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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11976480          
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_001637.1:c.82G>A
NM_001637.2:c.82G>A
NP_001628.1:p.Asp28Asn
NT_007819.16:g.36252630C>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 ss44779597 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11976480 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
ss17930878CSHL-HAPMAP|CSHL-HuCC-200402.chr7.NT_007819.14_36056155byFreqfwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga02/19/0410/26/06120Genomicunknown
ss22628680SSAHASNP|WGSA-200403-chr7.chr7.NT_007819.14_36056155fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga03/21/0403/21/04121Genomicunknown
ss22940830SSAHASNP|AACC-200403.chr7.NT_007819.14_36056155fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga03/22/0403/22/04121Genomicunknown
ss24005338PERLEGEN|afd1557312byFreqfwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga08/10/0409/13/04123Genomicunknown
ss44779597ABI|hCV16171136byFreqfwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga07/19/0511/03/06126Genomicunknown
ss48411845APPLERA_GI|hCV16171136byFreqfwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga09/28/0511/03/06126Genomicunknown
ss65730567ILLUMINA|Human1-rs11976480fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga10/10/0610/10/06127Genomicunknown
ss66540574ILLUMINA|HumanHap300v1.1_rs11976480fwd/TC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga11/09/0611/09/06127Genomicunknown
ss66972432ILLUMINA|HumanHap550v1.1_rs11976480fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga11/14/0611/14/06127Genomicunknown
ss67142306ILLUMINA|HumanHap650Yv1.0_rs11976480fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga11/14/0611/14/06127Genomicunknown
ss69012854PERLEGEN|PGP01557312byFreqfwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga01/30/0703/31/08127Genomicunknown
ss70403131ILLUMINA|HumanHap300v2.0_rs11976480fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga04/18/0711/18/07127Genomicunknown
ss70550659ILLUMINA|HumanHap550v3.0__rs11976480fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga04/20/0703/30/08130Genomicunknown
ss71086070ILLUMINA|HumanHap650Yv3.0_rs11976480fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga04/23/0704/23/07127Genomicunknown
ss74811887AFFY|SNP_M-286938fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga08/09/0708/09/07128Genomicunknown
ss75487726ILLUMINA|ILMN_Human_1M_rs11976480fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga08/28/0708/29/07129Genomicunknown
ss85167826KRIBB_YJKIM|KHS917068fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga12/04/0712/08/07130Genomicunknown
ss98255358HUMANGENOME_JCVI|1103652546831fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga03/31/0803/31/08130Genomicunknown
ss1135964661000GENOMES|NA19240_2008_12_16_1566281_chr7_36730197fwd/BC/Tcattcgagaggctgggcctggactggtcatgttggctggagaggccgaggactgaagaga12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11976480|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AAAATTCCAA TCGCCAATGA GGTGGAAGAG TTTTATGCCC AATTTAAACT AGTATGCTTT
 TTATTCACAT AGATGTATGT AGTGTCAATG TCTACTCTTA GACTCCACAT TTCTCTGTGT
 CAGTGAGGTT ACTGGTGCCT TACCTGGAAT CTTACAATTC TTGATTTAAT AAAATATGTG
 ATTTATTACG CAAGCAAAGT ACTGGATCCC ATTGTTATGT CTACATAGAA AATACAAAAA
 TATTTATTTG CATACCTACA CAGGTGTGCC CATTCGAGAG GCTGGGCCTG GACTGGTCAT
 Y
 GTTGGCTGGA GAGGCCGAGG ACTGAAGAGA CAGGAGCAAG AATAGAGGCG CCACCGTAAG
 GATTTTCCAG GGGGACTGCA TCTCCGAGCT ATGCACCCCA AGTGATCACC CGGCTTTGGA
 AGCTCCCAAC TGAGGGATGC TGGAGCTGAG GCTGCAGAAT CAATTGATCT CTCTCTCCTT
 CTCTTCCTCA CTCTCTTTGA CACACACACC CCACCCTCTC ACATACACAC TTTTCAATAA
 GTGTGAAGTG AATAAAAGCA CACATAAACA CTCACAGACC CACAGCTTGC TCTTGTTGGA

  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_007819 ABBA01056910
dbSNP Blast Analysis
UniGene Cluster ID
488007

  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
ss17930878 CHMJ Asian 74 IG 0.554 0.446
ss24005338 AFD_EUR_PANEL European 48 IG 0.500 0.375 0.125 0.584 0.688 0.312
AFD_AFR_PANEL African American 46 IG 0.913 0.087 1.000 0.957 0.043
AFD_CHN_PANEL Asian 48 IG 0.292 0.625 0.083 0.150 0.604 0.396
ss44779597 HapMap-CEU European 120 IG 0.450 0.433 0.117 0.317 0.667 0.333
HapMap-HCB Asian 90 IG 0.244 0.556 0.200 0.200 0.522 0.478
HapMap-JPT Asian 90 IG 0.244 0.533 0.222 0.403 0.511 0.489
HapMap-YRI Sub-Saharan African 120 IG 0.800 0.167 0.033 0.150 0.883 0.117
ss48411845 AGI_ASP population multiple 76 IG 0.684 0.263 0.053 0.479 0.816 0.184
ss69012854 HapMap-CEU European 120 GF 0.450 0.433 0.117 0.667 0.333
HapMap-HCB Asian 90 GF 0.244 0.556 0.200 0.522 0.478
HapMap-JPT Asian 90 GF 0.244 0.533 0.222 0.511 0.489
HapMap-YRI Sub-Saharan African 120 GF 0.800 0.167 0.033 0.883 0.117

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.431+/-0.173 1303 1091 276 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .