A research group at Tohoku Medical Megabank Organization (ToMMo) has successfully developed the Japonica Array which is the first ever SNP array optimized for Japanese population.
The aim of development of Japonica Array is not only to facilitate the prospective genomic cohort study conducted by ToMMo but also to make a contribution to the genomic medicine studies in Japan.

The array contains 659,253 SNPs, including tag SNPs for imputation, SNPs of Y chromosome and mitochondria, and SNPs related to previously reported genome-wide association studies and pharmacogenomics. The Japonica Array provides better imputation performance for Japanese individuals than the existing commercially available SNP arrays with both the 1KJPN^* panel and 1KGP panel (the International 1,000 genomes project).

*1KJPN：ToMMo constructed the reference panel, which contains 2,100 million single nucleotide polymorphisms (SNPs), from whole-genome sequence data of 1,070 Japanese individuals.

Article
Yosuke Kawai, Takahiro Mimori, Kaname Kojima, Naoki Nariai, Inaho Danjoh, Rumiko Saito, Jun Yasuda, Masayuki Yamamoto, Masao Nagasaki
"Japonica array: Improved genotype imputation by designing a population-specific SNP array with 1,070 Japanese individuals"
Journal of Human Genetics advance online publication, 25 June 2015; doi:10.1038/jhg.2015.68

The genotyping service of the Japonica Array is now provided by Toshiba Healthcare Company under the license from Tohoku University.
You can download the SNP list designed on Japonica Array from this website.
http://nagasakilab.csml.org/en/japonica