One million permutations were conducted per SNP, in which case or control status was randomly assigned to an individual in the dataset, keeping the total numbers of cases and controls consistent. For each permutation, logistic regression was used to test for the association between each SNP and myocardial infarction event 1 using an additive model. To determine whether the test statistic distribution differs by allele frequency we report the number of false positive "significant" tests by MAF at α = 10-4, 10-5, or 10-6. These threshold alpha values were selected because we could expect at least one false positive by chance using one million permutations. Statistical analysis was conducted using SAS version 9.1.3 (SAS Institute, Cary, NC) on a dedicated server.
