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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs219880          
refSNP ID: rs219880
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_000834.2:c.-19+50113G>A
NT_009714.16:g.6841723C>T
Links

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss1734764 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs219880 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss286013KWOK|OVLP-000621-246350fwd/BC/Taaaataaagcaccctagaacccagtaacacgggttactgtgatggttcactgcaatggtt06/30/0010/10/0379Genomic97 %
ss1734764KWOK|OVLP-000925-415453fwd/BC/Taaaataaagcaccctagaacccagtaacacgggttactgtgatggttcactgcaatggtt10/05/0010/10/0387Genomic97 %
ss11035191BCM_SSAHASNP|chr12.NT_009714.15_6841723fwd/BC/Taaaataaagcaccctagaacccagtaacacgggttactgtgatggttcactgcaatggtt07/01/0310/10/03116Genomicunknown
ss12208322WI_SSAHASNP|chr12.NT_009714.15_6841723fwd/BC/Taaaataaagcaccctagaacccagtaacacgggttactgtgatggttcactgcaatggtt07/04/0310/10/03116Genomicunknown
ss15642174SC_SNP|NT_009714.16_6841723fwd/BC/Taaaataaagcaccctagaacccagtaacacgggttactgtgatggttcactgcaatggtt11/17/0311/22/03120Genomicunknown
ss20906865SSAHASNP|WGSA-200403-chr12.chr12.NT_009714.16_6841723fwd/BC/Taaaataaagcaccctagaacccagtaacacgggttactgtgatggttcactgcaatggtt03/19/0403/19/04121Genomicunknown
ss88983391BCMHGSC_JDW|JWB-0522570fwd/BC/Taaaataaagcaccctagaacccagtaacacgggttactgtgatggttcactgcaatggtt02/26/0802/28/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs219880|allelePos=333|totalLen=904|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTGGGAAAGG CAGGTCTTAC GTTATGCTAA AGAAGATTTC CATTAGTGCT GGATATCTGC
 AAACTGTCTT CTGCTGTATA CCTGCTGTTA CTACGCTAGG CCTGAACAAA GCCCTGAGTG
 TCTAATGGAG CATCCAGCTT TCCTCTATCC TGTCACCTGT GAACAACAGC CTGCCATAAT
 GAGCTGCCTA GGTCCAATTT CCAAACTCCA TGTCAGTGGT TTGAATCTGA GCTTTACCAT
 TTACAAGCAG TCATGAAACT TAGGGTAAAC TACTTCACTT CCTTGATAAT TTCTTCATCT
 GCAAAATAAA GCACCCTAGA ACCCAGTAAC AC
 Y
 GGGTTACTGT GATGGTTCAC TGCAATGGTT AAGTGAGATA CATATTAAAG CACTCCAAAC
 ACCACAATAT GCTAAATAAA TAATTATTgg ctgggcgcag tggctcaaac ctgtaatctc
 agcactttgg gaggctgagg cgggcggatc acgaggtcta gagactgaaa ccatcctggc
 caaaatggtg aaaccccatc tctactaaca acacaaaaat tagctgggca tggtggcacg
 cacctgcagt cccagctact tgggaggctg aggcaggaga atcgcttgaa ccggggaggt
 ggaagctgca gtgagttgag actgtgccat tgcactccag cctgggcaac agagccagac
 tctgtctcaC aataaataga taaataaata aataaataaT ACAAGTTATT AACCTTATTT
 TTTAATAGAA TCTTATTATA ACCTTTGCTG ATAGGATTAT TAGACTGGTG ATTCAGAGAA
 ATATAAATAC ATGGGATCTT GATTTCAATG GGGGCATTTG GCCAAGTTTC CTATGAGATC
 TTTGAGACTA TAAGAGAGAA TGGTGGGCAG A

  GeneView back to top
GeneView via analysis of contig annotation: GRIN2B glutamate receptor, ionotropic, N-methyl D-aspartate 2B
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_009714->NM_000834
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_009714->NM_000834->NP_0008256841723reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs219880 maps exactly once on NCBI human chromosome 12
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
12NW_001838052.1448758413848101plusTalt_assembly_8HuRefHuRefview332
12NT_009714.16684172313974016plusCref_assemblyreferencereferenceview332
12NW_925328.1434205919227375plusTalt_assembly_1CeleraCeleraview332

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_009714 AC007916.9
dbSNP Blast Analysis

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .