Table 2 Adding a combination of rare SNPs to a common SNP significantly increases the signal of association with disease
Gene | Common SNP | Number of rare SNPs | p-value | SNP(s) removed | p-value |
|---|---|---|---|---|---|
MAP3K6 | C1S1886 | 4 | 2.13 × 10−8 | C1S18877 | 2.13 × 10−8 |
PTK2B | C8S911 | 9 | 1.08 × 10−7 | C8S936 | 2.9 × 10−3 |
|  |  |  |  | C8S900 | 5.12 × 10−9 |
|  |  |  |  | C8S900, C8S908 | 8.93 × 10−10 |
ETV6 | C12S860 | 2 | 5.53 × 10−7 | C12S863 | 3 × 10−4 |
|  |  |  |  | C12S861 | 6 × 10−4 |
BRCA1 | C17S2996 | 13 | 1.54 × 10−16 | C17S3009 | 1.97 × 10−21 |
|  |  |  |  | C17S3002, C17S3009 | 1.01 × 10−25 |
BRCA1 | C17S3006 | 13 | 4.45 × 10−11 | C17S3002 | 2.88 × 10−14 |
BRCA1 | C17S3010 | 13 | 7.27 × 10−10 | C17S3002 | 6.73 × 10−13 |
BRCA1 | C17S3014 | 13 | 5.33 × 10−9 | C17S3002 | 5.04 × 10−12 |
BRCA1 | C17S3016 | 13 | 1.31 × 10−10 | C17S3009 | 8.75 × 10−15 |
LOC645118 | C19S2844 | 1 | NS | C19S2846 | 9 × 10−4 |
TNK1 | C17S511 | 3 | NS | C17S515, C17S521 | 4.78 × 10−5 |
VNN1 | C6S5380 | 4 | NS | C6S5377, C6S5379 | 1.5 × 10−4 |