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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs4874143          
refSNP ID: rs4874143
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/129
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_052963.1:c.123-248C>T
NT_023684.17:g.378856G>A
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 ss44886610 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4874143 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
ss6734698WI_SSAHASNP|NT_023684.13_24190fwd/TA/Gcgtgtgctgctgagtcacggatcccaccaacccagctaagcgggaaagggcaagcccagc02/12/0310/10/03111Genomicunknown
ss17237774CSHL-HAPMAP|CSHL-HuAA-200402.chr8.NT_023684.16_346832fwd/TA/Gcgtgtgctgctgagtcacggatcccaccaacccagctaagcgggaaagggcaagcccagc02/17/0403/04/04120Genomicunknown
ss22706293SSAHASNP|WGSA-200403-chr8.chr8.NT_023684.16_346832fwd/TA/Gcgtgtgctgctgagtcacggatcccaccaacccagctaagcgggaaagggcaagcccagc03/21/0403/21/04121Genomicunknown
ss44886610ABI|hCV26237894fwd/TA/Gcgtgtgctgctgagtcacggatcccaccaacccagctaagcgggaaagggcaagcccagc07/19/0507/19/05126Genomicunknown
ss78168380HGSV|Cor12878_SNV_20070510.chr8_144485132fwd/TA/Gcgtgtgctgctgagtcacggatcccaccaacccagctaagcgggaaagggcaagcccagc10/17/0710/18/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4874143|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TGTGCTCCAG CTGTCTCCAC TTCACCCCGT CTTCGTGCTT CTCCTTCTCC CACCTAAAGA
 CGGAGACAGG ACGTGTCACT CTCCTGGGCC AGGCCCTGCA TGAGCCTCTT CCCCGCTCCC
 ACAGTGGCTC CTCCCTGTGG CTCCTAGCAG GTGAGCAGTG TGGCCTCCAC CTCACGGGGG
 AGGAAAACAA GGCCTGCAGA GGGAGGCAAC CCTACCTGAC CTCAGACCCC ATGCCCGTGT
 ACCCGCCCAT GCCCCCCACC TGCAGAGGCC CGTGTGCTGC TGAGTCACGG ATCCCACCAA
 R
 CCCAGCTAAG CGGGAAAGGG CAAGCCCAGC TAAGTGGGAA AGGCAACGTG CCTCTCCCAG
 GCTCTAGGGC CTCTCCCCAG ATGGGTCCCT TCAGAGCCGG TCTAGAATCT TCGGGAACCT
 CTCCATGGGA CCATTTCATT TGCTAAATAA AGGACCTGGC TGCTTATGAG AGAGCCCTGC
 CTCCGAGGAG CTGGGTGGAA GGGGGTCCAG CAGTGCAGCC AGTGGAGAGG CACCACAGCA
 GGGCGCAGGA CCGCCGCCCA CAGAGGATCG GGCAGGGTGG AAGGGTGGAA GAGGCAGGGC

  GeneView back to top
GeneView via analysis of contig annotation: TOP1MT topoisomerase (DNA) I, mitochondrial
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_023684->NM_052963
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_023684->NM_052963->NP_443195378856reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs4874143 maps exactly once on NCBI human chromosome 8
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
8NW_001839142.21751585139667016minusCalt_assembly_8HuRefHuRefview300
8NW_924018.11631155140723967plusGalt_assembly_1CeleraCeleraview300
8NT_023684.17378856144485132plusGref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023684
dbSNP Blast Analysis
GenBank HTGS Draft:
AF189001.3 AF276758.2

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/G
HWPG
ss44886610HapMap-CEUEuropean 114IG 1.000 1.000
HapMap-HCBAsian 86IG 1.000 1.000
HapMap-JPTAsian 86IG 1.000 1.000
HapMap-YRISub-Saharan African 114IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
27021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .