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Table 4 Replication of meta-analysis lead SNPs in an East African sample

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)

Genesa

P-value (meta-RE2 model)

P-value EAF

Beta EAF

SE EAF

MAF-EAF

Effectb (meta-EAF)

rs35397

T

5

33951116

SLC45A2

1.98 × 10− 24

0.605

−0.403

0.780

0.068

--

rs10160510

T

11

88614324

GRM5

8.87 × 10− 10

0.347

− 1.681

1.784

0.012

--

rs3098576

C

15

27858408

(GABRG3/OCA2)

8.90 × 10−09

0.438

0.303

0.391

0.436

- +

rs1448484

A

15

28283441

OCA2

3.73 × 10−10

4.43 × 10 − 04

−1.467

0.417

0.363

--

rs1667392

C

15

28533565

HERC2

4.64 × 10− 09

NA

NA

NA

NA

 

rs36194177

A

15

29118784

(APBA2)

4.95 × 10−10

NA

NA

NA

NA

 

rs2636060

A

15

29425936

FAM189A1

5.71 × 10− 10

0.323

−0.393

0.397

0.390

--

rs1426654

A

15

48426484

SLC24A5

6.32 × 10−39

6.89 × 10 −61

−7.775

0.452

0.243

--

rs10416746

A

19

3563982

(MFSD12)

1.01 × 10− 09

1.53 × 10 − 04

2.019

0.532

0.167

+ +

  1. EA Effect allele, Chr Chromosome, RE2 Han and Eskin’s random effects model, EAF East Africa, SE Standard error, MAF Minor allele frequency. Significant p-values after Bonferroni correction are highlighted in bold
  2. aFor variants located in intergenic regions, nearby genes are indicated in parenthesis
  3. bDirection of effect of the EA (− decreases melanin index, + increases melanin index)