10/20/2026

Added a Centromere and Satellite Regions column that reports the class of the centromeric or pericentromeric satellite region that overlaps each TR locus (for example, a human satellite 3 array, the alpha satellite array where the centromere forms, or a centromeric transition region between satellite arrays), based on the Miga lab's centromeric satellite annotation of hg38 [CenSatData]. 202,337 TR loci overlap one of these regions. The column can be used in custom filters in the filters form, and selected when exporting to TSV or JSON.

10/15/2026

Added HPRC256 population distributions and polymorphism metrics based on total allele length, as an alternative to the HPRC256 longest pure segment (LPS) metrics that existed before. This is particularly useful for studying polymorphic VNTRs with motif switches or other types of impure repeat sequences.
Updated TR annotations from GENCODE v49 to v50 (comprehensive gene set). The GENCODE track in IGV.js also now shows GENCODE v50 basic transcripts.

10/5/2026

Added ATaRVa export format.
Added optional columns summarizing massively parallel reporter assay (MPRA) results from [Zhang 2025] and ENCODE4. Also, added optional columns predicting splicing effects of TR variants, generated by computing SpliceAI scores for simulated expansions and contractions at 2,070,141 loci within Gencode v50 basic transcripts that were polymorphic (i.e. had at least 2 distinct allele sizes) in HPRC256.
Click the icon in the top-left above the search results table to enable these columns.
Added the TRExplorer v2.1 draft catalog as an option in the Search TR Catalog dropdown within the additional search filters form. The v2.1 catalog consists of all v2.0 loci plus 58,135 alternative locus definitions computed by extending the boundaries of some v2.0 definitions.
It's now possible to drag-drop a BED file onto the main search box to search for TRs within multiple regions. TXT or TSV files are also supported, and can be used to search for multiple LocusIds, regions, gene names or gene IDs listed one per line.

7/10/2026

Updates to the main search form:

Added the ability to upload a list of locus IDs, regions, gene names, and/or gene IDs (TXT/TSV/BED) to search for many at once.
Click the + button at the right edge of the search box to upload the file(s).
Updated the default result columns: added the σ_HPRC256 column and removed the RepeatMasker column.
To change the displayed columns, click the icon in the top-left above the search results table.

5/14/2026

Multiple updates to the main search form:

Added Stdev rank percentile (σ rank %) filters in the Polymorphism Filter dialog for HPRC256, AoU1027, and 10k10k
Improved the "Add custom filters..." feature in the Advanced Search form

5/11/2026

Multiple updates to locus-specific pages:

Added allele purity and allele methylation distributions from TRGT calls in HPRC256 data.
Allow population frequency, allele purity, and allele methylation plots to be stratified by population and/or sex.
Show TRGT consensus allele sequences decomposed into motifs using trviz.

3/5/2026

New custom filter feature at the bottom of the detailed filters form allows arbitrary filters to be set on database column(s).
Prev and Next above IGV for quickly traversing loci in the search results table
Export to TSV or JSON now shows a dialog that allows users to select the columns to include, and to choose how overlapping loci will be exported
Export to TRGT format shows a dialog that allows users to choose how to handle variation clusters and overlapping loci

2/2/2026

Database updated to include the latest set of known disease-associations from STRchive.
Added optional columns based on sc-eTRs from [Tanudisastro 2024] and PheWAS results from [Manigbas 2024].

1/16/2026

Database updated to the latest version of the v2 catalog.

1/7/2026

Updated to the latest draft release of TRExplorer catalog v2 and variation clusters
Updated population data from HPRC100 to HPRC256 (256 PacBio HiFi genomes)
Added non-coding annotations from the Talkowski lab, including ultra-conserved elements (UCEs), human accelerated regions (HARs), VISTA enhancers, fetal cortex enhancers/silencers, and ABC enhancer predictions
Added percentile rank display for polymorphism statistics (e.g., "top 1% by motif")

11/10/2025

Added separate locus-specific pages
Fixed IGV.js track loading speed - tracks now load much faster
Loaded TRExplorer catalog v2.0 draft which improves coverage of VNTRs by adding loci from the Vamos v2.1 catalog
Added motif frequencies computed via the Vamos v2.1 pipeline - shared by Bida Gu and Mark Chaisson. See [Gu et al. 2025]
Added new columns to the results table, including 'Motif Variability', 'Source', 'Repeat Masker', and others

10/31/2025

Fixed AoU1027 stdev values to be the standard deviation of the number of repeats of the longest pure segment. Previously, they were erroneously shown as the true value divided by the motif size.
Fixed IGV.js track loading speed - tracks now load much faster
Loaded TRExplorer catalog v2.0 draft which improves coverage of VNTRs by adding loci from the Vamos v2.1 catalog
Added motif frequencies computed via the Vamos v2.1 pipeline - shared by Bida Gu and Mark Chaisson. See [Gu et al. 2025]
Added new columns to the results table, including 'Motif Variability', 'Source', 'Repeat Masker', and others

