Permutation tests were conducted for all genes yielding at least 1 P-value <0.001, as well as for genes which yielded at least two SNPs with P-values <0.01, with an r2 <0.8 between those SNPs. This approach captured genes with single associated SNPs or genes with converging evidence for association from multiple SNPs. To take into account the LD structure across SNPs in a gene, Plink begins with the most significant SNP in the gene, removes SNPs with r2 >0.80, and continues this process for all SNPs with P <0.05 to obtain an independent group of associated SNPs. The P-value associated with the average test statistic across the remaining SNPs is compared across 10,000 permutation runs, yielding an empirical P-value for the gene based on the independent, significant SNPs observed in the gene.
