL - no_errors tier1 1506 9 0.59 554 180 24.42 NA 869586 TCGA-AB-3009 AML43 10 4423632 4423632 C T SNP LOC728544 XM_001127725.1 human genbank 54_36p 1 model intronic c.7-284 e2-284 0.001 - - - no_errors tier3 888 6 0.67 258 200 43.67 0 0 NA 869586 TCGA-AB-3009 AML43 10 8640977 8640977 C T SNP ENSG00000220584 ENST00000403012 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43902 NULL 0 - - - no_coding_region:pseudogene tier3 1142 18 1.55 268 206 43.46 0 0 NA 869586 TCGA-AB-3009 AML43 10 10282897 10282897 G A SNP ENSG00000200849 ENST00000363979 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-31683 NULL 0.001 - - - no_errors tier3 823 11 1.32 433 371 46.09 0 0 NA 869586 TCGA-AB-3009 AML43 10 10628016 10628016 C T SNP - - - - - - - - - - - - - - - tier2 704 8 1.12 155 125 44.64 0 0 NA 869586 TCGA-AB-3009 AML43 10 11104505 11104506 - T INS CUGBP2 NM_006561.2 human genbank 54_36p 1 reviewed intronic c.74+4373_74+4372 e1+4373 0.000:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 10 13681763 13681763 C A SNP PRPF18 NM_003675.3 human genbank 54_36p 1 reviewed intronic c.145-487 e3-487 0 - - - no_errors tier3 794 3 0.38 156 113 42.01 0 1 100 869586 TCGA-AB-3009 AML43 10 16956314 16956314 C T SNP CUBN NM_001081.3 human genbank 54_36p -1 reviewed intronic c.9236+65 e58+65 0 - - - no_errors tier3 819 6 0.73 274 239 46.59 0 0 0 869586 TCGA-AB-3009 AML43 10 19757104 19757104 G A SNP - - - - - - - - - - - - - - - tier3 957 4 0.42 350 335 48.91 0 0 NA 869586 TCGA-AB-3009 AML43 10 28556997 28556997 G A SNP MPP7 NM_173496.3 human genbank 54_36p -1 validated intronic c.37+10506 e1+10506 0.059 - - - no_errors tier3 581 9 1.53 302 187 38.24 0 0 0 869586 TCGA-AB-3009 AML43 10 28864676 28864677 - AGGGC INS WAC NM_016628.3 human genbank 54_36p 1 reviewed frame_shift_ins c.258_259 p.E87fs 1.000:1.000 NULL "HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain" - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 10 29201770 29201770 G A SNP LOC729601 XM_001130751.1 human genbank 54_36p -1 model 3_prime_untranslated_region c.*192 NULL 0 - - - no_errors tier3 638 8 1.24 226 217 48.98 0 0 NA 869586 TCGA-AB-3009 AML43 10 31062092 31062092 C A SNP LOC645954 XR_017086.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*28094 NULL 0.004 - - - no_errors tier3 739 12 1.6 158 75 32.19 0 0 NA 869586 TCGA-AB-3009 AML43 10 36958360 36958360 C T SNP ENSG00000207271 ENST00000384541 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3288 NULL 0 - - - no_errors tier3 199 6 2.91 14 3 16.67 0 0 NA 869586 TCGA-AB-3009 AML43 10 37691513 37691513 C T SNP LOC646360 XM_933553.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*20246 NULL 0 - - - no_errors tier2 419 4 0.94 122 116 48.74 0 0 NA 869586 TCGA-AB-3009 AML43 10 37762773 37762773 G T SNP - - - - - - - - - - - - - - - tier3 1033 6 0.58 374 291 43.76 0 0 NA 869586 TCGA-AB-3009 AML43 10 42523772 42523772 G A SNP LOC728064 XR_015196.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.01 - - - no_errors tier3 1000 11 1.09 347 274 44.12 0 0 0 869586 TCGA-AB-3009 AML43 10 45403334 45403334 G T SNP MARCH8 NM_001002265.1 human genbank 54_36p -1 validated intronic c.1+6355 e0+6355 0.078 - - - no_errors tier3 428 2 0.47 118 31 20.67 1 0 0 869586 TCGA-AB-3009 AML43 10 50307838 50307838 C T SNP LOC100128032 XM_001719050.1 human genbank 54_36p 1 model intronic c.27+10276 e1+10276 0 - - - no_errors tier3 871 15 1.69 273 258 48.59 0 0 NA 869586 TCGA-AB-3009 AML43 10 53476687 53476687 C A SNP PRKG1 ENST00000332193 human ensembl 54_36p 1 known 5_prime_untranslated_region c.-224465 NULL 0.028 - - - no_errors tier3 517 4 0.77 192 179 48.25 0 0 NA 869586 TCGA-AB-3009 AML43 10 53491665 53491665 G A SNP PRKG1 NM_006258.1 human genbank 54_36p 1 validated intronic c.841-638 e7-638 0 - - - no_errors tier3 273 6 2.15 259 225 46.49 0 0 NA 869586 TCGA-AB-3009 AML43 10 57607320 57607320 C T SNP - - - - - - - - - - - - - - - tier3 140 1 0.71 9 3 25 0 0 NA 869586 TCGA-AB-3009 AML43 10 60867451 60867451 C T SNP - - - - - - - - - - - - - - - tier3 563 9 1.57 128 103 44.59 0 0 NA 869586 TCGA-AB-3009 AML43 10 61596587 61596587 C A SNP ANK3 NM_020987.2 human genbank 54_36p -1 reviewed splice_site c.2551+1 e22+1 1 - - - no_errors tier1 787 10 1.25 358 207 36.64 1 100 869586 TCGA-AB-3009 AML43 10 62932225 62932225 A T SNP TMEM26 NM_178505.6 human genbank 54_36p -1 validated 5_prime_flanking_region c.-49380 NULL 0.007 - - - no_errors tier3 532 4 0.74 96 76 44.19 0 0 NA 869586 TCGA-AB-3009 AML43 10 65471530 65471530 C T SNP - - - - - - - - - - - - - - - tier3 292 3 1.02 140 146 51.05 0 0 NA 869586 TCGA-AB-3009 AML43 10 67606097 67606097 T C SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1885-73084 e13-73084 0.743 - - - no_errors tier3 541 7 1.28 175 156 47.13 0 0 NA 869586 TCGA-AB-3009 AML43 10 67745103 67745103 G C SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1733-34718 e12-34718 0 - - - no_errors tier3 1297 16 1.22 325 309 48.74 0 0 NA 869586 TCGA-AB-3009 AML43 10 67807862 67807862 T A SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1732+1054 e11+1054 0.017 - - - no_errors tier2 747 3 0.4 228 193 45.84 0 0 NA 869586 TCGA-AB-3009 AML43 10 67828365 67828365 G A SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1532-19249 e11-19249 0.277 - - - no_errors tier2 788 10 1.25 427 350 44.93 0 0 NA 869586 TCGA-AB-3009 AML43 10 68901253 68901253 G A SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.579+50353 e4+50353 0.018 - - - no_errors tier3 390 5 1.27 127 105 45.06 0 0 NA 869586 TCGA-AB-3009 AML43 10 70029424 70029424 C T SNP TET1 NM_030625.2 human genbank 54_36p 1 validated intronic c.1915-1320 e2-1320 0.001 - - - no_errors tier2 1233 7 0.56 262 201 43.41 0 0 0 869586 TCGA-AB-3009 AML43 10 72583478 72583478 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 10 73509568 73509568 G C SNP SPOCK2 NM_014767.1 human genbank 54_36p -1 validated intronic c.190-6894 e2-6894 0.001 - - - no_errors tier3 326 3 0.91 127 116 47.54 0 0 0 869586 TCGA-AB-3009 AML43 10 80716685 80716686 - AACTTCTC INS ZMIZ1 NM_020338.3 human genbank 54_36p 1 validated intronic c.426-2853_426-2852 e5-2852 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 10 83782638 83782638 G A SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.823+156739 e1+156739 0.005 - - - no_errors tier3 553 11 1.95 211 190 47.38 0 0 NA 869586 TCGA-AB-3009 AML43 10 83995484 83995484 A T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.824-112991 e2-112991 0.001 - - - no_errors tier3 686 0 0 128 109 45.99 0 0 NA 869586 TCGA-AB-3009 AML43 10 84453471 84453471 G T SNP NRG3 NM_001010848.3 human genbank 54_36p 1 validated intronic c.954-34842 e3-34842 0 - - - no_errors tier3 1756 27 1.51 511 315 38.14 0 0 NA 869586 TCGA-AB-3009 AML43 10 85411540 85411540 C T SNP LOC728050 XM_001126432.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*10756 NULL 0 - - - no_errors tier3 1033 6 0.58 434 350 44.64 0 0 NA 869586 TCGA-AB-3009 AML43 10 94405496 94405496 G A SNP HHEX NM_002729.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-34228 NULL 0.065 - - - no_errors tier2 492 6 1.2 115 96 45.5 13 8 38.1 869586 TCGA-AB-3009 AML43 10 94794402 94794402 C T SNP EXOC6 NM_019053.2 human genbank 54_36p 1 reviewed intronic c.2170-12269 e21-12269 0 - - - no_errors tier3 195 3 1.52 64 30 31.91 0 2 100 869586 TCGA-AB-3009 AML43 10 100068933 100068933 G A SNP - - - - - - - - - - - - - - - tier2 598 3 0.5 114 105 47.95 0 0 NA 869586 TCGA-AB-3009 AML43 10 101213454 101213454 C G SNP GOT1 NM_002079.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-33142 NULL 0.003 - - - no_errors tier2 1542 9 0.58 354 289 44.95 0 1 100 869586 TCGA-AB-3009 AML43 10 106595367 106595367 C T SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.695+2760 e2+2760 0 - - - no_errors tier3 1061 7 0.65 326 236 41.77 0 0 NA 869586 TCGA-AB-3009 AML43 10 106743384 106743384 C A SNP SORCS3 NM_014978.1 human genbank 54_36p 1 reviewed intronic c.954+16143 e4+16143 0.001 - - - no_errors tier2 1015 20 1.93 347 237 40.58 0 0 NA 869586 TCGA-AB-3009 AML43 10 107281839 107281839 C T SNP ENSG00000207068 ENST00000384340 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2568 NULL 0.001 - - - no_errors tier3 578 9 1.52 91 67 42.41 0 0 NA 869586 TCGA-AB-3009 AML43 10 108352378 108352378 A G SNP SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed intronic c.3165+4536 e23+4536 0 - - - no_errors tier3 3995 34 0.84 739 827 52.81 0 0 0 869586 TCGA-AB-3009 AML43 10 110925002 110925002 T G SNP - - - - - - - - - - - - - - - tier3 980 6 0.61 314 328 51.09 0 0 NA 869586 TCGA-AB-3009 AML43 10 111110033 111110033 C G SNP - - - - - - - - - - - - - - - tier3 687 8 1.15 347 240 40.82 0 0 NA 869586 TCGA-AB-3009 AML43 10 111441529 111441529 G C SNP LOC100132843 XR_037957.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*10558 NULL 0.404 - - - pseudogene tier3 1147 2 0.17 230 173 42.93 0 0 NA 869586 TCGA-AB-3009 AML43 10 117428688 117428688 C T SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.3796-48060 e27-48060 0 - - - no_errors tier3 462 5 1.07 266 229 45.98 0 0 NA 869586 TCGA-AB-3009 AML43 10 117570150 117570150 G A SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.3904-27228 e28-27228 0 - - - no_errors tier3 909 8 0.87 262 226 46.31 0 0 NA 869586 TCGA-AB-3009 AML43 10 117845864 117845864 G A SNP GFRA1 NM_005264.1 human genbank 54_36p -1 reviewed intronic c.880+292 e6+292 0 - - - no_errors tier3 1186 12 1 267 199 42.7 0 0 0 869586 TCGA-AB-3009 AML43 10 118139345 118139345 C T SNP PNLIPRP3 NM_001011709.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-38170 NULL 0.002 - - - no_errors tier3 564 7 1.22 162 135 45.45 0 0 NA 869586 TCGA-AB-3009 AML43 10 118726162 118726162 C T SNP KIAA1598 NM_018330.1 human genbank 54_36p -1 validated intronic c.111+2595 e2+2595 0.274 - - - no_errors tier3 898 6 0.66 270 251 48.18 0 0 NA 869586 TCGA-AB-3009 AML43 10 123174487 123174487 C T SNP ENSG00000222979 ENST00000411047 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*13783 NULL 0 - - - no_errors tier3 897 13 1.43 278 231 45.38 0 0 NA 869586 TCGA-AB-3009 AML43 10 124082289 124082289 T A SNP BTBD16 NM_144587.2 human genbank 54_36p 1 validated intronic c.1164+271 e12+271 0 - - - no_errors tier3 704 9 1.26 173 132 43.28 0 0 NA 869586 TCGA-AB-3009 AML43 10 124794442 124794442 T C SNP ACADSB NM_001609.3 human genbank 54_36p 1 reviewed intronic c.900+451 e7+451 0 - - - no_errors tier3 220 4 1.79 49 37 43.02 1 0 0 869586 TCGA-AB-3009 AML43 10 127227746 127227746 G A SNP - - - - - - - - - - - - - - - tier3 826 2 0.24 442 118 21.07 0 0 NA 869586 TCGA-AB-3009 AML43 10 128134394 128134394 T C SNP C10orf90 NM_001004298.2 human genbank 54_36p -1 validated intronic c.1897+3205 e6+3205 0.001 - - - no_errors tier3 1052 4 0.38 687 527 43.37 0 0 NA 869586 TCGA-AB-3009 AML43 10 130088113 130088113 C T SNP - - - - - - - - - - - - - - - tier3 808 11 1.34 489 363 42.61 0 0 NA 869586 TCGA-AB-3009 AML43 10 130656603 130656603 C T SNP - - - - - - - - - - - - - - - tier3 680 8 1.16 185 148 44.44 0 0 NA 869586 TCGA-AB-3009 AML43 10 131103876 131103876 G T SNP - - - - - - - - - - - - - - - tier3 1899 15 0.78 523 487 48.22 0 0 NA 869586 TCGA-AB-3009 AML43 10 132353514 132353514 C T SNP - - - - - - - - - - - - - - - tier3 577 13 2.2 287 237 45.23 0 0 NA 869586 TCGA-AB-3009 AML43 10 133849918 133849918 C T SNP DPYSL4 NM_006426.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-640 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 10 134588664 134588664 C T SNP LOC399829 XM_927466.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-49421 NULL 0 - - - no_errors tier2 54 1 1.82 39 39 50 0 0 NA 869586 TCGA-AB-3009 AML43 11 2093070 2093070 C T SNP IGF2AS NM_016412.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-25380 NULL 0.001 - - - no_errors tier3 479 3 0.62 119 76 38.97 0 0 NA 869586 TCGA-AB-3009 AML43 11 4697163 4697163 C T SNP OR51E2 NM_030774.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-36646 NULL 0.001 - - - no_errors tier2 1059 2 0.19 402 298 42.51 0 0 NA 869586 TCGA-AB-3009 AML43 11 7231970 7231970 G A SNP SYT9 NM_175733.2 human genbank 54_36p 1 provisional intronic c.145+1832 e1+1832 0.033 - - - no_errors tier3 527 0 0 252 62 19.75 0 0 NA 869586 TCGA-AB-3009 AML43 11 7401800 7401803 AGAG - DEL SYT9 NM_175733.2 human genbank 54_36p 1 provisional intronic c.1467+3358_1467+3355 e6+3358 0.000:0.001:0.001:0.009 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 13818946 13818946 C A SNP LOC729147 XM_001716508.1 human genbank 54_36p -1 model intronic c.144-13543 e3-13543 0 - - - no_errors tier3 2109 7 0.33 792 229 22.43 0 0 NA 869586 TCGA-AB-3009 AML43 11 13921326 13921326 G T SNP SPON1 ENST00000310358 human ensembl 54_36p 1 known 5_prime_flanking_region c.-19702 NULL 0.599 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 16766228 16766228 G T SNP PLEKHA7 NM_175058.3 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*982 NULL 0 - - - no_errors tier2 469 7 1.46 101 83 45.11 2 1 33.33 869586 TCGA-AB-3009 AML43 11 21157398 21157398 C T SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1427-50056 e14-50056 0 - - - no_errors tier3 438 6 1.35 73 57 43.85 0 0 NA 869586 TCGA-AB-3009 AML43 11 21441779 21441779 C T SNP NELL1 NM_006157.3 human genbank 54_36p 1 reviewed intronic c.1646-70717 e16-70717 0 - - - no_errors tier3 990 5 0.5 578 507 46.73 0 0 NA 869586 TCGA-AB-3009 AML43 11 23084461 23084461 C T SNP - - - - - - - - - - - - - - - tier3 339 4 1.16 164 66 28.57 1 0 0 869586 TCGA-AB-3009 AML43 11 23252161 23252161 C T SNP - - - - - - - - - - - - - - - tier3 733 14 1.87 357 298 45.43 0 0 NA 869586 TCGA-AB-3009 AML43 11 23414375 23414375 A T SNP - - - - - - - - - - - - - - - tier3 448 5 1.1 42 43 50.59 0 0 NA 869586 TCGA-AB-3009 AML43 11 26176637 26176637 C T SNP - - - - - - - - - - - - - - - tier3 406 7 1.69 70 49 40.5 0 0 NA 869586 TCGA-AB-3009 AML43 11 26600393 26600393 A T SNP ANO3 NM_031418.2 human genbank 54_36p 1 validated intronic c.1837-2192 e18-2192 0.002 - - - no_errors tier3 622 5 0.8 250 236 48.56 0 0 NA 869586 TCGA-AB-3009 AML43 11 28141801 28141801 T C SNP METT5D1 NM_152636.1 human genbank 54_36p 1 validated intronic c.271-47384 e2-47384 0.197 - - - no_errors tier2 351 0 0 84 82 48.81 0 2 100 869586 TCGA-AB-3009 AML43 11 29608177 29608177 G A SNP - - - - - - - - - - - - - - - tier3 588 4 0.68 137 135 49.63 0 0 NA 869586 TCGA-AB-3009 AML43 11 32374485 32374486 - GACCG INS WT1 NM_024426.3 human genbank 54_36p -1 reviewed frame_shift_ins c.1143_1142 p.A382fs 0.771:0.996 HMMPfam_WT1 "HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 11 32813764 32813764 C T SNP PRRG4 NM_024081.4 human genbank 54_36p 1 provisional intronic c.104-1016 e2-1016 0.006 - - - no_errors tier2 412 3 0.72 81 64 44.14 0 0 NA 869586 TCGA-AB-3009 AML43 11 35617793 35617793 G A SNP TRIM44 NM_017583.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23443 NULL 0 - - - no_errors tier3 1285 14 1.07 293 273 48.06 0 0 NA 869586 TCGA-AB-3009 AML43 11 36130208 36130208 G A SNP LDLRAD3 NM_174902.2 human genbank 54_36p 1 provisional intronic c.454+53621 e4+53621 0 - - - no_errors tier3 741 3 0.4 307 328 51.57 0 0 NA 869586 TCGA-AB-3009 AML43 11 37199515 37199515 G A SNP - - - - - - - - - - - - - - - tier3 173 1 0.57 73 56 43.41 0 0 NA 869586 TCGA-AB-3009 AML43 11 39886096 39886096 G T SNP ENSG00000221804 ENST00000408877 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-46376 NULL 0 - - - no_errors tier3 683 8 1.16 191 167 46.65 0 0 NA 869586 TCGA-AB-3009 AML43 11 40250680 40250680 G A SNP LRRC4C NM_020929.1 human genbank 54_36p -1 validated intronic c.1+19639 e0+19639 0 - - - no_errors tier3 167 0 0 16 6 27.27 0 0 NA 869586 TCGA-AB-3009 AML43 11 40618057 40618057 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 40678606 40678606 A C SNP - - - - - - - - - - - - - - - tier3 685 12 1.72 107 176 62.19 0 0 NA 869586 TCGA-AB-3009 AML43 11 42231838 42231838 A - DEL LOC387761 XM_373495.1 human genbank 54_36p -1 model frame_shift_del c.184 p.S62fs 0.003 NULL NULL - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 11 49764785 49764785 A - DEL ENSG00000219061 ENST00000405176 human ensembl 54_36p -1 known 3_prime_flanking_region c.*46480 NULL 0.014 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 67233955 67233955 G A SNP ALDH3B2 NM_000695.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-42973 NULL 0.002 - - - no_errors tier3 852 7 0.81 218 164 42.93 0 0 NA 869586 TCGA-AB-3009 AML43 11 68820412 68820412 C A SNP MYEOV NM_138768.2 human genbank 54_36p 1 validated missense c.919 p.L307I 0 NULL NULL - no_errors tier1 1287 18 1.38 130 130 50 NA 869586 TCGA-AB-3009 AML43 11 69511014 69511014 C A SNP LOC100127946 XM_001717040.1 human genbank 54_36p 1 model intronic c.58+1094 e1+1094 0 - - - no_errors tier3 962 20 2.04 242 217 47.28 0 0 NA 869586 TCGA-AB-3009 AML43 11 70110549 70110549 G A SNP SHANK2 NM_012309.1 human genbank 54_36p -1 reviewed intronic c.297+73032 e2+73032 0 - - - no_errors tier3 242 1 0.41 70 48 40.68 0 0 NA 869586 TCGA-AB-3009 AML43 11 70240166 70240166 G A SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.1781-17650 e21-17650 0.067 - - - no_errors tier3 362 0 0 67 59 46.83 0 0 NA 869586 TCGA-AB-3009 AML43 11 70313659 70313659 C A SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.1780+8537 e20+8537 0.029 - - - no_errors tier3 2285 37 1.59 286 212 42.57 0 0 NA 869586 TCGA-AB-3009 AML43 11 70339479 70339479 G A SNP SHANK2 ENST00000338508 human ensembl 54_36p -1 known intronic c.1496+4638 e18+4638 0 - - - no_errors tier3 377 10 2.58 32 62 65.96 0 0 NA 869586 TCGA-AB-3009 AML43 11 71333212 71333213 - G INS RNF121 NM_018320.4 human genbank 54_36p 1 reviewed intronic c.64-12709_64-12708 e2-12708 0.002:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 71402098 71402099 - CCCC INS NUMA1 NM_006185.2 human genbank 54_36p -1 validated frame_shift_ins c.4099_4098 p.C1366fs 0.996:0.977 NULL superfamily_Prefoldin - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 11 74692358 74692358 G A SNP ARRB1 NM_004041.3 human genbank 54_36p -1 validated intronic c.21-13627 e2-13627 0.017 - - - no_errors tier3 1257 13 1.02 572 164 22.28 17 1 5.56 869586 TCGA-AB-3009 AML43 11 78335902 78335902 C T SNP ODZ4 ENST00000278550 human ensembl 54_36p -1 known intronic c.494-43686 e3-43686 0.004 - - - no_errors tier2 738 8 1.07 381 76 16.63 0 0 NA 869586 TCGA-AB-3009 AML43 11 78591069 78591069 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 79669683 79669683 G A SNP - - - - - - - - - - - - - - - tier3 929 18 1.9 511 415 44.82 0 0 NA 869586 TCGA-AB-3009 AML43 11 84033038 84033038 T C SNP DLG2 NM_001364.1 human genbank 54_36p -1 reviewed intronic c.43-109616 e2-109616 0 - - - no_errors tier3 1105 13 1.16 341 252 42.5 0 0 NA 869586 TCGA-AB-3009 AML43 11 85646239 85646239 T A SNP EED NM_003797.2 human genbank 54_36p 1 reviewed missense c.587 p.L196Q 1 "HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40" "HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40" - no_errors tier1 662 2 0.3 235 210 47.19 37 31 45.59 869586 TCGA-AB-3009 AML43 11 88599343 88599343 C G SNP TYR NM_000372.4 human genbank 54_36p 1 reviewed intronic c.1037-1296 e3-1296 0 - - - no_errors tier3 677 14 2.02 322 235 42.19 0 0 NA 869586 TCGA-AB-3009 AML43 11 90927540 90927541 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 91626533 91626533 C T SNP - - - - - - - - - - - - - - - tier3 225 0 0 65 35 35 0 0 NA 869586 TCGA-AB-3009 AML43 11 91797028 91797028 C T SNP FAT3 NM_001008781.2 human genbank 54_36p 1 validated intronic c.3292+68810 e1+68810 0.002 - - - no_errors tier3 419 1 0.24 126 78 38.24 0 0 NA 869586 TCGA-AB-3009 AML43 11 93002621 93002621 G A SNP KIAA1731 ENST00000344196 human ensembl 54_36p 1 known 5_prime_flanking_region c.-72695 NULL 0.004 - - - no_errors tier3 1934 23 1.18 434 397 47.77 0 0 NA 869586 TCGA-AB-3009 AML43 11 96998106 96998106 A G SNP ENSG00000199315 ENST00000362445 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-35568 NULL 0.004 - - - no_errors tier3 741 4 0.54 332 289 46.46 0 0 NA 869586 TCGA-AB-3009 AML43 11 97690656 97690656 T A SNP - - - - - - - - - - - - - - - tier2 542 4 0.73 240 241 50.1 0 0 NA 869586 TCGA-AB-3009 AML43 11 99590148 99590150 TTC - DEL CNTN5 NM_014361.2 human genbank 54_36p 1 reviewed intronic c.1885-10486_1885-10484 e14-10484 0.000:0.001:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 100391923 100391923 A - DEL PGR NM_000926.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*23134 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 101246636 101246636 C T SNP KIAA1377 NM_020802.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-44590 NULL 0 - - - no_errors tier3 973 3 0.31 573 447 43.82 0 0 NA 869586 TCGA-AB-3009 AML43 11 102592234 102592235 - T INS DYNC2H1 NM_001080463.1 human genbank 54_36p 1 provisional intronic c.8832+437_8832+436 e55+437 0.000:0.000 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 104447886 104447886 G A SNP CASP1 NM_033292.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-36836 NULL 0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 0 869586 TCGA-AB-3009 AML43 11 106005732 106005732 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 106972356 106972356 C A SNP ELMOD1 NM_018712.1 human genbank 54_36p 1 validated intronic c.1+5011 e0+5011 0 - - - no_errors tier3 385 7 1.79 53 34 39.08 0 0 NA 869586 TCGA-AB-3009 AML43 11 112644644 112644645 - A INS NCAM1 ENST00000404693 human ensembl 54_36p 1 known intronic c.1509-1476_1475 e12-1475 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 112982090 112982091 - CCTCCCCC INS ENSG00000211178 ENST00000388443 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-43802 NULL 0.001:0.003 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 11 115844209 115844209 G A SNP - - - - - - - - - - - - - - - tier2 1137 9 0.79 301 259 46.25 0 0 NA 869586 TCGA-AB-3009 AML43 11 119952559 119952559 G A SNP - - - - - - - - - - - - - - - tier3 1012 7 0.69 383 299 43.84 0 0 NA 869586 TCGA-AB-3009 AML43 11 120711603 120711603 G A SNP SC5DL NM_001024956.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*28172 NULL 0 - - - no_errors tier3 1507 23 1.5 312 250 44.48 0 0 NA 869586 TCGA-AB-3009 AML43 11 121250028 121250028 C A SNP - - - - - - - - - - - - - - - tier3 895 14 1.54 304 237 43.81 0 0 NA 869586 TCGA-AB-3009 AML43 11 124577189 124577189 C T SNP PKNOX2 NM_022062.2 human genbank 54_36p 1 validated intronic c.1-32962 e1-32962 1 - - - no_errors tier2 598 7 1.16 127 103 44.78 0 0 NA 869586 TCGA-AB-3009 AML43 11 126161018 126161018 T C SNP KIRREL3 NM_032531.2 human genbank 54_36p -1 provisional intronic c.55+214543 e1+214543 0.003 - - - no_errors tier3 869 10 1.12 160 128 44.14 0 0 NA 869586 TCGA-AB-3009 AML43 11 129099192 129099192 C T SNP LOC729717 XM_001131119.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*37732 NULL 0.074 - - - no_errors tier3 953 16 1.65 362 327 47.25 0 0 NA 869586 TCGA-AB-3009 AML43 11 131087426 131087426 G A SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.83-199242 e2-199242 0 - - - no_errors tier3 906 0 0 383 279 42.15 0 0 NA 869586 TCGA-AB-3009 AML43 11 132525633 132525633 G A SNP OPCML NM_001012393.1 human genbank 54_36p -1 reviewed intronic c.62-207518 e2-207518 0 - - - no_errors tier3 1911 22 1.14 541 522 49.11 0 0 NA 869586 TCGA-AB-3009 AML43 12 1540410 1540410 C T SNP FBXL14 NM_152441.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*5765 NULL 0.001 - - - no_errors tier3 1276 8 0.62 314 241 43.35 1 0 0 869586 TCGA-AB-3009 AML43 12 3515374 3515374 C T SNP PRMT8 NM_019854.3 human genbank 54_36p 1 validated intronic c.76-4659 e2-4659 0 - - - no_errors tier3 1025 5 0.48 437 485 52.6 0 0 NA 869586 TCGA-AB-3009 AML43 12 6448244 6448244 G A SNP VAMP1 NM_014231.3 human genbank 54_36p -1 reviewed intronic c.2+1713 e1+1713 0.002 - - - no_errors tier2 1732 11 0.63 404 315 43.81 9 2 18.18 869586 TCGA-AB-3009 AML43 12 11600664 11600664 C T SNP ENSG00000221128 ENST00000408201 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-14418 NULL 0 - - - no_errors tier3 1400 12 0.85 714 214 22.99 1 1 50 869586 TCGA-AB-3009 AML43 12 13575457 13575457 G A SNP GRIN2B NM_000834.3 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*31527 NULL 0.008 - - - no_errors tier3 1558 29 1.83 668 650 49.32 0 0 NA 869586 TCGA-AB-3009 AML43 12 15513839 15513839 C T SNP PTPRO NM_030667.2 human genbank 54_36p 1 reviewed intronic c.76-14336 e2-14336 0.006 - - - no_errors tier3 936 19 1.99 266 195 42.3 0 0 NA 869586 TCGA-AB-3009 AML43 12 20925361 20925361 G A SNP SLCO1B3 NM_019844.2 human genbank 54_36p 1 validated intronic c.1497+140 e10+140 0 - - - no_errors tier3 272 2 0.72 65 72 52.55 0 0 NA 869586 TCGA-AB-3009 AML43 12 29479858 29479858 C T SNP OVCH1 NM_183378.2 human genbank 54_36p -1 validated intronic c.3265-1845 e27-1845 0.001 - - - no_errors tier3 765 20 2.55 283 249 46.8 0 0 NA 869586 TCGA-AB-3009 AML43 12 31412249 31412249 C T SNP FAM60A NM_021238.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-69844 NULL 0.027 - - - no_errors tier3 415 4 0.95 27 29 51.79 0 0 NA 869586 TCGA-AB-3009 AML43 12 31524470 31524470 A - DEL DENND5B NM_144973.3 human genbank 54_36p -1 validated intronic c.238-14 e3-14 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 12 37150181 37150181 C T SNP - - - - - - - - - - - - - - - tier2 624 8 1.27 186 134 41.88 0 0 NA 869586 TCGA-AB-3009 AML43 12 42005661 42005661 G A SNP ENSG00000215993 ENST00000401174 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-34011 NULL 0 - - - no_errors tier3 726 2 0.27 195 127 39.32 0 0 NA 869586 TCGA-AB-3009 AML43 12 44307912 44307912 G A SNP - - - - - - - - - - - - - - - tier2 582 6 1.02 215 153 41.58 0 0 NA 869586 TCGA-AB-3009 AML43 12 47152645 47152645 C T SNP ANP32D NM_012404.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-70 NULL 0.002 - - - no_errors tier3 574 8 1.37 148 94 38.68 0 0 NA 869586 TCGA-AB-3009 AML43 12 48739047 48739047 C G SNP ACCN2 NM_020039.2 human genbank 54_36p 1 reviewed silent c.231 p.L77 1 HMMPfam_ASC "HMMPfam_ASC,PatternScan_ASC" - no_errors tier1 1572 10 0.63 355 329 48.1 7 2 22.22 869586 TCGA-AB-3009 AML43 12 50955381 50955381 T C SNP KRT86 NM_002284.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-26587 NULL 0.003 - - - no_errors tier3 451 10 2.17 198 191 49.1 0 0 NA 869586 TCGA-AB-3009 AML43 12 62843551 62843551 G T SNP ENSG00000212298 ENST00000390996 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41289 NULL 0.005 - - - no_errors tier3 1059 16 1.49 351 331 48.53 0 0 NA 869586 TCGA-AB-3009 AML43 12 64216620 64216620 C T SNP - - - - - - - - - - - - - - - tier3 1048 7 0.66 342 226 39.79 0 0 NA 869586 TCGA-AB-3009 AML43 12 73564540 73564540 A G SNP - - - - - - - - - - - - - - - tier3 217 0 0 50 30 37.5 0 0 NA 869586 TCGA-AB-3009 AML43 12 76390199 76390199 C A SNP - - - - - - - - - - - - - - - tier3 459 4 0.86 54 65 54.62 0 0 NA 869586 TCGA-AB-3009 AML43 12 77981760 77981760 A T SNP SYT1 ENST00000261205 human ensembl 54_36p 1 known intronic c.1+16487 e0+16487 0 - - - no_errors tier3 NA NA NA NA NA NA 1 0 0 869586 TCGA-AB-3009 AML43 12 80061033 80061033 C T SNP ACSS3 NM_024560.2 human genbank 54_36p 1 validated missense c.797 p.A266V 0 "HMMPfam_AMP-binding,superfamily_Acetyl-CoA synthetase-like" "HMMPfam_AMP-binding,PatternScan_AMP_BINDING,superfamily_Acetyl-CoA synthetase-like" - no_errors tier1 592 2 0.34 203 207 50.49 NA 869586 TCGA-AB-3009 AML43 12 80305084 80305084 A C SNP PPFIA2 NM_003625.2 human genbank 54_36p -1 reviewed intronic c.763-2930 e7-2930 0 - - - no_errors tier3 589 6 1.01 175 211 54.66 0 0 NA 869586 TCGA-AB-3009 AML43 12 82431272 82431272 T A SNP - - - - - - - - - - - - - - - tier3 1495 29 1.9 322 236 42.29 0 0 NA 869586 TCGA-AB-3009 AML43 12 82550859 82550859 A T SNP - - - - - - - - - - - - - - - tier3 668 2 0.3 197 145 42.4 0 0 NA 869586 TCGA-AB-3009 AML43 12 82952593 82952593 A G SNP - - - - - - - - - - - - - - - tier2 381 2 0.52 96 82 46.07 0 0 NA 869586 TCGA-AB-3009 AML43 12 83466470 83466470 G C SNP - - - - - - - - - - - - - - - tier3 315 4 1.25 79 78 49.68 0 0 NA 869586 TCGA-AB-3009 AML43 12 84194039 84194039 A T SNP ALX1 NM_006982.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-4132 NULL 0 - - - no_errors tier3 113 0 0 9 9 50 0 0 NA 869586 TCGA-AB-3009 AML43 12 86504514 86504514 C T SNP - - - - - - - - - - - - - - - tier3 757 14 1.81 130 97 42.73 0 0 NA 869586 TCGA-AB-3009 AML43 12 87116911 87116911 T A SNP TMTC3 ENST00000266712 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*3354 NULL 0.532 - - - no_errors tier3 419 4 0.95 53 45 45.92 3 1 25 869586 TCGA-AB-3009 AML43 12 88004270 88004270 T C SNP - - - - - - - - - - - - - - - tier3 1256 11 0.87 468 333 41.57 0 0 NA 869586 TCGA-AB-3009 AML43 12 93846488 93846488 T C SNP NDUFA12 NM_018838.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*42859 NULL 0.003 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 12 95073406 95073406 T A SNP ELK3 NM_005230.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-68070 NULL 0 - - - no_errors tier3 1802 22 1.2 579 434 42.8 2 2 50 869586 TCGA-AB-3009 AML43 12 96881316 96881316 C T SNP - - - - - - - - - - - - - - - tier3 786 7 0.88 225 207 47.81 0 0 NA 869586 TCGA-AB-3009 AML43 12 97214456 97214456 C A SNP - - - - - - - - - - - - - - - tier2 1144 17 1.46 438 294 40.11 0 0 NA 869586 TCGA-AB-3009 AML43 12 105050145 105050145 C T SNP NUAK1 NM_014840.2 human genbank 54_36p -1 validated intronic c.240+6177 e1+6177 0.001 - - - no_errors tier3 974 11 1.12 254 238 48.37 0 0 NA 869586 TCGA-AB-3009 AML43 12 108709819 108709819 C T SNP TRPV4 NM_021625.3 human genbank 54_36p -1 reviewed intronic c.2208+769 e12+769 0.544 - - - no_errors tier3 659 4 0.6 174 126 42 0 0 NA 869586 TCGA-AB-3009 AML43 12 111596853 111596853 G T SNP MIRN1302-1 ENST00000408633 human ensembl 54_36p -1 known 3_prime_flanking_region c.*20369 NULL 0.002 - - - no_errors tier3 1519 14 0.91 399 293 42.34 0 0 NA 869586 TCGA-AB-3009 AML43 12 113491503 113491503 G T SNP LOC652191 XM_001716366.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*19454 NULL 0 - - - no_errors tier3 591 0 0 204 82 28.67 0 0 NA 869586 TCGA-AB-3009 AML43 12 116484385 116484385 T C SNP KSR2 NM_173598.4 human genbank 54_36p -1 validated intronic c.963-3624 e6-3624 0.004 - - - no_errors tier3 832 1 0.12 298 89 23 0 0 NA 869586 TCGA-AB-3009 AML43 12 124448371 124448371 C G SNP TMEM132B NM_052907.2 human genbank 54_36p 1 provisional intronic c.945-17659 e3-17659 0.331 - - - no_errors tier3 1960 12 0.61 604 392 39.36 0 0 NA 869586 TCGA-AB-3009 AML43 12 125623798 125623798 G A SNP ENSG00000209315 ENST00000386580 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*10350 NULL 0.001 - - - pseudogene tier2 1214 24 1.94 348 272 43.8 0 0 NA 869586 TCGA-AB-3009 AML43 12 126850425 126850425 C T SNP - - - - - - - - - - - - - - - tier3 825 17 2.02 397 328 45.24 0 0 NA 869586 TCGA-AB-3009 AML43 12 127808379 127808379 G A SNP SLC15A4 NM_145648.