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We developed a system that supports disease association studies to detect genes that may cause complex diseases. The main function of the system is to examine the possibility of each polymorphism being associated with a disease. Another important function is to perform linkage disequilibrium analysis and combine SNPs (single nucleotide polymorphisms) together into LDblocks (linkage-disequilibrium-blocks) to improve statistical power for association study. Those analyses can be efficiently performed using an analysis pipeline of the new system with handy tools for eliminating the inadequate data and so on. Consequently, the number of SNPs the system can analyze is about 30 to 50 times higher than by the standard manual procedures per unit of time. The new system also has a sophisticated visualization tool. The main viewer displays the genomic structure and is linked to another main viewer showing the in-depth analysis result. These viewers let the user easily check and make an interpretation of the results. The new system should provide significant assistance for the genome research of complex diseases.