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Table 3 Association of the meta-analysis top signals with the expression of key pigmentation genes (SLC45A2, TYR, OCA2 and SLC24A5)

From: Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations

SNP

EA

Chr

Position (GRCg37/hg19)

Note

P-value (meta-FE model)

Melanin

Gene

P-value (gene expression)

Expression

Chromosome 5 region (SLC45A2) lead SNPs (meta-analysis)

 rs35397

T

5

33951116

 

1.98E-24

↓

SLC45A2

3.95E-05

↑

 rs16891982

G

5

33951693

Non-synonymous

2.13E-23

↓

SLC45A2

4.78E-07

↑

Chromosome 5 region (SLC45A2) lead eQTLs

 rs35407

G

5

33946571

 

3.08E-15

↓

SLC45A2

2.11E-07

↑

 rs16891982

G

5

33951693

Non-synonymous

2.13E-23

↓

SLC45A2

4.78E-07

↑

Chromosome 11 region (GRM5/TYR) lead SNPs (meta-analysis)

 rs10160510

T

11

88614324

 

3.36E-10

↓

TYR

3.09E-03

↓

 rs10437581

A

11

88616875

 

4.89E-10

↓

TYR

2.26E-03

↓

 rs1042602

A

11

88911696

Non-synonymous

9.20E-10

↓

TYR

2.73E-02

↓

 rs12801588

G

11

88548272

 

9.62E-10

↓

TYR

1.98E-03

↓

Chromosome 11 region (GRM5/TYR) lead eQTLs

 rs28437494

G

11

88868611

 

0.102

↓

TYR

1.78E-06

↓

 rs4121729

G

11

88863140

 

0.038

↓

TYR

1.88E-06

↓

 rs7925346

T

11

88860927

 

0.035

↓

TYR

1.91E-06

↓

Chromosome 15 region (OCA2/HERC2/APBA2) lead SNPs (meta-analysis)

 rs3098576

C

15

27858408

 

8.90E-09

↓

OCA2

0.468

↓

 rs1448484

A

15

28283441

 

3.73E-10

↓

OCA2

0.022

↓

 rs12913832

G

15

28365618

 

3.18E-08

↓

OCA2

3.14E-23

↓

 rs1667392

C

15

28533565

 

4.64E-09

↓

OCA2

N/A

N/A

 rs36194177

G

15

29118784

 

4.95E-10

↓

OCA2

N/A

N/A

 rs2636060

A

15

29425936

 

5.71E-10

↓

OCA2

N/A

N/A

Chromosome 15 region (OCA2/HERC2/APBA2) lead eQTLs

 rs12913832

G

15

28365618

 

3.18E-08

↓

OCA2

3.14E-23

↓

 rs1129038

T

15

28356859

 

3.18E-08

↓

OCA2

1.24E-22

↓

Chromosome 15 region (SLC24A5) lead SNPs (meta-analysis)

 rs1426654

A

15

48426484

Non-synonymous

6.32E-39

↓

SLC24A5

0.218

↓

 rs2470102

A

15

48433494

 

2.19E-38

↓

SLC24A5

0.166

↓

Chromosome 15 region (SLC24A5) lead eQTLs

 N/A (no variants had nominal p-values < 0.01 in this region)

     

Chromosome 19 region (MFSD12) lead SNPs (meta-analysis)

 rs10416746

G

19

3563982

 

6.20E-09

↓

MFSD12

N/A

N/A

 rs112332856

T

19

3565599

 

2.31E-08

↓

MFSD12

N/A

N/A

Chromosome 15 region (MFSD12) lead eQTLs

 rs80204200

T

19

3529723

 

0.033761

↓

MFSD12

6.34E-04

↑

 rs7256261

A

19

3541615

 

4.88E-04

↓

MFSD12

1.64E-03

↑

  1. For comparative purposes, the table also reports the variants in each region with the strongest association to gene expression, and their respective p-values in the meta-analysis. The variants that appear as top signals in the meta-analysis and in the eQTL analysis are indicated in bold
  2. EA Effect allele, Chr Chromosome, FE model Fixed effects model
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BMC Genomic Data

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