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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs344784          
refSNP ID: rs344784
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:A/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_001005376.1:c.166+151A>T
NM_001005377.1:c.166+151A>T
NM_002659.2:c.166+151A>T
NT_011109.15:g.16439800T>A
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 ss1737589 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs344784 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
ss438742KWOK|OVLP-000621-347105rev/TA/Ttttcacacccaccagattggcaagcatttaaaatctgacaatacccgggttagtaaggat06/30/0010/10/0379Genomic99 %
ss561160SC_JCM|AC006953.1_20587fwd/BA/Tatccttactaacccgggtattgtcagattttaaatgcttgccaatctggtgggtgtgaaa07/12/0010/10/0380Genomicunknown
ss1229424KWOK|OVLP-000804-326921fwd/BA/Tatccttactaacccgggtattgtcagattttaaatgcttgccaatctggtgggtgtgaaa09/02/0010/10/0387Genomic97 %
ss1737589KWOK|OVLP-000925-500447byFreqfwd/BA/Tatccttactaacccgggtattgtcagattttaaatgcttgccaatctggtgggtgtgaaa10/05/0003/31/0887Genomic97 %
ss5607529PGA-UW-FHCRC|PLAUR-005172byFreqrev/TA/Ttttcacacccaccagattggcaagcatttaaaatctgacaatacccgggttagtaaggat12/23/0204/07/04111Genomicunknown
ss76838773AFFY|AFFY_6_1M_SNP_A-8700357rev/A/Tgattggcaagcatttaaaatctgacaataccc08/28/0708/30/07129Genomicunknown
ss84433255HGSV|Cor19240_SNV_20070510.chr19_48863422fwd/A/Tatccttactaacccgggtattgtcagattttaaatgcttgccaatctggtgggtgtgaaa11/30/0712/07/07130Genomicunknown
ss90982131BCMHGSC_JDW|JWB-1172391fwd/A/Tatccttactaacccgggtattgtcagattttaaatgcttgccaatctggtgggtgtgaaa02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs344784|allelePos=1183|totalLen=1465|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 TGTTCTTAAA GCTTATAAAA AACGTATCAT ATTCTGCAAC ATTTTTTTCC CTCTCAACCT
 TAGGTTTCTG AGATGTGTCC ACATTGGTAT CTGCAGCTCT ATTTCCTTCT TTAAGCTGCA
 GTAGAGCGCT CCATTATGTA ATTATTACCA CAGTGTTTCT CTTCTGCTGC TGACTTGCTG
 ACTGACATAA AGTCGTTTCC ATTTTCTTCT TTTCTTTCTT TCTCcccttc cttcctccct
 cctccctccc tccctccctg cctctctccg tccctccctc ccttcctctc tctctttctc
 tctctctctc ttcctttcct ttctttcttt ctttcttgag atggagtttt gctcttgtcg
 cccaggctgg agtgcaatgg cacaatctca gctcactgca acctccgcct cctgggttca
 aacaattctc ctgtctcagc ctcccgagta gctgggataa ctggtgcctg ccaccaagcc
 cggctaattt ttgtattttt tagtagagac agggtttcac catgttggcc aggctggtcc
 tgaactcctg acctcaggta atccacctgc ctcagcctcc caaagtgctg ggattacagg
 tgtgagccac catgcccggc cCACCTTTCT CTCTTTCGTT CAtttttttg acaggatctc
 gctctgtcgc ccaggctgga gtgcagtagc atgatctcag ctcactgcaa cctccacctc
 ccaggttcaa gcaattctcc tgtctcagcc tcccaagtag ctgagattac aggtgcgtgc
 caccacactc ggctaatttt tccttttttg tgtgtgtgtg gagacgggtg tttcaccatg
 ttggccagcc tggtcttgaa ctcctgacct caagcaattc atccgcctct gcctcccaaa
 gtgctggaaa tacaggtgtg agccagtgcc cagcctgttt ccaattttcc atgtcacaaa
 cattgctgct aagaacattc gtatacatgt gtccctgggt atatgtggcc aaggttcttt
 ggcatttctg catggcgagg agttgagctg tagcatatgt taatcttcat ctggactaga
 tattgccgaa tcgctctaag tggttgatgt gccaatttac tcccccacca cagacacggt
 ctgcaactcc acatccttac taacccgggt attgtcagat tt
 W
 taaatgcttg ccaatctggt gggtgtgaaa tgggctctcc ttgtttgttt gtttttagtt
 tgcatgtccc agttactggt gaGGAAGGTT TCTCAATCAC TCGCGTTCCA TGCTGCGCTG
 GAGGGGTGTG TGGGTTGGGG GGAAGCTCAC CTTCCCACAA GCGCACGATC GTGGTCCTGC
 AGAGGTCCTG TCCCAGGGCG CACTCTTCCA CACGGCAATC CCCGTTGGTC TTACACTGCA
 TGCACCGCAG GCCCCAAGAG GCTGGGGGAA GGAGGGAGAG GA

  GeneView back to top
GeneView via analysis of contig annotation: PLAUR plasminogen activator, urokinase receptor
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_011109->NM_001005376
svfunction
referenceNT_011109->NM_001005377
svfunction
referenceNT_011109->NM_002659
svfunction
HuRefNW_001838496->NM_001005376
svfunction
HuRefNW_001838496->NM_001005377
svfunction
HuRefNW_001838496->NM_002659
svfunction
CeleraNW_927217->NM_001005376
svfunction
CeleraNW_927217->NM_001005377
svfunction
CeleraNW_927217->NM_002659
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011109->NM_001005376->NP_00100537616439800reverseintron
referenceNT_011109->NM_001005377->NP_00100537716439800reverseintron
referenceNT_011109->NM_002659->NP_00265016439800reverseintron
HuRefNW_001838496->NM_001005376->NP_0010053766369030reverseintron
HuRefNW_001838496->NM_001005377->NP_0010053776369030reverseintron
HuRefNW_001838496->NM_002659->NP_0026506369030reverseintron
CeleraNW_927217->NM_001005376->NP_0010053766381323reverseintron
CeleraNW_927217->NM_001005377->NP_0010053776381323reverseintron
CeleraNW_927217->NM_002659->NP_0026506381323reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs344784 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
19NW_001838496.1636903040602656plusTalt_assembly_8HuRefHuRefview1182
19NW_927217.1638132340974552plusTalt_assembly_1CeleraCeleraview1182
19NT_011109.151643980048863422plusTref_assemblyreferencereferenceview1182

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AY194849 AC023970 AC023970.2
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC006953.1 NC_000019.8 AC023970.2

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/T
T/T
HWPA
T
ss1737589HapMap-CEUEuropean 120IG 0.117 0.667 0.217 0.450 0.550
HapMap-HCBAsian 90IG 0.356 0.511 0.133 0.611 0.389
HapMap-JPTAsian 90IG 0.244 0.556 0.200 0.522 0.478
ss5607529PGA-AFRICAN-PANELAfrican American 48IG 0.292 0.542 0.167 0.655 0.562 0.438
PGA-EUROPEAN-PANELEuropean 46IG 0.130 0.565 0.304 0.439 0.413 0.587

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.500+/-0.01321817690

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

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Revised: May 25, 2006 1:38 PM .