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Table 1 BCC susceptibility functional candidate genes identified via SMR analysis

From: Genetic and functional interaction network analysis reveals global enrichment of regulatory T cell genes influencing basal cell carcinoma susceptibility

probeID Chr Gene topSNP topSNP_bp A1 A2 Freq bGWAS PGWAS beQTL PeQTL bSMR PSMR PHEIDI
ENSG00000256049 1 PADI6 rs6678121 17719986 G T 0.344 − 0.097 9.60E−17 0.464 0.00E+00 − 0.208 1.80E−16 9.76E−22
ENSG00000179051 1 RCC2 rs12035179 17793114 C T 0.393 0.080 3.60E−13 0.207 1.19E−148 0.389 2.54E−12 8.16E−16
ENSG00000003400 2 CASP10 rs13005094 202092561 T C 0.474 0.059 6.50E−08 − 0.118 7.77E−50 − 0.500 3.82E−07 1.31E−11
ENSG00000064012 2 CASP8 rs7560328 202164837 A C 0.362 0.130 3.00E−31 − 0.207 7.38E−152 − 0.627 2.12E−26 1.90E−09
ENSG00000155749 2 ALS2CR12 rs2110690 202185132 G A 0.502 − 0.121 1.40E−28 − 0.157 7.92E−88 0.771 3.57E−22 2.89E−08
ENSG00000213090 2 AC007256.5 rs2540430 202368514 T A 0.302 0.105 2.20E−19 − 0.072 3.21E−17 − 1.456 7.41E−10 4.43E−05
ENSG00000082146 2 STRADB rs7575721 202256778 C T 0.321 0.094 2.60E−16 − 0.084 3.73E−26 − 1.120 9.39E−11 1.77E−08
ENSG00000163599 2 CTLA4 rs13030124 204694263 A G 0.430 0.085 1.00E−14 0.147 2.30E−70 0.576 1.35E−12 1.11E−07
ENSG00000049656 5 CLPTM1L rs13170453 1317481 G A 0.228 − 0.146 3.50E−27 0.090 5.61E−15 − 1.617 2.45E−10 1.37E−05
ENSG00000137265 6 IRF4 rs12526822 428486 A G 0.321 − 0.098 2.30E−16 − 0.070 1.81E−14 1.396 2.13E−08 3.22E−08
ENSG00000196126 6 HLA-DRB1 rs9271520 32589771 G A 0.350 − 0.092 2.20E−15 − 0.483 0.00E+00 0.190 3.97E−15 1.98E−14
ENSG00000237541 6 HLA-DQA2 rs9271520 32589771 G A 0.350 − 0.092 2.20E−15 0.613 0.00E+00 − 0.150 3.09E−15 1.22E−09
ENSG00000204267 6 TAP2 rs4148876 32796793 A G 0.071 − 0.114 2.90E−07 − 0.524 6.40E−274 0.218 3.82E−07 3.88E−04
ENSG00000112182 6 BACH2* rs72928038 90976768 A G 0.178 − 0.124 3.30E−17 − 0.290 9.04E−97 0.426 5.29E−15 3.10E−01
ENSG00000071242 6 RPS6KA2 rs2757050 167377165 T G 0.469 0.056 2.50E−07 0.316 0.00E+00 0.177 3.12E−07 1.14E−07
ENSG00000026297 6 RNASET2 rs393727 167398632 T A 0.469 0.056 2.20E−07 0.858 0.00E+00 0.065 2.22E−07 9.81E−06
ENSG00000197146 6 AL133458.1 rs408087 167398952 C T 0.469 0.056 2.10E−07 0.715 0.00E+00 0.079 2.15E−07 6.13E−07
ENSG00000227598 6 RP1-167A14.2 rs415987 167395375 G A 0.469 0.056 2.70E−07 0.304 0.00E+00 0.184 3.38E−07 3.31E−07
ENSG00000112486 6 CCR6 rs3093025 167532731 A G 0.438 − 0.065 3.90E−09 0.208 4.98E−148 − 0.311 9.30E−09 3.16E−04
ENSG00000245025 8 RP11-875O11.1 rs2241261 22876739 C T 0.476 − 0.056 4.00E−07 0.143 4.56E−73 − 0.390 1.05E−06 7.68E−05
ENSG00000173068 9 BNC2 rs12350739 16885017 G A 0.385 − 0.078 9.60E−12 − 0.255 1.01E−184 0.304 3.33E−11 1.72E−03
ENSG00000147883 9 CDKN2B rs2069422 22008026 G T 0.100 0.111 1.60E−10 − 0.659 0.00E+00 − 0.169 2.34E−10 2.71E−05
ENSG00000136824 9 SMC2* rs2122576 106870187 C A 0.395 0.064 8.30E−09 0.212 1.04E−138 0.299 1.97E−08 3.69E−02
ENSG00000236935 11 AP003774.1* rs479777 64107477 C T 0.344 0.068 2.50E−09 0.617 0.00E+00 0.110 2.85E−09 1.55E−01
ENSG00000111424 12 VDR* rs7975232 48238837 C A 0.480 − 0.063 9.00E−09 0.124 6.51E−56 − 0.503 6.65E−08 2.52E−01
ENSG00000261253 16 AC137932.6 rs1078578 89386934 G A 0.353 0.075 2.90E−11 − 0.119 9.58E−47 − 0.630 1.59E−09 5.89E−05
ENSG00000261118 16 RP11-104N10.1* rs4785687 89588896 A G 0.384 0.097 2.20E−18 − 0.060 1.11E−13 − 1.605 1.50E−08 4.58E−02
ENSG00000197912 16 SPG7 rs4785686 89587871 C A 0.417 − 0.083 5.60E−14 0.189 4.96E−128 − 0.441 7.25E−13 1.21E−06
ENSG00000167523 16 C16orf55 rs164749 89708224 G T 0.432 − 0.061 2.50E−08 0.114 2.28E−47 − 0.538 1.96E−07 1.82E−06
ENSG00000185324 16 CDK10 rs77651727 89708267 T C 0.076 0.096 1.50E−06 − 1.419 0.00E+00 − 0.067 1.68E−06 2.09E−04
ENSG00000158792 16 SPATA2L* rs396742 89768056 G C 0.422 − 0.065 1.00E−08 − 0.369 0.00E+00 0.175 1.39E−08 1.30E−02
ENSG00000158805 16 ZNF276 rs3743859 89846050 T C 0.412 0.052 2.30E−06 0.244 6.29E−198 0.213 3.07E−06 1.34E−23
ENSG00000204991 16 SPIRE2 rs2376879 89884822 G C 0.292 − 0.075 5.40E−10 0.360 0.00E+00 − 0.209 7.55E−10 1.43E−42
ENSG00000141013 16 GAS8 rs45583731 90106364 A C 0.428 0.068 4.40E−10 − 0.192 6.97E−91 − 0.355 2.50E−09 1.96E−10
ENSG00000141510 17 TP53* rs35850753 7578671 T C 0.018 0.282 7.00E−15 − 0.365 4.04E−21 − 0.772 1.93E−09 2.60E−01
ENSG00000091542 17 ALKBH5* rs2925138 18092509 A G 0.426 0.060 3.80E−08 0.157 1.63E−68 0.383 1.55E−07 3.76E−02
ENSG00000127666 19 TICAM1* rs10405449 4821949 T C 0.372 − 0.062 4.40E−08 0.217 5.05E−139 − 0.286 8.79E−08 5.72E−02
ENSG00000125780 20 TGM3 rs214787 2283667 C T 0.181 0.214 3.30E−58 − 0.357 0.00E+00 − 0.599 7.31E−50 1.55E−08
ENSG00000101421 20 CHMP4B* rs2626562 32409142 G A 0.530 0.053 1.50E−06 0.370 0.00E+00 0.142 1.74E−06 7.17E−01
ENSG00000125977 20 EIF2S2 rs6142101 32697845 G A 0.410 0.052 2.00E−06 − 0.243 7.51E−211 − 0.215 2.66E−06 2.07E−17
ENSG00000101460 20 MAP1LC3A rs6059919 33151545 G T 0.177 0.132 3.90E−22 − 0.642 0.00E+00 − 0.206 1.51E−21 7.05E−04
ENSG00000078804 20 TP53INP2* rs1884432 33342439 T C 0.182 0.127 5.70E−21 − 0.203 1.31E−72 − 0.626 8.03E−17 8.15E−02
ENSG00000198646 20 NCOA6* rs6058112 33322006 G C 0.179 0.131 4.70E−22 0.208 1.55E−77 0.632 1.01E−17 7.10E−02
ENSG00000131067 20 GGT7 rs4911164 33479488 G C 0.377 − 0.053 2.00E−06 0.201 1.44E−139 − 0.266 3.07E−06 4.36E−14
ENSG00000100991 20 TRPC4AP rs6058166 33656710 C G 0.394 0.054 9.00E−07 0.589 0.00E+00 0.093 9.40E−07 4.32E−11
ENSG00000100029 22 PES1* rs737953 30987861 G C 0.399 − 0.053 1.60E−06 0.174 1.57E−108 − 0.307 2.67E−06 2.08E−01
  1. Genes formatted in bold: decreased gene expression linked to increased risk of BCC. Genes not in bold: increased gene expression linked to increased risk of BCC. Genes denoted by asterisk (*): genes that passed the HEIDI test. Columns: Probe ID; Probe chromosome; Gene, gene name; Probe_bp, probe position; topSNP, SNP ID; topSNP_bp, top eQTL position; A1, effect allele; A2, alternative allele; Freq, frequency; bGWAS, GWAS effect; PGWAS, GWAS P value; beQTL, eQTL effect; PeQTL, eQTL P value; bSMR, SMR effect; PSMR, SMR P value; PHEIDI, HEIDI P value
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Genome Medicine

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