The MAGMA gene analysis was performed on the raw CD data using the PC regression model (MAGMA-main). Gene analyses with VEGAS and PLINK were performed using the mean SNP statistic for VEGAS and both the mean SNP statistic (PLINK-avg) and the top SNP statistic (PLINK-top) for PLINK. Pruning in PLINK was turned off for these analyses. An additional PLINK analysis using the mean SNP statistic with pruning set to its default (PLINK-prune) was performed as well.
