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.



What's New


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 is available under the MIT license, an Open Source Initiative approved license.

Questions or comments? Contact us via email.

LDassoc Tool

Interactively visualize association p-value results and linkage disequilibrium patterns for a genomic region of interest.


Browse
 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

LDhap Tool

Calculate population specific haplotype frequencies of all haplotypes observed for a list of query variants.


Browse

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RS Number Position (GRCh37) Allele Frequencies
Haplotype Count
Haplotype Frequency
Cluster Report Genome Browser
Haplotypes

LDmatrix Tool

Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics.


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SNP limit warning
Browse
Population codes

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LDpair Tool

Investigate correlated alleles for a pair of variants in high LD.


Population codes

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Cluster Report
Genome Browser
Cluster Report
Genome Browser
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Haplotypes Statistics
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R2:
Chi-sq:
p-value:





LDpair Results

LDpop Tool

Investigate allele frequencies and linkage disequilibrium patterns across 1000G populations.


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

LDproxy Tool

Interactively explore proxy and putatively functional variants for a query variant.


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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

LDtrait Tool

Search if a list of variants (or variants in LD with those variants) have previously been associated with a trait or disease.


Browse
Population codes
Thresholds
base pair window

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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 Details
Click a variant on the left to view details.
GWAS Catalog last updated on ...

SNPclip Tool

Find commercial genotyping platforms for variants.


Browse
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.

SNPchip Tool

Prune a list of variants by linkage disequilibrium.


Browse

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.

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'

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"}' 'https://ldlink.nci.nih.gov/LDlinkRest/ldtrait?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.

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