In gene-gene interaction (epistasis) analysis we commonly use the co-dominant models for both the SNPs that are tested for interaction. For example in R, we can do by constructing GLM models.

disease ~ snp1 * snp2

where snp1 and 2 will have three categories (wild,heterozygous and homozygous mutant) under a co-dominant model. This interaction can be also analyzed with SNPs regrouped using other models (for example under dominant model SNPs will have only two groups). But I never came across literature where researchers explored different inheritance models for interaction analysis. I would like to hear from people who work in this. It will be helpful if you can share any related article. Thanks