Table 1. Estimated type I error rates for each association testing procedure based on 1,000 samples from the null hypothesis with no risk variants at and subjects.

Method	Implementation Details	Common Variants	Common and Rare Variants
	Small Basis Cubic Splines	0.046	0.056
		0.044	0.055
FANOVA	Large Basis Cubic Splines	0.069	0.065
		0.065	0.063
	Large Basis Penalized Splines	0.053	0.045
		0.050	0.053
FLM		0.042	0.049
		0.040	0.056
SKAT		0.045	0.044

The rows highlighted in bold report type I error rates of the procedures after SNP genotype was relabeled to minimize the number of “2-0” or “0-2” flips.