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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2497070          
refSNP ID: rs2497070
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_130785.2:c.743-3522G>A
NM_199254.1:c.974-3522G>A
NT_024524.13:g.995815C>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 ss13172005 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2497070 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
ss3503266SC_JCM|AL590046.2_174579fwd/BC/Tggaaacttccttaactcaacaaagagaatcaccaaaatacctaccaggaacatcatatta09/24/0110/10/03100Genomicunknown
ss13172005SC_SNP|NT_009799.12_995815fwd/BC/Tggaaacttccttaactcaacaaagagaatcaccaaaatacctaccaggaacatcatatta10/22/0310/31/03119Genomicunknown
ss40401622ABI|hCV27326910fwd/BC/Tggaaacttccttaactcaacaaagagaatcaccaaaatacctaccaggaacatcatatta07/16/0507/17/05126Genomicunknown
ss89505213BCMHGSC_JDW|JWB-0634737fwd/BC/Tggaaacttccttaactcaacaaagagaatcaccaaaatacctaccaggaacatcatatta02/26/0802/28/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2497070|allelePos=2000|totalLen=2237|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 GAGATTcaag gttgaaatca acaaaaagaa acttctacat caatccagga aatgaaggaa
 gagataaaca tcttaataag aaatcaatca gaacttctgg aactaaaaaa attcacttaa
 ggaatttcaa aatacaactg aaaactttat caatagactg gacaaagtag aaaacataat
 ttcagagctt gaagactggt cttttgaact aatccagtca gacaaaaata aagaaaaaag
 attttttaaa agtgaagaaa gtcagaaata tgagattatg taaagtgacc aaacctacga
 attactggca tgccctagag agaaagagaa aaagaaaaca gcctggaaaa catatttgat
 ggaataattc gagaaaattt cttgaatctt gctagataga catctaagta cagtaaagcc
 agacagcacc tgtgagatac tataaaaaat gagcattacc aaggcatata ctcaccagac
 tgtccaaggt cactgtcaaa gaaaaagccc taaaggcact gcagaaaaag gccagatcac
 acacaaaggt agccccatca ggataacagc caaatccaac agcacatcaa aaagttcacc
 atcaagtaag cttcattcca aggatacaag gttcagcata tgcaaaccaa taaatgtgat
 tcaccacaca aacagaatta aacagaaacc acatgatcat ctcaatagat gcagaaaaaa
 aagcttttga taaaattcaa catctttctt gataaaaaaa aaacactcaa gaaactagga
 atcaaaggaa catacttcaa aatagagcca tGggccggat gcagtggctc acatctgtaa
 tcccagcact ttgggaggcc aaggcaggca gatcacttga ggtcaggagt tcaagaccag
 cctggccaac atagtgaaac tccgtcttta ctaaaaatac aaaaattagc caggcatggt
 ggtgcacacc tgtaatccca gtgactcaga aggctgaggc aggagaatcg cttgaaccca
 ggagtcggag gttgcagtga ctgagattgc accactgcat tccagcctgg gtgacagcaa
 gactccatct caaaaacaaa caagcaaaca aacaaacaaa caaaaaacag gctgggcacg
 gtggctcatg cctgtaatcc cagcactttg ggaggctggg gtgggtggat cacccgaggt
 caggagttcg agagcagcct ggccaacttg gtgaaaccct atctctacta aaaatacaaa
 aattagctgg gcgtggtggc aggcacttgt aatcccagct acttgggagg ctgagccagg
 agaatcactt gaacctgggg ggtggaggtt gcagtgagcc aagactgcgc cattgcactc
 cagcctgggc aacaagagca aaactccctc tcaaaaaaaa aaaaaaTAat ttcctttgca
 gcatcacgga tgcagctgga agtcattatc ctgagcaaat taatacagga acaaaaaacc
 aaataccgta tgttctcact cataagtgaa agctaaacaa tgggtgctca tggatatcaa
 ggtggcaata atggaccctg gggagttcta gacggggcac agcagaaaag ggcacaggtt
 gaaaaactaa ctattgggtc ctgtgctcag tacctgggtg atgcgatcac tcacacccca
 aacctcagca tcacacaata ttaccaataa acctgcatat gtacttccaa atctaaaaGT
 TAATTTATAC CAAAAATCTA AGCTCAAAAA GAAAAAAAAG TATTTTGCCC ATTAAAAAAC
 AAATAATAAA AAATACAAGA ATCATCCTTT Atcagaaatc tataataatg caatttatca
 tattcattga ttaaagaagt cataccttac aattatctca attaatgcag gaaaaagcat
 tcactaacat tcagcctgca cctgtgactt taaaaattaa caacaactag gaaacttcct
 taactcaaca aagagaatc
 Y
 accaaaatac ctaccaggaa catcatatta atgacataat attgacagca ttttctttaa
 agcctggaat taaacaaaaa tgccctctct tcactgtttc catttaacag tatactgcag
 agcctaacca gtgtagaaag tcaGTGTAGT AAGTAAATCT TTAGAATAAC TCCTTAATCT
 AATGAGAGAA TTTAGGAAGA TTTCTAGATG CAGGCTCAAC ATAAACAAAA ATTAATA

  GeneView back to top
GeneView via analysis of contig annotation: TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 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_024524->NM_130785
svfunction
referenceNT_024524->NM_199254
svfunction
HuRefNW_001838069->NM_130785
svfunction
HuRefNW_001838069->NM_199254
svfunction
CeleraNW_925473->NM_130785
svfunction
CeleraNW_925473->NM_199254
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_024524->NM_130785->NP_570141995815reverseintron
referenceNT_024524->NM_199254->NP_954863995815reverseintron
HuRefNW_001838069->NM_130785->NP_570141820691reverseintron
HuRefNW_001838069->NM_199254->NP_954863820691reverseintron
CeleraNW_925473->NM_130785->NP_570141812914reverseintron
CeleraNW_925473->NM_199254->NP_954863812914reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2497070 maps exactly once on NCBI human chromosome 13
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
13NW_001838069.1820691820691plusTalt_assembly_8HuRefHuRefview1999
13NW_925473.18129141077690plusCalt_assembly_1CeleraCeleraview1999
13NT_024524.1399581518913815plusCref_assemblyreferencereferenceview1999

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_009799 AL590076
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL590076.4 NC_000013.9 AL450318.10 AL590046.3

  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 .