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. +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. Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring +regions and constrain enhancer-promoter contacts.
The set contains five complementary sources:
The table below summarizes how each source's domains or boundaries were called and at what resolution:
-
Track Feature Calling method Resolution - Dixon 2012 Domains Directionality-index HMM 40 kb - ENCODE contact domains Domains Arrowhead (Juicer), ENCODE uniform Hi-C pipeline 5 kb + 3D Genome Browser 2.0 Domains Resource's own per-dataset TAD calls, shown verbatim 25 kb + ENCODE TADs Domains Arrowhead (Juicer), ENCODE uniform Hi-C pipeline (112 of 117 biosamples) 5 kb 3D Genome Browser 2.0 Domains Resource's own per-dataset TAD calls, shown verbatim 20 or 25 kb Schmitt 2016 Boundaries Insulation score 40 kb McArthur & Capra 2021 Boundaries (stability) Boundary sharing across 37 reprocessed cell-type maps 100 kb windows
-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. +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. Because TADs are called from Hi-C data analyzed in fixed-size bins, domain edges +are uncertain to roughly the bin size (from a few kilobases for the ENCODE 5 kb calls up to +about ±50 kb for the 100 kb stability windows), and the width of a boundary reflects +this precision, not a measured physical width. Domains do not cover the whole genome, and +the gaps between domains 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.
Each source was called independently by its original study or resource; the calling method and resolution for each are summarized in the table in the Description above. See the individual subtrack description pages for full methods, source publications, and assembly/liftOver details for each dataset.
The UCSC source for this track set is available on GitHub: doc/hg38/tad.txt (makedoc), makeDb/scripts/tad (build scripts), and trackDb/human/hg38/tad.ra (trackDb).
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 + +Topological domains in mammalian genomes identified by analysis of chromatin interactions. +Nature. 2012 Apr 11;485(7398):376-80. +DOI: 10.1038/nature11082; PMID: 22495300; PMC: PMC3356448
-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 +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 Feb 4;108(2):269-283. +DOI: 10.1016/j.ajhg.2021.01.001; PMID: 33545030; PMC: PMC7895846
-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 +Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, +Lander ES et al. + +A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. +Cell. 2014 Dec 18;159(7):1665-80. +DOI: 10.1016/j.cell.2014.11.021; PMID: 25497547; PMC: PMC5635824
-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 +Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL et al. + +A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. +Cell Rep. 2016 Nov 15;17(8):2042-2059. +DOI: 10.1016/j.celrep.2016.10.061; PMID: 27851967; PMC: PMC5478386
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 + +The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome +architecture. +Nucleic Acids Res. 2026 Jan 6;54(D1):D48-D54. +DOI: 10.1093/nar/gkaf1109; PMID: +41206958; PMC: PMC12807788