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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs9543961          
refSNP ID: rs9543961
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_203495.2:c.55-1652A>C
NM_203497.2:c.55-1652A>C
NT_024524.13:g.57086055T>G
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 ss21076528 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9543961 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
ss13239927SC_SNP|NT_024524.12_44680546fwd/BG/Tgatacatatatgaaaatgtccccagcagcttattcataatagccctaaactgaaaaccca10/22/0310/31/03119Genomicunknown
ss21076528SSAHASNP|WGSA-200403-chr13.chr13.NT_024524.13_57086055byFreqfwd/BG/Tgatacatatatgaaaatgtccccagcagcttattcataatagccctaaactgaaaaccca03/19/0410/26/06121Genomicunknown
ss40382366ABI|hCV1891489fwd/BG/Tgatacatatatgaaaatgtccccagcagcttattcataatagccctaaactgaaaaccca07/16/0507/17/05126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9543961|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=126
 AAAGGGGGAC CAAAAATTCC TCCTATCTCA GACTTTCTTT GCACCAATCT CCTACAGCAT
 TAAGTCCAAG CTAGTGCTGA CAAAAGGTTA ACATCTTTTA TAAGAAGATT GAATAAATTC
 ATTTTAAAGA AAAGTTCTCC ATATAAAAAt agaaaggcaa atcacaaaat aactacaaat
 ttctaataaa catatgaaaa tgtgctcacc ttaagaaaca aggaattaaa agccacaatt
 agataccact acacagctac caaaatggca aaaatttaag tctgaaaatt ccaagtattg
 gcaaggaagg atgtgaggca atgggaagtg tcacatgctg ttggtgaaag tgtaaactgg
 gccaatctat caaagagctg actttagcta gtaaaactga agctctgcat actgtgatcc
 aaattctact agggatagaa cttagaaaaa ctttttgaat atgtacacag gatacatata
 tgaaaatgtc cccagcagct
 K
 tattcataat agccctaaac tgaaaaccca aatgttcaac agaaataaaa tggataaatg
 aaatgctata cagcaatgaa aatgaacttc aattacacgt aaAACCAAAA ATATTTAAAA
 CAAGTCCAAA AGTtatgatt cagttcactt aaacttgaga aacaggtggt aaaactataa
 agagaatatg cctatccttt tggggtggag agaagtgggc attgattgaa gaggagcatc
 tggtgggctt ctgggggact ggtaacactc catttattga cttttgcttg tggttacacg
 agtgttcgct tttagataat tcattaactg tccatatttt gtgcactttt tgcatatatA
 GTCCAGAGAG AGCAATGTAA GTCAGTGACT ACATTTCTGG TTGAAAGGAA GAGTTTATTG
 TAGCCTAGGG AGTTAAGGGA AAGCTTTACA GAAGGCTTTA AGCTCCATTT TGAAGAATAA
 ACAGAACAGG AATTGAGGAA

  GeneView back to top
GeneView via analysis of contig annotation: COMMD6 COMM domain containing 6
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_203495
svfunction
referenceNT_024524->NM_203497
svfunction
HuRefNW_001838082->NM_203495
svfunction
HuRefNW_001838082->NM_203497
svfunction
CeleraNW_925506->NM_203495
svfunction
CeleraNW_925506->NM_203497
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_024524->NM_203495->NP_98709157086055reverseintron
referenceNT_024524->NM_203497->NP_98709357086055reverseintron
HuRefNW_001838082->NM_203495->NP_987091720702reverseintron
HuRefNW_001838082->NM_203497->NP_987093720702reverseintron
CeleraNW_925506->NM_203495->NP_98709111693212reverseintron
CeleraNW_925506->NM_203497->NP_98709311693212reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs9543961 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_001838082.172070256803501plusGalt_assembly_8HuRefHuRefview500
13NW_925506.11169321257003920plusTalt_assembly_1CeleraCeleraview500
13NT_024524.135708605575004055plusTref_assemblyreferencereferenceview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_024524
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL137244.28 NC_000013.9 AC213269.1

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/T
T/T
HWPG
T
ss21076528HapMap-CEUEuropean 102IG 0.255 0.745 0.251 0.127 0.873
HapMap-HCBAsian 88IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 116IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.064+/-0.16727021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .