TogoVar is a database that integrates and organizes related information of human genome variations. TogoVar provides information on the frequency of human variations especially for Japanese population collected across research projects. We generated two original dataset, JGA-NGS (125 samples of WES (Whole Exome Sequencing) data) and JGA-SNP (18 million samples of SNP-chip data) from deposited data in our NBDC Human Database. And, we integrated 3.5KJPN data of Tohoku Medical MegaBank, HGVD data of Kyoto University as Japanese population data, and ExAC data of Broad Institute as multi-population data. TogoVar provides collected annotation information related to the variations and phenotype that has been scattered, and it contributes for interpreting the variation as a one-stop service.