Estimated type I error probability for test of deviation from HWP of SNP₄, a SNP unassociated with secondary phenotype and primary disease (MAF = 10%), at 0.05 and 0.0001 significance levels in simulation studies^* using different approaches for HWP testing.

*Simulation studies were based on 1,000,000 replicates, each replicate with 2,000 cases in terms of primary disease and 2,000 controls frequency-matched on secondary phenotype. MAF: minor allele frequency. LRT_t: LRT approach, using presence and absence of secondary phenotype as cases and controls. mHWP_t: mHWP exact test, using presence and absence of secondary phenotype as cases and controls. LRT_d: LRT approach, using presence and absence of primary disease as cases and controls. mHWP_d: mHWP exact test, using presence and absence of primary disease as cases and controls. eLRT: extended LRT approach. emHWP: extended mHWP exact test. : prevalence of primary disease in general population. : prevalence of secondary phenotype in general population.