dbSNP News and Announcements

RELEASE: NCBI dbSNP Build 138 Phase I

Thu, 25 Apr 2013 23:00:00 EST

The following organisms are available in dbSNP Build 138 Phase I release:

organism: Danio rerio

tax_id: 7955

ss_cnt: 1516595

rs_cnt: 1441991

assembly_name: Zv9

assembly_number: 5.1

ftp: ftp://ftp.ncbi.nih.gov/snp/organisms/zebrafish_7955

organism: Gallus gallus

tax_id: 9031

ss_cnt: 12259245

rs_cnt: 9455444

assembly_name: Gallus_gallus_4.0

assembly_number: 3.1

ftp: ftp://ftp.ncbi.nih.gov/snp/organisms/chicken_9031

organism: Rattus norvegicus

tax_id: 10116

ss_cnt: 6473260

rs_cnt: 5076239

assembly_name: Rnor_5.0_Rn_Celera

assembly_number: 5.1

ftp: ftp://ftp.ncbi.nih.gov/snp/organisms/rat_10116

organism: Sus scrofa

tax_id: 9823

ss_cnt: 29090504

rs_cnt: 28702733

assembly_name: Sscrofa10.2

assembly_number: 4.1

ftp: ftp://ftp.ncbi.nih.gov/snp/organisms/pig_9823

The other 119 organisms included in this release do not have an assembly, but for those users who want to perform their own analysis, the data for these organisms are provided on the FTP site without mapping information or additional annotation. These organisms are also listed on the Build 138 Summary page without a genome build number: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?view+summary=view+summary&build_id=138.

=============================================

Component Availability Dates:

Component Date Available

dbSNP Web Query April 25, 2013

FTP Data April 25, 2013

Entrez Indexing May 2, 2013

=============================================

NOTES

* Build summary is available here (http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?view+summary=view+summary&build_id=138)

* All formats and conventions are described in ftp.ncbi.nih.gov/snp/00readme.txt. Please note that the README document is updated periodically only.

* Complete data for build 138 will be available in multiple formats at the ftp site for each organism as shown above.

* NEW: Beginning with this release, dbSNP will provide its data in VCF and BED files for those organisms whose rs clusters are mapped to an assembly. VCF and BED files for zebrafish (tax_id=7955), chicken (tax_id=9031), rat (tax_id=10116), and pig (tax_id=9823) are now available on the FTP site.

* The following organisms are scheduled for release later this year in the summer and fall:

organism tax_id assembly_name assembly_number

======== ===== ============== ================

Apis mellifera 7460 Amel_4.5 5.1

Arabidopsis thaliana 3702 gencoll_TAIR10 9.2

Bos taurus 9913 UMD31_Btau461 6.1

Caenorhabditis elegans 6239 WS195 9.1

Homo sapiens 9606 GRCh37.p10 37.5

Macaca mulatta 9544 Mmul 1.2

Mus musculus 10090 GRCm38.p1_Celera 38.2

Oryza sativa 4530 Oryza_sativa_Build_4.0 5.1

Ovis aries 9940 Oar_v3.1 1.1

Pan troglodytes 9598 Pan_troglodytes-2.1.4 3.2

Please contact snp-admin@ncbi.nlm.nih.gov to report any problems or if you have any questions.

Regards,

dbSNP Production Team

April 25, 2013

ANNOUNCEMENT: dbSNP Mouse BED (Browser Extensible Data) File Format Update

Wed, 10 Apr 2013 18:00:00 EST

ANNOUNCEMENT: dbSNP Mouse BED (Browser Extensible Data) File Format Update

The dbSNP BED format for mouse has been updated to comply with current standard BED specifications (https://genome.ucsc.edu/FAQ/FAQformat.html#format1 ); it has been QA tested and is compatible with standard BED tools and genome browser uploads such as the NCBI Remap Service (http://www.ncbi.nlm.nih.gov/genome/tools/remap), the UCSC Genome browser (https://genome.ucsc.edu/cgi-bin/hgGateway) and the EBI Genome Browser (http://www.ensembl.org).

The BED format update replaces dbSNP’s 30 field BED format (ftp://ftp.ncbi.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt) with a format that contains only three required fields and three optional fields:

Required Fields:

1. chrom: The name of the chromosome (e.g. chr1, chr2, etc.).

2. chromStart: The Reference SNP (rs) start position on the chromosome. Note: The first base in a chromosome is numbered 0.

3. chromEnd: The rs end position on the chromosome.

Optional Fields:

4. name: The dbSNP Reference SNP (rs) ID

5. score: dbSNP does not assign a score value, so this field will always contain a 0 .

6. strand: This field defines strand orientation as either “+”or “-“.

The dbSNP BED files for mouse are available on the dbSNP FTP site separated by chromosome (ftp://ftp.ncbi.nih.gov/snp/organisms/mouse_10090/). Updated BED files for other organisms will be available in future build releases, but we can also provide test BED files for your organism upon request.

Please send corrections and comments to snp-admin@ncbi.nlm.nih.gov.

Regards,

dbSNP Production Team

April 10, 2013

dbSNP Human Build 137 FTP Update

Wed, 09 Jan 2013 16:00:00 EST

dbSNP Human Build 137 FTP Update:

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/

Primarily, this update fixes RefSNP (rs) functional class reporting. RS positions have not changed; rather the interpretation of some rs functional classes relative to the gene has changed. These rs functional class changes include:

a. The reported functional class “near-gene-5” is now applied to neighboring genes when an rs is in proximity of multiple genes.

b. Fixed the incorrect reporting of functional classes “splice-3” and “splice-5” for rs located in genes that are in the reverse orientation with respect to genome. The incorrect reporting was inverted for ‘splice-5’ instead of ‘splice-3’ and vice versa.

c. The incorrect reporting of functional classes “UTR” and “nearGene” as functional class “cds-indel” has been corrected.

