Lead SNPs for univariate indicators and the common factors were identified using the clumping algorithm in PLINK.56 We defined LD-independent SNPs using an r2 threshold of 0.1 and a 500-kb window using the same 1000 Genomes Phase 3 reference panel used for obtaining MAF. For chromosomes 6 and 8 an additional pruning filter was used of 1Mb and r2 > 0.1 to account for long-range LD due to the MHC region and pericentric inversion, respectively. Increasing the pruning window further to 4Mb did not influence our findings on chromosome 6 or 8. The lead SNPs identified using PLINK were entered into DEPICT. Prioritized genes, enriched gene sets, and enriched tissues were identified using the standard false discovery rate of 5%.
