Identification of haplotype-specific differential TADs in GM12878. (A) Proportions of differential TADs identified between the paternal and maternal haplotypes. (B) Proportions of differential TADs on Chromosome X. (C) Example of a differential TAD encompassing TSIX and XIST. (D) Proportions of differential and nondifferential TADs containing no allele-specific genes or at least one allele-specific gene. (E) Example of a differential TAD containing the allele-biased gene TBL1X. (F) Single-cell Hi-C maps of the TBL1X TAD in maternal and paternal haplotypes, with RNA Pol II ChIA–PET interactions circled. (G) A differential TAD overlapping a maternal-specific deletion (Chr 22: 22,544,651–23,244,244), which includes the gene IGLL5. (H) Hi-C, RNA Pol II ChIA–PET, ChIP-seq, and RNA-seq signals at the IGLL5 locus visualized using the WashU Epigenome Browser (Li et al. 2022). (I) Single-cell Hi-C maps of the differential TAD across multiple cells, with ChIA–PET interactions circled.