BLAT Genome
JSNP Database Release Notes JSNP Database Release NotesChanges in Release 40
The Integrated mapping information is based on NCBI's build 37 version 3, Ensembl Human release 65 and rs number of dbSNP build135.
The rs number and the allele frequency information according to NCBI's dbSNP build 135 have been available.
Changes in Release 39
The Integrated mapping information is based on NCBI's build 37 version 2, Ensembl Human release 63 and rs number of dbSNP build134.
The rs number and the allele frequency information according to NCBI's dbSNP build 134 have been available.
Changes in Release 38
The Integrated mapping information is based on NCBI's build 37 version 1, Ensembl Human release 59 and rs number of dbSNP build131.
The rs number and the allele frequency information according to NCBI's dbSNP build 131 have been available.
Changes in Release 37
The Integrated mapping information is based on NCBI's build 37 version 1, Ensembl Human release 56 and rs number of dbSNP build130.
The rs number and the allele frequency information according to NCBI's dbSNP build 130 have been available.
XML files based on Screened information and XML files for data related to PCR region for primer design have been updated.
Changes in Release 36
The Integrated mapping information is based on NCBI's build 36 version 3, Ensembl Human release 54 and rs number of dbSNP build130.
The rs number and the allele frequency information according to NCBI's dbSNP build 130 have been available.
Changes in Release 35
The Integrated mapping information is based on NCBI's build 36 version 3, Ensembl Human release 50 and rs number of dbSNP build129.
The rs number and the allele frequency information according to NCBI's dbSNP build 129 have been available.
The threshold of mapping SNPs to genome sequence has been changed, the number of SNPs unmapped has been decreased.
Changes in Release 34
The genotypic datasets are released on "Genotype data summary".
The genotypic datasets are released on "Genotype data summary".
These datasets are the genotypic data of 191-195 Japanese samples from each of 35 diseases.
Each dataset provides almost 200,000 SNPs in autosomal chromosomes with genotyping information without individual genotype data.
Changes in Release 33
5 allele data by the SNP Research Center, RIKEN have been added, listed here.
SCG3 gene polymorphisms with genotype frequency information have been added, listed here.
The Integrated mapping information is based on NCBI's build 36 version 3, Ensembl Human release 49 and rs number of dbSNP build128.
The rs number and the allele frequency information according to NCBI's dbSNP build 128 have been available.
"Dump JSNP with XQuery" has been closed.
Changes in Release 32
The JSNP550typed is released. This new dataset consists of 515,286 SNPs with genotyping information participated by 934 Japanese volunteers.
The Integrated Maps provides a new track for JSNP550typed.
The Integrated mapping information is based on NCBI's build 36 version 2, Ensembl Human release 44 and rs number of dbSNP build127.
Changes in Release 31
6 allele frequency data by the SNP Research Center, RIKEN have been added, listed here.
The Integrated mapping information is based on NCBI's build 36 version 2, Ensembl Human release 44 and rs number of dbSNP build127.
The rs number and the allele frequency information according to NCBI's dbSNP build 127 have been available.
Changes in Release 30
'Search Genes' is available on the home page.
The Integrated mapping information is based on NCBI's build 36 version 2 reference and rs number of dbSNP build126.
Changes in Release 29
Links to related OMIM phenotype ID have been added.
The DrugBank information has been added and it is available to search using "Generic Name" of the drug.
Types of variations found in location in gene are shown.
The Integrated mapping information is based on NCBI's build 36 version 1 reference and rs number of dbSNP build126.
Changes in Release 28
The integrated map displays annotations on NCBI's build 36 version 1 of the human genome.
Statistics of Mapping Information on NCBI's build 36 version 1 of the human genome have been released.
The SNPs discovered by the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN) have been available to search and added in the ftp files.
"Dump JSNP with XQuery" has been available.
Changes in Release 27
ssID numbers from dbSNP database have been added to the new data of the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN).
The Locus Information has links to related mutation databases. The list of these databases is here. Links to HapMap and JMDBase have been added to the SNP Information.
The positions in GenBank sequences in a subset of deletion were amended in the ftp files and the XML files based on Screened information. The lists of these entries were posted in each file server.
Changes in Release 26
The SNPs discovered by the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN) have been available to search and added in the ftp files. These data have also been listed in SNPs 'in genes encoding a drug-metabolizing enzyme'. The number of these variations is 2,000.
The Integrated mapping information is based on NCBI's build 35 version 1 reference and rs number of dbSNP build125.
Changes in Release 25
Interleukin-18 gene polymorphisms with genotype frequency information have been added.
The allele frequency flat file's name and its data format have been changed.
