(A) Diagram of method used to measure differential allelic TF occupancy. First, chromatin was formaldehyde-fixed and sonicated. Cross-linked TF-binding complexes were then immunoprecipitated with an antibody specific for the TF of interest. The co-precipitated DNA was recovered and subjected to high-throughput single-end sequencing. Reads were aligned to maternal and paternal versions of the GM12878 genome according to data from the 1000 Genomes Project (The 1000 Genomes Project Consortium 2010). For each binding site, differential allelic occupancy was called when reads aligned to a single allele significantly more often than would be expected by random. (B) Spearman correlation of allelic imbalance at sites of TF co-occupancy throughout the genome. The color of the boxes indicates the correlation coefficient, with white indicating nonsignificant correlation (P > 0.05). The tree shows complete linkage hierarchical clustering. (C) We classified heterozygous variants by the number of TFs binding at that variant. Shown is the cumulative distribution of DNase I hypersensitivity signal at all occupied heterozygous variants in each class, as indicated in the legend. (D) For each class of heterozygous variants (as defined in C), the fractions of variants with phastCons score >0.5. Asterisks ([**] P < 0.01; [*] P < 0.05) indicate statistical significance compared to the uniquely bound variants as described in Methods.
