|
Your browser version may not work well with NCBI's Web applications. More information here...
|
Click on the image below to view the connections between Entrez SNP and other databases.
|
|
dbSNP is now incorporated into NCBI's Entrez system and can be queried using the same approach as the other Entrez databases such as PubMed and GenBank. The original database with additional information and search options are available here.
- Enter one or more search terms.
- Available search fields are listed below
- Use Limits to restrict your search by search field, chromosome, and other criteria.
Update: |
January 8, 2009 |
Updated query examples, organism list |
January 5, 2005 |
Updated search terms |
August 14, 2002 |
Add contig position tag [CTPOS] |
Below are search examples and available search fields.
Either the search fields or qualifiers (aliases) can be use for querying SNP (i.e. 103[CBID] is same as 103[Create Build ID]. Data type marked with an asterisk (*) indicates range searching is available.
Allele |
[ALLELE],[VARIATION],
[VARI] |
IUPAC |
Observed allele(s)
Example: N[ALLELE] |
Chromosome |
[CHR] |
Textnum |
Mapped chromosome number
Available values [1-22,W-Z, and Un (unknown)]
Example: 2[CHR] or X[CHR] |
Base Position |
[CHRPOS],[BPOS] |
Integer* |
Mapped chromosome position; use in conjunction with chromosome field [CHR]
Example: 7[CHR] AND 88556398:88580839[CHRPOS] |
Create Build ID |
[CREATE_BUILD],[CBID] |
Integer* |
SNP create build ID
Example: 103[CBID] |
Publication Date |
[CREATEDATE],[CDAT],[PDAT], [PUBDATE] |
Date* |
SNP create/publication date
Use the format YYYY/MM/DD; month and day are optional.
Example: "2005 07 13"[CDATE] |
Function Class |
[FXN_CLASS], [FUNC] |
Text |
Function Class:
locus region |
intron |
coding nonsynonymous |
mrna utr |
coding synonymous |
reference |
exception |
splice site |
Example: "coding synonymous"[FUNC]
|
Gene Name |
[GENE], [GENE_SYMBOL] |
Textnum |
Locus link symbol
Example: LPL[GENE] |
Genotype |
[GENOTYPE], [GTYPE] |
Boolean |
Genotype
Example: true[GTYPE] |
Heterozygosity |
[HET] |
Integer* |
Heterozygosity(%)
Example: 5[HET] |
Local SNP ID |
[LOC_SNP_ID] |
Textnum |
Submitter local SNP ID
Example: "TSC0227737"[LOC_SNP_ID] |
LocusLink ID |
[LOCUS_ID],[LID] |
Integer |
LocusLink ID number
Example: 4023[LID] |
Map Weight |
[WEIGHT],[MPWT],[HIT] |
Integer* |
SNP map weight info - the number of times a SNP map to the genome contig (range 1-10)
1 =
|
hit genome once, annotated on NT_ contigs |
2 =
|
hit genome twice, annotated on NT_ contigs with warning |
3 =
|
hit genome 3-9 times, not annotated |
10 =
|
hit 10+ times on genome, not annotated |
Example: 1[WEIGHT]
|
Method Class |
[METHOD_CLASS], [METHOD], [MCLS] |
Text |
Assay method used to identify SNP:
computed |
rflp |
dhplc |
sequence |
hybridize |
sscp |
other |
unknown |
Example: "sequence"[METHOD]
|
Accession.version |
[ACC] |
Textnum |
Search by nucleotide or protein accession and version number
Example: NT_030737.9[ACC] |
Contig Position |
[CTPOS] |
|
Mapped contig position; use in conjunction with contig accession field [ACC]
1000000:2000000[CTPOS] AND NT_034874[ACC] |
Reference SNP ID |
[RS] |
Integer* |
dbSNP assigned reference SNP ID (RS)
Example: rs709932[RS] |
Submitter SNP ID |
[SS] |
Integer* |
dbSNP assigned submitter SNP ID (SS)
Example: ss1487247[SS] |
SNP Class |
[SNP_CLASS], [SCLS] |
Text |
SNP Class/type:
heterozygous |
multinucleotide polymorphism |
in del |
named locus |
microsatellite |
no variation |
mixed |
snp |
Example: "snp"[SNP_CLASS]
|
Submitter Handle |
[HANDLE] |
Text |
Submitter handle
Example: "LEE"[HANDLE] |
Success Rate |
[SUCCESS_RATE], [SRATE] |
Integer* |
Success rate(%)
Example: 95[SRATE] |
Organism |
[ORGN],[TAX_ID] |
Text |
Organism name or Taxonomy ID number; use the prefix 'txid' before the Taxonomy ID number
Example: "human"[ORGN] , "mouse"[ORGN], or "txid9606"[ORGN] |
Update Build ID |
[UPD_BUILD],[UBID] |
Integer* |
SNP update build ID
Example: 102[UBID] |
Modification Date |
[UDATE], [UDAT], [MODDATE] |
Date* |
SNP modification/update date
Use the format YYYY/MM/DD; month and day are optional.
Example: "2005 09 27"[UDATE] |
Validation |
[VALIDATION] |
Text |
Validation status:
by cluster |
by submitter |
by frequency |
no info |
by 2hit 2allele |
by hapmap |
Example: "by cluster"[VALIDATION]
|
computed |
variation was mined from sequence alignment with software |
dhplc |
Denaturing High Pressure Liquid Chromatography used to detect SNP |
hybridize |
hybridization method (e.g. chip) was used to assay for variation |
other |
other method used to detect variation |
rflp |
variation in enzyme restriction site used to detect variation |
sequence |
samples were sequenced and resulting alignment used to define variation |
sscp |
single stranded conformational polymorphism used to detect variation |
unknown |
|
|
|
het |
variation has unknown sequence composition, but is observed to be heterozygous |
in del |
insertion deletion polymorophism, deletions represented by '-' in allele string |
microsat |
microsatellite / simple sequence repeat |
mixed |
|
mnp |
multiple nucleotide polymorphism (all alleles same length where length>1) |
named |
allele sequences defined by name tag instead of raw sequence, e.g. (Alu)/- |
no variation |
submission reports invariant region in surveyed sequence |
snp |
true single nucleotide polymorphism |
|
|
IUPAC code |
Meaning |
A |
A |
C |
C |
G |
G |
T |
T |
M |
A or C |
R |
A or G |
W |
A or T |
S |
C or G |
Y |
C or T |
K |
G or T |
V |
A or C or G |
H |
A or C or T |
D |
A or G or T |
B |
C or G or T |
N |
G or A or T or C |
|
|
Agelaius phoeniceus |
Alectoris |
Allium cepa |
Anopheles funestus |
Anopheles gambiae |
Apis mellifera |
Arabidopsis thaliana |
Bacillus anthracis |
Bison bison |
Bos indicus x Bos taurus |
Bos sp. |
Bos taurus |
Bubalus bubalis |
Caenorhabditis briggsae |
Caenorhabditis elegans |
Canis familiaris |
Capra hircus |
Cervus elaphus nelsoni |
Cooperia oncophora |
Corynespora cassiicola |
Danio rerio |
Drosophila melanogaster |
Equus caballus |
Felis catus |
Ficedula albicollis |
Ficedula hypoleuca |
Fusarium graminearum |
Gadus morhua |
Gallus gallus |
Glycine max |
Gorilla gorilla |
Gorilla gorilla gorilla |
Heterodera glycines |
Homo sapiens |
Hydroides elegans |
Litopenaeus vannamei |
Macaca fascicularis |
Macaca mulatta |
Malus x domestica |
Medicago truncatula |
Monodelphis domestica |
Mus musculus |
Mus spretus |
Oncorhynchus keta |
Oncorhynchus kisutch |
Oncorhynchus mykiss |
Oncorhynchus nerka |
Oncorhynchus tshawytscha |
Oreochromis niloticus |
Ornithorhynchus anatinus |
Oryza sativa |
Ovis aries |
Pan paniscus |
Pan troglodytes |
Pan troglodytes troglodytes |
Pan troglodytes verus |
Pinus pinaster |
Plasmodium falciparum |
Pongo pygmaeus |
Prunus dulcis |
Rattus norvegicus |
Rattus sp. |
Saccharum hybrid cultivar |
Salmo salar |
Schistosoma mansoni |
Solanum lycopersicum |
Staphylococcus aureus |
Sus scrofa |
Taeniopygia guttata |
Vitis vinifera |
Zea mays |
Zostera marina |
|
|
|
|