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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11580170          
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_024758.3:c.419G>A
NP_079034.3:p.Arg140Gln
NT_004873.16:g.2302582C>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 ss118519444 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11580170 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
ss16404986CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_004873.15_2286909byFreqfwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat02/17/0403/31/08120Genomicunknown
ss66700313ILLUMINA|HumanHap300v1.1_rs11580170fwd/TC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat11/09/0611/09/06127Genomicunknown
ss66932475ILLUMINA|HumanHap550v1.1_rs11580170fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat11/14/0611/14/06127Genomicunknown
ss67092496ILLUMINA|HumanHap650Yv1.0_rs11580170fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat11/14/0611/14/06127Genomicunknown
ss68759528PERLEGEN|PGP04763612byFreqfwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat01/30/0703/31/08127Genomicunknown
ss70394744ILLUMINA|HumanHap300v2.0_rs11580170fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat04/18/0711/18/07127Genomicunknown
ss70530215ILLUMINA|HumanHap550v3.0__rs11580170fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat04/20/0703/30/08130Genomicunknown
ss71060797ILLUMINA|HumanHap650Yv3.0_rs11580170fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat04/23/0704/23/07127Genomicunknown
ss75655472ILLUMINA|ILMN_Human_1M_rs11580170fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat08/28/0708/29/07129Genomicunknown
ss85100372KRIBB_YJKIM|KHS898881fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat12/04/0712/08/07130Genomicunknown
ss104805098KRIBB_YJKIM|KHS1114512fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat06/09/0806/09/08130Genomicunknown
ss1080146741000GENOMES|CEU.trio.12.15.2008_19636_chr1_15782331fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat12/15/0812/15/08130Genomicunknown
ss118519444ILLUMINA-UK|NA18507_000018826_NCBI36.1_chr1_15782331fwd/BC/Tgctacaattttctcataggcctcttgaattgccggcagctgtcctgaaggttgtaaagat01/21/0901/21/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11580170|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CACACACATA CACACACACG TGAAATATTC TCTCCCCAGG GATTAAAATA AATGAATTAC
 AATGCTCTCT TTCCTACTGT CTGCACATTT GCAGTGGCTT GCAGGGGAGA AGTAGCTGTA
 CTCAAGCCCC TGAGTACAGG ATAAGTAAAC CCTGAGTGCA GGGAACTACT CTGGCTCTTG
 CAGACTGACA TTACCCAAGG TCAGAGGAAT ACAGCCAGCT GCTACAATTT TCTCATAGGC
 CTCTTGAATT
 Y
 GCCGGCAGCT GTCCTGAAGG TTGTAAAGAT TGACATTCAC ATCGCCTAGG TCTGCAACCA
 TGAGGGACTG GAAGGGGAGG GCCCCCGTGC TAGGATTGAC TGTCCCAAGC ATCACTGATT
 CTTCCCGGAT GCGGCGAGGT CCGAATCTGC AGAAGGAAGA ATCATCCTGT CAGCCATCAT
 CTGCAGAGAT TTCAGGCTTT GCTTAGGCCA GGGCTTCTCA GCCTCAGCAA TTTGGGGCCA
 GATGATTCCG

  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_004873
dbSNP Blast Analysis
UniGene Cluster ID
461532

  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
ss16404986 HapMap-CEU European 120 IG 0.550 0.350 0.100 0.725 0.275
HapMap-HCB Asian 90 IG 0.867 0.133 0.933 0.067
HapMap-JPT Asian 90 IG 0.889 0.111 0.944 0.056
HapMap-YRI Sub-Saharan African 120 IG 0.150 0.500 0.350 0.400 0.600
ss68759528 HapMap-CEU European 120 GF 0.550 0.350 0.100 0.725 0.275
HapMap-HCB Asian 90 GF 0.867 0.133 0.933 0.067
HapMap-JPT Asian 90 GF 0.889 0.111 0.944 0.056
HapMap-YRI Sub-Saharan African 120 GF 0.150 0.500 0.350 0.400 0.600

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.400+/-0.200 1207 1002 270 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .