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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)