Table 3. Null simulation: empirical per-SNP type-I error rates from 1,000 permutations of case-control labels of 2 K individuals genotyped at 80 K SNPs.

Method	Error rate (per million SNPs)
	Additive only	Additive, dominant and recessive terms
NEG	6.44	12.8
DE	6.39	12.7
ATT	6.48	-

In each case the nominal per-SNP type-I error rate for the additive-only model was 10⁻⁵ ( = 10 per million SNPs).