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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs202080          
refSNP ID: rs202080
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
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_001014380.1:c.-15+1759A>G
NM_032116.3:c.-15+2150A>G
NT_024524.13:g.11859318T>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 ss265267 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs202080 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
ss265267KWOK|OVLP-000621-133405byFreqfwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat06/30/0010/25/0679Genomic97 %
ss842020SC_JCM|AL162380.5_65121fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat07/27/0010/10/0385Genomicunknown
ss1206467KWOK|OVLP-000804-78270fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat09/02/0010/10/0386Genomic97 %
ss1206811KWOK|OVLP-000804-83171fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat09/02/0010/10/0386Genomic97 %
ss3078910TSC-CSHL|TSC1172336fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat06/07/0110/10/0396Genomicunknown
ss6579957WI_SSAHASNP|NT_009799.11_11859318fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat02/12/0310/10/03111Genomicunknown
ss13163283SC_SNP|NT_009799.12_11859318fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat10/22/0310/31/03119Genomicunknown
ss21097116SSAHASNP|WGSA-200403-chr13.chr13.NT_024524.13_11859318fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat03/19/0403/19/04121Genomicunknown
ss40357093ABI|hCV2255604fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat07/16/0507/16/05126Genomicunknown
ss67215903ILLUMINA|HumanHap550v1.1_rs202080fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat11/14/0611/14/06127Genomicunknown
ss67609636ILLUMINA|HumanHap650Yv1.0_rs202080fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat11/14/0611/14/06127Genomicunknown
ss68194020ILLUMINA|HumanHap250Sv1.0_rs202080fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat12/06/0612/07/06127Genomicunknown
ss70694166ILLUMINA|HumanHap550v3.0__rs202080fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat04/20/0703/30/08130Genomicunknown
ss71259508ILLUMINA|HumanHap650Yv3.0_rs202080fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat04/23/0704/23/07127Genomicunknown
ss75915807ILLUMINA|ILMN_Human_1M_rs202080fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat08/28/0708/29/07129Genomicunknown
ss83384494KRIBB_YJKIM|KHS448820fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat12/04/0712/04/07130Genomicunknown
ss89568295BCMHGSC_JDW|JWB-0648907fwd/BC/Tactctagctaaaattcttcaatgactgcccatatcaagaaaaattctaaactctgaatat02/26/0802/28/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs202080|allelePos=993|totalLen=1738|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TCTCCCAGTT CTTCTTCCTC TATGCCTCCT AACTAGGGTC TCATTTGTAG GCTCCTCCCG
 CAAACACATA CACACAACTC tttttttttt tttttttcct gacacggagt ctcgctctgt
 caccaggctg gagtgcagca gcatgatctt ggctcactgc aacctctgcc tcctgggttc
 aagctattct cctgcctcag cctcctgagt agctgggact ataggtgtgc gccaccatgt
 ctagctaatt tttatatttt taggagaaac gaggtttcac catcttggcc aggatggtct
 cgatctcttg atctcctgat ctgcccgcct cagccttcca aagtgctggg attacaggcg
 cgagccactt cgcccggccT ACACACATTT CTTAAATGag agttccatat ccaaacctct
 tcctttttct tttctactca ttactccaat gtgagctggt ccattctccc ttgtagcttt
 aattacttat ctatatgcaa acttctaact ccagcctgct ctctctgaac tccagactaa
 aatgcacctc cacctgaata tcccatagga acctctaaca aatgctcaaa actcaactaa
 tatctttata tttcacccca ataaaaacca gctcctcctc atctcaatca acggattcac
 tattacctca gtcatgctag ccagaaactg aggaatcaat cagctaagag ttccaaatct
 aactcccaac atccaaactc ttatcaagtc atatcaattt tatctcttaa atattccttg
 aatccatgtc tttctgtaac tccaaatgct taattcagac tctcttcatt tctctactgg
 actttgtttt tttctattat acaactggct tttctactac ctgtaatgtt tcccctccca
 ggtccattct ctacactggg gctggagtta tctttctaaa atacaaatct gacgccacca
 ccactctagc taaaattctt caatgactgc cc
 Y
 atatcaagaa aaattctaaa ctctgaatat ggtgccaagt actttaagat ctggcctcAC
 CCACTAATTG CAAGTATTCT GGGAtccagt cattcagaac tacctagcgt ttcccaaata
 caaaatactg attcttcaat ctatcctttg cttattttgt gccatccatt tgtcctagaa
 tgactttcct catcatcact ccagtgaaag cttattcaac tattttaaca caagttaaaa
 gtcaaatcac actgaaggcc tcccctgact tccttagaca gagtcaggAT CTTTCTACTA
 AATGACAGAG AATGGTCAGT GCTTGAGAtc aggaccagac ccacctgggc tgaaatccca
 ggttcacacg ttaccagcta tgattttgag caaggcctct aaagcctgtt tcctcatctc
 taaaaatcag taactacttc accaactgtt ttgaggatta agtaaggagt tgcatgcaaa
 atactcctca cagcacctga catattcaat aaatgttact gttatGTGAT TATTTCCTCT
 GGGCTCCTAG AGCAACTTGC ACTTATCTCT ACCACACTAC TGTGATGACA AGACTGCcca
 tgcaggatac agactatctt ttttcatctc tttattctca ccacctggca taatgcctgg
 cacataggtt cctaacacat tttgaatgaa taaatAAAAT ACTTCAAACC TTATGTTGTA
 TCACATAAGG CCTCAATTTT GTTTT

  GeneView back to top
GeneView via analysis of contig annotation: KATNAL1 katanin p60 subunit A-like 1
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_024524->NM_001014380
svfunction
referenceNT_024524->NM_032116
svfunction
HuRefNW_001838071->NM_001014380
svfunction
HuRefNW_001838071->NM_032116
svfunction
CeleraNW_925473->NM_001014380
svfunction
CeleraNW_925473->NM_032116
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_024524->NM_001014380->NP_00101440211859318reverseintron
referenceNT_024524->NM_032116->NP_11549211859318reverseintron
HuRefNW_001838071->NM_001014380->NP_001014402534951forwardintron
HuRefNW_001838071->NM_032116->NP_115492534951forwardintron
CeleraNW_925473->NM_001014380->NP_00101440211684083reverseintron
CeleraNW_925473->NM_032116->NP_11549211684083reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs202080 maps exactly once on NCBI human chromosome 13
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
13NW_001838071.253495111696298minusGalt_assembly_8HuRefHuRefview992
13NW_925473.11168408311948859plusCalt_assembly_1CeleraCeleraview992
13NT_024524.131185931829777318plusTref_assemblyreferencereferenceview992

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_024524 AC002402 AL162380.5 AL356750.3
dbSNP Blast Analysis
GenBank HTGS Finished:
AC002402.1 AL356750.16 NC_000013.9

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss265267HapMap-CEUEuropean 118IG 0.966 0.034 1.000 0.983 0.017
HapMap-HCBAsian 86IG 0.884 0.116 0.752 0.942 0.058
HapMap-JPTAsian 88IG 0.795 0.205 0.898 0.102
HapMap-YRISub-Saharan African 120IG 0.850 0.133 0.017 0.343 0.917 0.083

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.118+/-0.21227021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .