Table 1. Top 10 cis- and top 10 trans-mQTLs identified in 268 African Americans (AAs).
SNPs | CpGs | SNP-CpG linear regression analysis | ||||||||||
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SNPs | Chr.a | Coordinatesa | Genes | SNP Type | CpGs | Chr.a | Coordinatesa | Genes | Allele | Betab | Pnominalc | qd |
Top 10 cis-mQTLs in AAs: | ||||||||||||
rs1800759 | 4 | 100065509 | ADH4 | Promoter | cg12011299 | 4 | 100065546 | ADH4 | C | 0.12 | 9.9E-100 | 6.7E-91 |
rs8028779 | 15 | 27034731 | GABRB3 | promoter | cg07763397 | 15 | 27020865 | GABRB3 | G | 0.09 | 4.6E-38 | 4.5E-30 |
rs2602836 | 4 | 100014805 | ADH5 | promoter | cg12011299 | 4 | 100065546 | ADH4 | G | 0.08 | 1.7E-37 | 6.7E-30 |
rs3828541 | 4 | 100042262 | ADH4 | Downstream | cg12011299 | 4 | 100065546 | ADH4 | G | 0.08 | 2.6E-34 | 1.8E-26 |
rs4486851 | 15 | 27022876 | GABRB3 | promoter | cg07763397 | 15 | 27020865 | GABRB3 | A | 0.07 | 9.5E-30 | 3.8E-22 |
rs732821 | 13 | 47472879 | HTR2A | promoter | cg06020661 | 13 | 47472138 | HTR2A | A | 0.08 | 8.7E-30 | 5.7E-22 |
rs1154415 | 4 | 99999033 | ADH5 | Intron | cg12011299 | 4 | 100065546 | ADH4 | G | 0.12 | 1.2E-26 | 4.3E-19 |
rs2851301 | 4 | 100010127 | ADH5 | promoter | cg12011299 | 4 | 100065546 | ADH4 | A | 0.12 | 1.2E-26 | 4.3E-19 |
rs13148577 | 4 | 100060836 | ADH4 | Intron | cg12011299 | 4 | 100065546 | ADH4 | A | 0.11 | 7.6E-26 | 2.6E-18 |
rs4147547 | 4 | 100127311 | ADH6 | Intron | cg12011299 | 4 | 100065546 | ADH4 | A | 0.11 | 8.0E-23 | 2.2E-15 |
Top 10 trans-mQTLs in AAs: | ||||||||||||
rs3097793 | 5 | 150617370 | CCDC69 - GM2A | intergenic | cg14150516 | 2 | 208394784 | CREB1 | A | 0.04 | 3.1E-43 | 6.5E-35 |
rs173567 | 5 | 150618829 | CCDC69 - GM2A | intergenic | cg14150516 | 2 | 208394784 | CREB1 | G | 0.04 | 3.8E-32 | 8.5E-25 |
rs628825 | 12 | 110436233 | ATXN2 | Intron | cg10959984 | 12 | 112204380 | ALDH2 | G | 0.00 | 3.2E-22 | 4.3E-15 |
rs11552148 | 16 | 48385957 | LONP2 | 3′ UTR | cg25195998 | 11 | 113345607 | DRD2 | G | -0.01 | 9.9E-22 | 1.8E-14 |
rs8055764 | 16 | 48384370 | LONP2 | Intron | cg25195998 | 11 | 113345607 | DRD2 | A | -0.01 | 6.6E-21 | 7.1E-14 |
rs11866529 | 16 | 48247523 | ABCC11 | Intron | cg25195998 | 11 | 113345607 | DRD2 | C | -0.01 | 5.5E-21 | 1.1E-13 |
rs8054314 | 16 | 48394330 | SIAH1 | Downstream | cg25195998 | 11 | 113345607 | DRD2 | A | -0.01 | 7.3E-21 | 1.1E-13 |
rs8190 | 16 | 48394626 | SIAH1 | 3′ UTR | cg25195998 | 11 | 113345607 | DRD2 | A | -0.01 | 7.3E-21 | 1.1E-13 |
rs153462 | 5 | 150605070 | CCDC69 | promoter | cg14150516 | 2 | 208394784 | CREB1 | G | 0.03 | 7.6E-20 | 5.9E-13 |
rs9926192 | 16 | 48306394 | LONP2 | Intron | cg25195998 | 11 | 113345607 | DRD2 | A | -0.01 | 4.2E-19 | 4.2E-12 |
Chromosomes and coordinates of SNPs and CpGs in GRCh37/hg19.
Regression coefficients by multiple linear regression analysis with adjustment for sex, age, ancestry proportion, and the status of alcohol dependence (AD).
Observed P values by multiple linear regression analysis with adjustment for sex, age, ancestry proportion, and the status of alcohol dependence (AD).
Adjusted P values by R package qvalue, controlling the False Discovery Rate (FDR) at 0.05.