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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:
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
coding nonsynon[FUNC] AND 1[CHR] Search SNPs with function class 'coding nonsynon' located on chromosome 1
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: 2002/01[CDATE]
Function Class [FXN_CLASS], [FUNC] Text Function Class:
locus region intron
coding nonsynon mrna utr
coding synon reference
exception splice site

Example: "coding synon"[FUNC]
Gene Name [GENE], [GENE_SYMBOL] Textnum Locus link symbol
Example: LPL[GENE]
Protein Description [PDSC] Text Protein description
Example: "liver expressed"[PDSC]
Gene Description [GDSC] Text Gene description
Example: "kinase"[Gene Description]
GO Terms [GO] Text Gene Ontology (GO) terms
Example: "receptor"[GO term]
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 [ACC] Textnum Search by nucleotide or protein accession
Example: AC000120[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]
Population Class [POP_CLASS],[POP],[PCLS] Text Population Classification based on geographic location:
central asia north america
central south africa north/east africa & middle east
central south america pacific
east asia unknown
europe west africa
multi national  

Example: "europe"[POP]
SNP Class [SNP_CLASS], [SCLS] Text SNP Class/type:
het mnp
in del named
microsat 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: 2002/01 [UDATE]
Validation [VALIDATION] Text Validation status:
by cluster by submitter
by frequency no info

Example: "by cluster"[VALIDATION]


Population Class:
central asia Samples from Russia and satellite Republics, Nations bordering Indian Ocean between East Asia and Persian Gulf regions.
central south africa Nations south of Equator, Madagascar & neighboring Island Nations.
central south america Samples from Mainland Central and South America, Island Nations of western Atlantic, Gulf of Mexico and Eastern Pacific.
east asia Samples from Eastern and South Eastern Mainland Asia, Northern Pacific Island Nations.
europe Samples from Europe north and west of Caucasus Mountains, Scandinavia, Atlantic Islands.
multi national samples that were designed to maximize measures of heterogeneity or sample human diversity in a global fashion. Examples OEFNER|GLOBAL and CEPH repository.
north america All samples north of Tropic of Cancer. This would include defined samples of U.S. Caucasians, African Americans and Hispanics and NCBI|NIHPDR.
north/east africa & middle east samples collected from North Africa (including Sahara desert), East Africa (south to Equator), Levant, Persian Gulf.
pacific Samples from Australia, New Zealand, Central and Southern Pacific Islands, Southeast Asian Peninsular/Island Nations.
unknown Samples with unknown geographic provenience that are not global in nature.
west africa Sub-Saharan Nations bordering Atlantic north of Congo River, and Central/Southern Atlantic Island Nations.
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:
Homo sapiens
Arabidopsis thaliana
Caenorhabditis elegans
Ficedula albicollis
Ficedula hypoleuca
Gallus gallus
Mus musculus
Pan troglodytes
Plasmodium falciparum
Rattus norvegicus



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Oct 13 2004 06:44:09