Table 1.
Results of the cis- and trans-eQTL mapping analyses.
| Summary statistics | Cis-eQTLs | Trans-eQTLs |
|---|---|---|
| Number of SNPs tested that pass QC | 1,962,237 | 4,542 (of which 2,082 are associated with complex traits at genome-wide significance, P < 5 × 10−8) |
| Number of probes tested that pass QC | 29,891 | 34,061 |
| Number of genes tested | 14,542 | 16,332 |
| Number of probes not mapping to genes | 9,260 | 18,018 |
| Number of statistical tests performed | 11,172,453 | 153,134,630 |
| Significance thresholds | Cis-eQTLs | Trans-eQTLs | ||
|---|---|---|---|---|
| Meta-analysis z-score | Meta-analysis p-value | Meta-analysis z-score | Meta-analysis p-value | |
| FDR < 0.05 significance | 3.824 | 1.31 × 10−4 | 5.022 | 5.12 × 10−7 |
| Bonferroni significance | 5.867 | 4.5 × 10−9 | 6.287 | 3.3 × 10−10 |
| cis-eQTL analysis | FDR < 0.05 significance | Bonferroni significance |
|---|---|---|
| Number of significant unique SNP-Probe pairs | 664,097 | 395,543 |
| Number of significant unique eQTL SNPs | 397,310 | 266,036 |
| Number of significant unique eQTL probes | 8,228 | 5,738 |
| Number of significant unique eQTL genes | 6,418 | 4,690 |
| Number of significant unique eQTL probes not mapping to genes | 636 | 326 |
| trans-eQTL analysis | FDR < 0.05 significance | Bonferroni significance |
|---|---|---|
| Number of significant unique SNP-Probe pairs | 1,513 | 643 |
| Number of significant unique eQTL SNPs | 346 | 200 |
| Number of significant unique eQTL probes | 494 | 240 |
| Number of significant unique eQTL genes | 430 | 223 |
| Number of significant unique eQTL probes not mapping to genes | 35 | 13 |