How To Use

1. Search SNVs

Go to search page (http://ijgvd.megabank.tohoku.ac.jp/search/).
The following search operations 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 maximum number of SNVs in one search operation 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:

Name Description
Position The position of genomic coordinate on the reference sequence (GRCh37/hg19).
rsID The rsid number in dbSNP database (dbsnp138).
Reference genome The version number of human genome reference. The all releases from iJGVD data are currently based on hg19 (GRCh37) coordinate.
Reference allele The nucleotide base to the reference allele.
Alternative allele The nucleotide base to the alternative allele. For the multi-allelic locus, the alternative allele base with the higher allele frequency is used.
Reference allele frequency (1KJPN) The reference allele frequency of 1KJPN to the SNV in the passed locus.
Reference allele count (1KJPN) The reference allele count of 1KJPN to the SNV in the passed locus.
Reference allele frequency (2KJPN) The reference allele frequency of 2KJPN to the SNV in the passed locus.
Reference allele count (2KJPN) The reference allele count of 2KJPN to the SNV in the passed locus.
Reference allele frequency (3.5KJPN, Passed) The reference allele frequency of 3.5KJPN to the SNV in the passed locus.
Reference allele count (3.5KJPN, Passed) The reference allele count of 3.5KJPN to the SNV in the passed locus.
Reference allele frequency (3.5KJPN, Filtered) The reference allele frequency of 3.5KJPN to the SNV in the filtered out locus.
Reference allele count (3.5KJPN, Filtered) The reference allele count of 3.5KJPN to the SNV in the filtered out locus.
Reference allele frequency (3.5KJPN, Multi-allelic) The reference allele frequency of 3.5KJPN to the SNV with the multi-allelic locus but biallelic status in 1KJPN or 2KJPN. The denominator of the reference allele frequency is the total allele count including all alternative-alleles.
Reference allele count (3.5KJPN, Multi-allelic) The reference allele count of 3.5KJPN to the SNV with the multi-allelic locus but biallelic status in 1KJPN or 2KJPN.
Alternative allele (3.5KJPN, Multi-allelic) The multi-allelic alternative nucleotide base to the reference allele. The order is sorted by allele frequencies in 3.5KJPN population. The denominator of the alternative allele frequency is the total allele count including all alternative-alleles.
Alternative allele frequency (1KJPN) The alternative allele frequency of 1KJPN to the SNV in the passed locus.
Alternative allele count (1KJPN) The alternative allele count of 1KJPN to the SNV in the passed locus.
Alternative allele frequency (2KJPN) The alternative allele frequency of 2KJPN to the SNV in the passed locus.
Alternative allele count (2KJPN) The alternative allele count of 2KJPN to the SNV in the passed locus.
Alternative allele frequency (3.5KJPN, Passed) The alternative allele frequency of 3.5KJPN to the SNV in the passed locus.
Alternative allele count (3.5KJPN, Passed) The alternative allele count of 3.5KJPN to the SNV in the passed locus.
Alternative allele frequency (3.5KJPN, Filtered) The alternative allele frequency of 3.5KJPN to the SNV in the filtered out locus.
Alternative allele count (3.5KJPN, Filtered) The alternative allele count of 3.5KJPN to the SNV in the filtered out locus.
Alternative allele frequency (3.5KJPN, Multi-allelic) The alternative allele frequency of 3.5KJPN to the SNV with the multi-allelic locus but biallelic status in 1KJPN or 2KJPN.
Alternative allele count (3.5KJPN, Multi-allelic) The alternative allele count of 3.5KJPN to the SNV with the multi-allelic locus but biallelic status in 1KJPN or 2KJPN.
Total allele count (1KJPN) The total allele count of 1KJPN to the SNV in the passed locus.
Total allele count (2KJPN) The total allele count of 2KJPN to the SNV in the passed locus.
Total allele count (3.5KJPN, Passed) The total allele count of 3.5KJPN to the SNV in the passed locus.
Total allele count (3.5KJPN, Filtered) The total allele count of 3.5KJPN to the SNV in the filtered out locus.
Total allele count (3.5KJPN, Multi-allelic) The total allele count of 3.5KJPN to the SNV with the multi-allelic locus but biallelic status in 1KJPN or 2KJPN.
Status The condition of the variant. If “passed”, the SNV is reliable in our rule. If “step1” to “step6” are given, the SNV is filtered out with the filtering rule. If “multiallelic” is given, the SNV location is multiallelic in 3.5KJPN while biallelic in 1KJPN or 2KJPN.
Gene Symbol If the target locus is in the gene body region, display the gene symbol.
Japonica Array v1 The SNP is designed in Japonica array version 1 (checked) or not. SNVs included in “Japonica array”, optimized genotyping chip for Japanese (http://nagasakilab.csml.org/en/japonica-snp-list), are indicated by “✔”
Genome Browser Link to the iJGVD genome browser.

