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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11594934          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_001003892.1:c.196G>A
NP_001003892.1:p.Asp66Asn
NT_008583.16:g.25369232C>T
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 ss16483523 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11594934 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
ss16483523CSHL-HAPMAP|CSHL-HuAA-200402.chr10.NT_008583.16_25369232byFreqfwd/BC/Taagcgagcctgggcctgggcacttactcatgccaatgtagagcttgggccagacctcgtt02/17/0403/31/08120Genomicunknown
ss74816103AFFY|SNP_M-311755fwd/BC/Taagcgagcctgggcctgggcacttactcatgccaatgtagagcttgggccagacctcgtt08/09/0708/09/07128Genomicunknown
ss76724557AFFY|AFFY_6_1M_SNP_A-8586058rev/TA/Gcaagctctacattggcatgagtaagtgcccag08/28/0708/30/07129Genomicunknown
ss77462420HGSV|Cor12156_SNV_20070510.chr10_76488083fwd/BC/Taagcgagcctgggcctgggcacttactcatgccaatgtagagcttgggccagacctcgtt10/09/0710/13/07129Genomicunknown
ss85463394HGSV|Cor18517_SNV_20070510.chr10_76488083fwd/BC/Taagcgagcctgggcctgggcacttactcatgccaatgtagagcttgggccagacctcgtt12/06/0712/09/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11594934|allelePos=501|totalLen=701|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 gctagctaaa ataaaagact acatttccca ggctcccttg cagctaggGG CAGGGGAAGT
 CTGGGATGGG ACTTTGCTTT CGGAAGATGC CCTTCtgctc tttctttccc tccaccctcc
 tgctgtctgg gtcctagagt tgatggctgg ggtcctggcg gcaatctggg accctgcagc
 acctggaggg aagaagccac gtccccagga cagtggcgca gaaacacagg agtctgagtc
 cctgatgacc ctgcagtggc cgtgccagcc ccagcccacc tccctctgca cttatatgtg
 agagagaaat aaacctctat cttgcctaag actttgttta ggttttctgt aatgtgaagg
 caagcccagc cctaactaat TGAGTTCTCA CAGAACGACT ACAAATTCCA AAGCCCATGG
 CTAGGAGGTG GCGCAGGGCG TGGCCTGGGG AGGGGCTGCT GCCTGCTCCC AAGCGAGCCT
 GGGCCTGGGC ACTTACTCAT
 Y
 GCCAATGTAG AGCTTGGGCC AGACCTCGTT GACGTGGGTG TACTGGGGAC TGCCCTTCCA
 GAAGAGCCGC TCCAGCTCAA AGGCTCCAGG GGTGCAGTAG TCCTCCTCCT CCCCTTCCTC
 CTCCATCTTC GGCGACAGCC TCTTGGCAGA TGAGTAGGCA TTCTTGAGGC TTGTCTTCAC
 TTCTCCAGAT GTCATTTTAG

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_008583
dbSNP Blast Analysis
UniGene Cluster ID
535090

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss16483523 HapMap-CEU European 116 IG 0.914 0.069 0.017 0.948 0.052
HapMap-HCB Asian 88 IG 0.909 0.091 0.955 0.045
HapMap-JPT Asian 86 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 116 IG 0.793 0.207 0.897 0.103

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.103+/-0.202 525 409 0 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .