Datasets | TogoVar

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

∗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 datasets

Variant dataset name Analysis method Liftover GRCh37 Target population Healthy subjects Affected subjects Sample size Number of alleles Author Version/Last updated
ClinVar Mixed 1,117,487 NCBI 2022/09/01
Genome Aggregation Database (gnomAD) genomes WGS Mixed 76,156 759,302,267 Broad Institute v3.1.2
Human Genetic Variation Database (HGVD) WES Japanese 1,208 549,623 Kyoto University Version 2.30
(2017/08/02)
ToMMo 14KJPN Allele Frequency Panel(14KJPN) WGS Japanese approx. 14,000 133,757,499 Tohoku Medical Megabank Organization v20211208r2

Note 1: TogoVar contains ClinVar variants only in the VCF file, GRCh38 positions of which were determined.
Note 2 : 14KJPN consists of SNVs (Autosome, chrX(PAR1+PAR2+XTR) and chrMT) and INDELs (Autosome and chrX(PAR1+PAR2+XTR)).

Non-variant datasets

Dataset name Version/Last update Description Author
Colil Obtained by API Information on citation relationships in life sciences literature DBCLS
GRCh38.p13 2019/3/1 Human genome reference sequence GRC
HGNC symbol report 2022/9/16 Approved human gene nomenclature and associated gene information HGNC
LitVar Obtained by API Information on papers in which the names of variants appear NCBI
PubTator Central 2022/9/20 Information on papers in which the names of variants appear NCBI
TogoGenome Comprehensive information on genomes DBCLS

Tools for data processing

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