Figure 3

Population specificity of mSNPs. (a) An example of an mSNP (between a CpG site near LDHC (chromosome 11, base 18390591), and rs2643856) that is found in both YRI and CEU. In both cases the T allele is associated with higher methylation. (b) Venn diagram of the overlap among CpG sites associated with an mSNP in YRI and/or CEU. Five CEU sites and eight YRI sites were excluded from the overlap analysis because they overlapped a SNP in the other population. (c) Example of an mSNP (between a CpG site near PLSCR2 (chromosome 3, base 147696535) and rs12489924) that is found in YRI but not CEU. No other SNPs in CEU within 100 kb of the CpG are associated with methylation at the site (r < 0.25 for all), indicating that the difference is unlikely to be due to differing LD between rs12489924 and the causal variant. (d) Scatter plot of all 86 YRI mSNPs, showing the strongest association found for that site in each population. Points are colored according to the significance of the difference in the associations within each population; most mSNP association strengths are significantly (P < 0.005) different between populations. The same plot for CEU mSNPs is shown in Figure S10 in Additional file 1. (e) Overlap of LCL mSNPs with brain mSNPs from two studies of European populations (similar to CEU). Both all CEU mSNPs and CEU-specific mSNPs show similar overlap of 40 to 42%, which is thus a minimum estimate for the extent of mSNPs shared between LCLs and brain. However, YRI-specific mSNPs show only 3.2% overlap, not significantly different from the 1.2% expected from any random set of CpG sites.