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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs206342          
refSNP ID: rs206342
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/G
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_000059.3:c.9257-1017C>G
NT_024524.13:g.13947809C>G
Links , Linkout

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 ss13329080 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs206342 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
ss270424KWOK|OVLP-000621-163368fwd/TC/Gcttttttttagtagaaaatggtgtttagatcaagatctggttgctagataggctcattac06/30/0010/10/0379Genomic97 %
ss999628KWOK|OVLP-000804-76871rev/BC/Ggtaatgagcctatctagcaaccagatcttgatctaaacaccattttctactaaaaaaaag09/02/0010/10/0386Genomic97 %
ss999910KWOK|OVLP-000804-78961fwd/TC/Gcttttttttagtagaaaatggtgtttagatcaagatctggttgctagataggctcattac09/02/0010/10/0386Genomic97 %
ss1740861KWOK|OVLP-000925-584518fwd/TC/Gcttttttttagtagaaaatggtgtttagatcaagatctggttgctagataggctcattac10/05/0010/10/0387Genomic97 %
ss1741118KWOK|OVLP-000925-591654fwd/TC/Gcttttttttagtagaaaatggtgtttagatcaagatctggttgctagataggctcattac10/05/0010/10/0387Genomic97 %
ss3677927SC_JCM|AC021571.3_128520fwd/TC/Gcttttttttagtagaaaatggtgtttagatcaagatctggttgctagataggctcattac09/24/0110/10/03100Genomicunknown
ss13329080SC_SNP|NT_024524.12_1542300byFreqfwd/TC/Gcttttttttagtagaaaatggtgtttagatcaagatctggttgctagataggctcattac10/22/0310/25/06119Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs206342|allelePos=1362|totalLen=2298|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=119
 TCCAGCTTTC CTAGCCTCAG TTCTATCCTG GTTTATCCCA GGATAGAATG GATAGCACCT
 ACCCATCTTT CACTTTAGAA TTTTATAACT CTTGgctagg cacagtggct catgcctgta
 atcccagcac tttgggaggc caaagcaggc agatcacttg aggccaggag ttcaagacca
 gcctggccaa catggcttga acccgggagg cgggggctgc ggtgacccaa gattgcacca
 ctgcacccta gcctaggcca cagagtgaga ctgcgtctca aaaaaaaaaa aaaaaaaTTA
 TAACtcttta ttttgaacta atttcagacc tttaaacaag ttgcaaaaat cgtggaattt
 ccaaatattc ctcacctagc ttcccctaat gttaacatct tgcataaccg tagtacaatt
 agaatcagaa agttaatagt ggtataatta ttacccatac tgtagatgta tttgaaaaat
 tgtttgagtt taaggtattt taccctgttt cccctttttt gttctgggat cccaaattgc
 atttagtcat ttttcccctg tattttctac cagtctttaa tacttcctgt cttctttttc
 atgatcatta tgcttttgaa tagactgata atgatcatta tgtttttgaa tagactgatc
 aattattttg tagcattccc ctcaatttga gttcgtctga tgttttctca tgactaggat
 gaagttatgc atttctggca agactaccac tgaagtgatg atgtgtcttt ctcagtacat
 catatcaagg ggttaatgat actgatctta atcacttgat taaggtgata atctgctggg
 tttctcctct gtacaataac ttcctttttc tttgtagtta ataaatatct tgagggagat
 tctttgagac tgaatcctat ttcacatcaa actagcattc atcagttgat tttgtttgca
 acaatgatta ctgtggtatt tgcctaatta tgatttttct ccctttcttt ccttctacat
 taattggaat tctataagga aaagctgtgc cctttccacc aatgtattta tttggttatt
 tatatcagta tggactcaag aacatttatt ttattctgca ggttaaaatt tggtaccttc
 attattttat tgtttaactt ttttttttta gctttgacca ttaggagctt tctcatatgg
 actcgtgtgt tctttcaacc agctttcttc actttttgaa cacttcctta ttttttgaca
 tcacaagatg ttccaagttc atcttatatg ttccctgccc tagtcttgga atcagccatt
 tctcttggct tctttttttt agtagaaaat ggtgtttaga t
 S
 caagatctgg ttgctagata ggctcattac tttactgtgg aggcatcagt actgccaggc
 cctctcagca gacagaggtg ggaaatgttt gtcttccatt ttggattccc tcatgtctag
 ttggatttgt ttgttggttg gtttattggg tatgtgaagt atcactgtgg ttctagggag
 tcagacctgt acaaaaagat atacttcatg tcacttcctc cttatccttg cagtcccaat
 cctaatcctc ctttttcccc cactcacacc ctgttccttt agtttctgag tttatccttc
 ctgatttctt ttgctcaaat gaacagatac atgtgtattt tcttatattc ccttcttcct
 tataagaagg ggaacatact ctagcctttc ttttatgctt ttctttttta actcaacact
 gtcctggaga tcagttcata gaaatcgtcc tcactctttt tttacagcta cgtggtacac
 cattgtttgg atgtaccaca gtttatccaa ctctatcctg tatatgagct aataaaagtt
 gcttccaata ttttataatt ataatgtttc agtgagtaac cttgttcata ggtgttttca
 tgaactttat gttcatgtgt attttactat tattagaggt ctatcttcag agaggagtac
 aagaaatggg attactgggt gcaaaggtaa atggatatgt gtctttgcta ggtattgcca
 aatttatctc cagaaatctt gcacaaatct gtactcctgt tagcaatgtg tgcgtatacc
 tgcttccaca tgacctcagt aaaagaatgt gttgtcatat tggtattgaa attttAGCAC
 TGTAAGCAAC AGGTCATTTT GGAAAACCTG AGCTTTCGCC AAATTCAGCT ATTTTGATTT
 GCTTTTATTA TTAGCATATA CCAAAATAAA TAGGCA

  GeneView back to top
GeneView via analysis of contig annotation: BRCA2 breast cancer 2, early onset
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_024524->NM_000059
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_024524->NM_000059->NP_00005013947809forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs206342 maps exactly once on NCBI human chromosome 13
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
13NW_001838072.1154824213779590plusCalt_assembly_8HuRefHuRefview1361
13NW_925473.11376983714034613plusCalt_assembly_1CeleraCeleraview1361
13NT_024524.131394780931865809plusCref_assemblyreferencereferenceview1361

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_024524 AL445212 Z73359 Z73359.1
dbSNP Blast Analysis
GenBank HTGS Finished:
AL445212.9 Z73359.1

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/G
G/G
HWPC
G
ss13329080HapMap-CEUEuropean 98IG 0.592 0.286 0.122 0.100 0.735 0.265
HapMap-HCBAsian 86IG 0.581 0.349 0.070 0.752 0.756 0.244
HapMap-JPTAsian 84IG 0.667 0.310 0.024 0.821 0.179
HapMap-YRISub-Saharan African 116IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.271+/-0.24927021000

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

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Revised: May 25, 2006 1:38 PM .