Clustering of significant sites of allele-specific histone modification in the H1 cell line by patterns of allele-specific modification. (A) All 51 significant sites clustered according to the allelic imbalance seen for each examined histone modification. The scale corresponds to the squared correlation of the observed allelic imbalances for each modification (as measured by the log of the respective binomial P-value) between corresponding pairs of sites. Sites showing the strongest evidence of being largely driven by H3K4me3 preferentially on one allele and H3K9me3 on the other are highlighted by the blue box (chr4:89004339, chr4:89004397, chr4:89004505, chr7:23729054, chr15:22751085). (B) Allelic imbalance for each histone modification at the sites forming cluster 5. Most modifications displayed no consistent evidence of allelic imbalance at these positions; however, H3K9me3 reads were found to preferentially contain allele ‘A’ at these sites (for this plot the allele chosen to be the ‘A’ allele at each site was the allele found more often in the H3K9me3 reads at each position).