We performed fine-mapping in each of the 10 selected 3Mb loci on chromosome 1 using methods based on SuSiE21, FINEMAP22,23, CAVIARBF20 and fastPAINTOR19. Following previous literature12,28 all methods used in-sample LD (i.e., summary LD information based on the genotypes of the same 337,491 individuals used to generate summary statistics), computed via LDstore28. For fastPAINTOR-, fastPAINTOR, SuSiE, and PolyFun + SuSiE, we specified a causal effect size variance using an estimator that we developed based on a modified version of HESS60 rather than using the estimator implemented in these methods, because it improved false discovery rate and power in most simulation settings (Supplementary Note, Supplementary Table 4).
