Table 3. Single associations of 12 SNPs previously involved in human eye colour variation with eye colour phenotype measures in the European study population (N = 3,087) controlled for age and sex in R 2 (P-values).
| SNP | Gene | Nopigm.# | Pheomelanin# | Eumelanin# | Saturation | Hue | Colour score | L | a* | b* | PIE score | T-index |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs1800407 | OCA2 | 1.0 (3.7e–08) | 1.0 (3.8e–08) | 0.1 (7.2e–02) | 0.5 (1.5e–04) | 0.1 (1.7e–01) | 0.0 (3.1e–03) | 0.0 (6.2e–01) | 0.0 (1.2e–01) | 0.0 (5.3e–07) | 0.0 (1.8e–07) | 0.0 (7.3e–01) |
| rs2070959 | UGT1A6 | 0.2 (1.4e–02) | 0.0 (2.7e–01) | 0.3 (1.7e–03) | 0.4 (9.0e–04) | 0.3 (3.1e–03) | 0.0 (1.1e–03) | 0.0 (8.9e–02) | 0.0 (1.6e–04) | 0.0 (7.5e–03) | 0.0 (2.1e–03) | 0.0 (3.2e–04) |
| rs9894429 | NPLOC4 | 0.0 (4.0e–01) | 0.0 (5.0e–01) | 0.0 (3.0e–01) | 0.1 (1.6e–01) | 0.0 (9.3e–01) | 0.0 (1.9e–01) | 0.0 (9.7e–01) | 0.0 (5.8e–01) | 0.0 (1.8e–01) | 0.0 (5.0e–01) | 0.0 (7.0e–01) |
| rs1129038$ | HERC2 | 49.2 (<1e–300) | 14.4 (7.4e–106) | 32.3 (2.4e–263) | 40.7 (<1e–300) | 25.7 (2.6e–201) | 4.4 (1.2e–160) | 2.3 (3.5e–117) | 15.3 (<1e–300) | 7.9 (4.2e–224) | 18.1 (0.0e + 00) | 11.3 (4.7e–269) |
| rs12203592 | IRF4 | 1.2 (5.2e–10) | 0.0 (6.0e–01) | 2.9 (3.3e–21) | 1.9 (7.2e–15) | 1.2 (5.4e–10) | 0.0 (2.2e–10) | 0.0 (1.2e–11) | 0.0 (5.9e–12) | 0.0 (3.0e–10) | 0.0 (2.7e–14) | 0.0 (9.3e–12) |
| rs1393350 | TYR | 0.6 (1.4e–05) | 0.4 (2.6e–04) | 0.3 (1.5e–03) | 0.8 (8.9e–07) | 0.2 (1.2e–02) | 0.0 (3.7e–05) | 0.0 (1.8e–01) | 0.0 (2.5e–04) | 0.0 (1.3e–05) | 0.0 (3.5e–07) | 0.0 (3.7e–03) |
| rs12913832$ | HERC2 | 49.7 (<1e–300) | 14.6 (1.8e–107) | 32.1 (1.3e–261) | 40.7 (0.0e + 00) | 26.1 (7.1e–205) | 4.3 (9.1e–159) | 2.4 (1.2e–119) | 15.4 (<1e–300) | 8.0 (7.9e–225) | 18.3 (0.0e + 00) | 11.4 (1.2e–270) |
| rs12896399 | SLC24A4 | 3.9 (9.2e–29) | 1.8 (1.1e–13) | 1.3 (1.8e–10) | 2.4 (6.1e–18) | 1.9 (1.2e–14) | 0.0 (3.1e–09) | 0.0 (2.6e–09) | 0.0 (3.9e–15) | 0.0 (1.6e–15) | 0.1 (3.2e–28) | 0.0 (7.2e–12) |
| rs3768056 | LYST | 0.1 (2.1e–01) | 0.0 (3.5e–01) | 0.0 (2.8e–01) | 0.1 (6.2e–02) | 0.0 (3.8e–01) | 0.0 (1.2e–01) | 0.0 (7.2e–01) | 0.0 (1.4e–01) | 0.0 (8.7e–02) | 0.0 (1.3e–01) | 0.0 (3.1e–01) |
| rs2835630 | DSCR9 | 0.0 (7.6e–01) | 0.0 (9.3e–01) | 0.0 (2.4e–01) | 0.0 (2.4e–01) | 0.0 (2.5e–01) | 0.0 (1.7e–01) | 0.0 (6.7e–01) | 0.0 (1.0e–01) | 0.0 (5.2e–01) | 0.0 (5.7e–01) | 0.0 (1.0e–01) |
| rs16891982 | SLC45A2 | 4.1 (5.2e–30) | 0.7 (2.4e–06) | 2.7 (2.9e–20) | 2.7 (2.9e–20) | 3.5 (2.0e–25) | 0.0 (7.0e–10) | 0.0 (8.3e–16) | 0.2 (1.4e–28) | 0.0 (7.0e–13) | 0.1 (1.1e–26) | 0.2 (2.2e–28) |
| rs1325127 | TYRP1 | 0.9 (7.5e–08) | 0.1 (4.2e–02) | 1.0 (2.7e–08) | 1.0 (3.2e–08) | 0.9 (1.2e–07) | 0.0 (1.4e–04) | 0.0 (5.7e–05) | 0.0 (5.9e–10) | 0.0 (1.1e–04) | 0.0 (3.4e–07) | 0.0 (1.0e–01) |
R2 values are provided in percentages, #estimated with the new computational approach introduced here, Bold values emphasize the strongest association within the quantitative phenotypes per SNP.$ The SNPs rs1129038 and rs12913832 are in strong LD (R2 = 0.99) and have no independent effects on the phenotype. Please refer to Supplementary Table S2 for betas.