Changes in Release 24
The allele frequency information in NCBI's dbSNP build 124 has been added to Allele Frequency Information.
Changes in Release 23
The integrated map displays annotations on NCBI's build 35 version 1 reference of the human genome.
Statistics of Mapping Information on NCBI's build 35 version 1 reference of the human genome have been released.
The allele frequency information in NCBI's dbSNP build 123 has been added to Allele Frequency Information.
The SNPs discovered by the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN) have been available to search and added in the ftp files. These data have also been listed in SNPs 'in genes encoding a drug-metabolizing enzyme'. The number of these variations is 5,608.
On the SNPs discovered by RIKEN, it is available to search using the GeneSymbol or the Accession and to display the GeneSymbol.
Search option to narrow down to the results with the OMIM ID has been available.
The 'Site map' is available.
Changes in Release 22
The allele frequency information in NCBI's dbSNP build 122 has been added to Allele Frequency Information.
The genotype frequency information in HapMap Project database has been added to Allele Frequency Information.
The integrated map has been enhanced. It is available to search and display the motif information related to JSNPs and dbSNP's rs_SNPs.
'Dump JSNP' has been available to search and get the JSNPs' or genes' list with many various related features in various formats.
Search help in detail has been provided in English.
Changes in Release 21
The integrated map displays annotations on NCBI's build 34 version 3 of the human genome.
Statistics of Mapping Information on NCBI's build 34 version 3 of the human genome have been released.
The allele frequency information in NCBI's dbSNP build 120 has been added to Allele Frequency Information.
The allele frequency in NCBI's dbSNP added to JSNP is available to search.
Display/Download option is available to select display fields of the extracted data and download them in Comma Separated Values(CSV) format.
Search help and Integrated Map's help are provided in Japanese.
Changes in Release 20
The integrated map displays annotations on NCBI's build 34 version 2 of the human genome.
Statistics of Mapping Information on NCBI's build 34 version 2 of the human genome have been released.
The allele frequency information in NCBI's dbSNP build 119 has been added to Allele Frequency Information.
Changes in Release 19
The integrated map displays annotations on NCBI's build 34 of the human genome.
Statistics of Mapping Information on NCBI's build 34 of the human genome have been released.
6 allele frequency data have been added, listed here.
The allele frequency information in NCBI's dbSNP build 117 has been added to Allele Frequency Information.
Changes in Release 18
The integrated map displays annotations on NCBI's build 33 of the human genome.
Statistics of Mapping Information on NCBI's build 33 of the human genome have been released.
3 allele frequency data have been added, listed here.
The allele frequency information in NCBI's dbSNP build 115 has been added to Allele Frequency Information.
Changes in Release 17
The integrated map displays annotations on NCBI's build 32 of the human genome.
Statistics of Mapping Information on NCBI's build 32 of the human genome have been released.
The allele frequency information in NCBI's dbSNP build 113 has been added to Allele Frequency Information.
XML filesXML files of SNP Information have been released.
The SNPs discovered by the Laboratory for Genotyping, the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN) have been available to search and added in the ftp files. These data have also been listed in SNPs 'in genes encoding a drug-metabolizing enzyme'. The number of these variations is 5,533.
Allele Frequency Information contributed by RIKEN has been added.
638 previously released entries have been amended, listed here.
The relation among existing JSNP entries has been added in 'reference ID'. We screened all newly submitted variations against existing JSNP entries to find the relations among them by blast homology between the flanking sequences. The number of the relations is 1,405 in the 17th data release.
Changes in Release 16
The integrated map displays annotations on NCBI's build 31 of the human genome.
ssID and rsID number from dbSNP database have been added to the data of the Laboratory for Genotyping, the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN).
Statistics of Mapping Information on NCBI's build 31 of the human genome have been released.
The relation among existing JSNP entries has been added in 'reference ID'. We screened all newly submitted variations against existing JSNP entries to find the relations among them by blast homology between the flanking sequences. The number of the relations is 1,256 in the 16th data release.
The new search option 'Search Genes' has been available to get a list of JSNP's variations mapped to the query gene with many various features of the gene.
'BLAT Genome' has been available to get a map with JSNP's variaions and a letter-by-letter alignment of the query sequence to the human genome.
Changes in Release 15
ssID number and rsID number from dbSNP database and Mapping Information have been added to the data of the Laboratory for Genotyping, the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN).
Statistics of Mapping Information have been added.
Changes in Release 14
60 previously released entries have been withdrawn, listed here.
JSNP ID numbers of 5 allele frequency data have been amended, listed here.
