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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs9270010          
refSNP ID: rs9270010
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:118/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_002124.1:c.101-775A>G
NT_007592.14:g.23411180T>C
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 ss12694966 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9270010 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
ss12694966SI_MHC_SNP|AL713966.7_119094_TCfwd/BC/Ttgttcttgaacacatgcccagatagacataacaacgtttaaaatgataaatgcaaaatga09/10/0310/10/03118Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9270010|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=118
 TTCAACAGCA CCCACCGCGT TCACCCTGTG AACACTTCCT TAGTGATGAC CTTGTGCCAG
 GCCTGCGCTG CCTCTAGGAA TCCAAACGAG GGAAAACAGA CCTCTCCACT CCTCTGGGGG
 AGCTTAAAGA GCAGTGAAAG CGATGGCCAA AAACCAAACA CACAAGAGCT TAGACAGCAA
 TGAGAAATAT CAGAAGTGTG GCGTTCTAGA GCAGAGAATA ATAGAAGATT CCCAGTTAAA
 TTTGGATTTc caataaatta tggttgtgta tctgaaattc agatttcact aggaacctgt
 attttatttg taactctaGC CCAACTTGCT AGTCAAACCT CAGAAGAAGG AGTGATTTAA
 TACTTCCTTG TGTTCTTGAA CACATGCCCA GATAGACATA
 Y
 ACAACGTTTA AAATGATAAA TGCAAAATGA ATGAAAGTTT CTCCTATACA TCAGAACTAG
 CAGCCCTTGC ATTTCTGTCC CCACTCTAAG AAACAGCCTG GTACATATGA ATATCAGAAA
 TTGTGTCAAT AATTCAGACA CAATATAGTC ACTACTCACT AATGATGGTC AAACTCTCAA
 ACTCTATAAT CAGAAAACCT GAATAAAAAC ACGATCTCTT CTACTTGGGT CAATTTTTAC
 CAACCATAAG CCTTTTTGTA ATCTATCAAA TGCATTTAAT AATAGCGTAA TCCTCACAGG
 ATTACCGTTA AGTGTAAAAT TAAATGATGA CACTTCTTAG CACTGATCAC ATAATAAACA
 CTCGAATACA TTCCCATTTT AACTTTTCTG ATCCTATAAC

  GeneView back to top
GeneView via analysis of contig annotation: HLA-DRB4 major histocompatibility complex, class II, DR beta 4
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: LOC100133661 similar to HLA class II histocompatibility antigen, DR-W53 beta chain
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
c6_QBLNT_113896->XM_001723414
function
c6_QBLNT_113896->XM_001723417
function
c6_QBLNT_113896->XM_001723419
function
HuRefNW_001841135->NM_021983
function
CeleraNW_923051->XM_001713857
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
c6_QBLNT_113896->XM_001723414->XP_001723466423584reverseintron
c6_QBLNT_113896->XM_001723417->XP_001723469423584reverseintron
c6_QBLNT_113896->XM_001723419->XP_001723471423584reverseintron
HuRefNW_001841135->NM_021983->NP_06881827094reverseintron
CeleraNW_923051->XM_001713857->XP_001713909140072forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs9270010 maps exactly once on NCBI human chromosome 6
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
6NW_923051.114007228381076minusGalt_assembly_1CeleraCeleraview400
6NG_002433.11168632522256plusCalt_haplotype_7DR53DR53view400
6NT_113891.1394267132631214plusCalt_assembly_3c6_COXc6_COXview400
6NT_113896.142358432632079plusCalt_assembly_4c6_QBLc6_QBLview400
6NT_007592.142341118032660908plusTref_assemblyreferencereferenceview400
UnNW_001841135.127094unplacedplusCalt_assembly_8HuRefHuRefview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AL713966.7
dbSNP Blast Analysis
GenBank HTGS Finished:
AL713966.7

  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 .