Table 3.
Association results for pigmentation phenotypes.
| trait | reported SNP | proxy SNP | r2 | minor allele | sample MAF | HapMap MAF | effect size | p-value | gene |
|---|---|---|---|---|---|---|---|---|---|
| eye darkness | rs12913832 | A | .222 | .208 | .998 | 2×10−68 | HERC2 | ||
| eye darkness | rs12896399 | rs1075830 | .615 | A | .460 | .308 | .167 | .003 | SLC24A |
| eye darkness | rs1393350 | A | .266 | .192 | −.154 | .02 | TYR | ||
| eye darkness | rs1408799 | T | .313 | .300 | .095 | .11 | TYRP1 | ||
| hair darkness | rs12913832 | A | .223 | .208 | .840 | 1×10−13 | HERC2 | ||
| hair darkness | rs12896399 | rs1075830 | .640 | A | .460 | .308 | .372 | 9×10−5 | SLC24A4 |
| hair darkness | rs12821256 | C | .095 | .142 | −.352 | .03 | KITLG | ||
| red hair | rs1805007 | T | .076 | .147 | 7.44 | 2×10−6 | MC1R | ||
| red hair | rs1015362 | T | .278 | .233 | .507 | .09 | ASIP | ||
| freckling | rs1805007 | T | .076 | .147 | .613 | 6×10−6 | MC1R | ||
| freckling | rs1042602 | A | .346 | .417 | −.223 | .005 | TY R | ||
| freckling | rs2153271 | rs1416742 | .949 | G | .384 | .373 | −.139 | .07 | BNC2 |
| freckling | rs619865 | A | .098 | .108 | .178 | .15 | ASIP | ||
| skin darkness | rs1805007 | T | .076 | .147 | −.267 | .005 | MC1R | ||
| skin darkness | rs1042602 | A | .346 | .417 | −.118 | .03 | TY R | ||
| skin darkness | rs619865 | A | .098 | .108 | −.156 | .07 | ASIP |
Eye darkness was reported on a 3-point scale. Hair darkness was recorded on 9-point scale. Red hair was recorded as a dichotomous trait, and its effect size is reported as an odds ratio. Freckling and skin darkness were recorded on 5-point scales. All effect sizes for non-dichotomous traits are reported as the expected change in trait value per each additional copy of the minor allele. All alleles are coded according to NCBI build 36 coordinates on the forward strand.