Please contact dbSNP at snp-admin@ncbi.nlm.nih.gov if you have questions or concerns.

The dbSNP Production Team

January 9, 2013

dbSNP Build 137 Mouse and Cow Release

Thu, 20 Sep 2012 23:00:00 EST

dbSNP Mouse_10090 and Cow_9913 (Bos taurus) Build 137 data are now available:

Mouse (tax_id 10900)

Mapped Assemblies: GRCm38 (GCF_000001635.20) and Mm_Celera (GCF_000002165.2)

New RS: 54562956

Total RS: 70036850

Cow (tax_id 9913)

Mapped Assemblies: Btau_4.6.1 (GCF_000003205.5) and Bos_taurus_UMD_3.1 (GCF_000003055.4)

New RS: 5522517

Total RS: 26539698

Component availability dates:

Component Date available

dbSNP web query September 20, 2012

FTP data September 20, 2012

Entrez indexing October 15, 2012

NOTES:

• All formats and conventions are described in ftp.ncbi.nih.gov/snp/00readme.txt. Please note that the README document is updated periodically only.

• The complete data for mouse and cow build 137 will be available in multiple formats at the following locations:

Mouse B137 (based on genomic assemblies GCF_000001635.20 and Mn_Celera GCF_000002165.2): ftp.ncbi.nih.gov/snp/organisms/mouse_10090

Cow B137 (based on Bos Taurus genomic assemblies GCF_000003205.5 and GCF_000003055.4): ftp.ncbi.nih.gov/snp/organisms/cow_9913

Please contact snp-admin@ncbi.nlm.nih.gov to report any problems or if you have any questions.

Regards,

dbSNP Production Team

September 20, 2012

RELEASE: NCBI dbSNP Build 137 for Human

Tue, 26 Jun 2012 22:00:00 EST

RELEASE: NCBI dbSNP Build 137 for Human

dbSNP Build 137 for Human (txid 9606)

===================================

This dbSNP build is based on Genome Reference Consortium (GRC) assembly GRCh37.p5, which is a patch release of GRCh37 that includes minor changes that are described in the README for this patch release: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p5/.

dbSNP build 137 includes new submissions from the 1000 Genomes Project phase I release (dbSNP Handle: 1000Genomes) and from the ClinSeq Sequencing Project (dbSNP handle: CLINSEQ-SNP). Listed below are the number of submitted SNPs (ss) and assigned Reference SNP (rs) clusters that are in B137 for these two submitters:

dbSNP Handle ss_cnt rs_cnt

------------------- -------- --------

1000GENOMES 2157571 2156169

CLINSEQ_SNP 374499 374497

Build Summary

-------------------

organism: Homo sapiens

tax_id: 9606

total_ss: 187,852,828

total_rs: 53,558,214

new_ss(since b135 release on Oct 13, 2011): 9,572,078

new_rs(since b135 release on Oct 13, 2011): 2,708,655

Component Availability Dates

--------------------------------------

Component Date Available

dbSNP web query June 26, 2012

FTP data June 26, 2012

Entrez Search June 26, 2012

**Please note that there is a slight discrepancy in the GMAF for B137 as well as in the MAF for two populations in B137 due to the presence of non-founder individuals in the populations used in the calculations. The effect of the non-founders on the calculations was minimal:

Population Total Size Extra Samples Discrepancy

Global 1092 3 0.27%

MXL 66 2 4.54%

LWK 97 1 1.03%

In the interest of expediency we released the data since the discrepancies were small, and will release a corrected version of the data at a future date.

* All formats and conventions for this build are described in ftp.ncbi.nlm.nih.gov/snp/00readme.txt. Please note that we update this README document only on a periodic basis.

* Complete data for build 137 will be available in multiple formats, and are separated by organism. The data are available at ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/

* The complete build summary for build 137 is available at:www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi

Updates and New Features for SNP Build 137

A. New BED FTP dump

dbSNP now provides data in dbSNP BED files. The data in these files are separated by chromosome and are available at: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/BED.

To see a general description of the BED file format and how it is used, see http://users.soe.ucsc.edu/~kent/gbd.html#BED

The BED contents were derived from dbSNP RS Docsum ASN.1 (ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.3.xsd). BED column descriptions and mapping to ASN.1 fields are described at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt.

B. Indel Clustering Adjustment

During the creation of B137, single base indel variations that collocated in a homopolymer stretch were merged into a single refSNP (rs) number. The resulting position of each merged indel refSNP was adjusted to start at the first base of the repeating nucleotide nearest the beginning of the homopolymer sequence. A total of 2,617,241 indel refSNPs were merged, giving a final total of 1,203,487 indel refSNPs

Merge histories for indel refSNPs are located at:

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/misc/indel_clustering_fix.README ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/misc/indel_clustering_fix.txt.gz

C. Variation Reporter Perl API

NCBI Variation Group has released a Perl module Variation:Reporter that will allow you to programmatically access the NCBI Variation Reporter service (http://www.ncbi.nlm.nih.gov/variation/tools/reporter/docs/help). The module can be downloaded from NCBI at ftp://ftp.ncbi.nlm.nih.gov/variation/tools/API/Variation.zip .

Instructions for using and installing the module are located in the README that comes in the module download.

D. Entrez SNP has a New Look

The Entrez SNP web site (http://www.ncbi.nlm.nih.gov/snp) is now live and has a new look and user interface similar to other NCBI resources to provide a more consistent user experience. Except for the new look and the removal of some reports (see NOTE below) which are more appropriate as downloads than web display, the search functions and reporting will remain the same for now. Gradually over the next year additional changes will be made to improve search functions and variation reporting.

NOTE: The following infrequently viewed reports have been removed from the Entrez web display:

XML

ASN.1

UID list (uilist)

Submitted SS exemplar (ssexemplar)

Merge Status (mergestatus)

Genotype xml (genxml)

Frequency xml (freqxml)

RefSNP Cluster Report (RSR) – Abbreviated version

Although the above reports will no longer be available as selected web display options, you can still access them using any of the following channels:

1. Entrez Web Search: Use the download option. See http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Displaying_and_Saving_a_Set_o for instructions on how to use the download option.

2. Entrez eUtils: http://dev.ncbi.nlm.nih.gov/books/NBK25501/

3. dbSNP build FTP dumps: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/

4. dbSNP batch query service: http://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html

Contact snp-admin@ncbi.nlm.ncbi.nih.gov if you have any questions or concerns regarding this change.

dbSNP Production Team

June 26, 2012

National Center for Biotechnology Information (NCBI)

National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

dbSNP Entrez New Look

Mon, 18 Jun 2012 20:00:00 EST

The Entrez SNP web site (http://www.ncbi.nlm.nih.gov/snp) is now live with a new look and user interface similar to other NCBI resources to provide user a consistent experience. Except for the new look and the removal of some reports (see NOTE below) which are more appropriate as downloads than web display, the search functions and reporting will remained the same for now. Then gradually over the next year additional changes will be made to improve search functions and variation reporting.

NOTE: The following infrequently viewed reports have been removed from the Entrez web display:

XML

ASN.1

UID list (uilist)

Submitted SS exemplar (ssexemplar)

Merge Status (mergestatus)

Genotype xml (genxml)

Frequency xml (freqxml)

RefSNP Cluster Report (RSR) – Abbreviated version

Although the above reports will no longer be available as selected web display options, you can still access them using any of the following channels:

1. Entrez Web Search: Use the download option. See http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Displaying_and_Saving_a_Set_o for instructions on how to use the download option.

2. Entrez eUtils: http://www.ncbi.nlm.nih.gov/books/NBK25501/

3. dbSNP build FTP dumps: ftp://ftp.ncbi.nih.gov/snp/organisms/

4. dbSNP batch query service: http://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html

Contact snp-admin@ncbi.nlm.ncbi.nih.gov if you have any questions or concerns regarding this upcoming change.

Regards,

dbSNP Team

dbSNP BED (Browser Extensible Data) File format

Mon, 19 Mar 2012 16:00:00 EST

The BED format is now available as output from dbSNP Batch query search (http://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html) . The dbSNP BED files were derived from dbSNP RS Docsum ASN.1 (ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.3.xsd). The dbSNP BED column descriptions and mapping to ASN.1 fields are described here (ftp://ftp.ncbi.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt).

For a general description of the BED file format and how it is used, see: http://users.soe.ucsc.edu/~kent/gbd.html#BED

dbSNP BED files will also be provided with the data separated by chromosome in upcoming dbSNP FTP dumps and in future build releases.

Please send corrections and comments to snp-admin@ncbi.nlm.nih.gov

Regards,

dbSNP Production Team

March 19, 2012

Build 136: FTP update for build specific SQL files for non-human organisms

Thu, 16 Feb 2012 16:00:00 EST

The SQL files below have been updated on dbSNP FTP site for the following organisms.

Arabidopsis (taxid 3702)

Chimpanzee (taxid 9598)

Macaque(taxid 9544)

Nematode (taxid 6239)

Pig (taxid 9823)

Rat (taxid 10116)

Orangutan (taxid 9601)

Zebrafish (taxid 7955)

The build specific files (b136_*) were missing from the regular build dumps and have been restored for each organism.

Base FTP URL - ftp://ftp.ncbi.nih.gov/snp/organisms/

./arabidopsis_3702/database/organism_data

./arabidopsis_3702/database/organism_data/b136_ContigInfo_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_ContigInfo_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_MapLinkInfo_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_MapLinkInfo_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_MapLink_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_MapLink_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_SNPContigLoc_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_SNPContigLoc_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_SNPContigLocusId_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_SNPContigLocusId_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_SNPContigProtein_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_SNPContigProtein_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_SNPMapInfo_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_SNPMapInfo_101.bcp.gz.md5

./arabidopsis_3702/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz

./arabidopsis_3702/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz.md5

./arabidopsis_3702/database/organism_schema

./arabidopsis_3702/database/organism_schema/arabidopsis_3702_constraint.sql.gz

./arabidopsis_3702/database/organism_schema/arabidopsis_3702_index.sql.gz

./arabidopsis_3702/database/organism_schema/arabidopsis_3702_table.sql.gz

./chimpanzee_9598/database/organism_schema

./chimpanzee_9598/database/organism_schema/chimpanzee_9598_constraint.sql.gz

./chimpanzee_9598/database/organism_schema/chimpanzee_9598_index.sql.gz

./chimpanzee_9598/database/organism_schema/chimpanzee_9598_table.sql.gz

./macaque_9544/database/organism_data

./macaque_9544/database/organism_data/b136_ContigInfo_101.bcp.gz

./macaque_9544/database/organism_data/b136_ContigInfo_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_MapLinkInfo_101.bcp.gz

./macaque_9544/database/organism_data/b136_MapLinkInfo_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_SNPContigLoc_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_SNPContigLoc_101.bcp.gz

./macaque_9544/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz

./macaque_9544/database/organism_data/b136_MapLink_101.bcp.gz

./macaque_9544/database/organism_data/b136_MapLink_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_SNPContigLocusId_101.bcp.gz

./macaque_9544/database/organism_data/b136_SNPContigLocusId_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_SNPContigProtein_101.bcp.gz

./macaque_9544/database/organism_data/b136_SNPContigProtein_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_SNPMapInfo_101.bcp.gz

./macaque_9544/database/organism_data/b136_SNPMapInfo_101.bcp.gz.md5

./macaque_9544/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz

./macaque_9544/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz.md5

./macaque_9544/database/organism_schema

./macaque_9544/database/organism_schema/macaque_9544_constraint.sql.gz

./macaque_9544/database/organism_schema/macaque_9544_index.sql.gz

./macaque_9544/database/organism_schema/macaque_9544_table.sql.gz

./nematode_6239/database/organism_data

./nematode_6239/database/organism_data/b136_ContigInfo_101.bcp.gz

./nematode_6239/database/organism_data/b136_ContigInfo_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_MapLinkInfo_101.bcp.gz

./nematode_6239/database/organism_data/b136_MapLink_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz

./nematode_6239/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_SNPContigLoc_101.bcp.gz

./nematode_6239/database/organism_data/b136_SNPContigLoc_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_MapLinkInfo_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_MapLink_101.bcp.gz

./nematode_6239/database/organism_data/b136_SNPContigLocusId_101.bcp.gz

./nematode_6239/database/organism_data/b136_SNPContigLocusId_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_SNPContigProtein_101.bcp.gz

./nematode_6239/database/organism_data/b136_SNPContigProtein_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_SNPMapInfo_101.bcp.gz

./nematode_6239/database/organism_data/b136_SNPMapInfo_101.bcp.gz.md5

./nematode_6239/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz

./nematode_6239/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz.md5

./nematode_6239/database/organism_schema

./nematode_6239/database/organism_schema/nematode_6239_constraint.sql.gz

./nematode_6239/database/organism_schema/nematode_6239_index.sql.gz

./nematode_6239/database/organism_schema/nematode_6239_table.sql.gz

./pig_9823/database/organism_data

./pig_9823/database/organism_data/b136_ContigInfo_103.bcp.gz

./pig_9823/database/organism_data/b136_ContigInfo_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_MapLinkInfo_103.bcp.gz

./pig_9823/database/organism_data/b136_MapLinkInfo_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_MapLink_103.bcp.gz

./pig_9823/database/organism_data/b136_MapLink_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_SNPChrPosOnRef_103.bcp.gz

./pig_9823/database/organism_data/b136_SNPChrPosOnRef_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_SNPContigLoc_103.bcp.gz

./pig_9823/database/organism_data/b136_SNPContigLoc_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_SNPContigLocusId_103.bcp.gz

./pig_9823/database/organism_data/b136_SNPContigLocusId_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_SNPContigProtein_103.bcp.gz

./pig_9823/database/organism_data/b136_SNPContigProtein_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_SNPMapInfo_103.bcp.gz

./pig_9823/database/organism_data/b136_SNPMapInfo_103.bcp.gz.md5

./pig_9823/database/organism_data/b136_SNPMapLinkProtein_103.bcp.gz

./pig_9823/database/organism_data/b136_SNPMapLinkProtein_103.bcp.gz.md5

./pig_9823/database/organism_schema

./pig_9823/database/organism_schema/pig_9823_constraint.sql.gz

./pig_9823/database/organism_schema/pig_9823_index.sql.gz

./pig_9823/database/organism_schema/pig_9823_table.sql.gz

./rat_10116/database/organism_data

./rat_10116/database/organism_data/b136_ContigInfo_101.bcp.gz

./rat_10116/database/organism_data/b136_ContigInfo_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_MapLinkInfo_101.bcp.gz

./rat_10116/database/organism_data/b136_MapLinkInfo_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_MapLink_101.bcp.gz

./rat_10116/database/organism_data/b136_MapLink_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_Remapped_101.bcp.gz

./rat_10116/database/organism_data/b136_Remapped_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz

./rat_10116/database/organism_data/b136_SNPChrPosOnRef_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_SNPContigLoc_101.bcp.gz

./rat_10116/database/organism_data/b136_SNPContigLoc_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_SNPContigLocusId_101.bcp.gz

./rat_10116/database/organism_data/b136_SNPContigLocusId_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_SNPContigProtein_101.bcp.gz

./rat_10116/database/organism_data/b136_SNPContigProtein_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_SNPMapInfo_101.bcp.gz

./rat_10116/database/organism_data/b136_SNPMapInfo_101.bcp.gz.md5

./rat_10116/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz

./rat_10116/database/organism_data/b136_SNPMapLinkProtein_101.bcp.gz.md5

./rat_10116/database/organism_schema

./rat_10116/database/organism_schema/rat_10116_constraint.sql.gz

./rat_10116/database/organism_schema/rat_10116_index.sql.gz

./rat_10116/database/organism_schema/rat_10116_table.sql.gz

./zebrafish_7955/database/organism_data

./zebrafish_7955/database/organism_data/b136_ContigInfo_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_SNPContigLocusId_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_SNPContigProtein_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_SNPContigProtein_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_SNPMapInfo_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_SNPChrPosOnRef_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_SNPContigLoc_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_SNPContigLoc_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_SNPContigLocusId_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_Remapped_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_SNPChrPosOnRef_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_Remapped_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_ContigInfo_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_MapLinkInfo_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_MapLinkInfo_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_MapLink_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_MapLink_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_SNPMapInfo_102.bcp.gz.md5

