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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1196497          
refSNP ID: rs1196497
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
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_002851.2:c.929-4961A>C
NT_007933.14:g.46815051A>C
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 ss1697210 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1196497 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
ss1697210KWOK|OVLP-000925-418357fwd/BG/Tcctgacaactattttatcttttattgttttgtttttttaagtttgtattaaatatattac10/05/0010/10/0387Genomic99 %
ss2564066SC_JCM|AC073471.3_82852rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg11/03/0010/10/0392Genomicunknown
ss2802352TSC-CSHL|TSC0969616fwd/BG/Tcctgacaactattttatcttttattgttttgtttttttaagtttgtattaaatatattac01/02/0110/10/0392Genomicunknown
ss3798905SC_JCM|AC073095.3_47452rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg09/25/0110/10/03100Genomicunknown
ss14577839WUGSC_SSAHASNP|chr7.NT_007933.13_46808165rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg11/05/0311/22/03120Genomicunknown
ss19724380CSHL-HAPMAP|CSHL-HuDD-200402.chr7.NT_007933.13_46808165rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg02/20/0403/04/04120Genomicunknown
ss20319501CSHL-HAPMAP|CSHL-HuFF-200402.chr7.NT_007933.13_46808165rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg02/21/0403/04/04120Genomicunknown
ss22578180SSAHASNP|WGSA-200403-chr7.chr7.NT_007933.13_46808165rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg03/21/0403/21/04121Genomicunknown
ss22961603SSAHASNP|AACC-200403.chr7.NT_007933.13_46808165rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg03/22/0403/22/04121Genomicunknown
ss77680805HGSV|Cor12156_SNV_20070510.chr7_121225426rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg10/09/0710/14/07129Genomicunknown
ss80817353HGSV|Cor18507_SNV_20070510.chr7_121225426rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg11/26/0711/26/07130Genomicunknown
ss93756563BCMHGSC_JDW|JWB-2366037rev/TA/Cgtaatatatttaatacaaacttaaaaaaacaaaacaataaaagataaaatagttgtcagg02/26/0803/05/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1196497|allelePos=201|totalLen=718|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 AGTGTTTACA TACATGTGAC CTTAACAAAT GCTAGTAACA ACCCACTGAC CTTCAAGAAG
 GTAAGTCTAC TAATGTATAA TTCATTATGA CGTTTTTTCA GGAAATTGTA CAAAATTTCT
 CATAGGTCAA AATATTATGC TACAAAGACA CTCCCTTTAT GCTACTCTGT CCTGACAACT
 ATTTTATCTT TTATTGTTTT
 K
 GTTTTTTTAA GTTTGTATTA AATATATTAC AATGCTAGCA AATGAGATTT GAAGTGCATC
 CATAATTCTA TTCAACAATT ATTTAAGAAC ACCTTAATCA TGAAAAACTT GAATAGTATA
 CCATACTCAC TGTGATATCT TGGCTGTCCA TATATACACA TGACAATGAT ACTAGTTATG
 AGTCAGTAGC ACGTTACATT CAagggactg tactgctttg caaattttag gtcatttaaa
 cctcaccaca accctatagg gtgaccattt ttaacttttc cattctatag gtgaagaaac
 tgaagcttgg ggagtttaag taagttgaca atttttatat gactaataag tattggtgct
 ggagtttaaa atcaagtcta ctgaacttta aggtctgatt ttcccccctg tgctttaGCA
 GGTCCCCGCT TCTTAGCAGA AAAACCTTGT AAGGTGGTAA GAAGGCAGCA TGAAAGCATC
 TGATGCCTGG AAGGCGTGCA TACAGTTGAA CTTAATC

  GeneView back to top
GeneView via analysis of contig annotation: PTPRZ1 protein tyrosine phosphatase, receptor-type, Z polypeptide 1
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_007933->NM_002851
function
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_007933->NM_002851->NP_00284246815051forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1196497 maps exactly once on NCBI human chromosome 7
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
7NW_001839071.29660010115994504plusGalt_assembly_8HuRefHuRefview200
7NW_923640.119199437116440686minusCalt_assembly_1CeleraCeleraview200
7NT_079596.221061702121026134minusCalt_assembly_2CRA_TCAGchr7v2CRA_TCAGchr7v2view200
7NT_007933.1446815051121418711minusAref_assemblyreferencereferenceview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007933 AC073095 AC073471 AC073471.3
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
byClusterUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .