Table 1 Single nucleotide polymorphisms identified in genome-wide analyses for circulating 25-hydroxyvitamin D concentrations

From: Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels

Gene

SNP

Chromosome: Position

Effect/reference allele

Allele frequency

Meta-GWAS estimates

Effect (Beta)

Standard Error

P-value

First stage discovery meta-GWAS (N = 79,366)

GC

rs3755967

4:72828262

T/C

0.28

−0.089

0.0023

4.74E–343

NADSYN1/ DHCR7

rs12785878

11:70845097

T/G

0.75

0.036

0.0022

3.80E–62

CYP2R1

rs10741657

11:14871454

A/G

0.4

0.031

0.0022

2.05E–46

CYP24A1

rs17216707

20:52165769

T/C

0.79

0.026

0.0027

8.14E–23

AMDHD1

rs10745742

12:94882660

T/C

0.4

0.017

0.0022

1.88E–14

SEC23A

rs8018720

14:38625936

C/G

0.82

−0.017

0.0029

4.72E–09

Replication data set 1: samples collected by EPIC (N = 40,562)

AMDHD1

rs10745742

12:94882660

T/C

0.41

0.041

0.0071

1.21E–08

SEC23A

rs8018720

14:38625936

C/G

0.83

−0.032

0.0093

5.24E–04

Replication data set 2: additional control samples collected by SOCCS (N=2195)

AMDHD1

rs10745742

12:94882660

T/C

0.37

0.045

0.021

0.03

SEC23A

rs8018720

14:38625936

C/G

0.81

−0.051

0.026

0.04

Pooled analysis (discovery meta-GWAS + replication 1 + replication 2) (N = 122,123)

AMDHD1

rs10745742

12:94882660

T/C

0.39

0.019

0.002

2.10E–20

SEC23A

rs8018720

14:38625936

C/G

0.82

−0.019

0.0027

1.11E–11

  1. In the pooled analysis, P heterogeneity = 0.003 for AMDHD1 rs10745742; P heterogeneity = 0.14 for SEC23A rs8018720.
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