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*36315 NULL 0 - - - no_errors tier3 3138 50 1.57 872 732 45.64 0 0 NA 869586 TCGA-AB-3009 AML43 12 128619257 128619257 C G SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.969-37554 e3-37554 0 - - - no_errors tier3 298 0 0 101 84 45.41 0 0 NA 869586 TCGA-AB-3009 AML43 12 128705131 128705131 C T SNP TMEM132D NM_133448.2 human genbank 54_36p -1 validated intronic c.968+45177 e2+45177 0.004 - - - no_errors tier3 612 13 2.08 71 87 55.06 0 0 NA 869586 TCGA-AB-3009 AML43 12 130170627 130170627 C T SNP GPR133 NM_198827.3 human genbank 54_36p 1 validated intronic c.2109-718 e20-718 0 - - - no_errors tier3 662 0 0 174 188 51.93 0 0 NA 869586 TCGA-AB-3009 AML43 13 19559062 19559062 G A SNP ZMYM2 ENST00000382874 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*908 NULL 0.005 - - - no_errors tier2 239 1 0.42 69 53 43.44 9 9 50 869586 TCGA-AB-3009 AML43 13 20228213 20228216 AGTT - DEL N6AMT2 NM_174928.1 human genbank 54_36p -1 provisional intronic c.144+1378_144+1375 e1+1378 0.031:0.025:0.022:0.020 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 20365587 20365587 C T SNP XPO4 NM_022459.4 human genbank 54_36p -1 validated intronic c.69+9222 e1+9222 0.017 - - - no_errors tier3 1103 18 1.6 366 324 46.96 1 3 75 869586 TCGA-AB-3009 AML43 13 24633630 24633630 C A SNP ENSG00000220865 ENST00000407591 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44557 NULL 0.013 - - - no_coding_region:pseudogene tier3 246 4 1.6 90 61 40.4 0 0 NA 869586 TCGA-AB-3009 AML43 13 32444064 32444064 G A SNP KL NM_004795.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-44515 NULL 0.006 - - - no_errors tier3 631 5 0.79 155 106 40.61 0 0 NA 869586 TCGA-AB-3009 AML43 13 33058730 33058730 G A SNP - - - - - - - - - - - - - - - tier3 536 2 0.37 132 102 43.22 1 0 0 869586 TCGA-AB-3009 AML43 13 35194627 35194627 C A SNP NBEA NM_015678.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*51499 NULL 0.002 - - - no_errors tier2 897 11 1.21 362 291 44.56 0 0 NA 869586 TCGA-AB-3009 AML43 13 35844364 35844364 C T SNP SPG20 NM_015087.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-36397 NULL 0.003 - - - no_errors tier3 1055 26 2.4 354 272 43.45 2 0 0 869586 TCGA-AB-3009 AML43 13 36262314 36262314 G T SNP RFXAP NM_000538.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29181 NULL 0.001 - - - no_errors tier3 1083 18 1.63 225 171 43.18 0 0 NA 869586 TCGA-AB-3009 AML43 13 36637852 36637852 C T SNP ENSG00000202395 ENST00000365525 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*642 NULL 0.687 - - - no_errors tier3 1064 8 0.74 505 443 46.68 0 0 NA 869586 TCGA-AB-3009 AML43 13 38218953 38218953 T A SNP FREM2 NM_207361.4 human genbank 54_36p 1 reviewed intronic c.5264-17488 e3-17488 0.004 - - - no_errors tier3 679 8 1.16 414 323 43.83 0 0 NA 869586 TCGA-AB-3009 AML43 13 40942534 40942534 C T SNP C13orf15 NM_014059.2 human genbank 54_36p 1 reviewed intronic c.407-80 e5-80 0 - - - no_errors tier3 1479 29 1.92 498 502 50.2 5 0 0 869586 TCGA-AB-3009 AML43 13 41628881 41628881 A G SNP DGKH NM_178009.3 human genbank 54_36p 1 reviewed intronic c.622+946 e5+946 0.015 - - - no_errors tier3 158 0 0 19 25 56.82 0 1 100 869586 TCGA-AB-3009 AML43 13 41643589 41643589 C T SNP DGKH NM_178009.3 human genbank 54_36p 1 reviewed intronic c.1368-2607 e12-2607 0.001 - - - no_errors tier3 1206 12 0.98 325 250 43.48 1 1 50 869586 TCGA-AB-3009 AML43 13 44270505 44270505 C T SNP LOC144817 XR_040343.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*1134 NULL 0 - - - no_errors tier3 943 16 1.66 235 184 43.81 0 0 NA 869586 TCGA-AB-3009 AML43 13 48126290 48126290 C T SNP - - - - - - - - - - - - - - - tier3 528 2 0.38 97 48 33.1 0 0 NA 869586 TCGA-AB-3009 AML43 13 52837723 52837723 T - DEL ENSG00000220990 ENST00000408063 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*2258 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 55428867 55428867 A - DEL HNF4GP1 ENST00000403841 human ensembl 54_36p -1 known 3_prime_flanking_region c.*42489 NULL 0 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 55752973 55752973 C G SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 56434844 56434844 A T SNP - - - - - - - - - - - - - - - tier3 233 7 2.92 155 115 42.59 0 0 0 869586 TCGA-AB-3009 AML43 13 56547920 56547920 T G SNP - - - - - - - - - - - - - - - tier2 417 8 1.87 226 155 40.68 0 0 0 869586 TCGA-AB-3009 AML43 13 57189099 57189099 C T SNP PCDH17 NM_001040429.2 human genbank 54_36p 1 reviewed intronic c.2798-7648 e4-7648 0.014 - - - no_errors tier2 547 2 0.36 303 61 16.76 0 0 NA 869586 TCGA-AB-3009 AML43 13 57300537 57300537 G A SNP - - - - - - - - - - - - - - - tier3 519 2 0.38 99 62 38.51 0 0 NA 869586 TCGA-AB-3009 AML43 13 58919452 58919452 A T SNP - - - - - - - - - - - - - - - tier2 748 2 0.27 205 57 21.76 0 0 NA 869586 TCGA-AB-3009 AML43 13 61836083 61836083 C T SNP LOC100133193 XR_039110.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*35553 NULL 0 - - - pseudogene tier3 283 0 0 98 64 39.26 0 0 NA 869586 TCGA-AB-3009 AML43 13 61836206 61836206 A T SNP LOC100133193 XR_039110.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*35676 NULL 0.083 - - - pseudogene tier3 149 0 0 9 10 52.63 0 0 NA 869586 TCGA-AB-3009 AML43 13 62067843 62067843 C T SNP - - - - - - - - - - - - - - - tier3 35 0 0 5 2 28.57 0 0 NA 869586 TCGA-AB-3009 AML43 13 62699194 62699194 C T SNP LOC729287 XM_001132996.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-64 NULL 0.009 - - - no_errors tier3 116 2 1.69 28 21 42.86 0 0 NA 869586 TCGA-AB-3009 AML43 13 64190847 64190847 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 65537506 65537506 A G SNP - - - - - - - - - - - - - - - tier3 214 3 1.38 25 13 34.21 0 0 NA 869586 TCGA-AB-3009 AML43 13 65882790 65882790 G A SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed intronic c.3341-105629 e4-105629 0.03 - - - no_errors tier3 1442 11 0.76 328 348 51.48 0 0 NA 869586 TCGA-AB-3009 AML43 13 66521030 66521030 G T SNP PCDH9 NM_203487.4 human genbank 54_36p -1 reviewed intronic c.3037-145292 e2-145292 0 - - - no_errors tier2 530 5 0.93 260 184 41.44 0 0 NA 869586 TCGA-AB-3009 AML43 13 67217152 67217152 G T SNP - - - - - - - - - - - - - - - tier3 614 2 0.32 225 132 36.97 0 0 NA 869586 TCGA-AB-3009 AML43 13 67769515 67769515 C A SNP ENSG00000217105 ENST00000405099 human ensembl 54_36p -1 known 5_prime_flanking_region c.-6102 NULL 0.009 - - - no_coding_region:pseudogene tier2 794 8 1 177 126 41.45 0 0 NA 869586 TCGA-AB-3009 AML43 13 68145004 68145004 C T SNP ENSG00000218340 ENST00000402052 human ensembl 54_36p 1 known 3_prime_flanking_region c.*38385 NULL 0.003 - - - no_coding_region:pseudogene tier3 220 1 0.45 92 67 42.14 0 0 NA 869586 TCGA-AB-3009 AML43 13 69993817 69993817 A T SNP - - - - - - - - - - - - - - - tier3 239 4 1.65 76 72 48.65 0 0 NA 869586 TCGA-AB-3009 AML43 13 80692580 80692580 G A SNP ENSG00000222486 ENST00000410554 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-45303 NULL 0.001 - - - no_errors tier2 760 17 2.19 192 181 48.53 0 0 NA 869586 TCGA-AB-3009 AML43 13 81410702 81410702 T C SNP - - - - - - - - - - - - - - - tier3 1110 12 1.07 402 328 44.87 0 0 NA 869586 TCGA-AB-3009 AML43 13 81853624 81853624 T A SNP - - - - - - - - - - - - - - - tier3 273 10 3.53 32 37 53.62 0 0 NA 869586 TCGA-AB-3009 AML43 13 89323401 89323401 C G SNP ENSG00000184837 ENST00000330770 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-39639 NULL 0.057 - - - no_coding_region:pseudogene tier2 440 4 0.9 130 122 48.41 0 0 NA 869586 TCGA-AB-3009 AML43 13 89699123 89699123 G A SNP MIRN622 ENST00000385123 human ensembl 54_36p 1 known 3_prime_flanking_region c.*17591 NULL 0 - - - no_errors tier3 1126 21 1.83 305 185 37.76 0 0 NA 869586 TCGA-AB-3009 AML43 13 90202612 90202612 C A SNP ENSG00000209120 ENST00000386385 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*29413 NULL 0 - - - pseudogene tier3 948 7 0.73 230 118 33.91 0 0 NA 869586 TCGA-AB-3009 AML43 13 91834507 91834507 C T SNP GPC5 NM_004466.4 human genbank 54_36p 1 reviewed intronic c.1561+239264 e7+239264 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 92652556 92652556 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-25155 NULL 0 - - - no_errors tier3 982 11 1.11 332 279 45.66 0 0 NA 869586 TCGA-AB-3009 AML43 13 93181483 93181483 C A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.320-98925 e3-98925 0 - - - no_errors tier3 1034 7 0.67 459 363 44.16 0 0 NA 869586 TCGA-AB-3009 AML43 13 94151983 94151983 C T SNP LOC100129538 XM_001714213.1 human genbank 54_36p -1 model intronic c.166+1718 e1+1718 0.001 - - - no_errors tier3 1119 7 0.62 398 344 46.3 0 0 NA 869586 TCGA-AB-3009 AML43 13 100115086 100115086 T C SNP TMTC4 NM_032813.1 human genbank 54_36p -1 validated intronic c.220-495 e3-495 0 - - - no_errors tier2 1043 6 0.57 547 520 48.73 6 1 14.29 869586 TCGA-AB-3009 AML43 13 101420364 101420364 T G SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.209-94717 e2-94717 0.015 - - - no_errors tier3 1286 8 0.62 371 282 43.19 0 0 NA 869586 TCGA-AB-3009 AML43 13 101449493 101449493 A T SNP FGF14 NM_175929.3 human genbank 54_36p -1 reviewed intronic c.209-123846 e2-123846 0 - - - no_errors tier3 321 3 0.93 79 47 37.3 0 0 NA 869586 TCGA-AB-3009 AML43 13 102829803 102829803 C T SNP - - - - - - - - - - - - - - - tier2 582 5 0.85 58 40 40.82 0 0 NA 869586 TCGA-AB-3009 AML43 13 103499293 103499296 TCTT - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 105717434 105717434 C T SNP - - - - - - - - - - - - - - - tier3 1329 32 2.35 489 447 47.71 0 0 NA 869586 TCGA-AB-3009 AML43 13 108073578 108073578 G A SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.1+26990 e0+26990 0 - - - no_errors tier3 1138 19 1.64 271 214 44.12 0 0 NA 869586 TCGA-AB-3009 AML43 13 111779588 111779588 G A SNP SOX1 NM_005986.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*8439 NULL 0 - - - no_errors tier3 421 3 0.71 92 86 48.31 0 0 NA 869586 TCGA-AB-3009 AML43 13 112326383 112326383 C T SNP TUBGCP3 NM_006322.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-36088 NULL 0.017 - - - no_errors tier2 559 5 0.88 230 183 44.31 0 0 NA 869586 TCGA-AB-3009 AML43 13 112390052 112390053 - TC INS ATP11A NM_032189.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2680 NULL 0.006:0.005 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 13 113159865 113159865 C T SNP DCUN1D2 NM_001014283.1 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*480 NULL 0 - - - no_errors tier3 502 9 1.76 142 83 36.89 27 26 49.06 869586 TCGA-AB-3009 AML43 14 23103149 23103149 C T SNP AP1G2 NM_003917.2 human genbank 54_36p -1 reviewed missense c.1037 p.R346Q 1 "HMMPfam_Adaptin_N,superfamily_ARM-type_fold" "HMMPfam_Adaptin_N,HMMPfam_Alpha_adaptinC2,HMMSmart_Alpha_adaptinC2,superfamily_Clath_adapt,superfamily_ARM-type_fold" - no_errors tier1 2568 35 1.34 670 596 47.08 66 74 52.86 869586 TCGA-AB-3009 AML43 14 23754911 23754911 A T SNP MDP-1 NM_138476.2 human genbank 54_36p -1 provisional intronic c.37+54 e1+54 0.081 - - - no_errors tier2 818 1 0.12 162 157 49.22 0 1 100 869586 TCGA-AB-3009 AML43 14 24483450 24483450 C T SNP STXBP6 NM_014178.6 human genbank 54_36p -1 provisional intronic c.154+30261 e1+30261 0 - - - no_errors tier3 443 11 2.42 149 129 46.4 0 0 NA 869586 TCGA-AB-3009 AML43 14 25426007 25426007 G T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 14 26041535 26041535 A T SNP NOVA1 NM_002515.2 human genbank 54_36p -1 reviewed intronic c.281-22346 e3-22346 0.007 - - - no_errors tier3 296 4 1.33 46 54 54 0 0 NA 869586 TCGA-AB-3009 AML43 14 26444248 26444248 G A SNP ENSG00000222899 ENST00000410967 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-22451 NULL 0 - - - no_errors tier2 357 1 0.28 66 92 58.23 0 0 NA 869586 TCGA-AB-3009 AML43 14 27399693 27399693 T C SNP - - - - - - - - - - - - - - - tier3 463 4 0.86 160 150 48.23 0 0 NA 869586 TCGA-AB-3009 AML43 14 31466328 31466328 C T SNP - - - - - - - - - - - - - - - tier3 1250 18 1.42 523 412 44.06 1 0 0 869586 TCGA-AB-3009 AML43 14 35171105 35171105 G T SNP GARNL1 NM_194301.1 human genbank 54_36p -1 provisional intronic c.4477+2426 e32+2426 0.032 - - - no_errors tier3 123 2 1.6 29 11 27.5 0 0 NA 869586 TCGA-AB-3009 AML43 14 41798835 41798835 T - DEL ENSG00000222084 ENST00000410152 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-40869 NULL 0.002 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 14 41858480 41858480 T A SNP ENSG00000222084 ENST00000410152 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*18665 NULL 0.007 - - - no_errors tier3 232 1 0.43 25 24 48.98 0 0 NA 869586 TCGA-AB-3009 AML43 14 42164751 42164751 C A SNP - - - - - - - - - - - - - - - tier3 446 6 1.33 251 217 46.37 0 0 NA 869586 TCGA-AB-3009 AML43 14 43834668 43834668 G C SNP - - - - - - - - - - - - - - - tier3 1032 9 0.86 248 201 44.77 0 0 NA 869586 TCGA-AB-3009 AML43 14 46259586 46259586 C T SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 14 46505564 46505564 T G SNP MDGA2 NM_182830.1 human genbank 54_36p -1 validated intronic c.926-8968 e5-8968 0.024 - - - no_errors tier3 246 1 0.4 26 26 50 0 0 NA 869586 TCGA-AB-3009 AML43 14 47724853 47724853 A T SNP - - - - - - - - - - - - - - - tier3 257 2 0.77 71 49 40.83 0 0 NA 869586 TCGA-AB-3009 AML43 14 50821980 50821980 C A SNP LOC283553 XR_017924.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-47887 NULL 0.002 - - - no_errors tier3 1324 5 0.38 457 414 47.53 0 0 0 869586 TCGA-AB-3009 AML43 14 56040270 56040270 G A SNP - - - - - - - - - - - - - - - tier2 897 3 0.33 180 59 24.69 0 0 NA 869586 TCGA-AB-3009 AML43 14 56054992 56054992 G T SNP - - - - - - - - - - - - - - - tier3 703 15 2.09 300 303 50.25 0 0 NA 869586 TCGA-AB-3009 AML43 14 56849033 56849033 A - DEL EXOC5 NM_006544.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-43914 NULL 0.007 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 14 56931759 56931759 T C SNP NAT12 NM_001011713.2 human genbank 54_36p 1 validated intronic c.772-1464 e2-1464 0.984 - - - no_errors tier3 197 3 1.5 59 35 37.23 1 0 0 869586 TCGA-AB-3009 AML43 14 57621356 57621356 G T SNP C14orf37 NM_001001872.2 human genbank 54_36p -1 predicted intronic c.2089+11839 e4+11839 0.001 - - - no_errors tier3 1046 6 0.57 347 219 38.69 0 0 NA 869586 TCGA-AB-3009 AML43 14 58145492 58145492 G A SNP DACT1 NM_016651.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-29182 NULL 0 - - - no_errors tier2 654 15 2.24 161 152 48.56 0 0 NA 869586 TCGA-AB-3009 AML43 14 60763542 60763542 G A SNP - - - - - - - - - - - - - - - tier3 953 10 1.04 325 328 50.23 0 0 NA 869586 TCGA-AB-3009 AML43 14 61210471 61210472 - AC INS HIF1A NM_001530.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-21805 NULL 0.009:0.023 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 14 61307948 61307949 - T INS SNAPC1 NM_003082.3 human genbank 54_36p 1 validated intronic c.534+2737_534+2736 e4+2737 0.051:0.071 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 14 62826386 62826386 T - DEL RHOJ NM_020663.3 human genbank 54_36p 1 provisional intronic c.499-963 e5-963 0.09 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 14 64839231 64839231 G A SNP RPL21P7 ENST00000398929 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35061 NULL 0.998 - - - no_start_codon tier2 1224 7 0.57 243 200 45.15 0 0 NA 869586 TCGA-AB-3009 AML43 14 66539860 66539860 A C SNP GPHN NM_020806.1 human genbank 54_36p 1 reviewed intronic c.964-20243 e10-20243 0.002 - - - no_errors tier3 366 0 0 185 65 26 0 0 NA 869586 TCGA-AB-3009 AML43 14 66927867 66927867 C T SNP PLEK2 NM_016445.1 human genbank 54_36p -1 provisional intronic c.772-651 e7-651 0.001 - - - no_errors tier2 641 5 0.77 170 143 45.4 0 0 NA 869586 TCGA-AB-3009 AML43 14 68436121 68436121 C A SNP ACTN1 NM_001102.3 human genbank 54_36p -1 reviewed intronic c.762+2826 e8+2826 0.148 - - - no_errors tier3 1351 26 1.89 301 258 46.07 1 1 50 869586 TCGA-AB-3009 AML43 14 69100487 69100487 C T SNP KIAA0247 NM_014734.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-94576 NULL 0 - - - no_errors tier3 613 7 1.13 202 149 42.45 0 0 NA 869586 TCGA-AB-3009 AML43 14 76800837 76800837 G A SNP MIRN1260 ENST00000408827 human ensembl 54_36p 1 known 5_prime_flanking_region c.-1477 NULL 0 - - - no_errors tier3 1742 11 0.63 433 300 40.93 0 0 NA 869586 TCGA-AB-3009 AML43 14 80562772 80562772 A T SNP TSHR NM_000369.2 human genbank 54_36p 1 reviewed intronic c.171-35473 e2-35473 0.001 - - - no_errors tier3 407 0 0 98 47 32.41 0 0 NA 869586 TCGA-AB-3009 AML43 14 84518986 84518986 A T SNP - - - - - - - - - - - - - - - tier3 420 6 1.41 190 140 42.42 0 0 NA 869586 TCGA-AB-3009 AML43 14 90435550 90435550 T C SNP RPS6KA5 NM_004755.2 human genbank 54_36p -1 validated intronic c.1380-31 e12-31 0 - - - no_errors tier3 662 2 0.3 361 88 19.6 4 2 33.33 869586 TCGA-AB-3009 AML43 14 94117856 94117856 G A SNP SERPINA5 NM_000624.4 human genbank 54_36p 1 validated intronic c.1+56 e0+56 0.001 - - - no_errors tier3 1183 12 1 280 234 45.53 0 0 NA 869586 TCGA-AB-3009 AML43 14 94135231 94135231 G A SNP SERPINA3 NM_001085.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15301 NULL 0 - - - no_errors tier2 954 29 2.95 228 214 48.42 0 0 NA 869586 TCGA-AB-3009 AML43 14 95469007 95469007 G A SNP LOC730125 XM_001134301.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*10132 NULL 0.024 - - - no_errors tier3 611 6 0.97 78 90 53.57 0 0 NA 869586 TCGA-AB-3009 AML43 14 99829178 99829178 C T SNP SLC25A29 NM_001039355.1 human genbank 54_36p -1 validated intronic c.163-56 e4-56 0.008 - - - no_errors tier2 130 1 0.76 92 65 41.4 1 0 0 869586 TCGA-AB-3009 AML43 14 101930188 101930188 T C SNP TECPR2 NM_014844.2 human genbank 54_36p 1 validated intronic c.220-13240 e2-13240 0.002 - - - no_errors tier3 1586 15 0.94 312 279 47.21 0 0 0 869586 TCGA-AB-3009 AML43 15 22289408 22289408 C T SNP - - - - - - - - - - - - - - - tier3 909 13 1.4 288 256 47.06 0 0 NA 869586 TCGA-AB-3009 AML43 15 24601542 24601543 - T INS GABRB3 ENST00000383015 human ensembl 54_36p -1 known intronic c.248+11064_248+11063 e2+11064 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 15 25745853 25745853 G A SNP OCA2 NM_000275.2 human genbank 54_36p -1 reviewed intronic c.2432+17847 e22+17847 0.005 - - - no_errors tier3 926 16 1.69 489 391 44.43 0 0 NA 869586 TCGA-AB-3009 AML43 15 30165141 30165141 G A SNP CHRNA7 NM_000746.3 human genbank 54_36p 1 reviewed intronic c.196-15657 e3-15657 0 - - - no_errors tier3 351 7 1.95 140 90 39.13 0 0 NA 869586 TCGA-AB-3009 AML43 15 35204470 35204470 A G SNP MEIS2 NM_170675.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-25511 NULL 0.981 - - - no_errors tier2 437 5 1.13 89 58 39.46 0 0 NA 869586 TCGA-AB-3009 AML43 15 36231034 36231034 G A SNP - - - - - - - - - - - - - - - tier3 1012 10 0.98 377 269 41.64 0 0 NA 869586 TCGA-AB-3009 AML43 15 36318140 36318140 C T SNP SPRED1 NM_152594.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-14539 NULL 0.001 - - - no_errors tier3 1244 9 0.72 276 240 46.51 0 0 NA 869586 TCGA-AB-3009 AML43 15 38135540 38135541 - TCGGA INS ENSG00000206058 ENST00000382724 human ensembl 54_36p 1 known intronic c.1-9174_9173 e1-9173 0.002:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 15 39384117 39384117 C T SNP NUSAP1 NM_018454.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28331 NULL 0.006 - - - no_errors tier3 1096 5 0.45 611 162 20.93 65 17 20.73 869586 TCGA-AB-3009 AML43 15 42095339 42095339 G A SNP FRMD5 NM_032892.3 human genbank 54_36p -1 validated intronic c.103-91540 e2-91540 0 - - - no_errors tier3 1156 5 0.43 240 219 47.71 0 0 NA 869586 TCGA-AB-3009 AML43 15 43790262 43790262 G A SNP SQRDL NM_021199.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*19742 NULL 0 - - - no_errors tier3 504 4 0.79 360 259 41.77 0 0 NA 869586 TCGA-AB-3009 AML43 15 52741139 52741139 G A SNP UNC13C NM_001080534.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*34536 NULL 0.084 - - - no_errors tier3 699 6 0.85 299 238 44.32 0 0 NA 869586 TCGA-AB-3009 AML43 15 55623697 55623697 C A SNP CGNL1 NM_032866.3 human genbank 54_36p 1 validated intronic c.3376-266 e15-266 0 - - - no_errors tier3 789 14 1.74 211 195 48.03 0 0 NA 869586 TCGA-AB-3009 AML43 15 61187432 61187432 C A SNP LACTB NM_032857.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13692 NULL 0.96 - - - no_errors tier3 1513 11 0.72 270 222 45.12 0 0 NA 869586 TCGA-AB-3009 AML43 15 64063387 64063387 G A SNP MEGF11 NM_032445.2 human genbank 54_36p -1 validated intronic c.170-1507 e3-1507 0.076 - - - no_errors tier3 1054 10 0.94 371 282 43.12 0 0 NA 869586 TCGA-AB-3009 AML43 15 65829689 65829689 G T SNP MAP2K5 NM_145160.2 human genbank 54_36p 1 reviewed intronic c.1134+1696 e19+1696 0.006 - - - no_errors tier3 1058 18 1.67 334 252 43 4 2 33.33 869586 TCGA-AB-3009 AML43 15 69291325 69291325 G A SNP THSD4 NM_024817.2 human genbank 54_36p 1 provisional intronic c.100-3103 e3-3103 0.034 - - - no_errors tier3 541 2 0.37 247 167 40.34 0 0 NA 869586 TCGA-AB-3009 AML43 15 77461201 77461201 G A SNP - - - - - - - - - - - - - - - tier3 949 11 1.15 550 408 42.59 1 2 66.67 869586 TCGA-AB-3009 AML43 15 81157623 81157623 C T SNP AP3B2 ENST00000261722 human ensembl 54_36p -1 known intronic c.114-2364 e2-2364 1 - - - no_errors tier2 1056 10 0.94 246 250 50.4 22 0 0 869586 TCGA-AB-3009 AML43 15 84614905 84614905 G A SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.1849+603 e12+603 0.003 - - - no_errors tier3 971 7 0.72 315 268 45.97 0 0 NA 869586 TCGA-AB-3009 AML43 15 84729981 84729981 G T SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.2237-11620 e16-11620 0.027 - - - no_errors tier3 307 2 0.65 199 142 41.64 0 0 NA 869586 TCGA-AB-3009 AML43 15 85034844 85034844 C G SNP AGBL1 NM_152336.2 human genbank 54_36p 1 validated intronic c.3083+16173 e21+16173 0 - - - no_errors tier3 1008 8 0.79 459 435 48.6 0 0 NA 869586 TCGA-AB-3009 AML43 15 85796054 85796054 C T SNP ENSG00000207150 ENST00000384421 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*22364 NULL 0 - - - no_errors tier3 1462 12 0.81 618 482 43.78 0 0 NA 869586 TCGA-AB-3009 AML43 15 91229444 91229444 A C SNP CHD2 NM_001271.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-16028 NULL 0.001 - - - no_errors tier3 183 6 3.17 30 45 60 14 29 67.44 869586 TCGA-AB-3009 AML43 15 93352910 93352911 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 15 93668521 93668521 G A SNP LOC400456 XM_001128315.2 human genbank 54_36p -1 model intronic c.370+2542 e2+2542 1 - - - no_errors tier2 575 1 0.17 193 137 41.52 0 0 NA 869586 TCGA-AB-3009 AML43 15 94242177 94242177 C T SNP - - - - - - - - - - - - - - - tier3 1043 11 1.04 427 322 42.99 0 0 NA 869586 TCGA-AB-3009 AML43 15 95463316 95463316 A G SNP ENSG00000215948 ENST00000401129 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-27730 NULL 0.006 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 15 95607153 95607153 C T SNP - - - - - - - - - - - - - - - tier3 663 11 1.63 285 265 48.09 0 0 NA 869586 TCGA-AB-3009 AML43 15 97094563 97094563 C T SNP IGF1R NM_000875.3 human genbank 54_36p 1 reviewed intronic c.640+25704 e2+25704 0.012 - - - no_errors tier2 793 8 1 197 185 48.43 1 0 0 869586 TCGA-AB-3009 AML43 15 98695666 98695666 C A SNP ADAMTS17 NM_139057.2 human genbank 54_36p -1 reviewed intronic c.450+3101 e2+3101 0.096 - - - no_errors tier3 649 7 1.07 242 228 48.51 1 0 0 869586 TCGA-AB-3009 AML43 16 1056286 1056286 T A SNP ENSG00000181791 ENST00000314015 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-1056286 NULL 0.03 - - - no_coding_region:pseudogene tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 16 4275072 4275072 T C SNP GLIS2 NM_032575.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-47211 NULL 0.004 - - - no_errors tier3 2355 35 1.46 30 334 91.76 0 0 NA 869586 TCGA-AB-3009 AML43 16 6727010 6727010 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+82358 e0+82358 0 - - - no_errors tier3 1169 40 3.31 45 677 93.77 0 0 NA 869586 TCGA-AB-3009 AML43 16 7071479 7071479 G T SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.27+29379 e1+29379 0.885 - - - no_errors tier2 561 6 1.06 37 241 86.69 0 0 NA 869586 TCGA-AB-3009 AML43 16 7907101 7907101 G A SNP ENSG00000222109 ENST00000410177 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-17667 NULL 0.001 - - - no_errors tier3 561 6 1.06 34 470 93.25 0 0 NA 869586 TCGA-AB-3009 AML43 16 10162241 10162241 C T SNP GRIN2A NM_000833.3 human genbank 54_36p -1 reviewed intronic c.414+19115 e1+19115 0 - - - no_errors tier3 831 13 1.54 34 326 90.56 0 0 NA 869586 TCGA-AB-3009 AML43 16 13958122 13958124 TAG - DEL ERCC4 NM_005236.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*8417 NULL 0.000:0.001:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 16 25864554 25864554 C T SNP HS3ST4 ENST00000331351 human ensembl 54_36p 1 known intronic c.735-189880 e2-189880 0 - - - no_errors tier3 1985 49 2.4 67 667 90.75 0 0 NA 869586 TCGA-AB-3009 AML43 16 27978208 27978208 C T SNP GSG1L NM_001109763.1 human genbank 54_36p -1 validated intronic c.349+3690 e1+3690 0.023 - - - no_errors tier3 593 11 1.82 38 225 85.55 0 0 NA 869586 TCGA-AB-3009 AML43 16 34278798 34278798 C G SNP LOC100131688 XM_001718246.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-41250 NULL 0 - - - no_errors tier3 600 7 1.15 174 128 42.38 0 0 NA 869586 TCGA-AB-3009 AML43 16 34581303 34581303 C A SNP LOC100130041 XR_037947.1 human genbank 54_36p 1 model rna NULL NULL 1 - - - pseudogene tier1 939 6 0.63 486 102 17.35 NA 869586 TCGA-AB-3009 AML43 16 34841397 34841397 T G SNP FLJ26245 XM_001718343.1 human genbank 54_36p 1 model intronic c.287+688 e4+688 0.005 - - - no_errors tier3 2942 25 0.84 1455 1141 43.9 0 0 NA 869586 TCGA-AB-3009 AML43 16 51059044 51059044 G T SNP TOX3 NM_001080430.1 human genbank 54_36p -1 provisional intronic c.153+878 e2+878 0.993 - - - no_errors tier3 494 7 1.4 242 174 41.83 0 0 NA 869586 TCGA-AB-3009 AML43 16 51123481 51123481 C T SNP TOX3 NM_001080430.1 human genbank 54_36p -1 provisional intronic c.87+14569 e1+14569 0.001 - - - no_errors tier3 722 4 0.55 252 250 49.8 0 0 NA 869586 TCGA-AB-3009 AML43 16 52994187 52994187 G A SNP - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 16 53962618 53962618 G A SNP IRX6 NM_024335.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*40900 NULL 0.036 - - - no_errors tier3 913 10 1.08 336 293 46.58 0 0 NA 869586 TCGA-AB-3009 AML43 16 57529049 57529049 G A SNP - - - - - - - - - - - - - - - tier3 897 20 2.18 398 240 37.62 0 0 NA 869586 TCGA-AB-3009 AML43 16 60412783 60412783 C G SNP CDH8 NM_001796.2 human genbank 54_36p -1 reviewed intronic c.836-265 e5-265 0.988 - - - no_errors tier3 1176 12 1.01 357 301 45.68 0 0 NA 869586 TCGA-AB-3009 AML43 16 60907206 60907206 G A SNP ENSG00000218786 ENST00000405014 human ensembl 54_36p 1 known 5_prime_flanking_region c.-41570 NULL 0 - - - no_coding_region:pseudogene tier2 536 6 1.1 235 186 44.18 0 0 NA 869586 TCGA-AB-3009 AML43 16 61642452 61642452 G T SNP - - - - - - - - - - - - - - - tier2 1398 13 0.92 528 408 43.59 0 0 NA 869586 TCGA-AB-3009 AML43 16 62479403 62479403 G C SNP - - - - - - - - - - - - - - - tier3 829 6 0.72 158 145 47.54 0 0 NA 869586 TCGA-AB-3009 AML43 16 62712754 62712754 T A SNP - - - - - - - - - - - - - - - tier3 984 5 0.51 321 305 48.72 0 0 NA 869586 TCGA-AB-3009 AML43 16 62829263 62829263 A T SNP LOC729217 XR_015483.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*22462 NULL 0 - - - pseudogene tier3 1389 10 0.71 508 133 20.75 0 0 NA 869586 TCGA-AB-3009 AML43 16 63209502 63209502 G T SNP - - - - - - - - - - - - - - - tier2 746 4 0.53 392 266 40.43 0 0 NA 869586 TCGA-AB-3009 AML43 16 65770615 65770615 C T SNP KIAA0895L NM_001040715.1 human genbank 54_36p -1 validated intronic c.847+219 e3+219 0.003 - - - no_errors tier3 770 9 1.15 276 217 44.02 6 3 33.33 869586 TCGA-AB-3009 AML43 16 66217970 66217970 C T SNP CTCF NM_006565.2 human genbank 54_36p 1 reviewed nonsense c.1369 p.R457* 1 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 1876 12 0.64 242 190 43.88 68 15 18.07 869586 TCGA-AB-3009 AML43 16 72877051 72877051 C T SNP PSMD7 NM_002811.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11263 NULL 0 - - - no_errors tier3 1511 18 1.18 277 215 43.7 0 2 100 869586 TCGA-AB-3009 AML43 16 74089247 74089247 G T SNP CHST6 NM_021615.4 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-18020 NULL 0.011 - - - no_errors tier3 480 3 0.62 204 165 44.72 0 0 NA 869586 TCGA-AB-3009 AML43 16 76733310 76733310 G A SNP WWOX NM_016373.1 human genbank 54_36p 1 reviewed intronic c.410-22271 e5-22271 0.999 - - - no_errors tier2 240 5 2.03 52 69 57.02 0 1 100 869586 TCGA-AB-3009 AML43 16 78153399 78153399 C A SNP MAF NM_005360.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*32459 NULL 0 - - - no_errors tier3 1659 11 0.66 514 378 42.38 0 0 NA 869586 TCGA-AB-3009 AML43 16 78455295 78455296 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 16 79588713 79588713 A G SNP C16orf61 NM_020188.3 human genbank 54_36p -1 validated intronic c.1-178 e1-178 0 - - - no_errors tier3 NA NA NA NA NA NA 11 0 0 869586 TCGA-AB-3009 AML43 16 82546470 82546470 G A SNP OSGIN1 NM_013370.3 human genbank 54_36p 1 validated intronic c.218-2276 e3-2276 0.007 - - - no_errors tier3 104 0 0 31 30 49.18 0 0 NA 869586 TCGA-AB-3009 AML43 16 84885805 84885805 C T SNP ENSG00000199949 ENST00000363079 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19175 NULL 1 - - - no_errors tier2 1400 10 0.71 394 310 44.03 0 0 NA 869586 TCGA-AB-3009 AML43 16 85959576 85959576 G A SNP FBXO31 NM_024735.3 human genbank 54_36p -1 validated intronic c.341-8103 e2-8103 0.065 - - - no_errors tier2 1309 12 0.91 389 288 42.54 1 0 0 869586 TCGA-AB-3009 AML43 17 5746607 5746607 C T SNP - - - - - - - - - - - - - - - tier3 1317 8 0.6 542 509 48.43 0 0 NA 869586 TCGA-AB-3009 AML43 17 13252186 13252187 - C INS - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 17 14981214 14981214 T G SNP - - - - - - - - - - - - - - - tier2 845 10 1.17 461 82 15.05 0 0 NA 869586 TCGA-AB-3009 AML43 17 16285101 16285101 C T SNP C17orf45 ENST00000347812 human ensembl 54_36p 1 known intronic c.387-12 e4-12 0 - - - no_errors tier3 783 16 2 143 110 43.48 3 6 66.67 869586 TCGA-AB-3009 AML43 17 17227878 17227878 G A SNP LOC100130734 XM_001716348.1 human genbank 54_36p 1 model missense c.1078 p.D360N 0.028 NULL NULL - no_errors tier1 NA NA NA NA NA NA 1231 0 869586 TCGA-AB-3009 AML43 17 18173889 18173889 G A SNP SHMT1 NM_004169.3 human genbank 54_36p -1 reviewed intronic c.1172-462 e10-462 0.004 - - - no_errors tier3 678 7 1.02 188 199 51.42 4 1 20 869586 TCGA-AB-3009 AML43 17 18225292 18225292 C T SNP EVPLL ENST00000399134 human ensembl 54_36p 1 known intronic c.64-114 e2-114 0.924 - - - no_errors tier3 471 5 1.05 194 175 47.43 0 0 NA 869586 TCGA-AB-3009 AML43 17 19562643 19562643 C T SNP SLC47A2 NM_152908.