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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6076535          
refSNP ID: rs6076535
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:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_144628.2:c.*453G>A
NT_011387.8:g.358777C>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 ss8396433 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6076535 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
ss8396433SC_SNP|NT_011387.8_358777fwd/BC/Ttcctttggcctcttgctctccatcccaagctgactccttcagcagcagccccctccttct04/17/0310/10/03114Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6076535|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=114
 TCAGGATCTT AGAAGCTCAT CCTTCTGATG AGAACTATTT TTTTTTCCGT GAAGGAACTA
 TTATTACTTT AAAAGTGAGG GTAATTTACA TATGGGGTGT ATATATTCTA AAAATAGTAA
 TAAAAGTACC TTTTATAAGC AATGTTGTGT GGCTTGTAGA AGAAAGCAGG GAGGAAAAAA
 AGGCAGGCAA AACTAGTCTA GGTCTAGGCC CTAAAAATGA GCTTCCTTCC CACTTGACTG
 GAAACGCCCA TGTGATTTCT AGGCTGAAAA TAGGTAGGAT TTAACGAGTA ACCTAGTTCC
 CTTCTGTCTC TGATTTCTGA TCAGCTGATG GAGCTGCTAG TAAGAGGGGC CGATCATGCT
 CCCAGACGAG TCCTTTGGCC TCTTGCTCTC CATCCCAAGC
 Y
 TGACTCCTTC AGCAGCAGCC CCCTCCTTCT GTGTCCATCT GATGCAGGCA AGCAGGAGCA
 GTAAGAGGGC ATCCCATGTT CCAGTTCACC TTCTATGGGG TGACTAGGAG GTTCCCGGTA
 ACTAGGGCAG CCCAGGCCCA GCAGGTTGCA AAAGCAGCTG CAAGCTTCAG AAACCCACTT
 CCTCCAACAC CAGGGAGGTG GCAGAGAGCC CATCCAAAAG CCCACTGGGA GAGGCATAAG
 ATTCTGTGCC AGGCCCCCAG GTCCCCTCTG TGTCAGGTAG GCTCTGCTAC TGGCCTCTGA
 AGTAAAGGCA AACACAAACG GGCAGGGCAG GGTGGCAGGA ATAAAAAACT CTGGACAGAA
 ACCCTTTTAA TAAAGGAAAT TCCACCCCTC CCAATCCTTC

  GeneView back to top
GeneView via analysis of contig annotation: TBC1D20 TBC1 domain family, member 20
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_011387->NM_144628
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011387->NM_144628->358777reverse18033' UTR

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6076535 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
20NT_011387.8358777366777plusCref_assemblyreferencereferenceview400
20NW_001838652.1370112370112plusCalt_assembly_8HuRefHuRefview400
20NW_927317.1370787513611plusCalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011387
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank HTGS Finished:GenBank mRNA:
NM_144628.2 AL121747.41 AK127062.1
UniGene Cluster ID
203514

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
HWPC
ss8396433HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 88IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 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
withHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .