New data release of SNVs for all allele frequencies from 3,554 Japanese individuals (3.5KJPN). In total, 37,067,715 qualified SNVs is released. In this release, additionally filtered out 12,866,823 SNVs and 165,439 multi-allelic SNVs but bi-allelic in 1KJPN or 2KJPN are distributed as separate data. The whole data is available upon sign and agreement with “Rules of Use” from the DOWNLOAD page. The allele frequencies more than or equal to 1% (total 7,892,880, passed 5,914,593, filtered out 1,978,287 and multi-allelic 38,699) can be explored on our iJGVD browser.