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Table 3 Association of the meta-analysis top signals with the expression of key pigmentation genes (SLC45A2, TYR, OCA2 and SLC24A5)

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) Note P-value (meta-FE model) Melanin Gene P-value (gene expression) Expression
Chromosome 5 region (SLC45A2) lead SNPs (meta-analysis)
 rs35397 T 5 33951116   1.98E-24 SLC45A2 3.95E-05
rs16891982 G 5 33951693 Non-synonymous 2.13E-23 SLC45A2 4.78E-07
Chromosome 5 region (SLC45A2) lead eQTLs
 rs35407 G 5 33946571   3.08E-15 SLC45A2 2.11E-07
rs16891982 G 5 33951693 Non-synonymous 2.13E-23 SLC45A2 4.78E-07
Chromosome 11 region (GRM5/TYR) lead SNPs (meta-analysis)
 rs10160510 T 11 88614324   3.36E-10 TYR 3.09E-03
 rs10437581 A 11 88616875   4.89E-10 TYR 2.26E-03
 rs1042602 A 11 88911696 Non-synonymous 9.20E-10 TYR 2.73E-02
 rs12801588 G 11 88548272   9.62E-10 TYR 1.98E-03
Chromosome 11 region (GRM5/TYR) lead eQTLs
 rs28437494 G 11 88868611   0.102 TYR 1.78E-06
 rs4121729 G 11 88863140   0.038 TYR 1.88E-06
 rs7925346 T 11 88860927   0.035 TYR 1.91E-06
Chromosome 15 region (OCA2/HERC2/APBA2) lead SNPs (meta-analysis)
 rs3098576 C 15 27858408   8.90E-09 OCA2 0.468
 rs1448484 A 15 28283441   3.73E-10 OCA2 0.022
rs12913832 G 15 28365618   3.18E-08 OCA2 3.14E-23
 rs1667392 C 15 28533565   4.64E-09 OCA2 N/A N/A
 rs36194177 G 15 29118784   4.95E-10 OCA2 N/A N/A
 rs2636060 A 15 29425936   5.71E-10 OCA2 N/A N/A
Chromosome 15 region (OCA2/HERC2/APBA2) lead eQTLs
rs12913832 G 15 28365618   3.18E-08 OCA2 3.14E-23
 rs1129038 T 15 28356859   3.18E-08 OCA2 1.24E-22
Chromosome 15 region (SLC24A5) lead SNPs (meta-analysis)
 rs1426654 A 15 48426484 Non-synonymous 6.32E-39 SLC24A5 0.218
 rs2470102 A 15 48433494   2.19E-38 SLC24A5 0.166
Chromosome 15 region (SLC24A5) lead eQTLs
 N/A (no variants had nominal p-values < 0.01 in this region)      
Chromosome 19 region (MFSD12) lead SNPs (meta-analysis)
 rs10416746 G 19 3563982   6.20E-09 MFSD12 N/A N/A
 rs112332856 T 19 3565599   2.31E-08 MFSD12 N/A N/A
Chromosome 15 region (MFSD12) lead eQTLs
 rs80204200 T 19 3529723   0.033761 MFSD12 6.34E-04
 rs7256261 A 19 3541615   4.88E-04 MFSD12 1.64E-03
  1. For comparative purposes, the table also reports the variants in each region with the strongest association to gene expression, and their respective p-values in the meta-analysis. The variants that appear as top signals in the meta-analysis and in the eQTL analysis are indicated in bold
  2. EA Effect allele, Chr Chromosome, FE model Fixed effects model