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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs864060          
refSNP ID: rs864060
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_001015053.1:c.98-6743T>G
NM_005474.4:c.95-6743T>G
NT_010783.14:g.831750A>C
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 ss1856091 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs864060 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
ss1279246KWOK|OVLP-000804-261703fwd/BG/Tgcccagctaatttttttttttttttttttgatctttagtagagacggggtttcaccatgt09/02/0010/10/0386Genomic92 %
ss1856091KWOK|OVLP-000925-221768fwd/BG/Tgcccagctaatttttttttttttttttttgatctttagtagagacggggtttcaccatgt10/06/0010/10/0387Genomic92 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs864060|allelePos=1025|totalLen=1369|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=87
 CCTCTTGTGA AGGCAGCTCC TCAGATCCAG GGAGTATCTG CACGGACCTC ATTTATGTTA
 TGTATAGACA TTCCAAACAG CGTAATAATG TCCCATGCCT TGTACTCTAC GCCCCTTGGG
 TCCCCTCCCC TCCTCCTAGC TTTCTGGGGC TGGTGGCTCC TGGAGCAGGG TCtttttttt
 tttttttttt tttttgagac ggagtcttgc tctgtcgcca aggctggagt gcagtggtgt
 gatcttggct cactgcaagc tccacctccc gggttcatgc cattctcctg cctcagcccc
 tcagcctccc aagtagctga gaatacaggc ctgccaccac acccagctaa ttttttgtgt
 ttttagtaga gacggtgttt caccgtgtta gccagggtgg tcttgatctc ctgacctcgt
 gatctgcctg tctcagcctc ccaaagtgct gggattacag gcatgagcca ctgtgcccgg
 ctGGAGCAGG GTCtttttaa aaattaattt tattttaggc caggcgcagt ggctcacgcc
 tgtaatccca gcactttggg aggctgaggc gggcggatca tgaggtcaag agattgagat
 catcctgacc aacatggtga aaccccgtct ctacctaaaa atacaaaaaa ttaggtgggt
 gtggtggcac atgcctgtag tcccagctat tcaggaggct gaggcaggag aatcgcttga
 acccagaagg cggaggttgc agtgagccga gatcacgcca ctgcactcca gcctggcgac
 agagcgagac tccgtctcca aaaaaaagaa aaaaaaaTTA CGTATGTATG TATGTAttta
 tttatttatt ttgagatgga gtctctccct gttgttgccc aggctggagt gcaatggcgc
 gatctcagct cactgcaacc tccacctcct gggttcaagt gattctcctg cctcagctgc
 ccgagtagct gggattacag gtgtgggcca ccatgcccag ctaatttttt tttttttttt
 tttg
 K
 atctttagta gagacggggt ttcaccatgt tggccaggct ggtctcaaac tcctgacctc
 gtgatctgcc cgccttggcc tctcaaagtg ctgggattac aggcatgaac cactgtgcct
 ggccttattt ttatatttat tttatGGAGC AGGGTCTTTT AGAGCTAGAT GCTAAGCCTC
 TTGGGTCTGC CAGGCAGGTC CACACTGTGC CAGCTCCCTC CCCCCAGGGC TTCTCTAGGG
 GGAACTATAG TTCCCATTTC CTTGCTGGCC AGGGTTCTTG TCACAGGGAT TCTTGAGTTG
 GAGATGTTGT CTCTGAGAGG GGGCTTGGAC CTGGGGTGCA GCTC

  GeneView back to top
GeneView via analysis of contig annotation: HDAC5 histone deacetylase 5
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_010783->NM_001015053
function
referenceNT_010783->NM_005474
function
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_010783->NM_001015053->NP_001015053831750reverseintron
referenceNT_010783->NM_005474->NP_005465831750reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs864060 maps exactly once on NCBI human chromosome 17
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
17NW_001838437.2135644937941878plusTalt_assembly_8HuRefHuRefview1024
17NW_926839.177308538886044minusAalt_assembly_1CeleraCeleraview1024
17NT_010783.1483175039533471minusAref_assemblyreferencereferenceview1024

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AC004150.8 AC023855.4
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
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .