We have shown for the first time that there are large numbers of methQTLs in human tissue. It is worth noting, however, that the CpG methylation sites assayed here have not been defined through experimental work; as such a proportion of these may be consistently non-methylated, and thus our estimate of the proportion of CpG sites with an associated methQTL may be an underestimate. As for mRNA expression, DNA methylation patterns are sufficiently different to predict the originating tissue; however, we also see that SNP variation strongly influences the level of DNA methylation at sites that show intermediate levels of methylation. The strength of effect for methQTLs is similar to those for eQTLs and as discussed above eQTLs and methQTLs tend to be found consistently across tissues, supporting the robustness of these loci. Additionally methQTLs also show cis-enrichment, suggesting that local genomic variants influence the propensity of a particular genomic site to be methylated.
