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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6438553          
refSNP ID: rs6438553
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_002093.2:c.477+2191T>A
NT_005612.15:g.26135175A>T
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 ss10092500 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6438553 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
ss10092500BCM_SSAHASNP|chr3.NT_005612.13_26039183byFreqfwd/TA/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa06/27/0305/17/04116Genomicunknown
ss11603746WI_SSAHASNP|chr3.NT_005612.13_26039183fwd/TA/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa07/03/0310/10/03116Genomicunknown
ss14230498BCM_SSAHASNP|chr3.NT_005612.14_26135175fwd/TA/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa11/05/0311/22/03119Genomicunknown
ss20178960CSHL-HAPMAP|CSHL-HuFF-200402.chr3.NT_005612.14_26135175fwd/TA/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa02/21/0403/04/04120Genomicunknown
ss24357546PERLEGEN|afd4021651byFreqfwd/TA/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa08/10/0409/13/04123Genomicunknown
ss44376705ABI|hCV11209018fwd/A/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa07/18/0507/18/05126Genomicunknown
ss65815541ILLUMINA|Human1-rs6438553fwd/TA/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa10/10/0610/10/06127Genomicunknown
ss78959902HGSV|Cor18507_SNV_20070510.chr3_121122719fwd/A/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa10/19/0710/21/07129Genomicunknown
ss92255854BCMHGSC_JDW|JWB-1655372fwd/A/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa02/26/0803/02/08129Genomicunknown
ss1108179921000GENOMES|NA19240_2008_12_16_707564_chr3_121122719fwd/A/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa12/16/0812/17/08130Genomicunknown
ss1124070801000GENOMES|CEU.trio.12.15.2008_790999_chr3_121122719fwd/A/Tcattggtacctatggaggatgctatggaatgactattataaattttcgtaaataaagaaa12/15/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6438553|allelePos=496|totalLen=1896|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 TGCTGGGTAG AATAAGTTAT TAATTATACT ACTATCATTG AGAAATGAAA TTTTCAATGT
 AAGAGAAAGG AAATACAAAT ATAAGATTAT TACAGTTAAG TAAAAACTCA TCGATTTTAT
 TTGAAAGTAT CAGTATGAAC TCATGGTGTA TTTATTTTTG GAAAAAAAGA AGATGCATTA
 CATCTGAGAA AATTACCCac atatttccta gctctgttcg ctaaaaagac ccagaaacaa
 taaccaatcc cgtgacaatt agcacctcta gcatccagac tgtggtctct aaataccacc
 tcccactaaa agaacaaggt cttcttgaag aaaaggttga ttctaagtct gaggaagaaa
 tgtgtaagat gaacttggaa tactttgtca tgttagaaag caaggaaacG Gtcaaatatt
 attaagactc acataagata ctttaaaaca acaaaacacc tcattcattg gtacctatgg
 aggatgctat ggaat
 W
 gactattata aattttcgta aataaagaaa agggatcaaa tacatttcct gtctttttat
 ataaactata tctcagggca caaatagttg atatgggaaa atctctcttt atgaaactat
 tccagcttat aaattaagaa ggaataataa cagtagacta tcaacatttt gtaaccttta
 atgaattaat gaatttaggc agtgatcatc aatggctact aacgtcagga aaagaaagac
 attatgttct tccttcagaa agcactcaat actacaaatg aagtggtcct gactcctacc
 aaaaatatat ttaattatca gttatctaac caccaatttg caggaaatat agatgaccaa
 agaacatact aattacacta cagaaattca gcaaaatcca gaccaagaaa gtataggtca
 aatgatccgg tttctttagc aacaaagttc aagagagaga aaaagagaac ctatggatta
 aaagaaacat tagaggcaca tcagccaatc acagtatata aaccttaact gaatgccaat
 tcaaaaatat aaacttaaaa aaatTATGTC ATAGGCAAAT ATAAACTGGG TATCTAATGA
 CACTAATGAA ATACCATTTA TTTTCATAGG TATGACAATG Gtaatttaat tacattttaa
 aaaataatat CCTggccagg cgtggtggct tgcgcctgta atctcagtac ttggggagtc
 ccagctggtg gatcaattga ggtcaggagt tcaagaccag cccagccaac atgatgaaac
 cacatctcca ctaaaaacac aaaaattagc tgggcatggt cgcgtgtgcc tgtaatccca
 gctacttggg aggctgaggc aggagaatcg cttgaaccca gagggtggag gttgcagtga
 gccgagattg tgccactgca ctccagcctg ggcaacagag tgaaaTgaag gaaggaagga
 aggaaggagg taggtaggta aggaggtagg ttaggtaggt aggtaggtag gtaggtaggg
 aaggagggaa ggaaggaagg aaggagggaa ggaaggaagg aaggaaggaa ggaaggaagg
 aaggaaggaa ggaagggagg agggaaAAAT AATAAAAAAG AACATCCTTA TCTATACATA
 AAGtatatat atactttata tataaatata tgatatacac tacatatagt atagtttata
 tataaatatg taatatacac tatagtatat atagtttata tattatatat acaatatata
 gtgtatatta tatatactat atatatatat GACTCCTTGC CAAAGTAATC TAGCTAACAA
 AAGTGCTTGA AGAACTTCta ttattattat tattattatt aGCTTATGCA AAATCCATCC
 AAAGAACTTC TATTATTAAT

  GeneView back to top
GeneView via analysis of contig annotation: GSK3B glycogen synthase kinase 3 beta
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_005612->NM_002093
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_005612->NM_002093->NP_00208426135175reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6438553 maps exactly once on NCBI human chromosome 3
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
3NW_001838881.2654269117015805minusTalt_assembly_8HuRefHuRefview495
3NW_921807.126234743118049073plusAalt_assembly_1CeleraCeleraview495
3NT_005612.1526135175121122719plusAref_assemblyreferencereferenceview495

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005612
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/T
T/T
HWPA
T
ss10092500HapMap-CEUEuropean 116IG 0.466 0.466 0.069 0.403 0.698 0.302
HapMap-HCBAsian 90IG 0.111 0.667 0.222 0.444 0.556
HapMap-JPTAsian 88IG 0.182 0.568 0.250 0.466 0.534
HapMap-YRISub-Saharan African 118IG 0.051 0.949 1.000 0.025 0.975
CHMJAsian 74IG 0.459 0.541
ss24357546AFD_EUR_PANELEuropean 48IG 0.333 0.458 0.208 0.752 0.562 0.438
AFD_AFR_PANELAfrican American 46IG 0.043 0.391 0.565 0.752 0.239 0.761
AFD_CHN_PANELAsian 48IG 0.167 0.333 0.500 0.251 0.333 0.667

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.478+/-0.10233226090

  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:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .