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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs4458268          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/130
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_002999.2:c.34T>C
NP_002990.2:p.Phe12Leu
NT_011362.9:g.9029906A>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 ss28459171 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4458268 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
ss5984905SC_JCM|NT_011362.7_9029905fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc01/10/0310/10/03111Genomicunknown
ss16246241CGAP-GAI|1490287rev/BC/Tgcccccgcccgtctgttcgcgctgctgctgtcttcgtaggcggagtcgccgagtcgatcc11/18/0311/22/03120cDNAunknown
ss19469946CSHL-HAPMAP|CSHL-HuDD-200402.chr20.NT_011362.8_9029906fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc02/20/0403/04/04120Genomicunknown
ss28459171KYUGEN|QH04009byFreqrev/BC/Tgcccccgcccgtctgttcgcgctgctgctgtcttcgtaggcggagtcgccgagtcggtgg07/07/0408/05/04123Genomicunknown
ss66683402ILLUMINA|HumanHap300v1.1_rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc11/09/0611/09/06127Genomicunknown
ss67337828ILLUMINA|HumanHap550v1.1_rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc11/14/0611/14/06127Genomicunknown
ss67734664ILLUMINA|HumanHap650Yv1.0_rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc11/14/0611/14/06127Genomicunknown
ss70805423ILLUMINA|HumanHap550v3.0__rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc04/20/0703/30/08130Genomicunknown
ss71384828ILLUMINA|HumanHap650Yv3.0_rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc04/23/0704/23/07127Genomicunknown
ss75690113ILLUMINA|ILMN_Human_1M_rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc08/28/0708/29/07129Genomicunknown
ss79182844ILLUMINA|HumanHap300v2.0_rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc04/18/0711/18/07130Genomicunknown
ss84273881KRIBB_YJKIM|KHS672966fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc12/04/0712/06/07130Genomicunknown
ss106190451BGI|BGI_rs4458268fwd/TA/Gccaccgactcggcgactccgcctacgaagacagcagcagcgcgaacagacgggcgggggc09/13/0806/18/09130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4458268|allelePos=97|totalLen=581|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GTCCAGAACA AAGGAGGCAC CGGCCTGCGC CCCCGCTTCG CCCCCAGCCC GGGAACCTCC
 AAGCACCCAC CGACTCGGCG ACTCCGCCTA CGAAGA
 R
 CAGCAGCAGC GCGAACAGAC GGGCGGGGGC CATGGCACCG CGGACTGGAG AAGGCGCGCA
 GGCTGCGGCG AGTGGNCCCG GGCGGGCGCG CCACCCATCT TATAGGCGGC CTACCGGCCC
 CGCCCCGGCC GCCCCCGCCC CGCCGCCCGC ACCCCGCCCG GAATTCCCCA GTGGAAGCGA
 GGCCTGCGGG GCACTGCGCC CGCCCGCGGA GTTGGAAACC CCAAGGGACC CGCCCTGCCC
 GAGCCCGCCG GCTCCTACTC AACCCCTAGT CCTACCCTCC GGGAGCTCCA ACTCCCTTTA
 TTTATTTGAC CCACTGCCAG GCAGGTCCCC AGAGATCACT GCGGCTAACC CCATTTTATA
 GTTGGGGAAA CTAAGGCCCA GGGACGGGAA GGACTTCCCT AGGGTGTTGA GTTTAGACCA
 GCCTTCATAC CGGGTGTGCT CCCCTCTGAA GACACAGAAC TTCCCAAATG GGATGTGACC
 GGTG

  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_011362.8 BM554308
dbSNP Blast Analysis
UniGene Cluster ID
252189

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss28459171 CP 156 AF 0.670 0.330
JPK2 200 AF 0.480 0.520
HapMap-CEU European 120 IG 0.517 0.367 0.117 0.343 0.700 0.300
HapMap-HCB Asian 90 IG 0.289 0.533 0.178 0.556 0.444
HapMap-JPT Asian 90 IG 0.133 0.511 0.356 0.389 0.611
HapMap-YRI Sub-Saharan African 120 IG 0.683 0.267 0.050 0.817 0.183

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.463+/-0.131 1207 1002 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
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN YES YES

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Revised: May 25, 2006 1:38 PM .