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Linkage Disequilibrium Proxy (LD proxy)

Definition
AI-generated

An LD proxy is a genetic variant that stands in for another variant because the two are correlated through linkage disequilibrium—often summarized by r² or D′—so association or instrument signal at one SNP partly reflects the other.

Topics
Population genetics
Related
Genome-Wide Association Study (GWAS) Horizontal Pleiotropy (MR) Instrumental Variable (IV)

Why it matters in GWAS

Lead GWAS SNPs frequently tag ungenotyped causal alleles via LD; in Mendelian randomization, correlated instruments complicate independence assumptions and motivate LD-aware clumping and sensitivity checks.

Example usage

"The exposure instrument was an LD proxy (r² > 0.8) for the published index SNP because that site was absent from the outcome study."

Genome-Wide Association Study (GWAS) Horizontal Pleiotropy (MR) Instrumental Variable (IV) LD Clumping Linkage Disequilibrium (LD) Mendelian Randomization (MR) Single Nucleotide Polymorphism (SNP)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Slatkin M. (2008). Linkage disequilibrium—understanding the evolutionary past and mapping the future. Nat Rev Genet.
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