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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs13439542          
refSNP ID: rs13439542
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/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_018688.4:c.*917A>G
NT_023666.17:g.852331T>C
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 ss23119492 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13439542 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
ss23119492WUGSC_SSAHASNP|WUGSC_WUchr2_SNPS_200403.chr8.NT_023666.16_852331byFreqfwd/BC/Tagagtgtgtcctccacagctcttcctactccctaggcttgcccgcgtgccctcccaccca03/22/0410/26/06121Genomicunknown
ss75050847ILLUMINA|ILMN_Human_1M_rs13439542fwd/BC/Tagagtgtgtcctccacagctcttcctactccctaggcttgcccgcgtgccctcccaccca08/28/0708/29/07129Genomicunknown
ss85739099HGSV|Cor18517_SNV_20070510.chr8_22533963fwd/BC/Tagagtgtgtcctccacagctcttcctactccctaggcttgcccgcgtgccctcccaccca12/06/0712/10/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs13439542|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTGTGTTCAG AATGTGGTAT TGGCTCTGGC CCAGCCTTCT CCCCTGTTAC CCATAATTCT
 TGCCTCTTTC CATAATCCGT GGTTTCAGTT TGACTTTGTA TATAAAGTTG GGGTTTTTTT
 TTTTTTTTTT TGGCTTGTTT TTTAAATAAA CCAAAGTCAA AAACAAACTG AGAGTGTGTC
 CTCCACAGCT CTTCCTACTC
 Y
 CCTAGGCTTG CCCGCGTGCC CTCCCACCCA GCGCCTCTGC TGGACCACGG TGCAGTTCGC
 TCCAGAAGGT GGGCCAGGGC CGGGGAGGTG CGCACACACC CCTGGCATGC TGGGCTGCCT
 GCTGGAGGGT GCTGCTGCTC CGTGGAGGGC AGCAGGCCCA GGAAGGGGTT TCCTCTGCTC
 GCCTAAGTTA CAGCACAATA

  GeneView back to top
GeneView via analysis of contig annotation: KIAA1967 KIAA1967
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: BIN3 bridging integrator 3
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_023666->NM_021174
svfunction
referenceNT_023666->NM_199205
svfunction
HuRefNW_001839127->NM_021174
svfunction
HuRefNW_001839127->NM_199205
svfunction
CeleraNW_923907->NM_021174
svfunction
CeleraNW_923907->NM_199205
svfunction
referenceNT_023666->NM_018688
svfunction
HuRefNW_001839127->NM_018688
svfunction
CeleraNW_923907->NM_018688
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_023666->NM_021174->NP_066997852331forward3' near gene
referenceNT_023666->NM_199205->NP_954675852331forward3' near gene
HuRefNW_001839127->NM_021174->NP_066997854266forward3' near gene
HuRefNW_001839127->NM_199205->NP_954675854266forward3' near gene
CeleraNW_923907->NM_021174->NP_06699710007710forward3' near gene
CeleraNW_923907->NM_199205->NP_95467510007710forward3' near gene
referenceNT_023666->NM_018688->852331reverse17763' UTR
HuRefNW_001839127->NM_018688->854266reverse17763' UTR
CeleraNW_923907->NM_018688->10007710reverse17763' UTR

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs13439542 maps exactly once on NCBI human chromosome 8
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
8NW_001839127.185426621021165plusTalt_assembly_8HuRefHuRefview200
8NW_923907.11000771021439872plusTalt_assembly_1CeleraCeleraview200
8NT_023666.1785233122533963plusTref_assemblyreferencereferenceview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023666
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC037459.16 NC_000008.9 AC022930.12
UniGene Cluster ID
553539

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss23119492HapMap-CEUEuropean 106IG 0.075 0.925 1.000 0.038 0.962
HapMap-HCBAsian 90IG 0.044 0.956 1.000 0.022 0.978
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 114IG 0.123 0.474 0.404 1.000 0.360 0.640

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.208+/-0.24627021000

  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 .