Description

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

The set contains three complementary sources:

• Dixon 2012 TADs – the original TAD domains in hESC and IMR90 cells (lifted from hg18).
• Schmitt 2016 boundaries – TAD boundaries across 21 human tissues and cell lines (native hg19).
• TAD boundary stability – how recurrent each boundary is across 37 cell-type maps (McArthur & Capra 2021; native hg19).

The table below summarizes how each of these tracks' domains or boundaries were called and at what resolution:

Track	Feature	Calling method	Resolution
Dixon 2012	Domains	Directionality-index HMM (lifted from hg18)	40 kb
Schmitt 2016	Boundaries	Insulation score (native hg19)	40 kb
McArthur & Capra 2021	Boundaries (stability)	Boundary sharing across 37 reprocessed cell-type maps (native hg19)	100 kb windows

Two further domain sources are available on the hg38 assembly:

• ENCODE TADs – TAD domains across 117 ENCODE human biosamples (hg38 only).
• 3D Genome Browser – TAD domains across 464 human Hi-C/Micro-C datasets (hg38 only).

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) and resolutions (40–100 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, 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.

Methods

Each source was called independently by its original study; 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/hg19.txt (makedoc), makeDb/scripts/tad (build scripts), and trackDb/human/hg19/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

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