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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs28394859          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:125/130
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_177998.1:c.721A>G
NP_819056.1:p.Ile241Val
NT_006051.17:g.291629T>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 ss48409264 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28394859 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
ss35123762SSAHASNP|TA-079.chr4_4322256fwd/BC/Tctcacctctctcaccactcacctgttgttagttcccaaaacccagagtgatgagccgttc03/11/05125Genomicunknown
ss48409264APPLERA_GI|hCV25743129rev/TA/Ggaacggctcatcactctgggttttgggaactaacaacaggtgagtggtgagagaggtgag09/28/0511/30/05126Genomicunknown
ss1116889361000GENOMES|NA19240_2008_12_16_814017_chr4_4255085fwd/BC/Tctcacctctctcaccactcacctgttgttagttcccaaaacccagagtgatgagccgttc12/16/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs28394859|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTATTTCTGC CGCAAACTGG ACCATGAGAA ATGGCCATCA GAATAATCAC CGTGGGTCTT
 ACAAGTCCCT GAGTCATGGA AGAAACCTTT AATTATGCTC AGTACACATC ACTTATGAGA
 GATTCAGGTT TTGGAAGATT TTCAACAACA GCGGGCTGTC TGGCTGATGC TGAGTTGGGT
 GGCCCTGCAG TTCTTTGGAA CCTGCACTCC ATCTCTGAAC TCTGTGGACT CTGCAGGTTT
 CCAAGACATT CCAACATGGC AGAAGGGCCA CTCACCTCTC TCACCACTCA CCTGTTGTTA
 Y
 GTTCCCAAAA CCCAGAGTGA TGAGCCGTTC CTTGTGCTCA TTGAGTTGGT GCTTTGACTC
 ATTGAGGACG CCATTGGCCC ACAGAAGCAG GTTGGTGAAC ACCGAGTGGA TCACCCCAAA
 CCTGAAAAAC ACAAGGACTC AGTTCTCAAG CAGCCCTGGG AGAGCCTCAG GCACCATGGG
 GTGAGACAGA CGTGTGCACA CAAATACATG GCTCCTTCTC AGCCATGATT CTGGTTTCAC
 CTGGCAGTTC AGGCTCTGGG TGGGCCCCCT GCCTGGCTGG GTGGGGCAGA TCCATAGAAC

  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
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
ss48409264 AGI_ASP population multiple 78 IG 0.026 0.974 1.000 0.013 0.987

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.025+/-0.110 39 39 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
byClusterwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .