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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs12336965          
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_182974.2:c.*14C>A
NT_019501.13:g.1424736G>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 ss18819486 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12336965 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
ss18819486SC_SNP|SC-CHR9-12_NA17119-200402.chr9.NT_019501.12_1231394byFreqfwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga02/20/0410/26/06120Genomicunknown
ss66669578ILLUMINA|HumanHap300v1.1_rs12336965fwd/TG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga11/09/0611/09/06127Genomicunknown
ss66999070ILLUMINA|HumanHap550v1.1_rs12336965fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga11/14/0611/14/06127Genomicunknown
ss67316766ILLUMINA|HumanHap650Yv1.0_rs12336965fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga11/14/0611/14/06127Genomicunknown
ss69305904PERLEGEN|PGP04761731byFreqfwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga01/30/0703/31/08127Genomicunknown
ss70408063ILLUMINA|HumanHap300v2.0_rs12336965fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga04/18/0711/18/07127Genomicunknown
ss70564209ILLUMINA|HumanHap550v3.0__rs12336965fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga04/20/0703/30/08130Genomicunknown
ss71103731ILLUMINA|HumanHap650Yv3.0_rs12336965fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga04/23/0704/23/07127Genomicunknown
ss74813260AFFY|SNP_M-289311fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga08/09/0708/09/07128Genomicunknown
ss75558098ILLUMINA|ILMN_Human_1M_rs12336965fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga08/28/0708/29/07129Genomicunknown
ss85209450KRIBB_YJKIM|KHS928706fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga12/04/0712/08/07130Genomicunknown
ss1091337891000GENOMES|CEU.trio.12.15.2008_2270042_chr9_137655750fwd/BG/Tggaggagaaaatgcaagatcccagctgtatctggtgataacagctaggtgggtttattga12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12336965|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 ATTTATTTGG GAAGGATGTA AATTTGTATG TCTCTAAAAA ATGGAAGGTC TTAAGACTTC
 CCTCATTTAT AAGAAATTGC CGTGATTCAT TTATTCGTCA TAAACCTCAT GGCGTAATTC
 ATAATTTCCT CTGGGAATCA TGTGCGACCT TGACGTATTG GATCTGTGGA GGAGGAGAAA
 ATGCAAGATC CCAGCTGTAT
 K
 CTGGTGATAA CAGCTAGGTG GGTTTATTGA GGTAAAAATA TTTGTTAAGG TGCTTTTCAT
 AAGTGCTATT GAGTCCATTT TTGATGTCAT GAATAACTCC GTTCAGATAT TCTTTGATGA
 AGTCTAAAAT ATTATGGGGT GTGCCACCAA CCATCAAGTT GCCATAATAG AAATCTCCCT
 GTCCAAACGG GATGCAAGCT

  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_019501
dbSNP Blast Analysis
UniGene Cluster ID
522491

  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
ss18819486 HapMap-CEU European 120 IG 0.633 0.333 0.033 0.752 0.800 0.200
HapMap-HCB Asian 90 IG 0.644 0.333 0.022 0.584 0.811 0.189
HapMap-JPT Asian 88 IG 0.614 0.341 0.045 1.000 0.784 0.216
HapMap-YRI Sub-Saharan African 120 IG 0.633 0.350 0.017 0.317 0.808 0.192
ss69305904 HapMap-CEU European 120 GF 0.633 0.350 0.017 0.808 0.192
HapMap-HCB Asian 90 GF 0.644 0.333 0.022 0.811 0.189
HapMap-JPT Asian 90 GF 0.622 0.333 0.044 0.789 0.211
HapMap-YRI Sub-Saharan African 120 GF 0.633 0.350 0.017 0.808 0.192
Concordant Genotype Total Sample G/G G/T T/T
ss18819486 1206 753 387 43
ss69305904 269 172 91 6
RefSNP Genotype Summary Total Individual G/G G/T T/T
rs12336965 1207 769 393 44
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
637 ss18819486 T/T CSHL-HAPMAP HapMap-CEU NA12892 CEPH1463.16 r27_ch9_CEU_illumina:human_1m_beadchip 718112
637 ss69305904 G/T CSHL-HAPMAP HapMap-CEU NA12892 CEPH1463.16 chr9-HapMap-CEU
Genotype data submitted for1207 samples from1207 individualsIndividual with multiple genotypes submission:270

  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 .