To facilitate the comparison, several additional SNP-wise gene-set analyses were performed in MAGMA with test-statistics matching those of PLINK-avg, PLINK-top and VEGAS: mean χ 2 (MAGMA-mean) and top χ 2 (MAGMA-top) on the raw CD data to match the two PLINK analyses, and mean χ 2 using CD SNP p-values and with either HapMap reference data (MAGMA-pval) to match VEGAS or with 1,000 Genomes reference data (MAGMA-pval-1K). The SNP summary statistics used for VEGAS and MAGMA-pval were computed using PLINK ‘--assoc’.
