We conducted single variant tests on inverse normalized phenotypes in EPACTS using EMMAX (Kang et al., 2010), which produces a genetic kinship matrix that is used to correct for population stratification and familial structure. Depending on the endophenotype, there were approximately 14 million variants with a minor allele count greater than three that were tested for association with an endophenotype, resulting in an approximate Bonferroni correction of 4 × 10−9 to obtain genome-wide significance. At this threshold, no single variant was significant. Q-Q plots and Manhattan plots for each endophenotype are available in the supporting information.
