A complex interplay between transcription factors (TFs) and the genome regulates
transcription. However, connecting variation in genome sequence with variation in TF
binding and gene expression is challenging due to environmental differences between
individuals and cell types. To address this problem, we measured genome-wide differential
allelic occupancy of 24 TFs and EP300 in a human lymphoblastoid cell line GM12878.
Overall, 5% of human TF binding sites have an allelic imbalance in occupancy. At many …

Results Transcription factors often cluster together on the same alleles in regions of open
chromatin To survey the allelic cis-regulatory landscape, we performed ChIP-seq on 24
sequence-specific human TFs and the transcriptional co-activator EP300 in a
lymphoblastoid cell line (LCL), GM12878, generated by EBV immortalization of cells from a
female (Supplemental Table 1). Whole genome sequencing has been performed on this cell
line and on LCLs derived from both of her parents (The 1000 Genomes Project Consortium …