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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs10853952          
refSNP ID: rs10853952
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:C
Clinical Association:unknown
HGVS Names
NM_014963.2:c.-126-9533G>A
NT_011255.14:g.1103934C>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 ss44173572 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10853952 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
ss16809607CSHL-HAPMAP|CSHL-HuAA-200402.chr19.NT_011255.14_1103934fwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg02/17/0410/26/06120Genomicunknown
ss18308384SC_SNP|SC-CHR1_NA07340-200402.chr19.NT_011255.14_1103934fwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg02/20/0403/04/04120Genomicunknown
ss19409359CSHL-HAPMAP|CSHL-HuDD-200402.chr19.NT_011255.14_1103934fwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg02/20/0403/04/04120Genomicunknown
ss21553671SSAHASNP|WGSA-200403-chr19.chr19.NT_011255.14_1103934fwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg03/20/0403/20/04121Genomicunknown
ss44173572ABI|hCV11695405byFreqfwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg07/18/0511/03/06126Genomicunknown
ss69222246PERLEGEN|PGP04858237fwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg01/30/0701/30/07127Genomicunknown
ss75112626ILLUMINA|ILMN_Human_1M_rs10853952fwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg08/28/0708/29/07129Genomicunknown
ss90879370BCMHGSC_JDW|JWB-1135171fwd/BC/Tagcctcaccgccccataccccaggagcccagtgcttctctcacagggaaaggtgtactgg02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10853952|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 CCAACCACGG GCAGAGGCCA CCGCTCCCGA GCTTGGACCC TGCCACGCGC AGGCACAGGC
 CAGGCGGCGC CGGGGAAGCC TGGGGGCCCC AGACCGGCCC AGCACCGCCT GACATTTCTC
 AAGCATGCTG GGGGACGGCC CCTCAATTTA GGATGAGGAC GAGGTGGGCC CGGCAGGAGG
 GCAGGAGCCG GGGTCCAGGG CGAGCAAGTT CTCCCCGCCC CACGAGGAAC GGCAGTGGCC
 CCGGTTGCCT GGAGGTGGAA GGGGCACTGC AGCCTCACCG CCCCATACCC CAGGAGCCCA
 Y
 GTGCTTCTCT CACAGGGAAA GGTGTACTGG CCAGACTCAG CGCCCTGAGG ACGGGGTCGG
 AACCCAGCGC CCAGGAAGCT CCCCTCCCCC CGACCAAGGA CCTCCCTCCA GGTGGGTCCT
 CTGGAAACTC AGGCCCGCGG CCATCACGGC CCCTCTCCTG GGAGGGCTCA AGGGTGTTGG
 CCGTGGGGGC TTCACACTGC ACCCCGATTT CGAGGGAAGC CCCTGCCCAT GGCTTCCGGG
 GCCTTCCGGA GGGGCCAAGG GGCGGTGCCA TGGGAGGGAA AGTTCCCAAG CTCGGAGATG

  GeneView back to top
GeneView via analysis of contig annotation: SBNO2 strawberry notch homolog 2 (Drosophila)
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_011255->NM_014963
svfunction
HuRefNW_001838476->NM_014963
svfunction
CeleraNW_927173->NM_014963
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011255->NM_014963->NP_0557781103934reverseintron
HuRefNW_001838476->NM_014963->NP_055778929998reverseintron
CeleraNW_927173->NM_014963->NP_055778358834reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs10853952 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_001838476.1929998940799plusTalt_assembly_8HuRefHuRefview300
19NW_927173.13588341100110plusTalt_assembly_1CeleraCeleraview300
19NT_011255.1411039341114934plusCref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011255
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC120982.2 NC_000019.8 AC011553.3

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss44173572HapMap-CEUEuropean 118IG 0.492 0.492 0.017 0.050 0.737 0.263
HapMap-HCBAsian 90IG 0.200 0.578 0.222 0.317 0.489 0.511
HapMap-JPTAsian 88IG 0.386 0.455 0.159 1.000 0.614 0.386
HapMap-YRISub-Saharan African 116IG 0.793 0.155 0.052 0.020 0.871 0.129

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.425+/-0.1792702102700

  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 .