The abundance of cis QTL for CpG methylation and mRNA expression prompted us to examine the distribution of cis methQTLs and eQTLs (Figure 2C–2L). This revealed that both the number of significant methQTLs and the strength of association between SNP and DNA methylation level were inversely correlated with physical distance between the genetic and epigenetic variants in question (Figure 2C–2F). Furthermore, this relationship was also evident for cis eQTLs (Figure 2H–2K). The average distance between correlated cis SNP and trait was 81Kb for CpG sites and 121Kb for mRNA transcripts. The largest effect QTLs for both cis methQTLs and eQTLs tended to be present in all four tissues tested (Figure 2G and 2L). Of the mRNA transcripts where a cis eQTL was significantly detected in at least one brain region 53% have been previously reported. This number increased to 70% when analysis is limited to those transcripts with a cis eQTL consistently detected in all four tissues [2]–[4] (Table S2).
