The full logistic model has the form ln(P1−P)=α+β1g+β2s+β3G1+β4G2, where G1 codes genotype status at rs16969968 with a recessive model (determined from the best model analysis) and G2 codes the second SNP with the primary, log-additive model. We test for the effect of each SNP by removing it from the model and calculating the likelihood ratio chi-square with one df.
