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Lead Variant

Definition
AI-generated

A lead variant is the primary associated variant used to label an association signal or locus, typically the variant with the smallest p-value within that signal.

Topics
GWAS
Related
Sentinel Variant Top Variant Index Variant

Why it matters in GWAS

"Lead variant" is the most common formal wording in GWAS and QTL reporting. It provides a consistent anchor for locus naming, regional plots, replication checks, and downstream follow-up analyses.

Example usage

"The regional plot showed strong LD around the lead variant, but fine-mapping left multiple plausible causal candidates."

Sentinel Variant Top Variant Index Variant Regional Plot Conditional Association Analysis Linkage Disequilibrium (LD)
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

  • Uffelmann E, et al. (2021). Genome-wide association studies. Nat Rev Methods Primers. https://doi.org/10.1038/s43586-021-00056-9
  • Buniello A, et al. (2019). The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. https://doi.org/10.1093/nar/gky1120
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