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Effect Allele

Definition
AI-generated

The effect allele is the allele whose association with the trait is reported by the signed effect in summary statistics—the allele with respect to which betas or log odds ratios are defined.

Topics
Core genetics
Related
Allele Alternative Allele Effect Size

Why it matters in GWAS

Meta-analysis, PRS, and MR require harmonizing effect direction so all cohorts use the same effect allele; flipping mistakes invert association signs.

Example usage

"We flipped summary stats so A1 always denoted the effect allele reported in column BETA."

Allele Alternative Allele Effect Size Reference Allele
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

← eCAVIAR Effect Size →

Last updated (UTC · Git history)