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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs607939          
refSNP ID: rs607939
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:83/129
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_005993.4:c.951-1497T>C
NT_010663.14:g.976361T>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 ss20034887 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs607939 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
ss780046SC_JCM|AC068584.2_178077fwd/BC/Ttggaatcttgacgtggctcagctgggtcccggtcagggtctctcctgaggcttcttaaac07/27/0010/10/0383Genomicunknown
ss4977540YUSUKE|IMS-JST148440rev/TA/Ggtttaagaagcctcaggagagaccctgaccgggacccagctgagccacgtcaagattcca08/12/0210/10/03108Genomicunknown
ss12412328WI_SSAHASNP|chr17.NT_010663.13_970304fwd/BC/Ttggaatcttgacgtggctcagctgggtcccggtcagggtctctcctgaggcttcttaaac07/04/0310/10/03116Genomicunknown
ss20034887CSHL-HAPMAP|CSHL-HuFF-200402.chr17.NT_010663.14_976361fwd/BC/Ttggaatcttgacgtggctcagctgggtcccggtcagggtctctcctgaggcttcttaaac02/21/0403/04/04120Genomicunknown
ss21381704SSAHASNP|WGSA-200403-chr17.chr17.NT_010663.14_976361fwd/BC/Ttggaatcttgacgtggctcagctgggtcccggtcagggtctctcctgaggcttcttaaac03/19/0403/19/04121Genomicunknown
ss77400080HGSV|Cor12156_SNV_20070510.chr17_78355543fwd/BC/Ttggaatcttgacgtggctcagctgggtcccggtcagggtctctcctgaggcttcttaaac10/09/0710/12/07129Genomicunknown
ss82930662HGSV|Cor18956_SNV_20070510.chr17_78355543fwd/BC/Ttggaatcttgacgtggctcagctgggtcccggtcagggtctctcctgaggcttcttaaac11/30/0712/03/07130Genomicunknown
ss90681797BCMHGSC_JDW|JWB-1057104fwd/BC/Ttggaatcttgacgtggctcagctgggtcccggtcagggtctctcctgaggcttcttaaac02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs607939|allelePos=312|totalLen=812|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GTAGAGTTTA GGGGAGAGTG GGGGCTGGGG TGCACCTGCC TGTAGAGTTT AGGGGAGAGT
 GGGGGCTGGG GTGTGCCTGC CTGTGGGGTG TTGGGGAAGA GTGGGGGCTG GGGTGTGCCT
 GCTCGTGGGG CATTAGGCAT CTTGCTGGGT GTCTGATGGT CTCCGCCACG GTCCTAAGAT
 GGCTGATGAT ACTCTCTTCA taccagttac cctacattac agtgtacccc gaaatttagc
 agcttaaaca gtgcactttt tcctcacagt tttggtgggt ctggaatctt gacgtggctc
 agctgggtcc c
 Y
 ggtcagggtc tctcctgagg ctTCTTaaac agtgcacttt ttcctcacag ttttggtggg
 tctggaatct tgacgtggct cagctgggtc cctggttagg gtctctcctg aggcttcttg
 aaggcgccgg cctggccact gccgtctcaa ggcctgcatt gctggggggt gtgcttccat
 gctcctcatg ggttgctgtc gggacccggt gccttgtggg ctgttggtgg ggacctgttt
 gaagtcctta ccatgtgggc ccctccgcag ggcagtgcac agcatggtag ctggcttcat
 tggagGCTGA GAGGCGGGTG GAAACCACGG CTGTTTGGAA GGTGGCAGCT CTCACCAGAC
 TCTGCGTATT CTGTTCCTTG GGAGGGAATC ATTGGGCCCA GGCCACACCC CGTGTGAGAG
 GAACGCTAGG CGGTGGGGGT CGTGGGCTGT CTTGGAAACT GCCCCCCTCC TTGTTTCCTA
 GACTTGGAAA CTGAGTCCCA

  GeneView back to top
GeneView via analysis of contig annotation: TBCD tubulin folding cofactor D
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_010663->NM_005993
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010663->NM_005993->NP_005984976361forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs607939 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_001838459.11010669..101073276163740..76163803plusNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNalt_assembly_8HuRefHuRefview244..362
17NW_926918.11786273377357332plusCalt_assembly_1CeleraCeleraview311
17NT_010663.1497636178355543plusTref_assemblyreferencereferenceview311

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022037.1 AC068014
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, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .