Fig. 2

a CpGs showing significant (q < 0.01) imbalanced methylation, significant (q < 0.1) allelic methylation, and significant (q < 0.1) non-allelic methylation. Percentages indicate the proportion of the total significant CpGs found in any of these three sets (n = 962,557 of the 2,233,846 CpGs tested in all three tests). b Counts of CpGs showing allele-specific (AS)-genetic (ASM q < 0.1), non-allele-specific (NAS)-genetic (ASM q ≥ 0.1 and mQTL < 0.1), epigenetic (GIT q < 0.01, ASM and mQTL ≥ 0.1), and no (GIT q > 0.01, ASM and mQTL q ≥ 0.1) associations. Frequencies are plotted for all the CpGs, and also for CpGs in each of the ChromHMM regions. TSS transcription start site. c Fold change of the rate of putatively epigenetic (GIT q < 0.01, ASM and mQTL q ≥ 0.1) versus genetic (ASM or mQTL q < 0.1). ***Ratios with Fisher p < 0.0001; all other p values were >0.05. d Distribution of allelic ratios at significant GIT and ASM CpGs, for H3K27ac and H3K4me1 in normal T cells