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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11120301          
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:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_020197.1:c.1290T>G
NM_020197.2:c.1290T>G
NP_064582.1:p.Ile430Met
NP_064582.2:p.Ile430Met
NT_021877.18:g.8027894T>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 ss48405197 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11120301 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
ss16250339CGAP-GAI|1499813fwd/BG/Ttccatatatttctgagatcaaacaggaaatgaaagccactgaaactatgcagcatttcag11/18/0311/22/03120cDNAunknown
ss18081544SC_SNP|SC-CHR1_NA11321-200402.chr1.NT_021877.16_7946021fwd/BG/Ttccatatatttctgagatcaaacaggaaatgaaagccactgaaactatgcagcatttcag02/20/0403/04/04120Genomicunknown
ss48405197APPLERA_GI|hCV25621132byFreqrev/TA/Cctgaaatgctgcatagtttcagtggctttcatttcctgtttgatctcagaaatatatgga09/28/0511/03/06126Genomicunknown
ss65725165ILLUMINA|Human1-rs11120301fwd/BG/Ttccatatatttctgagatcaaacaggaaatgaaagccactgaaactatgcagcatttcag10/10/0610/10/06127Genomicunknown
ss68792448PERLEGEN|PGP04783103byFreqfwd/BG/Ttccatatatttctgagatcaaacaggaaatgaaagccactgaaactatgcagcatttcag01/30/0703/31/08127Genomicunknown
ss74810671AFFY|SNP_M-184036fwd/BG/Ttccatatatttctgagatcaaacaggaaatgaaagccactgaaactatgcagcatttcag08/09/0708/09/07128Genomicunknown
ss74885964ILLUMINA|ILMN_Human_1M_rs11120301fwd/BG/Ttccatatatttctgagatcaaacaggaaatgaaagccactgaaactatgcagcatttcag08/28/0708/29/07129Genomicunknown
ss76676359AFFY|AFFY_6_1M_SNP_A-8537780rev/TA/Cagtttcagtggctttcatttcctgtttgatct08/28/0708/30/07129Genomicunknown
ss83110916HGSV|Cor18555_SNV_20070510.chr1_210898510fwd/BG/Ttccatatatttctgagatcaaacaggaaatgaaagccactgaaactatgcagcatttcag11/27/0712/04/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11120301|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 CAGTGAGCGG AGATCGCACC ACTGCACTCC AGCCTGGGCG ACAGAGCGAG ACTCCGTCTC
 AAAATAAATA AATAAATTAA AATAAAAACA GGTCCTGGTG GAGAACATAG GCTCTAATGG
 CCAGTTTGCA TCCTGTGCCT TAAAGCAGAG AGATCCAACT TAAAGTTACC CTGGGTGGAG
 GTGTGAGGAG ATTGGCTTCT AGGCTCTCAT TGTTTGTCTT GCTTTTTCCT AGGCCATTGC
 AATCATGGAA GTAGCTCACG GCAAAGATCA TCCATATATT TCTGAGATCA AACAGGAAAT
 K
 GAAAGCCACT GAAACTATGC AGCATTTCAG TTTTCATTTA AACACTTAGT TCAGAAACCT
 TAAAGGATTT GAATATTTCA AATTGCACAC GTCACTCCAG CATCTCTGTA AAATAATTGG
 AATGAAAATA CTTCTTGCAC TTAAACACTG CACATGCCGT ACTTTGAGGT TAGTCTGAAT
 CTTGAACTTT AATACCAAAT TAATTTTGAA TGCTTTTGTT TCCTAAGAGA TAATGGCATG
 GTTTCATATG TTATACTTTG GACAGAGTTT TAAAAATGGA ATTATTTTTT CTTTCATGCC

  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_021877 BI763458
dbSNP Blast Analysis
UniGene Cluster ID
66170

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source G/G
 G/T
 T/T
 HWP G
 T
ss48405197 HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 90 IG 0.156 0.422 0.422 0.584 0.367 0.633
HapMap-JPT Asian 86 IG 0.140 0.535 0.326 0.479 0.407 0.593
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
AGI_ASP population multiple 76 IG 0.026 0.974 1.000 0.013 0.987
ss68792448 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 0.156 0.422 0.422 0.367 0.633
HapMap-JPT Asian 90 GF 0.133 0.533 0.333 0.400 0.600
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.257+/-0.250 809 632 270 0

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

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Revised: May 25, 2006 1:38 PM .