Determination of the human genome sequence will enable analysis of one entire set of genes (genome). Single nucleotide polymorphism (SNP) is now increasingly a focus of attention because of its important role in the genetic background of common disease. In Japan, we have identified 190,000 SNPs in two years and also established high-throughput genotyping system as part of SNP projects started in 2000. Using such infrastructure, we are now advancing to the next phase: identification of common disease-related genes by genome-wide association studies.