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Table 4 Validated meQTL-CpG pairs

From: meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes

meQTL SNP

Chromosome

Associated gene

No. of paired CpGs*

rs301799

1

RERE

2

rs1890946

1

NRDC

1

rs72710803

1

AL122019

2

rs7585722

2

RNF103-CHMP3

2

rs4346585

3

SOCS5P3, ZKSCAN7-AS1

3

rs13084037

3

KLHDC8B

2

rs7624336

3

TKT

1

rs6783233

3

LOC101926953

1

rs7685686

4

HTT

5

rs34937911

4

SLC30A9

1

rs60157091

5

KIF2A

1

rs200949

6

HIST1H1B

7

rs7758630

6

LOC107984041

1

rs1933802

6

HACE1--[]--LIN28B

2

rs3823624

7

MAD1L1

9

rs2043539

7

TMEM106B

2

rs7030813

9

PAX5

1

rs2670139

9

DENND1A

1

rs198457

11

-

4

rs7117514

11

SHANK2

1

rs3213572

12

SPPL3

1

rs1343605

13

OLFM4--[]

1

rs4772087

13

STK24

1

rs1045430

14

AREL1

1

rs62091461

18

RAB27B

1

rs7241572

18

KCNG2

6

rs12624433

20

SLC12A5

1

rs5995992

22

RBX1---[]-EP300

3

  1. *Validation analysis was run by applying lm models between the methylation level and genetic dominant model, adjusting for age and sex The Benjamini-Hochberg multiple-testing adjustment was applied to the p values. A CpG site was paired with the meQTL SNP if the adjusted p value < 0.05
  2. meQTL methylation quantitative trait locus, SNP single nucleotide polymorphism