Welcome to LDlink

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.

SNPchip

Find commercial genotyping platforms for variants.

SNPclip

Prune a list of variants by linkage disequilibrium.


What's New

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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.

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

Questions or comments? Contact us via email.

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 Use example GWAS data
ldassoc population codes
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LDassoc legend

View R2 data in UCSC Genome Browser View scoring scheme for FORGEdb scores 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 FORGEdb RegulomeDB HaploReg Functional Class
RS Number Chr Position (GRCh37) Alleles MAF Distance D' R2 Correlated Alleles Association P-value FORGEdb RegulomeDB HaploReg Functional Class
Download association data for all variants
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Population codes Warning: Selecting 2 or more sub-populations at a time significantly slows down query time and ties up limited system resources.
Tissue codes
Thresholds
base pair window
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Variants in LD with GTEx QTL
Genes with GTEx QTL
Tissues with GTEx QTL
Variants with Warnings
Query RS Number Position (GRCh37) R2 D' Gene Symbol Gencode ID Tissue Non-effect Allele Freq Effect Allele Freq Effect Size P-value
Query Variants with Warnings
Variant Position (GRCh37) Details
Click a variant on the left to view details.
GTEx v8
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ldhap population codes
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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
You are using a version of Firefox that does not render tool tips properly in the output interactive plot
Population codes Warning: Selecting 2 or more sub-populations at a time significantly slows down query time and ties up limited system resources.
base pair window
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LDproxy legend

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

Proxy Variants

RS Number Chr Position (GRCh37) Alleles MAF Distance D' R2 Correlated Alleles FORGEdb RegulomeDB HaploReg Functional Class
RS Number Chr Position (GRCh37) Alleles MAF Distance D' R2 Correlated Alleles FORGEdb RegulomeDB HaploReg Functional Class
Download all proxy variants
Browse
Population codes Warning: Selecting 2 or more sub-populations at a time significantly slows down query time and ties up limited system resources.
Thresholds
base pair window
loading icon Estimated calculation time: _
Error
Warning
Variants in LD with GWAS Catalog
RS Number
Variants with Warnings
Details for rs1234
GWAS Trait RS Number Position (GRCh37) Alleles R2 D' LDpair Risk Allele Frequency Beta or OR Effect Size (95% CI) P-value GWAS Catalog
Query Variants with Warnings
Variant Position (GRCh37) Details
Click a variant on the left to view details.
GWAS Catalog last updated on ...
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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 (GRCh37) Alleles Details
Variants With Warnings
RS Number Position (GRCh37) 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)

LDlink API 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.

LDexpress

curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "pop": "YRI+CEU", "tissues": "Adipose_Subcutaneous+Adipose_Visceral_Omentum", "r2_d": "r2", "r2_d_threshold": "0.1", "p_threshold": "0.1", "window": "500000", "genome_build": "grch37"}' 'https://ldlink.nci.nih.gov/LDlinkRest/ldexpress?token=faketoken123'

LDhap

curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldhap?snps=rs3%0Ars4&pop=ALL&genome_build=grch38&token=faketoken123'

LDmatrix

							curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldmatrix?snps=rs3%0Ars4%0Ars148890987&pop=CEU&r2_d=d&genome_build=grch38_high_coverage&token=faketoken123'

Note: GET requests can support up to 300 SNPs.

							curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "pop": "CEU","r2_d": "d", "genome_build": "grch37"}' 'https://ldlink.nci.nih.gov/LDlinkRest/ldmatrix?token=faketoken123'

Note: POST requests can support up to 2,500 SNPs.

LDpair

							curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldpair?var1=rs3&var2=rs4&pop=CEU%2BYRI%2BCHB&genome_build=grch37&json_out=false&token=faketoken123'

Note: GET requests only support 1 SNP pair.

							curl -k -H "Content-Type: application/json" -X POST -d '{"snp_pairs": [["rs3", "rs4"], ["rs7837688", "rs4242384"]], "pop": "CEU+YRI+CHB","genome_build": "grch37", "json_out": true}' 'https://ldlink.nci.nih.gov/LDlinkRest/ldpair?token=faketoken123'

Note: POST requests can support up to 10 SNP pairs. If more than 1 SNP pair is provided, a JSON response will always be returned.

LDpop

curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldpop?var1=rs3&var2=rs4&pop=CEU%2BYRI%2BCHB&r2_d=r2&genome_build=grch37&token=faketoken123'

LDproxy

curl -k -X GET 'https://ldlink.nci.nih.gov/LDlinkRest/ldproxy?var=rs3&pop=MXL&r2_d=r2&window=500000&genome_build=grch37&token=faketoken123'

LDtrait

curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "pop": "YRI", "r2_d": "r2", "r2_d_threshold": "0.1", "window": "500000", "genome_build": "grch37"}' 'https://ldlink.nci.nih.gov/LDlinkRest/ldtrait?token=faketoken123'

SNPchip

curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4\nrs17795812", "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+I_GDA-C+I_GSA-v3C", "genome_build": "grch37"}' '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", "genome_build": "grch37"}' 'https://ldlink.nci.nih.gov/LDlinkRest/snpclip?token=faketoken123'

Note: LDassoc is not currently accessible via programmatic access.

LDlink Citations

Thank you for using LDlink! If you use LDlink in any publication please cite the LDlink manuscript and any relevant module publications:


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.

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.

Alexander TA, Machiela MJ. LDpop: an interactive online tool to calculate and visualize geographic LD patterns. BMC Bioinformatics. 2020 Jan 10.

Myers TA, Chanock SJ, Machiela MJ. LDlinkR: An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations. Front. Genet. 2020 Feb 28.

LDlink Version History