We have released the new whole-genome reference panel with 3554 individuals of Japanese. The panel contains about qualified 37 million SNVs and about 13 million candidate SNVs. You can access the data from our integrative Japanese Genome Variation Database (iJGVD)
Tohoku University Tohoku Medical Megabank Organization
[NEWS] The locations and allele frequencies of SNVs of 3,554 Japanese individuals by whole genome sequences is available
http://www.megabank.tohoku.ac.jp/english/timeline/20170928_01/