Category Archives: Update

New data release of SNV frequency data (3.5KJPN)

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.

Maintenance

iJGVD will be unavailable in the following period due to the maintenance.

Date: Mar 21st (Mon), 2016
Time: 10:45-15:30 (Japan Standard Time)

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Maintenance

iJGVD will be unavailable in the following period due to the maintenance.

Date: Jan 29th (Fri), 2016
Time: 12:00-13:00 (Japan Standard Time)

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New feature: “Probe locations for Japonica Array”

We recently designed a genotyping chip, “Japonica Array”, which was optimized for the Japanese population (Kawai et al. 2015). The probe locations for Japonica Array on autosomes are shown in the genome browser in iJGVD. Please use “full screen view” of the genome browser, and check the box for “japonica array probe site” in the available tracks.

Publication: Yosuke Kawai, Takahiro Mimori, Kaname Kojima, Naoki Nariai, Inaho Danjo, Rumiko Saito, Jun Yasuda, Masayuki Yamamoto and Masao Nagasaki (2015) “Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals” Journal of Human Genetics (AOP)
http://www.nature.com/jhg/journal/vaop/ncurrent/full/jhg201568a.html

See also:
SNP list of Japonica array
http://nagasakilab.csml.org/en/japonica-snp-list

Maintenance

iJGVD will be unavailable in the following period due to the maintenance.

Date: May 11th (Mon), 2015
Time: 10:00-11:00 (Japan Standard Time)

We are sorry for the inconvenience.

Maintenance

iJGVD will be unavailable in the following period due to the maintenance.

Date: February 4th (Wed), 2015
Time: 10:00-12:00 (Japan Standard Time)

We are sorry for the inconvenience.