Table 2 Summary of the VV lead SNPs for novel loci and their colocalized genes.

From: Genome-wide association study of varicose veins identifies a protective missense variant in GJD3 enriched in the Finnish population

Lead variant

Chr:pos:ref/alta

Alt AFb

Effect (β)c

P

Variant typed

Finnish enrichmente

Nearest genes

Colocalized gene expressionf

rs17032325

1:8238488:G/A

0.095

0.128

1.6 × 10−8

Regulatory region

3.41

SLC45A1

–

rs76077063

1:9471381C/T

0.046

0.189

2.9 × 10−9

Intergenic

15.68

SLC25A33

SPSB1

rs3738814

1:17005181:A/G

0.484

−0.083

7.2 × 10−10

Intron

1.19

ATP13A2

MFAP2

rs6662887

1:91709357:C/T

0.297

−0.087

4.0 × 10−9

Intron

0.92

TGFBR3

–

rs11589479

1:155060832:G/A

0.139

0.121

4.0 × 10−10

Splice region

0.89

ADAM15

–

rs72749413

1:198091159:C/T

0.129

−0.12

1.9 × 10−9

Intergenic

1.33

NEK7

NEK7

rs192335285

1:218434159:C/T

2.54e-3

0.77

2.5 × 10−8

Synonymous

56.13

TGFB2

–

rs11118774

1:221612617:G/A

0.398

−0.081

2.7 × 10−9

Regulatory

1.31

DUSP10

–

rs10049210

3:157079584.T/C

0.332

−0.081

1.5 × 10−8

Upstream gene

0.80

LEKR1

TIPARP

rs493410

3:170754426:G/T

0.252

0.089

9.0 × 10−9

Intron

1.34

CLDN11

–

rs2189759

5:131047353:G/A

0.150

0.13

9.4 × 10−12

Intergenic

2.41

HINT1

–

rs708461

5:132751125:G/C

0.201

0.10

7.7 × 10−9

3-prime UTR

2.49

CCNI2, SEPT8

AFF4, HINT1, KIF3A

rs1294414

6:6740133:A/G

0.641

−0.077

3.9 × 10−8

Intergenic

1.01

LY86

–

rs1981030

9:91455019:T/C

0.244

0.10

2.2 × 10−11

Intergenic

1.50

NFIL3

–

rs635634

9:133279427:T/C

0.801

−0.010

2.7 × 10−9

Upstream gene

0.99

ABO

–

rs7295096

12:27644972:A/G

0.827

0.10

1.9 × 10−8

Intron

1.06

PPFIBP1

–

rs7321631

13:37543414:T/C

0.552

−0.08

1.1 × 10−8

Intron

1.12

POSTN

POSTN

rs4403927

13:39767008:G/T

0.362

−0.079

4.0 × 10−8

Intron

0.91

COG6

–

rs1657686

17:21313652:T/C

0.502

−0.0749

2.6 × 10−8

Missense

1.21

MAP2K3

–

rs76327840

17:39247659:G/C

0.0137

−0.44

1.8 × 10−13

Intron

28.0

FBXL20

–

rs201955556

17:40363641:G/T

0.014

−0.47

1.0 × 10−14

Missense

69.16

GJD3

–

rs200702391

17:41515873:G/C

0.0153

−0.44

2.3 × 10−12

Intron

51.9

KRT16

–

rs149387021

17:42696125:C/T

0.0156

−0.32

5.9 × 10−9

Synonymous

29.0

CNTNAP1

–

rs182510184

17:44645052:A/G

0.0272

−0.24

4.4 × 10−8

Upstream gene

49.1

MEIOC

–

rs2165846

17:46864000:A/G

0.482

0.084

3.8 × 10−10

Intron

1.20

WNT9B

–

rs3746106

19:1250110:C/A

0.424

−0.077

1.7 × 10−8

5-prime UTR

0.98

MIDN

–

rs2836405g

21:38444848:G/A

0.536

0.086

3.1 × 10−8

Intron

1.03

ERG

–

rs5979390

23:11277189:C/T

0.29

−0.079

2.2 × 10−9

Intron

1.34

ARHGAP6

ARHGAP6

rs35318931

23:38149868:G/A

0.062

−0.15

1.2 × 10−9

Missense

0.69

SRPX

–

  1. Novel susceptibility loci genome-wide significantly associated (P < 5 × 10−8) with varicose veins are shown.
  2. aLead variant position is given in genome build GRCh38.
  3. bThe reported alternative allele frequency (AF) is observed in the FinnGen data.
  4. cThe associated effect (β) of each variant is the logarithm of the odds ratio.
  5. dThe variant types we obtained using the Ensembl Variant Effect Predictor72.
  6. eThe Finnish enrichment of each lead variant is with respect to non-Finnish non-Estonian Europeans (NFEEs) in the gnomAD database30, v2.1.1.
  7. fColocalized gene expression refers to the genes with a cis-eQTL variant in GTEx V8 tissues considered relevant to VV etiopathology (adipose, arterial and nerve tissues)16,17, such that within a locus the associations with gene expression levels and varicose veins risk were shared for variant with a high posterior probability (PP.H4 > 0.8).
  8. gFemale-specifically associated lead variant.
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