JSNP

2023/06/29

Web Site: (Closed) http://snp.ims.u-tokyo.ac.jp/index.html
Note: http://biosciencedbc.jp/moved-jsnp-biosciencedbc-jp
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/jsnp/

A database of about 197,000 polymorphisms in Japanese population, with annotations such as genes, positions, amino acid substitutions

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Polymorphism Sequence
  3. Allele Frequency
  4. Screening Information
  5. Mapping Information
  6. Integrated List
  7. Flat Files
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "JSNP" data.
File README_e.html (English)
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2.2 Polymorphism Sequence

Data name Polymorphism Sequence
Description of data contents

Information on polymorphisms (SNPs and insertions/deletions) and their flanking sequences

Derived from "Flat files" ftp://ftp.hgc.jp/pub/hgc/db/snp/imsSNP140508.fas and ftp://ftp.hgc.jp/pub/hgc/db/snp/imsIND140508.fas
File jsnp_seq.zip (10.6 MB)

Data items are the following:
Data itemDescription
Database Name

database name

JSNP_SNP: single nucleotide polymorphism

JSNP_InsDel_IND: insertion/deletion

JSNP_InsDel_MIC: microsatelite
JSNP ID

JSNP ID

ID starting with IMS-JST: from IMS and JST

ID starting with ssj: from RIKEN SNP Research Center or from Tokyo Women's Medical University
Allele Frequency (only in SimpleSearch pages) link to Allele Frequency of the same JSNP ID
Screening Information (only in SimpleSearch pages) link to Screening Information of the same JSNP ID
Mapping Information (only in SimpleSearch pages) link to Mapping Information of the same JSNP ID
Integrated List (only in SimpleSearch pages) link to Integrated List of the same JSNP ID
dbSNP ss# dbSNP ss (submitted SNP) number assigned
dbSNP rs# dbSNP rs (reference SNP) number assigned
5' Flanking Sequence 5' flanking sequence
Observed allele observed
3' Flanking Sequence 3' flanking sequence
Offset in Flanking Sequence position of the polymorphism in the flanking sequence
Total Length total length of the flanking sequence
Accession No. accession No. of the sequence for polymorphism screening
Offset in Record position of the polymorphism in the sequence for polymorphism screening
Comment Type

1: the polymorphism overlaps with a repetitive sequence

2: the flanking sequence overlaps with a repetitive sequence
Gene Symbol

gene where the polymorphism is found

(information from LocusLink, GenBank and Unigene)
JSNP previous ID

JSNP previous ID

(IDs of IMS-JST104817 to IMS-JST105472 and IMS-JST075266 to IMS-JST075585 are reassigned with ssj IDs)
JSNP reference ID

JSNP reference ID

(where multiple JSNP IDs are assigned to the same polymorphism)
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2.3 Allele Frequency

Data name Allele Frequency
Description of data contents

Polymorphism allele frequencies in Japanese.
Out of 84651 polymorphisms, 13 and 39 SNPs are assayed in three (POP_*) and two (RIKEN_japanese_*) panels, respectively.

Derived from "Flat files" ftp://ftp.hgc.jp/pub/hgc/db/snp/alleleFreq140508.txt
File jsnp_allele_freq.zip (1.4 MB)

Data items are the following:
Data itemDescription
JSNP ID JSNP ID
Panel_ID ID of the pool of Japanese individuals where the frequency was examined
  • JBIC-allele - 752 anonymous unrelated Japanese volunteers
  • RIKEN-allele - 893 anonymous unrelated Japanese volunteers
  • POP_102 - 144 unrelated Japanese volunteers with rheumatoid arthritis under informed consent
  • POP_103 - 16 unrelated Japanese volunteers with adult-onset Still's disease under informed consent
  • POP_104 - 92 healthy unrelated Japanese volunteers under informed consent
  • RIKEN_japanese_normal_weight - 711 unrelated japanese normal weight volunteers ( body mass index <= 25kg/m2 )
  • RIKEN_japanese_obese - 796 unrelated japanese obese patients ( body mass index >= 30kg/m2 )
dbSNP ss# dbSNP ss (submitted SNP) number assigned
dbSNP rs# dbSNP rs (reference SNP) number assigned
allele-1 allele-1
allele-2 allele-2
allele-1 frequency allele-1 frequency
allele-2 frequency allele-2 frequency
the number of chromosomes examined the number of chromosomes where the frequency was examined (sample size)
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2.4 Screening Information

Data name Screening Information
Description of data contents

Information from polymorphism screening experiments.

Derived from "Each Type of variation Found in Location in Gene" in "Data Contributions" http://snp.ims.u-tokyo.ac.jp/data_roots.html .
File jsnp_screen.zip (15.6 MB)

Data items are the following:
Data itemDescription
JSNP ID JSNP ID
In Gene type of gene region where the polymorphism
  • promoter*1: annotated in GenBank entries
  • promoter*2: predicted by GENSCAN
  • promoter*3: putative promoter (1.5kb upstream of the initiation position of mRNA records in the RefSeq)
  • CDS*1: annotated in GenBank entries either positively or passively
  • CDS*2: predicted by GENSCAN
  • CDS*3: extracted by homology search with cDNA
  • exon*1: annotated in GenBank entries either positively or passively
  • exon*3: extracted by homology search with mRNA/cDNA/Unigene records
  • intron*1: annotated in GenBank entries or intervened by Exon*1 and CDS*1
  • intron*2: intervened by CDS*2
  • intron*3: intervened by exon*3 and CDS*3
  • others: surrounding regions of genes
Type type of polymorphisms
  • SNP: single nucleotide polymorphism
  • IND: insertion/deletion
  • MIC: microsatelite
Frequencies minor allele frequencies in dbSNP; number in brackets means JSNP original allele frequency
allele allele observed
dbSNP ss# dbSNP ss (submitted SNP) number assigned
dbSNP rs# dbSNP rs (reference SNP) number assigned
HGVbase-ID ID in HGCbase
5' assay 5' flanking sequence
3' assay 3' flanking sequence
Screened Accession accession No. of the sequence for polymorphism screening
Screened Position position of the polymorphism in the sequence for polymorphism screening
Screened Symbol gene name related to the sequence for polymorphism screening
Screened OMIM-ID OMIM ID related to the sequence for polymorphism screening
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2.5 Mapping Information

Data name Mapping Information
Description of data contents

Information from mapping polymorphisms on the genome.

Derived from "Dump JSNP" http://snp.ims.u-tokyo.ac.jp/map/cgi-bin/Dump/snp_region_filter.cgi .
File jsnp_dump.zip (24 MB)

Data items are the following:
Data itemDescription
snp_id ID of JSNP
snp_type snp type: SNP or IND (insertion/deletion)
5_flank_seq 5'-flanking sequence of the snp
na_var nucleic acids variation
3_flank_seq 3'-flanking sequence of the snp
for_primer forward primer sequence for e-PCR
back_primer backward primer sequence
product_size PCR product size
freq_minor minor allele frequency of the snp (-1: no frequency information) from JSNP
freq_major major allele frequency of the snp from JSNP
chr chromosome number that the snp is mapped
chr_start start position of the snp in the chromosome
chr_end end position of the snp in the chromosome
chr_direct direction of the flanking sequences against the chromosome
contig_acc ACC of genomic contig (RefSeq NT) that the snp is mapped
contig_start start position of the snp in the genomic contig
contig_end end position of the snp in the genomic contig
contig_direct direction of the flanking sequences against the genomic contig
hit_count number of hit (mapped positions of the snp against genome)
gene_na_acc ACC of a gene (RefSeq NM/XM) that the snp is mapped
gene_aa_acc ACC of the gene (RefSeq NP/XP) that the snp is mapped
symbol symbol of gene that the snp is mapped
locus_id ID of gene (LocusLink) that the snp is mapped
gene_direct

direction of the flanking sequences against the direction of the gene:

if the directions of the flanking sequences and of the gene are the same, this is "+"; otherwise "-".
str_type gene structure that the snp is mapped: CDS, exon, intron, 5'-UTR, 3'-UTR
aa_var amino acids variation
codon_var codon variation
codon_posi snp postion in the codon
dbsnp_rs_id dbSNP rs (reference SNP) number assigned
dbsnp_ss_id dbSNP ss (submitted SNP) number assigned
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2.6 Integrated List

Data name Integrated List
Description of data contents

List of  data from "Mapping Information" and "Screening Information" put together every polymorphism (unless the polymorphism is mapped on two or more chromosomes).

