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 151. 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.
LDpop: Investigate allele frequencies and linkage disequilibrium patterns across 1000G populations. Input is two RS numbers and populations of interest.
LDproxy: Interactively explore proxy and putatively functional variants for a query variant. Input is an RS number 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.
SNPclip: Prune a list of variants by linkage disequilibrium. Input is a list of variant RS numbers (one per line) and a population group.

News and Updates

Interested in accessing LDlink's API using R?
Check out the new LDlinkR package now available on CRAN.
Bogged down organizing authors and affiliations on journal title pages for large studies?
Check out AuthorArranger and conquer title pages in seconds!

Citations:
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.

Machiela MJ, Chanock SJ. LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation. Bioinformatics. 2017 Sept 12. PMID: 28968746.

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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SNP limit warning
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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
Population codes

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rs#1 rs#2 LD

rs#1 Allele Frequency

rs#2 Allele Frequency


Population N rs#1 Allele Freq rs#2 Allele Freq R2 D' LDpair
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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

Limit search results to only SNPs on the selected arrays (unselect all)


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SNP Chip List
RS Number Position (GRCh37)

Welcome to LDlink Programmatic Access!

LDlink modules are also accessible via command line from a terminal. This programmatic access facilitates researchers who are interested in performing batch queries. The syntax is similar to the web address link created for queries on the webpage. Generally text output is returned that is the same as the file a user would download from the online site. Please register below for an access token required for your API call. Once registered, your access token will be emailed to you.


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


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Examples of command line arguments are listed below for each module. Replace the example token in token=faketoken123 with your own registered token.

LDhap

curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldhap?snps=rs3%0Ars4&pop=ALL&token=faketoken123'

LDmatrix

							curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldmatrix?snps=rs3%0Ars4%0Ars148890987&pop=CEU&r2_d=d&token=faketoken123'
						

Note: GET request can support up to 300 SNPs.

							curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "pop": "CEU","r2_d": "d"}' 'https://ldlink.nci.nih.gov/LDlinkRest/ldmatrix?&token=faketoken123'
						

Note: POST request can support up to 1,000 SNPs.

LDpair

curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldpair?var1=rs3&var2=rs4&pop=CEU%2BYRI%2BCHB&token=faketoken123'

LDpop

curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldpop?var1=rs3&var2=rs4&pop=CEU%2BYRI%2BCHB&r2_d=r2&token=faketoken123'

LDproxy

curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldproxy?var=rs3&pop=MXL&r2_d=r2&token=faketoken123'

SNPchip

curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "platforms":"A_10X+A_250N+A_250S+A_50H+A_50X+A_AFR+A_ASI+A_CHB2+A_DMETplus+A_EAS+A_EUR+A_Exome1A+A_Exome319+A_Hu+A_Hu-CHB+A_LAT+A_Onco+A_OncoCNV+A_SNP5.0+A_SNP6.0+I_100+I_1M+I_1M-D+I_240S+I_300+I_300-D+I_550v1+I_550v3+I_610-Q+I_650Y+I_660W-Q+I_CNV-12+I_CNV370-D+I_CNV370-Q+I_CVD+I_CardioMetab+I_Core-12+I_CoreE-12v1+I_CoreE-12v1.1+I_CoreE-24v1+I_CoreE-24v1.1+I_Cyto-12v2+I_Cyto-12v2.1+I_Cyto-12v2.1f+I_Cyto850+I_Exome-12+I_Exon510S+I_Immuno-24v1+I_Immuno-24v2+I_Linkage-12+I_Linkage-24+I_ME-Global-8+I_NS-12+I_O1-Q+I_O1S-8+I_O2.5-4+I_O2.5-8+I_O2.5E-8v1+I_O2.5E-8v1.1+I_O2.5E-8v1.2+I_O2.5S-8+I_O5-4+I_O5E-4+I_OE-12+I_OE-12f+I_OE-24+I_OEE-8v1+I_OEE-8v1.1+I_OEE-8v1.2+I_OEE-8v1.3+I_OZH-8v1+I_OZH-8v1.1+I_OZH-8v1.2+I_OncoArray+I_Psyc-24v1+I_Psyc-24v1.1"}' 'https://ldlink.nci.nih.gov/LDlinkRest/snpchip?token=faketoken123'

SNPclip

curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "pop": "YRI", "r2_threshold": "0.1", "maf_threshold": "0.01"}' 'https://ldlink.nci.nih.gov/LDlinkRest/snpclip?token=faketoken123'

Note: LDassoc is not currently accessible via programmatic access.