Table 2.

Inflation before and after principal component correction

Model	$\hat{\lambda }$without PC adjustment	$\hat{\lambda }$with PC adjustment
Single-SNP tests*	1.070	1.077
Main-effects	1.101	1.059
Main+adj	1.092	1.052
Haplotype	1.064	1.037

Comparison of inflation in median test statistics ($\hat{\lambda }$) for each model with and without principal components. *Single-SNP tests without PC adjustment were Cochran-Armitage trend statistics which are not able to incorporate PC adjustment. The single-SNP statistics with PC adjustment are the 1 d.f. logistic regression.