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. Author manuscript; available in PMC: 2015 Mar 1.
Published in final edited form as: Hum Genet. 2014 Jun 3;133(9):1093–1104. doi: 10.1007/s00439-014-1452-2

Table 2. Top 10 cis- and top 10 trans-mQTLs identified in 143 European Americans (EAs).

SNPs CpGs SNP-CpG linear regression analysis
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
a

Chromosomes and coordinates of SNPs and CpGs in GRCh37/hg19.

b

Regression coefficients by multiple linear regression analysis with adjustment for sex, age, ancestry proportion, and the status of alcohol dependence (AD).

c

Observed P values by multiple linear regression analysis with adjustment for sex, age, ancestry proportion, and the status of alcohol dependence (AD).

d

Adjusted P values by R package qvalue, controlling the False Discovery Rate (FDR) at 0.05.