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-2183 NULL 0.006 - - - no_errors tier3 530 1 0.19 86 98 52.97 0 0 NA 869586 TCGA-AB-3009 AML43 17 20787873 20787873 C T SNP CCDC144NL NM_001004306.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-47948 NULL 0 - - - no_errors tier3 721 13 1.77 222 152 40.64 0 0 NA 869586 TCGA-AB-3009 AML43 17 21861423 21861423 G T SNP LOC100131001 XM_001723720.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-26155 NULL 0.001 - - - no_errors tier3 309 5 1.58 89 81 47.65 0 0 NA 869586 TCGA-AB-3009 AML43 17 25062077 25062077 C T SNP SSH2 NM_033389.2 human genbank 54_36p -1 reviewed intronic c.108-7871 e3-7871 0 - - - no_errors tier3 1479 30 1.98 423 314 42.43 4 8 66.67 869586 TCGA-AB-3009 AML43 17 26587107 26587107 C T SNP NF1 NM_001042492.2 human genbank 54_36p 1 reviewed nonsense c.3916 p.R1306* 1 "HMMPfam_RasGAP,HMMSmart_SM00323,superfamily_GTPase activation domain GAP" "HMMSmart_SM00516,HMMPfam_RasGAP,HMMSmart_SM00323,PatternScan_RAS_GTPASE_ACTIV_1,superfamily_GTPase activation domain GAP" - no_errors tier1 769 5 0.64 43 229 84.19 1 16 94.12 869586 TCGA-AB-3009 AML43 17 27317311 27317311 G A SNP SUZ12 NM_015355.2 human genbank 54_36p 1 reviewed missense c.488 p.G163D 1 NULL "PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,HMMPfam_VEFS-Box" - no_errors tier1 192 3 1.54 14 100 4 54 93.1 869586 TCGA-AB-3009 AML43 17 29638693 29638693 A T SNP CCL11 NM_002986.2 human genbank 54_36p 1 reviewed intronic c.189-24 e3-24 0 - - - no_errors tier3 459 8 1.71 303 237 43.89 0 0 NA 869586 TCGA-AB-3009 AML43 17 35203222 35203222 G A SNP IKZF3 NM_012481.3 human genbank 54_36p -1 reviewed intronic c.164-510 e4-510 0.007 - - - no_errors tier3 1559 14 0.89 577 445 43.5 0 0 0 869586 TCGA-AB-3009 AML43 17 35336721 35336721 C G SNP ORMDL3 NM_139280.1 human genbank 54_36p -1 provisional intronic c.1+542 e0+542 0.001 - - - no_errors tier2 621 8 1.27 156 111 41.57 0 0 0 869586 TCGA-AB-3009 AML43 17 36960500 36960500 T A SNP KRT13 NM_153490.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-45172 NULL 0.001 - - - no_errors tier3 1836 13 0.7 348 341 49.49 0 0 NA 869586 TCGA-AB-3009 AML43 17 38492196 38492196 G C SNP BRCA1 NM_007294.2 human genbank 54_36p -1 reviewed intronic c.4186-4078 e11-4078 0.966 - - - no_errors tier3 1038 9 0.86 266 233 46.69 1 0 0 869586 TCGA-AB-3009 AML43 17 41464770 41464770 C T SNP KIAA1267 NM_015443.2 human genbank 54_36p -1 validated silent c.3237 p.A1079 0.003 NULL NULL - no_errors tier1 1127 12 1.05 296 296 49.83 25 36 59.02 869586 TCGA-AB-3009 AML43 17 44156725 44156725 G T SNP LOC100132903 XM_001726558.1 human genbank 54_36p 1 model missense c.104 p.G35V 0 NULL NULL - no_errors tier1 608 2 0.33 151 135 47.2 NA 869586 TCGA-AB-3009 AML43 17 45903937 45903937 C T SNP ACSF2 NM_025149.4 human genbank 54_36p 1 validated intronic c.1323+442 e11+442 0.001 - - - no_errors tier3 1204 12 0.98 385 312 44.7 4 1 20 869586 TCGA-AB-3009 AML43 17 52504691 52504691 C T SNP AKAP1 NM_003488.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33134 NULL 0.001 - - - no_errors tier3 643 3 0.46 302 52 14.69 0 0 NA 869586 TCGA-AB-3009 AML43 17 53937533 53937534 - GGTCAG INS MTMR4 NM_004687.4 human genbank 54_36p -1 validated intronic c.1104-200_1104-199 e11-199 0.000:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 17 55365250 55365250 A T SNP RPS6KB1 NM_003161.2 human genbank 54_36p 1 reviewed intronic c.689-1063 e8-1063 0.002 - - - no_errors tier3 883 8 0.9 207 168 44.68 1 1 50 869586 TCGA-AB-3009 AML43 17 56755423 56755423 T C SNP BCAS3 NM_001099432.1 human genbank 54_36p 1 validated intronic c.2471-45047 e23-45047 0.441 - - - no_errors tier3 801 1 0.12 107 85 44.27 2 2 50 869586 TCGA-AB-3009 AML43 17 65996414 65996414 T A SNP - - - - - - - - - - - - - - - tier3 428 1 0.23 94 63 39.87 0 0 NA 869586 TCGA-AB-3009 AML43 17 66124108 66124108 G T SNP - - - - - - - - - - - - - - - tier3 1081 10 0.92 255 200 43.96 0 0 NA 869586 TCGA-AB-3009 AML43 17 67097763 67097763 A C SNP LOC124685 XR_040247.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 1341 14 1.03 438 379 46.39 0 0 NA 869586 TCGA-AB-3009 AML43 17 67400601 67400601 C T SNP - - - - - - - - - - - - - - - tier2 1289 14 1.07 460 371 44.59 0 0 NA 869586 TCGA-AB-3009 AML43 17 67884705 67884705 A - DEL ENSG00000211264 ENST00000388529 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*47851 NULL 0.289 - - - pseudogene tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 17 72195638 72195638 C T SNP MXRA7 NM_001008528.1 human genbank 54_36p -1 validated intronic c.406+152 e2+152 0.001 - - - no_errors tier3 382 6 1.54 133 115 46.37 0 0 NA 869586 TCGA-AB-3009 AML43 17 72401240 72401240 G A SNP MGAT5B NM_198955.2 human genbank 54_36p 1 validated intronic c.363-8992 e3-8992 0.001 - - - no_errors tier3 427 2 0.47 174 33 15.94 1 0 0 869586 TCGA-AB-3009 AML43 17 74668164 74668164 C T SNP uc010dhs.1 ENST00000338834 human ensembl 54_36p -1 known intronic c.1-44739 e1-44739 0.024 - - - no_errors tier2 301 1 0.33 88 75 46.01 0 0 NA 869586 TCGA-AB-3009 AML43 17 76214324 76214324 G A SNP KIAA1303 NM_020761.2 human genbank 54_36p 1 validated intronic c.265+136 e2+136 0 - - - no_errors tier3 NA NA NA NA NA NA 0 1 100 869586 TCGA-AB-3009 AML43 17 78575203 78575203 A T SNP B3GNTL1 NM_001009905.1 human genbank 54_36p -1 validated intronic c.343-9519 e5-9519 0.002 - - - no_errors tier3 639 5 0.78 291 288 49.74 2 2 50 869586 TCGA-AB-3009 AML43 18 368469 368469 C T SNP COLEC12 NM_130386.2 human genbank 54_36p -1 validated intronic c.59-20947 e3-20947 0 - - - no_errors tier3 812 4 0.49 248 223 47.15 0 0 NA 869586 TCGA-AB-3009 AML43 18 6593666 6593666 C T SNP LOC100130480 XM_001722554.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*13123 NULL 0.015 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 8803690 8803690 G A SNP KIAA0802 NM_015210.3 human genbank 54_36p 1 predicted intronic c.2859+459 e10+459 0.011 - - - no_errors tier3 1243 7 0.56 522 411 44.05 0 0 0 869586 TCGA-AB-3009 AML43 18 10252033 10252033 T C SNP - - - - - - - - - - - - - - - tier3 1420 14 0.98 530 446 45.7 0 0 NA 869586 TCGA-AB-3009 AML43 18 11156222 11156222 G A SNP - - - - - - - - - - - - - - - tier3 1112 5 0.45 278 249 47.25 0 0 NA 869586 TCGA-AB-3009 AML43 18 14588945 14588945 C A SNP ENSG00000215214 ENST00000399809 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-14264 NULL 0.041 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 18267507 18267507 G A SNP CTAGE1 NM_172241.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-15735 NULL 0.009 - - - no_errors tier3 630 13 2.02 125 76 37.81 0 0 NA 869586 TCGA-AB-3009 AML43 18 18370824 18370824 C T SNP - - - - - - - - - - - - - - - tier2 601 3 0.5 231 189 44.89 0 0 NA 869586 TCGA-AB-3009 AML43 18 23487973 23487973 C T SNP - - - - - - - - - - - - - - - tier3 573 3 0.52 197 145 42.4 0 0 NA 869586 TCGA-AB-3009 AML43 18 23513588 23513588 C G SNP - - - - - - - - - - - - - - - tier3 1006 21 2.04 378 279 42.27 0 0 NA 869586 TCGA-AB-3009 AML43 18 26146117 26146118 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 26875514 26875514 G A SNP DSC3 NM_001941.3 human genbank 54_36p -1 reviewed intronic c.69+1042 e1+1042 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 28716219 28716219 G A SNP - - - - - - - - - - - - - - - tier3 703 2 0.28 124 71 36.41 0 0 NA 869586 TCGA-AB-3009 AML43 18 32301437 32301437 C T SNP FHOD3 NM_025135.2 human genbank 54_36p 1 validated intronic c.338-34456 e4-34456 0 - - - no_errors tier3 745 6 0.8 235 160 40.51 0 0 NA 869586 TCGA-AB-3009 AML43 18 33019829 33019829 G A SNP KIAA1328 NM_020776.1 human genbank 54_36p 1 validated intronic c.1523+12787 e9+12787 0.023 - - - no_errors tier3 184 3 1.6 16 21 56.76 0 0 0 869586 TCGA-AB-3009 AML43 18 33422881 33422881 T - DEL BRUNOL4 NM_020180.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-23279 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 36688146 36688146 C T SNP - - - - - - - - - - - - - - - tier3 1967 19 0.96 489 422 46.32 0 0 NA 869586 TCGA-AB-3009 AML43 18 40600060 40600061 - GT INS SETBP1 NM_015559.1 human genbank 54_36p 1 validated intronic c.324+64265_324+64264 e1+64265 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 44059580 44059580 G A SNP C18orf12 XR_040899.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*26374 NULL 0 - - - no_errors tier3 1286 10 0.77 265 222 45.59 0 0 NA 869586 TCGA-AB-3009 AML43 18 46473871 46473871 C T SNP MAPK4 NM_002747.3 human genbank 54_36p 1 reviewed intronic c.547-21576 e2-21576 0 - - - no_errors tier3 1131 9 0.79 292 236 44.7 0 0 NA 869586 TCGA-AB-3009 AML43 18 51548336 51548336 G A SNP - - - - - - - - - - - - - - - tier3 737 10 1.34 350 324 48.07 0 0 NA 869586 TCGA-AB-3009 AML43 18 53088803 53088803 G A SNP ENSG00000202240 ENST00000365370 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*14028 NULL 0.001 - - - no_errors tier3 945 26 2.67 484 418 46.34 0 0 NA 869586 TCGA-AB-3009 AML43 18 56979477 56979477 C T SNP - - - - - - - - - - - - - - - tier3 2022 21 1.02 828 702 45.82 0 0 NA 869586 TCGA-AB-3009 AML43 18 59684865 59684865 G A SNP SERPINB2 NM_002575.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-24794 NULL 0 - - - no_errors tier3 906 4 0.44 185 145 43.94 0 0 NA 869586 TCGA-AB-3009 AML43 18 59945136 59945136 C T SNP C18orf20 ENST00000397982 human ensembl 54_36p -1 known intronic c.1+21853 e0+21853 0.001 - - - no_errors tier2 376 2 0.53 74 15 16.85 0 0 NA 869586 TCGA-AB-3009 AML43 18 63759016 63759016 G A SNP - - - - - - - - - - - - - - - tier3 489 1 0.2 156 108 40.91 0 0 NA 869586 TCGA-AB-3009 AML43 18 64074927 64074928 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 64227606 64227606 T - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 64854142 64854142 G A SNP CCDC102B NM_001093729.1 human genbank 54_36p 1 validated intronic c.1435-18105 e7-18105 0.004 - - - no_errors tier3 537 8 1.47 252 196 43.75 0 0 NA 869586 TCGA-AB-3009 AML43 18 66639122 66639122 T C SNP - - - - - - - - - - - - - - - tier3 581 3 0.51 242 80 24.84 0 0 NA 869586 TCGA-AB-3009 AML43 18 71942227 71942227 G A SNP - - - - - - - - - - - - - - - tier3 1072 13 1.2 401 322 44.54 0 0 NA 869586 TCGA-AB-3009 AML43 18 73098218 73098218 T - DEL GALR1 NM_001480.3 human genbank 54_36p 1 reviewed intronic c.732+1051 e2+1051 0.003 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 18 73166661 73166661 G A SNP - - - - - - - - - - - - - - - tier3 1443 6 0.41 469 295 38.56 0 0 NA 869586 TCGA-AB-3009 AML43 18 73498391 73498391 G A SNP - - - - - - - - - - - - - - - tier3 342 6 1.72 106 60 36.14 0 0 NA 869586 TCGA-AB-3009 AML43 19 1339089 1339089 G A SNP NDUFS7 NM_024407.4 human genbank 54_36p 1 reviewed intronic c.53+243 e2+243 0.04 - - - no_errors tier3 NA NA NA NA NA NA 4 0 0 869586 TCGA-AB-3009 AML43 19 5773127 5773127 G A SNP NRTN NM_004558.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2050 NULL 0 - - - no_errors tier3 823 26 3.06 158 174 52.41 2 0 0 869586 TCGA-AB-3009 AML43 19 10770237 10770238 - GCCATCGT INS DNM2 NM_001005360.1 human genbank 54_36p 1 reviewed frame_shift_ins c.1411_1412 p.T471fs 1.000:1.000 HMMPfam_Dynamin_M "HMMPfam_Dynamin_M,HMMPfam_Dynamin_N,HMMSmart_SM00053,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_GED,HMMSmart_SM00302,PatternScan_DYNAMIN,superfamily_PH domain-like,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 19 16858458 16858458 G C SNP F2RL3 NM_003950.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-2543 NULL 0 - - - no_errors tier3 293 2 0.68 137 80 36.87 0 0 NA 869586 TCGA-AB-3009 AML43 19 18858533 18858533 G A SNP LASS1 NM_198207.3 human genbank 54_36p -1 reviewed intronic c.410-2457 e3-2457 0.013 - - - no_errors tier2 851 10 1.16 94 92 49.46 0 0 NA 869586 TCGA-AB-3009 AML43 19 19511501 19511501 C T SNP CILP2 NM_153221.2 human genbank 54_36p 1 validated silent c.78 p.T26 0.003 NULL "HMMPfam_TSP_1,HMMSmart_TSP1,superfamily_TSP1,HMMSmart_IGc2,superfamily_CarboxypepD_reg,HMMPfam_I-set,superfamily_SSF48726" - no_errors tier1 465 4 0.85 122 121 49.39 NA 869586 TCGA-AB-3009 AML43 19 33034534 33034534 C T SNP LOC100131141 XR_036861.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*45522 NULL 0 - - - pseudogene tier3 593 10 1.65 449 398 46.93 0 0 NA 869586 TCGA-AB-3009 AML43 19 34625104 34625104 C T SNP LOC284395 XM_378787.3 human genbank 54_36p -1 model intronic c.180-13547 e2-13547 0 - - - no_errors tier3 467 11 2.3 165 124 42.76 0 0 NA 869586 TCGA-AB-3009 AML43 19 35677114 35677114 G A SNP ZNF536 NM_014717.1 human genbank 54_36p 1 provisional intronic c.2171-40480 e2-40480 0 - - - no_errors tier3 597 9 1.49 219 195 47.1 0 0 NA 869586 TCGA-AB-3009 AML43 19 35924138 35924138 G A SNP - - - - - - - - - - - - - - - tier3 939 7 0.74 211 191 47.51 0 0 NA 869586 TCGA-AB-3009 AML43 19 37239780 37239780 G A SNP - - - - - - - - - - - - - - - tier3 1390 18 1.28 497 417 45.62 0 0 NA 869586 TCGA-AB-3009 AML43 19 37745682 37745683 - T INS PDCD5 NM_004708.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-18326 NULL 0.421:0.436 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 19 37855446 37855446 G A SNP ANKRD27 NM_032139.2 human genbank 54_36p -1 validated intronic c.1+2371 e0+2371 0 - - - no_errors tier2 777 2 0.26 266 195 42.3 2 1 33.33 869586 TCGA-AB-3009 AML43 19 38636663 38636663 C T SNP PEPD NM_000285.2 human genbank 54_36p -1 validated intronic c.671+9078 e9+9078 0.021 - - - no_errors tier3 904 8 0.87 280 258 47.87 2 0 0 869586 TCGA-AB-3009 AML43 19 39063795 39063795 C T SNP ENSG00000222442 ENST00000410510 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46327 NULL 0 - - - no_errors tier3 399 1 0.25 89 62 41.06 0 0 NA 869586 TCGA-AB-3009 AML43 19 40534990 40534990 G A SNP FFAR1 NM_005303.1 human genbank 54_36p 1 provisional silent c.696 p.T232 0.663 "HMMPfam_7tm_1,superfamily_SSF81321" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321" - no_errors tier1 363 3 0.82 114 125 52.3 NA 869586 TCGA-AB-3009 AML43 19 40611308 40611308 C T SNP FFAR2 NM_005306.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-21149 NULL 0.062 - - - no_errors tier3 1197 29 2.37 55 37 40.22 0 0 NA 869586 TCGA-AB-3009 AML43 19 42941321 42941321 A T SNP ZNF573 NM_152360.2 human genbank 54_36p -1 provisional intronic c.1+206 e0+206 0 - - - no_errors tier3 279 2 0.71 30 11 26.83 1 0 0 869586 TCGA-AB-3009 AML43 19 44661403 44661403 G C SNP DLL3 NM_016941.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20052 NULL 0.007 - - - no_errors tier2 1332 6 0.45 316 92 22.44 0 0 NA 869586 TCGA-AB-3009 AML43 19 47108048 47108048 C T SNP LOC390937 XM_372730.1 human genbank 54_36p -1 model intronic c.319+797 e2+797 0.001 - - - no_errors tier2 323 6 1.81 91 59 39.33 2 2 50 869586 TCGA-AB-3009 AML43 19 53413830 53413830 C A SNP CARD8 NM_014959.2 human genbank 54_36p -1 reviewed intronic c.985+110 e6+110 0 - - - no_errors tier3 583 2 0.34 243 44 15.33 5 0 0 869586 TCGA-AB-3009 AML43 19 55857216 55857216 C T SNP SHANK1 NM_016148.2 human genbank 54_36p -1 validated missense c.6304 p.D2102N 1 "HMMPfam_SAM_1,HMMSmart_SM00454,superfamily_SAM/Pointed domain" "HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,superfamily_SAM/Pointed domain,HMMPfam_SH3_2" - no_errors tier1 1108 1 0.09 265 199 42.89 6 5 45.45 869586 TCGA-AB-3009 AML43 19 57830425 57830425 G A SNP ZNF83 NM_001105549.1 human genbank 54_36p -1 validated intronic c.1-207 e1-207 0.001 - - - no_errors tier3 533 6 1.11 58 68 53.97 4 1 20 869586 TCGA-AB-3009 AML43 19 58432183 58432183 G T SNP ZNF677 NM_182609.2 human genbank 54_36p -1 provisional missense c.1609 p.H537N 0.931 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" "HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667" - no_errors tier1 575 3 0.52 108 70 39.11 1 100 869586 TCGA-AB-3009 AML43 19 58999238 58999238 C T SNP NLRP12 NM_144687.2 human genbank 54_36p -1 reviewed intronic c.2415-50 e6-50 0.001 - - - no_errors tier3 791 2 0.25 136 114 45.42 0 0 NA 869586 TCGA-AB-3009 AML43 19 60555201 60555201 G A SNP COX6B2 NM_144613.4 human genbank 54_36p -1 validated intronic c.267-1221 e4-1221 0.034 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 19 62068178 62068178 C T SNP PEG3 NM_006210.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-40343 NULL 0 - - - no_errors tier2 944 9 0.94 374 371 49.73 0 0 NA 869586 TCGA-AB-3009 AML43 19 63216065 63216065 G A SNP ZNF606 NM_025027.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-11566 NULL 0.99 - - - no_errors tier3 745 6 0.8 261 221 45.57 1 0 0 869586 TCGA-AB-3009 AML43 20 842287 842287 G A SNP ANGPT4 NM_015985.2 human genbank 54_36p -1 reviewed intronic c.309+2262 e1+2262 0.003 - - - no_errors tier3 6184 103 1.64 1028 868 45.78 0 0 NA 869586 TCGA-AB-3009 AML43 20 3603624 3603625 - G INS ADAM33 ENST00000360630 human ensembl 54_36p -1 known splice_region_ins c.369+10_369+9 e4+10 0.000:0.000 - - - no_stop_codon tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 20 4260112 4260112 C A SNP - - - - - - - - - - - - - - - tier3 707 14 1.94 220 199 47.49 0 0 NA 869586 TCGA-AB-3009 AML43 20 5556509 5556509 C T SNP RP5-1022P6.2 NM_019593.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-23451 NULL 0 - - - no_errors tier3 1627 22 1.33 331 257 43.71 0 0 NA 869586 TCGA-AB-3009 AML43 20 11740319 11740319 T C SNP LOC728450 XM_001131473.2 human genbank 54_36p -1 model intronic c.12-1232 e2-1232 0.009 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 20 11897877 11897878 - A INS BTBD3 NM_014962.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*45563 NULL 0.127:0.138 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 20 13605323 13605323 A C SNP TASP1 NM_017714.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-46598 NULL 0.001 - - - no_errors tier3 966 11 1.12 63 83 56.85 0 0 NA 869586 TCGA-AB-3009 AML43 20 15227176 15227176 A G SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.540+68469 e6+68469 0.005 - - - no_errors tier3 1034 12 1.15 486 433 47.12 0 0 NA 869586 TCGA-AB-3009 AML43 20 15733935 15733935 C T SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.646-57455 e9-57455 0 - - - no_errors tier3 1059 23 2.12 414 307 42.58 0 0 NA 869586 TCGA-AB-3009 AML43 20 21076958 21076958 T C SNP NCRNA00153 ENST00000246027 human ensembl 54_36p 1 known intronic c.405+2663 e4+2663 0 - - - no_errors tier3 538 13 2.36 93 87 48.33 0 1 100 869586 TCGA-AB-3009 AML43 20 21453856 21453856 A T SNP NKX2-2 NM_002509.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11549 NULL 0 - - - no_errors tier3 776 7 0.89 293 297 50.25 0 0 NA 869586 TCGA-AB-3009 AML43 20 22441415 22441415 G A SNP - - - - - - - - - - - - - - - tier3 2031 15 0.73 312 255 44.89 0 0 NA 869586 TCGA-AB-3009 AML43 20 24902759 24902759 G A SNP C20orf3 NM_020531.2 human genbank 54_36p -1 validated intronic c.329-386 e4-386 0.001 - - - no_errors tier3 788 17 2.11 331 270 44.93 1 0 0 869586 TCGA-AB-3009 AML43 20 33485469 33485469 A T SNP GDF5 NM_000557.2 human genbank 54_36p -1 reviewed silent c.1158 p.T386 0.507 NULL "HMMPfam_TGFb_propeptide,HMMPfam_TGF_beta,HMMSmart_TGFB,PatternScan_TGF_BETA_1,superfamily_SSF57501" - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 20 37978602 37978602 C T SNP HSPEP1 ENST00000404611 human ensembl 54_36p -1 known 3_prime_flanking_region c.*16376 NULL 0.058 - - - no_coding_region:pseudogene tier3 1473 18 1.21 509 438 46.06 0 0 NA 869586 TCGA-AB-3009 AML43 20 48432454 48432455 - GGGCCAGAG INS ENSG00000222505 ENST00000410573 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*46682 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 20 50410533 50410533 G A SNP - - - - - - - - - - - - - - - tier3 789 5 0.63 337 288 46.08 0 0 NA 869586 TCGA-AB-3009 AML43 20 53981980 53981980 G T SNP CBLN4 NM_080617.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*25040 NULL 0 - - - no_errors tier3 1022 15 1.44 248 206 45.37 0 0 NA 869586 TCGA-AB-3009 AML43 20 56588797 56588797 C T SNP ENSG00000221174 ENST00000408247 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-24749 NULL 0.008 - - - no_errors tier3 1993 35 1.72 439 428 49.31 0 0 NA 869586 TCGA-AB-3009 AML43 20 57500227 57500227 C T SNP LOC645605 XM_001716708.1 human genbank 54_36p -1 model intronic c.135+2876 e1+2876 0.004 - - - no_errors tier3 1797 11 0.61 357 306 46.15 0 0 NA 869586 TCGA-AB-3009 AML43 20 59147387 59147387 C T SNP - - - - - - - - - - - - - - - tier3 646 7 1.07 70 110 61.11 0 0 NA 869586 TCGA-AB-3009 AML43 20 59694017 59694017 G A SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.170-57997 e3-57997 0.004 - - - no_errors tier3 1521 17 1.1 217 196 47.46 0 0 NA 869586 TCGA-AB-3009 AML43 20 60494666 60494666 A T SNP GATA5 NM_080473.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-10694 NULL 0.001 - - - no_errors tier3 130 2 1.52 21 12 36.36 0 0 NA 869586 TCGA-AB-3009 AML43 20 61097191 61097191 C T SNP LOC100128172 XM_001724178.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-23008 NULL 0 - - - no_errors tier3 1162 12 1.02 157 131 45.49 0 0 NA 869586 TCGA-AB-3009 AML43 20 61196445 61196445 G A SNP HAR1A NR_003244.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-6644 NULL 0 - - - no_errors tier3 222 0 0 27 43 61.43 0 0 NA 869586 TCGA-AB-3009 AML43 21 15397360 15397361 - T INS NRIP1 ENST00000318948 human ensembl 54_36p -1 known 5_prime_flanking_region c.-134976 NULL 0.001:0.014 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 21 16144190 16144190 C T SNP USP25 NM_013396.3 human genbank 54_36p 1 validated intronic c.2337+7460 e18+7460 0 - - - no_errors tier3 271 2 0.73 37 35 48.61 0 0 0 869586 TCGA-AB-3009 AML43 21 16338704 16338704 C T SNP C21orf34 NM_001005732.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-26601 NULL 0.001 - - - no_errors tier3 655 3 0.46 138 89 39.21 0 0 NA 869586 TCGA-AB-3009 AML43 21 19075723 19075723 A G SNP - - - - - - - - - - - - - - - tier3 534 6 1.11 203 188 48.08 0 0 NA 869586 TCGA-AB-3009 AML43 21 19352744 19352744 A C SNP - - - - - - - - - - - - - - - tier3 190 2 1.04 10 16 61.54 0 0 NA 869586 TCGA-AB-3009 AML43 21 21921868 21921868 A C SNP ENSG00000198434 ENST00000358086 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*6776 NULL 0.244 - - - no_coding_region:pseudogene tier2 875 6 0.68 262 226 46.22 0 0 NA 869586 TCGA-AB-3009 AML43 21 23932660 23932660 C T SNP - - - - - - - - - - - - - - - tier2 512 8 1.54 191 156 44.96 0 0 NA 869586 TCGA-AB-3009 AML43 21 24117139 24117139 C A SNP - - - - - - - - - - - - - - - tier3 1135 8 0.7 274 199 41.98 0 1 100 869586 TCGA-AB-3009 AML43 21 24167684 24167684 G A SNP - - - - - - - - - - - - - - - tier3 676 12 1.74 131 101 43.53 0 0 NA 869586 TCGA-AB-3009 AML43 21 24984752 24984752 C A SNP - - - - - - - - - - - - - - - tier3 136 5 3.55 19 10 34.48 0 0 NA 869586 TCGA-AB-3009 AML43 21 27892746 27892746 A G SNP - - - - - - - - - - - - - - - tier2 1350 16 1.17 754 662 46.75 0 0 NA 869586 TCGA-AB-3009 AML43 21 30692169 30692169 C T SNP KRTAP13-2 NM_181621.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-25767 NULL 0.046 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 21 35174739 35174740 - GGCTA INS RUNX1 NM_001754.2 human genbank 54_36p -1 reviewed frame_shift_ins c.493_492 p.G164fs 1.000:1.000 "superfamily_p53-like transcription factors,HMMPfam_Runt" "superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI" - no_errors tier1 NA NA NA NA NA NA NA 869586 TCGA-AB-3009 AML43 21 35543051 35543051 A G SNP - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 21 37017631 37017631 C T SNP SIM2 NM_005069.3 human genbank 54_36p 1 reviewed intronic c.543+330 e5+330 0 - - - no_errors tier3 1158 9 0.77 281 272 49.1 0 0 NA 869586 TCGA-AB-3009 AML43 21 37380897 37380897 T A SNP TTC3 ENST00000354749 human ensembl 54_36p 1 known 5_prime_untranslated_region c.-531 NULL 0.005 - - - no_errors tier3 890 10 1.11 441 452 50.56 2 2 50 869586 TCGA-AB-3009 AML43 21 38837308 38837308 A C SNP ERG NM_004449.1 human genbank 54_36p -1 validated intronic c.39+32148 e1+32148 0.001 - - - no_errors tier3 945 9 0.94 200 216 51.92 0 0 NA 869586 TCGA-AB-3009 AML43 21 44204493 44204493 G A SNP AGPAT3 NM_001037553.1 human genbank 54_36p 1 reviewed intronic c.178+325 e1+325 0.001 - - - no_errors tier3 2450 33 1.33 534 415 43.73 18 7 28 869586 TCGA-AB-3009 AML43 21 46795914 46795914 T C SNP DIP2A NM_015151.1 human genbank 54_36p 1 reviewed intronic c.2840-61 e24-61 0 - - - no_errors tier3 194 4 2.02 58 50 46.3 2 2 50 869586 TCGA-AB-3009 AML43 22 18037304 18037304 G A SNP SEPT5 NM_002688.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-44808 NULL 0.017 - - - no_errors tier3 658 9 1.35 134 152 53.15 0 0 NA 869586 TCGA-AB-3009 AML43 22 26058330 26058330 G A SNP - - - - - - - - - - - - - - - tier2 1097 17 1.53 450 352 43.89 0 0 NA 869586 TCGA-AB-3009 AML43 22 27622622 27622622 C A SNP ZNRF3 NM_032173.2 human genbank 54_36p 1 validated intronic c.1+12568 e0+12568 0.985 - - - no_errors tier3 1559 17 1.08 450 347 43.54 1 0 0 869586 TCGA-AB-3009 AML43 22 30654997 30654997 C A SNP YWHAH NM_003405.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-15723 NULL 0.005 - - - no_errors tier3 1361 25 1.8 181 156 46.15 0 2 100 869586 TCGA-AB-3009 AML43 22 31549562 31549562 G A SNP SYN3 NM_003490.1 human genbank 54_36p -1 reviewed intronic c.711+41340 e5+41340 0.025 - - - no_errors tier3 1432 14 0.97 421 316 42.88 0 0 0 869586 TCGA-AB-3009 AML43 22 33807628 33807628 A G SNP ISX NM_001008494.1 human genbank 54_36p 1 validated intronic c.230-883 e2-883 0 - - - no_errors tier3 1340 2 0.15 329 307 48.27 0 0 NA 869586 TCGA-AB-3009 AML43 22 37565854 37565854 T G SNP NPTXR NM_014293.2 human genbank 54_36p -1 reviewed intronic c.624+3332 e1+3332 0.002 - - - no_errors tier3 217 2 0.91 72 52 41.94 0 0 NA 869586 TCGA-AB-3009 AML43 22 37566187 37566187 G T SNP NPTXR NM_014293.2 human genbank 54_36p -1 reviewed intronic c.624+2999 e1+2999 0.001 - - - no_errors tier3 254 4 1.55 115 74 39.15 1 0 0 869586 TCGA-AB-3009 AML43 22 38685367 38685367 C T SNP GRAP2 NM_004810.2 human genbank 54_36p 1 reviewed intronic c.171-638 e3-638 0.001 - - - no_errors tier3 580 16 2.68 83 142 62.83 2 0 0 869586 TCGA-AB-3009 AML43 22 38693185 38693185 G A SNP GRAP2 NM_004810.2 human genbank 54_36p 1 reviewed intronic c.460-807 e5-807 0 - - - no_errors tier3 1502 16 1.05 333 223 40.11 4 0 0 869586 TCGA-AB-3009 AML43 22 40994686 40994687 - A INS LOC388906 XM_001716802.1 human genbank 54_36p 1 model intronic c.94-795_94-794 e2-794 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 869586 TCGA-AB-3009 AML43 22 43811533 43811533 C T SNP PHF21B NM_138415.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-27439 NULL 0.005 - - - no_errors tier3 1102 11 0.99 393 374 48.7 0 0 NA 869586 TCGA-AB-3009 AML43 22 45357133 45357133 G A SNP CELSR1 NM_014246.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-45402 NULL 0.002 - - - no_errors tier3 446 1 0.22 144 53 26.63 14 4 22.22 869586 TCGA-AB-3009 AML43 22 47301588 47301588 G A SNP FAM19A5 ENST00000402357 human ensembl 54_36p 1 known intronic c.112+37408 e1+37408 0 - - - no_errors tier3 86 3 3.37 24 32 57.14 0 0 NA 869586 TCGA-AB-3009 AML43 22 47525066 47525066 C T SNP FAM19A5 ENST00000402357 human ensembl 54_36p 1 known intronic c.391-6591 e4-6591 0.003 - - - no_errors tier3 192 0 0 84 58 40.28 0 0 NA 509754 TCGA-AB-3011 AML07 X 668051 668051 G A SNP LOC100134439 XM_001713974.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-48278 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 429 6 1.37 202 124 37.92 0 0 NA 509754 TCGA-AB-3011 AML07 X 3324052 3324052 A G SNP MXRA5 NM_015419.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-52178 NULL 0.001 - - - no_errors tier3 458 13 2.76 367 254 40.84 0 0 NA 509754 TCGA-AB-3011 AML07 X 14087330 14087330 G T SNP - - - - - - - - - - - - - - - tier2 550 16 2.82 543 420 43.48 0 0 NA 509754 TCGA-AB-3011 AML07 X 24790014 24790014 T - DEL POLA1 NM_016937.2 human genbank 54_36p 1 validated intronic c.4029+18299 e34+18299 0.292 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 509754 TCGA-AB-3011 AML07 X 28749597 28749597 G A SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.82+32134 e1+32134 0.003 - - - no_errors tier3 371 2 0.54 533 159 22.98 0 0 NA 509754 TCGA-AB-3011 AML07 X 28749608 28749608 T G SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.82+32145 e1+32145 0 - - - no_errors tier3 354 2 0.56 511 142 21.75 0 0 NA 509754 TCGA-AB-3011 AML07 X 32964118 32964118 C A SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.32-15880 e2-15880 0 - - - no_errors tier3 114 1 0.87 161 108 40.15 0 0 NA 509754 TCGA-AB-3011 AML07 X 42894217 42894217 T C SNP - - - - - - - - - - - - - - - tier3 117 3 2.5 96 77 44.51 0 0 NA 509754 TCGA-AB-3011 AML07 X 46801649 46801649 T A SNP PHF16 NM_001077445.1 human genbank 54_36p 1 reviewed intronic c.1562-864 e10-864 0.05 - - - no_errors tier3 466 10 2.1 234 167 41.65 3 0 0 509754 TCGA-AB-3011 AML07 X 49330039 49330039 A C SNP ENSG00000220450 ENST00000407777 human ensembl 54_36p -1 known 5_prime_flanking_region c.-9805 NULL 0.071 - - - no_coding_region:pseudogene tier3 476 9 1.85 273 221 44.47 0 0 NA 509754 TCGA-AB-3011 AML07 X 55410339 55410339 T A SNP LOC100130725 XM_001720978.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*13947 NULL 0.074 - - - no_errors tier3 390 10 2.49 365 247 40.23 0 0 NA 509754 TCGA-AB-3011 AML07 X 68123370 68123370 G T SNP - - - - - - - - - - - - - - - tier3 571 20 3.38 238 160 40.2 0 0 NA 509754 TCGA-AB-3011 AML07 X 68188218 68188218 A T SNP - - - - - - - - - - - - - - - tier3 1275 60 4.48 273 150 35.38 0 0 NA 509754 TCGA-AB-3011 AML07 X 68188219 68188219 G C SNP - - - - - - - - - - - - - - - tier3 1261 57 4.3 271 147 35.08 0 0 NA 509754 TCGA-AB-3011 AML07 X 69611066 69611066 C G SNP DLG3 NM_021120.1 human genbank 54_36p 1 validated intronic c.1406-4659 e10-4659 0.001 - - - no_errors tier3 226 7 3 117 88 42.93 1 0 0 509754 TCGA-AB-3011 AML07 X 70428422 70428422 C A SNP NONO NM_007363.1 human genbank 54_36p 1 reviewed missense c.223 p.R75S 1 "HMMSmart_SM00360,superfamily_RNA-binding domain RBD" "HMMPfam_RRM_1,HMMSmart_SM00360,HMMPfam_NOPS,superfamily_RNA-binding domain RBD" - no_errors tier1 215 4 1.83 132 40 23.26 71 87 55.06 509754 TCGA-AB-3011 AML07 X 85205195 85205195 G T SNP CHM NM_000390.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-16003 NULL 0.12 - - - no_errors tier3 388 4 1.02 215 148 40.77 0 0 NA 509754 TCGA-AB-3011 AML07 X 88050699 88050699 T A SNP ENSG00000220636 ENST00000405067 human ensembl 54_36p 1 known 3_prime_flanking_region c.