Table 2.
Chromatin marks are enriched on meQTL SNPs.
| control | cis only | trans only | cis + trans | |||||
|---|---|---|---|---|---|---|---|---|
| cell line | mark | proportion | proportion | fold change | proportion | fold change | proportion | fold change |
| SAEC | CTCF | 11.8% | 35.3% | 3.0 | 29.6% | 2.5 | 45.4% | 3.8 |
| DnaseI | 25.4% | 54.0% | 2.1 | 45.8% | 1.8 | 59.6% | 2.3 | |
| H3K27me3 | 20.4% | 34.1% | 1.7 | 25.4% | 1.2 | 42.9% | 2.1 | |
| H3K4me3 | 4.8% | 29.7% | 6.2 | 18.0% | 3.8 | 39.9% | 8.3 | |
| H3K36m3 | 13.4% | 36.8% | 2.7 | 22.8% | 1.7 | 45.4% | 3.4 | |
| HAEC | H3K27me3 | 17.5% | 25.3% | 1.4 | 15.6% | 0.9 | 33.2% | 1.9 |
| H3K4me3 | 7.6% | 37.0% | 4.9 | 25.0% | 3.3 | 54.9% | 7.2 | |
| H3K9-14Ac | 17.3% | 47.6% | 2.8 | 32.3% | 1.9 | 65.3% | 3.8 | |
meQTL SNPs were enriched in chromatin marks, including CTCF binding sites, DNaseI hypersensitive sites and histone marks from small airway epithelial cells (SAEC) from ENCODE and human alveolar epithelial cells (hAEC) from our laboratory. A SNP is determined to be related with a regulatory region if the SNP or any LD-related SNP (r2≥0.8) resides in the ChIP-Seq peaks of the regulatory regions. Enrichment for cis-meQTL SNPs without trans effects (“cis only”), trans-meQTL SNPs without cis effects (“trans only”) and SNPs with both trans and cis effects (“cis+trans”). The baseline proportion (control set) was calculated based on SNPs not associated with meQTLs and with minor allele frequencies and local CpG probe density matching to the meQTL SNPs. The fold changes were calculated using the control set as baseline.