Skip to content

Index Variant

Definition
AI-generated

An index variant is the representative variant used to label an association signal or locus, typically the strongest associated variant in that region after the study's selection procedure.

Topics
GWAS
Related
Lead Variant Sentinel Variant Top Variant

Why it matters in GWAS

GWAS pipelines and catalogs often need one identifier per signal for reporting, clumping, annotation, and downstream lookups. "Index variant" is a common label for that reporting anchor, even when multiple correlated variants remain plausible causal candidates.

Example usage

"We defined one index variant per locus by LD clumping and then mapped nearby genes for functional follow-up."

Lead Variant Sentinel Variant Top Variant LD Clumping Fine-Mapping
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
← Independent variable Induced Pluripotent Stem Cell (iPSC) →

Last updated (UTC · Git history)