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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1273328          
refSNP ID: rs1273328
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_001083962.1:c.549+23957T>G
NM_003199.2:c.549+23957T>G
NT_025028.13:g.784497A>C
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 ss1981895 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1273328 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
ss1981895KWOK|OVLP-000925-738416fwd/BG/Tatttttttttttttttttttttttttttttgctgctgctctttaaggcactcttgcatag10/06/0010/10/0387Genomic80 %
ss21477881SSAHASNP|WGSA-200403-chr18.chr18.NT_025028.13_784497rev/TA/Cctatgcaagagtgccttaaagagcagcagcaaaaaaaaaaaaaaaaaaaaaaaaaaaaat03/20/0403/20/04121Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1273328|allelePos=230|totalLen=740|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=121
 TAGATTTGAG TACTAACACA TCAGCAGAAA TTATATTTTT AAGTACATAC ATAATTCTCA
 GGCCAGTCGT GTTTGGTGCT CCAAAAAGAT TTGTGATTGA ATATCTTTGC TCCATTGGGA
 AGAGTTTAGC ATGGTGCTGT ATTTTTATAA TTCTTTTTTC CATTTTAGCA GACTTCACCT
 AAGTCTATTT TAGGTGGAGA tttttttttt tttttttttt ttttttttt
 K
 GCTGCTGCTC TTTAAGGCAC TCTTGCATAG AGGAAACAGC AGAGGAGACA CAAGGAAATG
 CACTCTCCTT TATAACATGC TGCTGATTCT CTGAACTAGG TGTCCTCTCA TTTAAGCCTC
 AAAAGAAGCT GTGTATTAAC TAGATGAAGG AACTAACACT CAAACCTGTG ATACAGCTTG
 GCCAGAGTCA CACTGCTGGG GAGCAGCAAG GTTACTCATC AAGATGTGTC TGACCCTCAA
 GTTTAAGTGC TCTGATTTAA TAACTTTGCT CACACCCTGA TTCCAGTGTC TTAGTAGCTT
 TTGATCTATA AAATGTCATC TAAGGATCTT TGAGCCTTAA TTCTTTGTCT TTAAAGTGGG
 AATGATAATA CCTGCCACAG AGTACTAGTT ATGGAGATTA AATAAGTGAA GGCAATTATT
 ATATGTTCTT TAAATTGTGT GTCACTGTAC TGTGCATGTA TTAAGTGTCG TTTTATTAGC
 AAATATCTTT TTGATGGGTA GATGTTTACC

  GeneView back to top
GeneView via analysis of contig annotation: TCF4 transcription factor 4
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_025028->NM_001083962
function
referenceNT_025028->NM_003199
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_025028->NM_001083962->NP_001077431784497reverseintron
referenceNT_025028->NM_003199->NP_003190784497reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1273328 maps exactly once on NCBI human chromosome 18
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
18NW_001838469.178660049703251minusAalt_assembly_8HuRefHuRefview229
18NW_927106.18304583^830458449711000^49711001minus-alt_assembly_1CeleraCeleraview229..229
18NT_025028.1378449751144631minusAref_assemblyreferencereferenceview229

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_025028 AP001493.2
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
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .