LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.
LDhap: Calculate population specific haplotype frequencies of all haplotypes observed for a list of query SNPs. Input is a list of SNP RS numbers (one per line) and a population group.
LDmatrix: Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics. Input is a list of SNP RS numbers (one per line) and a population group.
LDpair: Investigate correlated alleles for a pair of SNPs in high LD. Input is two RS numbers and a population group.
LDproxy: Interactively explore proxy and putatively functional SNPs for a query SNP. Input is an RS number and a population group.
Mitchell Machiela in collaboration with NCI’s Center for Biomedical Informatics and Information Technology (CBIIT).
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LDlink: A web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.
Machiela MJ, Chanock SJ.
Bioinformatics. 2015 Jul 2. pii: btv402.