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Reference SNP (refSNP) Cluster Report: rs17421158                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/151
Map to Genome Build:108/Weight 1
Validation Status:byFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/T (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.00004/4 (ExAC)
A=0.00006/8 (TOPMED)
HGVS Names
  • CM000663.2:g.25301003T>A
  • NC_000001.10:g.25627494T>A
  • NC_000001.11:g.25301003T>A
  • NG_007494.1:g.33514T>A
  • NM_001127691.2:c.544T>A
  • NM_001282867.1:c.46T>A
  • NM_001282868.1:c.544T>A
  • NM_001282869.1:c.544T>A
  • NM_001282870.1:c.544T>A
  • NM_001282871.1:c.544T>A
  • NM_001282872.1:c.544T>A
  • NM_001321772.1:c.-67+36037A>T
  • NM_016124.4:c.544T>A
  • NP_001121163.1:p.Ser182Thr
  • NP_001269796.1:p.Ser16Thr
  • NP_001269797.1:p.Ser182Thr
  • NP_001269798.1:p.Ser182Thr
  • NP_001269799.1:p.Ser182Thr
  • NP_001269800.1:p.Ser182Thr
  • NP_001269801.1:p.Ser182Thr
  • NP_057208.2:p.Ser182Thr
  • NR_135787.1:n.1215+36037A>T
  • NR_135788.1:n.277+36975A>T
  • NR_135789.1:n.1215+36037A>T
  • XP_005246016.1:p.Ser182Thr
  • XP_005246017.1:p.Ser182Thr
  • XP_005246018.1:p.Ser182Thr
  • XP_005246019.1:p.Ser182Thr
  • XP_005246020.1:p.Ser182Thr
  • XP_016857504.1:p.Ser182Thr
  • XR_946736.1:n.699T>A
  • XR_946737.1:n.699T>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 ss453939147 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17421158 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
ss4419875LEE|e534291fwd/BA/Tatctacgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcctctac04/26/0210/10/03138cDNAunknown
ss24817612SEQUENOM|sqnm216604fwd/BA/Tatctacgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcctctac06/18/0406/18/04123cDNAunknown
ss4539391471000GENOMES|20101123_snps_106377_chr1_25627494fwd/A/Tatctacgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcctctac07/20/1107/20/11135Genomicunknown
ss1685398781EVA_EXAC|EVA_EXAC_194599fwd/A/Tcgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcc03/04/1503/04/15144Genomicunknown
ss2731264765GNOMAD|exomes_rs17421158fwd/A/Tcgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcc05/17/1705/17/17151Genomicunknown
ss2746262110GNOMAD|coding_rs17421158fwd/A/Tcgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcc05/17/1705/17/17151Genomicunknown
ss2752822974GNOMAD|rs17421158fwd/A/Tcgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcc05/17/1705/17/17151Genomicunknown
ss3071294056TOPMED|TOPMed_freeze_5?chr1:25,301,003fwd/A/Tcgtgttcgcagcctattttgggctgctgtggcctggtgcctgccaaagcc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17421158|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=151
 GGGCTGGGTA AGCTCTGAAC ACCAGTCTCA TGGCTTCAAG TCACACCTCC TAAGTGAAGC
 TCTGAACTTT CTCCAAGGAC TATCAGGGCT TGCCCCGGGC AGAGGATGCC GACACTCACT
 GCTCTTACTG GGTTTTATTG CAGACAGACT ACCACATGAA CATGATGCAC ATCTACGTGT
 TCGCAGCCTA TTTTGGGCTG
 W
 CTGTGGCCTG GTGCCTGCCA AAGCCTCTAC CCGAGGGAAC GGAGGATAAA GATCAGACAG
 CAACGATACC CAGTTTGTCT GCCATGCTGG GTAAGGACAA GGTGGGGTGA GTGGTCTCCT
 ACTTGGGCTG AGCAGAATGG CTCAGAAAAG GCTCTGGCTG AAAAAATCTC CCTCCTTTAC
 CAAGTTCCCC TGGGTGTCTG

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm216604 Z97026 Hs.108380
dbSNP Blast Analysis
UniGene Cluster ID
269364
3D structure mapping
NP_001121163  NP_057208  

  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.
SourceT/T
HWPA
T
ss1685398781ExAc_Aggregated_Populations111908AF 0.000035740.99996424
ss24817612ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0060000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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