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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2440039          
refSNP ID: rs2440039
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/129
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_001092.3:c.1450+2696T>C
NM_021962.2:c.1561+2696T>C
NT_010718.15:g.559953A>G
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 ss21399728 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2440039 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
ss3419892SC_JCM|AC015884.7_143503fwd/TA/Ggagggttcacagggtcagagggagggttcggaaggggctgggggagggctcacagggtca09/24/0110/10/03100Genomicunknown
ss21399728SSAHASNP|WGSA-200403-chr17.chr17.NT_035414.4_559953fwd/TA/Ggagggttcacagggtcagagggagggttcggaaggggctgggggagggctcacagggtca03/19/0403/20/04121Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2440039|allelePos=501|totalLen=832|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=121
 TCAGAGGGAG GGTTCCGGAA GGGGCTGGGG GAGGGGTCAC AGGGTCAGAG GGAGGGTTCA
 GGAAGGGGCT GGGGGAGGGC TCACAGGGTC AGAGGGAGGG TTCCGGAAGG GGCTGGGGGA
 GGGGTCACAG GGTCAGAGCG AGGGTTCCGG AAGGGGCTGG GGGAGGGCTC ACAGGGTCAG
 AGGGAGGGTT CCggaagggg ctgggggagg gttcacaggg tcagagggag ggttccggaa
 ggggctgggg gaggggtcac agggtcagag ggagggttcc ggaaggggct gggggagggg
 tcacagggtc agagggaggg ttccggaagg ggctggggga ggggtcacag ggtcagaggg
 agggttccgg aaggggctgg gggagggCTC ACAGGGTCAG AGGGAGGGTT CCGGAAGGGG
 CTGGGGGAGG GTTCACAGGG TCAGAGGGAG GGTTCCGGAA GGGGCTGGGG GAGGGTTCAC
 AGGGTCAGAG GGAGGGTTCG
 R
 GAAGGGGCTG GGGGAGGGCT CACAGGGTCA GAGGGAGGGT TCCGGAACGG GCTGGGGGAG
 GGTTCACAGG GTCAGAGGGA GGGTTCCGGA AGGAGCTGGG GACGGCTCAC AGGGTCAGAG
 CGAGGGTTCC GGAGTCAGAC CATCTGGGTC CACACCCCAG CTCTGCACAG ATCACCTCCC
 TTCTCTCCCC AGGTTCCTGT CTGCACAGCA GGAAAAGTCA TGGTGCCTAC ACCCTGGGCC
 TGCCTGTCCA GAGGTCCTGA GTTTACCACG GCTGAAGACA CAGGGCCTCA CCTCTGAGTG
 AGAACAGACA TATGAGTGGG TCAGGGGTGG C

  GeneView back to top
GeneView via analysis of contig annotation: ABR active BCR-related gene
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_010718->NM_001092
svfunction
referenceNT_010718->NM_021962
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010718->NM_001092->NP_001083559953reverseintron
referenceNT_010718->NM_021962->NP_068781559953reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2440039 maps exactly once on NCBI human chromosome 17
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
17NW_001838403.1554898863728plusGalt_assembly_8HuRefHuRefview500
17NT_010718.15559953903329plusAref_assemblyreferencereferenceview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_035414 AC016292
dbSNP Blast Analysis

  Population Diversity back to top
There is no frequency data.

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

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Revised: May 25, 2006 1:38 PM .