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 7.3.0 Release (07/31/2026)

Fixed atomic token lock acquisition to prevent concurrent race conditions

Fixed stale-lock cleanup, reliably releasing locks older than timeout

Closed LDlinkRestWeb compute bypass to prevent unauthorized access

Added runtime-based quota with auto-block/unblock to manage usage

Added Redis caching for lock-status checks and runtime counters to reduce database load (See Version History)

LDlink 7.1.0 Release (05/08/2026)

Added Liability Scale to LDscore's Heritability Analysis and Genetic Correlation

Updated LDpop to support automatic submission

Credit references added to all modules

Python updated to 3.13

LDlink 7.0.0 Release (03/19/2026)

Credit reference added to LDscore

Removed filename restrictions for LDScore input files

Fixed heritability and correlation concurrency issue

Fixed genome build mismatches for LDassoc, LDexpress, LDhap, LDproxy, SNPclip

Added file input validation for LDscore (heritability, correlation and ldscore) module

Updated urllib3 to address security vulnerabilities and boto3 dependency issues

Mongo DB migrated to a new AWS account

Python updated to 3.11

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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.