We used KGG 2.5 [37, 38] to conduct gene-based tests of GWAS results. We used publicly available 1000 Genomes Phase 1 Version 3 (European subsample) linkage disequilibrium (LD) files to build the “analysis genome” by position, for autosomes only. We included extended gene lengths of 5kb at the 5’ and 3’ ends. SNPs in high LD (r2>.9) were considered connected; those in low LD (r2<.02) were considered independent. We used the HYST test option. A Benjamini and Hochberg [39] false discovery rate (FDR) of 0.05 was used, and q-values are reported where appropriate.
