expected given the observed set of SNP p values in the GWAS. Gene sets required at least two signals to be tested to remove the possibility of a small gene set being deemed significantly enriched based on one signal. An important modification to the original ALIGATOR method is that significant genes in the same gene set that are less than 1 Mb apart (and thus could be explained by the same association signal) were counted as a single signal. SNPs within the boundaries of a gene (genome build 36.3) were assigned to that gene: if SNPs mapped to more than one gene, they were assigned to all such genes. Using this method, 203,663 SNPs were assigned to 14,929 genes. As before (32), the significant genes included the top 5% of all genes represented by SNPs, which was a total of 746 genes with at least one SNP (p<0.0054).
