Cis methylation QTLs. (a) Quantile-quantile (QQ) plot describing the enrichment of association signal in cis compared to the permuted data (90% confidence band shaded). (b) The cis-meQTL SNPs were enriched for association signal at additional CpG-sites near to the CpG-site for which they are meQTLs. The 180 best-associated SNPs were tested for association to probes that fell within 2 kb (red), within 2 kb to 10 kb (purple), and within 10 kb to 50 kb (blue) of the original best-associated CpG-site. The majority (96%) of probes within 2 kb (red) were in the same CGI as the best-associated probe. (c) Spatial distribution of cis-meQTLs with respect to the CpG-site as estimated by the hierarchical model.