Table 2 Genome-wide significant common loci associated with retinol in the larger meta-analysis (METSIM + INTERVAL + ATBC + PLCO)

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

Lead SNP (Stouffer)

Locus

Closest gene (TSS)

EA/NEA

Z-score (METSIM +  INTERVAL)

Z-score (METSIM + INTERVAL + PLCO + ATBC)

PGWAS

PHet

Reported by Mondul et al.22

rs1260326

2:27598097-27752871

GCKR

T/C

6.242

6.714

1.90e−11

0.06

Yes

rs6601299

8:9167797-9224907

PPP1R3B

T/C

−6.197

−6.137

8.41e−10

0.004

Yes

rs11187547

10:95279771-95360964

RBP4

A/G

8.769

10.691

1.12e−26

0.11

No

rs11865979

16:79696939-79756197

MAF

T/C

5.575

6.103

1.04e−9

0.887

Yes

rs4799581

18:29068068-29230411

TTR

T/C

−7.998

−11.065

1.85e−28

9.72e−6

No

rs6029188

20:39152458-39234223

MAFB

A/G

−5.908

−6.407

1.48e−10

0.299

Yes

  1. Lead SNP based on statistical significance from sample size weighted (Stouffer) meta-analysis for SNPs available in this extended analysis. Constituent GWAS was performed using multiple linear regression Loci boundaries as defined by FUMA (hg19 coordinates). 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 Z score is given for the full extended meta-analysis as well as the smaller METSIM + INTERVAL analysis in terms of sample size. 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 from the extended meta-analysis. Bolded loci are known retinol signals. The last column refers to whether they were genome-wide significant in the previous Mondul et al. retinol GWAS (ATBC + PLCO)22.
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