*321 NULL 0.998 - - - no_coding_region:pseudogene tier2 156 1 0.63 83 64 43.54 0 0 NA 509754 TCGA-AB-3011 AML07 X 102595867 102595867 G C SNP RAB40A NM_080879.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*45640 NULL 0.013 - - - no_errors tier3 386 5 1.28 473 139 22.71 0 0 NA 509754 TCGA-AB-3011 AML07 X 121224584 121224584 C T SNP - - - - - - - - - - - - - - - tier2 67 1 1.47 100 52 34.21 0 0 NA 509754 TCGA-AB-3011 AML07 X 141065298 141065298 C G SNP ENSG00000217283 ENST00000402189 human ensembl 54_36p -1 known 5_prime_flanking_region c.-980 NULL 0 - - - no_coding_region:pseudogene tier3 405 9 2.16 295 222 42.94 0 0 NA 509754 TCGA-AB-3011 AML07 X 142028297 142028297 T C SNP ENSG00000202473 ENST00000365603 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*22168 NULL 0.004 - - - no_errors tier3 276 7 2.47 284 236 45.38 0 0 NA 509754 TCGA-AB-3011 AML07 X 142353526 142353526 G A SNP ENSG00000221505 ENST00000408578 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*8133 NULL 0.167 - - - no_errors tier3 291 1 0.34 212 43 16.86 0 0 NA 509754 TCGA-AB-3011 AML07 X 149761195 149761195 G A SNP CD99L2 NM_031462.2 human genbank 54_36p -1 validated intronic c.68-10771 e2-10771 0 - - - no_errors tier2 862 41 4.52 749 598 44.39 2 0 0 509754 TCGA-AB-3011 AML07 1 20336131 20336131 C T SNP PLA2G2F NM_022819.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-2377 NULL 0 - - - no_errors tier3 122 2 1.61 69 39 36.11 0 0 NA 509754 TCGA-AB-3011 AML07 1 45783422 45783422 A G SNP NASP NM_172164.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-46068 NULL 0.001 - - - no_errors tier3 807 7 0.86 216 50 18.8 0 0 NA 509754 TCGA-AB-3011 AML07 1 51798766 51798766 C T SNP EPS15 NM_001981.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-41275 NULL 0.976 - - - no_errors tier2 338 6 1.74 270 160 37.21 0 1 100 509754 TCGA-AB-3011 AML07 1 63486369 63486369 G T SNP ENSG00000216223 ENST00000402761 human ensembl 54_36p 1 known 5_prime_flanking_region c.-14003 NULL 0.001 - - - no_coding_region:pseudogene tier3 91 1 1.09 77 62 44.6 0 0 NA 509754 TCGA-AB-3011 AML07 1 64522146 64522146 G A SNP UBE2U NM_152489.1 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*39742 NULL 0 - - - no_errors tier3 606 19 3.03 434 272 38.53 0 0 NA 509754 TCGA-AB-3011 AML07 1 72306273 72306273 A C SNP NEGR1 NM_173808.2 human genbank 54_36p -1 validated intronic c.177-132691 e2-132691 0.015 - - - no_errors tier3 104 0 0 112 41 26.8 13 3 18.75 509754 TCGA-AB-3011 AML07 1 81350296 81350296 A G SNP ENSG00000216938 ENST00000402913 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-12589 NULL 0.016 - - - no_coding_region:pseudogene tier3 190 5 2.56 225 172 43.32 0 0 NA 509754 TCGA-AB-3011 AML07 1 98682373 98682373 T G SNP - - - - - - - - - - - - - - - tier3 316 14 4.23 334 221 39.82 0 0 NA 509754 TCGA-AB-3011 AML07 1 105515057 105515057 C A SNP - - - - - - - - - - - - - - - tier2 127 6 4.51 107 48 30.97 0 0 NA 509754 TCGA-AB-3011 AML07 1 114146054 114146054 C T SNP RSBN1 NM_018364.3 human genbank 54_36p -1 validated intronic c.704-3873 e2-3873 0.059 - - - no_errors tier3 138 10 6.76 145 83 36.4 0 4 100 509754 TCGA-AB-3011 AML07 1 120885446 120885446 C A SNP - - - - - - - - - - - - - - - tier3 132 6 4.35 129 79 37.98 0 0 NA 509754 TCGA-AB-3011 AML07 1 187755691 187755691 G T SNP - - - - - - - - - - - - - - - tier2 64 3 4.48 97 62 38.99 0 0 NA 509754 TCGA-AB-3011 AML07 1 188585864 188585864 C T SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional intronic c.237-68361 e2-68361 0 - - - no_errors tier3 596 7 1.16 460 124 21.2 0 0 NA 509754 TCGA-AB-3011 AML07 1 189157754 189157754 C G SNP - - - - - - - - - - - - - - - tier3 923 41 4.25 413 262 38.81 0 0 NA 509754 TCGA-AB-3011 AML07 1 196300839 196300839 T C SNP - - - - - - - - - - - - - - - tier3 95 0 0 132 89 40.27 0 0 NA 509754 TCGA-AB-3011 AML07 1 206672607 206672607 C T SNP - - - - - - - - - - - - - - - tier3 368 8 2.12 247 180 42.06 0 0 NA 509754 TCGA-AB-3011 AML07 1 234000297 234000297 G A SNP LYST NM_000081.2 human genbank 54_36p -1 reviewed intronic c.5785-77 e18-77 0.001 - - - no_errors tier3 349 4 1.12 342 73 17.59 0 1 100 509754 TCGA-AB-3011 AML07 1 240191074 240191074 C T SNP ENSG00000213026 ENST00000391847 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32047 NULL 0.007 - - - no_coding_region:pseudogene tier3 1271 13 1.01 366 143 28.09 0 0 NA 509754 TCGA-AB-3011 AML07 1 245987765 245987765 G A SNP OR1C1 NM_012353.2 human genbank 54_36p -1 validated silent c.567 p.C189 0.993 "HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like" "HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like" - no_errors tier1 926 26 2.73 423 310 42.23 NA 509754 TCGA-AB-3011 AML07 2 6457047 6457047 G A SNP - - - - - - - - - - - - - - - tier3 300 9 2.91 239 176 42.41 0 0 NA 509754 TCGA-AB-3011 AML07 2 13433157 13433157 C T SNP - - - - - - - - - - - - - - - tier3 128 3 2.29 137 91 39.91 0 0 NA 509754 TCGA-AB-3011 AML07 2 25886617 25886617 G A SNP ENSG00000187536 ENST00000338274 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-25886617 NULL 1 - - - no_coding_region:pseudogene tier2 596 24 3.86 273 166 37.81 3 3 50 509754 TCGA-AB-3011 AML07 2 29854386 29854386 C A SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.668-60319 e2-60319 0.002 - - - no_errors tier2 626 15 2.34 273 144 34.53 0 0 NA 509754 TCGA-AB-3011 AML07 2 51280385 51280385 T C SNP LOC730100 XR_041273.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.018 - - - no_errors tier3 264 6 2.22 238 154 39.29 0 0 NA 509754 TCGA-AB-3011 AML07 2 51584850 51584850 C A SNP ENSG00000220872 ENST00000405610 human ensembl 54_36p 1 known 5_prime_flanking_region c.-6850 NULL 0.002 - - - no_coding_region:pseudogene tier3 537 2 0.37 416 108 20.61 0 0 NA 509754 TCGA-AB-3011 AML07 2 54149124 54149124 G A SNP ACYP2 NM_138448.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-47216 NULL 0.002 - - - no_errors tier3 443 4 0.89 306 91 22.92 1 1 50 509754 TCGA-AB-3011 AML07 2 77549096 77549096 C A SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+49856 e2+49856 0 - - - no_errors tier3 199 2 0.99 180 65 26.53 0 0 NA 509754 TCGA-AB-3011 AML07 2 77866184 77866184 A G SNP - - - - - - - - - - - - - - - tier3 212 7 3.18 189 163 46.31 0 0 NA 509754 TCGA-AB-3011 AML07 2 97379666 97379666 G T SNP - - - - - - - - - - - - - - - tier3 517 18 3.35 221 148 40.11 0 0 0 509754 TCGA-AB-3011 AML07 2 97712506 97712506 T C SNP ZAP70 NM_001079.3 human genbank 54_36p 1 reviewed intronic c.564-3272 e3-3272 0.114 - - - no_errors tier2 218 2 0.91 164 56 25.45 1 1 50 509754 TCGA-AB-3011 AML07 2 99912909 99912909 G A SNP AFF3 NM_001025108.1 human genbank 54_36p -1 reviewed intronic c.948+76617 e5+76617 0.01 - - - no_errors tier3 282 8 2.75 265 48 15.34 2 0 0 509754 TCGA-AB-3011 AML07 2 150798253 150798253 G A SNP - - - - - - - - - - - - - - - tier3 315 9 2.76 269 197 42.27 0 0 NA 509754 TCGA-AB-3011 AML07 2 176684244 176684245 - T INS RPLP1P4 ENST00000405359 human ensembl 54_36p -1 known intronic c.345-87609_87610 e2-87608 0.987:0.984 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 509754 TCGA-AB-3011 AML07 2 189205531 189205531 G A SNP GULP1 NM_016315.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*38548 NULL 0.005 - - - no_errors tier3 218 4 1.79 170 98 36.57 0 0 NA 509754 TCGA-AB-3011 AML07 2 199843332 199843332 T - DEL SATB2 NM_015265.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*1847 NULL 0.996 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 509754 TCGA-AB-3011 AML07 2 208821358 208821358 G T SNP IDH1 NM_005896.2 human genbank 54_36p -1 reviewed missense c.394 p.R132S 1 "HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" "HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like" - no_errors tier1 308 7 2.22 204 119 36.84 29 43 59.72 509754 TCGA-AB-3011 AML07 2 209995928 209995928 C A SNP MAP2 NM_001039538.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-230212 NULL 0.001 - - - no_errors tier3 178 4 2.2 87 100 53.19 0 0 NA 509754 TCGA-AB-3011 AML07 2 230077005 230077005 A G SNP DNER NM_139072.3 human genbank 54_36p -1 validated intronic c.1147+8738 e6+8738 0 - - - no_errors tier3 255 7 2.67 266 153 36 0 0 NA 509754 TCGA-AB-3011 AML07 2 235253544 235253544 G A SNP - - - - - - - - - - - - - - - tier3 830 6 0.72 364 125 25.51 0 0 NA 509754 TCGA-AB-3011 AML07 3 2245722 2245722 C T SNP CNTN4 NM_175607.1 human genbank 54_36p 1 reviewed intronic c.1-110140 e1-110140 0 - - - no_errors tier3 219 1 0.45 275 57 17.17 0 0 NA 509754 TCGA-AB-3011 AML07 3 17643816 17643816 G T SNP TBC1D5 NM_014744.1 human genbank 54_36p -1 validated intronic c.1-3407 e1-3407 0 - - - no_errors tier3 307 7 2.22 283 184 39.4 11 5 31.25 509754 TCGA-AB-3011 AML07 3 17726460 17726460 C T SNP TBC1D5 NM_014744.1 human genbank 54_36p -1 validated intronic c.1+29379 e0+29379 0.005 - - - no_errors tier3 191 1 0.52 166 60 26.43 5 5 50 509754 TCGA-AB-3011 AML07 3 47889837 47889837 A T SNP MAP4 NM_002375.1 human genbank 54_36p -1 reviewed intronic c.2323-1243 e10-1243 0 - - - no_errors tier3 566 13 2.25 207 159 43.44 5 6 54.55 509754 TCGA-AB-3011 AML07 3 62421168 62421168 G A SNP CADPS NM_003716.3 human genbank 54_36p -1 reviewed intronic c.3636+4914 e26+4914 0 - - - no_errors tier3 632 6 0.94 403 43 9.64 0 0 NA 509754 TCGA-AB-3011 AML07 3 85452361 85452361 A T SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+360852 e1+360852 0.078 - - - no_errors tier3 378 8 2.07 336 247 42.29 0 0 NA 509754 TCGA-AB-3011 AML07 3 96951961 96951961 T C SNP - - - - - - - - - - - - - - - tier3 166 8 4.6 80 63 44.06 0 0 NA 509754 TCGA-AB-3011 AML07 3 104530587 104530587 A C SNP - - - - - - - - - - - - - - - tier3 791 11 1.37 535 144 21.21 0 0 NA 509754 TCGA-AB-3011 AML07 3 130924323 130924324 AG - DEL TMCC1 NM_001017395.2 human genbank 54_36p -1 validated intronic c.577-51527_577-51526 e2-51526 0.445:0.421 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 509754 TCGA-AB-3011 AML07 3 133171138 133171138 C T SNP CPNE4 NM_130808.1 human genbank 54_36p -1 reviewed intronic c.1-64160 e1-64160 0.159 - - - no_errors tier2 319 6 1.85 249 133 34.82 0 0 NA 509754 TCGA-AB-3011 AML07 3 144791675 144791675 C T SNP SLC9A9 NM_173653.2 human genbank 54_36p -1 validated intronic c.756-11420 e7-11420 0 - - - no_errors tier2 361 13 3.47 261 183 41.22 0 0 NA 509754 TCGA-AB-3011 AML07 3 154919293 154919293 C G SNP - - - - - - - - - - - - - - - tier3 104 5 4.59 127 35 21.6 0 0 NA 509754 TCGA-AB-3011 AML07 3 157747715 157747715 A C SNP SSR3 NM_007107.2 human genbank 54_36p -1 reviewed intronic c.359+1673 e3+1673 0.006 - - - no_errors tier2 303 9 2.88 244 182 42.72 2 1 33.33 509754 TCGA-AB-3011 AML07 3 166696202 166696202 T G SNP - - - - - - - - - - - - - - - tier3 74 1 1.33 84 33 28.21 0 0 NA 509754 TCGA-AB-3011 AML07 4 3634062 3634062 C T SNP LOC100129786 XM_001719840.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-19956 NULL 0 - - - no_errors tier3 1140 64 5.32 164 117 41.64 0 0 0 509754 TCGA-AB-3011 AML07 4 18022627 18022627 A T SNP - - - - - - - - - - - - - - - tier3 986 4 0.4 443 158 26.29 0 0 NA 509754 TCGA-AB-3011 AML07 4 33789087 33789087 C A SNP - - - - - - - - - - - - - - - tier3 205 3 1.44 200 133 39.7 0 0 NA 509754 TCGA-AB-3011 AML07 4 64218690 64218690 C A SNP - - - - - - - - - - - - - - - tier3 58 2 3.33 62 50 44.64 0 0 NA 509754 TCGA-AB-3011 AML07 4 68596789 68596789 T G SNP TMPRSS11F NM_207407.2 human genbank 54_36p -1 validated 3_prime_flanking_region c.*5433 NULL 0.381 - - - no_errors tier3 173 6 3.35 109 72 39.78 0 0 NA 509754 TCGA-AB-3011 AML07 4 70811998 70811998 T C SNP CSN1S1 NM_001890.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20865 NULL 0 - - - no_errors tier3 108 1 0.91 121 77 38.89 0 0 NA 509754 TCGA-AB-3011 AML07 4 97647300 97647300 G A SNP ENSG00000201837 ENST00000364967 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*40892 NULL 0 - - - no_errors tier3 188 1 0.52 222 32 12.6 0 0 NA 509754 TCGA-AB-3011 AML07 4 105548413 105548413 G A SNP - - - - - - - - - - - - - - - tier3 444 13 2.84 355 161 31.2 0 0 NA 509754 TCGA-AB-3011 AML07 4 128261426 128261426 G T SNP - - - - - - - - - - - - - - - tier2 612 17 2.69 329 257 43.86 0 0 NA 509754 TCGA-AB-3011 AML07 4 150146812 150146812 G A SNP - - - - - - - - - - - - - - - tier3 153 6 3.77 155 86 35.68 0 0 NA 509754 TCGA-AB-3011 AML07 4 161710813 161710813 G T SNP ENSG00000208632 ENST00000385897 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-4872 NULL 0.001 - - - pseudogene tier3 132 0 0 149 45 23.2 0 0 NA 509754 TCGA-AB-3011 AML07 4 168173901 168173901 C A SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated intronic c.245-15712 e4-15712 0.002 - - - no_errors tier2 176 1 0.56 259 73 21.99 0 0 NA 509754 TCGA-AB-3011 AML07 4 190067892 190067892 G T SNP - - - - - - - - - - - - - - - tier3 377 6 1.55 396 103 20.6 0 0 NA 509754 TCGA-AB-3011 AML07 5 2886388 2886388 A G SNP ENSG00000215233 ENST00000399855 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-44742 NULL 0 - - - no_coding_region:pseudogene tier3 99 4 3.88 75 43 36.44 0 0 NA 509754 TCGA-AB-3011 AML07 5 2886394 2886394 A G SNP ENSG00000215233 ENST00000399855 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-44748 NULL 0.01 - - - no_coding_region:pseudogene tier3 96 4 4 69 43 38.39 0 0 NA 509754 TCGA-AB-3011 AML07 5 15940705 15940705 C A SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.128-40294 e3-40294 0.004 - - - no_errors tier3 482 11 2.23 243 154 38.6 0 0 NA 509754 TCGA-AB-3011 AML07 5 26078063 26078063 C T SNP ENSG00000222560 ENST00000410628 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*29171 NULL 0 - - - no_errors tier3 261 16 5.69 183 109 37.33 0 0 NA 509754 TCGA-AB-3011 AML07 5 31753392 31753392 G A SNP - - - - - - - - - - - - - - - tier3 698 12 1.68 245 157 38.96 0 0 NA 509754 TCGA-AB-3011 AML07 5 37997932 37997932 C T SNP - - - - - - - - - - - - - - - tier2 226 10 4.24 240 158 39.5 0 0 NA 509754 TCGA-AB-3011 AML07 5 38002332 38002332 T C SNP - - - - - - - - - - - - - - - tier3 315 5 1.56 258 210 44.87 0 0 NA 509754 TCGA-AB-3011 AML07 5 40992292 40992292 C T SNP C7 NM_000587.2 human genbank 54_36p 1 reviewed intronic c.1260+880 e10+880 0.001 - - - no_errors tier3 393 5 1.25 566 136 19.37 0 0 0 509754 TCGA-AB-3011 AML07 5 50895976 50895976 G A SNP - - - - - - - - - - - - - - - tier2 122 1 0.81 182 53 22.55 0 0 NA 509754 TCGA-AB-3011 AML07 5 70870793 70870793 T C SNP BDP1 NM_018429.2 human genbank 54_36p 1 reviewed intronic c.5929+132 e27+132 0 - - - no_errors tier3 139 3 2.1 68 44 39.29 5 2 28.57 509754 TCGA-AB-3011 AML07 5 84911083 84911083 A T SNP LOC645181 XR_017382.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*29372 NULL 0.011 - - - pseudogene tier3 59 2 3.28 83 107 56.02 0 0 NA 509754 TCGA-AB-3011 AML07 5 86526052 86526052 G A SNP ENSG00000196836 ENST00000355023 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*23460 NULL 0.001 - - - no_coding_region:pseudogene tier3 234 4 1.68 259 155 37.44 0 0 NA 509754 TCGA-AB-3011 AML07 5 92791137 92791137 G T SNP - - - - - - - - - - - - - - - tier2 335 8 2.33 268 196 42.15 0 0 NA 509754 TCGA-AB-3011 AML07 5 97917622 97917622 C A SNP LOC642909 XR_016221.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-14544 NULL 0.002 - - - pseudogene tier3 152 9 5.59 157 74 31.9 0 0 NA 509754 TCGA-AB-3011 AML07 5 106065448 106065448 A G SNP - - - - - - - - - - - - - - - tier3 108 1 0.91 115 81 41.12 0 0 NA 509754 TCGA-AB-3011 AML07 5 125195967 125195967 C T SNP - - - - - - - - - - - - - - - tier2 224 1 0.44 155 92 37.1 0 0 NA 509754 TCGA-AB-3011 AML07 5 152488165 152488165 T C SNP - - - - - - - - - - - - - - - tier3 409 14 3.31 415 258 38.34 0 0 NA 509754 TCGA-AB-3011 AML07 5 155236915 155236915 C G SNP ENSG00000200275 ENST00000363405 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*31773 NULL 0 - - - no_errors tier3 253 9 3.44 232 130 35.91 0 0 NA 509754 TCGA-AB-3011 AML07 5 170770152 170770153 - TCTG INS NPM1 NM_002520.1 human genbank 54_36p 1 validated frame_shift_ins c.863_864 p.W288fs 1.000:1.000 NULL "HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain" - no_errors tier1 NA NA NA NA NA NA NA 509754 TCGA-AB-3011 AML07 6 49492356 49492356 C T SNP CENPQ NM_018132.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-53493 NULL 0.085 - - - no_errors tier3 837 33 3.79 385 315 44.94 0 0 NA 509754 TCGA-AB-3011 AML07 6 53241489 53241489 A G SNP ELOVL5 NM_021814.3 human genbank 54_36p -1 provisional 3_prime_untranslated_region c.*395 NULL 0.999 - - - no_errors tier2 154 3 1.91 124 60 32.43 22 6 21.43 509754 TCGA-AB-3011 AML07 6 62914004 62914004 C T SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.219+31045 e2+31045 0.002 - - - no_errors tier3 153 3 1.9 191 111 36.75 0 0 NA 509754 TCGA-AB-3011 AML07 6 62914006 62914006 T G SNP KHDRBS2 NM_152688.2 human genbank 54_36p -1 validated intronic c.219+31043 e2+31043 0.006 - - - no_errors tier3 151 3 1.95 184 109 37.2 0 0 NA 509754 TCGA-AB-3011 AML07 6 68241670 68241670 C A SNP ENSG00000211117 ENST00000388382 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-7750 NULL 0 - - - pseudogene tier3 123 5 3.91 157 73 31.6 0 0 NA 509754 TCGA-AB-3011 AML07 6 79965690 79965690 C T SNP HMGN3 NM_004242.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*2434 NULL 0.007 - - - no_errors tier3 252 5 1.95 119 90 43.06 1 0 0 509754 TCGA-AB-3011 AML07 6 81500866 81500866 G A SNP - - - - - - - - - - - - - - - tier3 205 5 2.37 311 220 41.35 0 0 NA 509754 TCGA-AB-3011 AML07 6 109800043 109800043 C G SNP CD164 NM_006016.1 human genbank 54_36p -1 validated intronic c.371-1680 e5-1680 0.104 - - - no_errors tier3 501 19 3.64 366 230 38.59 68 61 47.29 509754 TCGA-AB-3011 AML07 6 162170932 162170932 G A SNP PARK2 NM_004562.2 human genbank 54_36p -1 reviewed intronic c.735-44002 e7-44002 0 - - - no_errors tier3 204 4 1.92 141 95 40.25 0 0 NA 509754 TCGA-AB-3011 AML07 6 164896559 164896559 T C SNP - - - - - - - - - - - - - - - tier3 485 4 0.82 452 259 36.43 0 0 NA 509754 TCGA-AB-3011 AML07 7 8855964 8855964 C G SNP LOC100134670 XM_001725702.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-25941 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 85 5 5.56 95 80 45.71 0 0 NA 509754 TCGA-AB-3011 AML07 7 46363699 46363699 C T SNP - - - - - - - - - - - - - - - tier3 442 12 2.64 440 306 40.96 0 0 NA 509754 TCGA-AB-3011 AML07 7 52924670 52924670 T C SNP - - - - - - - - - - - - - - - tier3 255 2 0.77 158 103 39.31 0 0 NA 509754 TCGA-AB-3011 AML07 7 63315756 63315756 A G SNP ZNF679 ENST00000255746 human ensembl 54_36p 1 known 5_prime_flanking_region c.-31175 NULL 0.957 - - - no_errors tier2 138 0 0 56 15 20.83 0 0 NA 509754 TCGA-AB-3011 AML07 7 70448416 70448416 G A SNP WBSCR17 NM_022479.1 human genbank 54_36p 1 reviewed intronic c.422+9761 e2+9761 0 - - - no_errors tier3 437 13 2.89 229 136 37.16 0 0 NA 509754 TCGA-AB-3011 AML07 7 86493363 86493363 G T SNP KIAA1324L NM_152748.1 human genbank 54_36p -1 validated intronic c.1+13992 e0+13992 0.01 - - - no_errors tier3 367 12 3.17 263 154 36.93 0 0 NA 509754 TCGA-AB-3011 AML07 7 88084410 88084410 C T SNP ENSG00000211518 ENST00000390184 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-23361 NULL 0.004 - - - no_errors tier3 336 3 0.88 238 189 44.26 0 0 NA 509754 TCGA-AB-3011 AML07 7 118815164 118815164 T A SNP - - - - - - - - - - - - - - - tier3 205 1 0.48 128 92 41.82 0 0 NA 509754 TCGA-AB-3011 AML07 7 144697342 144697342 G T SNP - - - - - - - - - - - - - - - tier3 116 9 7.14 92 73 44.24 0 0 NA 509754 TCGA-AB-3011 AML07 8 15818302 15818302 T G SNP - - - - - - - - - - - - - - - tier3 180 1 0.55 172 64 27.12 0 0 NA 509754 TCGA-AB-3011 AML07 8 34680594 34680594 C A SNP - - - - - - - - - - - - - - - tier3 138 1 0.72 204 75 26.88 0 0 NA 509754 TCGA-AB-3011 AML07 8 57614212 57614212 G A SNP LOC389662 XR_016813.2 human genbank 54_36p -1 model intronic c.NULL NULL 0.001 - - - pseudogene tier3 404 8 1.94 182 135 42.59 0 0 NA 509754 TCGA-AB-3011 AML07 8 63034029 63034029 C T SNP - - - - - - - - - - - - - - - tier3 346 5 1.42 258 185 41.67 0 0 NA 509754 TCGA-AB-3011 AML07 8 70999419 70999419 C T SNP ENSG00000222906 ENST00000410974 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-1584 NULL 0 - - - no_errors tier3 339 6 1.74 194 108 35.53 0 0 NA 509754 TCGA-AB-3011 AML07 8 78279557 78279557 T A SNP - - - - - - - - - - - - - - - tier3 127 2 1.55 150 82 35.34 0 0 NA 509754 TCGA-AB-3011 AML07 8 78279566 78279566 A C SNP - - - - - - - - - - - - - - - tier3 126 3 2.33 138 78 35.94 0 0 NA 509754 TCGA-AB-3011 AML07 8 92327641 92327641 C A SNP SLC26A7 NM_134266.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3415 NULL 0 - - - no_errors tier3 157 2 1.26 193 62 24.31 0 0 NA 509754 TCGA-AB-3011 AML07 8 97053382 97053382 G A SNP - - - - - - - - - - - - - - - tier2 900 12 1.31 417 111 20.94 0 0 NA 509754 TCGA-AB-3011 AML07 8 97980714 97980714 C T SNP PGCP NM_016134.2 human genbank 54_36p 1 provisional intronic c.849+19305 e3+19305 0.001 - - - no_errors tier3 198 8 3.88 169 170 50.15 1 0 0 509754 TCGA-AB-3011 AML07 8 105242865 105242865 G T SNP RIMS2 NM_001100117.1 human genbank 54_36p 1 validated intronic c.3335-83455 e20-83455 0 - - - no_errors tier3 237 1 0.42 333 91 21.46 0 0 NA 509754 TCGA-AB-3011 AML07 8 113631801 113631801 T - DEL CSMD3 NM_198123.2 human genbank 54_36p -1 validated intronic c.4564+275 e27+275 0.041 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 509754 TCGA-AB-3011 AML07 8 116040618 116040618 C T SNP - - - - - - - - - - - - - - - tier3 223 16 6.69 241 175 41.97 0 0 NA 509754 TCGA-AB-3011 AML07 8 124908314 124908314 G A SNP FER1L6 NM_001039112.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-129106 NULL 0 - - - no_errors tier3 569 3 0.52 394 129 24.62 0 0 NA 509754 TCGA-AB-3011 AML07 9 11279051 11279051 C T SNP - - - - - - - - - - - - - - - tier3 231 8 3.35 181 124 40.52 0 0 NA 509754 TCGA-AB-3011 AML07 9 111406619 111406619 C T SNP PALM2 NM_053016.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-36344 NULL 0.682 - - - no_errors tier3 554 27 4.62 509 354 41.02 0 0 NA 509754 TCGA-AB-3011 AML07 9 117391624 117391624 G A SNP - - - - - - - - - - - - - - - tier3 183 0 0 356 87 19.64 0 0 NA 509754 TCGA-AB-3011 AML07 9 132403117 132403117 G A SNP FUBP3 NM_003934.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-41772 NULL 0.131 - - - no_errors tier3 339 13 3.68 83 64 43.54 0 0 NA 509754 TCGA-AB-3011 AML07 9 136662352 136662352 G T SNP COL5A1 NM_000093.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-11503 NULL 0.001 - - - no_errors tier3 72 2 2.7 20 32 61.54 0 0 NA 509754 TCGA-AB-3011 AML07 9 137971444 137971444 C T SNP UBAC1 NM_016172.2 human genbank 54_36p -1 validated intronic c.877-18 e8-18 0.001 - - - no_errors tier2 75 2 2.6 58 45 43.69 2 4 66.67 509754 TCGA-AB-3011 AML07 10 1856346 1856346 G A SNP - - - - - - - - - - - - - - - tier3 933 36 3.7 354 219 38.22 0 0 NA 509754 TCGA-AB-3011 AML07 10 4448959 4448959 C T SNP LOC100128356 XM_001719204.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*23240 NULL 0 - - - no_errors tier3 482 19 3.78 308 170 35.27 0 0 NA 509754 TCGA-AB-3011 AML07 10 9352760 9352760 C T SNP LOC728494 XM_001722163.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*41387 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier2 228 9 3.8 122 72 37.11 0 0 NA 509754 TCGA-AB-3011 AML07 10 23841923 23841923 A G SNP LOC729432 XM_001130241.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*18216 NULL 0.037 - - - no_errors tier3 353 6 1.67 280 189 40.3 0 0 NA 509754 TCGA-AB-3011 AML07 10 26012361 26012361 C T SNP ENSG00000218015 ENST00000405352 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35322 NULL 0.006 - - - no_coding_region:pseudogene tier3 280 1 0.35 214 106 33.12 0 0 NA 509754 TCGA-AB-3011 AML07 10 31544410 31544410 C T SNP ENSG00000209675 ENST00000386940 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-44124 NULL 0.002 - - - pseudogene tier3 327 2 0.61 267 80 23.05 0 0 NA 509754 TCGA-AB-3011 AML07 10 42878789 42878789 T A SNP RET NM_020975.4 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-13924 NULL 0.005 - - - no_errors tier3 77 3 3.7 31 34 52.31 0 0 NA 509754 TCGA-AB-3011 AML07 10 67776373 67776373 A G SNP CTNNA3 NM_013266.1 human genbank 54_36p -1 validated intronic c.1732+32543 e11+32543 0.001 - - - no_errors tier3 138 6 4.17 157 114 41.91 0 0 NA 509754 TCGA-AB-3011 AML07 10 73395648 73395648 C T SNP CHST3 NM_004273.4 human genbank 54_36p 1 reviewed intronic c.1+1190 e0+1190 0 - - - no_errors tier2 210 11 4.95 314 256 44.83 0 0 NA 509754 TCGA-AB-3011 AML07 10 79135062 79135062 T C SNP ENSG00000213514 ENST00000394628 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-25477 NULL 0.001 - - - no_coding_region:pseudogene tier3 659 38 5.42 395 297 42.86 0 1 100 509754 TCGA-AB-3011 AML07 10 83132827 83132827 T G SNP - - - - - - - - - - - - - - - tier3 47 2 4.08 93 71 43.03 0 0 NA 509754 TCGA-AB-3011 AML07 10 116910155 116910155 T A SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.1004+190 e6+190 0.003 - - - no_errors tier3 101 4 3.81 234 141 37.6 0 0 NA 509754 TCGA-AB-3011 AML07 10 117047961 117047961 T C SNP ATRNL1 NM_207303.2 human genbank 54_36p 1 validated intronic c.2416-1573 e16-1573 0.588 - - - no_errors tier3 93 7 6.93 191 124 39.37 0 0 NA 509754 TCGA-AB-3011 AML07 10 123033262 123033262 A G SNP - - - - - - - - - - - - - - - tier3 213 9 4.05 240 159 39.85 0 0 NA 509754 TCGA-AB-3011 AML07 10 128944134 128944134 G T SNP DOCK1 ENST00000398025 human ensembl 54_36p 1 known intronic c.3085-1455 e30-1455 0 - - - no_errors tier3 382 5 1.29 220 55 20 0 0 NA 509754 TCGA-AB-3011 AML07 11 8666236 8666236 G A SNP RPL27A NM_000990.4 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*2307 NULL 0.004 - - - no_errors tier2 677 27 3.84 306 197 39.09 17 23 57.5 509754 TCGA-AB-3011 AML07 11 26039268 26039268 A C SNP - - - - - - - - - - - - - - - tier3 287 3 1.03 205 79 27.72 0 0 NA 509754 TCGA-AB-3011 AML07 11 31042440 31042440 C A SNP uc001msu.1 ENST00000342355 human ensembl 54_36p -1 known intronic c.1448+152 e12+152 0.998 - - - no_errors tier2 216 5 2.26 237 155 39.54 0 0 NA 509754 TCGA-AB-3011 AML07 11 39063880 39063880 G A SNP - - - - - - - - - - - - - - - tier2 138 6 4.17 130 62 32.29 0 0 NA 509754 TCGA-AB-3011 AML07 11 79338135 79338135 G A SNP - - - - - - - - - - - - - - - tier3 298 0 0 211 85 28.72 0 0 NA 509754 TCGA-AB-3011 AML07 11 91269128 91269128 C A SNP - - - - - - - - - - - - - - - tier3 379 15 3.8 179 95 34.67 0 0 NA 509754 TCGA-AB-3011 AML07 11 108178989 108178989 C T SNP DDX10 NM_004398.2 human genbank 54_36p 1 reviewed intronic c.1966-35394 e14-35394 0.002 - - - no_errors tier3 308 6 1.91 199 124 38.39 1 0 0 509754 TCGA-AB-3011 AML07 11 115637423 115637423 G A SNP - - - - - - - - - - - - - - - tier2 618 3 0.48 269 92 25.48 0 0 NA 509754 TCGA-AB-3011 AML07 11 126973112 126973112 C T SNP - - - - - - - - - - - - - - - tier3 235 0 0 394 116 22.75 0 0 NA 509754 TCGA-AB-3011 AML07 12 17157555 17157555 C G SNP ENSG00000212358 ENST00000391056 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-41849 NULL 0 - - - no_errors tier3 292 13 4.25 177 124 41.06 0 0 NA 509754 TCGA-AB-3011 AML07 12 18554116 18554116 A G SNP PIK3C2G ENST00000266497 human ensembl 54_36p 1 known intronic c.3200+4454 e22+4454 0.063 - - - no_errors tier3 113 8 6.61 121 111 47.84 0 0 NA 509754 TCGA-AB-3011 AML07 12 28014166 28014166 T A SNP PTHLH NM_198965.2 human genbank 54_36p -1 reviewed intronic c.1+59 e0+59 0.007 - - - no_errors tier2 196 4 2 210 77 26.74 0 0 NA 509754 TCGA-AB-3011 AML07 12 45890871 45890871 A G SNP FAM113B ENST00000321382 human ensembl 54_36p 1 known intronic c.1-5401 e1-5401 0.16 - - - no_errors tier3 131 1 0.76 96 69 41.57 1 0 0 509754 TCGA-AB-3011 AML07 12 84188148 84188148 A G SNP ALX1 NM_006982.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-10023 NULL 0.007 - - - no_errors tier3 110 5 4.35 66 52 44.07 0 0 NA 509754 TCGA-AB-3011 AML07 13 26906981 26906981 G A SNP GTF3A ENST00000381140 human ensembl 54_36p 1 known missense c.854 p.R285H 1 "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" "HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers" - no_errors tier1 876 34 3.74 361 245 40.43 127 199 61.04 509754 TCGA-AB-3011 AML07 13 29330257 29330257 A T SNP UBL3 NM_007106.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-8582 NULL 0.018 - - - no_errors tier3 365 3 0.81 196 132 40.12 0 0 NA 509754 TCGA-AB-3011 AML07 13 54154358 54154358 T G SNP - - - - - - - - - - - - - - - tier3 92 2 2.13 62 38 38 0 0 NA 509754 TCGA-AB-3011 AML07 13 56154643 56154643 A C SNP - - - - - - - - - - - - - - - tier3 34 0 0 48 15 23.81 0 0 NA 509754 TCGA-AB-3011 AML07 13 62634534 62634534 T A SNP LOC729287 XM_001132996.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*20896 NULL 0.282 - - - no_errors tier3 109 1 0.9 227 63 21.65 0 0 NA 509754 TCGA-AB-3011 AML07 13 82762292 82762292 G T SNP ENSG00000222791 ENST00000410859 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*7915 NULL 0 - - - no_errors tier3 183 3 1.6 166 110 39.86 0 0 NA 509754 TCGA-AB-3011 AML07 13 95952146 95952146 C A SNP HS6ST3 NM_153456.2 human genbank 54_36p 1 validated intronic c.708-330599 e2-330599 0 - - - no_errors tier3 380 7 1.8 229 154 40.1 0 0 NA 509754 TCGA-AB-3011 AML07 14 41886250 41886250 G A SNP ENSG00000222084 ENST00000410152 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*46435 NULL 0.012 - - - no_errors tier3 247 12 4.62 166 91 35.41 0 0 NA 509754 TCGA-AB-3011 AML07 14 84870937 84870937 A G SNP - - - - - - - - - - - - - - - tier3 193 7 3.5 145 120 45.11 0 0 NA 509754 TCGA-AB-3011 AML07 15 36075880 36075880 C T SNP TMCO5A NM_152453.2 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*45153 NULL 0.003 - - - no_errors tier3 362 1 0.28 377 97 20.46 0 0 NA 509754 TCGA-AB-3011 AML07 15 83523852 83523852 C T SNP LOC727858 XM_001126151.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-24595 NULL 0.03 - - - no_errors tier3 94 2 2.08 55 34 38.2 0 0 NA 509754 TCGA-AB-3011 AML07 15 84395039 84395039 G T SNP - - - - - - - - - - - - - - - tier3 381 9 2.31 195 56 22.31 0 0 NA 509754 TCGA-AB-3011 AML07 16 8179918 8179918 T C SNP - - - - - - - - - - - - - - - tier3 776 40 4.9 449 299 39.81 0 0 NA 509754 TCGA-AB-3011 AML07 17 5642206 5642206 C T SNP - - - - - - - - - - - - - - - tier3 524 14 2.59 360 290 44.41 0 0 NA 509754 TCGA-AB-3011 AML07 17 14544415 14544415 C T SNP LOC388339 XM_371019.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*4703 NULL 0.004 - - - pseudogene tier3 460 16 3.36 366 283 43.61 0 0 NA 509754 TCGA-AB-3011 AML07 17 25695121 25695121 G T SNP CPD NM_001304.