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LD Clumping

Definition
AI-generated

LD clumping groups variants in linkage disequilibrium around each genome-wide significant “index” SNP (typically the best p-value in the region) and retains one variant per group, yielding a non-redundant list of lead associations for reporting, follow-up, or polygenic scores.

Topics
Population genetics
URL
https://www.cog-genomics.org/plink/1.9/postproc#clump
Related
Fine-Mapping Genome-Wide Association Study (GWAS) Linkage Disequilibrium (LD)

Why it matters in GWAS

Without clumping, correlated signals inflate the apparent number of independent loci; clumping gives a clearer map of distinct association peaks and is standard in catalog-style summaries and some PRS workflows.

Example usage

"LD Clumping structure informed clumping, fine-mapping, and interpretation of nearby association peaks."

Fine-Mapping Genome-Wide Association Study (GWAS) Linkage Disequilibrium (LD) Multiple Testing Correction PLINK Polygenic Risk Score (PRS) PRS Clumping and Thresholding PRSice-2 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

  • PLINK 1.9 --clump: https://www.cog-genomics.org/plink/1.9/postproc#clump
  • PLINK 2.0 --clump: https://www.cog-genomics.org/plink/2.0/postproc#clump
← Law of segregation Linkage Disequilibrium Proxy (LD proxy) →

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