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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)