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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs11465412          
refSNP ID: rs11465412
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
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_021155.2:c.*1855C>T
NT_077812.2:g.410066G>A
Links

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 ss15355191 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11465412 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
ss15355191IIPGA-WEISS-MARTINEZ|IIPGA-CD209_11337byFreqfwd/BC/Tcaggcctgagccacngcgcccngnctctcccacgttcttgaactcgggcagcacatcctc11/14/0304/07/04120Genomicunknown
ss74814899AFFY|SNP_M-307860fwd/BC/Tcaggcctgagccaccgcgcccagtctctcccacgttcttgaactcgggcagcacatcctc08/09/0708/09/07128Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11465412|allelePos=101|totalLen=201|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=128
 TTGACCAGGA TGGTCTNGAT CTCTTGACCT CGTGATTCGC CCGCCGCGTC CTCCCAAAGT
 GCTGGGATTA CAGGCCTGAG CCACNGCGCC CNGNCTCTCC
 Y
 CACGTTCTTG AACTCGGGCA GCACATCCTC ACAGAAATCT AGGAACTGTT GGTAGGTTTC
 TTCCTCGCTG TACTCCAGGC TTGCTTCGGA GTCATAGTCA

  GeneView back to top
GeneView via analysis of contig annotation: CD209 CD209 molecule
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_077812->NM_021155
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_077812->NM_021155->410066reverse30793' UTR

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs11465412 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
19NW_001838480.28704777476132plusCalt_assembly_8HuRefHuRefview100
19NW_927173.169362097677485minusGalt_assembly_1CeleraCeleraview100
19NT_077812.24100667712070minusGref_assemblyreferencereferenceview100

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_077812.1
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank mRNA:
NM_021155.2 AF290886.1 AK293089.1
UniGene Cluster ID
278694

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss15355191D-0African American 46IG 0.609 0.391 0.251 0.804 0.196
E-0European 40IG 0.900 0.100 1.000 0.950 0.050
E-1European 6IG 1.000 1.000
HapMap-CEUEuropean 116IG 1.000 1.000
HapMap-HCBAsian 88IG 1.000 1.000
HapMap-JPTAsian 86IG 1.000 1.000
HapMap-YRISub-Saharan African 116IG 0.948 0.034 0.017 0.966 0.034
Concordant GenotypeTotal SampleC/CC/TT/T
ss15355191306285111
RefSNP Genotype SummaryTotal IndividualC/CC/TT/T
rs11465412308285111
Discordant Genotypes:
Indiviudal
SampleID		SubSNP(ss)GenotypePopulation
Handle		Submitter
Population		Submitter
SampleID		SampleID
Alias		Submission
Batch		NCBI
ProbeID
162ss15355191C/TIIPGA-WEISS-MARTINEZE-0E0232.5
162ss15355191C/CCSHL-HAPMAPHapMap-CEUNA07019CEPH1340.02r23_ch19_CEU_bcm:genotype_0002
348ss15355191C/TIIPGA-WEISS-MARTINEZE-0E0052.5
348ss15355191C/CCSHL-HAPMAPHapMap-CEUNA10860CEPH1362.01r23_ch19_CEU_bcm:genotype_0002
Genotype data submitted for317 samples from308 individualsIndividual with multiple genotypes submission:9

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .