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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs34825130          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:126/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_182701.1:c.157T>C
NP_874360.1:p.Tyr53His
NT_007592.14:g.19336863A>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 ss38347288 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs34825130 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
ss38347288EGP_SNPS|GPX6-006905byFreqfwd/BC/Ttatggagccctcaccctcaacggcgaggagacatccaattcaagcagtttgcaggcaagc07/07/0511/02/06126Genomicunknown
ss78815616HGSV|Cor18507_SNV_20070510.chr6_28586591rev/TA/Ggcttgcctgcaaactgcttgaattggatgtctcctcgccgttgagggtgagggctccata10/19/0710/20/07129Genomicunknown
ss116371502ILLUMINA-UK|NA18507_000041263_NCBI36.1_chr6_28586591rev/TA/Ggcttgcctgcaaactgcttgaattggatgtctcctcgccgttgagggtgagggctccata01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs34825130|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 ATTTAGAAGA CATAAATTCT AGCTATGGCA TCAGCTCTAA CTAAAAATTT TACTTGGAAA
 GATCCCTTCA GTTCTTAGAA TTTCAAGATA TTACATGAAG GGTCTTCGAG TGTTTTGAAA
 AAGTCCACAA ATGTTGGGAA TTATTTTTTA TCTTATATCG TTATGGTTAT TTTTGTAAAA
 TTCCAGGTGG ATTGCAACAA AGGGGTAACA GGCACCATCT ATGAGTATGG AGCCCTCACC
 CTCAACGGCG AGGAG
 Y
 ACATCCAATT CAAGCAGTTT GCAGGCAAGC ACGTCCTGTT TGTCAATGTG GCCGCCTATT
 GAGGCTTGGC AGCTCAGTAT CCTGGTAAGA ACTCACGTTT CAACTCTTTT GGAAGCAGCA
 TTGCCAGATA GCCATATTCT AATTCCAGAA GGTTTTACCA ATGTGTTATT GGAGGATGCG
 ATGGGAGAAC TGATCAGGTG ACTCTACCTC CCTAAATGCT GCTCCTGCTC TGCTCCTTAG
 AATATCAGGA TAATT

  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
DQ088982
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
ss38347288 EGP_YORUB-PANEL Sub-Saharan African 22 AF 0.091 0.909 1.000 0.045 0.955
EGP_HISP-PANEL Hispanic 42 AF 1.000 1.000
EGP_CEPH-PANEL European 40 AF 1.000 1.000
EGP_AD-PANEL African American 30 AF 0.067 0.933 1.000 0.033 0.967
EGP_ASIAN-PANEL Asian 46 AF 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.022+/-0.102 95 95 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
byClusterbyFreq UNKNOWN UNKNOWN YES

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Revised: May 25, 2006 1:38 PM .