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-35004 NULL 0.004 - - - no_errors tier3 236 2 0.84 206 63 23.42 0 0 NA 509754 TCGA-AB-3011 AML07 17 28117565 28117565 G A SNP MYO1D NM_015194.1 human genbank 54_36p -1 provisional intronic c.831+1202 e7+1202 0.001 - - - no_errors tier2 249 7 2.7 130 114 46.72 0 0 0 509754 TCGA-AB-3011 AML07 17 28418287 28418287 G T SNP ACCN1 NM_183377.4 human genbank 54_36p -1 reviewed intronic c.987+21707 e3+21707 0.001 - - - no_errors tier3 330 9 2.65 248 219 46.9 0 0 NA 509754 TCGA-AB-3011 AML07 17 38193916 38193916 C T SNP WNK4 NM_032387.3 human genbank 54_36p 1 validated missense c.2005 p.R669W 0.975 NULL "HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase" - no_errors tier1 201 14 6.48 144 110 43.14 NA 509754 TCGA-AB-3011 AML07 17 47835793 47835793 C T SNP - - - - - - - - - - - - - - - tier3 268 7 2.55 226 128 36.16 0 0 NA 509754 TCGA-AB-3011 AML07 17 48882836 48882836 G A SNP - - - - - - - - - - - - - - - tier3 116 1 0.85 107 60 35.93 0 0 NA 509754 TCGA-AB-3011 AML07 17 49332956 49332956 G A SNP - - - - - - - - - - - - - - - tier3 57 0 0 63 27 30 0 0 NA 509754 TCGA-AB-3011 AML07 17 67857507 67857507 T A SNP ENSG00000211264 ENST00000388529 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*20653 NULL 1 - - - pseudogene tier2 527 12 2.22 303 228 42.94 0 0 NA 509754 TCGA-AB-3011 AML07 18 4826541 4826541 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 509754 TCGA-AB-3011 AML07 18 5490295 5490295 C A SNP EPB41L3 NM_012307.2 human genbank 54_36p -1 provisional intronic c.1-11102 e1-11102 1 - - - no_errors tier2 158 1 0.63 150 44 22.68 0 0 NA 509754 TCGA-AB-3011 AML07 18 37160612 37160612 C T SNP - - - - - - - - - - - - - - - tier3 185 11 5.61 116 80 40.82 0 0 NA 509754 TCGA-AB-3011 AML07 18 38513476 38513476 C A SNP - - - - - - - - - - - - - - - tier3 230 2 0.86 354 84 19.18 0 0 NA 509754 TCGA-AB-3011 AML07 18 47890139 47890139 G T SNP - - - - - - - - - - - - - - - tier3 211 7 3.2 171 140 45.02 0 0 NA 509754 TCGA-AB-3011 AML07 19 21912857 21912857 C T SNP ZNF208 NM_007153.2 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*32468 NULL 0 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 32 1 3.03 34 27 44.26 0 0 0 509754 TCGA-AB-3011 AML07 19 54397072 54397072 G A SNP TRPM4 NM_017636.2 human genbank 54_36p 1 provisional missense c.2993 p.G998D 0.061 HMMPfam_Ion_trans HMMPfam_Ion_trans - no_errors tier1 65 4 5.8 90 69 43.12 NA 509754 TCGA-AB-3011 AML07 20 8466337 8466337 T C SNP PLCB1 NM_015192.2 human genbank 54_36p 1 reviewed intronic c.247-90604 e4-90604 0.02 - - - no_errors tier3 342 11 3.11 292 187 39.04 8 7 46.67 509754 TCGA-AB-3011 AML07 20 15971517 15971517 G A SNP MACROD2 NM_080676.1 human genbank 54_36p 1 validated intronic c.1231+1594 e16+1594 0.006 - - - no_errors tier3 262 10 3.65 216 120 35.71 0 0 NA 509754 TCGA-AB-3011 AML07 20 21283662 21283662 T C SNP XRN2 NM_012255.3 human genbank 54_36p 1 reviewed intronic c.2020+152 e21+152 0.233 - - - no_errors tier3 49 0 0 78 42 35 7 17 70.83 509754 TCGA-AB-3011 AML07 20 32166819 32166819 G - DEL EIF2S2 NM_003908.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-3242 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 509754 TCGA-AB-3011 AML07 20 38472401 38472401 G A SNP - - - - - - - - - - - - - - - tier3 301 4 1.31 253 73 22.39 0 0 NA 509754 TCGA-AB-3011 AML07 20 54086532 54086532 G T SNP - - - - - - - - - - - - - - - tier3 544 17 3.01 321 245 43.29 0 0 NA 509754 TCGA-AB-3011 AML07 21 16780477 16780477 G T SNP C21orf34 NM_001005734.1 human genbank 54_36p 1 validated intronic c.315-1204 e4-1204 0 - - - no_errors tier2 261 4 1.5 253 151 37.38 0 0 NA 509754 TCGA-AB-3011 AML07 21 23442616 23442616 C T SNP ENSG00000216619 ENST00000406433 human ensembl 54_36p 1 known 3_prime_flanking_region c.*45349 NULL 0.002 - - - no_coding_region:pseudogene tier3 196 4 2 148 92 38.33 0 0 NA 509754 TCGA-AB-3011 AML07 21 27701405 27701405 A T SNP EIF4A1P ENST00000407743 human ensembl 54_36p -1 known 5_prime_flanking_region c.-39268 NULL 0.001 - - - no_coding_region:pseudogene tier3 302 11 3.5 377 281 42.71 0 0 NA 509754 TCGA-AB-3011 AML07 21 28130492 28130492 G A SNP - - - - - - - - - - - - - - - tier3 106 3 2.75 83 47 36.15 0 0 NA 509754 TCGA-AB-3011 AML07 21 40335466 40335466 C T SNP DSCAM NM_001389.3 human genbank 54_36p -1 validated intronic c.5686+702 e32+702 0.005 - - - no_errors tier3 189 2 1.04 208 118 35.98 0 0 NA 509754 TCGA-AB-3011 AML07 22 21754424 21754424 T - DEL GNAZ NM_002073.2 human genbank 54_36p 1 reviewed intronic c.1+11668 e0+11668 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 Y 7070377 7070377 G A SNP ENSG00000216561 ENST00000402762 human ensembl 54_36p -1 known 5_prime_flanking_region c.-35834 NULL 0.046 - - - no_coding_region:pseudogene tier2 812 1 0.12 69 671 90.68 0 0 NA 673778 TCGA-AB-3012 AML13 Y 8206792 8206792 A - DEL RBMY2KP ENST00000404997 human ensembl 54_36p -1 known 5_prime_flanking_region c.-1563 NULL 0 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 Y 11695289 11695289 C T SNP - - - - - - - - - - - - - - - tier3 422 0 0 33 190 84.82 0 0 NA 673778 TCGA-AB-3012 AML13 Y 17201001 17201001 T A SNP - - - - - - - - - - - - - - - tier3 408 0 0 914 131 12.54 0 0 NA 673778 TCGA-AB-3012 AML13 X 19020872 19020872 G A SNP GPR64 NM_001079858.1 human genbank 54_36p -1 validated intronic c.1-10087 e1-10087 0.002 - - - no_errors tier3 1117 1 0.09 69 633 89.91 0 1 100 673778 TCGA-AB-3012 AML13 X 29046745 29046745 C A SNP IL1RAPL1 NM_014271.3 human genbank 54_36p 1 reviewed intronic c.83-164231 e2-164231 0.005 - - - no_errors tier3 527 0 0 668 272 28.94 0 0 NA 673778 TCGA-AB-3012 AML13 X 32062643 32062643 C T SNP DMD NM_004006.2 human genbank 54_36p -1 reviewed intronic c.6438+82311 e44+82311 0 - - - no_errors tier3 415 0 0 233 347 59.62 0 0 NA 673778 TCGA-AB-3012 AML13 X 69333738 69333738 T C SNP DGAT2L6 NM_198512.1 human genbank 54_36p 1 provisional intronic c.86-2108 e2-2108 0.019 - - - no_errors tier2 1027 1 0.1 97 872 89.9 0 0 NA 673778 TCGA-AB-3012 AML13 X 83015361 83015361 C A SNP CYLC1 NM_021118.1 human genbank 54_36p 1 provisional missense c.989 p.T330K 0.027 NULL NULL - no_errors tier1 809 2 0.25 96 734 88.43 NA 673778 TCGA-AB-3012 AML13 X 84847587 84847587 G T SNP - - - - - - - - - - - - - - - tier3 222 0 0 281 48 14.59 0 0 NA 673778 TCGA-AB-3012 AML13 X 97285110 97285110 G A SNP - - - - - - - - - - - - - - - tier3 497 0 0 486 309 38.77 0 0 NA 673778 TCGA-AB-3012 AML13 X 98091339 98091340 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 X 109766869 109766869 C T SNP ENSG00000220162 ENST00000406794 human ensembl 54_36p 1 known 3_prime_untranslated_region c.*109766869 NULL 0.027 - - - no_coding_region:pseudogene tier3 806 1 0.12 771 110 12.47 0 0 NA 673778 TCGA-AB-3012 AML13 X 110533000 110533000 C G SNP DCX NM_000555.2 human genbank 54_36p -1 reviewed intronic c.608-1786 e3-1786 0 - - - no_errors tier3 691 2 0.29 109 714 86.44 0 0 NA 673778 TCGA-AB-3012 AML13 X 112096240 112096240 C A SNP ENSG00000217750 ENST00000405507 human ensembl 54_36p 1 known 3_prime_flanking_region c.*48595 NULL 0.009 - - - no_coding_region:pseudogene tier3 508 0 0 67 622 90.28 0 0 NA 673778 TCGA-AB-3012 AML13 X 127566672 127566672 G A SNP ENSG00000223339 ENST00000411407 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*18808 NULL 0.003 - - - no_errors tier3 650 1 0.15 47 331 87.34 0 0 NA 673778 TCGA-AB-3012 AML13 X 133345232 133345232 T A SNP PHF6 NM_001015877.1 human genbank 54_36p 1 reviewed intronic c.240+5430 e2+5430 0.007 - - - no_errors tier3 348 0 0 57 591 91.2 0 0 0 673778 TCGA-AB-3012 AML13 X 135709099 135709099 G A SNP ARHGEF6 NM_004840.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-18392 NULL 0 - - - no_errors tier2 1487 3 0.2 650 444 40.51 0 0 NA 673778 TCGA-AB-3012 AML13 X 140274787 140274787 C T SNP ENSG00000220346 ENST00000407507 human ensembl 54_36p 1 known 5_prime_flanking_region c.-27866 NULL 0.006 - - - no_coding_region:pseudogene tier2 581 1 0.17 75 607 89 0 0 NA 673778 TCGA-AB-3012 AML13 X 141820566 141820566 T C SNP ENSG00000208499 ENST00000385764 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-31055 NULL 0.307 - - - pseudogene tier3 238 0 0 46 419 90.11 0 0 NA 673778 TCGA-AB-3012 AML13 X 142968647 142968647 C A SNP - - - - - - - - - - - - - - - tier3 547 1 0.18 243 489 66.62 0 0 NA 673778 TCGA-AB-3012 AML13 X 145155874 145155874 C A SNP - - - - - - - - - - - - - - - tier2 343 1 0.29 321 136 29.76 0 0 NA 673778 TCGA-AB-3012 AML13 X 152133458 152133458 G T SNP ENSG00000218770 ENST00000403785 human ensembl 54_36p -1 known 5_prime_flanking_region c.-17922 NULL 0 - - - no_coding_region:pseudogene tier3 454 0 0 117 176 59.86 0 0 NA 673778 TCGA-AB-3012 AML13 1 5489323 5489323 G A SNP - - - - - - - - - - - - - - - tier3 889 0 0 469 401 46.04 0 0 NA 673778 TCGA-AB-3012 AML13 1 9369079 9369079 C T SNP SPSB1 NM_025106.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*18858 NULL 0.002 - - - no_errors tier2 797 1 0.13 400 330 45.08 0 0 NA 673778 TCGA-AB-3012 AML13 1 10150617 10150617 T A SNP UBE4B NM_001105562.1 human genbank 54_36p 1 reviewed intronic c.3199-164 e24-164 0 - - - no_errors tier2 1208 0 0 1155 150 11.45 2 0 0 673778 TCGA-AB-3012 AML13 1 16440747 16440747 C T SNP LOC645652 XM_928668.1 human genbank 54_36p -1 model intronic c.166-241 e3-241 0.004 - - - no_errors tier3 566 1 0.18 296 246 45.39 8 13 61.9 673778 TCGA-AB-3012 AML13 1 16915186 16915186 C T SNP ESPNP ENST00000270691 human ensembl 54_36p -1 known intronic c.194+3860 e1+3860 0.007 - - - no_start_codon tier3 1419 4 0.28 621 156 20.08 0 0 NA 673778 TCGA-AB-3012 AML13 1 29726645 29726645 C T SNP ENSG00000219178 ENST00000404255 human ensembl 54_36p -1 known 5_prime_flanking_region c.-30653 NULL 0 - - - no_coding_region:pseudogene tier3 761 1 0.13 523 271 34.13 0 0 NA 673778 TCGA-AB-3012 AML13 1 31285449 31285449 C T SNP PUM1 NM_001020658.1 human genbank 54_36p -1 reviewed intronic c.364-11151 e2-11151 0.009 - - - no_errors tier3 1051 2 0.19 422 150 26.22 3 2 40 673778 TCGA-AB-3012 AML13 1 38727633 38727633 G A SNP - - - - - - - - - - - - - - - tier3 2533 6 0.24 1007 841 45.41 0 0 NA 673778 TCGA-AB-3012 AML13 1 43656888 43656888 G A SNP C1orf84 ENST00000406439 human ensembl 54_36p 1 known intronic c.880-1104 e8-1104 0.065 - - - no_errors tier3 1519 2 0.13 856 725 45.74 0 0 0 673778 TCGA-AB-3012 AML13 1 43887372 43887372 A G SNP JMJD2A NM_014663.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-4062 NULL 0.69 - - - no_errors tier2 449 1 0.22 277 257 47.95 1 0 0 673778 TCGA-AB-3012 AML13 1 59472451 59472451 C T SNP - - - - - - - - - - - - - - - tier3 1024 0 0 813 588 41.94 0 0 NA 673778 TCGA-AB-3012 AML13 1 64736624 64736624 G A SNP CACHD1 NM_020925.2 human genbank 54_36p 1 validated intronic c.45+27411 e1+27411 0.002 - - - no_errors tier3 693 3 0.43 328 270 45 0 0 NA 673778 TCGA-AB-3012 AML13 1 68926008 68926008 G A SNP - - - - - - - - - - - - - - - tier2 670 0 0 978 767 43.93 0 0 NA 673778 TCGA-AB-3012 AML13 1 74349160 74349160 C T SNP LRRIQ3 NM_001105659.1 human genbank 54_36p -1 inferred intronic c.708-1335 e4-1335 0 - - - no_errors tier3 992 2 0.2 710 606 45.98 0 0 NA 673778 TCGA-AB-3012 AML13 1 79617501 79617501 C T SNP - - - - - - - - - - - - - - - tier2 568 4 0.7 470 359 43.2 0 0 NA 673778 TCGA-AB-3012 AML13 1 80476770 80476770 A G SNP ENSG00000218484 ENST00000402916 human ensembl 54_36p 1 known 5_prime_flanking_region c.-44855 NULL 0 - - - no_coding_region:pseudogene tier3 500 0 0 331 263 44.28 0 0 NA 673778 TCGA-AB-3012 AML13 1 80911067 80911067 A G SNP - - - - - - - - - - - - - - - tier3 269 0 0 356 298 45.5 0 0 NA 673778 TCGA-AB-3012 AML13 1 81114311 81114311 T C SNP - - - - - - - - - - - - - - - tier2 816 4 0.49 763 712 48.21 0 0 NA 673778 TCGA-AB-3012 AML13 1 81752466 81752466 T C SNP LPHN2 ENST00000370725 human ensembl 54_36p 1 known intronic c.1-66683 e1-66683 0.001 - - - no_errors tier3 399 0 0 84 339 80.14 0 0 NA 673778 TCGA-AB-3012 AML13 1 86874200 86874200 G A SNP CLCA3 ENST00000284054 human ensembl 54_36p 1 known intronic c.301-27 e3-27 0.002 - - - no_errors tier3 275 0 0 346 278 44.55 0 0 NA 673778 TCGA-AB-3012 AML13 1 90747891 90747891 A G SNP - - - - - - - - - - - - - - - tier3 799 2 0.25 1484 382 20.47 0 0 NA 673778 TCGA-AB-3012 AML13 1 97990432 97990432 C T SNP DPYD NM_000110.3 human genbank 54_36p -1 reviewed intronic c.234-11809 e4-11809 0 - - - no_errors tier3 187 3 1.58 228 226 49.78 0 0 0 673778 TCGA-AB-3012 AML13 1 98369218 98369218 G T SNP - - - - - - - - - - - - - - - tier3 511 0 0 555 422 43.15 0 0 NA 673778 TCGA-AB-3012 AML13 1 101113353 101113353 T C SNP EXTL2 NM_001033025.1 human genbank 54_36p -1 validated intronic c.505-779 e4-779 0 - - - no_errors tier3 697 1 0.14 669 549 45.07 2 0 0 673778 TCGA-AB-3012 AML13 1 101313213 101313213 A G SNP DPH5 NM_001077394.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49626 NULL 0.186 - - - no_errors tier2 614 0 0 929 653 41.28 1 1 50 673778 TCGA-AB-3012 AML13 1 106141135 106141136 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 1 109825976 109825976 C T SNP SYPL2 NM_001040709.1 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*2283 NULL 0.052 - - - no_errors tier2 826 1 0.12 261 208 44.35 0 0 NA 673778 TCGA-AB-3012 AML13 1 112122071 112122071 C T SNP KCND3 NM_004980.3 human genbank 54_36p -1 reviewed intronic c.1518+510 e5+510 0 - - - no_errors tier3 2771 6 0.22 777 626 44.62 0 0 NA 673778 TCGA-AB-3012 AML13 1 115269725 115269725 C T SNP SYCP1 NM_003176.2 human genbank 54_36p 1 validated intronic c.1801-697 e21-697 0 - - - no_errors tier3 524 2 0.38 397 305 43.45 0 0 NA 673778 TCGA-AB-3012 AML13 1 116593657 116593657 G A SNP ENSG00000221040 ENST00000408113 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-29094 NULL 0.002 - - - no_errors tier3 1773 0 0 816 674 45.2 0 0 NA 673778 TCGA-AB-3012 AML13 1 148510573 148510573 T G SNP C1orf54 ENST00000369102 human ensembl 54_36p 1 known intronic c.1-738 e1-738 0.002 - - - no_errors tier3 1027 3 0.29 393 330 45.64 0 0 NA 673778 TCGA-AB-3012 AML13 1 157641996 157641996 G A SNP OR10J9P ENST00000404061 human ensembl 54_36p -1 known 5_prime_untranslated_region c.-157641996 NULL 0.002 - - - no_coding_region:pseudogene tier3 434 1 0.23 509 362 41.56 0 0 NA 673778 TCGA-AB-3012 AML13 1 166689502 166689502 G T SNP ENSG00000215833 ENST00000400977 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-2450 NULL 0.015 - - - no_coding_region:pseudogene tier3 1359 1 0.07 1242 988 44.25 0 0 NA 673778 TCGA-AB-3012 AML13 1 179456646 179456646 G A SNP ENSG00000179452 ENST00000319701 human ensembl 54_36p 1 known 5_prime_flanking_region c.-15501 NULL 0.656 - - - no_errors tier2 968 2 0.21 538 387 41.75 0 0 NA 673778 TCGA-AB-3012 AML13 1 187148885 187148885 T C SNP - - - - - - - - - - - - - - - tier3 334 0 0 419 177 29.7 0 0 NA 673778 TCGA-AB-3012 AML13 1 188473990 188473990 T A SNP FAM5C NM_199051.1 human genbank 54_36p -1 provisional intronic c.619-3760 e4-3760 0 - - - no_errors tier3 123 1 0.81 359 192 34.85 0 0 NA 673778 TCGA-AB-3012 AML13 1 193022788 193022788 A T SNP - - - - - - - - - - - - - - - tier3 614 0 0 584 446 43.3 0 0 NA 673778 TCGA-AB-3012 AML13 1 209044386 209044386 C G SNP KCNH1 NM_172362.3 human genbank 54_36p -1 reviewed intronic c.1463-255 e8-255 0.011 - - - no_errors tier3 659 0 0 638 451 41.34 0 0 NA 673778 TCGA-AB-3012 AML13 1 210462704 210462704 G A SNP LOC643143 XM_931358.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*2743 NULL 0 - - - no_errors tier2 1154 1 0.09 590 371 38.61 0 0 NA 673778 TCGA-AB-3012 AML13 1 211606017 211606017 G A SNP - - - - - - - - - - - - - - - tier3 985 0 0 556 482 46.35 0 0 NA 673778 TCGA-AB-3012 AML13 1 212206066 212206066 C A SNP PROX1 NM_002763.3 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-30436 NULL 0 - - - no_errors tier3 2565 4 0.16 620 489 44.09 0 0 NA 673778 TCGA-AB-3012 AML13 1 216213967 216213967 C A SNP - - - - - - - - - - - - - - - tier3 571 0 0 1052 114 9.78 0 0 NA 673778 TCGA-AB-3012 AML13 1 217941399 217941399 G A SNP ENSG00000222688 ENST00000410756 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*37967 NULL 0.015 - - - no_errors tier3 2901 4 0.14 1678 1340 44.4 0 0 NA 673778 TCGA-AB-3012 AML13 1 221674373 221674373 A G SNP C1orf65 NM_152610.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*39061 NULL 0.003 - - - no_errors tier3 1211 5 0.41 460 349 43.09 0 0 NA 673778 TCGA-AB-3012 AML13 1 229300963 229300963 C T SNP ENSG00000220221 ENST00000405247 human ensembl 54_36p -1 known 3_prime_flanking_region c.*19237 NULL 0.001 - - - no_coding_region:pseudogene tier3 1650 5 0.3 989 747 43.03 0 0 NA 673778 TCGA-AB-3012 AML13 1 230741956 230741956 G A SNP LOC729336 XM_001129978.2 human genbank 54_36p -1 model intronic c.1318-23979 e6-23979 0.001 - - - no_errors tier3 1126 0 0 859 668 43.69 0 0 NA 673778 TCGA-AB-3012 AML13 1 235714362 235714362 G A SNP RYR2 NM_001035.2 human genbank 54_36p 1 reviewed intronic c.1709-7367 e18-7367 0.001 - - - no_errors tier3 642 0 0 483 390 44.62 0 0 NA 673778 TCGA-AB-3012 AML13 1 239032800 239032800 A - DEL RGS7 NM_002924.4 human genbank 54_36p -1 validated intronic c.1359+27 e15+27 0.007 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 1 243508101 243508101 C T SNP KIF26B NM_018012.3 human genbank 54_36p 1 provisional intronic c.466-88658 e3-88658 0.893 - - - no_errors tier3 1737 3 0.17 1029 807 43.91 1 0 0 673778 TCGA-AB-3012 AML13 2 5458300 5458300 G A SNP - - - - - - - - - - - - - - - tier3 588 2 0.34 515 302 36.78 0 0 NA 673778 TCGA-AB-3012 AML13 2 6253626 6253626 C T SNP - - - - - - - - - - - - - - - tier2 740 3 0.4 1154 812 41.28 0 0 NA 673778 TCGA-AB-3012 AML13 2 8031511 8031511 G A SNP - - - - - - - - - - - - - - - tier2 1114 3 0.27 644 528 45.01 0 0 NA 673778 TCGA-AB-3012 AML13 2 14032425 14032425 T C SNP - - - - - - - - - - - - - - - tier3 411 1 0.24 394 272 40.78 0 0 NA 673778 TCGA-AB-3012 AML13 2 19703474 19703474 C T SNP - - - - - - - - - - - - - - - tier2 843 3 0.35 436 337 43.54 0 0 NA 673778 TCGA-AB-3012 AML13 2 22084915 22084915 A T SNP - - - - - - - - - - - - - - - tier3 2614 3 0.11 1038 730 41.27 0 0 NA 673778 TCGA-AB-3012 AML13 2 29668597 29668597 C T SNP ALK NM_004304.3 human genbank 54_36p -1 reviewed intronic c.953-60111 e4-60111 0 - - - no_errors tier3 639 0 0 358 253 41.41 0 0 NA 673778 TCGA-AB-3012 AML13 2 33026912 33026912 T C SNP LTBP1 NM_206943.2 human genbank 54_36p 1 reviewed intronic c.494+523 e1+523 0 - - - no_errors tier2 238 2 0.83 141 102 41.98 0 0 0 673778 TCGA-AB-3012 AML13 2 33455831 33455831 G A SNP LTBP1 NM_206943.2 human genbank 54_36p 1 reviewed intronic c.4714+11757 e31+11757 0 - - - no_errors tier2 1325 1 0.08 793 668 45.69 0 0 0 673778 TCGA-AB-3012 AML13 2 33521766 33521766 C T SNP RASGRP3 NM_170672.1 human genbank 54_36p 1 validated intronic c.1-4625 e1-4625 0 - - - no_errors tier3 589 1 0.17 423 345 44.92 0 0 NA 673778 TCGA-AB-3012 AML13 2 35082739 35082739 A T SNP LOC730189 XM_001719191.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*30511 NULL 0 - - - no_start_codon:pseudogene:no_stop_codon tier3 437 0 0 470 78 14.23 0 0 NA 673778 TCGA-AB-3012 AML13 2 35495389 35495389 C T SNP - - - - - - - - - - - - - - - tier3 908 1 0.11 661 79 10.68 0 0 NA 673778 TCGA-AB-3012 AML13 2 45223252 45223252 C T SNP ENSG00000205054 ENST00000378479 human ensembl 54_36p -1 known 3_prime_flanking_region c.*32558 NULL 0.012 - - - no_errors tier2 1662 7 0.42 654 547 45.51 0 0 NA 673778 TCGA-AB-3012 AML13 2 47213429 47213429 A G SNP C2orf61 NM_173649.1 human genbank 54_36p -1 predicted intronic c.400-2526 e4-2526 0.015 - - - no_errors tier3 1071 0 0 500 392 43.9 0 1 100 673778 TCGA-AB-3012 AML13 2 56281300 56281300 G C SNP CCDC85A NM_001080433.1 human genbank 54_36p 1 provisional intronic c.1240+7221 e2+7221 0.023 - - - no_errors tier3 818 1 0.12 502 437 46.54 0 0 NA 673778 TCGA-AB-3012 AML13 2 64308585 64308585 A G SNP - - - - - - - - - - - - - - - tier3 1562 2 0.13 653 577 46.87 0 0 NA 673778 TCGA-AB-3012 AML13 2 64662696 64662696 A G SNP AFTPH NM_203437.1 human genbank 54_36p 1 validated intronic c.2539+785 e7+785 0.999 - - - no_errors tier2 261 1 0.38 370 253 40.61 2 2 50 673778 TCGA-AB-3012 AML13 2 65725056 65725056 G A SNP LOC100131818 XM_001725646.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-10432 NULL 0.004 - - - no_errors tier3 1208 0 0 814 538 39.79 0 0 NA 673778 TCGA-AB-3012 AML13 2 67006182 67006182 G A SNP - - - - - - - - - - - - - - - tier3 917 0 0 675 547 44.65 0 0 NA 673778 TCGA-AB-3012 AML13 2 72116297 72116297 G A SNP - - - - - - - - - - - - - - - tier3 337 0 0 329 265 44.61 0 0 NA 673778 TCGA-AB-3012 AML13 2 74922309 74922309 C T SNP HK2 NM_000189.4 human genbank 54_36p 1 reviewed intronic c.63+7031 e1+7031 0 - - - no_errors tier3 1426 5 0.35 405 341 45.47 4 4 50 673778 TCGA-AB-3012 AML13 2 76078448 76078448 G A SNP - - - - - - - - - - - - - - - tier3 467 0 0 568 365 39.08 0 0 NA 673778 TCGA-AB-3012 AML13 2 77594063 77594063 C T SNP LRRTM4 ENST00000409911 human ensembl 54_36p -1 known intronic c.1554+4889 e2+4889 0 - - - no_errors tier3 748 0 0 982 403 29.1 0 0 NA 673778 TCGA-AB-3012 AML13 2 79068820 79068820 C G SNP REG3G NM_001008387.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-37908 NULL 0.002 - - - no_errors tier3 876 0 0 880 689 43.86 0 0 NA 673778 TCGA-AB-3012 AML13 2 83042935 83042935 A C SNP - - - - - - - - - - - - - - - tier3 540 1 0.18 389 305 43.95 0 0 NA 673778 TCGA-AB-3012 AML13 2 104081007 104081007 G A SNP LOC728838 XM_001128590.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*4148 NULL 0.005 - - - no_errors tier3 823 0 0 612 461 42.92 0 0 NA 673778 TCGA-AB-3012 AML13 2 107372282 107372282 G A SNP - - - - - - - - - - - - - - - tier3 603 1 0.16 628 479 43.19 0 0 NA 673778 TCGA-AB-3012 AML13 2 111349371 111349371 T C SNP ACOXL NM_001105516.2 human genbank 54_36p 1 validated intronic c.789-33466 e10-33466 0.005 - - - no_errors tier3 477 1 0.21 631 494 43.87 0 0 NA 673778 TCGA-AB-3012 AML13 2 115836513 115836513 G A SNP DPP10 NM_020868.2 human genbank 54_36p 1 reviewed intronic c.271+18555 e3+18555 0 - - - no_errors tier3 464 0 0 467 296 38.74 0 0 0 673778 TCGA-AB-3012 AML13 2 116478861 116478861 A G SNP - - - - - - - - - - - - - - - tier3 1286 4 0.31 1063 540 33.67 0 0 NA 673778 TCGA-AB-3012 AML13 2 119197357 119197357 T G SNP - - - - - - - - - - - - - - - tier2 1359 2 0.15 628 429 40.47 0 0 NA 673778 TCGA-AB-3012 AML13 2 123059708 123059708 T C SNP - - - - - - - - - - - - - - - tier3 263 1 0.38 313 271 46.4 0 0 NA 673778 TCGA-AB-3012 AML13 2 125441547 125441547 G A SNP ENSG00000206726 ENST00000383999 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-21719 NULL 0 - - - no_errors tier3 871 2 0.23 466 334 41.75 0 0 NA 673778 TCGA-AB-3012 AML13 2 126002889 126002889 A C SNP - - - - - - - - - - - - - - - tier3 913 0 0 843 580 40.7 0 0 NA 673778 TCGA-AB-3012 AML13 2 133921381 133921381 G A SNP NAP5 NM_207363.2 human genbank 54_36p -1 validated intronic c.69+70118 e1+70118 0 - - - no_errors tier3 1641 8 0.48 1248 1005 44.61 0 0 NA 673778 TCGA-AB-3012 AML13 2 154721642 154721642 C T SNP GALNT13 NM_052917.2 human genbank 54_36p 1 validated intronic c.311+16378 e2+16378 0.002 - - - no_errors tier3 1066 0 0 1180 827 41.21 0 0 NA 673778 TCGA-AB-3012 AML13 2 163619322 163619322 C T SNP - - - - - - - - - - - - - - - tier3 839 0 0 356 286 44.55 0 0 NA 673778 TCGA-AB-3012 AML13 2 167614149 167614149 T C SNP XIRP2 NM_152381.2 human genbank 54_36p 1 validated intronic c.409-86516 e2-86516 0.003 - - - no_errors tier3 275 0 0 475 357 42.86 0 0 NA 673778 TCGA-AB-3012 AML13 2 184095444 184095444 G A SNP - - - - - - - - - - - - - - - tier2 1242 1 0.08 544 240 30.57 0 0 NA 673778 TCGA-AB-3012 AML13 2 188178449 188178449 G A SNP - - - - - - - - - - - - - - - tier3 435 0 0 393 310 43.97 0 0 NA 673778 TCGA-AB-3012 AML13 2 195548862 195548862 T C SNP - - - - - - - - - - - - - - - tier3 1271 1 0.08 622 482 43.62 0 1 100 673778 TCGA-AB-3012 AML13 2 199858753 199858753 G A SNP SATB2 NM_015265.2 human genbank 54_36p -1 validated intronic c.1741-13113 e10-13113 1 - - - no_errors tier2 1651 1 0.06 1396 973 41.07 0 0 0 673778 TCGA-AB-3012 AML13 2 199860141 199860141 G A SNP SATB2 NM_015265.2 human genbank 54_36p -1 validated intronic c.1741-14501 e10-14501 0.091 - - - no_errors tier2 1220 0 0 926 761 45.11 0 0 0 673778 TCGA-AB-3012 AML13 2 199902618 199902618 C T SNP SATB2 NM_015265.2 human genbank 54_36p -1 validated intronic c.1174-740 e7-740 0 - - - no_errors tier3 873 0 0 768 406 34.52 0 0 0 673778 TCGA-AB-3012 AML13 2 202355526 202355526 C T SNP ALS2 NM_020919.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-13673 NULL 0.626 - - - no_errors tier2 532 1 0.19 265 166 38.43 0 0 NA 673778 TCGA-AB-3012 AML13 2 205892199 205892199 G A SNP PARD3B NM_152526.5 human genbank 54_36p 1 validated intronic c.2444+17529 e17+17529 0 - - - no_errors tier3 1294 1 0.08 802 654 44.86 0 0 NA 673778 TCGA-AB-3012 AML13 2 206529869 206529869 C T SNP INO80D NM_017759.4 human genbank 54_36p -1 validated 3_prime_flanking_region c.*47468 NULL 0.034 - - - no_errors tier3 1217 1 0.08 673 539 44.4 0 0 NA 673778 TCGA-AB-3012 AML13 2 208978305 208978305 G C SNP PTH2R NM_005048.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-1709 NULL 0.064 - - - no_errors tier2 381 1 0.26 307 191 38.28 0 0 0 673778 TCGA-AB-3012 AML13 2 210356581 210356581 C A SNP C2orf21 NM_182587.1 human genbank 54_36p 1 validated intronic c.601-2454 e5-2454 0.005 - - - no_errors tier2 611 0 0 413 208 33.49 0 0 NA 673778 TCGA-AB-3012 AML13 2 211633700 211633700 C G SNP - - - - - - - - - - - - - - - tier2 1106 0 0 721 546 43.09 0 0 NA 673778 TCGA-AB-3012 AML13 2 211986367 211986367 C A SNP ERBB4 NM_005235.1 human genbank 54_36p -1 reviewed intronic c.3135+7044 e25+7044 0.003 - - - no_errors tier3 2608 9 0.34 787 270 25.47 0 0 NA 673778 TCGA-AB-3012 AML13 2 213169231 213169231 G A SNP - - - - - - - - - - - - - - - tier3 474 0 0 421 302 41.66 0 0 NA 673778 TCGA-AB-3012 AML13 2 216038012 216038012 C A SNP FN1 NM_212482.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-29242 NULL 0.339 - - - no_errors tier3 1297 2 0.15 840 581 40.8 0 0 NA 673778 TCGA-AB-3012 AML13 2 222862922 222862922 G C SNP PAX3 NM_181459.4 human genbank 54_36p -1 reviewed intronic c.586+4208 e4+4208 0.003 - - - no_errors tier3 812 3 0.37 526 382 42.02 0 0 NA 673778 TCGA-AB-3012 AML13 2 224112065 224112065 G C SNP - - - - - - - - - - - - - - - tier3 885 0 0 1066 140 11.61 0 0 NA 673778 TCGA-AB-3012 AML13 2 226346305 226346305 C T SNP - - - - - - - - - - - - - - - tier3 837 0 0 438 286 39.39 0 0 NA 673778 TCGA-AB-3012 AML13 2 226941700 226941700 G A SNP - - - - - - - - - - - - - - - tier2 2533 4 0.16 1274 1017 44.35 0 0 NA 673778 TCGA-AB-3012 AML13 2 232848379 232848380 - T INS DIS3L2 NM_152383.4 human genbank 54_36p 1 validated intronic c.1659+11985_1659+11984 e12+11985 0.005:0.002 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 2 236181491 236181491 G A SNP AGAP1 NM_001037131.1 human genbank 54_36p 1 validated intronic c.164-101071 e2-101071 0.001 - - - no_errors tier3 743 2 0.27 400 321 44.4 0 0 NA 673778 TCGA-AB-3012 AML13 2 237321102 237321102 A G SNP - - - - - - - - - - - - - - - tier2 750 3 0.4 536 399 42.63 0 0 NA 673778 TCGA-AB-3012 AML13 2 237986957 237986957 G A SNP COL6A3 NM_004369.3 human genbank 54_36p -1 reviewed intronic c.1+378 e0+378 0 - - - no_errors tier3 851 0 0 524 457 46.59 0 0 0 673778 TCGA-AB-3012 AML13 2 240403453 240403453 C A SNP ENSG00000213827 ENST00000396488 human ensembl 54_36p 1 known intronic c.70-2541 e3-2541 0.013 - - - no_start_codon:no_stop_codon tier3 2067 0 0 471 419 47.08 1 0 0 673778 TCGA-AB-3012 AML13 3 10401646 10401646 C T SNP ATP2B2 NM_001001331.2 human genbank 54_36p -1 reviewed intronic c.1000+306 e7+306 0.002 - - - no_errors tier3 1152 2 0.17 339 262 43.59 0 0 NA 673778 TCGA-AB-3012 AML13 3 21196941 21196941 G T SNP ENSG00000221659 ENST00000408732 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-42104 NULL 0 - - - no_errors tier3 294 0 0 252 148 36.91 0 0 NA 673778 TCGA-AB-3012 AML13 3 21276149 21276149 A G SNP - - - - - - - - - - - - - - - tier2 852 1 0.12 544 481 46.93 0 0 NA 673778 TCGA-AB-3012 AML13 3 25317834 25317834 G A SNP RARB ENST00000404969 human ensembl 54_36p 1 known intronic c.178+126764 e1+126764 0 - - - no_errors tier3 1403 4 0.28 830 588 41.41 0 0 NA 673778 TCGA-AB-3012 AML13 3 26594989 26594989 C G SNP LRRC3B NM_052953.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-131179 NULL 0 - - - no_errors tier3 867 1 0.12 701 504 41.76 0 0 NA 673778 TCGA-AB-3012 AML13 3 27089906 27089906 T C SNP NEK10 ENST00000396636 human ensembl 54_36p -1 known 3_prime_flanking_region c.*37861 NULL 0.996 - - - no_errors tier3 978 1 0.1 646 471 42.09 0 0 NA 673778 TCGA-AB-3012 AML13 3 31825452 31825452 A C SNP OSBPL10 NM_017784.3 human genbank 54_36p -1 reviewed intronic c.729+21084 e4+21084 0 - - - no_errors tier3 767 2 0.26 593 457 43.52 0 0 NA 673778 TCGA-AB-3012 AML13 3 36118717 36118717 G A SNP - - - - - - - - - - - - - - - tier3 926 1 0.11 604 433 41.67 0 0 NA 673778 TCGA-AB-3012 AML13 3 36244686 36244686 G C SNP LOC100133753 XM_001718068.