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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs4253030          
refSNP ID: rs4253030
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:A
Clinical Association:unknown
HGVS Names
NM_000124.1:c.543+319A>G
NT_017696.14:g.1542911T>C
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 ss5608996 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4253030 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
ss5608996EGP_SNPS|ERCC6-009588byFreqfwd/TA/Gtgaaaatattgttagtcaaaaatgcattaatacactgaaaaacctatcttaaagtcaaaa01/08/0304/07/04111Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4253030|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=111
 TAGGAAGTAT TTTAAAAAGT GCTTATAAGA TGTGAAGCAA ATACTTATAA TTACAATAGA
 GAAATTTTGG GTTTCTTTTG TATGTTTAAT CTTTCTGCTG TTTTCCTTTA ACATCCCATT
 CTATTGCATT TAAAAAAACA CACATACATA GACACACACA TCCATACGTA TAcagttgct
 ccttgattta caacagggtt acatcccgac aaacccatcg taaattgaaa atattgttag
 tcaaaaatgc attaa
 R
 tacactgaaa aacctatcTT AAAGTCAAAA TATTGTAAGT CAAACCATAG TTAAGTCcag
 aggctcctca gtttataatg gggttatgcc ctgataaacc catcacaaag ttgaaaaatt
 gcaagtcAGA CCATGATAAG TTGGAGACCA TCTGTGTATT TGAGAAAAGT TCCTTTTTGG
 TGTTGCTTGC CTCACTTGGG CGCACTTCCT TAGTTTTCCT GCATCACCAT TTCTTTGGCC
 TGGCTTAGGG TCACA

  GeneView back to top
GeneView via analysis of contig annotation: ERCC6 excision repair cross-complementing rodent repair deficiency, complementation group 6
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_017696->NM_000124
svfunction
HuRefNW_001837975->NM_000124
svfunction
CeleraNW_924685->NM_000124
svfunction
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_017696->NM_000124->NP_0001151542911reverseintron
HuRefNW_001837975->NM_000124->NP_000115334337forwardintron
CeleraNW_924685->NM_000124->NP_0001151366696reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs4253030 maps exactly once on NCBI human chromosome 10
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
10NW_924685.1136669644324542minusTalt_assembly_1CeleraCeleraview255
10NW_001837975.233433745003226plusAalt_assembly_8HuRefHuRefview255
10NT_017696.14154291150408453minusTref_assemblyreferencereferenceview255

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AY204752
dbSNP Blast Analysis
GenBank HTGS Finished:
AC073366.4 AL138760.14 NC_000010.9

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
HWPA
G
ss5608996PDR90Global 178IG 0.933 0.067 0.752 0.966 0.034
HapMap-CEUEuropean 106IG 1.000 1.000
HapMap-HCBAsian 82IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.026+/-0.11127024000

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

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Revised: May 25, 2006 1:38 PM .