LDlink is a web-based application designed to explore population-specific haplotype structure and link correlated alleles of possible functional variants. It consists of several bioinformatic modules that query single nucleotide polymorphisms (SNPs) in specific population groups to generate haplotype tables and interactive plots. The tool utilizes Phase 3 haplotype data from the 1000 Genomes Project to calculate pairwise metrics of linkage disequilibrium (LD), search for proxies in high LD, and enumerate 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. The tool is free and publicly available at http://analysistools.nci.nih.gov/LDlink/. It aims to facilitate fine mapping of disease susceptibility regions and assist in characterizing functional variants based on genotype-phenotype associations with potential clinical utility.LDlink is a web-based application designed to explore population-specific haplotype structure and link correlated alleles of possible functional variants. It consists of several bioinformatic modules that query single nucleotide polymorphisms (SNPs) in specific population groups to generate haplotype tables and interactive plots. The tool utilizes Phase 3 haplotype data from the 1000 Genomes Project to calculate pairwise metrics of linkage disequilibrium (LD), search for proxies in high LD, and enumerate 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. The tool is free and publicly available at http://analysistools.nci.nih.gov/LDlink/. It aims to facilitate fine mapping of disease susceptibility regions and assist in characterizing functional variants based on genotype-phenotype associations with potential clinical utility.