Welcome to LDlink!

LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups. All population genotype data originates from Phase 3 of the 1000 Genomes Project and variant RS numbers are indexed based on dbSNP build 142. Only bi-allelic variants are permitted as input. LDlink includes the following components:

LDhap: Calculate population specific haplotype frequencies of all haplotypes observed for a list of query variants. Input is a list of variant RS numbers (one per line) and a population group.
LDmatrix: Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics. Input is a list of variant RS numbers (one per line) and a population group.
LDpair: Investigate correlated alleles for a pair of variants in high LD. Input is two RS numbers and a population group.
LDproxy: Interactively explore proxy and putatively functional variants for a query variant. Input is an RS number and a population group.
SNPclip: Prune a list of variants by linkage disequilibrium. Input is a list of variant RS numbers (one per line) and a population group.
SNPchip: Find commercial genotyping platforms for variants. Input is a list of variant RS numbers (one per line) and desired arrays.

News and Updates

03/10/2016 -- New features in LDlink 2.0.

  • 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

09/30/2015 -- New features in LDlink 1.1.

  • 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.

Citation: Machiela MJ, Chanock SJ. LDlink a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants. Bioinformatics. 2015 Jul 2. PMID: 26139635.

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.

Questions or comments? Contact us via email.

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RS Number Position (GRCh37) Allele Frequencies
Haplotype Count
Haplotype Frequency
Haplotypes
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Haplotypes Statistics
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LDproxy legend

View R2 data in UCSC Genome Browser View scoring scheme for RegulomeDB scores

Proxy Variants

RS Number Chr Position (GRCh37) Alleles MAF Distance D' R2 Correlated Alleles RegulomeDB HaploReg Functional Class
RS Results Chr Position (GRCh37) Alleles MAF Distance D' R2 Correlated Alleles RegulomeDB HaploReg Functional Class
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Thresholds

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LD Thinned Variant List
RS Number
Variants with Warnings
Details for rs1234
RS Number Position Alleles Details
Variants With Warnings
RS Number Position Alleles Details
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Filter by array 0 Illumina array(s) and 0 Affymetrix array(s) selected

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SNP Chip List
RS Number Position (GRCh37)