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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6104180          
refSNP ID: rs6104180
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_002951.2:c.1753+533A>T
NT_011362.9:g.915946A>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 ss8430056 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6104180 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
ss8430056SC_SNP|NT_011362.7_915946fwd/BA/Tcaaatcacttaagcatttctgaggcttttgtgctattggatcaggggtgccttgcatttc04/17/0310/10/03114Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6104180|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=114
 TGGCCTTTTA GGACAGTTAA TACGAAGATA AACCTGTTTG GTCCATCACT TAGAACAGCT
 GTCATTATAT TGGGCTTTGT TGTACTGTGC CACTGTTGGC AGACCATTTA CCCTCAGTTA
 ATAACCCTGT TTATTTCCAG AGATTACTCA CTTATCGTAT CTTTACATTG AGCAATCTTC
 CTGGATGAAG AGCATTAATG CAGTTTCCAA AGGTTATCTT TCCCCACGCT ATCGATCTTC
 ACATTTGCTG CCGGCTCTGT CTGTGTAGTA ATAGAAAACA GTCCTTTCCA CAGTCAGACA
 TGCTATCCTG CATCGTTCTC TGGAGACCTT AGGACTTCAA CAGCCTAAAC ATAACAAGAC
 AGTAAATTCA CAAATCACTT AAGCATTTCT GAGGCTTTTG
 W
 TGCTATTGGA TCAGGGGTGC CTTGCATTTC ACTGTGACTT TAAttttttg ttcgttgttt
 tttttttttt gagacagggt cttactctgt cacccaggct ggagtgcagt ggtgcattca
 tggctcactg cagccttgac ctcccagact caggtgatcc tcccacctca gcctccagag
 cagctgggac tccaggcttg tgtcaccaca tttagctagt atttgtattt tttgtagaga
 cggggtcttg ctgtgttcag agctggtctt gaactcctag gctcaagcag tcttcccgcc
 tttggcctcc cagagtgcta ggattatagg tgtgagccac cacgcctggc cTGACCTTAA
 TATTTTTAAA ATTCTTTGCC TCTTTCAGGA GTCACTATCT

  GeneView back to top
GeneView via analysis of contig annotation: RPN2 ribophorin II
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_011362->NM_002951
function
HuRefNW_001838665->NM_002951
function
CeleraNW_927339->NM_002951
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011362->NM_002951->NP_002942915946forwardintron
HuRefNW_001838665->NM_002951->NP_002942918525forwardintron
CeleraNW_927339->NM_002951->NP_0029426073411forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6104180 maps exactly once on NCBI human chromosome 20
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
20NW_927339.1607341132570302plusAalt_assembly_1CeleraCeleraview400
20NW_001838665.191852532598614plusAalt_assembly_8HuRefHuRefview400
20NT_011362.991594635296445plusAref_assemblyreferencereferenceview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011362
dbSNP Blast Analysis
GenBank HTGS Finished:
AL031659.9

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/T
HWPA
T
ss8430056HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 84IG 0.976 0.024 1.000 0.988 0.012
HapMap-JPTAsian 84IG 1.000 1.000
HapMap-YRISub-Saharan African 108IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.005+/-0.05027021000

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

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Revised: May 25, 2006 1:38 PM .