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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs5742796          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_001344.1:c.247G>A
NM_001344.2:c.247G>A
NP_001335.1:p.Ala83Thr
NT_026437.11:g.4043938C>T
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 ss7986505 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5742796 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
ss7986505EGP_SNPS|DAD1-014926fwd/TA/Gctgagaatacagatcaacccacagaacaaacggatttccaaggcatctccccagagcgag04/01/0301/23/04114Genomicunknown
ss74876702ILLUMINA|ILMN_Human_1M_rs5742796fwd/TA/Gctgagaatacagatcaacccacagaacaaacggatttccaaggcatctccccagagcgag08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5742796|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=129
 Ttgtatatgc tataatttat ccattttact gttgatagac attagattgt ttccagtttg
 gggctatctg ggtatcattt ctgtgtatgc cctttgatgt atatatgcat tcatttctgt
 tagAGTAGAA TTGTTGGGTC CTCGGGTATG TCTGTGTTCA TTAGCATATT TATTTTATAC
 TTCTATATAA TCATTTTTTT GTGTTTTGCT TCTTGTGCAG TTTGCCTGAG AATACAGATC
 AACCCACAGA ACAAA
 R
 CGGATTTCCA AGGCATCTCC CCAGAGCGAG CCTTTGCTGA TTTTCTCTTT GCCAGCACCA
 TCCTGCACCT TGTTGTCATG AACTTTGTTG GCTGAATCAT TCTCATTTAC TTAATTGAGG
 AGTAGGAGAC TAAAAGAATG TAAGTGATGA TCATAGTCCT TGTCCTATAA TGTTGATTTT
 AGGAAGAGAA ATTGGATGGG ACTGGTTTTG ATCATGGTTG GCCAGGCTCC CATACTGCTA
 TTGACATTTG CAGAA

  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
AY259117
dbSNP Blast Analysis
UniGene Cluster ID
82890

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/G
 G/G
 HWP A
 G
ss7986505 PDR90 Global 174 IG 0.011 0.989 1.000 0.006 0.994
HapMap-CEU European 116 IG 1.000 1.000
HapMap-HCB Asian 88 IG 1.000 1.000
HapMap-JPT Asian 86 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 116 IG 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.003+/-0.041 692 549 0 0

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

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Revised: May 25, 2006 1:38 PM .