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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs200657          
refSNP ID: rs200657
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
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 ss84663111 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs200657 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
ss263589KWOK|OVLP-000621-125548fwd/BC/Tcatgcccctccccagcctcccatcttccctcatgctgtgcccctgatagcacaagcccag06/30/0010/10/0379Genomic97 %
ss1034147KWOK|OVLP-000804-449698byFreqfwd/BC/Tcatgcccctccccagcctcccatcttccctcatgctgtgcccctgatagcacaagcccag09/02/0010/25/0689Genomic97 %
ss2546037SC_JCM|AC063977.3_115609fwd/BC/Tcatgcccctccccagcctcccatcttccctcatgctgtgcccctgatagcacaagcccag11/03/0010/10/03104Genomicunknown
ss84663111HGSV|Cor19129_SNV_20070510.chr19_56317011fwd/BC/Tcatgcccctccccagcctcccatcttccctcatgctgtgcccctgatagcacaagcccag12/06/0712/07/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs200657|allelePos=501|totalLen=701|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TCCTCCAAAT GTCACCCTTT TCATCCACTG TACTCATGAG CCAGTGGGTG CTGTAACTTC
 CCTTCCTGAA CAATGTCTCC CGTCATGCCC TCCTTGCTTA GTCCCCTGTC CTCCATCAGC
 ATGACCAGGC CCTTTGCTGT CTTTTTTTTT TTTTTTTTTT TGAAGATGAA GTTTCGCTCT
 TGTCGTCCAG GCTGGAGTGC GGTGGCAGGA TCTCGGCTCA CTGCAACCTC CGCCTCCTTG
 GTTCAAGTGA TTCTCCTGCC TCAGCCTTCT GAGTAGCTGG GATTACAGGA GCATGCCACC
 ATGCCTGGCT AATTTTTGTA CTTTTAGTAG AAACAACTTT TCACCATGTT GGTCAGGGTG
 GTCTCGAACT CCTTGACCTC AGGTGATCCA ACCGCCTTGG CCTCCCAAAG TGCTGGGGTT
 ACAGATCTGA GCCGCCGCAC CCAGCCTCTT TGCTGTCTTG ATCATTGTTC CATGCCCCTC
 CCCAGCCTCC CATCTTCCCT
 Y
 CATGCTGTGC CCCTGATAGC ACAAGCCCAG AAAGACCTTC CTGTACCCAG TACCAGCCCC
 ACCCCTTCCT GGCCCAGAGT CCCCTGTGAC TCCTCGGCAC CCTCAGTCTA AGCTCCTCAG
 CTGGTCATGC CCCAACACCT CCATGTCCCC TTGGAAGACC CCAGATATAT GTGCAGGTCT
 CTTCATCTGC CAGACTGTTT

  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:  rs200657 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
19NW_001838498.2430750747958399minusAalt_assembly_8HuRefHuRefview490
19NW_927284.198456948677285plusTalt_assembly_1CeleraCeleraview490
19NT_011109.152389338956317011plusTref_assemblyreferencereferenceview490

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AC063977 AC026638 AC063977.3
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1034147HapMap-CEUEuropean 118IG 1.000 1.000
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 0.367 0.483 0.150 1.000 0.608 0.392

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.289+/-0.24727021000

  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_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .