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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs10082916          
refSNP ID: rs10082916
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/129
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
NM_000966.4:c.184+1701G>A
NT_029419.11:g.15762751C>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 ss13937680 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10082916 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
ss13937680WI_SSAHASNP|chr12.NT_029419.10_15762751byFreqfwd/BC/Ttctgtctctgaaattgctctttcccccgccttcaatcaccttctcttggccccagttgaa11/05/0310/25/06119Genomicunknown
ss16168288SC_SNP|NT_029419.10_15762751fwd/BC/Ttctgtctctgaaattgctctttcccccgccttcaatcaccttctcttggccccagttgaa11/18/0311/22/03120Genomicunknown
ss66942832ILLUMINA|HumanHap650Yv1.0_rs10082916fwd/BC/Ttctgtctctgaaattgctctttcccccgccttcaatcaccttctcttggccccagttgaa11/14/0611/14/06127Genomicunknown
ss70984847ILLUMINA|HumanHap650Yv3.0_rs10082916fwd/BC/Ttctgtctctgaaattgctctttcccccgccttcaatcaccttctcttggccccagttgaa04/23/0704/23/07127Genomicunknown
ss75374548ILLUMINA|ILMN_Human_1M_rs10082916fwd/BC/Ttctgtctctgaaattgctctttcccccgccttcaatcaccttctcttggccccagttgaa08/28/0708/29/07129Genomicunknown
ss1135576521000GENOMES|NA19240_2008_12_16_2461278_chr12_51905712fwd/BC/Ttctgtctctgaaattgctctttcccccgccttcaatcaccttctcttggccccagttgaa12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10082916|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTCTTTCCAG TGGAGCTGCC AGCCCAGCCT AGTCACCCCT TTCACATACA GACACACAAC
 CCTCTGCGTG CCCCCTCCTG GAAGCAGGGC GCCTTCTCTT CTACCTCTGT CTCTGCGCTC
 GTGGAGCCAT GAAGGATGTG CGTTTATCTT TTTGTCTTTT TCTCTCCAAC TCTGTCTCTG
 AAATTGCTCT TTCCCCCGCC
 Y
 TTCAATCACC TTCTCTTGGC CCCAGTTGAA GCCTTCTCTT AACCAGCTTG GAACCCCCAC
 CTGTAATGGC CTGGCCAGGA GGAATGACTA CCAACTGGGA GGAGAGGGGT CCCAGAGGGA
 GGAGGAGAGG AGAGGCCCAA GCCTTGGCTG CTGTCAGCAC TCAAAGGCTT AACCCAAAGA
 GGGCAGGCCT GGGGAACAAG

  GeneView back to top
GeneView via analysis of contig annotation: RARG retinoic acid receptor, gamma
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_029419->NM_000966
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_029419->NM_000966->NP_00095715762751reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs10082916 maps exactly once on NCBI human chromosome 12
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
12NW_001838059.188771350661553plusCalt_assembly_8HuRefHuRefview200
12NT_029419.111576275151905712plusCref_assemblyreferencereferenceview200
12NW_925395.189189953268070plusCalt_assembly_1CeleraCeleraview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_029419
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss13937680HapMap-CEUEuropean 120IG 0.917 0.083 0.752 0.958 0.042
HapMap-HCBAsian 90IG 0.978 0.022 1.000 0.989 0.011
HapMap-JPTAsian 90IG 0.978 0.022 1.000 0.989 0.011
HapMap-YRISub-Saharan African 120IG 0.650 0.333 0.017 0.403 0.817 0.183

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.129+/-0.21927021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .