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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs12002220          
refSNP ID: rs12002220
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
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
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 ss18009111 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12002220 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
ss18009111CSHL-HAPMAP|CSHL-HuCC-200402.chr9.NT_023935.16_18736635byFreqfwd/BC/Taaaaattgattggaaagtacagagggttccgcacaattcctactccccccacctgtttcc02/19/0410/26/06120Genomicunknown
ss22860509SSAHASNP|WGSA-200403-chr9.chr9.NT_023935.16_18736635fwd/BC/Taaaaattgattggaaagtacagagggttccgcacaattcctactccccccacctgtttcc03/21/0403/22/04121Genomicunknown
ss43354820ABI|hCV26567742fwd/BC/Taaaaattgattggaaagtacagagggttccgcacaattcctactccccccacctgtttcc07/18/0507/18/05126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12002220|allelePos=331|totalLen=766|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=126
 TATTGATAAA GATTACAAGC CATCTAATTC GTTTTAATGA AATATATATC CTAGGACTTC
 ATCAAACACC TCATTGATGA GTTCACACTT TTCCTAAATT TTAAATTTAT ATGCACACTT
 ACCTGCTCAT TTCTCACTGA ATTTGATTCA GTTGAATCCA ACAGATGTTT ATTGAGTTCC
 CACTGTATGT TCTAGGAAGG CAAATAATGT TTTCTTCAAG TCTTCCATCT CTGTTCCTCT
 TTTCTTTCTT Tattactaga ctttttttaa aaagcacttt tagttttaag gcaattttag
 aaaaattgat tggaaagtac agagggttcc
 Y
 gcacaattcc tactcccccc acctgtttcc tctattattt acattctgtg ttatattact
 gtggcacact cgttacaact gatgaaccaa tactggtatt ttattattaa ctaaagtctt
 cgatttacat tagttccttc ttagtgttgt tcattctatg cattttgaca aatgtataat
 gtcatgtatt cactattaga atatcataca gagtttcatc tccctaaatt ccctgGAAGC
 ATTCTGTATT AACCTAGAAG GGATCTTAAA TCAAATTTTT TCGTTTACAG CTTCACTTCT
 TAAAGCTTCT GGATCTAGTA TTTCTTTTTT GCCCATTATT TAAAAAATTA AGTGAGATTT
 TGCATGCCAT TTGAATTCAA AAGTTGGTCT CTCTGTGGTA CACATCTCCT CAAATGATTA
 ACTATTTATG TTGAA

  GeneView back to top
GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs12002220 maps exactly once on NCBI human chromosome 9
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
9NW_001839222.190351359396326plusTalt_assembly_8HuRefHuRefview330
9NW_924484.11852138260141346plusCalt_assembly_1CeleraCeleraview330
9NT_023935.171873663588761923plusCref_assemblyreferencereferenceview330

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023935
dbSNP Blast Analysis
GenBank HTGS Finished:
AL158149.14

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss18009111HapMap-CEUEuropean 120IG 0.867 0.133 0.584 0.933 0.067
HapMap-HCBAsian 90IG 0.733 0.156 0.111 0.001 0.811 0.189
HapMap-JPTAsian 88IG 0.727 0.205 0.068 0.100 0.830 0.170
HapMap-YRISub-Saharan African 118IG 0.864 0.136 0.584 0.932 0.068

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.204+/-0.24627021000

  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 .