The SNPs discovered by the Laboratory for Genotyping,the SNP Research Center, the Institute of Physical and Chemical Research(RIKEN) have been available to search and added in the ftp files. These data have also been listed in SNPs 'in genes encoding a drug-metabolizing enzyme'. The number of these variations is 4,867.
The relation among existing JSNP entries has been added in 'reference ID'.We screened all newly submitted variations against existing JSNP entries to find the relations among them by blast homology between the flanking sequences.The number of the relations is 1,252 in the 14th data release.
5'UTR and 3'UTR as position in gene for searching JSNP database have been available.
Search option to narrow down to the results with nonsynonymous amino acid substitution has been available.
The integrated map displays annotations on NCBI's build 30 of the human genome.
Changes in Release 13
The search option to the mapping information has been extended
The new JSNP ID form starting from ssj has been added for the variation data submitted to JSNP database.
The SNPs discovered by the Laboratory for Genotyping,the SNP Research Center, the Institute of Physical and Chemical Research(RIKEN) have been available to search and added in the ftp files. These data have also been listed in SNPs 'in genes encoding a drug-metabolizing enzyme'. The number of these variations is 3,451.
JSNP ID number IMS-JST075266-075585 and IMS-JST104817-105472 consisting of 976 SNPs submitted by RIKEN have been replaced with ssj form ID, listed here. And due to the change of JSNP ID number, the contents of Screened Sequence (Accession No. & Position in Sequence) in SNP information page have been also changed.
The relation among existing JSNP entries has been added in 'reference ID'.We screened all newly submitted variations against existing JSNP entries to find the relations among them by blast homology between the flanking sequences.The number of the relations is 848 in the 13th data release.
The integrated map displays annotations on NCBI's build 30 of the human genome.
Changes in Release 12
The SNPs discovered by the laboratory for Genotyping, the SNP Research Center, RIKEN have been added in the list of 'in genes encoding a drug-metabolizing enzyme'. The number of these data is 3,451.
The integrated map displays annotations on NCBI's build 30 of the human genome.
Changes in Release 11
The allele frequency flat file has been added in FTP server.
The allele frequency of 106 entries were amended because of reexamination, listed here.
The reverse outputs by computed error in allele frequency of 1,259 entries were amended, listed here.
The allele frequency information of IMS-JST000487 was amended.
The observed allele of IMS-JST026852 was amended.
Changes in Release 10
Gene and amino acid substitution information derived from Integrated Map has been added in SNP information page.
A view of SNP position on the NCBI contig sequence has been added. It also shows the gene information and repeat sequence position.
Difference between the JSNP screened sequence and the NCBI contig has been added.
Search option to narrow down to the results with allele frequency has been available.
Changes in Release 9
Allele Frequency Information contributed by JBIC has been added.The "list up genes in Access Map" bar in a Chromosome Integrated Map provides the link to a View of the conceptual amino acid translation for the gene or EST of interest.
List by Official gene symbol is improved.
The positions in GenBank sequences of 101 entries were amended, listed here.
Changes in Release 8
Integrated Maps which display mapping data from JSNP and public resources including dbSNP, UniSTS, UniGene, Model mRNA (XM_nnnnnn) derived from NCBI Genome Annotation on NCBI Genomic Contig have been released.Integrated Mapping Information search is available to make free text queries against marker name, marker alias, gene symbol, UniGene cluster ID(Hs.nnnnn), Model mRNA RefSeq(XM_nnnnnn) and UniSTS ID.
Integrated Mapping Information is added to a SNP information page.
Changes in Release 7
Microsatellite variations extracted from ins/del variations using trf and tandyman have been released.Keyword search is available to make queries against dbSNP ss number, dbSNP rs number and HGBASE ID whose SNP has been already deposited in dbSNP or HGBASE. FTP data format is changed by adding dbSNP IDs.
Changes in Release 6
Laboratory for Genotyping, The SNP Research Center, RIKEN has contributed to SNPs in genes encoding a drug-metabolizing enzyme.A snp was withdrawn from the previous release and the positions in GenBank sequences of 196 entries were amended, listed here.
Changes in Release 5
Advanced search features which allow users to make queries by genes and cytogenetic locations have been released.
Changes in Release 4
Trace View is available from the alleles on "View SNP position in Genbank record".219 previously released entries have been withdrawn, listed here.
Changes in Release 3
Keyword search is available to make free-text queries against Accession number, SNP ID, gene name and chromosome number.In the column of "SNP's position in gene", the entries located in "Surrounding region of exon" are divided into introns and surrounding regions of exons.
