Because of its accessibility and ease of use, we recommend using FUMA to find near-independent genome-wide significant “lead SNPs”. FUMA conducts conventional linkage-disequilibrium (LD) informed pruning (“clumping”). The default settings are sensible to use in most cases. FUMA computes LD with the publicly available European subsample of the 1000 Genomes Phase 3 reference panel as the default setting (though, researchers should depart from this default to match the genetic ancestry of the summary statistics being evaluated). The default settings largely overlap with those of the original study on EXT (importantly, the LD r2 threshold of 0.1 to define lead SNPs is identical), though the original study used a larger restricted-access reference panel that combined the 1000 Genomes Phase 3 reference panel with other reference data.4.How similar are gene-property analyses when using down-sampled GWASs?
