A haplotype map database by using validated single nucleotide polymorphism (SNP) information for the world and Japanese rice collections. The association of SNP allele frequencies with quantitative trait loci (QTLs) and functionally characterized genes could be clarified by using two other databases, Q-TARO and OGRO, constructed on the same platform. The allele frequency of each SNP can be visualized in the SNP genome browser similar to the human HapMap database. To obtain information on SNPs in any genomic region and to design cleaved amplified polymorphic sequence (CAPS) markers, we also constructed a tool for SNP searches and design of primer pairs. We also provide information for a core set of 768 SNPs selected for the analysis of genetic diversity and QTL mapping in the world rice collection.