INTERSNP is a software for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). Our software product implements

• A logistic regression framework as well as log-linear models for joint analysis of multiple SNPs.
  

• Automatic handling of SNP annotation and pathway information

• Methods to account for multiple testing, in particular, Monte-Carlo simulations to judge genome-wide significance.