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*37270 NULL 0.01 - - - no_start_codon:pseudogene:no_stop_codon tier3 1800 1 0.06 1159 150 11.45 0 0 NA 673778 TCGA-AB-3012 AML13 3 38396248 38396248 A G SNP XYLB NM_005108.2 human genbank 54_36p 1 reviewed intronic c.1291+411 e15+411 0.001 - - - no_errors tier3 976 2 0.2 640 502 43.88 0 0 0 673778 TCGA-AB-3012 AML13 3 54906809 54906809 C T SNP CACNA2D3 NM_018398.2 human genbank 54_36p 1 reviewed intronic c.2368+872 e26+872 0 - - - no_errors tier3 590 0 0 720 539 42.81 0 0 NA 673778 TCGA-AB-3012 AML13 3 55814813 55814813 G A SNP ERC2 NM_015576.1 human genbank 54_36p -1 validated intronic c.2565-70827 e14-70827 0.001 - - - no_errors tier3 617 1 0.16 604 530 46.7 0 0 NA 673778 TCGA-AB-3012 AML13 3 65849079 65849079 T C SNP MAGI1 NM_001033057.1 human genbank 54_36p -1 reviewed intronic c.313+149632 e1+149632 0.002 - - - no_errors tier3 1221 5 0.41 1250 970 43.69 0 0 NA 673778 TCGA-AB-3012 AML13 3 71428134 71428134 G T SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.1+3527 e0+3527 0 - - - no_errors tier2 1284 1 0.08 767 592 43.53 8 8 50 673778 TCGA-AB-3012 AML13 3 71603672 71603672 A G SNP FOXP1 NM_032682.1 human genbank 54_36p -1 reviewed intronic c.1+21595 e0+21595 0 - - - no_errors tier3 1182 4 0.34 847 610 41.87 3 2 40 673778 TCGA-AB-3012 AML13 3 74026149 74026149 C T SNP - - - - - - - - - - - - - - - tier2 842 1 0.12 676 533 44.09 0 0 NA 673778 TCGA-AB-3012 AML13 3 74650044 74650044 G A SNP CNTN3 NM_020872.1 human genbank 54_36p -1 validated intronic c.55+2855 e1+2855 0.001 - - - no_errors tier3 902 2 0.22 840 203 19.44 0 0 NA 673778 TCGA-AB-3012 AML13 3 77382339 77382339 G A SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.388+152158 e2+152158 0 - - - no_errors tier3 560 0 0 573 443 43.6 0 0 NA 673778 TCGA-AB-3012 AML13 3 77454181 77454181 T C SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.389-155074 e3-155074 0.061 - - - no_errors tier2 402 0 0 434 308 41.45 0 0 NA 673778 TCGA-AB-3012 AML13 3 77741484 77741484 A C SNP ROBO2 NM_002942.1 human genbank 54_36p 1 reviewed intronic c.3293+1689 e21+1689 0 - - - no_errors tier3 488 1 0.2 284 213 42.77 0 0 0 673778 TCGA-AB-3012 AML13 3 77990696 77990696 A - DEL ENSG00000206891 ENST00000384164 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-47011 NULL 0 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 3 84040687 84040687 G A SNP - - - - - - - - - - - - - - - tier3 444 1 0.22 329 297 47.44 0 0 NA 673778 TCGA-AB-3012 AML13 3 84075944 84075944 C G SNP - - - - - - - - - - - - - - - tier3 399 0 0 326 234 41.79 0 0 NA 673778 TCGA-AB-3012 AML13 3 85291701 85291701 T C SNP CADM2 ENST00000407528 human ensembl 54_36p 1 known intronic c.61+200192 e1+200192 0.006 - - - no_errors tier3 503 2 0.4 478 327 40.57 0 0 NA 673778 TCGA-AB-3012 AML13 3 86197499 86197499 T G SNP CADM2 NM_153184.2 human genbank 54_36p 1 validated missense c.1124 p.I375R 1 NULL "HMMSmart_4.1m,HMMSmart_IGc2,HMMSmart_IG,HMMPfam_V-set,HMMPfam_ig,HMMPfam_C2-set_2,superfamily_SSF48726" - no_errors tier1 953 3 0.31 500 378 42.95 NA 673778 TCGA-AB-3012 AML13 3 96462902 96462902 C T SNP - - - - - - - - - - - - - - - tier3 763 2 0.26 792 348 30.53 0 0 NA 673778 TCGA-AB-3012 AML13 3 97524736 97524736 T C SNP LOC644063 XR_016547.2 human genbank 54_36p 1 model 5_prime_flanking_region c.-26158 NULL 0.03 - - - pseudogene tier3 428 0 0 500 263 34.42 0 0 NA 673778 TCGA-AB-3012 AML13 3 97654652 97654652 A G SNP ENSG00000216136 ENST00000401317 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-19708 NULL 0.006 - - - no_errors tier3 480 1 0.21 481 364 43.08 0 0 NA 673778 TCGA-AB-3012 AML13 3 98026055 98026055 G T SNP EPHA6 NM_001080448.2 human genbank 54_36p 1 provisional intronic c.385+9513 e1+9513 0 - - - no_errors tier3 864 0 0 472 201 29.87 0 0 NA 673778 TCGA-AB-3012 AML13 3 100099918 100099918 A G SNP DCBLD2 NM_080927.3 human genbank 54_36p -1 validated intronic c.205+2738 e1+2738 0.002 - - - no_errors tier2 514 0 0 365 314 46.11 0 0 NA 673778 TCGA-AB-3012 AML13 3 106830472 106830472 G T SNP CBLB NM_170662.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*30032 NULL 0.023 - - - no_errors tier3 963 0 0 899 647 41.77 0 0 NA 673778 TCGA-AB-3012 AML13 3 113510948 113510948 C T SNP CD200 NM_001004196.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-23802 NULL 1 - - - no_errors tier2 261 0 0 383 275 41.79 0 0 NA 673778 TCGA-AB-3012 AML13 3 115371677 115371677 C T SNP DRD3 NM_000796.3 human genbank 54_36p -1 reviewed intronic c.270+1583 e1+1583 0 - - - no_errors tier3 1092 0 0 467 384 45.12 0 0 NA 673778 TCGA-AB-3012 AML13 3 116068832 116068832 C T SNP ZBTB20 NM_015642.3 human genbank 54_36p -1 provisional intronic c.1+33009 e0+33009 0.001 - - - no_errors tier3 1290 1 0.08 929 404 30.28 1 0 0 673778 TCGA-AB-3012 AML13 3 118192138 118192138 A G SNP ENSG00000200372 ENST00000363502 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-25374 NULL 0.001 - - - no_errors tier3 1118 2 0.18 614 549 47.21 0 0 NA 673778 TCGA-AB-3012 AML13 3 125893051 125893051 C A SNP KALRN NM_001024660.2 human genbank 54_36p 1 reviewed intronic c.7378-2290 e52-2290 0.225 - - - no_errors tier3 1869 2 0.11 1106 860 43.74 0 0 NA 673778 TCGA-AB-3012 AML13 3 135257004 135257004 G T SNP SLCO2A1 NM_005630.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-25668 NULL 0.017 - - - no_errors tier3 894 1 0.11 265 126 32.23 0 0 NA 673778 TCGA-AB-3012 AML13 3 148994850 148994850 C T SNP - - - - - - - - - - - - - - - tier3 1007 1 0.1 673 534 44.21 0 0 NA 673778 TCGA-AB-3012 AML13 3 155733457 155733457 A T SNP - - - - - - - - - - - - - - - tier3 1000 3 0.3 675 582 46.3 0 0 NA 673778 TCGA-AB-3012 AML13 3 157716700 157716700 C T SNP KCNAB1 NM_172160.3 human genbank 54_36p 1 reviewed intronic c.866-53 e11-53 0.011 - - - no_errors tier3 614 4 0.65 491 501 50.45 0 0 NA 673778 TCGA-AB-3012 AML13 3 166758424 166758424 C T SNP - - - - - - - - - - - - - - - tier3 438 3 0.68 727 311 29.96 0 0 NA 673778 TCGA-AB-3012 AML13 3 174298238 174298238 C T SNP SPATA16 NM_031955.4 human genbank 54_36p -1 validated intronic c.612+19366 e1+19366 0.977 - - - no_errors tier2 721 0 0 1009 778 43.32 0 0 NA 673778 TCGA-AB-3012 AML13 3 175253068 175253068 T A SNP NLGN1 NM_014932.2 human genbank 54_36p 1 reviewed intronic c.647-222731 e3-222731 0.002 - - - no_errors tier3 899 5 0.55 714 499 41.1 0 0 NA 673778 TCGA-AB-3012 AML13 3 177407957 177407957 G T SNP - - - - - - - - - - - - - - - tier3 724 0 0 252 191 43.02 0 0 NA 673778 TCGA-AB-3012 AML13 3 177530917 177530917 T C SNP - - - - - - - - - - - - - - - tier3 840 3 0.36 1425 1196 45.61 0 0 NA 673778 TCGA-AB-3012 AML13 3 181211245 181211246 CT - DEL PEX5L NM_016559.1 human genbank 54_36p -1 provisional intronic c.21+25815_21+25814 e1+25815 0.000:0.000 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 3 185658277 185658277 C T SNP LOC730218 XM_001132993.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*18403 NULL 0.016 - - - no_errors tier3 1653 3 0.18 499 392 43.85 0 0 NA 673778 TCGA-AB-3012 AML13 3 193346132 193346132 C T SNP FGF12 NM_021032.4 human genbank 54_36p -1 reviewed intronic c.614-1522 e5-1522 0 - - - no_errors tier3 1451 2 0.14 819 548 40.09 0 0 NA 673778 TCGA-AB-3012 AML13 4 3551601 3551601 T G SNP FLJ35424 XR_040705.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.007 - - - no_errors tier3 952 0 0 654 101 13.36 0 0 NA 673778 TCGA-AB-3012 AML13 4 3764106 3764106 G A SNP ADRA2C NM_000683.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*24586 NULL 0.003 - - - no_errors tier3 687 0 0 228 165 41.98 0 0 NA 673778 TCGA-AB-3012 AML13 4 4567430 4567430 C A SNP STX18 NM_016930.2 human genbank 54_36p -1 validated intronic c.168+26995 e1+26995 0 - - - no_errors tier3 504 1 0.2 996 134 11.86 0 0 0 673778 TCGA-AB-3012 AML13 4 9786701 9786701 G A SNP - - - - - - - - - - - - - - - tier2 788 1 0.13 455 344 43 0 0 NA 673778 TCGA-AB-3012 AML13 4 11658415 11658415 T C SNP - - - - - - - - - - - - - - - tier3 789 1 0.13 626 474 43.09 0 0 NA 673778 TCGA-AB-3012 AML13 4 21633878 21633878 T A SNP - - - - - - - - - - - - - - - tier3 627 0 0 410 331 44.67 0 0 NA 673778 TCGA-AB-3012 AML13 4 23123867 23123867 G A SNP - - - - - - - - - - - - - - - tier2 1076 1 0.09 871 771 46.95 0 0 NA 673778 TCGA-AB-3012 AML13 4 23612018 23612018 C A SNP - - - - - - - - - - - - - - - tier3 1063 3 0.28 616 461 42.8 1 0 0 673778 TCGA-AB-3012 AML13 4 28760604 28760604 A G SNP - - - - - - - - - - - - - - - tier3 700 0 0 663 315 32.21 0 0 NA 673778 TCGA-AB-3012 AML13 4 28773631 28773631 A T SNP - - - - - - - - - - - - - - - tier3 530 1 0.19 685 271 28.32 0 0 NA 673778 TCGA-AB-3012 AML13 4 30039522 30039522 G A SNP - - - - - - - - - - - - - - - tier3 1662 0 0 1164 316 21.34 0 0 NA 673778 TCGA-AB-3012 AML13 4 31036566 31036566 C T SNP - - - - - - - - - - - - - - - tier3 1270 2 0.16 492 329 39.98 0 0 NA 673778 TCGA-AB-3012 AML13 4 31616824 31616824 T C SNP LOC100133713 XM_001715885.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-12028 NULL 0.002 - - - no_start_codon:pseudogene:no_stop_codon tier3 437 0 0 402 207 33.93 0 0 NA 673778 TCGA-AB-3012 AML13 4 34261391 34261391 C T SNP LOC727819 XM_001125877.2 human genbank 54_36p 1 model intronic c.128+40308 e1+40308 1 - - - no_errors tier2 1134 1 0.09 567 409 41.86 0 0 NA 673778 TCGA-AB-3012 AML13 4 43215398 43215398 G T SNP - - - - - - - - - - - - - - - tier3 1173 0 0 730 542 42.58 0 0 NA 673778 TCGA-AB-3012 AML13 4 48271967 48271967 T C SNP FRYL NM_015030.1 human genbank 54_36p -1 validated missense c.2770 p.M924V 1 superfamily_ARM repeat superfamily_ARM repeat - no_errors tier1 390 0 582 308 34.61 18 11 37.93 673778 TCGA-AB-3012 AML13 4 59178976 59178976 T C SNP - - - - - - - - - - - - - - - tier3 325 0 0 458 325 41.45 0 0 NA 673778 TCGA-AB-3012 AML13 4 62754316 62754316 C T SNP - - - - - - - - - - - - - - - tier3 545 1 0.18 603 444 42.37 0 0 NA 673778 TCGA-AB-3012 AML13 4 63513162 63513162 A G SNP - - - - - - - - - - - - - - - tier3 330 0 0 598 467 43.77 0 0 NA 673778 TCGA-AB-3012 AML13 4 64527668 64527668 C T SNP - - - - - - - - - - - - - - - tier3 448 0 0 385 76 16.49 0 0 NA 673778 TCGA-AB-3012 AML13 4 64767545 64767546 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 4 68420764 68420764 G T SNP TMPRSS11D NM_004262.2 human genbank 54_36p -1 reviewed intronic c.8+11475 e1+11475 0.022 - - - no_errors tier3 354 2 0.56 465 317 40.54 0 0 NA 673778 TCGA-AB-3012 AML13 4 72341739 72341739 C A SNP SLC4A4 NM_001098484.2 human genbank 54_36p 1 reviewed intronic c.253+1759 e2+1759 0 - - - no_errors tier3 1548 9 0.58 1113 830 42.67 0 0 NA 673778 TCGA-AB-3012 AML13 4 85307615 85307615 G A SNP - - - - - - - - - - - - - - - tier2 1412 1 0.07 960 691 41.83 0 0 NA 673778 TCGA-AB-3012 AML13 4 86777665 86777665 C T SNP ARHGAP24 NM_001025616.2 human genbank 54_36p 1 validated intronic c.180+66767 e1+66767 0.006 - - - no_errors tier2 420 1 0.24 358 266 42.63 0 0 NA 673778 TCGA-AB-3012 AML13 4 95582746 95582746 T C SNP PDLIM5 NM_006457.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-12717 NULL 0.001 - - - no_errors tier2 409 0 0 321 241 42.88 0 0 NA 673778 TCGA-AB-3012 AML13 4 97362819 97362819 G A SNP - - - - - - - - - - - - - - - tier2 1269 1 0.08 684 530 43.66 0 0 NA 673778 TCGA-AB-3012 AML13 4 98590278 98590278 C T SNP ENSG00000216036 ENST00000401217 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-36702 NULL 0.025 - - - no_errors tier3 276 2 0.72 544 290 34.69 0 0 NA 673778 TCGA-AB-3012 AML13 4 103197258 103197258 G C SNP BANK1 NM_017935.1 human genbank 54_36p 1 validated intronic c.1970-3133 e12-3133 0.003 - - - no_errors tier3 1722 3 0.17 1232 537 30.36 0 0 0 673778 TCGA-AB-3012 AML13 4 105222614 105222614 C T SNP - - - - - - - - - - - - - - - tier3 487 0 0 534 404 43.07 0 0 NA 673778 TCGA-AB-3012 AML13 4 109351729 109351729 G A SNP LOC644993 XM_932570.1 human genbank 54_36p 1 model intronic c.259+11165 e3+11165 0 - - - no_errors tier3 1170 1 0.09 610 440 41.9 0 0 NA 673778 TCGA-AB-3012 AML13 4 109538572 109538572 C A SNP - - - - - - - - - - - - - - - tier3 6226 6 0.1 747 549 42.3 0 0 NA 673778 TCGA-AB-3012 AML13 4 112249593 112249593 G A SNP - - - - - - - - - - - - - - - tier2 962 2 0.21 492 386 43.86 0 0 NA 673778 TCGA-AB-3012 AML13 4 117228398 117228398 A G SNP - - - - - - - - - - - - - - - tier3 321 0 0 424 355 45.51 0 0 NA 673778 TCGA-AB-3012 AML13 4 121085785 121085785 G A SNP ENSG00000200553 ENST00000363683 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-1949 NULL 0 - - - no_errors tier3 583 0 0 645 453 41.22 0 0 NA 673778 TCGA-AB-3012 AML13 4 128130797 128130797 C A SNP ENSG00000199862 ENST00000362992 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*37915 NULL 0.001 - - - no_errors tier3 698 0 0 643 486 43.05 0 0 NA 673778 TCGA-AB-3012 AML13 4 134260577 134260577 A T SNP PCDH10 NM_032961.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30169 NULL 0.009 - - - no_errors tier3 620 0 0 578 460 44.23 0 0 NA 673778 TCGA-AB-3012 AML13 4 134304670 134304670 G T SNP PCDH10 NM_032961.1 human genbank 54_36p 1 reviewed intronic c.3103+783 e4+783 0 - - - no_errors tier3 690 0 0 565 278 32.98 0 0 NA 673778 TCGA-AB-3012 AML13 4 136246522 136246522 C T SNP LOC729551 XM_001130594.2 human genbank 54_36p 1 model 3_prime_flanking_region c.*8376 NULL 0.006 - - - no_errors tier3 392 3 0.76 374 329 46.73 0 0 NA 673778 TCGA-AB-3012 AML13 4 136298657 136298657 G A SNP - - - - - - - - - - - - - - - tier3 553 1 0.18 583 511 46.67 0 0 NA 673778 TCGA-AB-3012 AML13 4 137249738 137249738 A G SNP - - - - - - - - - - - - - - - tier2 647 0 0 726 542 42.71 0 0 NA 673778 TCGA-AB-3012 AML13 4 137689996 137689996 C T SNP - - - - - - - - - - - - - - - tier3 962 2 0.21 1761 420 19.26 0 0 NA 673778 TCGA-AB-3012 AML13 4 137845008 137845008 G C SNP - - - - - - - - - - - - - - - tier3 658 0 0 763 95 11.06 0 0 NA 673778 TCGA-AB-3012 AML13 4 139335508 139335508 G T SNP SLC7A11 NM_014331.3 human genbank 54_36p -1 validated intronic c.792-9660 e7-9660 0.015 - - - no_errors tier3 722 0 0 751 602 44.43 0 0 NA 673778 TCGA-AB-3012 AML13 4 150405383 150405383 T C SNP - - - - - - - - - - - - - - - tier3 968 0 0 577 482 45.51 0 0 NA 673778 TCGA-AB-3012 AML13 4 155541209 155541209 G T SNP DCHS2 ENST00000339452 human ensembl 54_36p -1 known intronic c.2053-23163 e2-23163 0 - - - no_errors tier2 2380 5 0.21 1491 317 17.53 0 0 NA 673778 TCGA-AB-3012 AML13 4 159695729 159695729 G T SNP RXFP1 NM_021634.2 human genbank 54_36p 1 provisional intronic c.50-17571 e2-17571 0.001 - - - no_errors tier3 357 1 0.28 371 281 43.1 0 0 NA 673778 TCGA-AB-3012 AML13 4 160048590 160048590 G A SNP C4orf45 NM_152543.2 human genbank 54_36p -1 validated intronic c.546+7182 e4+7182 0.273 - - - no_errors tier2 366 1 0.27 363 274 43.01 0 1 100 673778 TCGA-AB-3012 AML13 4 164685617 164685617 A G SNP MARCH1 NM_017923.2 human genbank 54_36p -1 validated intronic c.520+581 e3+581 0.001 - - - no_errors tier3 1209 3 0.25 1087 745 40.67 0 0 0 673778 TCGA-AB-3012 AML13 4 167707403 167707403 G T SNP - - - - - - - - - - - - - - - tier2 235 0 0 362 254 41.17 0 0 NA 673778 TCGA-AB-3012 AML13 4 168034012 168034012 G A SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated intronic c.598+12844 e6+12844 0 - - - no_errors tier2 736 1 0.14 1186 309 20.64 0 0 NA 673778 TCGA-AB-3012 AML13 4 168235398 168235398 C T SNP SPOCK3 NM_016950.1 human genbank 54_36p -1 validated intronic c.198+5566 e2+5566 0.004 - - - no_errors tier3 1005 3 0.3 678 187 21.59 0 0 NA 673778 TCGA-AB-3012 AML13 4 169808578 169808578 C T SNP PALLD NM_016081.3 human genbank 54_36p 1 validated intronic c.909-17338 e2-17338 0 - - - no_errors tier3 643 1 0.16 318 258 44.79 0 0 NA 673778 TCGA-AB-3012 AML13 4 182951041 182951041 G A SNP LOC728191 XM_001126817.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*27376 NULL 1 - - - no_errors tier2 659 0 0 703 555 44.08 0 0 NA 673778 TCGA-AB-3012 AML13 4 187022043 187022043 A G SNP SORBS2 NM_021069.1 human genbank 54_36p -1 reviewed intronic c.1-88529 e1-88529 0.009 - - - no_errors tier3 349 0 0 556 432 43.72 0 0 NA 673778 TCGA-AB-3012 AML13 4 187454990 187454990 C T SNP KLKB1 NM_000892.3 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*38630 NULL 0.002 - - - no_errors tier3 2966 3 0.1 1310 515 28.2 0 0 NA 673778 TCGA-AB-3012 AML13 4 188527624 188527624 G A SNP - - - - - - - - - - - - - - - tier3 1170 4 0.34 668 332 33.17 0 0 NA 673778 TCGA-AB-3012 AML13 5 2924154 2924154 C T SNP - - - - - - - - - - - - - - - tier3 865 1 0.12 589 459 43.76 0 0 NA 673778 TCGA-AB-3012 AML13 5 3242552 3242553 - A INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 5 3569743 3569743 C T SNP - - - - - - - - - - - - - - - tier3 1845 2 0.11 1322 654 33.08 1 0 0 673778 TCGA-AB-3012 AML13 5 5070139 5070139 G A SNP ENSG00000215231 ENST00000399853 human ensembl 54_36p 1 known 5_prime_flanking_region c.-21495 NULL 0.001 - - - no_errors tier3 827 0 0 854 101 10.58 0 0 NA 673778 TCGA-AB-3012 AML13 5 5930416 5930416 G A SNP - - - - - - - - - - - - - - - tier3 1420 2 0.14 611 453 42.46 0 0 NA 673778 TCGA-AB-3012 AML13 5 7669518 7669518 C T SNP ADCY2 NM_020546.2 human genbank 54_36p 1 reviewed intronic c.571-9762 e4-9762 0.002 - - - no_errors tier3 928 0 0 667 585 46.65 0 0 NA 673778 TCGA-AB-3012 AML13 5 11094542 11094542 G A SNP CTNND2 NM_001332.2 human genbank 54_36p -1 validated intronic c.2789-18451 e17-18451 0.012 - - - no_errors tier2 537 4 0.74 535 418 43.82 0 0 NA 673778 TCGA-AB-3012 AML13 5 12101509 12101509 G C SNP - - - - - - - - - - - - - - - tier3 673 1 0.15 605 529 46.65 0 0 NA 673778 TCGA-AB-3012 AML13 5 15826864 15826864 G A SNP FBXL7 NM_012304.3 human genbank 54_36p 1 reviewed intronic c.128-154135 e3-154135 0 - - - no_errors tier3 893 1 0.11 481 409 45.96 0 0 NA 673778 TCGA-AB-3012 AML13 5 19645264 19645264 C T SNP CDH18 NM_004934.2 human genbank 54_36p -1 reviewed intronic c.811+3036 e4+3036 0 - - - no_errors tier3 687 0 0 1274 115 8.27 0 0 NA 673778 TCGA-AB-3012 AML13 5 26981561 26981561 T A SNP CDH9 NM_016279.3 human genbank 54_36p -1 reviewed intronic c.229-29772 e2-29772 0.055 - - - no_errors tier3 630 0 0 488 388 44.24 0 0 NA 673778 TCGA-AB-3012 AML13 5 29269446 29269446 C T SNP - - - - - - - - - - - - - - - tier3 238 0 0 362 173 32.28 0 0 NA 673778 TCGA-AB-3012 AML13 5 29860747 29860747 A C SNP - - - - - - - - - - - - - - - tier3 723 1 0.14 998 105 9.5 0 0 NA 673778 TCGA-AB-3012 AML13 5 34324234 34324234 C A SNP - - - - - - - - - - - - - - - tier2 395 1 0.25 242 235 49.06 0 0 NA 673778 TCGA-AB-3012 AML13 5 52678578 52678578 G A SNP - - - - - - - - - - - - - - - tier2 1050 3 0.28 799 336 29.53 0 0 NA 673778 TCGA-AB-3012 AML13 5 65471820 65471820 C T SNP SFRS12 NM_001077199.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-4141 NULL 0.011 - - - no_errors tier3 917 1 0.11 692 558 44.6 1 0 0 673778 TCGA-AB-3012 AML13 5 72548498 72548498 C T SNP TMEM174 NM_153217.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*42750 NULL 0.038 - - - no_errors tier2 415 1 0.24 298 208 41.11 0 0 NA 673778 TCGA-AB-3012 AML13 5 78989793 78989793 A G SNP PAPD4 NM_173797.1 human genbank 54_36p 1 validated intronic c.1071+1213 e10+1213 0 - - - no_errors tier3 349 0 0 416 308 42.48 1 4 80 673778 TCGA-AB-3012 AML13 5 83612138 83612138 A G SNP EDIL3 NM_005711.3 human genbank 54_36p -1 reviewed intronic c.68-26352 e2-26352 0.001 - - - no_errors tier2 844 3 0.35 740 577 43.81 0 0 NA 673778 TCGA-AB-3012 AML13 5 97756600 97756600 G T SNP ENSG00000211351 ENST00000388616 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-17177 NULL 1 - - - pseudogene tier2 91 1 1.09 116 79 40.51 0 0 NA 673778 TCGA-AB-3012 AML13 5 101268814 101268814 C A SNP - - - - - - - - - - - - - - - tier3 517 2 0.39 494 392 44.24 0 0 NA 673778 TCGA-AB-3012 AML13 5 101624611 101624611 A C SNP SLCO4C1 NM_180991.4 human genbank 54_36p -1 validated intronic c.1022-689 e6-689 0.024 - - - no_errors tier3 617 1 0.16 720 587 44.91 0 0 0 673778 TCGA-AB-3012 AML13 5 105696236 105696236 C T SNP - - - - - - - - - - - - - - - tier3 679 0 0 564 449 44.24 0 0 NA 673778 TCGA-AB-3012 AML13 5 106438416 106438416 C A SNP - - - - - - - - - - - - - - - tier3 1377 0 0 1183 977 45.19 0 0 NA 673778 TCGA-AB-3012 AML13 5 106575058 106575058 G A SNP - - - - - - - - - - - - - - - tier3 500 0 0 733 543 42.55 0 0 NA 673778 TCGA-AB-3012 AML13 5 108278662 108278662 T C SNP FER NM_005246.2 human genbank 54_36p 1 reviewed intronic c.1236+17214 e8+17214 0.05 - - - no_errors tier3 780 3 0.38 531 381 41.68 1 1 50 673778 TCGA-AB-3012 AML13 5 114165351 114165351 T G SNP - - - - - - - - - - - - - - - tier3 798 1 0.13 958 784 44.95 0 0 NA 673778 TCGA-AB-3012 AML13 5 116334277 116334277 C T SNP - - - - - - - - - - - - - - - tier3 833 1 0.12 505 396 43.85 0 0 NA 673778 TCGA-AB-3012 AML13 5 119401962 119401962 T G SNP - - - - - - - - - - - - - - - tier3 506 0 0 600 151 20.08 0 0 NA 673778 TCGA-AB-3012 AML13 5 124600244 124600244 T C SNP - - - - - - - - - - - - - - - tier3 529 0 0 857 337 28.15 0 0 NA 673778 TCGA-AB-3012 AML13 5 126812459 126812459 G A SNP MEGF10 NM_032446.2 human genbank 54_36p 1 validated intronic c.2857-231 e21-231 0.002 - - - no_errors tier3 612 0 0 496 393 44.16 0 0 0 673778 TCGA-AB-3012 AML13 5 132729081 132729081 A G SNP FSTL4 NM_015082.1 human genbank 54_36p -1 validated intronic c.409+35248 e3+35248 0.866 - - - no_errors tier3 282 0 0 201 153 43.22 0 0 NA 673778 TCGA-AB-3012 AML13 5 140740112 140740113 - A INS PCDHGA2 NM_018915.2 human genbank 54_36p 1 reviewed intronic c.2424+38966_2424+38965 e1+38966 0.000:0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 5 144404609 144404609 T C SNP - - - - - - - - - - - - - - - tier2 1327 2 0.15 570 423 42.6 0 0 NA 673778 TCGA-AB-3012 AML13 5 144404611 144404611 A T SNP - - - - - - - - - - - - - - - tier2 1324 0 0 570 422 42.54 0 0 NA 673778 TCGA-AB-3012 AML13 5 155680120 155680120 C T SNP SGCD NM_000337.5 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-9045 NULL 0 - - - no_errors tier3 579 0 0 399 307 43.48 0 0 NA 673778 TCGA-AB-3012 AML13 5 162129385 162129385 C T SNP ENSG00000208481 ENST00000385746 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-14194 NULL 0 - - - pseudogene tier3 380 0 0 701 462 39.62 0 0 NA 673778 TCGA-AB-3012 AML13 5 171106887 171106887 C T SNP LOC644994 XM_928062.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-38594 NULL 0.007 - - - no_errors tier3 1608 0 0 1084 899 45.29 0 0 NA 673778 TCGA-AB-3012 AML13 5 174310600 174310600 T G SNP ENSG00000204754 ENST00000377300 human ensembl 54_36p -1 known intronic c.447+25458 e1+25458 0.001 - - - no_errors tier3 1911 3 0.15 1575 687 29.92 0 0 NA 673778 TCGA-AB-3012 AML13 6 4535147 4535147 C T SNP KU-MEL-3 XR_040426.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-20748 NULL 0 - - - no_errors tier3 1357 0 0 1522 178 10.47 0 0 NA 673778 TCGA-AB-3012 AML13 6 8098892 8098892 G A SNP - - - - - - - - - - - - - - - tier3 1394 0 0 665 560 45.64 0 0 NA 673778 TCGA-AB-3012 AML13 6 17339388 17339388 G A SNP ENSG00000209103 ENST00000386368 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-6063 NULL 0.001 - - - pseudogene tier3 1409 2 0.14 764 613 44.42 0 0 NA 673778 TCGA-AB-3012 AML13 6 21369127 21369127 G T SNP CDKAL1 NM_017774.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*29878 NULL 0.014 - - - no_errors tier3 996 0 0 442 204 31.58 0 0 NA 673778 TCGA-AB-3012 AML13 6 33168856 33168856 G A SNP ENSG00000172899 ENST00000308384 human ensembl 54_36p -1 novel 5_prime_untranslated_region c.-33168856 NULL 0.009 - - - no_coding_region:pseudogene tier3 1297 6 0.46 939 452 32.49 0 0 0 673778 TCGA-AB-3012 AML13 6 45003334 45003334 G A SNP SUPT3H NM_181356.2 human genbank 54_36p -1 provisional intronic c.945+5034 e10+5034 0 - - - no_errors tier3 532 0 0 478 354 42.55 1 0 0 673778 TCGA-AB-3012 AML13 6 46519278 46519278 G - DEL RCAN2 ENST00000306764 human ensembl 54_36p -1 known intronic c.225+13170 e1+13170 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 6 47478053 47478053 T C SNP - - - - - - - - - - - - - - - tier3 1130 2 0.18 542 430 44.19 0 0 NA 673778 TCGA-AB-3012 AML13 6 50097803 50097803 G C SNP DEFB111 NM_001037497.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-196 NULL 0.001 - - - no_errors tier3 430 0 0 493 377 43.28 0 0 NA 673778 TCGA-AB-3012 AML13 6 50146953 50146953 T - DEL DEFB112 NM_001037498.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-22630 NULL 0.001 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 6 52120439 52120439 C T SNP IL17A NM_002190.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-38750 NULL 0 - - - no_errors tier3 545 0 0 717 539 42.88 0 0 NA 673778 TCGA-AB-3012 AML13 6 53739807 53739807 C T SNP LRRC1 NM_018214.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-28207 NULL 0.001 - - - no_errors tier3 1221 2 0.16 807 617 43.3 0 0 NA 673778 TCGA-AB-3012 AML13 6 58720410 58720410 A C SNP - - - - - - - - - - - - - - - tier3 826 0 0 720 543 42.96 0 0 NA 673778 TCGA-AB-3012 AML13 6 64201795 64201795 G A SNP ENSG00000218048 ENST00000402043 human ensembl 54_36p 1 known 5_prime_flanking_region c.-6835 NULL 0.001 - - - no_coding_region:pseudogene tier3 1309 1 0.08 589 463 44.01 0 0 NA 673778 TCGA-AB-3012 AML13 6 69514397 69514397 A T SNP BAI3 NM_001704.2 human genbank 54_36p 1 reviewed intronic c.757+108352 e1+108352 0.001 - - - no_errors tier3 1502 0 0 1105 864 43.86 0 0 NA 673778 TCGA-AB-3012 AML13 6 71929556 71929556 C T SNP ENSG00000207180 ENST00000384451 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-19480 NULL 0 - - - no_errors tier3 1185 3 0.25 790 547 40.88 0 0 NA 673778 TCGA-AB-3012 AML13 6 72679682 72679682 C T SNP RIMS1 NM_014989.3 human genbank 54_36p 1 validated intronic c.164+26071 e1+26071 0.002 - - - no_errors tier3 496 4 0.8 340 241 41.34 0 0 NA 673778 TCGA-AB-3012 AML13 6 74784072 74784072 G A SNP ENSG00000217268 ENST00000406296 human ensembl 54_36p -1 known 5_prime_flanking_region c.-12824 NULL 0.004 - - - no_coding_region:pseudogene tier3 706 1 0.14 848 614 42 0 0 NA 673778 TCGA-AB-3012 AML13 6 76892963 76892963 G A SNP ENSG00000222652 ENST00000410720 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33586 NULL 0.002 - - - no_errors tier3 2072 2 0.1 1365 1057 43.62 0 0 NA 673778 TCGA-AB-3012 AML13 6 77487262 77487262 C A SNP - - - - - - - - - - - - - - - tier3 747 0 0 697 405 36.75 0 0 NA 673778 TCGA-AB-3012 AML13 6 85210685 85210685 A G SNP ENSG00000214465 ENST00000398372 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-13447 NULL 0.013 - - - no_coding_region:pseudogene tier3 2107 7 0.33 1196 916 43.35 0 0 NA 673778 TCGA-AB-3012 AML13 6 89750642 89750642 T A SNP RNGTT NM_003800.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-20795 NULL 0.283 - - - no_errors tier3 809 2 0.25 651 87 11.77 0 0 NA 673778 TCGA-AB-3012 AML13 6 91597740 91597740 C T SNP - - - - - - - - - - - - - - - tier3 926 0 0 592 431 42.05 0 0 NA 673778 TCGA-AB-3012 AML13 6 97903296 97903296 C T SNP - - - - - - - - - - - - - - - tier3 692 1 0.14 819 180 18.02 0 0 NA 673778 TCGA-AB-3012 AML13 6 102890439 102890439 G A SNP - - - - - - - - - - - - - - - tier2 217 0 0 255 179 41.15 0 0 NA 673778 TCGA-AB-3012 AML13 6 104262514 104262514 C A SNP - - - - - - - - - - - - - - - tier3 391 0 0 375 290 43.61 0 0 NA 673778 TCGA-AB-3012 AML13 6 104283954 104283954 T C SNP - - - - - - - - - - - - - - - tier3 605 0 0 707 349 33.02 0 0 NA 673778 TCGA-AB-3012 AML13 6 111978268 111978268 A T SNP LOC643749 XR_041903.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.279 - - - no_errors tier3 567 0 0 365 282 43.52 2 3 60 673778 TCGA-AB-3012 AML13 6 114965106 114965106 C T SNP - - - - - - - - - - - - - - - tier3 964 1 0.1 787 570 41.94 0 0 NA 673778 TCGA-AB-3012 AML13 6 121008021 121008021 C G SNP ENSG00000200310 ENST00000363440 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-41445 NULL 0.011 - - - no_errors tier3 902 8 0.88 742 685 47.97 0 0 NA 673778 TCGA-AB-3012 AML13 6 126217564 126217564 A G SNP NCOA7 NM_181782.1 human genbank 54_36p 1 validated intronic c.51-295 e2-295 0.002 - - - no_errors tier3 785 1 0.13 653 444 40.36 0 0 0 673778 TCGA-AB-3012 AML13 6 126560011 126560011 A T SNP - - - - - - - - - - - - - - - tier3 936 0 0 452 418 48.05 0 0 NA 673778 TCGA-AB-3012 AML13 6 128722782 128722782 C A SNP PTPRK NM_002844.1 human genbank 54_36p -1 validated intronic c.223+37622 e2+37622 0.008 - - - no_errors tier3 836 0 0 810 572 41.36 0 0 NA 673778 TCGA-AB-3012 AML13 6 132173561 132173561 G A SNP ENPP1 NM_006208.2 human genbank 54_36p 1 reviewed intronic c.84+2453 e1+2453 0.008 - - - no_errors tier3 539 1 0.19 397 53 11.78 0 0 NA 673778 TCGA-AB-3012 AML13 6 135910261 135910261 C A SNP AHI1 NM_017651.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-55193 NULL 0.104 - - - no_errors tier3 307 0 0 727 328 31.03 0 0 NA 673778 TCGA-AB-3012 AML13 6 139602147 139602147 G T SNP TXLNB NM_153235.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*3209 NULL 0 - - - no_errors tier2 959 1 0.1 874 434 33.18 0 0 NA 673778 TCGA-AB-3012 AML13 6 141906337 141906337 T C SNP - - - - - - - - - - - - - - - tier3 632 1 0.16 518 497 48.97 0 0 NA 673778 TCGA-AB-3012 AML13 6 149318187 149318187 G T SNP UST NM_005715.2 human genbank 54_36p 1 validated intronic c.527+1407 e4+1407 0.051 - - - no_errors tier3 709 0 0 803 187 18.89 0 0 NA 673778 TCGA-AB-3012 AML13 6 151567200 151567200 T A SNP AKAP12 NM_005100.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-36191 NULL 0.004 - - - no_errors tier3 1827 3 0.16 693 540 43.69 0 0 NA 673778 TCGA-AB-3012 AML13 6 161429282 161429282 T C SNP MAP3K4 NM_005922.2 human genbank 54_36p 1 reviewed intronic c.2823+306 e10+306 0.001 - - - no_errors tier3 841 1 0.12 901 776 46.27 0 0 0 673778 TCGA-AB-3012 AML13 6 168341682 168341682 G A SNP - - - - - - - - - - - - - - - tier3 959 0 0 528 397 42.78 0 0 NA 673778 TCGA-AB-3012 AML13 7 3272288 3272288 C T SNP SDK1 NM_152744.1 human genbank 54_36p 1 validated 5_prime_flanking_region c.-35457 NULL 0 - - - no_errors tier3 1527 1 0.07 575 458 44.21 0 0 NA 673778 TCGA-AB-3012 AML13 7 15183588 15183588 C T SNP TMEM195 NM_001004320.1 human genbank 54_36p -1 provisional 3_prime_flanking_region c.*23847 NULL 0 - - - no_errors tier3 686 0 0 694 497 41.73 0 0 NA 673778 TCGA-AB-3012 AML13 7 19329865 19329865 T C SNP - - - - - - - - - - - - - - - tier3 697 0 0 761 447 37 0 0 NA 673778 TCGA-AB-3012 AML13 7 24829212 24829212 T A SNP OSBPL3 NM_015550.2 human genbank 54_36p -1 reviewed intronic c.1885-2830 e16-2830 0.008 - - - no_errors tier3 915 2 0.22 643 506 43.96 0 1 100 673778 TCGA-AB-3012 AML13 7 27329790 27329790 C T SNP LOC392008 XR_017366.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-20384 NULL 0 - - - no_errors tier3 1310 1 0.08 861 603 41.16 0 0 NA 673778 TCGA-AB-3012 AML13 7 27378740 27378740 G C SNP ENSG00000219101 ENST00000401976 human ensembl 54_36p -1 known 5_prime_flanking_region c.-43063 NULL 0.005 - - - no_coding_region:pseudogene tier3 1577 1 0.06 634 486 43.28 0 0 NA 673778 TCGA-AB-3012 AML13 7 27921586 27921586 T A SNP JAZF1 NM_175061.3 human genbank 54_36p -1 reviewed intronic c.189-20026 e3-20026 0.999 - - - no_errors tier3 659 0 0 496 409 45.09 1 1 50 673778 TCGA-AB-3012 AML13 7 36832138 36832138 G A SNP ELMO1 NM_014800.1 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*29543 NULL 0.002 - - - no_errors tier2 1093 1 0.09 1306 631 32.56 0 0 NA 673778 TCGA-AB-3012 AML13 7 38686861 38686861 G A SNP AMPH NM_001635.2 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-49385 NULL 0.002 - - - no_errors tier3 914 4 0.43 597 497 45.39 0 0 NA 673778 TCGA-AB-3012 AML13 7 42261337 42261337 T - DEL GLI3 NM_000168.5 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31960 NULL 0.02 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 7 45568264 45568264 C T SNP ADCY1 NM_021116.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-12404 NULL 0.006 - - - no_errors tier3 1168 1 0.09 244 185 43.12 0 0 NA 673778 TCGA-AB-3012 AML13 7 52688597 52688597 T C SNP - - - - - - - - - - - - - - - tier3 505 0 0 470 354 42.91 0 0 NA 673778 TCGA-AB-3012 AML13 7 53886041 53886041 A T SNP FLJ45974 XR_040790.