The significance of the association of each of the five clinical phenotypes with up to 17,567 autosomal genes was tested using the versatile gene-based test for genome-wide association studies (VEGAS) approach (Liu et al., 2010). For each gene, VEGAS uses as a test statistic the sum of the individual test statistics for SNPs lying within ± 50 kb of the 5’ and 3’ UTR for that gene. To determine the significance level of the observed test statistic, a null distribution is generated using Monte Carlo methods and based on the LD structure of the SNPs within each gene as determined from a reference sample. In our case, we used as the reference the CEU HapMap sample.