Derived from "Show List by Chromosome" of "Show List of SNPs" http://snp.ims.u-tokyo.ac.jp/search_list.html .
File jsnp_list.zip (17.9 MB)

Data items are the following:
Data itemDescription
JSNP ID JSNP ID
Chromosome Chromosome number
Location cytogenetic band
Evidence of Location

information source of cytogenic band

- GenBank "/chromosome" and "/map"

- EntrezGene "CHR" and "MAP"

- UniGene "CHROMOSOME" and "CYTOBAND"
In Gene Type of gene region
  • promoter*1: Annotated in GenBank entries
  • promoter*2: Predicted by GENSCAN
  • promoter*3: Putative promoter (1.5kb upstream of the initiation position of mRNA records in the RefSeq)
  • CDS*1: Annotated in GenBank entries either positively or passively
  • CDS*2: Predicted by GENSCAN
  • CDS*3: Extracted by homology search with cDNA
  • exon*1: Annotated in GenBank entries either positively or passively
  • exon*3: Extracted by homology search with mRNA/cDNA/Unigene records
  • intron*1: Annotated in GenBank entries or intervened by Exon*1 and CDS*1
  • intron*2: Intervened by CDS*2
  • intron*3: Intervened by exon*3 and CDS*3
  • others: surrounding regions of genes
Type type of polymorphisms
  • SNP: single nucleotide polymorphism
  • IND: insertion/deletion
  • MIC: microsatelite
Frequencies minor allele frequencies in dbSNP, number in brackets means JSNP original allele frequency
allele allele observed
dbSNP ss# dbSNP ss (submitted SNP) number assigned
dbSNP rs# dbSNP rs (reference SNP) number assigned
HGVBase-ID ID in HGCbase
5' assay 5' flanking sequence
3' assay 3' flanking sequence
Mapping Accession accession No. of the mapped sequence
Mapping Position position of the polymorphism in the mapped sequence
Mapping Symbol gene name relevant to the mapped sequence
Mapping OMIM-ID OMIM ID relevant to the mapped sequence
Screened Accession accession No. of the sequence for polymorphism screening
Screened Position position of the polymorphism in the sequence for polymorphism screening
Screened Symbol gene name relevant to the sequence for polymorphism screening
Screened OMIM-ID OMIM ID relevant to the sequence for polymorphism screening
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2.7 Flat Files

Data name Flat Files
Description of data contents

Information on polymorphisms (SNPs and insertions/deletions) and their flanking sequences, and polymorphism allele frequencies in Japanese.

Provided as "Flat files" ftp://ftp.hgc.jp/pub/hgc/db/snp/ .
File jsnp_flat_files (128 MB)
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3. License

Last updated : 2023/06/29

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

 

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "JSNP © The University of Tokyo and Japan Science and Technology Agency (JST) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

https://form2.jst.go.jp/s/contact_nbdc

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2016/12/06 Description of the original site (http://snp.ims.u-tokyo.ac.jp/index.html) is updated.
2016/02/01 JSNP English archive site is opened.
2000/07/07 JSNP (http://snp.ims.u-tokyo.ac.jp/index.html) is opened.
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5. Literature

Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y.
JSNP: a database of common gene variations in the Japanese population
Nucleic Acids Research, 30:158-162, 2002
PMID: 11752280

Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T.
Gene-based SNP discovery as part of the Japanese Millennium Genome Project : identification of 190,562 genetic variations in the human genome.
Journal of Human Genetics, 2002;47(11):605-610
PMID: 12436197

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6. Contact address

When you have any question about "JSNP", contact the following:

https://form2.jst.go.jp/s/contact_nbdc

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