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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs17884212          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:124/130
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
NG_008150.1:g.906T>C
NM_172002.3:c.489A>G
NP_741999.3:p.Ile163Met
NT_011520.11:g.8532486A>G
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 ss48402977 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17884212 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
ss28531578EGP_SNPS|CHEK2-000132byFreqfwd/BC/Ttgcgagtttttcattgatttccattatttcatgaggaattgcctgtccatttcataatct11/08/0401/27/05124Genomicunknown
ss48402977APPLERA_GI|hCV25958715byFreqrev/TA/Gagattatgaaatggacaggcaattcctcatgaaataatggaaatcaatgaaaaactcgca09/28/0511/03/06126Genomicunknown
ss69274795PERLEGEN|PGP17792727byFreqrev/TA/Gagattatgaaatggacaggcaattcctcatgaaataatggaaatcaatgaaaaactcgca01/30/0703/31/08127Genomicunknown
ss74897296ILLUMINA|ILMN_Human_1M_rs17884212fwd/BC/Ttgcgagtttttcattgatttccattatttcatgaggaattgcctgtccatttcataatct08/28/0708/29/07129Genomicunknown
ss86348618CANCER-GENOME|33516rev/TA/Gagattatgaaatggacaggcaattcctcatgaaataatggaaatcaatgaaaaactcgca01/25/0801/25/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17884212|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 TTTGTATTTT CAGTAGAGAC AGGGTTTTAC CATGTTGGCC AGGCTGATCT TGAACTCCTG
 ACCTCAGGTG ATCCACTTGC CTTGGCCTCC CAAAGTGCTG GGATTATAGG CGTGAGCCAC
 TGCACCCGGG CCATTATATA CTCTACGTTC ATTTTTCACT AATCCTTGGA CAAGTGTTCA
 TAACAGCAAT GAAATACATT CAGTGCTATT TTATCTTTCA CCTTTGACAA TGGATTCAAT
 CTCTTTCATG GCAGCTTCAC TTTCAGCTTC TGCGAGTTTT TCATTGATTT CCATTATTTC
 Y
 ATGAGGAATT GCCTGTCCAT TTCATAATCT GTCCTTTCAG GAATCTCTAT TCCATGGAGC
 TTTAGCTATT GGGGTAGAAA GCAAGAAAAA TAAGTTGAAG AAGCTATGGG CAGAGTAATG
 TAAATCCTAC TCATCCATTA GGAAATAATA CCACTAATAG AGAAAACTGC AACTGTCCCG
 ATAATGAAAG ACTAAGGGGT ATCAAAAGCT TGGACTGAAA CAGAAATGCT GGAATGGGAT
 TTCCACTCAT GCTACCCAAA ACTATGTGAC CTTGGTGTGA TCTTGGGGTA GTCATTCCTC

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NC_000022.8
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/T
 T/T
 HWP C
 T
ss28531578 PDR90 Global 164 IG 0.024 0.976 1.000 0.012 0.988
ss48402977 AGI_ASP population multiple 76 IG 0.105 0.895 0.752 0.053 0.947
ss69274795 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.217 0.783 0.108 0.892

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.056+/-0.158 828 678 90 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreq UNKNOWN UNKNOWN YES

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Revised: May 25, 2006 1:38 PM .