./zebrafish_7955/database/organism_data/b136_SNPMapLinkProtein_102.bcp.gz

./zebrafish_7955/database/organism_data/b136_SNPMapLinkProtein_102.bcp.gz.md5

./zebrafish_7955/database/organism_schema

./zebrafish_7955/database/organism_schema/zebrafish_7955_index.sql.gz

./zebrafish_7955/database/organism_schema/zebrafish_7955_table.sql.gz

./zebrafish_7955/database/organism_schema/zebrafish_7955_constraint.sql.gz

./orangutan_9601/database/organism_schema

./orangutan_9601/database/organism_schema/orangutan_9601_constraint.sql.gz

./orangutan_9601/database/organism_schema/orangutan_9601_index.sql.gz

./orangutan_9601/database/organism_schema/orangutan_9601_table.sql.gz

./orangutan_9601/database/organism_data

./orangutan_9601/database/organism_data/b136_ContigInfo_100.bcp.gz

./orangutan_9601/database/organism_data/b136_ContigInfo_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_MapLinkInfo_100.bcp.gz

./orangutan_9601/database/organism_data/b136_MapLinkInfo_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_MapLink_100.bcp.gz

./orangutan_9601/database/organism_data/b136_MapLink_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_SNPChrPosOnRef_100.bcp.gz

./orangutan_9601/database/organism_data/b136_SNPChrPosOnRef_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_SNPContigLoc_100.bcp.gz

./orangutan_9601/database/organism_data/b136_SNPContigLoc_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_SNPContigLocusId_100.bcp.gz

./orangutan_9601/database/organism_data/b136_SNPContigLocusId_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_SNPContigProtein_100.bcp.gz

./orangutan_9601/database/organism_data/b136_SNPContigProtein_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_SNPMapInfo_100.bcp.gz

./orangutan_9601/database/organism_data/b136_SNPMapInfo_100.bcp.gz.md5

./orangutan_9601/database/organism_data/b136_SNPMapLinkProtein_100.bcp.gz

./orangutan_9601/database/organism_data/b136_SNPMapLinkProtein_100.bcp.gz.md5

Build 135: Human SNPSubSNPLinkHistory.bcp.gz FTP file update

Wed, 15 Feb 2012 13:00:00 EST

The database file SNPSubSNPLinkHistory.bcp.gz has been updated on the FTP site to record the history of submitted SNP (ss) numbers that were withdrawn by submitter when build 135 was released.

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/SNPSubSNPLinkHistory.bcp.gz

Please contact snp-admin@ncbi.nlm.nih.gov if you have any questions or concerns.

Regards,

dbSNP Production Team

February 15, 2012

National Center for Biotechnology Information (NCBI)

National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

Build 135: Human FTP ASN1_flat Format Update

Thu, 26 Jan 2012 20:00:00 EST

The following new refSNP (rs) attributes have been added to ASN1_flat files on the FTP site (ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat/).  1)      Clinical significance 2)      Minor Allele Frequency (MAF)/Global minor allele frequency (GMAF) 3)      Suspect Variations 4)      Allele Origin **This update contains only additions of the new attributes and that the rest of the data has not changed from previous Build 135 dumps. **RS attribute descriptions are located at: http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html

Please visit this link for further details (http://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2012q1/000115.html)

RELEASE: NCBI dbSNP Build 136 for arabidopsis, chimpanzee, macaque, nematode, orangutan, pig, rat, and zebrafish

Thu, 26 Jan 2012 20:00:00 EST

===================================================
dbSNP Build 136
=================================================== Component availability dates:       Component                 Date available
      dbSNP web query           Jan 26, 2012
      FTP data                  Jan 26, 2012
      Entrez indexing           Jan 26, 2012
      Blast database  Pending

* The complete build summary for 136 is available
at:www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi
===================================================
Build 136 is based on the following NCBI genomes:
=================================================== organism tax_id assembly_name
========        ====== =============
arabidopsis 3702 TAIR10
chimpanzee 9598 Pan_troglodytes-2.1.4
macaque         9544 Mmul_051212
nematode 6239 WS195
orangutan 9601 P_pygmaeus_2.0.2
pig         9823 Sscrofa10.2
rat         10116 RGSC_v3.4
zebrafish 7955 Zv9 ===================================================
Entrez Search
===================================================
arabidopsis: http://www.ncbi.nlm.nih.gov/snp?Term=txid3702
chimpanzee: http://www.ncbi.nlm.nih.gov/snp?Term=txid9598
macaque: http://www.ncbi.nlm.nih.gov/snp?Term=txid9544
nematode: http://www.ncbi.nlm.nih.gov/snp?Term=txid6239
orangutan: http://www.ncbi.nlm.nih.gov/snp?Term=txid9601
pig: http://www.ncbi.nlm.nih.gov/snp?Term=txid9823
rat: http://www.ncbi.nlm.nih.gov/snp?Term=txid10116
zebrafish: http://www.ncbi.nlm.nih.gov/snp?Term=txid7955 ===================================================
FTP Downloads
===================================================
* The complete data for build 136 will be available at
ftp.ncbi.nih.gov/snp/organisms/ in multiple formats.
* All formats and conventions are described in
ftp.ncbi.nih.gov/snp/00readme.txt. Please note that the README document is
updated periodically. arabidopsis: ftp://ftp.ncbi.nih.gov/snp/organisms/arabidopsis_3702/
chimpanzee: ftp://ftp.ncbi.nih.gov/snp/organisms/chimpanzee_9598/
macaque: ftp://ftp.ncbi.nih.gov/snp/organisms/macaque_9544/
nematode: ftp://ftp.ncbi.nih.gov/snp/organisms/nematode_6239/
orangutan: ftp://ftp.ncbi.nih.gov/snp/organisms/orangutan_9601/
pig: ftp://ftp.ncbi.nih.gov/snp/organisms/pig_9823/
rat: ftp://ftp.ncbi.nih.gov/snp/organisms/rat_10116/
zebrafish: ftp://ftp.ncbi.nih.gov/snp/organisms/zebrafish_7955/
Please contact snp-admin@ncbi.nlm.nih.gov if you have any question or to report a problem. Regards, dbSNP Production Team
Jan 26, 2012
National Center for Biotechnology Information (NCBI)
National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

New NCBI Variation Reporter Tool

Tue, 22 Nov 2011 13:00:00 EST

NCBI Variation Reporter

The Variation Reporter (http://www.ncbi.nlm.nih.gov/variation/tools/reporter/ )

is designed to expedite access to information which may be available about

sequence variation at one or thousands of locations on a genome. In other words,

whether you need to interpret variation you have identified in one individual in

one gene, or from a large resequencing project, Variation Reporter is the tool

for you. Specifically, you provide variant calls made in your research or

testing and we will try to match these calls to variants that are in dbSNP or

dbVar. If we can match your submitted variant to a known variant, we will

provide you with detailed information concerning known alleles for that

location. If we cannot match a submitted variant to a known variant, we will

calculate whether that variant has a predicted consequence based on NCBI genome

annotation.

Online Help: http://www.ncbi.nlm.nih.gov/variation/tools/reporter/docs/help

Write to Help Desk: http://1.usa.gov/vyQyJp

dbSNP Build 135 human VCF and genotype XML FTP files are available

Mon, 21 Nov 2011 13:00:00 EST

Human VCF Files

Data in the VCF (Variant Call Format) for human is available on the dbSNP ftp site:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF
For more information see:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/000-README.html
and
http://www.1000genomes.org/node/101

Human Genotype XML by Gene

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/genotype_by_gene/

Please send any questions or report any problems to snp-admin at
ncbi.nlm.nih.gov.

Regards,

dbSNP Production Team
November 21, 2011
National Center for Biotechnology Information (NCBI)
National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Help Desk: snp-admin at ncbi.nlm.nih.gov

=================
dbSNP Announcements
=================
Email: http://www.ncbi.nlm.nih.gov/mailman/listinfo/dbsnp-announce
RSS: http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=dbsnpnews

dbSNP Build 135: FTP Genotype XML and VCF download updates

Thu, 10 Nov 2011 12:00:00 EST

A) Human Genotype XML files for Build 135 are now available.

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/genotype/

IMPORTANT RELEASE NOTE: Due to the volume of data, 1000 Genomes genotype is

not loaded directly to dbSNP and therefore it's not included in dbSNP genotype

XML dumps, web search, and eUtils search and retrieval systems. We're currently

developing a new system for archiving, searching, and retrieving genotype for

large dataset which we hope will be available later in 2012.

For now, users can download the genotype data directly from 1000 Genomes FTP

site (http://www.1000genomes.org/data).

B) Status updates:

1) Human Genotype XML by Gene

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/genotype_by_gene/

The files are being prepared and estimated to be ready early next week.

2) Human VCF Files

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/

Files are currently being QA for release next week.

Please send any questions or report any problems to snp-admin at

ncbi.nlm.nih.gov.

Regards,

dbSNP Production Team

November 10, 2011

National Center for Biotechnology Information (NCBI)

National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

Help Desk: snp-admin at ncbi.nlm.nih.gov

=================

dbSNP Announcements

=================

Email: http://www.ncbi.nlm.nih.gov/mailman/listinfo/dbsnp-announce

RSS: http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=dbsnpnews

dbSNP Build 135 Entrez and FTP Release

Tue, 08 Nov 2011 11:00:00 EST

Entrez has been updated to include dbSNP Build 135 for human based on NCBI genome build GRCh37.3. This release include new submissions from the 1000 Genomes Project Phase I release (http://1.usa.gov/rhf62b).

Entrez Search: http://www.ncbi.nlm.nih.gov/snp
dbSNP Entrez eUtils Help: http://www.ncbi.nlm.nih.gov/SNP/SNPeutils.htm
eUtils General Help : http://www.ncbi.nlm.nih.gov/books/NBK25500/
Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils): http://www.ncbi.nlm.nih.gov/books/NBK1058/

FTP files for Build 135 are now available on the ftp site (ftp://ftp.ncbi.nih.gov/snp/organisms/).

IMPORTANT: Please see notes concerning recent updates if you downloaded human FTP files between Nov. 3, 2011 and Nov. 7, 2011 (http://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2011q4/000111.html).

The complete data for Build 135:Human are available at
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ in multiple formats
****NOTE: Genotype XML Files****
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/genotype/
The genotype xml files in the above directory at are currently being prepared. Another announcement will be sent when they're ready.
All formats and conventions are described in 00readme.txt file.
ftp://ftp.ncbi.nih.gov/snp/00readme.txt.
For those downloading SQL database format, the updated SQL schemas are here:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_schema
Other organisms that are also included in this release are in the following subdirectories (listed below) under ftp://ftp.ncbi.nih.gov/snp/organisms/.
bony_fish_8187
bony_fish_8235
eucalyptus_urophylla_99020
fusarium_5518
rubbertree_3981
stickleback_69293
sweet_cherry_42229

Please send any questions or report any problems to snp-admin at ncbi.nlm.nih.gov.

Regards,

dbSNP Production Team

RELEASE: NCBI dbSNP Build 135 for human

Thu, 13 Oct 2011 22:00:00 EST

RELEASE: NCBI dbSNP Build 135 for human
                         dbSNP Build 135 for human (txid 9606)
===================================
This release is based on NCBI genome build GRCh37.3 that included assembly
changes described here (http://1.usa.gov/fIk86S) and include new submissions
from 1000 Genomes Project Phase I release (http://1.usa.gov/rhf62b). dbSNP Handle    ss_cnt  rs_cnt
------------ -------  -------
1000GENOMES* 57911353 39484957 *Includes Pilot 1,2,3 and Phase I June 2011 release (http://bit.ly/q8a5Wy)
Build Summary
------------- organism: Homo sapiens
tax_id: 9606
total_ss: 178,140,838
total_rs: 52,345,594
new_ss(since b134 release on Aug.8, 2011): 167,018
new_rs(since b134 release on Aug.8, 2011): 12,632,872
Component availability dates:       Component                 Date available
      dbSNP web query           October 13, 2011
      BLAST databases           October 24, 2011 (estimated)
      FTP data                  October 24, 2011 (estimated)
      Entrez Search           October 24, 2011 (estimated)


* All formats and conventions are described in
ftp.ncbi.nih.gov/snp/00readme.txt. Please note that the README document is
updated periodically.
* The complete data for build 135 will be available in multiple formats by
organisms at
ftp://ftp.ncbi.nih.gov/snp/organisms/
* The complete build summary for build 135 is available
at:www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi Important updates and new features: 1) About dbSNP:
Content in dbSNP is not limited to single nucleotide polymorphisms (SNPs), but
stores information about multiple small-scale variations that include
insertions/deletions, microsatellites, and non-polymorphic variants. dbSNP also
stores common and rare variations along with their genotypes and allele
frequencies. Most importantly, dbSNP includes clinically significant human
variations as well as benign polymorphisms. dbSNP also aggregates user assertions for these variations, including its
clinical assertion, minor allele frequencies, the likelihood that the variation
is a false positive, and whether the allele origin is germline or somatic.
For detail descriptions, please visit the following site:
(http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html).
2) New Feature: Filtered VCF files
dbSNP is preparing specially filtered VCF data files to provide reasonable
subsets of dbSNP selected to act as surrogates for 'polymorphic' or 'rare'
variants. These subsets are defined using minor allele frequencies (MAF) and
sources (http://1.usa.gov/qWA9oE), and the individual files include the following: 1) MAF
> 0.01 based on 1000 Genomes populations, 2) MAF > 0.01 for any population
submitted to dbSNP, 3) MAF > 0.01 for all populations submitted to dbSNP. A
separate announcement will be sent when these files are available on the FTP
site (ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/) for dbSNP human
Build 135 in a few weeks.   3) Known Issues: Due to the volume of data, 1000Genomes genotype is not loaded directly to dbSNP
so it's not reported in "new ss/rs with genotype" count. However, the global
minor allele frequency (MAF) will be calculated and included with the build
release (http://1.usa.gov/pVHRaA).   The genotype data can be download directly
from 1000Genomes FTP site (http://www.1000genomes.org/data).
dbSNP Production Team
October 13, 2011
National Center for Biotechnology Information (NCBI)
National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
RSS: http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=dbsnpnews
Help Desk: snp-admin@ncbi.nlm.nih.gov

RELEASE: dbSNP Build 134 Human Entrez Search

Thu, 01 Sep 2011 17:00:00 EST

Entrez has been updated to include dbSNP build 134 for human.

Entrez Search:

http://www.ncbi.nlm.nih.gov/snp

dbSNP Entrez eUtils Help:

http://www.ncbi.nlm.nih.gov/SNP/SNPeutils.htm

eUtils General Help :

http://www.ncbi.nlm.nih.gov/books/NBK25500/

Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils):

http://www.ncbi.nlm.nih.gov/books/NBK1058/

Please contact info at ncbi.nlm.nih.gov or snp-admin at ncbi.nlm.nih.gov for technical questions

regarding the Entrez search and retrieval system.

Regards,

dbSNP Production Team

September 1, 2011

dbSNP build 134 FTP dumps

Fri, 26 Aug 2011 00:00:00 EST

FTP files for Build 134:Human are now available on the ftp site.

-- The complete data for Build 134:Human are available at

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ in multiple formats.

-- All formats and conventions are described in 00readme.txt file.

ftp://ftp.ncbi.nih.gov/snp/00readme.txt.

-- For those downloading SQL database format, the updated SQL schemas

are here:

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_schema

Please send any questions or report any problems to snp-admin at ncbi.nlm.nih.gov.

Regards,

dbSNP Production Team

dbSNP Build 134 VCF release

Wed, 17 Aug 2011 13:00:00 EST

dbSNP Build 134 VCF files for human are available on the FTP site. ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ Please contact (snp-admin@ncbi.nlm.nih.gov) if you have any questions or to report a problem.

RELEASE: NCBI dbSNP Build 134 for human

Mon, 15 Aug 2011 15:00:00 EST

dbSNP Build 134 for human (txid 9606)
===================================
This release is based on Genome Reference Consortium (GRC) assembly GRCh37.p2,
which is a patch release of GRCh37 that has minor changes described in a README
document(http://bit.ly/mQjIii). dbSNP build 134 includes new submissions from
the 1000 Genomes Project interim phase I release(dbSNP Handle: 1000Genomes)and
the NHLBI Exome Sequencing Project (dbSNP handle: NHLBI-ESP).
handle          ss_cnt  rs_cnt
-------  -------  -------
1000GENOMES* 15893853 14877247
NHLBI-ESP         526799 526799
Build 134 added 18 new organisms [6,038,585 submissions(ss#)]to dbSNP.
Overall, with these new organisms included, build 134 added 108,182,122 new
ss# to dbSNP representing a total of 86 organisms.
Component availability dates:       Component                 Date available
      dbSNP web query           August 15, 2011
      BLAST databases           August 22, 2011 (estimated)
      FTP data                  August 22, 2011 (estimated)
      Entrez indexing           August 22, 2011 (estimated)


* All formats and conventions are described in ftp.ncbi.nih.gov/snp/00readme.txt.
Please note that the README document is updated only periodically. * The complete data for build 134 will be available in multiple formats sorted by
organism at ftp://ftp.ncbi.nih.gov/snp/organisms/ * The complete build summary for 134 is available
at: www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi Recent updates and new features: 1) dbSNP logo change (http://www.ncbi.nlm.nih.gov/projects/SNP/) As there has been confusion about the types of variations dbSNP actually contains,
the dbSNP logo text was changed from "Single Nucleotide Polymorphism" to
"Short Genetic Variations". We hope that this change will reflect the wide
range of dbSNP's variation content, and thereby prevent any future misunderstandings. In spite of its name, dbSNP is not limited to single nucleotide polymorphisms
(SNPs), but stores information about multiple small-scale variations that
include insertions/deletions, microsatellites, and non-polymorphic variants.
dbSNP also stores common and rare variations along with their genotypes and
allele frequencies. Most importantly, dbSNP includes clinically significant variations, and should
NOT be assumed to hold only benign polymorphisms.
2) New refSNP Attributes dbSNP has added new attributes that allow searching and filtering of human variation
by clinical significance, allele origin, minor allele frequency, and suspected false
SNPs. See http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html
for more information and examples of the changes these filters have on RefSNP pages.
3) New dbSNP News Web Feed A new RSS feed for brief announcements that highlight recent enhancements and changes
to the dbSNP database is now available at:
http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=dbsnpnews
4) Gene ID added to VCF (Variant Call Format) for human Data in the Variant Call Format is available on the dbSNP ftp site:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF For more information see:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/000-README.txt
and
http://www.1000genomes.org/node/101
dbSNP Production Team
August 15, 2011
National Center for Biotechnology Information (NCBI)
National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

dbSNP new attributes

Thu, 09 Jun 2011 16:00:00 EST

New attributes have been added to dbSNP to allow search and filtering of human variation by the following characteristics:

1. Allele Origin: The rs report summarizes the reported origin(s) of the variant allele asserted by each submitter for the submitted SNP (ss) . Current values are germline, somatic, and unknown.

2. Clinical significance: The significance of the indicated allele.

3. Global minor allele frequency (MAF): dbSNP is reporting the minor allele frequency for each rs included in a default global population. Since this is being provided to distinguish common polymorphism from rare variants, the MAF is actually the second most frequent allele value. In other words, if there are 3 alleles, with frequencies of 0.50, 0.49, and 0.01, the MAF will be reported as 0.49. The current default global population is 1000Genome phase 1 genotype data from 629 worldwide individuals, released in the 08-04-2010 dataset.

4. Suspect: Variation suspected to be false positive due to artifacts of the presence of a paralogous sequence in the genome (Musumeci et al. 2010) (Sudmant et al. 2010) or evidence suggested sequencing error or computation artifacts.

RELEASE: NCBI dbSNP Build 133 for cow and updates for grape, macaque, and soybean

Wed, 23 Mar 2011 10:00:00 EST

dbSNP Build 133 for cow (txid 9913) This release is based on NCBI genome build 5.2 that included Btau_4.2 and UMD_3.1 assemblies. A total of 9493419 Reference SNP (rs) are in this release including more than 5 million new rs added since the last release.

Updates for grape, macaque, and soybean Minor updates with no additional new annotations were performed on grape (txid 29760), macaque (txid 9541), and soybean (txid 3847) to include these organisms in Entrez search and the FTP dumps. 
 Entrez Search Cow: http://www.ncbi.nlm.nih.gov/snp?Term=txid9913 
Grape: http://www.ncbi.nlm.nih.gov/snp?Term=txid29760
Macaque: http://www.ncbi.nlm.nih.gov/snp?Term=txid9541
Soybean: http://www.ncbi.nlm.nih.gov/snp?Term=txid3847 
 
FTP
Cow: ftp://ftp.ncbi.nih.gov/snp/organisms/cow_9913
Grape: ftp://ftp.ncbi.nih.gov/snp/organisms/grape_29760/
Macaque: ftp://ftp.ncbi.nih.gov/snp/organisms/macaque_9541
Soybean: ftp://ftp.ncbi.nih.gov/snp/organisms/soybean_3847

Gene report FTP site update

Wed, 02 Feb 2011 11:00:00 EST

Gene report FTP site (ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/gene_report/)
has been updated on Feb 1st, 2011. It now has 3416 genes (compared with 3171 before
the udpate).

New dbSNP BLAST page

Tue, 01 Feb 2011 11:00:00 EST

The New dbSNP BLAST page is now available with a new user interface.    It has been designed to be consistent with other NCBI BLAST Web Pages and more intuitive to use with easier access to many different organisms.   Please update your bookmarks as the old site (http://www.ncbi.nlm.nih.gov/projects/SNP/snp_blastByOrg.cgi)  will be retired soon from service.