Fig. 1: Characterization of the identified meQTLs.

a The locations of the meQTLs are shown relative to the CpG sites. b Proportion of variance (PVE; aka SNP heritability) in methylation levels estimated for all CpG sites (left three plots), CpGs without detectable meQTLs (middle three plots), and CpGs with detectable meQTLs (right three plots). PVE explained by all SNPs is referred to as total PVE (orange), which is partitioned into a component that is explained by cis-SNPs (cis-PVE; green) and another component that is explained by trans-SNPs (trans-PVE; purple). In the boxplots, the center line, box limits and whiskers denote the median, upper and lower quartiles, and 1.5× interquartile range, respectively. c Mean beta value distribution stratified by locations relative to gene regions. Beta values are the ratio of the normalized intensity of the methylated bead type to the combined normalized locus intensity, which range from 0 (hypomethylated) to 1 (hypermethylated). The gene body and intergenic regions are more hypermethylated, the TSS1500 and TSS200 are more hypomethylated. d Mean beta value distribution stratified by locations relative to CpG islands. The open sea is more hypermethylated and the CpG island is more hypomethylated. e Enrichment odds ratio of meCpGs, together with the 95% CI, is computed for CpG sites residing in different annotated genomic regions. CpG sites with meQTLs are enriched in intergenic region, gene body and open sea regions, and depleted in TSS regions, 3’ and 5’ UTR, 1st exon and CpG island. Bar graphs show odds ratios; error bars show 95% confidence intervals. f Enrichment odds ratio of meCpGs, together with the 95% CI, is computed for CpG sites residing in 15 different chromatin states as defined by the Roadmap Epigenomics project through ChromHMM in blood samples. Bar graphs show odds ratios; error bars show 95% confidence intervals. Statistics were computed based on a sample size of n = 961 and for 728,578 CpG sites.