Integrative Japanese Genome Variation Database (iJGVD; http://ijgvd.megabank.tohoku.ac.jp/) provides data of genomic variations obtained by whole-genome sequencing of Japanese individuals who participate the genome cohort study of ToMMo.  The current release provides SNV frequency data obtained from the 1070 individuals. The first release contains data of about 4,300,000 SNVs selected by the criteria: (1) they are on autosomes, (2) they exist at least 5.0 % frequency in the 1070 individuals, and (3) they have been reported in dbSNP138.