Welcome to

LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups. Each included application is specialized for querying and displaying unique aspects of linkage disequilibrium.

LDassoc

Interactively visualize association p-value results and linkage disequilibrium patterns for a genomic region of interest.

LDexpress

Search if a list of variants (or variants in LD with those variants) is associated with gene expression in multiple tissue types.

LDhap

Calculate population specific haplotype frequencies of all haplotypes observed for a list of query variants.

LDmatrix

Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics.

LDpair

Investigate correlated alleles for a pair of variants in high LD.

LDpop

Investigate allele frequencies and linkage disequilibrium patterns across 1000G populations.

LDproxy

Interactively explore proxy and putatively functional variants for a query variant.

LDtrait

Search if a list of variants (or variants in LD with those variants) have previously been associated with a trait or disease.

LDscore

Calculate LD scores and perform LD score regression.

SNPchip

Find commercial genotyping platforms for variants.

SNPclip

Prune a list of variants by linkage disequilibrium.

What's New

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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 (See Version History)

LDlinkR

Interested in accessing LDlink's API using R?
Check out the new LDlinkR package now available on CRAN.

GWAS Explorer

Visualize and interact with genome-wide association study results from PLCO Atlas.
Check out GWAS Explorer.

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Credits

LDlink was developed by Mitchell Machiela in collaboration with NCI's Center for Biomedical Informatics and Information Technology (CBIIT). Support comes from the Division of Cancer Epidemiology and Genetics Informatics Tool Challenge.

This work utilized the computational resources of the NIH STRIDES Initiative (https://cloud.nih.gov) through the Other Transaction agreement [AWS: OT2OD027852]

LDlink's source code is available under the MIT license, an Open Source Initiative approved license.

Questions or comments? Contact us via email.