Table 1. Summary of testa pigmentation GWAS.
| SNP (Relevance) | S4_61667908 (tan1-a allele) | S4_61862778 (tags Tan1, -0.2 Mb) | S4_61121403 (tags Tan1, -0.5 Mb) | S4_62353772 (tags Tan1, +0.7 Mb) |
|---|---|---|---|---|
| Small association panel (n = 142) | ||||
| GLM | 230 (3 × 10−7) | 1 (4 × 10−11) | 2 (5 × 10−11) | 38 (8 × 10−8) |
| CMLM (K) | 82 (2 × 10−5) | 3 (6 × 10-8) | 1 (2 × 10−8) | 159,802 (0.76) |
| CMLM (Q + K) | 82 (2 × 10−5) | 3 (6 × 10−8) | 1 (2 × 10−8) | 159,802 (0.76) |
| MLM (K) | 176 (1 × 10−6) | 2 (7 × 10−10) | 1 (7 × 10−10) | 12 (8 × 10−9) |
| Large association panel (n = 336) | ||||
| GLM | 9 (1 × 10−14) | 3 (2 × 10−17) | 14 (4 × 10−15) | 1 (2 × 10−22) |
| GLM (Q) | 1 (9 × 10−15) | 3 (5 × 10−12) | 5 (2 × 10−10) | 14 (2 × 10−8) |
| CMLM (K) | 69,491 (0.76) | 77,062 (0.86) | 1 (1 × 10−11) | 61,782 (0.64) |
| CMLM (Q + K) | 14355 (0.09) | 39,506 (0.33) | 1 (9 × 10−11) | 3381 (0.01) |
| MLM (K) | 1 (2 × 10−13) | 115,088 (0.83) | 2 (1 × 10−11) | 87,702 (0.57) |
| Loss-of-function | 1 (3 × 10−19) | 4 (1 × 10−13) | 22 (1 × 10−9) | 26 (2 × 10−9) |
Mapping results for various GWAS models giving the rank of the given SNP of 265,487 SNPs (P values in parenthesis). GWAS, genome-wide association studies; GLM, general linear model; CMLM, compressed mixed linear model; MLM, mixed linear model; SNP, single-nucleotide polymorphism.