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Table 5 Follow-up of previous GWAS genome-wide signals in our meta-analysis

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)

Gene

Reported P-value*

Ref.

P-value meta†

Beta meta

SE meta

Effectg (study-meta)

P-value Cuba

P-value Cape Verde

P-value GALA II

P-value SAGE II

rs35395

T

5

33948589

SLC45A2

5.30 × 10−08

a

1.98 × 10−24

−0.321

0.032

--

1.26 × 10− 12

5.05 × 10− 08

1.28 × 10− 05

0.0094

rs16891982

G

5

33951693

SLC45A2

9.71 × 10− 10

b

2.13 × 10−23

−0.317

0.032

--

3.31 × 10− 11

3.04 × 10− 07

1.83 × 10− 06

0.0052

rs6602666

G

10

13606490

BEND7-PRPF18

4.58 × 10− 09

b

5.10 × 10− 03

0.129

0.046

+ +

0.9235

0.7941

2.53 × 10− 05

0.0139

rs11230664

C

11

61076372

DDB1/ TMEM138

2.10 × 10− 09

d

5.20 × 10− 04

0.121

0.035

+ +

0.3660

0.0004

0.7934

0.2027

rs7120594

T

11

61080557

DDB1/ TMEM138

1.20 × 10− 08

d

0.016

0.087

0.036

+ +

0.6213

0.0050

0.8055

0.4503

rs2513329

C

11

61106892

DDB1

5.20 × 10−07

c

2.20 × 10− 04

− 0.129

0.035

--

0.3281

0.0002

0.7934

0.1744

rs7948623

A

11

61137147

DDB1/ TMEM138

2.20 × 10−11

d

0.179

−0.074

0.055

--

NA

0.0922

0.8261

0.9972

rs10831496

G

11

88557991

GRM5

1.20 × 10−08

a

9.25 × 10− 08

0.168

0.032

+ +

0.0498

1.34 × 10− 09

0.0917

0.9202

rs1800404

T

15

28235773

OCA2

1.60 × 10−08

d

8.92 × 10− 06

−0.137

0.031

--

0.2368

0.0004

0.0618

0.0120

rs4932620

C

15

28514281

HERC2

3.20 × 10−09

d

5.03 × 10− 03

−0.258

0.092

--

NA

0.0014

0.7298

0.3685

rs4424881

T

15

29261716

APBA2

6.10 × 10−09

a

5.44 × 10− 07

0.158

0.032

+ +

0.8845

2.60 × 10− 07

0.0229

0.0149

rs1426654

G

15

48426484

SLC24A5

3.91 × 10−24; 2.62 × 10−14; 5.5 × 10−62; 9.8 × 10−9

a; b; d; e

6.32 × 10− 39

0.403

0.031

+ +

4.95 × 10− 07

2.87 × 10−23

6.39 × 10− 08

5.62 × 10− 08

rs139343937

A

16

80256441

LOC102724084

1.56 × 10− 08

f

3.45 × 10− 06

− 0.248

0.053

--

1.69 × 10− 08

0.3206

NA

NA

rs56203814

T

19

3544892

MFSD12

3.60 × 10−18

d

0.157

0.076

0.054

+ +

0.4032

0.1792

0.6323

0.1051

rs10424065

T

19

3545022

MFSD12

5.10 × 10−20

d

0.048

0.093

0.047

+ +

0.0184

0.0039

0.3854

0.0916

rs6510760

A

19

3565253

MFSD12

6.50 × 10−15

d

3.24 × 10− 06

0.164

0.035

+ +

0.8013

4.42 × 10− 06

0.2545

0.0096

rs112332856

C

19

3565599

MFSD12

3.80 × 10−16

d

2.31 × 10− 08

0.197

0.035

+ +

0.2740

1.21 × 10− 06

0.1604

0.0031

  1. EA Effect allele, Chr Chromosome, Ref Reference of studied population
  2. * P-value reported for rs2513329 corresponds to a Bayesian analysis
  3. †All the p-values reported for the BEND7-PRPF18, DDB1/TMEM138, OCA2/HERC2/APBA2, LOC102724084 and MFSD12 regions are the p-values obtained after conditioning for the SLC24A5 and SLC45A2 signals
  4. aBeleza et al., 2013 [6]
  5. bHernandez-Pacheco et al., 2017 [8]
  6. cLloyd-Jones et al., 2017 [7]
  7. dCrawford et al.,2017 [10]
  8. eMartin et al., 2017 [11]
  9. fThis study
  10. gDirection of effect of the EA (− decreases melanin index, + increases melanin index)
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BMC Genomic Data

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