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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs28483498          
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:C
Clinical Association:unknown
HGVS Names
NG_008843.1:g.46656C>T
NM_153717.2:c.1115C>T
NP_714928.1:p.Thr372Met
NT_006051.17:g.1842024C>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 ss76896896 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28483498 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
ss35235506SSAHASNP|TA-079.chr4_5872651fwd/BC/Tgtttctttttgcaggacgccctggagaggagatggggcgggcgcacatggcaaaagtgat03/11/05125Genomicunknown
ss48404359APPLERA_GI|hCV25937054byFreqrev/TA/Gatcacttttgccatgtgcgcccgccccatctcctctccagggcgtcctgcaaaaagaaac09/28/0511/03/06126Genomicunknown
ss68889120PERLEGEN|PGP04818118byFreqfwd/BC/Tgtttctttttgcaggacgccctggagaggagatggggcgggcgcacatggcaaaagtgat01/30/0703/31/08127Genomicunknown
ss74875864ILLUMINA|ILMN_Human_1M_rs28483498fwd/BC/Tgtttctttttgcaggacgccctggagaggagatggggcgggcgcacatggcaaaagtgat08/28/0708/29/07129Genomicunknown
ss76896896SI_EXO|NT_006051.17_1842024fwd/BC/Tgtttctttttgcaggacgccctggagaggagatggggcgggcgcacatggcaaaagtgat09/20/0709/20/07129Genomicunknown
ss1128742041000GENOMES|CEU.trio.12.15.2008_904818_chr4_5805480fwd/BC/Tgtttctttttgcaggacgccctggagaggagatggggcgggcgcacatggcaaaagtgat12/15/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs28483498|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CCTCCACAGC CCTGTGGGGG CCACAGGGCC AGATTGGCCG GGGGAGATGA CTATAAGCCA
 GGTGGCTTTT CCTCCTTGAC CGTTTGTAAA TCTGGATTCC CTCCTAGGAG GGTGGCCCTC
 TGGGGAGCGC TACTGGTGAC TAAGTGCCTA CATGCTAAGC TGCGTCAGCC TCCCCGCACC
 CTAGGAGAGA CACTTAATCC CCACCTCGGG GGCAGACGCA GATCTCGCTC ATGAAGGAGA
 GGGGGAGTTC ATCCCTCTGA GCTCCGCTCT CCCAGGCAGT GCCATTAGTT AATGACCCTG
 GTGGCTTCTT CTCAGCTGTT AATTAACATG CCCTGGTGGT TCCCAGGACA CCCCAGCTAT
 GGTCCTGTGT GTTTCTTTTT GCAGGACGCC CTGGAGAGGA
 Y
 GATGGGGCGG GCGCACATGG CAAAAGTGAT TGAGTTTCTG AAGCTGCAAG TCCAGGAGGA
 GACCAGGTGC CGGCTGGCTG CCATCTCCCA CGGCCTGGAG CTGCTGGCTG GTGAGGGGAA
 GCTGTCCGGG CGGCAGAAGG AGGAGCTGCT CACGCAGCAG CACAAGGCCT TCTGGCAGGA
 GGCAGAGCGC TTCAGCCGGG GTGAGCCGTG GGCATGGGTG CCGCCGTCCA CAACACTGGC
 CTTCTGGGTC CCTGGGGCTG TGCAGTGAGA GGGCTGGCAG CCTGGGGCAG TGTGCCCATG
 ATGCCGGGCA CAGGCTGCCT TTCTGCTTCT GCCCTAGGGA CTGGGTCACT GGGCTGCTCT
 CTGGGGCTCT CTTCCCTTCT CTGTACAGCA GAGTCCATGA

  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
NT_006051.17
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss48404359 AGI_ASP population multiple 76 IG 0.789 0.211 0.479 0.895 0.105
ss68889120 HapMap-CEU European 120 GF 0.900 0.100 0.450 0.550
HapMap-HCB Asian 90 GF 0.911 0.089 0.456 0.544
HapMap-JPT Asian 90 GF 0.022 0.978 0.511 0.489
HapMap-YRI Sub-Saharan African 120 GF 0.033 0.933 0.033 0.500 0.500

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.496+/-0.042 1245 1040 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
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .