Distribution of methylation patterns across the genome. (a) Methylation patterns for CpG-sites on autosomes, X-chromosome, and in the vicinity of imprinted genes. Methylation values are plotted for 77 individuals at 21,289 autosomal CpG-sites (left), for 43 females at 997 CpG-sites on the X-chromosome (middle), and for 77 individuals at 153 CpG-sites in 33 imprinted genes (right). (b) Methylation levels with respect to the TSS (negative distances are upstream from the TSS), where the line represents running median levels in sliding windows of 300 bp. (c) Correlations in methylation levels for all pair-wise CpG-sites (black), and for CpG-sites where both probes are in the same CGI (red), or where at least one probe is outside of CGIs (blue). Lines indicate smoothed spline fits of the mean rank pairwise correlation between CpG-sites in 100 bp windows, weighted by the number of probe pairs. (d) Methylation levels inside and outside of annotation categories, including CpG Islands (CGIs) for probes within 100 bp of the TSS, and histone modifications and transcription factor (TF) binding sites for all probes (see Additional file 1).