TogoVar datasets (GRCh37)

Variant frequencies for which you can apply for use of individual-level data∗1 to the NBDC human databases∗2

Click the links at the Included controlled-access datasets to apply for use of individual-level data

Variant dataset nameAnalysis methodTarget populationHealthy subjectsAffected subjectsSample sizeNumber of variants
(# of sites)
Included controlled-access datasets
GEM Japan Whole Genome Aggregation (GEM-J WGA) PanelWGSJapanese7,60995,863,463
(90,280,248)
6 datasets
JGA-NGSWESJapanese1254,679,025
7 datasets
JGA-SNPSNP-ChipJapanese183,8841,249,7243 datasets

∗1:fastq/bam/cel files and/or lists of genotype data etc.
∗2:Japanese Genotype-phenotype Archive (JGA) / AMED Genome group sharing Database (AGD)

Other variant frequency datasets

Variant dataset nameAnalysis methodTarget populationHealthy subjectsAffected subjectsSample sizeNumber of alleles
(# of sites)
AuthorVersion/Last updated
Genome Aggregation Database (gnomAD) exomesWESMixed125,74817,209,972Broad Institutev2.1.1
Genome Aggregation Database (gnomAD) genomesWGSMixed15,708261,942,336Broad Institutev2.1.1
Human Genetic Variation Database (HGVD)WESJapanese1,208554,461
(501,556)
Kyoto UniversityVersion 2.30
(2017/08/02)
ToMMo 8.3KJPN Allele Frequency Panel(8.3KJPN)WGSJapanese8,38095,085,851
(79,359,228)
Tohoku Medical Megabank Organizationv20200831

Note: 8.3KJPN consists of SNVs (Autosome, chrX(PAR1+PAR2+XTR) and chrMT) and INDELs (Autosome and chrX(PAR1+PAR2+XTR)).

Non-variant frequency datasets

Dataset nameVersion/Last updateDescriptionAuthor
ClinVar2024/01/08Clinical significance of variantsNCBI
ColilObtained by APIInformation on citation relationships in life sciences literatureDBCLS
GRCh37.p132013/06/28Human genome reference sequenceGRC
GWAS Catalog2024/05/28Catalog of human genome-wide association studiesNHGRI-EBI
HGNC symbol report2024/05/28Approved human gene nomenclature and associated gene informationHGNC
LitVarObtained by APIInformation on papers in which the names of variants appearNCBI
PubMed2024/04/26Information on papersNCBI
PubTator Central2024/01/04Information on papers in which the names of variants appearNCBI

Note: TogoVar obtained ClinVar variants from the VCF filethat contains only variants for which GRCh37 positions were determined.

Tools for data processing

NameVer.DescriptionAuthor
bcftoolsSplit multiallelic sites into biallelic variantsGenome Research Ltd.
BioReTExecute programs for variant discovery from NGS data in proper orderAmelieff
Variant Effect Predictor (VEP)Ensembl release 110Add annotations like gene names, consequences or deleterious predictions (AlphaMissense, SIFT and Polyphen) to variantsEMBL-EBI