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LDlink Version History

LDlink 6.0.0 Release (12/05/2025)

  • Modernized UI Technology with update from jQuery to Next.js and React's component-based architecture
  • Improved site's UI responsiveness, layouts and error/warning messaging

LDlink 5.8.2 Release (11/7/2025)

  • Pinned the LDscore version to avoid updates

LDlink 5.8.1 Release (10/29/2025)

  • Updated the python script to not delete the GWAS catalog table when the program fails to download data from the source

LDlink 5.8.0 Release (08/27/2025)

  • Added GET methods for the LDexpress and LDtrait API endpoints
  • Added examples of the GET methods for the LDexpress and LDtrait to the API Access page

LDlink 5.7.0 Release (06/18/2025)

  • Added LDscore module

LDlink 5.6.8 Release (06/21/2024)

  • Removed domain change notice
  • Added USA government official flag banner
  • Specified numpy version

LDlink 5.6.7 Release (02/21/2024)

  • Forge DB Scores update

LDlink 5.6.6 Release (10/20/2023)

  • Updated ForgeDB link to new server
  • Updated HaploReg link to new version
  • Added shutdown alert in the header
  • Fixed the input patterns which should allow only one snp for LDproxy, ldpair and ldpop

LDlink 5.6.5 Release (8/11/2023)

  • Added more citations for LDtrait and LDexpress
  • Added PUBMEDID(PMID) for LDtrait outputs

LDlink 5.6.4 Release (7/6/2023)

  • Replaced CDN-hosted assets

LDlink 5.6.3 Release (6/1/2023)

  • Fixed LDassoc Upload Issues

LDlink 5.6.2 Release (5/15/2023)

  • Domain URL migrated from ldlink.nci.nih.gov to ldlink.nih.gov
  • Application logo changed

LDlink 5.6.1 Release (5/3/2023)

  • Fixed download button which can not load file in new tab for Chrome and Firefox

LDlink 5.6.0 Release (4/20/2023)

  • Migrated to serverless architecture for improved performance, reliability, and scalability.

LDlink 5.5.2 Release (3/25/2023)

  • Fix the multiallelic error message for LDpair

LDlink 5.5.1 Release (11/15/2022)

  • Add a link to FORGEdb scoring scheme for LDassoc and LDproxy

LDlink 5.5.0 Release (11/03/2022)

  • Publicly available scores from FORGEdb are used by LDlink's LDassoc and LDproxy and LDMatrix modules.
  • Added Global Diversity Array_Confluence (I_GDA-C) and Illumina Global Screening version 3_Confluence (I_GSA-v3C) to SNPChip.
  • Provide a warning when the input on LDtrait can potentially cause a server timeout.
  • Fixed the broken link for View R2 data in UCGC Genome Browse

LDlink 5.4.2 Release (09/13/2022)

  • Fix the output format for LDpair. It should be text file for api call

LDlink 5.4.1 Release (09/01/2022)

  • Provide more useful error message for LDpair if varient is not in 1000G

LDlink 5.4.0 Release (08/08/2022)

  • Internal code refactoring for performance improvements

LDlink 5.3.3 Release (05/24/2022)

  • Revise SNPclip sort order, use user supplied input format;
  • Fix LDpair multiallelic query for second SNP input

LDlink 5.3.2 Release (05/06/2022)

  • Fix LDmatrix plotting for unsorted query variants.

LDlink 5.3.1 Release (04/28/2022)

  • Improve ability to catch SNPs missing in 1000G data.

LDlink 5.3 Release (04/05/2022)

  • Add ability to submit batch LDpair inputs to single API requests.
  • Fix behavior when a SNP's 1000G position does not match dbSNP.

LDlink 5.2 Release (01/03/2022)

  • dbSNP build updated from version 151 to 155.
  • Add support for GRCh38 genomic coordinates.
  • Add support for genetic map recombination rates in chromosome X.
  • Add ability to collapsed gene transcripts in LDmatrix and LDproxy.

