Fig. 3: Brisbane plot showing signal density and levels of pleiotropy of 2,293 genome-wide significant loci identified by fastASSET analysis across 116 traits.

We define significant SNPs as those that have fastASSET p-value \( < \, 5\times {10}^{-8}\) (two-sided) and clump them to obtain 10,628 independent SNPs (\({r}^{2} \, < \, 0.1\)), which we then group into 2293 loci whose lead SNPs (strongest association within a locus) are at least 500 kb apart. Each dot represents the lead SNP of a locus, and the y axis is the number of independent significant SNPs within 100 kb from the lead SNP. In a dots are colored by the number of traits associated with the lead SNP as reported by fastASSET. In b–e dots are colored by the proportion of significant SNPs in a locus (within 100 kb from the lead SNP) that fall into each category of pleiotropy. b Color represents proportion of significant SNPs that are trait-specific (associated with 1 trait). c Color represents proportion of significant SNPs that are associated with 2–5 traits. d Color represents proportion of significant SNPs that are associated with 6–10 traits. e Color represents proportion of significant SNPs that are associated with > 10 traits. Nearly half (1094) of the loci harbor at least two independent genome-wide significant SNPs within 100 kb of the lead SNP (including the lead SNP itself); 248 (11%) loci harbor at least 5 significant SNPs within 100 kb of the lead SNP. See Supplementary Data 6 for details.