Figure 5. Power to detect a SNP–SNP interaction effect as function of the proportion of variance explained by the interaction.

Each condition was simulated 1,000 times with 15,000 individuals. For simplicity, both SNPs were assigned the same allelic frequency (MAF) as well as the same SNP-Y β coefficient (i.e. β₁ = β₂). Upper panel: Power to identify either SNP₁ or SNP₂ as an “interacting” SNP using Levene's test with a P-value threshold of 0.05 (black), 0.01 (red) and 1.5×10⁻⁷ (green; to account for 340,000 tests using Bonferroni correction). Also shown is the power to detect the interaction itself with a linear regression interaction P-value cut-off of 4.3×10⁻¹³ (blue; chosen to account for all possible pairwise interactions between 340,000 SNPs). Lower panel: The variance per genotype is illustrated as a function of the fraction of the total variance of the quantitative trait explained by the interaction. The homozygous major allele genotype is drawn in black, the heterozygous genotype in red and the homozygous minor allele genotype in green.