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Table 3 Association of GWAS loci with gene expression. Three genes, SEMA4A, UNC13D, and WBP2 were nominally associated with WMH

From: Whole blood gene expression and white matter Hyperintensities

GWAS SNP

Risk allelea

Locus

P value (GWAS association with WMH) [46]

Association of SNPs with gene expression by eQTL analysis [44]

Association of eGene expression with WMH (current study)

eGene

P value

Direction on gene expressionb

Effect sizea

SEc

P value

rs4072479

C

17q25.1

4.6E-14

WBP2

1.0E-10

↓

−0.020

0.010

4.6E-02

rs8067275

T

17q25.1

1.9E-13

MYO15B

2.3E-05

↑

0.003

0.005

0.52

rs9894244

A

17q25.1

5.2E-10

GALK1

2.9E-06

↓

0.001

0.004

0.79

rs9894244

A

17q25.1

5.2E-10

ITGB4

2.9E-06

↓

−0.001

0.003

0.79

rs7216615

C

17q25.1

1.1E-09

H3F3B

9.2E-29

↓

−0.007

0.008

0.38

rs34143128

C

17q25.1

2.4E-09

ACOX1

9.1E-50

↓

0.003

0.009

0.75

rs1135889

A

17q25.1

8.8E-09

UNC13D

4.5E-11

↓

−0.010

0.004

6.1E-03

rs1135889

A

17q25.1

8.8E-09

EXOC7

9.1E-05

↓

−0.009

0.006

0.86

rs1135889

A

17q25.1

8.8E-09

ZACN

9.1E-05

↓

−0.001

0.005

0.86

rs2984613

C

1q22

2.0E-08

C1orf85

6.5E-23

↓

−0.003

0.007

0.65

rs2984613

C

1q22

2.0E-08

TMEM79

6.5E-23

↓

0.005

0.007

0.65

rs2984613

C

1q22

2.0E-08

SMG5

3.3E-20

↓

0.002

0.005

0.72

rs2984613

C

1q22

2.0E-08

PAQR6

1.6E-16

↓

0.001

0.006

0.89

rs2984613

C

1q22

2.0E-08

PMF1

7.3E-10

↑

−0.001

0.005

0.91

rs2984613

C

1q22

2.0E-08

SEMA4A

2.4E-08

↓

−0.022

0.006

3.4E-04

rs10883865

G

10q24.33

4.6E-08

AS3MT

7.9E-26

↓

0.011

0.010

0.30

rs10883865

G

10q24.33

4.6E-08

USMG5

7.7E-07

↑

0.015

0.011

0.19

  1. aRisk allele respresnts the allele that was associated with increased risk of WMH
  2. bDirection of effect: ↓indicates the risk allele was associated with decreased gene expression, whereas ↑ indicates the risk allele was associated with increased gene expression
  3. c SE standard error
  4. Genes with P-value less than 0.05 were marked in bold text