in PLINK (v1.90b3v) on all 1000 permuted data sets for each phenotype, and Z scores were calculated for the shuffled data in the same manner as the observed data. An empirical threshold was drawn at the 95th percentile highest-ranked Z score (an empirical α = 0.05) among the 1000 permuted sets for each phenotype, and we concluded that there was a significant enrichment of associations if the number of observed hits met or exceeded this empirical threshold. Empirical thresholds are provided in Table 2. As is evident in the Results, the permutation analyses provided a rather conservative test of enrichment.
