Table 1 Genome-wide significant common loci associated with retinol (METSIM + INTERVAL)

From: Genetic influences on circulating retinol and its relationship to human health

Lead SNP (Stouffer)

Locus

Closest Gene (TSS)

EA/NEA

EAF NFE/FIN

Z

PGWAS

PHet

Reported by Mondul et al.22

rs1260326

2:27598097-27752871

GCKR

T/C

0.409/0.358

6.242

4.32e−10

0.023

No

rs34898035

2:122078406-122084285

TFCP2L1

A/G

0.042/0.027

−5.677

1.37e−8

0.190

No

rs11762406

7:114014488-114286611

FOXP2

A/C

0.092/0.085

−5.526

3.28e−8

0.104

No

rs6601299

8:9167797-9224907

PPP1R3B

T/C

0.17/0.10

−6.197

5.76e−10

0.004

No

rs10882283

10:95295876-95360964

RBP4

A/C

0.622/0.664

9.789

1.26e−22

0.192

Yes

rs12149203

16:79696939-79756197

MAF

C/G

0.708/0.726

5.668

1.45e−8

0.841

No

rs1667226

18:29134171-29190174

TTR

A/T

0.481/0.507

−8.405

4.27e−17

0.06

Yes

rs6029188

20:39142516-39234223

MAFB

A/G

0.637/0.662

−5.908

3.47e−9

0.147

No

  1. Lead SNP based on statistical significance from sample size weighted (Stouffer) meta-analysis. Loci boundaries as defined by FUMA (hg19 coordinates). Constituent GWAS was performed using multiple linear regression. The closest gene by transcription start site (TSS) is listed. EA = effect allele, that is, allele to which the effect size relates, NEA = non-effect allele. The effect allele frequency (EAF) is given from gnomAD v2.1.1 for non-Finnish Europeans (NFE) and Finnish Europeans (FIN). Z-score from the Stouffer meta-analysis. The PGWAS (statistical significance of association) and PHet (Heterogeneity between input effect sizes P value derived from Cochran’s Q) are also from the Stouffer meta-analysis. Bolded loci are known retinol signals. The far right column denotes whether they were genome-wide significant in the previous Mondul et al. retinol GWAS (ATBC + PLCO)22.
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