Table 1.
Enrichments of 14,118 cis-meQTL-CpGs in regulatory genomic elements
| Annotation | Ratio meQTL (%) | Ratio non-meQTL (%) | P-value | q-value | OR (95% CI) |
|---|---|---|---|---|---|
| Roadmap E071 flanking active TSS | 13.2 | 10.1 | 1.4 × 10−27 | 2.7 × 10−25 | 1.353 (1.282–1.427) |
| Roadmap E071 weak repr. PolyComb | 12.5 | 10.7 | 3.4 × 10−10 | 6.5 × 10−08 | 1.191 (1.128–1.257) |
| Roadmap E071 H3K27me3 | 49.5 | 46.0 | 2.1 × 10−14 | 4.1 × 10−12 | 1.148 (1.108–1.189) |
| Roadmap E071 H3K4me1 | 72.1 | 69.1 | 5.5 × 10−13 | 1.0 × 10−10 | 1.154 (1.109–1.200) |
| Roadmap E071 H3K4me3 | 59.1 | 56.1 | 6.9 × 10−12 | 1.3 × 10−09 | 1.133 (1.093–1.175) |
| UCSC CGI shore | 31.3 | 27.6 | 4.0 × 10−20 | 7.6 × 10−18 | 1.198 (1.153–1.245) |
| Brain intermediate methylation regions | 9.8 | 5.6 | 1.3 × 10−74 | 2.4 × 10−72 | 1.835 (1.724–1.953) |
| Duke DNase I HS cerebellum | 30.9 | 28.4 | 8.4 × 10−10 | 1.6 × 10−07 | 1.128 (1.085–1.172) |
| Duke DNase I HS cerebrum frontal | 41.7 | 39.7 | 4.6 × 10−06 | 8.7 × 10−04 | 1.087 (1.049–1.127) |
| Encode (Tfbs) CTCF | 17.3 | 13.6 | 8.3 × 10−31 | 1.6 × 10−28 | 1.329 (1.267–1.394) |
| Encode (Tfbs) RAD21 | 8.4 | 7.5 | 5.7 × 10−05 | 1.1 × 10−02 | 1.142 (1.071–1.218) |
| Encode (Tfbs) SMC3 | 5.2 | 4.5 | 1.9 × 10−04 | 3.7 × 10−02 | 1.167 (1.076–1.265) |
| Encode (Tfbs) POLR2A | 30.8 | 29.2 | 2.1 × 10−04 | 4.0 × 10−02 | 1.075 (1.035–1.117) |
Co-localization of cis-meQTL-CpGs to genomic annotations of 189 regulatory elements were compared with control-CpG sites matched for β-value (n = 98,826). Significant enrichments after Bonferroni correction (q-value) are shown
OR odds ratio with 95% confidence interval