Changes in Release 2
Japanese page is released.This release provides Graphical View of each Genbank entries. This shows annotations (gene, exon, intron, CDS, mRNA, 5'-UTR, 3'-UTR) described in each Genbank entries, Screening Regions and SNP positions related with a certain Genbank entry. This view is linked to SNP information pages and SNPs list of Accession No. pages.
This release presents repeat sequence information for each SNP entries and masked sequence by RepeatMasker with options of "Do not mask simple repeats and low complexity DNA". FTP data format is changed by adding these information.
3 previously released entries have been withdrawn, listed here.
JSNP Database Release History
Release Date Total Number of SNPs Total Number of SNPs
with allele frequencyComment -------- --------------- --------------------- --------------------- ---------------------------------------------------------- 40 Mar 22, 2012 197,195 84,651 mapped on NCBI's build 37 version 3 of the human genome. 39 Oct 14, 2011 197,195 84,651 mapped on NCBI's build 37 version 2 of the human genome. 38 Oct 18, 2010 197,195 84,651 mapped on NCBI's build 37 version 1 of the human genome. 37 Nov 26, 2009 197,195 84,651 mapped on NCBI's build 37 version 1 of the human genome. 36 Aug 11, 2009 197,195 84,651 mapped on NCBI's build 36 version 3 of the human genome. - Jul 23, 2009 - - genotype frequency dataset of esophageal cancer study added. 35 Oct 28, 2008 197,195 84,651 mapped on NCBI's build 36 version 3 of the human genome. 34 Jun 12, 2008 - - genotypic datasets:35 diseases added 33 Apr 21, 2008 197,195 84,651 mapped on NCBI's build 36 version 3 of the human genome. 32 Oct 31, 2007 515,286 515,286 a new dataset:JSNP550typed added 31 Jun 25, 2007 197,157 84,618 mapped on NCBI's build 36 version 2 of the human genome. 30 Jan 11, 2007 197,157 84,612 mapped on NCBI's build 36 version 2 of the human genome. 29 Sep 5, 2006 197,157 84,612 mapped on NCBI's build 36 version 1 of the human genome. 28 May 30, 2006 197,157 84,612 mapped on NCBI's build 36 version 1 of the human genome. 27 Jan 11, 2006 197,151 84,612 mapped on NCBI's build 35 version 1 of the human genome. 26 Nov 17, 2005 197,151 84,612 mapped on NCBI's build 35 version 1 of the human genome. 25 Sep 7, 2005 195,151 84,612 mapped on NCBI's build 35 version 1 of the human genome. 24 May 16, 2005 195,134 84,599 mapped on NCBI's build 35 version 1 of the human genome. 23 Nov 25, 2004 195,134 84,599 mapped on NCBI's build 35 version 1 of the human genome. 22 Sep 15, 2004 195,059 84,566 mapped on NCBI's build 34 version 3 of the human genome. 21 May 20, 2004 195,059 84,566 mapped on NCBI's build 34 version 3 of the human genome. 20 Mar 31, 2004 195,059 84,566 mapped on NCBI's build 34 version 2 of the human genome. 19 Dec 3, 2003 195,059 84,566 6 allele frequency data have been added.
mapped on NCBI's build 34 of the human genome.18 July 31, 2003 195,059 84,560 3 allele frequency data have been added.
mapped on NCBI's build 33 of the human genome17 May 30. 2003 195,059 84,557 dbSNP Information and XML files have been added.
mapped on NCBI's build 32 of the human genome16 Mar 12. 2003 194,393 78,570 rsID number have been added to RIKEN data.
mapped on NCBI's build 31 of the human genome15 Jan 23. 2003 194,393 78,570 ssID number and rsID number have been added to RIKEN data.
mapped on NCBI's build 30 of the human genome14 Dec 25. 2002 194,393 78,570 60 entries have been withdrawn.
mapped on NCBI's build 30 of the human genome13 Oct 21. 2002 193,037 78,570 976 entries replaced with ssj ID.
mapped on NCBI's build 30 of the human genome12 Oct 1. 2002 190,562 78,570 ftp files as same as release 11.
mapped on NCBI's build 30 of the human genome11 Jul 17. 2002 190,562 78,570 10 Mar 26. 2002 164,117 48,143 9 Jan 23. 2002 151,727 24,335 8 Oct 11. 2001 117,427 7 Aug 9. 2001 104,192 6 Jun 11. 2001 77,141 1 entry has been withdrawn. 5 Mar 30. 2001 56,332 4 Dec 26. 2000 34,064 219 entries have been withdrawn. 3 Oct 20. 2000 22,882 2 Aug 10. 2000 10,131 3 entries have been withdrawn. 1 Jul 7. 2000 6,830
