Fig. 2: Characterization of the conditional meQTLs.

a Histogram shows the number of meCpGs (y axis) that harbor different numbers of independent meQTLs (x axis). We displayed meCpGs that harbor up to 19 independent meQTLs, with the detailed number of meQTLs listed above each bar. A large fraction of meCpGs harbor a small number of independent meQTLs. b Density plot shows the distance from meQTL to the corresponding meCpG. The density plot is stratified by the number of meQTLs: meCpGs with one, two, three, four, five or more, and 10 or more independent meQTLs. Dashed lines represent the median distance between meQTL and meCpG in the six stratified groups. c The proportion of variance (PVE) in methylation levels explained by SNPs are higher for meCpGs that harbor a larger number of independent meQTLs. In the boxplots, the center line, box limits and whiskers denote the median, upper and lower quartiles, and 1.5× interquartile range, respectively. d–g Left: Histograms of mean beta value distribution stratified by locations relative to CpG islands (d: CpG islands; e: CpG shores; f: CpG shelves; g: Open sea). Right: Enrichment odds ratios of CpG sites in different functional groups. The CpG sites are stratified by the number of meQTLs. In each stratified set of CpGs in the functional groups, we only calculate odd ratios for the sets with at least 100 CpGs. Error bars show 95% confidence intervals. Statistics were computed based on a sample size of n = 961 and for 728,578 CpG sites.