Mechanistically, disease‐associated SNPs may be found in DNA regulatory regions where the genetic variation affects cognate binding of transcription factor complexes, effecting on the expression of disease‐relevant genes (Harismendy et al, 2011). ...variation in the methylation of a DNA regulatory region (either increased or decreased methylation) can also alter the binding of transcription factor complexes and regulate both distal and proximal gene expression (Choy et al, 2010; Jones & Takai, 2001; Phillips & Corces, 2009; Weaver et al, 2004). On the basis that increased DNA methylation may be a means of regulating transcription factor complex binding and therefore mark genomic regions that are important to control by methylation (Choy et al, 2010; Jones & Takai, 2001), our findings support the notion that sites of heterogeneous genetic variation in one subpopulation are functionally relevant to the corresponding subpopulation, but sites of heterogeneous genetic variation of a different subpopulation, are not.