Systematic investigation of interindividual variation of DNA methylation in human whole blood

Interindividual genetic variability is well characterised, but we still lack a complete catalogue of loci displaying variable and stable epigenetic patterns. Here, we report a catalogue of stable and variable interindividual DNA methylation in human whole blood by analysing the DNA methylation patterns in 3642 individuals using the IlluminaEPIC array. Our results showed that 41,216 CpGs display stable methylation (SMPs) and 34,972 CpGs display variable methylation levels (VMPs). This catalogue will be a useful resource for interpretation of results when associating epigenetic signals to phenotypes. We observed that SMPs are highly enriched in CpG islands, depleted at CpG shelves and open sea regions of the genome. In addition, we found that the VMPs were under higher genetic control than the SMPs and that trans mQTL pairs are often located in the same TAD or connected by chromatin loops. A subset of these VMPs (784) were classified as putative epialleles and our results demonstrate that these loci located in regulatory regions exhibit a link with gene expression.