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Reference SNP (refSNP) Cluster Report: rs200503540                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:137/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreq
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (FWD)
Allele Origin:
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0775/988 (ExAC)
T=0.0400/5022 (TOPMED)
HGVS Names
  • CM000663.2:g.17452C>A
  • CM000663.2:g.17452C>T
  • NC_000001.10:g.17452C>T
  • NC_000001.11:g.17452C>A
  • NC_000001.11:g.17452C>T
  • NR_024540.1:n.588-84G>A
  • NR_024540.1:n.588-84G>T
  • NR_106918.1:n.-16G>A
  • NR_106918.1:n.-16G>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss491581586 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs200503540 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
ss491581586CLINSEQ_SNP|SNV-chr1-7315fwd/BC/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc03/06/1203/12/12137Genomicunknown
ss538305548BILGI_BIOE|chr1_17452fwd/BC/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc08/22/1208/22/12138Genomicunknown
ss647514757SSMP|1_17452fwd/BC/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc12/14/1202/09/15138Genomicunknown
ss1685216861EVA_EXAC|EXAC_0.3.1:g17452c>tfwd/C/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc03/04/1503/04/15144Genomicunknown
ss1917958137WEILL_CORNELL_DGM|SNV:chr1:17452fwd/BC/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc10/16/1510/16/15147Genomicunknown
ss2147483692USC_VALOUEV|NC_000001.10:g.17452C>Tfwd/C/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc11/17/1611/17/16150Genomicunknown
ss2697372911GRF|rs200503540fwd/C/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc02/13/1702/13/17151Genomicunknown
ss2746168707GNOMAD|coding_rs200503540fwd/C/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc05/17/1705/17/17151Genomicunknown
ss2750601993GNOMAD|rs200503540fwd/C/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc05/17/1705/17/17151Genomicunknown
ss2986141485SWEGEN|NC_000001.10:g.17452C>Tfwd/C/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc05/30/1705/30/17151Genomicunknown
ss3343271478CSHL|rs200503540fwd/C/Tctctcccacatcatcaggggcacaggtgcactgtggggtcccaggcctcc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs200503540|allelePos=26|totalLen=51|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 CTCTCCCACA TCATCAGGGG CACAG
 H
 GTGCACTGTG GGGTCCCAGG CCTCC

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

  Population Diversity (Alleles in RefSNP orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
HWPC
T
ss1685216861ExAc_Aggregated_Populations 75912AF 0.984468880.01553114
ss491581586CSAgilent 297GF0.993000030.007000001.000000000.996500020.00350000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.143+/-0.2260000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqUNKNOWNUNKNOWNUNKNOWN