How To Use

1. Search SNVs

Go to search page (http://ijgvd.megabank.tohoku.ac.jp/).
The following search methods are available.

1-1. Search by gene symbol

Enter any gene symbol for human genes in the box, such as “ALDH2”, then click “Search” button.
The gene symbols in this database are according to HGNC (http://www.genenames.org/) .
For example, when you want to get SNVs of “NRF2” gene, “NFE2L2” is the approved gene symbol.

1-2. Search by rsSNP ID

Enter rs SNP ID of dbSNP (http://www.ncbi.nlm.nih.gov/SNP/) in the box, such as “rs671”,
then click “Search” button. You can inquire the genetic polymorphisms of your interest in dbSNP and get their IDs.

1-3. Search by genomic region

Specify chromosome and the genomic coordinate range, e.g., 23444-44455.
The number of SNVs in output is limited to 1000.

1-4. Jump to chromosome on the browser

Click chromosome number at the bottom of “Search page”.

 

2. Look for the details of SNV

SNV data is provided as follows:

Position: position of genomic coordinate on the reference sequence (GRCh37/hg19).
Reference allele: nucleotide base on the reference sequence.
Alternative allele: nucleotide base that differs from the reference sequence.
Allele frequency: Proportion of reference or alternative allele among the total alleles for the subjects.

Allele count: Count for reference or alternative allele in the subjects.
Japonica array: SNVs included in “Japonica array”, a newly developed genotyping chip (http://nagasakilab.csml.org/en/japonica-snp-list), are indidated by “✔”. 

 

3. Save data of SNVs with their frequencies

Click “Download Table”, then the table will be saved in CSV format.

 

4. Contact us

Please send e-mails to the following address:
ijgvdATig-nagalabDOTmegabankDOTtohokuDOTacDOTjp
(Please replace “AT” with “@” and “DOT” with “.”)

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