This track set displays topologically associating domains (TADs) and TAD boundaries in the human genome, assembled from published Hi-C studies. TADs are self-interacting regions of the genome, typically hundreds of kilobases to about a megabase, and themselves nested, with smaller contact domains contained within larger top-level TADs. Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring regions and constrain enhancer-promoter contacts. Disruption of a TAD boundary can rewire gene regulation and cause disease, and TADs are widely used to nominate candidate target genes for non-coding variants.
The set contains three complementary sources:
Two further domain sources are available on the hg38 assembly:
The domain track (Dixon) answers "are my variant and a candidate gene in the same TAD?" and helps prioritize target genes at non-coding GWAS loci. The boundary tracks (Schmitt, stability) answer "does my structural variant disrupt an insulating boundary?" and help interpret the regulatory impact of deletions, duplications, and inversions.
Each source is shown as a separate track because TAD calls are not directly comparable across studies: different algorithms (directionality index/HMM, insulation score) and resolutions (40–100 kb) produce different calls of the same underlying biology. Domains are drawn as boxes spanning each self-interacting region; boundaries are drawn as the short bins that divide adjacent domains. Because calls are made on binned data, domain edges are uncertain to roughly the caller's bin size, and the bin width of a boundary feature reflects this localization precision, not a measured physical width. Domains do not tile the genome end to end; the gaps between domain boxes are inter-domain or unorganized regions, not display artifacts.
See the individual subtrack description pages for full methods, source publications, and assembly/liftOver details for each dataset. In brief: Dixon domains were called with the directionality-index HMM at 40 kb (lifted from hg18); Schmitt boundaries with the insulation-score method at 40 kb; and the boundary-stability track counts, per 100 kb window, how many of 37 re-processed cell-type maps share a boundary (McArthur & Capra 2021). The Schmitt and stability tracks are native to hg19.
The raw data can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API. The underlying bigBed files can be downloaded from our download server.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376-80. doi:10.1038/nature11082
McArthur E, Capra JA. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. Am J Hum Genet. 2021;108(2):269-283. doi:10.1016/j.ajhg.2021.01.001
Schmitt AD, Hu M, Jung I, Xu Z, et al. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Rep. 2016;17(8):2042-2059. doi:10.1016/j.celrep.2016.10.061