We applied MTAG16 to variants with MAF>1% from the final meta-analysis results for each phenotype, using the other four phenotypes to increase power for locus discovery. Genomic controls and LD Intercept tests of the MTAG results were well controlled (Supplementary Table 29), and Manhattan and QQ plots well-behaved (Supplementary Figures 16 and 17). GCTA-COJO58 was used to identify conditionally independent variants (listed in Supplementary Table 12). All loci were plotted with LocusZoom, visually inspected, with suspicious loci identified (e.g., those without LD support; see Supplementary Table 30) removed from further consideration. Additional details, including testing of MTAG model assumptions, are provided in the Supplementary Note. Finally, we also applied Genomic SEM59 to our five phenotypes to formally model and factor their correlation structure. See Supplementary Figure 18, Supplementary Table 31, and the Supplementary Note for further details.
