This track set displays topologically associating domains (TADs) and TAD boundaries in the human genome, assembled from several 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 five complementary sources:
The domain tracks (Dixon, ENCODE, 3D Genome Browser) answer "are my variant and a candidate gene in the same TAD?" and help 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. Because the domain tracks are nested (ENCODE calls smaller sub-TAD contact domains; Dixon and the 3D Genome Browser call larger top-level TADs), "which TAD?" is answered at different scales by different tracks.
Each source is shown as a separate track because TAD calls are not directly comparable across studies: different algorithms (directionality index/HMM, insulation score, Arrowhead) and resolutions (5–100 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 (from a few kilobases for the ENCODE 5 kb calls up to about ±50 kb for the 100 kb stability bins), 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. The ENCODE and 3D Genome Browser tracks each contain many biosamples and are browsable with a faceted selector on their track configuration pages; a small default set is shown and the rest are enabled through the facets.
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; Schmitt boundaries with the insulation-score method at 40 kb; ENCODE contact domains with Arrowhead (Juicer) on the ENCODE uniform Hi-C pipeline; the 3D Genome Browser domains are that resource's own per-dataset TAD calls (25 kb) across 464 human datasets, shown verbatim (format normalization only); 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 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
Rao SS, Huntley MH, Durand NC, Stamenova EK, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665-80. doi:10.1016/j.cell.2014.11.021
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
Yu S, Fu Y, Wong JH, Wang J, Zhao H, Zhao J, Yue F. The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome architecture. Nucleic Acids Res. 2026;54(D1):D48-D54. doi:10.1093/nar/gkaf1109