LDlink 5.1 Release (05/25/2021)

  • Improved filtering options on LDexpress data table.
  • Allow scientific notation as input for LDexpress P-value threshold.

LDlink 5.0 Release (11/06/2020)

  • LDexpress released for searching variants that are associated with gene expression in multiple tissue types.

LDlink 4.2.0 Release (09/21/2020)

  • Add ability to LDproxy to adjust base pair window size.

LDlink 4.1.0 Release (04/29/2020)

  • Add ability to LDtrait to adjust base pair window size.

LDlink 4.0.3 Release (04/06/2020)

  • Fix population dropdown UI cut short by module container.

LDlink 4.0.2 Release (03/20/2020)

  • Fix P-value and 95% CI columns in LDtrait to reflect GWAS Catalog.
  • Add timestamp of when LDtrait GWAS Catalog was last updated.
  • Fix browser forward/back functionality.

LDlink 4.0.1 Release (03/10/2020)

  • Fix SNPchip array labels not displaying correctly.

LDlink 4.0 Release (03/10/2020)

  • LDtrait released for searching variants that have been associated with a trait or disease.
  • Fix correlated allele calculation for LDassoc, LDmatrix, LDpair, and LDproxy.
  • Combine R2 and D' coloring for LDmatrix plots.
  • Home page redesign.

LDlink 3.9 Release (12/10/2019)

  • Add population details, P-value, and Chi-sq to LDpop export table.

LDlink 3.8 Release (10/31/2019)

  • Upgrade backend from Python 2 to Python 3.

LDlink 3.7.2 Release (08/23/2019)

  • Fix variant inputs by genomic coordinates for chromosomes X and Y.

LDlink 3.7.1 Release (07/30/2019)

  • Fix collapsed gene transcripts in LDassoc.

LDlink 3.7 Release (05/09/2019)

  • Return LDpop API results in tab-delimited format.

LDlink 3.6 Release (04/03/2019)

  • Add ability to make POST requests to LDmatrix with up to 1000 variants.
  • Restrict concurrent requests to the API.

LDlink 3.5 Release (03/18/2019)

  • LDpop released for visualizing LD patterns across 1000G populations.

LDlink 3.4 Release (02/06/2019)

  • Correct dbsnp positions for delins, ins, and del type variants.
  • Improve query performance from genomic coordinate and rsid inputs.

LDlink 3.3 Release (12/24/2018)

  • LDlink API access now requires registration. Please register using the API Access tab.
  • dbSNP build updated from version 142 to 151.
  • Genomic coordinates can now be used to query variants for each module.
  • Improvements have been made to error messages from programmatic access.
  • Refresh user interface.

LDlink 3.2 Release (08/01/2018)

  • Update Bokeh interactive plotting library to release 0.13.0.
  • Add ability to export Bokeh plots to high quality images (SVG, PDF, PNG, and JPEG).
  • Merge gene plot and main plot into one image during export.
  • Fix errors with SNPclip output when variants are not found in 1000G VCF file.

LDlink 3.0 Release (04/01/2017)

  • LDassoc released for visualizing association results.
  • Programmatic Access of LDlink via terminal commands.
  • Update Bokeh interactive plotting library to release 0.12.2.
  • Improve performance of allele matching algorithm.
  • Better table sorting on absolute value of distance.
  • Refine exported UCSC data tracks (link at bottom of interactive plots).

LDlink 2.0 Release (03/10/2016)

  • SNPclip released for LD pruning a list of variants.
  • SNPchip released for finding variants on commercial genotyping arrays.
  • Minor tweaks to improve visualization of indel output.
  • Correct p-value rounding to zero in LDpair.
  • Fix errors when variants map to the same position in 1000G VCF file

LDlink 1.1 Release (09/30/2015)

  • Indels are now accepted as input in all LDlink modules.
  • LDproxy output table now returns all data with options to sort by columns and search output.
  • LDhap haplotypes are now color coded by alleles for easier viewing.
  • LDmatrix now includes a R2/D' toggle for plotting R2 or D' matrices.
  • Minor tweaks to improve visualization on a variety of device screen sizes.