LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants
Open accessAbstract
UNLABELLED: Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants. AVAILABILITY AND IMPLEMENTATION: LDlink is a free and publically available web tool which can be accessed at http://analysistools.nci.nih.gov/LDlink/. CONTACT: mitchell.machiela@nih.gov.
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The two HFE SNPs are in low linkage disequilibrium (LD r2 < 0.01) in combined European populations.
“The two SNPs in the HFE gene were in low linkage disequilibrium (LD r2 < 0.01) when considering combined European populations with the LDlink resource [2,17].”
From Associations of genetically determined iron status across the phenome: A mendelian randomization study (2019) · cites this paper as [17]
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- Authors
- Machiela, M. J., & Chanock, S. J.
- Affiliations
- Division of Cancer Epidemiology and Genetics (US)
- Corresponding author
- Machiela, Mitchell J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-07-02
- Volume
- 31
- Issue
- 21
- Pages
- 3555-3557
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4626747
- OpenAlex
- W2166320441
- Cited by
- 2,069
- References
- 7
- Citations by year
- 2026: 156 · 2025: 236 · 2024: 346 · 2023: 244 · 2022: 235 · 2021: 278 · 2020: 210 · 2019: 155 · 2018: 104 · 2017: 75 · 2016: 26 · 2015: 2 · 2014: 1
- FWCI
- 47.43
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- public-domain
- Locations
- Bioinformatics (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute
- Center for Biomedical Informatics and Information Technology, National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- linkage disequilibrium, haplotype structure, single nucleotide polymorphisms, 1000 Genomes Project, disease susceptibility loci, functional variants, web-based bioinformatics tool, interactive visualization
- MeSH terms
- Alleles, Chromosome Mapping, Haplotypes, Humans, Software, Linkage Disequilibrium, Genetic Predisposition to Disease, Internet, Polymorphism, Single Nucleotide, Population Groups
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