mQTLs are preferentially close to CpG sites. (A) Distribution of the mQTL to CpG probe distances for all correlated SNP-CpG pairs at 5% FDR. For each CpG probe, when more than one SNP is significantly correlated, a single one is retained as having either the most significant correlation (gray bars) or being located closest to the CpG probe (black bars). (B) Quantile-quantile plot of SNP/CpG probe Spearman’s rho P-values, grouped by pairwise distances. For each CpG probe included in the mQTL analysis, the most strongly correlated SNP within 250 kb was identified and the P-value obtained included in the set of P-values to be plotted for the distance bin in question. All SNPs in linkage disequilibrium with the selected SNP (R2 > 0.8) were removed, and the next most strongly correlated SNP was taken, until all SNPs within the range of the CpG probe in question were considered. The number of significant mQTLs decays with distance, but is still more than expected by chance at distances greater than 100 kb.