Fig. 1

Allele-specific associations in 1-7HB2 cells with Region Capture Hi-C (RC-Hi-C) for selected imprinted loci. a IGF2-KCNQ1, with the known IGF2 and H19 enhancer interactions labelled 1 and 2. b SNRPN locus. c DLK1 locus. For each locus, the full (diploid) contact matrix (binned at 10kb resolution) is presented, showing the average of all interactions. Below the diploid contact matrix is the TAD insulation score [50], the CTCF track, and the gene track, with imprinted genes annotated. The positions of DMRs with imprinting control functions are highlighted with arrows above the CTCF track for each matrix. Adjacent to the diploid matrices are the haplotype phased allele-specific matrices (A1 above and A2 below) and a subtraction matrix highlighting the differences between the alleles. Enrichment of A1 relative to A2 (blue), enrichment of A2 relative to A1 (red), the scale bar represents distance-normalized differences between A1 and A2. A SNP density track is included to indicate areas of reduced SNP densities that cannot be haplophased. Allelic differences in these regions cannot be called. Coordinates refer to genome build GRCh37/hg19