Figure 2. Effect of meSNPs on methylation at nearby CpG sites. (A) Near-range effect of meSNPs. For 1,562 CpG-changing (including CpG-loss and CpG-gain) SNPs that have significant meQTL (P-value < 10⁻⁹) to a CpG site within 100 bp, we plot their SNP-CpG distance (X-coordinate) vs. their meQTL effect sizes (Y-coordinate). Both CpG-loss and CpG-gain SNP genotypes are oriented such that the CpG-carrying allele is coded as 0 and the non-CpG-carrying allele is coded as 1. (B and C) Effect of meSNP beyond immediate neighborhood. We plotted the distribution of cis-meQTL signals surrounding 812 meSNPs in the GOLDN data, before (B) and after (C) adjusting for meSNPs. The center is the location of the meSNPs. The X-axis represents the relative position of the SNP to the central meSNPs, organized into 101 equal-sized bins, each covering 198 bp. The Y-axis represents similar bins for the relative position of the CpG to the meSNPs. Color of the heatmap represents the number of meQTLs found at the distance bin.