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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs3135838          
refSNP ID: rs3135838
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:103/129
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_000142.2:c.109+540C>T
NM_022965.1:c.109+540C>T
NT_006081.18:g.301962C>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 ss28528382 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3135838 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
ss4384015COX|FGFR3-347fwd/BC/Tccgaccctgcccctgcctgggggccgaggggcttccccgtgggtgcgcgccgagctccag02/28/0210/10/03103Genomicunknown
ss14616414WI_SSAHASNP|chr4.NT_037623.4_299565fwd/BC/Tccgaccctgcccctgcctgggggccgaggggcttccccgtgggtgcgcgccgagctccag11/05/0311/22/03119Genomicunknown
ss28528382EGP_SNPS|FGFR3-001785byFreqfwd/BC/Tccgaccctgcccctgcctgggggccgaggggcttccccgtgggtgcgcgccgagctccag11/06/0401/27/05124Genomicunknown
ss82531701HGSV|Cor19240_SNV_20070510.chr4_1763541fwd/BC/Tccgaccctgcccctgcctgggggccgaggggcttccccgtgggtgcgcgccgagctccag11/30/0712/03/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3135838|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTGTCGGGAG GGCGCGGGGG GCCCCATTTC CACGATTCCC GCTGTTGTTA TTCGGGTTCT
 GCGCAGACGG AAAGTTCCCA TTGTTGGCGT CCCCCTCCCC CGGGCCCCAG TTTGTGGCCA
 GCTTCAGCCA AGGCGAGAGA CCGGACTTCT AAGGGTGGGT GTGCGCGTCA GCGAAGCCCG
 GCCCCTGCCC GCCCGAAGAG GCAGCAGCCT CCAGCGTCCC CGCTGCCGAC CCTGCCCCTG
 CCTGGGGGCC GAGGG
 Y
 GCTTCCCCGT GGGTGCGCGC CGAGCTCCAG GCAAGCGAGG GGCGCGTGTC CCAGCGTCGC
 GGGCCCTAGA CTGGGCTGGC GGTCCAGGTC CCGCGGGACG TCGAGGGTCT GAAGGGAGGT
 CCCAAGGGGC GAGGGGAGGG GAAGGGGCGC CCGGCCGGAC CTGCACACGC GCCGCGGTTC
 CTCGTGGGCC GGGCCGAGAG CTCCGGTGCC GCCGCCGCGT ACACCCGCAG CCGGCTCCGG
 ACGGGCGAGG GGGGC

  GeneView back to top
GeneView via analysis of contig annotation: FGFR3 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism)
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_006081->NM_000142
svfunction
referenceNT_006081->NM_022965
svfunction
HuRefNW_001838896->NM_000142
svfunction
HuRefNW_001838896->NM_022965
svfunction
CeleraNW_921918->NM_000142
svfunction
CeleraNW_921918->NM_022965
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_006081->NM_000142->NP_000133301962forwardintron
referenceNT_006081->NM_022965->NP_075254301962forwardintron
HuRefNW_001838896->NM_000142->NP_0001332014950reverseintron
HuRefNW_001838896->NM_022965->NP_0752542014950reverseintron
CeleraNW_921918->NM_000142->NP_0001331708826forwardintron
CeleraNW_921918->NM_022965->NP_0752541708826forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs3135838 maps exactly once on NCBI human chromosome 4
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
4NW_921918.117088261708826plusCalt_assembly_1CeleraCeleraview255
4NW_001838896.220149501739184minusGalt_assembly_8HuRefHuRefview255
4NT_006081.183019621766108plusCref_assemblyreferencereferenceview255

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_037623
dbSNP Blast Analysis
GenBank HTGS Finished:
AC016773.8 NC_000004.10

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
HWPC
T
ss28528382PDR90Global 168IG 0.893 0.107 0.655 0.946 0.054

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.101+/-0.201909000

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

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Revised: May 25, 2006 1:38 PM .