genotyping have brought a great deal of attention to association studies for common complex diseases. The two-loci analysis was recently developed (Marchini et al, 2005) but multi-loci analyses are expected to find even stronger disease associations. Results: A novel combinatorial method for finding disease-associated multi-SNP combinations was developed. Multi-SNP combinations significantly associating with diseases were found. For Crohn's disease data (Daly, et al., 2001), a few associated multi-SNP combinations with multiple-testing-adjusted to p < 0.05 were found, while no single SNP or pair of SNPs showed significant association. For a dataset for an autoimmune disorder (Ueda, et al., 2003), a few previously unknown associated multi-SNP combinations were found. For tickborne encephalitis virus-induced disease, a multi-SNP combination within a group of genes showing a high degree of linkage disequilibrium significantly associated with the severity of the disease was found
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