6/18/2025

Added FAQ page

5/25/2025

Initial release of TRExplorer

10/20/2026	Added a Centromere and Satellite Regions column that reports the class of the centromeric or pericentromeric satellite region that overlaps each TR locus (for example, a human satellite 3 array, the alpha satellite array where the centromere forms, or a centromeric transition region between satellite arrays), based on the Miga lab's centromeric satellite annotation of hg38 [CenSatData]. 202,337 TR loci overlap one of these regions. The column can be used in custom filters in the filters form, and selected when exporting to TSV or JSON.
10/15/2026	Added HPRC256 population distributions and polymorphism metrics based on total allele length, as an alternative to the HPRC256 longest pure segment (LPS) metrics that existed before. This is particularly useful for studying polymorphic VNTRs with motif switches or other types of impure repeat sequences. Updated TR annotations from GENCODE v49 to v50 (comprehensive gene set). The GENCODE track in IGV.js also now shows GENCODE v50 basic transcripts.
10/5/2026	Added ATaRVa export format. Added optional columns summarizing massively parallel reporter assay (MPRA) results from [Zhang 2025] and ENCODE4. Also, added optional columns predicting splicing effects of TR variants, generated by computing SpliceAI scores for simulated expansions and contractions at 2,070,141 loci within Gencode v50 basic transcripts that were polymorphic (i.e. had at least 2 distinct allele sizes) in HPRC256. Click the icon in the top-left above the search results table to enable these columns. Added the TRExplorer v2.1 draft catalog as an option in the Search TR Catalog dropdown within the additional search filters form. The v2.1 catalog consists of all v2.0 loci plus 58,135 alternative locus definitions computed by extending the boundaries of some v2.0 definitions. It's now possible to drag-drop a BED file onto the main search box to search for TRs within multiple regions. TXT or TSV files are also supported, and can be used to search for multiple LocusIds, regions, gene names or gene IDs listed one per line.
7/10/2026	Updates to the main search form: Added the ability to upload a list of locus IDs, regions, gene names, and/or gene IDs (TXT/TSV/BED) to search for many at once. Click the + button at the right edge of the search box to upload the file(s). Updated the default result columns: added the σ_HPRC256 column and removed the RepeatMasker column. To change the displayed columns, click the icon in the top-left above the search results table.
5/14/2026	Multiple updates to the main search form: Added Stdev rank percentile (σ rank %) filters in the Polymorphism Filter dialog for HPRC256, AoU1027, and 10k10k Improved the "Add custom filters..." feature in the Advanced Search form
5/11/2026	Multiple updates to locus-specific pages: Added allele purity and allele methylation distributions from TRGT calls in HPRC256 data. Allow population frequency, allele purity, and allele methylation plots to be stratified by population and/or sex. Show TRGT consensus allele sequences decomposed into motifs using trviz.
3/5/2026	New custom filter feature at the bottom of the detailed filters form allows arbitrary filters to be set on database column(s). Prev and Next above IGV for quickly traversing loci in the search results table Export to TSV or JSON now shows a dialog that allows users to select the columns to include, and to choose how overlapping loci will be exported Export to TRGT format shows a dialog that allows users to choose how to handle variation clusters and overlapping loci
2/2/2026	Database updated to include the latest set of known disease-associations from STRchive. Added optional columns based on sc-eTRs from [Tanudisastro 2024] and PheWAS results from [Manigbas 2024].
1/16/2026	Database updated to the latest version of the v2 catalog.
1/7/2026	Updated to the latest draft release of TRExplorer catalog v2 and variation clusters Updated population data from HPRC100 to HPRC256 (256 PacBio HiFi genomes) Added non-coding annotations from the Talkowski lab, including ultra-conserved elements (UCEs), human accelerated regions (HARs), VISTA enhancers, fetal cortex enhancers/silencers, and ABC enhancer predictions Added percentile rank display for polymorphism statistics (e.g., "top 1% by motif")
11/10/2025	Added separate locus-specific pages Fixed IGV.js track loading speed - tracks now load much faster Loaded TRExplorer catalog v2.0 draft which improves coverage of VNTRs by adding loci from the Vamos v2.1 catalog Added motif frequencies computed via the Vamos v2.1 pipeline - shared by Bida Gu and Mark Chaisson. See [Gu et al. 2025] Added new columns to the results table, including 'Motif Variability', 'Source', 'Repeat Masker', and others
10/31/2025	Fixed AoU1027 stdev values to be the standard deviation of the number of repeats of the longest pure segment. Previously, they were erroneously shown as the true value divided by the motif size. Fixed IGV.js track loading speed - tracks now load much faster Loaded TRExplorer catalog v2.0 draft which improves coverage of VNTRs by adding loci from the Vamos v2.1 catalog Added motif frequencies computed via the Vamos v2.1 pipeline - shared by Bida Gu and Mark Chaisson. See [Gu et al. 2025] Added new columns to the results table, including 'Motif Variability', 'Source', 'Repeat Masker', and others
6/18/2025	Added FAQ page
5/25/2025	Initial release of TRExplorer