Correlation of methylation levels between neighboring CpG sites. The x-axis represents the genomic distance in bases between the neighboring CpG sites, or assayed CpG sites that are adjacent in the genome. Different colors and points represent subsets of the CpG sites genome-wide, including pairs of CpG sites that are not adjacent in the genome but that are the specified distance apart (non-adjacent). The CGI shore and shelf CpG sites are truncated at 4,000 bp, which is the length of the CGI shore and shelf regions. The solid horizontal line represents the background (absolute value correlation or mean squared Euclidean distance, MED) level from 50,000 pairs of CpG sites from different chromosomes. (A) Absolute value of the correlation between neighboring sites across all individuals (y-axis). The lines represent cubic smoothing splines fitted to the correlation data. (B) Median MED was calculated (y-axis) across pairs of CpG sites within the genomic distance window (x-axis). bp, base pair; CGI, CpG island; MED, mean squared Euclidean distance.