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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1053959          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_012212.2:c.79T>G
NP_036344.1:p.Ser27Ala
NT_008470.18:g.21680829C>A
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 ss19786825 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053959 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
ss1531587LEE|558919fwd/BG/Tcctactaatagtgactttgagttgaagacactgagctcccacccttaaaaaatggagagg09/13/0010/10/0386cDNAunknown
ss4396034LEE|ge558919fwd/BG/Tcctactaatagtgactttgagttgaagacactgagctcccacccttaaaaaatggaggta04/25/0210/10/03108cDNAunknown
ss4420754LEE|e558919fwd/BG/Tcctactaatagtgactttgagttgaagacactgagctcccacccttaaaaaatggagagg04/26/0210/10/03106cDNAunknown
ss16250420CGAP-GAI|1500008fwd/BG/Tcctactaatagtgactttgagttgaagacactgagctcccacccttaaaaaatggagagg11/18/0311/22/03120cDNAunknown
ss19786825CSHL-HAPMAP|CSHL-HuDD-200402.chr9.NT_008470.16_16021152rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg02/20/0403/04/04123Genomicunknown
ss22854960SSAHASNP|WGSA-200403-chr9.chr9.NT_008470.16_16021152rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg03/21/0403/22/04123Genomicunknown
ss24787760SEQUENOM|sqnm76287byFreqrev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg06/18/0411/02/06123cDNAunknown
ss28498514MGC_GENOME_DIFF|37540590-C16021152Arev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg08/20/0408/20/04126cDNAunknown
ss28513437MGC_GENOME_DIFF|BC035228x37540590-C16021152Arev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg08/25/0408/25/04126cDNAunknown
ss43807076ABI|hCV1348802byFreqrev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg07/18/0511/03/06126Genomicunknown
ss48401257APPLERA_GI|hCV1348802byFreqrev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg09/28/0511/03/06126Genomicunknown
ss77156741HGSV|Cor12156_SNV_20070510.chr9_111439179rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg10/09/0710/11/07129Genomicunknown
ss78058785HGSV|Cor12878_SNV_20070510.chr9_111439179rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg10/17/0710/17/07129Genomicunknown
ss81842222HGSV|Cor19240_SNV_20070510.chr9_111439179rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg11/30/0712/01/07130Genomicunknown
ss84325415HGSV|Cor18517_SNV_20070510.chr9_111439179rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg12/06/0712/07/07130Genomicunknown
ss97824546HUMANGENOME_JCVI|1103652161396rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg03/30/0803/30/08130Genomicunknown
ss105696267BGI|BGI_rs1053959rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg09/10/0806/18/09130Genomicunknown
ss1090060111000GENOMES|CEU.trio.12.15.2008_2237469_chr9_113399445rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg12/15/0812/16/08130Genomicunknown
ss1149447001000GENOMES|NA19240_2008_12_16_2022610_chr9_113399445rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg12/18/0812/19/08130Genomicunknown
ss115785423ILLUMINA-UK|NA18507_000115836_NCBI36.1_chr9_113399445rev/TA/Ctacctccattttttaagggtgggagctcagtgtcttcaactcaaagtcactattagtagg01/15/0901/16/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053959|allelePos=201|totalLen=701|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 GATGGGATTT GAGGATATTG TAATTGTGCT GTCTGGTCTC AGTTTGACGG CTAGAGAACT
 GTTAGAATGC AGTCACTTCA TGGCAGTTGA CTACATATTT ACTGTGTTCT AGGAGCTTCA
 GGATGGTTCG TACTAAGACA TGGACCCTGA AGAAGCACTT TGTTGGCTAT CCTACTAATA
 GTGACTTTGA GTTGAAGACA
 K
 CTGAGCTCCC ACCCTTAAAA AATGGAGGTA AGTCATACTA AAAATATTTC AGAGTTGGAA
 GGGACtgtat cagttagctt ttgctgcata acaaactacc ccaaagttta gtgactttaa
 gcaacaacgg tttattagtt cacaattctt tgggttggca atttgggctg agttaagctg
 ggtggttctt cttaggtctc atctggggta aatggttaat ttaggatggg ccttgctcac
 atgtctgctg attagcaggc tttctgttgg ggtgcatgcc ttagttctca tctatgtggc
 ctttctagca ggctagcttg agctctattc ttatagtggc cccatagatc tagagcagca
 gtagttggca agctccaatg tgcaagcact ttctcttttt tttttttttt tttttttgag
 acagagtctt gctctgttgc ccaggttgga gtgcagtggc atgattttgg ctcactgcaa
 cctctgcctt ctgggtccaa

  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
dbSTS GenBank
sqnm76287 NT_008470 ABBA01042728 BC035228 BG252194 Hs.114670
dbSNP Blast Analysis
UniGene Cluster ID
546348

  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
ss24787760 CEPH 184 AF 0.460 0.540
ss43807076 AoD_African_American 90 AF 0.430 0.570
AoD_Caucasian 92 AF 0.410 0.590
AoD_Chinese 90 AF 0.260 0.740
AoD_Japanese 90 AF 0.490 0.510
ss48401257 AGI_ASP population multiple 76 IG 0.132 0.474 0.395 1.000 0.368 0.632

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.465+/-0.127 40 39 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
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .