LDlink

LDlink calculates pairwise linkage disequilibrium (LD) metrics and identifies proxy single nucleotide polymorphisms (SNPs) and haplotypes across population groups using 1000 Genomes Project phase 3 haplotype data to support mapping of disease-associated loci and prioritization of putative functional variants.

Key Features:

• Reference dataset: Uses 1000 Genomes Project phase 3 haplotype data as the reference panel for analyses.
• Pairwise LD metrics: Computes pairwise linkage disequilibrium metrics between SNPs for specified population groups.
• Proxy SNP identification: Searches for proxy SNPs in high linkage disequilibrium with query variants.
• Haplotype enumeration: Enumerates all observed haplotypes within specified population groups and generates haplotype tables.
• Population-specific SNP queries: Queries single nucleotide polymorphisms (SNPs) across defined ancestral or population groups.
• Visualization outputs: Produces visualizations summarizing LD structure and haplotype distributions.
• Correlated allele linking: Links correlated alleles and highlights putative functional variants for downstream interpretation.

Scientific Applications:

• Mapping disease-associated loci: Supports identification of genomic regions and proxy variants associated with common and rare disease susceptibility.
• Functional variant prioritization: Aids prioritization of putative functional alleles by highlighting correlated variants.
• Population genetics analyses: Enables investigation of population-specific LD structure and haplotype composition.
• Haplotype-based interpretation: Facilitates interpretation of trait-associated loci by enumerating haplotypes and their allele correlations.

Methodology:

Analyses use 1000 Genomes Project phase 3 haplotype data to compute pairwise LD metrics, identify proxy SNPs in high LD, enumerate observed haplotypes, generate haplotype tables, and link correlated alleles with emphasis on putative functional variants.