3.1.2. Differential Methylation of CpG Sites

## 1. Proportions of Differentially Methylated CpG Sites by Region

Considering CpG sites, the majority of CpG sites are mapped to the gene body (36%), open sea (34%), and island (32%) regions (Table 6). A large proportion of the promoter region (66%) overlapped with CpG islands, and the promoter region also showed overlap with the TSS200 and TSS1500 regions (25% and 24%, respectively) (Supplementary Figure S1). Analysis of individual CpG sites revealed few identifiable differentially methylated sites and roughly a balance of hypo- and hypermethylated sites (SmartSVA method, Table 6). In spite of the relatively low numbers of differentially methylated sites, we estimated that 9% (*n* = 27,276) of CpG sites were actually non-null. Out of all CpG sites represented in our analytical dataset (*n* = 313,161), 4–9% were estimated to be non-null CpG sites across individual gene regions (Table 6). Relatively fewer numbers of differentially methylated CpG sites were observed in analyses excluding SmartSVA (Supplementary Table S2).
