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SNP

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.

Search using wild-card(*), ranging(:), AND, OR, and NOT operators:
Example Description
BRC*[Gene Name] Search SNPs on all genes with names starting with the letter 'BRC' (ie. BRCA1 and BRCA2)
1:5[HET] Search SNPs with heterozygosity between 1 and 5 percent
1[CHR] AND (nonsense[Function_Class] OR missense[Function_Class] OR frameshift[Function_Class]) Search SNPs located on chromosome 1 with function class 'nonsense', or 'missense', or 'frame-shift'
1[CHR] OR 2[CHR] Search all SNPs on chromosome 1 or 2
1[CHR] OR 2[CHR] NOT unknown[METHOD] Search all SNPs on chromosome 1 or 2 detected by all methods except 'unknown'.
1[WEIGHT] AND (1[CHR] OR 2[CHR]) NOT (unknown[METHOD] OR computed[METHOD]) Search all SNPs with weight 1 on chromosome 1 or 2 detected by all methods except 'unknown' or 'computed'.

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.

Search Field Qualifier Type Description
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]


Method Class:
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
SNP Class:
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
Allele(s):
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
Organism:
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