Table 2. The variance explained (R 2) for the three sets of SNPs tested (all, HLA only and non-HLA) at the different thresholds tested.
| Variance explained (delta R2) | P values | |||||
|---|---|---|---|---|---|---|
| Threshold (-log10(P)) | All | non-HLA | HLA only | All | Non-HLA | HLA only |
| 5 × 10−8 | 0.327 | 0.041 | 0.259 | 1.1 × 10−69 | 1.3 × 10−17 | 5.6 × 10−66 |
| 0.01 | 0.343 | 0.045 | 0.25 | 2.0 × 10−73 | 3.6 × 10−18 | 5.7 × 10−66 |
| 0.05 | 0.349 | 0.017 | 0.294 | 9.2 × 10−75 | 8.3 × 10−10 | 3.1 × 10−71 |
| 0.1 | 0.321 | 0.005 | 0.31 | 1.3 × 10−58 | 0.006 | 2.0 × 10−70 |
| 0.2 | 0.281 | 8.9 × 10−5 | 0.323 | 3.8 × 10−47 | 0.081 | 1.5 × 10−70 |
| 0.3 | 0.266 | 7.5 × 10−6 | 0.328 | 5.6 × 10−43 | 0.128 | 2.3 × 10−71 |
| 0.4 | 0.196 | 2.8 × 10−5 | 0.291 | 6.4 × 10−26 | 0.213 | 2.2 × 10−62 |
| 0.5 | 0.225 | 4.0 × 10−4 | 0.334 | 3.7 × 10−26 | 0.318 | 5.3 × 10−72 |
P values were calculated for the difference in score between cases and controls using Student's t test.