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-38929 NULL 0.354 - - - no_errors tier3 81 0 0 236 170 41.67 0 0 NA 673778 TCGA-AB-3012 AML13 7 53920573 53920573 G A SNP - - - - - - - - - - - - - - - tier3 698 0 0 653 544 45.41 0 0 NA 673778 TCGA-AB-3012 AML13 7 57586176 57586176 C T SNP - - - - - - - - - - - - - - - tier3 456 0 0 457 323 41.3 0 0 NA 673778 TCGA-AB-3012 AML13 7 63056402 63056402 C T SNP LOC100129126 XM_001715328.1 human genbank 54_36p -1 model intronic c.661-4526 e8-4526 0.001 - - - no_errors tier2 1482 3 0.2 918 98 9.64 0 0 NA 673778 TCGA-AB-3012 AML13 7 71688820 71688820 C A SNP ENSG00000188463 ENST00000389196 human ensembl 54_36p -1 known intronic c.1017-10180 e10-10180 0.07 - - - no_errors tier3 1249 1 0.08 903 516 36.36 0 3 100 673778 TCGA-AB-3012 AML13 7 77927693 77927693 G A SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.1045+29321 e6+29321 0.037 - - - no_errors tier3 661 0 0 544 420 43.48 0 0 NA 673778 TCGA-AB-3012 AML13 7 78203186 78203186 G T SNP MAGI2 NM_012301.3 human genbank 54_36p -1 reviewed intronic c.419-108695 e3-108695 0 - - - no_errors tier3 262 0 0 592 302 33.71 0 0 NA 673778 TCGA-AB-3012 AML13 7 80385414 80385414 C G SNP SEMA3C NM_006379.2 human genbank 54_36p -1 validated intronic c.1+666 e0+666 0.792 - - - no_errors tier2 362 0 0 315 246 43.77 0 0 0 673778 TCGA-AB-3012 AML13 7 81651605 81651605 C T SNP CACNA2D1 NM_000722.2 human genbank 54_36p -1 reviewed intronic c.295-13744 e4-13744 0 - - - no_errors tier3 282 0 0 211 105 33.23 0 0 NA 673778 TCGA-AB-3012 AML13 7 83053700 83053700 G A SNP SEMA3E NM_012431.1 human genbank 54_36p -1 provisional intronic c.115+61980 e1+61980 0 - - - no_errors tier3 428 1 0.23 425 337 44.23 0 0 NA 673778 TCGA-AB-3012 AML13 7 97170705 97170705 C T SNP TAC1 NM_003182.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-29156 NULL 0 - - - no_errors tier3 454 0 0 432 362 45.59 0 0 NA 673778 TCGA-AB-3012 AML13 7 102821166 102821166 G A SNP SLC26A5 NM_198999.1 human genbank 54_36p -1 validated intronic c.972-417 e8-417 0.065 - - - no_errors tier3 562 0 0 423 287 40.37 0 0 NA 673778 TCGA-AB-3012 AML13 7 107813036 107813036 C T SNP NRCAM NM_001037132.1 human genbank 54_36p -1 reviewed intronic c.1+14080 e0+14080 0 - - - no_errors tier2 839 0 0 1016 752 42.53 0 0 NA 673778 TCGA-AB-3012 AML13 7 111440842 111440842 C T SNP DOCK4 NM_014705.3 human genbank 54_36p -1 reviewed intronic c.38-9420 e2-9420 0 - - - no_errors tier3 1035 0 0 888 739 45.42 0 1 100 673778 TCGA-AB-3012 AML13 7 113020351 113020351 C T SNP - - - - - - - - - - - - - - - tier2 392 1 0.25 261 186 41.61 0 1 100 673778 TCGA-AB-3012 AML13 7 115928358 115928358 G A SNP CAV2 NM_001233.3 human genbank 54_36p 1 reviewed intronic c.338+621 e2+621 0 - - - no_errors tier2 349 0 0 178 156 46.71 0 1 100 673778 TCGA-AB-3012 AML13 7 116714307 116714307 C T SNP WNT2 NM_003391.2 human genbank 54_36p -1 reviewed intronic c.854-8633 e5-8633 0.008 - - - no_errors tier3 1014 0 0 918 396 30.14 0 0 NA 673778 TCGA-AB-3012 AML13 7 123454798 123454798 C T SNP - - - - - - - - - - - - - - - tier2 430 0 0 491 55 10.07 0 0 NA 673778 TCGA-AB-3012 AML13 7 126443834 126443834 A T SNP GRM8 NM_000845.2 human genbank 54_36p -1 reviewed intronic c.727+89952 e2+89952 0.172 - - - no_errors tier2 1100 1 0.09 1277 926 42 0 0 NA 673778 TCGA-AB-3012 AML13 7 134648001 134648001 C T SNP CNOT4 NM_013316.1 human genbank 54_36p -1 validated 3_prime_flanking_region c.*50176 NULL 0.008 - - - no_errors tier3 947 2 0.21 809 611 43 0 0 NA 673778 TCGA-AB-3012 AML13 7 135136775 135136775 T C SNP ENSG00000222219 ENST00000410287 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3378 NULL 0 - - - no_errors tier2 1049 3 0.29 553 465 45.63 0 0 NA 673778 TCGA-AB-3012 AML13 7 145212294 145212294 G A SNP - - - - - - - - - - - - - - - tier3 1273 1 0.08 1688 340 16.77 0 0 NA 673778 TCGA-AB-3012 AML13 7 146944978 146944978 G A SNP CNTNAP2 NM_014141.4 human genbank 54_36p 1 reviewed intronic c.1898-22153 e13-22153 0 - - - no_errors tier3 652 0 0 572 432 42.94 0 0 NA 673778 TCGA-AB-3012 AML13 7 149041943 149041943 G A SNP KRBA1 ENST00000255992 human ensembl 54_36p 1 known 5_prime_flanking_region c.-5720 NULL 0 - - - no_errors tier2 204 0 0 78 81 50.62 0 0 NA 673778 TCGA-AB-3012 AML13 7 150246270 150246270 C T SNP KCNH2 NM_000238.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*27116 NULL 0 - - - no_errors tier2 1449 2 0.14 828 337 28.9 0 0 NA 673778 TCGA-AB-3012 AML13 7 155375990 155375990 C T SNP LOC100132381 XM_001715638.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-1480 NULL 0.006 - - - no_errors tier3 371 0 0 59 46 43.81 0 0 NA 673778 TCGA-AB-3012 AML13 7 155623753 155623753 G A SNP LOC393076 XR_016902.1 human genbank 54_36p 1 model intronic c.NULL NULL 0.004 - - - no_errors tier3 1381 5 0.36 357 281 43.97 0 0 NA 673778 TCGA-AB-3012 AML13 8 4833470 4833470 T C SNP CSMD1 NM_033225.4 human genbank 54_36p -1 validated intronic c.85+5792 e1+5792 0.002 - - - pseudogene:no_stop_codon:bad_bp_length_for_coding_region tier3 465 0 0 317 67 17.45 0 0 NA 673778 TCGA-AB-3012 AML13 8 10551884 10551884 A G SNP RP1L1 ENST00000329335 human ensembl 54_36p -1 known intronic c.1-33744 e1-33744 0 - - - no_errors tier3 971 1 0.1 601 528 46.77 0 0 NA 673778 TCGA-AB-3012 AML13 8 13519385 13519385 G A SNP C8orf48 ENST00000297324 human ensembl 54_36p 1 known 3_prime_flanking_region c.*49554 NULL 0 - - - no_errors tier3 364 0 0 301 243 44.67 0 0 NA 673778 TCGA-AB-3012 AML13 8 14648389 14648389 C T SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.40-191583 e2-191583 0 - - - no_errors tier3 560 0 0 504 435 46.28 0 0 NA 673778 TCGA-AB-3012 AML13 8 14989792 14989792 C T SNP SGCZ NM_139167.2 human genbank 54_36p -1 reviewed intronic c.39+149673 e1+149673 0 - - - no_errors tier3 510 0 0 488 351 41.74 0 0 NA 673778 TCGA-AB-3012 AML13 8 15302705 15302705 T A SNP - - - - - - - - - - - - - - - tier3 1095 1 0.09 991 248 20.02 0 0 NA 673778 TCGA-AB-3012 AML13 8 15532570 15532570 G A SNP TUSC3 NM_006765.2 human genbank 54_36p 1 reviewed intronic c.308+7441 e2+7441 0 - - - no_errors tier3 929 0 0 910 686 42.96 0 0 0 673778 TCGA-AB-3012 AML13 8 19429553 19429553 C T SNP CSGALNACT1 NM_018371.1 human genbank 54_36p -1 validated intronic c.1-21632 e1-21632 0.001 - - - no_errors tier3 1059 5 0.47 742 651 46.73 3 1 25 673778 TCGA-AB-3012 AML13 8 20825025 20825025 C T SNP - - - - - - - - - - - - - - - tier3 1369 6 0.44 632 467 42.45 0 0 NA 673778 TCGA-AB-3012 AML13 8 21448254 21448254 C T SNP - - - - - - - - - - - - - - - tier3 3093 1 0.03 1086 851 43.87 0 0 NA 673778 TCGA-AB-3012 AML13 8 23577774 23577774 C T SNP NKX3-1 NM_006167.3 human genbank 54_36p -1 validated 3_prime_flanking_region c.*16905 NULL 0.042 - - - no_errors tier3 1531 1 0.07 786 590 42.88 0 0 NA 673778 TCGA-AB-3012 AML13 8 29246701 29246701 C T SNP DUSP4 NM_001394.5 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*3761 NULL 1 - - - no_errors tier3 921 2 0.22 352 239 40.3 0 0 NA 673778 TCGA-AB-3012 AML13 8 30698428 30698428 G A SNP GSR NM_000637.2 human genbank 54_36p -1 validated intronic c.306+6161 e1+6161 0.006 - - - no_errors tier3 803 0 0 209 165 44.12 0 0 0 673778 TCGA-AB-3012 AML13 8 36350185 36350185 G A SNP - - - - - - - - - - - - - - - tier3 900 2 0.22 962 752 43.82 0 0 NA 673778 TCGA-AB-3012 AML13 8 37038178 37038178 G C SNP - - - - - - - - - - - - - - - tier3 681 3 0.44 629 509 44.61 0 0 NA 673778 TCGA-AB-3012 AML13 8 38507789 38507789 G A SNP C8orf86 NM_207412.1 human genbank 54_36p -1 predicted 5_prime_flanking_region c.-2477 NULL 0.818 - - - no_errors tier2 332 0 0 294 198 40.24 0 0 NA 673778 TCGA-AB-3012 AML13 8 40440764 40440764 G A SNP - - - - - - - - - - - - - - - tier3 903 2 0.22 1099 280 20.29 0 0 NA 673778 TCGA-AB-3012 AML13 8 41042734 41042734 A T SNP ENSG00000206867 ENST00000384140 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*33060 NULL 0.001 - - - no_errors tier3 836 6 0.71 953 705 42.47 0 0 NA 673778 TCGA-AB-3012 AML13 8 52412680 52412680 G A SNP PXDNL NM_144651.4 human genbank 54_36p -1 validated intronic c.4146+2057 e21+2057 0.002 - - - no_errors tier3 1071 1 0.09 503 455 47.35 0 0 NA 673778 TCGA-AB-3012 AML13 8 57589793 57589793 G A SNP LOC389662 XR_016813.2 human genbank 54_36p -1 model intronic c.NULL NULL 0 - - - pseudogene tier3 927 3 0.32 733 548 42.75 0 0 NA 673778 TCGA-AB-3012 AML13 8 58786508 58786508 C A SNP LOC100130588 XM_001719422.1 human genbank 54_36p -1 model intronic c.126+75163 e2+75163 0.002 - - - no_errors tier3 1247 3 0.24 1066 851 44.32 0 0 NA 673778 TCGA-AB-3012 AML13 8 64023962 64023962 C T SNP NKAIN3 NM_173688.2 human genbank 54_36p 1 provisional intronic c.532+30336 e5+30336 0 - - - no_errors tier3 431 1 0.23 831 381 31.41 0 0 NA 673778 TCGA-AB-3012 AML13 8 65408358 65408359 - A INS LOC100130155 XM_001720219.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40205 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 8 69215655 69215655 C T SNP PREX2 NM_024870.2 human genbank 54_36p 1 validated intronic c.4087+2349 e33+2349 0 - - - no_errors tier3 822 0 0 822 584 41.51 0 0 NA 673778 TCGA-AB-3012 AML13 8 72231075 72231075 G A SNP EYA1 NM_000503.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*43054 NULL 0 - - - no_errors tier3 1252 1 0.08 648 490 43.06 0 0 NA 673778 TCGA-AB-3012 AML13 8 76566604 76566604 C T SNP HNF4G ENST00000354370 human ensembl 54_36p 1 known intronic c.1+1606 e0+1606 0 - - - no_errors tier3 1212 0 0 789 469 37.19 0 0 NA 673778 TCGA-AB-3012 AML13 8 80082549 80082549 C G SNP - - - - - - - - - - - - - - - tier3 1357 2 0.15 1163 762 39.56 0 0 NA 673778 TCGA-AB-3012 AML13 8 82397007 82397007 C T SNP LOC100131721 XM_001716134.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-40534 NULL 0.001 - - - no_errors tier3 855 1 0.12 697 577 45.18 0 0 NA 673778 TCGA-AB-3012 AML13 8 84839688 84839688 G C SNP - - - - - - - - - - - - - - - tier3 592 0 0 789 373 32.07 0 0 NA 673778 TCGA-AB-3012 AML13 8 89581935 89581935 C T SNP - - - - - - - - - - - - - - - tier3 469 0 0 933 241 20.51 0 0 NA 673778 TCGA-AB-3012 AML13 8 90031506 90031506 C T SNP - - - - - - - - - - - - - - - tier3 667 0 0 402 271 40.21 0 0 NA 673778 TCGA-AB-3012 AML13 8 95326583 95326583 G A SNP CDH17 NM_004063.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-50494 NULL 0 - - - no_errors tier3 2429 2 0.08 791 624 44.1 0 0 NA 673778 TCGA-AB-3012 AML13 8 101809238 101809238 G A SNP PABPC1 NM_002568.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-6251 NULL 0.005 - - - no_errors tier3 581 1 0.17 361 31 7.91 0 0 NA 673778 TCGA-AB-3012 AML13 8 106514616 106514616 G A SNP ZFPM2 NM_012082.3 human genbank 54_36p 1 reviewed intronic c.200-11068 e3-11068 0.001 - - - no_errors tier3 1083 0 0 962 407 29.73 0 0 NA 673778 TCGA-AB-3012 AML13 8 109595414 109595414 C T SNP TTC35 NM_014673.3 human genbank 54_36p 1 provisional 3_prime_flanking_region c.*27411 NULL 0.025 - - - no_errors tier3 530 0 0 1468 136 8.46 0 0 NA 673778 TCGA-AB-3012 AML13 8 115029562 115029562 A C SNP ENSG00000206719 ENST00000383992 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-2729 NULL 0.006 - - - no_errors tier3 697 1 0.14 670 543 44.77 0 0 NA 673778 TCGA-AB-3012 AML13 8 118833261 118833261 C T SNP EXT1 NM_000127.2 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*47871 NULL 0.002 - - - no_errors tier3 1483 0 0 760 597 43.96 0 0 NA 673778 TCGA-AB-3012 AML13 8 125267041 125267041 C T SNP ENSG00000214803 ENST00000399016 human ensembl 54_36p -1 known 3_prime_flanking_region c.*22622 NULL 0.01 - - - no_start_codon tier2 1079 0 0 947 712 42.84 1 0 0 673778 TCGA-AB-3012 AML13 8 133116597 133116597 A G SNP OC90 NM_001080399.2 human genbank 54_36p -1 validated intronic c.680-334 e9-334 0.001 - - - no_errors tier3 789 1 0.13 969 743 43.37 0 0 NA 673778 TCGA-AB-3012 AML13 8 133420223 133420223 C T SNP KCNQ3 NM_004519.2 human genbank 54_36p -1 reviewed intronic c.386+141353 e1+141353 0 - - - no_errors tier3 2379 4 0.17 709 640 47.34 0 0 NA 673778 TCGA-AB-3012 AML13 8 136573822 136573822 G A SNP KHDRBS3 NM_006558.1 human genbank 54_36p 1 provisional intronic c.89-28840 e2-28840 0.001 - - - no_errors tier3 421 3 0.71 520 458 46.83 0 0 NA 673778 TCGA-AB-3012 AML13 8 138534503 138534503 A G SNP - - - - - - - - - - - - - - - tier3 579 1 0.17 1245 304 19.63 0 0 NA 673778 TCGA-AB-3012 AML13 9 1329761 1329761 G C SNP ENSG00000202383 ENST00000365513 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*5808 NULL 0.002 - - - no_errors tier3 720 0 0 478 342 41.71 0 0 NA 673778 TCGA-AB-3012 AML13 9 12093623 12093623 T C SNP - - - - - - - - - - - - - - - tier3 409 0 0 632 273 30.13 0 0 NA 673778 TCGA-AB-3012 AML13 9 12383941 12383941 C T SNP - - - - - - - - - - - - - - - tier3 1571 4 0.25 748 618 45.18 0 0 NA 673778 TCGA-AB-3012 AML13 9 20403512 20403513 - T INS MLLT3 NM_004529.2 human genbank 54_36p -1 validated intronic c.1125+206_1125+205 e5+206 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 9 22031305 22031305 T C SNP CDKN2BAS NR_003529.3 human genbank 54_36p 1 validated intronic c.NULL NULL 0 - - - no_errors tier3 728 4 0.55 763 613 44.55 0 0 NA 673778 TCGA-AB-3012 AML13 9 22596705 22596705 G A SNP - - - - - - - - - - - - - - - tier3 910 4 0.44 641 549 46.13 0 0 NA 673778 TCGA-AB-3012 AML13 9 27854005 27854005 G A SNP - - - - - - - - - - - - - - - tier2 941 2 0.21 710 549 43.54 0 0 NA 673778 TCGA-AB-3012 AML13 9 28748120 28748120 T C SNP LINGO2 NM_152570.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-807451 NULL 0.008 - - - no_errors tier3 936 0 0 888 414 31.75 0 0 NA 673778 TCGA-AB-3012 AML13 9 31663232 31663232 A G SNP ENSG00000217739 ENST00000402171 human ensembl 54_36p -1 known 5_prime_flanking_region c.-28074 NULL 0.073 - - - no_coding_region:pseudogene tier3 880 0 0 740 601 44.82 0 0 NA 673778 TCGA-AB-3012 AML13 9 67983131 67983131 C T SNP LOC642236 XR_041085.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-37936 NULL 0.002 - - - no_errors tier2 263 1 0.38 361 127 26.02 0 0 NA 673778 TCGA-AB-3012 AML13 9 75923333 75923333 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 9 80772039 80772039 C T SNP - - - - - - - - - - - - - - - tier2 578 1 0.17 370 263 41.55 0 0 NA 673778 TCGA-AB-3012 AML13 9 93672933 93672933 C A SNP ROR2 NM_004560.2 human genbank 54_36p -1 reviewed intronic c.97+79037 e1+79037 0.006 - - - no_errors tier3 663 2 0.3 1231 149 10.79 0 0 NA 673778 TCGA-AB-3012 AML13 9 100931544 100931544 A G SNP TGFBR1 NM_004612.1 human genbank 54_36p 1 reviewed intronic c.343+341 e2+341 0 - - - no_errors tier3 679 0 0 484 366 43.01 2 1 33.33 673778 TCGA-AB-3012 AML13 9 117952418 117952418 A G SNP PAPPA NM_002581.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-3855 NULL 0 - - - no_errors tier2 1259 3 0.24 420 341 44.75 0 0 NA 673778 TCGA-AB-3012 AML13 9 121881301 121881301 C T SNP - - - - - - - - - - - - - - - tier3 1880 0 0 1551 405 20.69 0 0 NA 673778 TCGA-AB-3012 AML13 9 126631849 126631849 C T SNP WDR38 NM_001045476.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-23783 NULL 0 - - - no_errors tier3 311 0 0 94 81 46.29 0 0 NA 673778 TCGA-AB-3012 AML13 9 131490690 131490690 G C SNP PRRX2 NM_016307.3 human genbank 54_36p 1 reviewed intronic c.259+22464 e1+22464 0.034 - - - no_errors tier3 2239 2 0.09 337 280 45.38 0 0 NA 673778 TCGA-AB-3012 AML13 9 135445823 135445823 C T SNP DBH NM_000787.3 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-45492 NULL 0 - - - no_errors tier3 821 0 0 466 357 43.27 0 0 NA 673778 TCGA-AB-3012 AML13 9 138635922 138635923 - G INS EGFL7 NM_016215.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46634 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 10 3596296 3596296 A T SNP LOC100134102 XM_001718244.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-49757 NULL 0.001 - - - no_start_codon:pseudogene:no_stop_codon tier3 732 2 0.27 548 457 45.47 0 0 NA 673778 TCGA-AB-3012 AML13 10 7096080 7096080 C A SNP - - - - - - - - - - - - - - - tier3 1363 0 0 979 827 45.77 0 0 NA 673778 TCGA-AB-3012 AML13 10 7810663 7810663 C T SNP ITIH2 NM_002216.2 human genbank 54_36p 1 validated intronic c.1279+866 e11+866 0.04 - - - no_errors tier3 1344 0 0 904 678 42.86 0 0 NA 673778 TCGA-AB-3012 AML13 10 15779364 15779364 T C SNP ITGA8 NM_003638.1 human genbank 54_36p -1 provisional intronic c.344-9321 e3-9321 0 - - - no_errors tier3 957 1 0.1 361 359 49.86 0 0 NA 673778 TCGA-AB-3012 AML13 10 25830191 25830191 G A SNP GPR158 NM_020752.2 human genbank 54_36p 1 validated intronic c.1404+34537 e5+34537 0 - - - no_errors tier3 1127 3 0.26 996 868 46.44 0 0 NA 673778 TCGA-AB-3012 AML13 10 26110307 26110307 G A SNP ENSG00000223019 ENST00000411087 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*32439 NULL 0.201 - - - no_errors tier3 340 0 0 551 403 42.2 0 0 NA 673778 TCGA-AB-3012 AML13 10 27480468 27480468 C T SNP YME1L1 NM_139312.2 human genbank 54_36p -1 reviewed intronic c.34-2493 e2-2493 0.018 - - - no_errors tier3 608 2 0.33 408 312 43.33 1 1 50 673778 TCGA-AB-3012 AML13 10 33057760 33057760 A G SNP C10orf68 NM_024688.2 human genbank 54_36p 1 validated intronic c.590-61 e7-61 0.009 - - - no_errors tier3 379 0 0 435 335 43.51 0 0 0 673778 TCGA-AB-3012 AML13 10 35081933 35081933 T A SNP PARD3 NM_019619.2 human genbank 54_36p -1 provisional intronic c.121-56580 e2-56580 0.008 - - - no_errors tier3 1675 3 0.18 812 640 44.05 0 0 NA 673778 TCGA-AB-3012 AML13 10 37470639 37470639 G A SNP ANKRD30A NM_052997.2 human genbank 54_36p 1 validated intronic c.653-13 e7-13 0 - - - no_errors tier3 284 0 0 171 155 47.55 0 0 NA 673778 TCGA-AB-3012 AML13 10 53443693 53443693 T C SNP PRKG1 NM_006258.1 human genbank 54_36p 1 validated intronic c.763-40557 e6-40557 0.002 - - - no_errors tier3 1234 2 0.16 482 329 40.57 0 0 NA 673778 TCGA-AB-3012 AML13 10 56316715 56316715 A G SNP PCDH15 ENST00000373957 human ensembl 54_36p -1 known intronic c.1+10501 e0+10501 0.001 - - - no_errors tier3 463 0 0 336 279 45.37 0 0 NA 673778 TCGA-AB-3012 AML13 10 64858546 64858546 C G SNP JMJD1C NM_032776.2 human genbank 54_36p -1 validated intronic c.168+36715 e1+36715 0.048 - - - no_errors tier3 385 4 1.03 569 426 42.73 1 2 66.67 673778 TCGA-AB-3012 AML13 10 79988382 79988382 G A SNP LOC100132987 XM_001716093.1 human genbank 54_36p 1 model intronic c.388-1282 e4-1282 0 - - - no_errors tier3 479 0 0 325 218 40 0 0 NA 673778 TCGA-AB-3012 AML13 10 83524706 83524706 C A SNP - - - - - - - - - - - - - - - tier3 872 1 0.11 1133 524 31.6 0 0 NA 673778 TCGA-AB-3012 AML13 10 85412655 85412655 T C SNP LOC728050 XM_001126432.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*9641 NULL 0.045 - - - no_errors tier3 906 1 0.11 957 243 20.25 0 0 NA 673778 TCGA-AB-3012 AML13 10 95886365 95886365 A C SNP PLCE1 NM_016341.3 human genbank 54_36p 1 validated intronic c.1492+4159 e2+4159 0 - - - no_errors tier2 956 1 0.1 548 366 40.04 0 0 NA 673778 TCGA-AB-3012 AML13 10 102909648 102909648 C T SNP TD1 NM_001085398.1 human genbank 54_36p -1 validated 5_prime_flanking_region c.-69996 NULL 0.023 - - - no_errors tier2 812 6 0.73 435 352 44.67 0 0 NA 673778 TCGA-AB-3012 AML13 10 104651302 104651303 - T INS AS3MT NM_020682.3 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*855 NULL 0.000:0.000 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 10 108357874 108357874 T A SNP SORCS1 NM_001013031.1 human genbank 54_36p -1 reviewed intronic c.3034-829 e23-829 0.002 - - - no_errors tier3 1498 0 0 1005 729 41.99 0 0 NA 673778 TCGA-AB-3012 AML13 10 111031968 111031968 C T SNP ENSG00000200217 ENST00000363347 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*42474 NULL 0.01 - - - no_errors tier3 638 0 0 1271 280 18.01 0 0 NA 673778 TCGA-AB-3012 AML13 10 111307835 111307835 G T SNP ENSG00000218906 ENST00000404325 human ensembl 54_36p 1 known 3_prime_flanking_region c.*29079 NULL 0 - - - no_coding_region:pseudogene tier2 1791 0 0 1616 743 31.5 0 0 NA 673778 TCGA-AB-3012 AML13 10 122051669 122051669 C A SNP - - - - - - - - - - - - - - - tier3 1104 0 0 1130 784 40.94 0 0 NA 673778 TCGA-AB-3012 AML13 10 125767932 125767932 C T SNP GALNAC4S-6ST NM_015892.2 human genbank 54_36p -1 validated intronic c.1347+2830 e5+2830 0.255 - - - no_errors tier3 833 1 0.12 484 418 46.24 0 0 NA 673778 TCGA-AB-3012 AML13 10 131371626 131371626 A T SNP MGMT NM_002412.3 human genbank 54_36p 1 validated intronic c.126-24523 e2-24523 0.001 - - - no_errors tier3 473 1 0.21 280 226 44.66 1 1 33.33 673778 TCGA-AB-3012 AML13 11 8491420 8491420 T A SNP - - - - - - - - - - - - - - - tier3 1950 3 0.15 702 553 43.96 0 0 NA 673778 TCGA-AB-3012 AML13 11 20640996 20640996 C T SNP - - - - - - - - - - - - - - - tier3 1145 1 0.09 329 231 41.25 0 0 NA 673778 TCGA-AB-3012 AML13 11 24504893 24504894 - T INS - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 11 26719154 26719154 C T SNP - - - - - - - - - - - - - - - tier3 1471 1 0.07 1042 805 43.56 0 0 NA 673778 TCGA-AB-3012 AML13 11 30164513 30164513 A C SNP - - - - - - - - - - - - - - - tier3 519 1 0.19 804 555 40.84 0 0 NA 673778 TCGA-AB-3012 AML13 11 35902328 35902328 C T SNP - - - - - - - - - - - - - - - tier2 852 1 0.12 374 285 43.25 0 0 NA 673778 TCGA-AB-3012 AML13 11 41712164 41712164 T G SNP - - - - - - - - - - - - - - - tier2 731 2 0.27 1060 128 10.77 0 0 NA 673778 TCGA-AB-3012 AML13 11 46486106 46486106 C G SNP - - - - - - - - - - - - - - - tier2 1272 0 0 1124 588 34.29 2 0 0 673778 TCGA-AB-3012 AML13 11 49817482 49817482 G T SNP - - - - - - - - - - - - - - - tier3 621 0 0 240 35 12.73 0 0 NA 673778 TCGA-AB-3012 AML13 11 79109243 79109243 G A SNP - - - - - - - - - - - - - - - tier3 633 2 0.31 559 457 44.94 0 0 NA 673778 TCGA-AB-3012 AML13 11 79366756 79366756 T A SNP - - - - - - - - - - - - - - - tier3 1202 4 0.33 976 764 43.91 0 0 NA 673778 TCGA-AB-3012 AML13 11 82742904 82742904 C T SNP - - - - - - - - - - - - - - - tier3 885 2 0.22 1153 211 15.46 0 0 NA 673778 TCGA-AB-3012 AML13 11 82846372 82846372 A - DEL - - - - - - - - - - - - - - - tier2 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 11 83532408 83532408 C T SNP - - - - - - - - - - - - - - - tier3 392 1 0.25 571 526 47.95 0 0 NA 673778 TCGA-AB-3012 AML13 11 89854161 89854161 T C SNP - - - - - - - - - - - - - - - tier3 487 0 0 460 409 47.07 0 0 NA 673778 TCGA-AB-3012 AML13 11 110399542 110399542 C T SNP ENSG00000200168 ENST00000363298 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*16490 NULL 0 - - - no_errors tier3 2434 2 0.08 2038 1447 41.47 0 0 NA 673778 TCGA-AB-3012 AML13 11 111776847 111776847 C T SNP ENSG00000206772 ENST00000384045 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-48252 NULL 0.001 - - - no_errors tier3 1892 0 0 506 431 45.9 0 0 NA 673778 TCGA-AB-3012 AML13 11 119084977 119084977 C T SNP PVRL1 NM_002855.4 human genbank 54_36p -1 validated intronic c.79+19418 e1+19418 0 - - - no_errors tier3 1097 4 0.36 232 194 45.54 1 1 50 673778 TCGA-AB-3012 AML13 11 125426084 125426084 C T SNP CDON NM_016952.4 human genbank 54_36p -1 validated intronic c.1+12247 e0+12247 0.005 - - - no_errors tier3 1002 0 0 446 323 42 0 0 NA 673778 TCGA-AB-3012 AML13 11 126481051 126481051 C A SNP - - - - - - - - - - - - - - - tier3 1566 6 0.38 1257 341 21.31 0 0 NA 673778 TCGA-AB-3012 AML13 11 131655168 131655168 C T SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed intronic c.527-27625 e5-27625 0.002 - - - no_errors tier3 461 1 0.22 922 403 30.42 0 0 NA 673778 TCGA-AB-3012 AML13 11 131734711 131734711 T A SNP NTM NM_001048209.1 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*24461 NULL 0.001 - - - no_errors tier3 800 0 0 501 403 44.53 0 0 NA 673778 TCGA-AB-3012 AML13 11 134210931 134210931 C T SNP - - - - - - - - - - - - - - - tier3 762 3 0.39 285 160 35.96 0 0 NA 673778 TCGA-AB-3012 AML13 12 5429959 5429959 C T SNP NTF3 NM_001102654.1 human genbank 54_36p 1 reviewed intronic c.18+18190 e1+18190 0.001 - - - no_errors tier2 1371 4 0.29 1328 1084 44.94 0 0 NA 673778 TCGA-AB-3012 AML13 12 11789043 11789043 C A SNP ETV6 NM_001987.4 human genbank 54_36p 1 reviewed intronic c.34-7608 e2-7608 0.286 - - - no_errors tier3 1326 6 0.45 1250 930 42.64 13 11 45.83 673778 TCGA-AB-3012 AML13 12 11883488 11883500 ATCGATCTCCTCA - DEL ETV6 NM_001987.4 human genbank 54_36p 1 reviewed frame_shift_del c.311_323 p.Y104fs 0.995:0.881:0.929:0.995:0.992:1.000:1.000:1.000:1.000:1.000:0.984:1.000:1.000 "HMMPfam_SAM_PNT,HMMSmart_SM00251,superfamily_SAM/Pointed domain" "HMMPfam_Ets,HMMSmart_SM00413,PatternScan_ETS_DOMAIN_2,HMMPfam_SAM_PNT,HMMSmart_SM00251,superfamily_SAM/Pointed domain,superfamily_""Winged helix"" DNA-binding domain" - no_errors tier1 NA NA NA NA NA NA NA 673778 TCGA-AB-3012 AML13 12 14483291 14483291 A G SNP ATF7IP NM_018179.3 human genbank 54_36p 1 validated intronic c.1929+823 e4+823 0.002 - - - no_errors tier3 392 0 0 922 688 42.68 0 2 100 673778 TCGA-AB-3012 AML13 12 15974520 15974520 G A SNP DERA NM_015954.2 human genbank 54_36p 1 validated intronic c.31+18905 e1+18905 0 - - - no_errors tier3 421 0 0 825 381 31.59 0 0 0 673778 TCGA-AB-3012 AML13 12 26542314 26542314 A G SNP ITPR2 NM_002223.2 human genbank 54_36p -1 validated intronic c.5074-2854 e38-2854 0.003 - - - no_errors tier3 461 1 0.22 796 232 22.52 0 0 0 673778 TCGA-AB-3012 AML13 12 41654221 41654221 T A SNP - - - - - - - - - - - - - - - tier2 750 1 0.13 477 386 44.73 0 1 100 673778 TCGA-AB-3012 AML13 12 54299838 54299838 G T SNP OR10P1 NM_206899.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-17105 NULL 0.334 - - - no_errors tier2 1561 4 0.25 786 566 41.86 0 0 NA 673778 TCGA-AB-3012 AML13 12 57487072 57487072 A G SNP - - - - - - - - - - - - - - - tier3 719 0 0 780 539 40.86 0 0 NA 673778 TCGA-AB-3012 AML13 12 61277128 61277128 G A SNP MON2 NM_015026.2 human genbank 54_36p 1 validated 3_prime_untranslated_region c.*4332 NULL 0.2 - - - no_errors tier2 663 0 0 407 198 32.62 9 3 25 673778 TCGA-AB-3012 AML13 12 61776214 61776214 A G SNP - - - - - - - - - - - - - - - tier3 1118 2 0.18 1552 1252 44.63 0 0 NA 673778 TCGA-AB-3012 AML13 12 65028070 65028070 A T SNP HELB NM_033647.2 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*9921 NULL 1 - - - no_errors tier2 872 0 0 1007 676 40.12 8 6 42.86 673778 TCGA-AB-3012 AML13 12 70859924 70859924 C T SNP - - - - - - - - - - - - - - - tier3 429 1 0.23 537 79 12.78 0 0 NA 673778 TCGA-AB-3012 AML13 12 77657987 77657987 A G SNP - - - - - - - - - - - - - - - tier3 619 0 0 912 624 40.49 0 0 NA 673778 TCGA-AB-3012 AML13 12 84528188 84528188 G A SNP ENSG00000213268 ENST00000393210 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*42037 NULL 0.007 - - - no_coding_region:pseudogene tier3 845 2 0.24 1166 486 29.4 0 0 NA 673778 TCGA-AB-3012 AML13 12 88387602 88387602 C T SNP WDR51B NM_172240.1 human genbank 54_36p -1 provisional intronic c.810+667 e7+667 0 - - - no_errors tier3 1311 6 0.45 1088 855 43.96 0 0 0 673778 TCGA-AB-3012 AML13 12 89513881 89513881 C T SNP - - - - - - - - - - - - - - - tier2 978 1 0.1 659 495 42.89 0 0 NA 673778 TCGA-AB-3012 AML13 12 93029822 93029822 G T SNP PLXNC1 NM_005761.1 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-37057 NULL 0.001 - - - no_errors tier3 1049 0 0 548 420 43.3 0 0 NA 673778 TCGA-AB-3012 AML13 12 97757815 97757815 G T SNP ANKS1B NM_152788.2 human genbank 54_36p -1 validated intronic c.2779-7770 e18-7770 0 - - - no_errors tier3 1044 2 0.19 550 438 44.2 0 0 NA 673778 TCGA-AB-3012 AML13 12 100049448 100049448 C G SNP ANO4 NM_178826.3 human genbank 54_36p 1 validated 3_prime_flanking_region c.*4469 NULL 0.002 - - - no_errors tier3 881 1 0.11 561 607 51.92 0 0 NA 673778 TCGA-AB-3012 AML13 12 104911924 104911924 C T SNP - - - - - - - - - - - - - - - tier3 1248 1 0.08 426 331 43.61 0 0 NA 673778 TCGA-AB-3012 AML13 12 105719377 105719377 C A SNP RIC8B NM_018157.2 human genbank 54_36p 1 validated intronic c.133-13227 e3-13227 0.272 - - - no_errors tier3 962 2 0.21 715 505 41.39 2 2 50 673778 TCGA-AB-3012 AML13 12 105719378 105719378 T C SNP RIC8B NM_018157.2 human genbank 54_36p 1 validated intronic c.133-13226 e3-13226 0.309 - - - no_errors tier3 972 1 0.1 718 512 41.63 2 2 50 673778 TCGA-AB-3012 AML13 12 121922780 121922780 G A SNP VPS37B NM_024667.2 human genbank 54_36p -1 validated intronic c.112-1219 e2-1219 0.002 - - - no_errors tier3 915 1 0.11 410 283 40.84 4 2 33.33 673778 TCGA-AB-3012 AML13 12 125452272 125452272 T C SNP LOC100128554 XM_001719470.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-43193 NULL 0.004 - - - no_errors tier3 653 1 0.15 447 332 42.62 0 0 NA 673778 TCGA-AB-3012 AML13 12 127020940 127020940 C T SNP - - - - - - - - - - - - - - - tier3 928 1 0.11 538 415 43.5 0 0 NA 673778 TCGA-AB-3012 AML13 12 127705905 127705905 G T SNP TMEM132C ENST00000315208 human ensembl 54_36p 1 known intronic c.154-14010 e2-14010 0.015 - - - no_errors tier3 757 0 0 1173 876 42.69 0 0 NA 673778 TCGA-AB-3012 AML13 12 130998360 130998360 G A SNP EP400 NM_015409.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-12758 NULL 0 - - - no_errors tier3 875 2 0.23 290 220 43.05 0 0 NA 673778 TCGA-AB-3012 AML13 13 21152456 21152456 G A SNP FGF9 NM_002010.2 human genbank 54_36p 1 reviewed intronic c.278-725 e2-725 0 - - - no_errors tier3 357 1 0.28 282 194 40.76 0 0 NA 673778 TCGA-AB-3012 AML13 13 22707043 22707043 T A SNP SGCG NM_000231.2 human genbank 54_36p 1 reviewed intronic c.297+192 e2+192 0.033 - - - no_errors tier3 352 0 0 994 132 11.71 0 0 NA 673778 TCGA-AB-3012 AML13 13 31205995 31205995 C T SNP RXFP2 NM_130806.3 human genbank 54_36p 1 validated 5_prime_flanking_region c.-5755 NULL 0.005 - - - no_errors tier3 976 1 0.1 480 382 44.32 0 0 NA 673778 TCGA-AB-3012 AML13 13 32113945 32113946 - T INS PDS5B NM_015032.2 human genbank 54_36p 1 validated intronic c.1-6946_6945 e1-6945 0.012:0.020 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 13 37436766 37436766 A T SNP ENSG00000217350 ENST00000403854 human ensembl 54_36p -1 known 3_prime_flanking_region c.*28456 NULL 0.034 - - - no_coding_region:pseudogene tier2 745 0 0 630 511 44.79 0 0 NA 673778 TCGA-AB-3012 AML13 13 43492623 43492623 G C SNP ENSG00000179611 ENST00000325496 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*49288 NULL 0.008 - - - no_coding_region:pseudogene tier3 1119 1 0.09 777 593 43.25 0 0 NA 673778 TCGA-AB-3012 AML13 13 46313983 46313983 G A SNP HTR2A NM_000621.2 human genbank 54_36p -1 validated intronic c.614-6208 e3-6208 0 - - - no_errors tier3 1086 1 0.09 746 544 42.14 0 0 NA 673778 TCGA-AB-3012 AML13 13 46731748 46731748 C T SNP ENSG00000220245 ENST00000403833 human ensembl 54_36p 1 known 5_prime_flanking_region c.-47470 NULL 0 - - - no_coding_region:pseudogene tier3 1397 3 0.21 1263 534 29.65 0 0 NA 673778 TCGA-AB-3012 AML13 13 49890235 49890235 A T SNP - - - - - - - - - - - - - - - tier3 1067 3 0.28 896 697 43.7 0 0 0 673778 TCGA-AB-3012 AML13 13 50361992 50361992 T C SNP RNASEH2B NM_024570.