NCBI
dbSNP
Attention: This page will be retired!
This legacy RefSNP page contains old data from dbSNP build 151 (March 2018) and is no longer maintained. Please update your links and bookmarks to use the re-designed RefSNP Report page.
Spacer gif

Spacer gif
Reference SNP (refSNP) Cluster Report: rs200139083                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:137/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0002/27 (ExAC)
A=0.0006/3 (1000 Genomes)
A=0.00003/4 (TOPMED)
HGVS Names
  • CM000663.2:g.931108G>A
  • NC_000001.10:g.866488G>A
  • NC_000001.11:g.931108G>A
  • NM_152486.2:c.305+19G>A
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 ss487561411 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs200139083 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
ss4875614111000GENOMES|20110521_exome_10_chr1_866488fwd/TA/Gggcgtcctgcaggtaggagccgtgctgtgctgcataagagggggccgtgactcccctccc02/10/1202/13/12137Genomicunknown
ss491581631CLINSEQ_SNP|SNV-chr1-856351fwd/TA/Gcctgcaggtaggagccgtgctgtgctgcataagagggggccgtgactccc03/06/1203/12/12137Genomicunknown
ss12893425801000GENOMES|PHASE3_V1_7476fwd/A/Gcctgcaggtaggagccgtgctgtgctgcataagagggggccgtgactccc08/16/1408/16/14142Genomicunknown
ss1685217365EVA_EXAC|EXAC_0.3.1:g866488g>afwd/A/Gcctgcaggtaggagccgtgctgtgctgcataagagggggccgtgactccc03/04/1503/04/15144Genomicunknown
ss2730987012GNOMAD|exomes_rs200139083fwd/A/Gcctgcaggtaggagccgtgctgtgctgcataagagggggccgtgactccc05/17/1705/17/17151Genomicunknown
ss2746169484GNOMAD|coding_rs200139083fwd/A/Gcctgcaggtaggagccgtgctgtgctgcataagagggggccgtgactccc05/17/1705/17/17151Genomicunknown
ss2750649476GNOMAD|rs200139083fwd/A/Gcctgcaggtaggagccgtgctgtgctgcataagagggggccgtgactccc05/17/1705/17/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs200139083|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CCTCGTTCAC TGCCCAGGGC TGTGGCCCAG CGGGGCACTG ACCCGAGACA GGTCTGCGCA
 CGCCCTGCTA TCCTGAGGCT GGGGTCAGGG GCCTCCAGAG CAACATGGAC CTTCTGCTTC
 CCTTCCTGCA GAGTCCACAC CCACTGGGAC GTGAACATCT CTTTCCGAGA GGCGTCCTGC
 AGGTAGGAGC CGTGCTGTGC
 R
 TGCATAAGAG GGGGCCGTGA CTCCCCTCCC TCCCTCCCAC CCCTGACCGT GCCCTGCTGT
 CTGCTGTCCG CTGTCTCAGC GTGAGCTGAT GCTGTGATGC TGGCTGAGTG TCTGCCAGGT
 TTGACATGTG CTGCAAGGTT GTCCCCCATC CCGGGAGGCA GACAGTGTTG CACCCAGTTG
 GGACTGAGGG ACCCCAGACC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/G
G/G
HWPA
G
ss1289342580EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.000800000.99919999
AMR 694AF 1.00000000
SAS 978AF 0.002000000.99800003
ss1685217365ExAc_Aggregated_Populations121246AF 0.000222690.99977732
ss491581631CSAgilent 925GF0.002000000.998000031.000000000.001000000.99900001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0150000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN