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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6641662          
refSNP ID: rs6641662
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_001079855.1:c.150-2918A>T
NM_003918.2:c.243-2918A>T
NT_011757.15:g.650865A>T
Links

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 ss17286567 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6641662 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
ss8542996SC_SNP|NT_025302.11_500545fwd/TA/Tataaacatgaatagattaaaattcctttttaaaagataggctttctgaatgggaaaataa05/23/0310/10/03116Genomicunknown
ss17286567CSHL-HAPMAP|CSHL-HuAA-200402.chrX.NT_025302.12_450790fwd/TA/Tataaacatgaatagattaaaattcctttttaaaagataggctttctgaatgggaaaataa02/17/0411/02/05120Genomicunknown
ss19805265CSHL-HAPMAP|CSHL-HuDD-200402.chrX.NT_025302.12_450790fwd/TA/Tataaacatgaatagattaaaattcctttttaaaagataggctttctgaatgggaaaataa02/20/0403/04/04120Genomicunknown
ss20984478SSAHASNP|WGSA-200403-chrX.chrX.NT_025302.12_450790fwd/TA/Tataaacatgaatagattaaaattcctttttaaaagataggctttctgaatgggaaaataa03/19/0403/19/04121Genomicunknown
ss43710094ABI|hCV1977183fwd/A/Tataaacatgaatagattaaaattcctttttaaaagataggctttctgaatgggaaaataa07/18/0507/18/05126Genomicunknown
ss84587201HGSV|Cor18517_SNV_20070510.chrX_2762464fwd/A/Tataaacatgaatagattaaaattcctttttaaaagataggctttctgaatgggaaaataa12/06/0712/07/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6641662|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 ccctgtgacc tgcatgtaca catccagatg gccggttcct gccttaactg atgacattcc
 accacaaaag aagtgaaaat ggcctgttcc tgccttaact aatgacatta tcttgtgaaa
 ttccttctcc tggctcatcc tggctcaaaa gctcccctac tgagcacctt tcgaccccca
 ctcctgccca ccagagaaca accccccttt gactgtaatt ttccttgacc tacccaaatc
 ttataaaacg gccccacccc tatctccctt cgctgactct cttttcggac tcagcccacc
 tgcacctagg tgaaataaac agccttgttg ctcacacaaa gcctgtttgg tggtctcttc
 acacggacgG GAGTGAAAAC TGAAGAAATA GAAAATCTGA TATATGTAAA AAAGGGAAAA
 TAATATAAAA TGAAACTGCA GGACTCAATC CAAATATAAC CGTGATCATA ATAAACATGA
 ATAGATTAAA ATTCCTTTTT
 W
 AAAAGATAGG CTTTCTGAAT GGGAAAATAA ACATAAAATC CGGACATACA GTAGTGTAGG
 AGGCAGCTTA ATTAAAAACA AACAAAATGT TGAAAATAAA TGGATGCATT TGATATGATT
 CTGTTCCACT ATCCAATCTA AGTAATGGTC AATTGTTTTA TAGATTGTTC TTCAGTTGTt
 tgttgttgtt gttgttgttt tgagacagag cctcgctctg tcgcccaggc cggagtgcag
 tggcacgatc tcagctcatt gcaacctctg cctcccaggt tcaagcaatt ctcatgcctc
 agcctccaga gtagctggga ttagtttccc gccaccgcac ccggctagtt tttgtatttt
 tagtagagac ggggtttcac cttgttggcc aggctggtct cgaactcctg atgtcaggtg
 atccacctgc ctaggcctcc caaggtgctg gaattacagg catgagcccc tgtgcccagc
 cTTCAGTTTG GTTTTGTCCA

  GeneView back to top
GeneView via analysis of contig annotation: GYG2 glycogenin 2
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_011757->NM_001079855
function
referenceNT_011757->NM_003918
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011757->NM_001079855->NP_001073324650865forwardintron
referenceNT_011757->NM_003918->NP_003909650865forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6641662 maps exactly once on NCBI human chromosome X
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
XNW_001842356.1710529710529plusTalt_assembly_8HuRefHuRefview500
XNT_011757.156508652779103plusAref_assemblyreferencereferenceview500
XNW_927700.114477987049516plusAalt_assembly_1CeleraCeleraview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_025302
dbSNP Blast Analysis

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .