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 (Version 5) of the 1000 Genomes Project and variant RS numbers are indexed based on dbSNP build 142. Where coordinates are specified, GRCh37/hg19 is used. Only bi-allelic variants are permitted as input. LDlink includes the following modules:

LDassoc: Interactively visualize association p-value results and linkage disequilibrium patterns for a genomic region of interest. Input is a tab or space delimited association output file and a population group.
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

04/01/2017 -- New features in LDlink 3.0.

  • LDassoc released for visualizing association results.
  • Programatic 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).

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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 Use example GWAS data
base pair window

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LDassoc legend

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

  • Number of Individuals: 2504
  • SNPs in Region: 2451
  • Run time: 6.39 seconds

Association Results

RS Number Chr Position (GRCh37) Alleles MAF Distance D' R2 Correlated Alleles Association P-value RegulomeDB HaploReg Functional Class
RS Results Chr Position (GRCh37) Alleles MAF Distance D' R2 Correlated Alleles Association P-value RegulomeDB HaploReg Functional Class
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RS Number Position (GRCh37) Allele Frequencies
Haplotype Count
Haplotype Frequency
Cluster Report Genome Browser
Haplotypes
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Population codes

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Population codes

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Cluster Report
Genome Browser
Cluster Report
Genome Browser
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Haplotypes Statistics
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LDpair Results
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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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Population codes
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
Click a variant on the left to view details.
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Filter by array Collapse 0 Illumina array(s) and 0 Affymetrix array(s) selected

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SNP Chip List
RS Number Position (GRCh37)