Nature Reviews Genetics just published an excellent paper on interaction analysis by Heather Cordell. This masterfully written review starts by defining interaction, then delving into strategies to statistically model it in human genetics studies. She covers several regression-based procedures, Bayesian approaches, data-mining methods, and other related techniques, referring the reader to the pertinent publications and software (usually free) available to perform these analyses. The review wraps up with a discussion of the biological interpretation of statistical models of interaction.
Genome-wide association studies: Detecting gene–gene interactions that underlie human diseases (NRG Advance Online)