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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs13233338          
refSNP ID: rs13233338
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_001061.2:c.337-12393C>G
NM_030984.1:c.337-12393C>G
NT_007914.14:g.215149C>G
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 ss22579397 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13233338 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
ss22579397SSAHASNP|WGSA-200403-chr7.chr7.NT_007914.13_215149fwd/BC/Gaccatccccacctccctcgacactctttcatactcttcccagcctctggtaaccatcatt03/21/0403/21/04121Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs13233338|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=121
 GCTTGAGCAA CAGAGCGAGA CCCTGTCCga gagagagaga gagacgcaag agagagaaac
 agagagagaT GGCGGTATAA ATTCTCGTGG TTATTCTAGT TCTTTTGGTT CCATATATCT
 GTTTACAGGA ATCAGCTTGT CAATTTTTAA AATGtttaat ttttgtgagt atatagtagg
 tgtatacatt tatggggtat atgaaatatt ttgatacatg catgtatcat gcatgcatga
 tacatgcatg caatgtataa taatcacatc agggtaaatg gggaatccac catctcaagc
 atttttcctt tctttgtgtt acaaacaatc caattataat catttatttt tttgccctgt
 cttatggtgc tgatctttcg gttattttaa aacctgcaat taaattatta ttgactatag
 tcaccaaata ctaggtctta ttcacttttt ctattttttt ccacccatta accatcccca
 cctccctcga cactctttca
 S
 tactcttccc agcctctggt aaccatcatt ctactatctc catgagttca attgttttac
 tttttagctc ctacaaataa gtgagaacat gccaattttg tccttctgtg cctggcttat
 ttcgtttaac aaaatgacct ccagctctat ccatgttgtt gcaaatggca ggcttttatt
 cttttttatg gctgaattgt actcccattg tatatatgta ccacgttttc tttatgcagt
 tgtctgttaa tggacactta ggtgcttcca aatttggctc ttgtgaatag tgctgcaata
 aacatgggtg tgcagatatc tctttgatat actgatttcc tttctttggg gtatatacct
 agcagtggga ttactggatc atatggtagc tctattttta gtttttttag ttttttgagg
 cgcctccaaa ctgttctcca tagtgattgt cctaatttac atttgcacca acagtgtatg
 tgggttccct tttctccaca

  GeneView back to top
GeneView via analysis of contig annotation: TBXAS1 thromboxane A synthase 1 (platelet)
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_007914->NM_001061
function
referenceNT_007914->NM_030984
function
HuRefNW_001839073->NM_001061
function
HuRefNW_001839073->NM_030984
function
CeleraNW_923640->NM_001061
function
CeleraNW_923640->NM_030984
function
CRA_TCAGchr7v2NT_079596->NM_001061
function
CRA_TCAGchr7v2NT_079596->NM_030984
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_007914->NM_001061->NP_001052215149forwardintron
referenceNT_007914->NM_030984->NP_112246215149forwardintron
HuRefNW_001839073->NM_001061->NP_001052218203forwardintron
HuRefNW_001839073->NM_030984->NP_112246218203forwardintron
CeleraNW_923640->NM_001061->NP_00105237104383forwardintron
CeleraNW_923640->NM_030984->NP_11224637104383forwardintron
CRA_TCAGchr7v2NT_079596->NM_001061->NP_00105238988107forwardintron
CRA_TCAGchr7v2NT_079596->NM_030984->NP_11224638988107forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs13233338 maps exactly once on NCBI human chromosome 7
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
7NW_001839073.1218203133917750plusCalt_assembly_8HuRefHuRefview500
7NW_923640.137104383134345632plusCalt_assembly_1CeleraCeleraview500
7NT_079596.238988107138952539plusCalt_assembly_2CRA_TCAGchr7v2CRA_TCAGchr7v2view500
7NT_007914.14215149139270066plusCref_assemblyreferencereferenceview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007914
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
HWPC
ss22579397HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
27021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
withHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .