Table 3.
P values (Wilcoxon rank-sum test) for GWAS SNPs and eQTLs. Comparisons are shown between GWAS index SNPs and tag SNPs hitting regulatory elements. Also shown are comparisons between GWAS index SNPs and control SNPs matched for frequency, functional consequence, and GWAS array availability. Additionally, comparisons between eQTLs and tag SNPs hitting regulatory elements are shown. The best performing individual annotation is also reported.
| Dataset | n | Comparison | Score | P value |
|---|---|---|---|---|
| GWAS | 2,115 | Regulatory GWAS vs. Tag SNPs | Eigen | 1.2E-05 |
| Eigen-PC | 4.0E-06 | |||
| CADD-score v1.0 | 5.9E-04 | |||
| CADD-score v1.1 | 2.0E-04 | |||
| GWAVA (TSS) | 4.1E-06 | |||
| TFBS num | 4.9E-05 | |||
|
| ||||
| GWAS | 2,115 | Regulatory GWAS vs. Other SNPs | Eigen | 1.6E-09 |
| Eigen-PC | 2.0E-13 | |||
| CADD-score v1.0 | 2.0E-06 | |||
| CADD-score v1.1 | 8.6E-07 | |||
| GWAVA (TSS) | 7.4E-13 | |||
| TFBS sum | 5.6E-09 | |||
|
| ||||
| GWAS | 10,718 | GWAS vs. Matched Controls | Eigen | 6.9E-08 |
| Eigen-PC | 3.5E-13 | |||
| CADD-score v1.0 | 1.0E-04 | |||
| CADD-score v1.1 | 5.2E-07 | |||
| GWAVA (TSS) | 2.5E-09 | |||
| H3K4Me1 | 4.0E-11 | |||
|
| ||||
| eQTLs | 676 | Regulatory eQTLs vs. Tag SNPs | Eigen | 1.8E-10 |
| Eigen-PC | 7.0E-23 | |||
| CADD-score v1.0 | 3.1E-04 | |||
| CADD-score v1.1 | 4.3E-05 | |||
| GWAVA (TSS) | 1.3E-03 | |||
| H3K4Me3 | 2.2E-24 | |||
|
| ||||
| eQTLs | 676 | Regulatory eQTLs vs. Other SNPs | Eigen | 5.9E-13 |
| Eigen-PC | 2.6E-27 | |||
| CADD-score v1.0 | 2.8E-04 | |||
| CADD-score v1.1 | 2.1E-05 | |||
| GWAVA (TSS) | 7.3E-08 | |||
| H3K4Me3 | 3.8E-25 | |||