 

3. Save data of SNVs with their frequencies

Click “Copy”, then the table will be copied to the clipbord (in your desktop machine).

Click “TSV”, then the table will be saved to your local machine within TSCSV format.

“Column visibility” can change the visible status of each column in the table. In the default setting all columns are displayed.

 

4. Passed, Filtered and Multi-allelic SNVs in 3.5KJPN

The relationship of SNVs for passed, filtered and multiallelic in 3.5KJPN are given in the schematic diagram below. We recommend to use passed SNVs as the most reliable SNV set among them. The filtered and multialleic SNVs do not guarantee the quality from the false discovery rate in the original 1KJPN paper (Nagasaki et al Nat Comm 2015).

In the iJGVD browser, the allele frequency with more than or equal to 1% can be searched for 3.5KJPN with our security policy (1KJPN and 2KJPN are 5%). The complete SNV set including rare variants can be downloaded from the download link after the approvement of the data transfer agreement.

The total SNV numbers of each panel and data accessibility are summarized.

Panel status Distributed allele frequency Data accessibility Total number of SNVs
1KJPN passed 5% or more iJGVD browser 4,301,546
1KJPN passed all frequency Text download (need DTA) 21,221,195
2KJPN passed 5% or more iJGVD browser 4,267,828
2KJPN passed all frequency Text download (need DTA) 27,997,593
3.5KJPN passed 1% or more iJGVD browser 5,914,593
3.5KJPN filtered 1% or more iJGVD browser 1,978,287
3.5KJPN multi-allelic 1% or more iJGVD browser 38,699
3.5KJPN passed all frequency Text download (need DTA) 37,067,715
3.5KJPN filtered all frequency Text download (need DTA) 12,866,823
3.5KJPN multi-allelic all frequency Text download (need DTA) 165,439

5. Filter steps in 3.5KJPN

For the SNVs matched to the filtering condition is stored as “SNV (filtered)”. The matched condition is given in the “condition” column in the searched result. The meaning of the status is summarized in the following table. The more details of each filtering step please refer to the original paper (Nagasaki et al Nat Comm 2015).

Category Total SNVs Matched SNVs Description
Step1 (Multi-allelic) 50,099,977 165,439 Multi-allelic SNVs in 3.5KJPN but bi-allelic in 1KJPN and 2KJPN.
Step2 49,934,538 1,373,119 Depth filter (in naïve call, an alternative variant is detected but disappeared with the sequence depth filter, e.g. miscall with CNV, somatic call or misalignment.)
Step3 48,561,419 2,835,609 Depth filter (more than 10% individuals does not fit into the reliable sequence depth range.)
Step4 45,725,810 6,969,032 SNVs in high repeatetive regions.
Step5 38,756,778 1,267,757 SNVs are not detected in other alignment tool and variant caller.
Step6 37,489,021 421,306 The SNVs’s hardy weinberg equilibrium is less than or equal to 0.00001.
Passed 37,067,715 13,032,262

6. Contact us

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

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