PolyFun specifies prior causal probabilities in proportion to per-SNP heritability estimates: (1)P(βi≠0|ai)∝var[βi|ai], where βi is the causal effect size of SNP i in standardized units (the number of standard deviations increase in phenotype per 1 standard deviation increase in genotype), ai is the vector of functional annotations of SNP i, and var[βi|ai] is the estimated per-SNP heritability of SNP i from step 4 (Methods).
