I’m curious about the basis on which you are assigning a probability of causality without a method like mendelian randomisation, or something that tries to assign a probability of an effect based on interpreting the biology like a coding of the output of something like SnpEff to an approximate probability of effect.
Using finemapping. I.e. assuming a model where nonzero additive effects are sparsely distributed among SNPs, you can do Bayesian math to infer how probable each SNP is to have a nonzero effect and its expected effect size conditional on observed GWAS results. Things like SnpEff can further help by giving you a better prior.
Using finemapping. I.e. assuming a model where nonzero additive effects are sparsely distributed among SNPs, you can do Bayesian math to infer how probable each SNP is to have a nonzero effect and its expected effect size conditional on observed GWAS results. Things like SnpEff can further help by giving you a better prior.
(For people reading this thread who want an intro to finemapping this lecture is a great place to start for a high level overview https://www.youtube.com/watch?v=pglYf7wocSI)