Exploring 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. LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups. LDlink consists of four modules for interactively exploring linkage disequilibrium: LDhap, LDmatrix, LDpair, and LDproxy. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Haplotype tables and interactive plots generated by LDlink are tailored for investigators interested in mapping common and uncommon disease susceptibility loci with a focus on linking correlated alleles and highlighting potentially functional variants.
All population genotype data for LDlink and its modules originates from Phase 3 of the 1000 Genomes Project. The genotyped set is complete with all individuals having called genotypes at every included locus. Ancestral super-populations include African, Ad-mixed American, East Asian, European, and South Asian. LDlink is flexible to allow for any combination of 1000 Genomes Project super or sub-populations as input. For query input, LDlink uses dbSNP build 142 to reference SNP (RS) numbers and extract genomic coordinates. The current implementation of LDlink only accepts bi-allelic SNPs as input.
Machiela MJ, Chanock SJ. LDlink: A web-based application for exploring population-specific haplotype structure and linking correlated alleles of potentially functional variants. Bioinformatics 2015. DOI: 10.1093/bioinformatics/btv402.