Description

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. Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring regions and constrain enhancer-promoter contacts.

The set contains five complementary sources:

• Dixon 2012 TADs – the original TAD domains in hESC and IMR90 cells (lifted from hg18).
• ENCODE TADs – TAD domains across 117 ENCODE human biosamples (hg38 only), 112 of them called with Arrowhead by the ENCODE uniform Hi-C pipeline, browsable by a faceted selector (organ, biosample type, assay, life stage, calls). The Arrowhead calls are finer-resolution (5 kb) contact domains, smaller than the Dixon TADs.
• 3D Genome Browser – TAD domains across 464 human Hi-C/Micro-C datasets (normal and cancer, baseline and perturbation), exactly as called and published by the 3D Genome Browser, browsable by a faceted selector (organ, cell type, assay, condition, treatment, provenance, year, study).
• Schmitt 2016 boundaries – TAD boundaries across 21 human tissues and cell lines.
• TAD boundary stability – how recurrent each boundary is across 37 cell-type maps (McArthur & Capra 2021).

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 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

Display Conventions and Configuration

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.

Methods

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).

Data Access

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.

References

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 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 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, 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, 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 Jan 6;54(D1):D48-D54. DOI: 10.1093/nar/gkaf1109; PMID: 41206958; PMC: PMC12807788