Fig. 3

SNPs explained a greater proportion of inter-individual variation in DNA methylation in infant cord blood (CB) than in infant cord tissue (CT): SNP-associated CpGs detected in each infant tissue. a Pie charts show the percentage of CpGs in each infant tissue whose inter-individual variation could be explained by SNPs (out of all CpGs which showed inter-individual variation in the infant tissue). A CpG whose inter-individual variation could be explained by SNPs (SNP-associated) was defined to be one where the most significant association between the CpG and cis-SNPs (all SNPs on the same chromosome as CpG) attained a P value < 5 × 10^–8, the commonly used Bonferroni threshold for genome-wide association studies (corresponding to testing for 10⁶ independent SNPs across the genome at a family-wise Type 1 error rate of 0.05). b Overlap between SNP-associated, non-SNP-associated (but variable), and non-variable CpGs in the two tissues. Only CpGs which showed inter-individual variation in at least one tissue were included (N = 98,124). Examining each tissue separately, each of these 98,124 CpGs can either be SNP-associated, not SNP-associated, or not variable in each tissue. The number of CpGs in each of these three sets in each tissue is shown in the bottom left bar chart (for each tissue the number of CpGs from the three sets will sum to 98,124). Collectively, the 98,124 CpGs can be grouped into eight categories. The bottom right panel identifies each of these eight categories, with the solid black dots representing the sets being considered. For example, the extreme right column identifies the group of CpGs that are SNP-associated in both tissues. The top bar chart shows the number of CpGs in each of these eight categories. For example, 7822 CpGs were SNP-associated in both tissues