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Table 2 Top genome-wide significant SNPs in conditional meta-analysis and on each independent study

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

SNP Chr Position (GRCg37/hg19) EA/ NEA Genesa Fixed Effects Modelb Random Effects Modelc P-value Cochran’s Q I2
P-value Beta SD Q P-value
rs10160510 11 88614324 T/A GRM5 3.36E-10 −0.248 0.039 7.54E-11 11.078 0.011 72.920
rs3098576 15 27858408 T/C (GABRG3/OCA2) 8.90E-09 0.182 0.032 1.30E-08 2.883 0.410 0.000
rs1448484 15 28283441 G/A OCA2 3.73E-10 0.213 0.034 5.83E-10 2.237 0.525 0.000
rs1667392 15 28533565 C/G HERC2 4.64E-09 −0.268 0.046 6.65E-09 1.048 0.306 4.580
rs36194177 15 29118784 A/G (APBA2) 4.95E-10 0.229 0.037 2.58E-10 9.281 0.026 67.676
rs2636060 15 29425936 A/G FAM189A1 5.71E-10 −0.231 0.037 8.79E-10 3.433 0.330 12.611
rs10416746 19 3563982 A/G (MFSD12) 1.01E-09 0.309 0.051 1.55E-09 3.947 0.267 24.002
  1. The table presents the results of the meta-analysis after conditioning for SLC24A5 rs1426654 and SLC45A2 rs35397, which had very strong effects in the original meta-analysis (p = 6.32 × 10− 39, and rs35397, p = 1.98 × 10− 24, respectively)
  2. Chr Chromosome, EA Effect allele, NEA Non-effect allele, SD Standard deviation, M Posterior probability of an existent effect on each study, I2 Heterogeneity statistic, NA Marker not genotyped
  3. aFor variants located in intergenic regions, nearby genes are indicated in parenthesis
  4. bFixed effects model, as computed in Metasoft
  5. cHan and Eskin’s Random Effects Model