Description

Tandem repeats are among the most polymorphic loci in the genome due to high rates of repeat unit insertions and deletions caused primarily by polymerase slippage during DNA replication. The Tandem Repeat Variation track contains a collection of tracks displaying population-level genetic variation at tandem repeat loci across the human genome. Short tandem repeats (STRs), also known as microsatellites, are consecutive repetitions of 1-6 nucleotide motifs. Variable Number Tandem Repeats (VNTRs) are tandem repeats of typically 7-100 bp.

This super track provides genome-wide tandem repeat annotations, allele frequency data from large-scale population cohorts, and curated disease-associated STR loci.

Note that the gnomAD track container also includes an STR variation track, which is not part of the container here.

Tracks in this collection

Not every track is available on every assembly. The list below covers the whole collection; the track configuration page for this assembly shows the ones you can actually turn on here. STRchive is on hg19, hg38 and hs1 (T2T-CHM13); the rest are hg38 only.

• WebSTR (hg38 only) — 1.7 million STR loci from the EnsembleTR panel with allele frequency data from the 1000 Genomes Project (3,550 individuals across five continental populations). See the WebSTR track documentation for full details.
• TRExplorer (hg38 only) — 5.6 million tandem repeat loci (STRs and VNTRs) from the TRExplorer catalog at the Broad Institute, with population allele frequency data from TenK10K, HPRC256, and AoU1027 cohorts. See the TRExplorer track documentation for full details.
• STRchive (hg19, hg38, hs1) — disease-associated tandem repeat loci curated from published literature, with pathogenic repeat thresholds, inheritance modes, and disease annotations. See the STRchive track documentation for full details.
• ToMMo 61K STR (hg38 only) — 174,300 STR loci with allele count distributions from 61,000 Japanese individuals (Tohoku Medical Megabank Organization), genotyped with Expansion Hunter. See the ToMMo STR track documentation for full details.
• 1KG Vienna ONT VNTR (hg38 only) — 361,362 VNTR loci with allele statistics from 1,019 samples of the 1000 Genomes Oxford Nanopore long-read sequencing project (Vienna), genotyped with VAMOS. Unlike the other STR tracks which use short-read data, this track is based on long-read sequencing which can span longer tandem repeat regions. See the Vienna VNTR track documentation for full details.

Credits

Thanks to the data providers of the individual tracks listed above. See each track's documentation page for specific credits.