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Reference SNP (refSNP) Cluster Report: rs142925159                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreq
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=0.0002/17 (ExAC)
A=0.0005/6 (GO-ESP)
A=0.0002/31 (TOPMED)
HGVS Names
  • CM000663.2:g.25284633G>A
  • NC_000001.10:g.25611124G>A
  • NC_000001.11:g.25284633G>A
  • NG_007494.1:g.17144G>A
  • NM_001127691.2:c.209G>A
  • NM_001282867.1:c.-286G>A
  • NM_001282868.1:c.209G>A
  • NM_001282869.1:c.209G>A
  • NM_001282870.1:c.209G>A
  • NM_001282871.1:c.209G>A
  • NM_001282872.1:c.209G>A
  • NM_001321772.1:c.-66-37604C>T
  • NM_016124.4:c.209G>A
  • NP_001121163.1:p.Arg70Gln
  • NP_001269797.1:p.Arg70Gln
  • NP_001269798.1:p.Arg70Gln
  • NP_001269799.1:p.Arg70Gln
  • NP_001269800.1:p.Arg70Gln
  • NP_001269801.1:p.Arg70Gln
  • NP_057208.2:p.Arg70Gln
  • NR_135787.1:n.1216-37604C>T
  • NR_135788.1:n.278-37604C>T
  • NR_135789.1:n.1216-37604C>T
  • XP_005246016.1:p.Arg70Gln
  • XP_005246017.1:p.Arg70Gln
  • XP_005246018.1:p.Arg70Gln
  • XP_005246019.1:p.Arg70Gln
  • XP_005246020.1:p.Arg70Gln
  • XP_005246021.1:p.Arg70Gln
  • XP_016857504.1:p.Arg70Gln
  • XR_946736.1:n.364G>A
  • XR_946737.1:n.364G>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 ss341945877 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs142925159 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
ss341945877NHLBI-ESP|ESP2500-chr1-25611124fwd/TA/Gttggcttgggcttcctcacctcgagtttccgagacacagctggagcagtgtggccttcaa03/25/1103/25/11134Genomicunknown
ss491289425EXOME_CHIP|nonsyn_5652_chr_1_25611124fwd/TA/Gttggcttgggcttcctcacctcgagtttccgagacacagctggagcagtgtggccttcaa03/05/1203/05/12137Genomicunknown
ss1685398668EVA_EXAC|EVA_EXAC_194475fwd/A/Gttgggcttcctcacctcgagtttccgagacacagctggagcagtgtggcc03/04/1503/04/15144Genomicunknown
ss2731264603GNOMAD|exomes_rs142925159fwd/A/Gttgggcttcctcacctcgagtttccgagacacagctggagcagtgtggcc05/17/1705/17/17151Genomicunknown
ss2746262056GNOMAD|coding_rs142925159fwd/A/Gttgggcttcctcacctcgagtttccgagacacagctggagcagtgtggcc05/17/1705/17/17151Genomicunknown
ss2752821595GNOMAD|rs142925159fwd/A/Gttgggcttcctcacctcgagtttccgagacacagctggagcagtgtggcc05/17/1705/17/17151Genomicunknown
ss3071291169TOPMED|TOPMed_freeze_5?chr1:25,284,633fwd/A/Gttgggcttcctcacctcgagtttccgagacacagctggagcagtgtggcc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs142925159|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 GGCATGTTAT GTTATCCCCA TTATTCAGTT GAGAACATTG AGGCTCAAAG AGGCAAAGTA
 ACTTGACCAA ATACTTGTAA ACGATCTTGC ATGCCCCTTC CAGCTGCCAT TTAGTAAGAC
 TCTAATTTCA TACCACCCTA AATCTCGTCT GCTTCCCCCT CGTCCTTCTC GCCATCTCCC
 CACCGAGCAG TTGGCCAAGA TCTGACCGTG ATGGCGGCCA TTGGCTTGGG CTTCCTCACC
 TCGAGTTTCC
 R
 GAGACACAGC TGGAGCAGTG TGGCCTTCAA CCTCTTCATG CTGGCGCTTG GTGTGCAGTG
 GGCAATCCTG CTGGACGGCT TCCTGAGCCA GTTCCCTTCT GGGAAGGTGG TCATCACACT
 GTTCAGGTAT TGGGATGGTG GCTGGATCAC TTCTGGGTCA TAGAGGGAAT GGACCCCGAA
 AGGACAGGTT CCAGAAGATC TGGGATATTG CCCCCTCTCT GTCTAGCACC AGTGCTGTGC
 AATATTTAGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
3D structure mapping
NP_001121163  NP_057208  

  Population Diversity (Alleles in RefSNP orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss1685398668ExAc_Aggregated_Populations111150AF 0.000152950.99984705
ss341945877ESP_Cohort_Populations 4054GF 0.000493340.999506651.000000000.000246670.99975336

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0130000

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

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