Table 2. Top 10 cis- and top 10 trans-mQTLs identified in 143 European Americans (EAs).
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 EAs: | ||||||||||||
rs1800759 | 4 | 100065509 | ADH4 | Promoter | cg12011299 | 4 | 100065546 | ADH4 | A | -0.15 | 2.7E-53 | 1.4E-44 |
rs2602836 | 4 | 100014805 | ADH5 | Promoter | cg12011299 | 4 | 100065546 | ADH4 | A | -0.14 | 1.3E-39 | 3.4E-31 |
rs732821 | 13 | 47472879 | HTR2A | Promoter | cg06020661 | 13 | 47472138 | HTR2A | G | -0.07 | 2.9E-27 | 2.2E-19 |
rs1126670 | 4 | 100052733 | ADH4 | Exon | cg12011299 | 4 | 100065546 | ADH4 | C | -0.13 | 1.7E-26 | 2.7E-19 |
rs1126671 | 4 | 100048414 | ADH4 | Exon | cg12011299 | 4 | 100065546 | ADH4 | A | -0.13 | 1.7E-26 | 2.7E-19 |
rs6837685 | 4 | 100049145 | ADH4 | Intron | cg12011299 | 4 | 100065546 | ADH4 | G | -0.13 | 1.7E-26 | 2.7E-19 |
rs1126673 | 4 | 100045616 | ADH4 | Exon | cg12011299 | 4 | 100065546 | ADH4 | G | -0.13 | 1.9E-26 | 3.3E-19 |
rs4699710 | 4 | 100051819 | ADH4 | Intron | cg12011299 | 4 | 100065546 | ADH4 | G | -0.13 | 1.9E-26 | 3.3E-19 |
rs6532798 | 4 | 100054827 | ADH4 | Intron | cg12011299 | 4 | 100065546 | ADH4 | G | -0.13 | 1.9E-26 | 3.3E-19 |
rs10017466 | 4 | 100055800 | ADH4 | Intron | cg12011299 | 4 | 100065546 | ADH4 | G | -0.13 | 3.0E-26 | 4.8E-19 |
Top 10 trans-mQTLs in EAs: | ||||||||||||
rs3097793 | 5 | 150617370 | CCDC69 - GM2A | intergenic | cg14150516 | 2 | 208394784 | CREB1 | A | 0.04 | 1.2E-33 | 2.0E-25 |
rs173567 | 5 | 150618829 | CCDC69 - GM2A | intergenic | cg14150516 | 2 | 208394784 | CREB1 | G | 0.04 | 4.5E-33 | 5.8E-25 |
rs6536733 | 4 | 141069646 | MAML3 | Intron | cg23463131 | 16 | 10276410 | GRIN2A | G | 0.02 | 1.7E-29 | 1.5E-21 |
rs17005603 | 4 | 141083754 | MAML3 | Promoter | cg23463131 | 16 | 10276410 | GRIN2A | G | 0.02 | 8.2E-26 | 3.5E-18 |
rs153462 | 5 | 150605070 | CCDC69 | Promoter | cg14150516 | 2 | 208394784 | CREB1 | G | 0.03 | 6.5E-18 | 3.7E-11 |
rs7917960 | 10 | 113155506 | ADRA2A - GPAM | intergenic | cg15408490 | 12 | 112204591 | ALDH2 | A | -0.05 | 8.7E-17 | 8.2E-10 |
rs9420082 | 10 | 113166617 | ADRA2A - GPAM | intergenic | cg15408490 | 12 | 112204591 | ALDH2 | G | -0.05 | 2.7E-16 | 1.8E-09 |
rs10885154 | 10 | 113151980 | ADRA2A - GPAM | intergenic | cg15408490 | 12 | 112204591 | ALDH2 | A | -0.05 | 2.6E-15 | 2.0E-08 |
rs4372376 | 10 | 113231124 | ADRA2A - GPAM | intergenic | cg15408490 | 12 | 112204591 | ALDH2 | A | -0.05 | 1.5E-14 | 9.8E-08 |
rs7896658 | 10 | 113176902 | ADRA2A - GPAM | intergenic | cg15408490 | 12 | 112204591 | ALDH2 | G | -0.05 | 2.0E-14 | 1.3E-07 |
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.