tooluniverse-gwas-finemapping

Credible Sets

A credible set is a minimal set of variants that contains the causal variant with high confidence (typically 95% or 99%). Each variant in the set has a posterior probability of being causal, computed using methods like:

• SuSiE (Sum of Single Effects)
• FINEMAP (Bayesian fine-mapping)
• PAINTOR (Probabilistic Annotation INtegraTOR)

Posterior Probability

The probability that a specific variant is causal, given the GWAS data and LD structure. Higher posterior probability = more likely to be causal.

Locus-to-Gene (L2G) Predictions

L2G scores integrate multiple data types to predict which gene is affected by a variant:

• Distance to gene (closer = higher score)
• eQTL evidence (expression changes)
• Chromatin interactions (Hi-C, promoter capture)
• Functional annotations (coding variants, regulatory regions)

L2G scores range from 0 to 1, with higher scores indicating stronger gene-variant links.