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Reference SNP (refSNP) Cluster Report: rs41267489                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:127/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0001/14 (ExAC)
A=0.0044/22 (1000 Genomes)
A=0.00002/2 (TOPMED)
HGVS Names
  • CM000663.2:g.25290666T>A
  • CM000663.2:g.25290666T>C
  • NC_000001.10:g.25617157T>A
  • NC_000001.10:g.25617157T>C
  • NC_000001.11:g.25290666T>A
  • NC_000001.11:g.25290666T>C
  • NG_007494.1:g.23177T>A
  • NG_007494.1:g.23177T>C
  • NM_001127691.2:c.361T>A
  • NM_001127691.2:c.361T>C
  • NM_001282867.1:c.-134T>A
  • NM_001282867.1:c.-134T>C
  • NM_001282868.1:c.361T>A
  • NM_001282868.1:c.361T>C
  • NM_001282869.1:c.361T>A
  • NM_001282869.1:c.361T>C
  • NM_001282870.1:c.361T>A
  • NM_001282870.1:c.361T>C
  • NM_001282871.1:c.361T>A
  • NM_001282871.1:c.361T>C
  • NM_001282872.1:c.361T>A
  • NM_001282872.1:c.361T>C
  • NM_001321772.1:c.-66-43637A>G
  • NM_001321772.1:c.-66-43637A>T
  • NM_016124.4:c.361T>A
  • NM_016124.4:c.361T>C
  • NP_001121163.1:p.Leu121=
  • NP_001121163.1:p.Leu121Met
  • NP_001269797.1:p.Leu121=
  • NP_001269797.1:p.Leu121Met
  • NP_001269798.1:p.Leu121=
  • NP_001269798.1:p.Leu121Met
  • NP_001269799.1:p.Leu121=
  • NP_001269799.1:p.Leu121Met
  • NP_001269800.1:p.Leu121=
  • NP_001269800.1:p.Leu121Met
  • NP_001269801.1:p.Leu121=
  • NP_001269801.1:p.Leu121Met
  • NP_057208.2:p.Leu121=
  • NP_057208.2:p.Leu121Met
  • NR_135787.1:n.1216-43637A>G
  • NR_135787.1:n.1216-43637A>T
  • NR_135788.1:n.278-43637A>G
  • NR_135788.1:n.278-43637A>T
  • NR_135789.1:n.1216-43637A>G
  • NR_135789.1:n.1216-43637A>T
  • XP_005246016.1:p.Leu121=
  • XP_005246016.1:p.Leu121Met
  • XP_005246017.1:p.Leu121=
  • XP_005246017.1:p.Leu121Met
  • XP_005246018.1:p.Leu121=
  • XP_005246018.1:p.Leu121Met
  • XP_005246019.1:p.Leu121=
  • XP_005246019.1:p.Leu121Met
  • XP_005246020.1:p.Leu121=
  • XP_005246020.1:p.Leu121Met
  • XP_005246021.1:p.Leu121=
  • XP_005246021.1:p.Leu121Met
  • XP_016857504.1:p.Leu121=
  • XP_016857504.1:p.Leu121Met
  • XR_946736.1:n.516T>A
  • XR_946736.1:n.516T>C
  • XR_946737.1:n.516T>A
  • XR_946737.1:n.516T>C
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 ss52053994 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs41267489 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
ss52053994SI_EXO|NT_004610.17_8441509fwd/A/Tcccagtattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgctgtct03/29/0603/29/06127Genomicunknown
ss553907090TISHKOFF|snp_chr1_25617157fwd/A/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc11/22/1211/22/12138Genomicunknown
ss12900891131000GENOMES|PHASE3_V1_783440fwd/A/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc08/16/1408/16/14142Genomicunknown
ss1685398710EVA_EXAC|EVA_EXAC_194520fwd/A/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc03/04/1503/04/15144Genomicunknown
ss1685398711EVA_EXAC|EVA_EXAC_194521fwd/C/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc03/04/1503/04/15144Genomicunknown
ss2731264676GNOMAD|exomes_rs41267489fwd/A/C/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc05/17/1705/17/17151Genomicunknown
ss2746262083GNOMAD|coding_rs41267489fwd/A/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc05/17/1705/17/17151Genomicunknown
ss2752822160GNOMAD|rs41267489fwd/A/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc05/17/1705/17/17151Genomicunknown
ss3071292305TOPMED|TOPMed_freeze_5?chr1:25,290,666fwd/A/Ttattcggctggccaccatgagtgcttgtcggtgctgatctcagtggatgc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs41267489|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 GGCAGCAGAA AAGAAGACTG GGCAGAATCC CAGTTATCAG ATCCCCTGAG GGAACAGTCA
 CCCCGATCAC CCTCAGTCAG ATGAGTGTGT GTAGATCAAT GCCTCATAGA TGAAGGCACT
 GAGGCACAGA GTGGTTAAGT CATCTGCCAG ACCACATGGC TCAGGGTGCA GAGGCCACCT
 TAACGGGAGA AGAGATGGTC ACTCCACTCT GCAGCATCAG CGCCCAGGTG GGTAGAAATC
 TTGTCTTCTA TTCCCACAGA AAGTAGGTGC CCAACAGTGT TTGTTGAAAG AATGAATGAA
 TGAATGAATG AATGAATGAA TGAGTGAGAG GCATCCTTCC TTCTCAGTCG TCCTGGCTCT
 CCCTCTCTCC CCCAGTATTC GGCTGGCCAC CATGAGTGCT
 H
 TGTCGGTGCT GATCTCAGTG GATGCTGTCT TGGGGAAGGT CAACTTGGCG CAGTTGGTGG
 TGATGGTGCT GGTGGAGGTG ACAGCTTTAG GCAACCTGAG GATGGTCATC AGTAATATCT
 TCAACGTGAG TCATGGTGCT GGGAGGAGGG ACCTGGGAGA AAAGGGCCAA AAGCTCCATT
 TGGTGGGGTT TCCAGGGTTT TGAAAAATAA AGACAACCTG TAATCCCAGC TACTTGGGAG
 GTTGAGGAGG GAAGATCACT TGAGGCCAGG AGTTTGAGAC CAGCCTGGGC ATCATAGCAA
 GATCCTCATC TCTAAAAAGT AATTTTTTCT AAATTATCCA GTTGTGGTGG CATGCACCTG
 TAGTCTCAGT TACTCAGGAG GCTGAGGTGT GAGTTGGAAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004610.17
dbSNP Blast Analysis
3D structure mapping
NP_001121163  NP_057208  

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

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPA
C
T
ss1290089113EAS 1008AF 1.00000000
EUR 1006AF 0.01090000 0.98909998
AFR 1322AF 0.00300000 0.99700004
AMR 694AF 0.00140000 0.99859995
SAS 978AF 0.00610000 0.99390000
ss1685398710ExAc_Aggregated_Populations111567AF 0.00013445 0.99986553
ss1685398711ExAc_Aggregated_Populations111553AF 0.000008960.99999106

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0120000

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

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