Type I error rates for HIPO observed in datasets simulated under covariance structure estimated from studies of blood lipids.

See S1 Table 1a and 1b for detailed settings. Summary-level association statistics are simulated for 4 traits using genetic and phenotypic covariance matrices estimated from Global Lipids Genetics Consortium (GLGC) data, with and without population stratification. The results for HIPO-D1 and the most heritable trait are listed. Reported are the average of genome-wide type I error rates across 100 simulations, under significance thresholds p<0.05, p<0.01 and p<0.001.