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-20222 NULL 0.002 - - - no_errors tier2 561 0 0 379 326 46.24 0 1 100 673778 TCGA-AB-3012 AML13 13 52243046 52243046 T - DEL LECT1 NM_007015.1 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-31209 NULL 0 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 13 54206697 54206697 T A SNP - - - - - - - - - - - - - - - tier3 380 0 0 443 348 43.99 0 0 NA 673778 TCGA-AB-3012 AML13 13 54987108 54987108 A T SNP - - - - - - - - - - - - - - - tier2 988 0 0 1356 198 12.72 0 0 NA 673778 TCGA-AB-3012 AML13 13 57939076 57939076 C T SNP LOC341689 XR_017487.1 human genbank 54_36p 1 model intronic c.NULL NULL 0 - - - no_errors tier3 1073 1 0.09 1107 105 8.65 0 0 NA 673778 TCGA-AB-3012 AML13 13 58753045 58753045 G T SNP - - - - - - - - - - - - - - - tier2 839 0 0 819 378 31.53 0 0 NA 673778 TCGA-AB-3012 AML13 13 65217028 65217028 G C SNP ENSG00000181836 ENST00000321014 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*43037 NULL 0.006 - - - no_coding_region:pseudogene tier3 779 3 0.38 659 470 41.63 0 0 NA 673778 TCGA-AB-3012 AML13 13 67641697 67641697 A T SNP - - - - - - - - - - - - - - - tier3 467 0 0 294 141 32.41 0 0 NA 673778 TCGA-AB-3012 AML13 13 67770057 67770057 G A SNP ENSG00000217105 ENST00000405099 human ensembl 54_36p -1 known 5_prime_flanking_region c.-6644 NULL 0.001 - - - no_coding_region:pseudogene tier3 1001 0 0 685 444 39.33 0 0 NA 673778 TCGA-AB-3012 AML13 13 68485961 68485961 C A SNP ENSG00000219035 ENST00000382463 human ensembl 54_36p 1 known 3_prime_flanking_region c.*27764 NULL 0 - - - no_coding_region:pseudogene tier2 842 4 0.47 592 468 44.15 0 0 NA 673778 TCGA-AB-3012 AML13 13 68669807 68669807 T C SNP - - - - - - - - - - - - - - - tier3 624 0 0 534 228 29.84 0 0 NA 673778 TCGA-AB-3012 AML13 13 75195600 75195600 G T SNP LMO7 NM_005358.5 human genbank 54_36p 1 reviewed intronic c.297-3566 e4-3566 0 - - - no_errors tier2 419 0 0 442 365 45.23 0 0 0 673778 TCGA-AB-3012 AML13 13 76023985 76023985 C T SNP - - - - - - - - - - - - - - - tier3 691 1 0.14 891 382 29.94 0 0 NA 673778 TCGA-AB-3012 AML13 13 77703379 77703379 G A SNP - - - - - - - - - - - - - - - tier2 773 0 0 950 656 40.8 0 0 NA 673778 TCGA-AB-3012 AML13 13 77903810 77903810 G A SNP ENSG00000219197 ENST00000404519 human ensembl 54_36p 1 known 3_prime_flanking_region c.*8482 NULL 0 - - - no_coding_region:pseudogene tier3 773 0 0 780 568 42.04 0 0 NA 673778 TCGA-AB-3012 AML13 13 78125818 78125818 C G SNP RNF219 NM_024546.3 human genbank 54_36p -1 validated intronic c.72+5367 e1+5367 0.001 - - - no_errors tier3 1235 0 0 806 348 30.16 0 0 0 673778 TCGA-AB-3012 AML13 13 81486814 81486814 C G SNP - - - - - - - - - - - - - - - tier3 350 0 0 272 188 40.78 0 0 NA 673778 TCGA-AB-3012 AML13 13 81489422 81489422 C A SNP - - - - - - - - - - - - - - - tier3 736 3 0.41 480 381 44.25 0 0 NA 673778 TCGA-AB-3012 AML13 13 82305782 82305782 C T SNP ENSG00000216454 ENST00000404510 human ensembl 54_36p 1 known 3_prime_flanking_region c.*9510 NULL 0.004 - - - no_coding_region:pseudogene tier3 893 2 0.22 470 178 27.47 0 0 NA 673778 TCGA-AB-3012 AML13 13 85736226 85736226 A G SNP ENSG00000214181 ENST00000397726 human ensembl 54_36p 1 novel 3_prime_flanking_region c.*8706 NULL 0 - - - no_coding_region:pseudogene tier3 540 0 0 749 606 44.69 0 0 NA 673778 TCGA-AB-3012 AML13 13 85920125 85920125 T A SNP - - - - - - - - - - - - - - - tier3 483 0 0 699 90 11.41 0 0 NA 673778 TCGA-AB-3012 AML13 13 86472323 86472323 G A SNP - - - - - - - - - - - - - - - tier3 711 1 0.14 645 518 44.5 0 0 NA 673778 TCGA-AB-3012 AML13 13 87222117 87222117 G A SNP - - - - - - - - - - - - - - - tier3 791 0 0 757 654 46.32 0 0 NA 673778 TCGA-AB-3012 AML13 13 89762491 89762491 C A SNP - - - - - - - - - - - - - - - tier3 1662 5 0.3 1578 658 29.4 0 0 NA 673778 TCGA-AB-3012 AML13 13 93816450 93816450 G A SNP GPC6 NM_005708.3 human genbank 54_36p 1 reviewed intronic c.1153-16219 e7-16219 0 - - - no_errors tier3 592 2 0.34 622 281 31.08 0 0 NA 673778 TCGA-AB-3012 AML13 13 98961387 98961387 T A SNP TM9SF2 NM_004800.1 human genbank 54_36p 1 provisional intronic c.172-6482 e2-6482 0.002 - - - no_errors tier2 509 1 0.2 396 284 41.76 1 2 66.67 673778 TCGA-AB-3012 AML13 13 108335798 108335798 C T SNP MYO16 NM_015011.1 human genbank 54_36p 1 validated intronic c.1487+2263 e12+2263 0.026 - - - no_errors tier3 610 1 0.16 703 301 29.92 0 0 NA 673778 TCGA-AB-3012 AML13 13 109693485 109693485 G A SNP COL4A1 NM_001845.4 human genbank 54_36p -1 reviewed intronic c.85-403 e2-403 0 - - - no_errors tier2 532 0 0 359 281 43.77 0 0 NA 673778 TCGA-AB-3012 AML13 13 110152269 110152269 C A SNP CARS2 NM_024537.1 human genbank 54_36p -1 provisional intronic c.276-366 e3-366 0 - - - no_errors tier3 653 3 0.46 319 246 43.54 0 1 100 673778 TCGA-AB-3012 AML13 13 112227091 112227092 - T INS TUBGCP3 NM_006322.4 human genbank 54_36p -1 provisional intronic c.1555+2165_1555+2164 e13+2165 0.001:0.001 - - - no_errors tier2 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 13 114036766 114036766 C T SNP CDC16 NM_001078645.1 human genbank 54_36p 1 reviewed intronic c.1097+2515 e12+2515 0.005 - - - no_errors tier3 422 0 0 389 288 42.48 1 1 50 673778 TCGA-AB-3012 AML13 14 18182216 18182216 C T SNP ENSG00000215398 ENST00000400208 human ensembl 54_36p 1 known intronic c.107+1843 e1+1843 0.011 - - - no_start_codon tier3 227 0 0 370 97 20.77 0 0 NA 673778 TCGA-AB-3012 AML13 14 23680748 23680748 A T SNP REC8 NM_001048205.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-30854 NULL 0.974 - - - no_errors tier2 932 8 0.85 279 218 43.69 0 1 100 673778 TCGA-AB-3012 AML13 14 24789043 24789043 C G SNP ENSG00000179020 ENST00000323440 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*17067 NULL 0 - - - no_coding_region:pseudogene tier3 657 1 0.15 811 506 38.42 0 0 NA 673778 TCGA-AB-3012 AML13 14 26636172 26636172 A G SNP - - - - - - - - - - - - - - - tier3 656 0 0 693 597 46.17 0 0 NA 673778 TCGA-AB-3012 AML13 14 27055241 27055241 T A SNP LOC728755 XM_001128377.2 human genbank 54_36p -1 model intronic c.201+140248 e2+140248 0 - - - no_errors tier3 1226 0 0 1365 158 10.36 0 0 NA 673778 TCGA-AB-3012 AML13 14 28070548 28070548 T C SNP - - - - - - - - - - - - - - - tier3 511 0 0 683 534 43.88 0 0 NA 673778 TCGA-AB-3012 AML13 14 40142647 40142647 C T SNP - - - - - - - - - - - - - - - tier3 580 0 0 437 211 32.51 0 0 NA 673778 TCGA-AB-3012 AML13 14 45389907 45389907 C A SNP - - - - - - - - - - - - - - - tier3 526 0 0 850 572 40.2 0 0 NA 673778 TCGA-AB-3012 AML13 14 47153950 47153950 A G SNP MDGA2 ENST00000399232 human ensembl 54_36p -1 known intronic c.73+59520 e1+59520 0 - - - no_errors tier2 674 0 0 347 260 42.76 0 0 NA 673778 TCGA-AB-3012 AML13 14 47813175 47813175 C T SNP - - - - - - - - - - - - - - - tier2 867 0 0 1206 929 43.43 0 0 NA 673778 TCGA-AB-3012 AML13 14 53648357 53648357 G A SNP - - - - - - - - - - - - - - - tier3 1156 0 0 671 538 44.46 0 0 NA 673778 TCGA-AB-3012 AML13 14 55007011 55007011 G A SNP TBPL2 NM_199047.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-29995 NULL 0.009 - - - no_errors tier3 1278 5 0.39 403 352 46.62 1 0 0 673778 TCGA-AB-3012 AML13 14 56337666 56337666 A G SNP OTX2 NM_021728.2 human genbank 54_36p -1 reviewed 3_prime_untranslated_region c.*540 NULL 1 - - - no_errors tier2 976 2 0.2 382 57 12.98 0 0 NA 673778 TCGA-AB-3012 AML13 14 59872524 59872524 C T SNP PPM1A NM_021003.4 human genbank 54_36p 1 reviewed 3_prime_flanking_region c.*43571 NULL 0.009 - - - no_errors tier3 1669 1 0.06 698 545 43.81 0 0 NA 673778 TCGA-AB-3012 AML13 14 64299257 64299257 C T SNP SPTB NM_001024858.4 human genbank 54_36p -1 validated intronic c.6345+3940 e31+3940 0.004 - - - no_errors tier3 2749 2 0.07 536 378 41.36 0 1 100 673778 TCGA-AB-3012 AML13 14 65662164 65662164 C T SNP - - - - - - - - - - - - - - - tier3 668 0 0 631 264 29.43 0 0 NA 673778 TCGA-AB-3012 AML13 14 79314557 79314557 A G SNP NRXN3 NM_004796.1 human genbank 54_36p 1 reviewed intronic c.2806-26651 e14-26651 0.001 - - - no_errors tier2 1786 1 0.06 1599 1292 44.69 0 0 0 673778 TCGA-AB-3012 AML13 14 81565557 81565557 A - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 14 82232337 82232338 - A INS ENSG00000213346 ENST00000393582 human ensembl 54_36p -1 novel 5_prime_flanking_region c.-3185 NULL 0.227:0.284 - - - no_coding_region:pseudogene tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 14 83071657 83071657 C T SNP - - - - - - - - - - - - - - - tier2 740 1 0.13 463 314 40.41 0 0 NA 673778 TCGA-AB-3012 AML13 14 83243494 83243494 C T SNP ENSG00000210408 ENST00000387673 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-43004 NULL 0 - - - pseudogene tier3 520 1 0.19 500 475 48.62 0 0 NA 673778 TCGA-AB-3012 AML13 14 89612836 89612836 C T SNP KCNK13 NM_022054.2 human genbank 54_36p 1 reviewed intronic c.334+14200 e1+14200 0.006 - - - no_errors tier3 1324 0 0 434 343 43.92 0 0 NA 673778 TCGA-AB-3012 AML13 14 95883013 95883013 C T SNP ATG2B NM_018036.5 human genbank 54_36p -1 validated intronic c.325+256 e2+256 0.004 - - - no_errors tier3 465 0 0 329 207 38.55 0 0 0 673778 TCGA-AB-3012 AML13 14 98149263 98149263 C G SNP - - - - - - - - - - - - - - - tier3 1466 7 0.47 710 615 46.31 0 0 NA 673778 TCGA-AB-3012 AML13 14 105017271 105017271 G A SNP CRIP2 NM_001312.2 human genbank 54_36p 1 provisional 3_prime_untranslated_region c.*236 NULL 0.001 - - - no_errors tier3 105 1 0.94 25 16 39.02 1 0 0 673778 TCGA-AB-3012 AML13 15 18666170 18666170 T C SNP LOC646090 XR_017120.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*26920 NULL 0.016 - - - pseudogene tier3 888 1 0.11 556 208 27.15 0 0 NA 673778 TCGA-AB-3012 AML13 15 20080335 20080335 C G SNP LOC646396 XM_001726976.1 human genbank 54_36p 1 model 3_prime_flanking_region c.*8058 NULL 0.005 - - - no_errors tier3 401 0 0 480 218 31.19 0 0 NA 673778 TCGA-AB-3012 AML13 15 21803341 21803341 T C SNP - - - - - - - - - - - - - - - tier3 516 0 0 707 461 39.44 0 0 NA 673778 TCGA-AB-3012 AML13 15 25973189 25973189 C T SNP OCA2 NM_000275.2 human genbank 54_36p -1 reviewed intronic c.228-22285 e2-22285 0.002 - - - no_errors tier3 606 0 0 486 272 35.84 0 0 NA 673778 TCGA-AB-3012 AML13 15 27212632 27212632 C T SNP APBA2 ENST00000382938 human ensembl 54_36p 1 known intronic c.735-21865 e7-21865 0 - - - no_errors tier3 138 0 0 29 29 50 0 0 NA 673778 TCGA-AB-3012 AML13 15 29279902 29279902 C T SNP LOC283710 XM_211174.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*22874 NULL 0.031 - - - no_errors tier3 326 0 0 159 136 45.79 0 0 NA 673778 TCGA-AB-3012 AML13 15 30998025 30998025 A T SNP FMN1 NM_001103184.1 human genbank 54_36p -1 provisional intronic c.2557+7642 e6+7642 0.004 - - - no_errors tier3 1207 0 0 825 667 44.68 0 0 NA 673778 TCGA-AB-3012 AML13 15 31860210 31860210 G A SNP RYR3 NM_001036.3 human genbank 54_36p 1 validated intronic c.9268+376 e65+376 0 - - - no_errors tier3 1121 0 0 906 449 33.14 0 1 100 673778 TCGA-AB-3012 AML13 15 32163527 32163527 G A SNP C15orf24 NM_020154.2 human genbank 54_36p -1 validated 3_prime_untranslated_region c.*300 NULL 0.955 - - - no_errors tier2 389 1 0.26 383 275 41.79 1 3 75 673778 TCGA-AB-3012 AML13 15 40428888 40428888 G A SNP GANC NM_198141.2 human genbank 54_36p 1 reviewed missense c.2434 p.E812K 1 NULL "HMMPfam_Glyco_hydro_31,PatternScan_GLYCOSYL_HYDROL_F31_1,superfamily_(Trans)glycosidases" - no_errors tier1 1453 0 962 691 41.8 18 4 18.18 673778 TCGA-AB-3012 AML13 15 40804573 40804573 A C SNP CDAN1 NM_138477.2 human genbank 54_36p -1 validated intronic c.3558+61 e27+61 0.001 - - - no_errors tier3 1366 4 0.29 445 470 51.37 7 2 22.22 673778 TCGA-AB-3012 AML13 15 42294488 42294488 T C SNP FRMD5 NM_032892.3 human genbank 54_36p -1 validated 5_prime_flanking_region c.-19944 NULL 0.746 - - - no_errors tier2 823 0 0 562 381 40.4 0 0 NA 673778 TCGA-AB-3012 AML13 15 45624065 45624065 C G SNP ENSG00000221202 ENST00000408275 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*7899 NULL 0.005 - - - no_errors tier2 1701 0 0 1175 880 42.78 0 0 NA 673778 TCGA-AB-3012 AML13 15 57355339 57355340 - C INS MYO1E NM_004998.2 human genbank 54_36p -1 validated intronic c.4-3400_4-3399 e2-3399 0.025:0.027 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 15 64236834 64236834 A G SNP MEGF11 NM_032445.2 human genbank 54_36p -1 validated intronic c.1-33442 e1-33442 0 - - - no_errors tier3 809 0 0 570 430 43 0 0 NA 673778 TCGA-AB-3012 AML13 15 67527336 67527336 C A SNP KIF23 NM_138555.4 human genbank 54_36p 1 reviewed 3_prime_untranslated_region c.*136 NULL 0.138 - - - no_errors tier3 963 4 0.41 869 355 28.96 13 5 27.78 673778 TCGA-AB-3012 AML13 15 67660737 67660737 T C SNP - - - - - - - - - - - - - - - tier3 1011 1 0.1 407 353 46.26 0 0 NA 673778 TCGA-AB-3012 AML13 15 87161334 87161334 A C SNP ACAN NM_013227.2 human genbank 54_36p 1 reviewed intronic c.1+13290 e0+13290 0 - - - no_errors tier3 671 0 0 338 267 44.06 0 0 NA 673778 TCGA-AB-3012 AML13 15 95354146 95354146 C G SNP - - - - - - - - - - - - - - - tier3 670 0 0 407 269 39.79 0 0 NA 673778 TCGA-AB-3012 AML13 15 96258345 96258345 T G SNP ARRDC4 NM_183376.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-46751 NULL 0.035 - - - no_errors tier3 1053 1 0.09 779 635 44.88 0 0 NA 673778 TCGA-AB-3012 AML13 15 96406660 96406660 G A SNP LOC728459 XM_001129411.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*39804 NULL 0.006 - - - no_errors tier3 1144 0 0 746 604 44.71 0 0 NA 673778 TCGA-AB-3012 AML13 16 2752700 2752701 - TC INS SRRM2 NM_016333.3 human genbank 54_36p 1 validated frame_shift_ins c.2170_2171 p.S724fs 1.000:1.000 NULL HMMPfam_cwf21 - no_errors tier1 NA NA NA NA NA NA NA 673778 TCGA-AB-3012 AML13 16 5414500 5414500 C T SNP - - - - - - - - - - - - - - - tier2 832 6 0.71 454 438 49.05 0 0 NA 673778 TCGA-AB-3012 AML13 16 6078407 6078407 G A SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1+68413 e0+68413 0.691 - - - no_errors tier3 981 4 0.4 645 580 47.31 0 0 NA 673778 TCGA-AB-3012 AML13 16 6244966 6244966 A G SNP A2BP1 NM_018723.1 human genbank 54_36p 1 reviewed intronic c.1-62031 e1-62031 0 - - - no_errors tier2 1294 2 0.15 594 451 43.08 0 0 NA 673778 TCGA-AB-3012 AML13 16 11064866 11064866 G A SNP CLEC16A NM_015226.2 human genbank 54_36p 1 validated intronic c.2116+2486 e19+2486 0.005 - - - no_errors tier3 775 1 0.13 637 483 43.09 1 0 0 673778 TCGA-AB-3012 AML13 16 17311067 17311067 A G SNP XYLT1 NM_022166.3 human genbank 54_36p -1 validated intronic c.402+48303 e2+48303 0.201 - - - no_errors tier3 1427 0 0 1014 862 45.8 12 6 33.33 673778 TCGA-AB-3012 AML13 16 45289910 45289910 C A SNP VPS35 NM_018206.4 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-9364 NULL 0 - - - no_errors tier2 885 2 0.23 475 355 42.67 0 0 NA 673778 TCGA-AB-3012 AML13 16 52869976 52869976 C T SNP LOC728792 XM_001719288.1 human genbank 54_36p 1 model 5_prime_flanking_region c.-40946 NULL 0.012 - - - no_errors tier3 2332 1 0.04 428 299 40.96 0 0 NA 673778 TCGA-AB-3012 AML13 16 53371211 53371211 G A SNP - - - - - - - - - - - - - - - tier3 1032 0 0 653 485 42.58 0 0 NA 673778 TCGA-AB-3012 AML13 16 55024365 55024365 T C SNP NUDT21 NM_007006.2 human genbank 54_36p -1 reviewed intronic c.663-219 e7-219 0 - - - no_errors tier3 558 2 0.36 222 178 44.5 0 0 0 673778 TCGA-AB-3012 AML13 16 61139911 61139911 G A SNP - - - - - - - - - - - - - - - tier3 804 2 0.25 649 614 48.5 0 0 NA 673778 TCGA-AB-3012 AML13 16 63199045 63199045 G A SNP - - - - - - - - - - - - - - - tier3 1105 3 0.27 762 580 43.19 0 0 NA 673778 TCGA-AB-3012 AML13 16 66163880 66163880 C - DEL CTCF NM_006565.2 human genbank 54_36p 1 reviewed intronic c.1+1212 e0+1212 0.876 - - - no_errors tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 16 72205451 72205451 C T SNP - - - - - - - - - - - - - - - tier3 720 1 0.14 914 385 29.55 0 0 NA 673778 TCGA-AB-3012 AML13 16 75203250 75203250 C T SNP - - - - - - - - - - - - - - - tier3 924 1 0.11 457 395 46.36 0 0 NA 673778 TCGA-AB-3012 AML13 16 80241300 80241300 C T SNP CMIP NM_198390.2 human genbank 54_36p 1 validated intronic c.376-2009 e4-2009 0.001 - - - no_errors tier3 770 0 0 640 95 12.89 3 1 25 673778 TCGA-AB-3012 AML13 16 83632832 83632832 G A SNP KIAA0513 NM_014732.2 human genbank 54_36p 1 validated intronic c.1+13874 e0+13874 0.035 - - - no_errors tier3 922 1 0.11 406 287 41.29 0 0 NA 673778 TCGA-AB-3012 AML13 16 85702758 85702758 G A SNP LOC730018 XM_001132101.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*29324 NULL 0.007 - - - no_errors tier3 740 0 0 471 409 46.32 0 0 NA 673778 TCGA-AB-3012 AML13 16 86689902 86689902 C T SNP LOC400553 XM_001132183.1 human genbank 54_36p -1 model intronic c.434+1899 e2+1899 0.003 - - - no_errors tier3 354 0 0 189 151 44.28 0 0 NA 673778 TCGA-AB-3012 AML13 17 9200033 9200033 T C SNP STX8 NM_004853.1 human genbank 54_36p -1 provisional intronic c.643+22561 e7+22561 0.001 - - - no_errors tier3 1684 2 0.12 619 472 43.26 2 2 50 673778 TCGA-AB-3012 AML13 17 12271838 12271838 G A SNP - - - - - - - - - - - - - - - tier3 1318 3 0.23 1518 413 21.35 0 0 NA 673778 TCGA-AB-3012 AML13 17 13218464 13218464 G - DEL - - - - - - - - - - - - - - - tier3 NA NA NA NA NA NA 0 0 NA 673778 TCGA-AB-3012 AML13 17 19388366 19388366 G A SNP SLC47A1 NM_018242.2 human genbank 54_36p 1 validated intronic c.237+1967 e2+1967 0 - - - no_errors tier3 748 3 0.4 268 235 46.53 0 0 NA 673778 TCGA-AB-3012 AML13 17 23373772 23373772 T C SNP NLK NM_016231.4 human genbank 54_36p 1 validated 5_prime_flanking_region c.-20255 NULL 0.002 - - - no_errors tier3 883 0 0 430 322 42.82 0 0 NA 673778 TCGA-AB-3012 AML13 17 27613399 27613399 C T SNP RHBDL3 NM_138328.2 human genbank 54_36p 1 validated 5_prime_flanking_region c.-3923 NULL 0.014 - - - no_errors tier3 1164 3 0.26 221 184 45.32 0 0 NA 673778 TCGA-AB-3012 AML13 17 32246740 32246740 C T SNP LOC727862 XM_001125987.2 human genbank 54_36p -1 model 3_prime_flanking_region c.*46463 NULL 0.004 - - - no_errors tier3 1691 3 0.18 455 367 44.54 0 0 NA 673778 TCGA-AB-3012 AML13 17 43248265 43248265 C T SNP OSBPL7 NM_145798.2 human genbank 54_36p -1 reviewed intronic c.1119+207 e11+207 0 - - - no_errors tier2 734 13 1.74 253 214 45.73 2 0 0 673778 TCGA-AB-3012 AML13 17 44894092 44894092 T C SNP NGFR NM_002507.2 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-33687 NULL 0.003 - - - no_errors tier2 1846 5 0.27 519 386 42.46 0 0 NA 673778 TCGA-AB-3012 AML13 17 46021102 46021102 T G SNP CACNA1G NM_018896.3 human genbank 54_36p 1 validated intronic c.2302-1729 e10-1729 0.031 - - - no_errors tier3 706 1 0.14 470 351 42.75 0 0 NA 673778 TCGA-AB-3012 AML13 17 47335092 47335092 G A SNP CA10 NM_001082533.1 human genbank 54_36p -1 reviewed intronic c.279+28257 e3+28257 0.003 - - - no_errors tier3 1006 1 0.1 1710 1223 41.64 0 0 NA 673778 TCGA-AB-3012 AML13 17 54320922 54320922 C T SNP PPM1E NM_014906.3 human genbank 54_36p 1 reviewed intronic c.465-66870 e2-66870 0.018 - - - no_errors tier3 856 0 0 638 256 28.64 0 0 NA 673778 TCGA-AB-3012 AML13 17 58440860 58440860 C T SNP TANC2 NM_025185.3 human genbank 54_36p 1 validated intronic c.67+141 e1+141 0 - - - no_errors tier3 587 0 0 579 453 43.85 0 0 NA 673778 TCGA-AB-3012 AML13 17 62930050 62930050 A G SNP PITPNC1 NM_012417.2 human genbank 54_36p 1 reviewed intronic c.49-29330 e2-29330 0.002 - - - no_errors tier3 1053 2 0.19 537 431 44.48 0 0 0 673778 TCGA-AB-3012 AML13 17 65033825 65033825 A G SNP MAP2K6 NM_002758.3 human genbank 54_36p 1 reviewed intronic c.742-481 e10-481 0.036 - - - no_errors tier3 1471 2 0.14 693 542 43.82 1 1 50 673778 TCGA-AB-3012 AML13 17 67411737 67411737 T C SNP - - - - - - - - - - - - - - - tier3 660 2 0.3 941 148 13.57 0 0 NA 673778 TCGA-AB-3012 AML13 18 1492647 1492647 C T SNP LOC100130320 XR_038508.1 human genbank 54_36p -1 model 5_prime_flanking_region c.-18938 NULL 0.001 - - - pseudogene tier2 1140 1 0.09 1137 578 33.66 0 0 NA 673778 TCGA-AB-3012 AML13 18 10666837 10666837 G A SNP FAM38B NM_022068.1 human genbank 54_36p -1 predicted intronic c.1118+907 e8+907 0.001 - - - no_errors tier3 1088 0 0 785 648 45 0 0 NA 673778 TCGA-AB-3012 AML13 18 10953922 10953922 G T SNP - - - - - - - - - - - - - - - tier3 919 1 0.11 676 575 45.89 0 0 NA 673778 TCGA-AB-3012 AML13 18 19043823 19043823 G A SNP CABLES1 NM_001100619.2 human genbank 54_36p 1 validated intronic c.1011-4116 e4-4116 0 - - - no_errors tier3 472 0 0 374 326 46.57 1 0 0 673778 TCGA-AB-3012 AML13 18 22680256 22680256 G A SNP AQP4 NM_001650.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*9917 NULL 0.392 - - - no_errors tier3 1635 7 0.43 1201 810 40.2 0 0 NA 673778 TCGA-AB-3012 AML13 18 36415813 36415813 C T SNP - - - - - - - - - - - - - - - tier3 390 0 0 299 285 48.8 0 0 NA 673778 TCGA-AB-3012 AML13 18 37510556 37510556 A C SNP - - - - - - - - - - - - - - - tier3 1843 3 0.16 2065 201 8.86 0 0 NA 673778 TCGA-AB-3012 AML13 18 40706607 40706607 T C SNP SETBP1 NM_015559.1 human genbank 54_36p 1 validated intronic c.378+3361 e2+3361 0 - - - no_errors tier3 1025 5 0.49 826 622 42.93 0 0 NA 673778 TCGA-AB-3012 AML13 18 45442195 45442195 G A SNP - - - - - - - - - - - - - - - tier3 1915 3 0.16 476 407 45.89 0 0 NA 673778 TCGA-AB-3012 AML13 18 47900425 47900425 A C SNP - - - - - - - - - - - - - - - tier3 655 1 0.15 534 407 43.16 0 0 NA 673778 TCGA-AB-3012 AML13 18 51718024 51718024 T C SNP - - - - - - - - - - - - - - - tier3 1279 2 0.16 1436 215 13.01 0 0 NA 673778 TCGA-AB-3012 AML13 18 59251584 59251584 A G SNP VPS4B NM_004869.3 human genbank 54_36p -1 reviewed 5_prime_flanking_region c.-11112 NULL 0 - - - no_errors tier3 925 1 0.11 347 297 46.12 0 0 NA 673778 TCGA-AB-3012 AML13 18 62138414 62138414 G T SNP - - - - - - - - - - - - - - - tier3 522 2 0.38 703 99 12.34 0 0 NA 673778 TCGA-AB-3012 AML13 18 63707740 63707740 A T SNP - - - - - - - - - - - - - - - tier3 436 0 0 401 50 11.09 0 0 NA 673778 TCGA-AB-3012 AML13 18 74211246 74211246 C T SNP - - - - - - - - - - - - - - - tier3 639 3 0.47 348 306 46.65 0 0 NA 673778 TCGA-AB-3012 AML13 18 74443236 74443236 T G SNP LOC100132713 XM_001714438.1 human genbank 54_36p 1 model intronic c.2314-1249 e15-1249 0.984 - - - no_errors tier2 660 1 0.15 437 267 37.87 0 0 NA 673778 TCGA-AB-3012 AML13 19 13336222 13336222 C T SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known intronic c.784+909 e5+909 0.005 - - - no_errors tier3 1304 0 0 460 350 43.21 0 0 0 673778 TCGA-AB-3012 AML13 19 13485174 13485174 A T SNP CACNA1A ENST00000325084 human ensembl 54_36p -1 known 5_prime_flanking_region c.-7136 NULL 0 - - - no_errors tier2 640 3 0.46 306 247 44.5 0 0 NA 673778 TCGA-AB-3012 AML13 19 21416650 21416650 C T SNP ZNF493 NM_001076678.2 human genbank 54_36p 1 validated 3_prime_flanking_region c.*17024 NULL 0 - - - no_errors tier3 248 0 0 172 136 44.16 3 4 57.14 673778 TCGA-AB-3012 AML13 19 33347191 33347191 C G SNP - - - - - - - - - - - - - - - tier3 2222 2 0.09 1173 945 44.6 0 0 NA 673778 TCGA-AB-3012 AML13 19 34014643 34014643 T C SNP - - - - - - - - - - - - - - - tier2 1190 0 0 901 90 9.07 0 0 NA 673778 TCGA-AB-3012 AML13 19 36186138 36186138 A C SNP - - - - - - - - - - - - - - - tier3 2039 3 0.15 1090 797 42.21 0 0 NA 673778 TCGA-AB-3012 AML13 19 44481248 44481248 G A SNP SAMD4B NM_018028.2 human genbank 54_36p 1 provisional 5_prime_flanking_region c.-58126 NULL 0 - - - no_errors tier2 1042 3 0.29 302 224 42.5 1 2 66.67 673778 TCGA-AB-3012 AML13 19 47827165 47827165 C T SNP ENSG00000219845 ENST00000407179 human ensembl 54_36p -1 known intronic c.NULL NULL 0.014 - - - no_coding_region:pseudogene tier3 1078 1 0.09 277 211 43.24 0 0 NA 673778 TCGA-AB-3012 AML13 19 52567974 52567974 G A SNP DHX34 NM_014681.4 human genbank 54_36p 1 reviewed missense c.1942 p.V648I 0.984 NULL "HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_HA2,HMMPfam_DUF1605,HMMSmart_SM00487,PatternScan_RUBREDOXIN,superfamily_P-loop containing nucleoside triphosphate hydrolases" - no_errors tier1 203 0 87 67 43.51 8 1 11.11 673778 TCGA-AB-3012 AML13 19 56663851 56663851 C T SNP SIGLEC8 NM_014442.2 human genbank 54_36p -1 validated 5_prime_flanking_region c.-10398 NULL 0 - - - no_errors tier3 616 1 0.16 270 237 46.56 0 0 NA 673778 TCGA-AB-3012 AML13 20 3158541 3158541 G A SNP SLC4A11 NM_032034.2 human genbank 54_36p -1 validated intronic c.1538-119 e13-119 0 - - - no_errors tier3 191 0 0 126 104 45.22 1 0 0 673778 TCGA-AB-3012 AML13 20 13296445 13296445 T C SNP GAPDP2 ENST00000406370 human ensembl 54_36p 1 known 5_prime_flanking_region c.-24879 NULL 0.002 - - - no_coding_region:pseudogene tier3 975 0 0 556 499 47.3 0 1 100 673778 TCGA-AB-3012 AML13 20 17038119 17038119 A C SNP - - - - - - - - - - - - - - - tier3 1536 1 0.06 1042 791 43.11 0 0 NA 673778 TCGA-AB-3012 AML13 20 24317265 24317265 T A SNP - - - - - - - - - - - - - - - tier3 1169 0 0 1017 729 41.73 0 0 NA 673778 TCGA-AB-3012 AML13 20 24737649 24737649 C T SNP - - - - - - - - - - - - - - - tier3 511 0 0 255 178 40.92 0 0 NA 673778 TCGA-AB-3012 AML13 20 30698142 30698142 G C SNP ENSG00000198547 ENST00000360785 human ensembl 54_36p -1 known intronic c.585+2576 e2+2576 0 - - - no_errors tier3 2372 0 0 270 258 48.86 1 1 50 673778 TCGA-AB-3012 AML13 20 37392453 37392453 C T SNP ENSG00000220679 ENST00000403085 human ensembl 54_36p -1 known 5_prime_flanking_region c.-472 NULL 0.003 - - - no_coding_region:pseudogene tier3 1414 1 0.07 871 426 32.82 0 0 NA 673778 TCGA-AB-3012 AML13 20 38476906 38476906 A G SNP - - - - - - - - - - - - - - - tier3 658 1 0.15 372 259 41.05 0 0 NA 673778 TCGA-AB-3012 AML13 20 38511896 38511896 A G SNP - - - - - - - - - - - - - - - tier3 879 0 0 726 628 46.38 0 0 NA 673778 TCGA-AB-3012 AML13 20 38646589 38646589 G A SNP - - - - - - - - - - - - - - - tier3 1219 2 0.16 796 684 46.22 0 0 NA 673778 TCGA-AB-3012 AML13 20 40321722 40321722 G A SNP PTPRT NM_133170.5 human genbank 54_36p -1 reviewed intronic c.2233+10729 e14+10729 0 - - - no_errors tier3 825 2 0.24 590 467 44.18 0 0 NA 673778 TCGA-AB-3012 AML13 20 41454558 41454558 G A SNP ENSG00000201021 ENST00000364151 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-12969 NULL 0 - - - no_errors tier3 1206 4 0.33 570 494 46.38 0 0 NA 673778 TCGA-AB-3012 AML13 20 46019293 46019293 G A SNP LOC100130589 XM_001722384.1 human genbank 54_36p -1 model 3_prime_flanking_region c.*20598 NULL 0 - - - no_errors tier3 1470 2 0.14 853 563 39.73 0 0 NA 673778 TCGA-AB-3012 AML13 20 49294317 49294317 C G SNP - - - - - - - - - - - - - - - tier2 771 0 0 546 500 47.8 0 0 NA 673778 TCGA-AB-3012 AML13 20 51757199 51757199 G A SNP - - - - - - - - - - - - - - - tier3 3103 3 0.1 1568 265 14.43 0 0 NA 673778 TCGA-AB-3012 AML13 20 52873915 52873915 A C SNP ENSG00000210815 ENST00000388080 human ensembl 54_36p -1 novel 3_prime_flanking_region c.*35718 NULL 0.012 - - - pseudogene tier3 906 0 0 525 381 42.01 0 0 NA 673778 TCGA-AB-3012 AML13 20 53073758 53073758 C T SNP - - - - - - - - - - - - - - - tier3 1132 0 0 647 248 27.71 0 0 NA 673778 TCGA-AB-3012 AML13 20 53883130 53883130 G A SNP - - - - - - - - - - - - - - - tier3 1720 2 0.12 1296 900 40.96 0 0 NA 673778 TCGA-AB-3012 AML13 20 53997320 53997320 C T SNP CBLN4 NM_080617.4 human genbank 54_36p -1 reviewed 3_prime_flanking_region c.*9700 NULL 0 - - - no_errors tier3 913 0 0 484 335 40.85 0 0 NA 673778 TCGA-AB-3012 AML13 20 54694672 54694672 G A SNP ENSG00000221416 ENST00000408489 human ensembl 54_36p 1 novel 5_prime_flanking_region c.-32677 NULL 0 - - - no_errors tier3 839 2 0.24 400 276 40.65 0 0 NA 673778 TCGA-AB-3012 AML13 20 56562736 56562736 T G SNP APCDD1L NM_153360.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-39567 NULL 0.003 - - - no_errors tier3 921 2 0.22 324 316 49.38 0 0 NA 673778 TCGA-AB-3012 AML13 20 59378659 59378659 G A SNP CDH4 NM_001794.2 human genbank 54_36p 1 reviewed intronic c.169+115271 e2+115271 0.001 - - - no_errors tier3 918 4 0.43 420 317 43.01 0 0 NA 673778 TCGA-AB-3012 AML13 20 61221229 61221229 C T SNP HAR1B NR_003245.1 human genbank 54_36p -1 provisional 5_prime_flanking_region c.-17113 NULL 0.001 - - - no_errors tier3 578 0 0 266 125 31.89 0 0 NA 673778 TCGA-AB-3012 AML13 21 22221013 22221013 G T SNP - - - - - - - - - - - - - - - tier3 403 0 0 361 287 44.29 0 0 NA 673778 TCGA-AB-3012 AML13 21 24271419 24271419 A T SNP - - - - - - - - - - - - - - - tier3 320 0 0 316 258 44.87 0 0 NA 673778 TCGA-AB-3012 AML13 21 37422602 37422602 T C SNP TTC3 NM_001001894.1 human genbank 54_36p 1 validated intronic c.1298-571 e15-571 0 - - - no_errors tier3 679 2 0.29 644 567 46.82 2 10 83.33 673778 TCGA-AB-3012 AML13 21 39773939 39773939 A T SNP SH3BGR NM_007341.1 human genbank 54_36p 1 validated intronic c.501+4928 e3+4928 0.019 - - - no_errors tier3 638 1 0.16 349 358 50.56 0 0 0 673778 TCGA-AB-3012 AML13 21 44402663 44402663 G A SNP LOC100129890 XM_001722818.1 human genbank 54_36p -1 model intronic c.1855+1080 e13+1080 0 - - - no_errors tier3 852 3 0.35 285 114 28.5 4 3 42.86 673778 TCGA-AB-3012 AML13 22 18457143 18457143 T G SNP DGCR8 NM_022720.5 human genbank 54_36p 1 validated intronic c.881-49 e3-49 0 - - - no_errors tier3 1445 0 0 647 78 10.74 4 1 20 673778 TCGA-AB-3012 AML13 22 20654724 20654724 C T SNP TOP3B NM_003935.3 human genbank 54_36p -1 reviewed missense c.439 p.V147M 0.984 "superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00436,HMMPfam_Toprim" "PatternScan_TOPOISOMERASE_I_PROK,superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00436,HMMSmart_SM00437,HMMSmart_SM00493,HMMPfam_Toprim,HMMPfam_Topoisom_bac" - no_errors tier1 596 0 265 187 41.37 15 15 50 673778 TCGA-AB-3012 AML13 22 21362993 21362993 T A SNP ENSG00000183169 ENST00000402027 human ensembl 54_36p -1 known 5_prime_flanking_region c.-46437 NULL 0 - - - no_errors tier3 445 1 0.22 322 233 41.98 0 0 0 673778 TCGA-AB-3012 AML13 22 28018596 28018596 G T SNP EWSR1 NM_005243.2 human genbank 54_36p 1 reviewed splice_site c.1164+1 e11+1 1 - - - no_errors tier1 1118 0 753 176 18.95 13 9 26.47 673778 TCGA-AB-3012 AML13 22 28892764 28892764 T C SNP HORMAD2 NM_152510.2 human genbank 54_36p 1 provisional intronic c.820-9288 e10-9288 0.014 - - - no_errors tier3 651 1 0.15 696 559 44.47 0 0 NA 673778 TCGA-AB-3012 AML13 22 29936230 29936230 T C SNP LIMK2 NM_001031801.1 human genbank 54_36p 1 reviewed 5_prime_flanking_region c.-38473 NULL 0 - - - no_errors tier3 1110 11 0.98 254 181 41.61 0 0 0 673778 TCGA-AB-3012 AML13 22 33986566 33986566 G A SNP HMGXB4 NM_001003681.1 human genbank 54_36p 1 validated intronic c.1-1750 e1-1750 0 - - - no_errors tier3 835 1 0.12 303 221 42.18 2 1 33.33 673778 TCGA-AB-3012 AML13 22 44092796 44092796 A G SNP FAM118A NM_001104595.1 human genbank 54_36p 1 validated intronic c.1-4120 e1-4120 0 - - - no_errors tier3 673 0 0 372 238 38.95 3 2 40 673778 TCGA-AB-3012 AML13 22 46400982 46400982 C T SNP FLJ46257 XR_041673.1 human genbank 54_36p -1 model intronic c.NULL NULL 0.009 - - - no_errors tier3 751 1 0.13 288 202 41.14 0 0 NA 673778 TCGA-AB-3012 AML13 22 48056181 48056181 C T SNP - - - - - - - - - - - - - - - tier2 481 1 0.21 343 219 38.9 0 0 NA