Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression

We quantitatively interrogate these relationships by comparing Hi-C and molecular phenotype data across cell types and haplotypes. While chromatin loops consistently form across different cell types, subtle quantitative differences in contact frequency are associated with larger changes in gene expression and H3K27ac. Across haplotypes, we find larger differences in contact frequency at imprinted and copy number variable loci. We find most changes in contact frequency are smaller across haplotypes than cell types; however, the proportional relationship between these changes and those in gene expression and regulation are consistent. This suggests that subtle changes in contact propensity have a biologically meaningful role in gene regulation and could be a mechanism by which regulatory genetic variants in loop anchors mediate effects on expression. The raw data files for these processed files can be obtained through dbGaP accession phs000924. Examination of phased HiC, RNA-seq, H3K27AC ChIP-seq, and ATAC-seq across two cell types and seven individuals. Multiple replicates for non-hic data are separate. HiC replicates have been merged Raw data requires controlled access and is deposited at dbGaP http://www.ncbi.nlm.nih.gov/gap/?term=phs000924