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Reference SNP (refSNP) Cluster Report: rs41282026                 ** With Likely benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:127/144
Map to Genome Build:107/Weight
Validation Status:byClusterbyFreq
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G/T (FWD)
Allele Origin:A:germline
G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Likely benign allele [ClinVar]
MAF/MinorAlleleCount:NA
MAF Source:
HGVS Names
  • NC_000020.10:g.43034732G>A
  • NC_000020.10:g.43034732G>T
  • NC_000020.11:g.44406092G>A
  • NC_000020.11:g.44406092G>T
  • NG_009818.1:g.55292G>A
  • NG_009818.1:g.55292G>T
  • NM_000457.4:c.150G>A
  • NM_000457.4:c.150G>T
  • NM_001030003.2:c.84G>A
  • NM_001030003.2:c.84G>T
  • NM_001030004.2:c.84G>A
  • NM_001030004.2:c.84G>T
  • NM_001258355.1:c.129G>A
  • NM_001258355.1:c.129G>T
  • NM_001287182.1:c.75G>A
  • NM_001287182.1:c.75G>T
  • NM_001287183.1:c.75G>A
  • NM_001287183.1:c.75G>T
  • NM_001287184.1:c.75G>A
  • NM_001287184.1:c.75G>T
  • NM_175914.4:c.84G>A
  • NM_175914.4:c.84G>T
  • NM_178849.2:c.150G>A
  • NM_178849.2:c.150G>T
  • NM_178850.2:c.150G>A
  • NM_178850.2:c.150G>T
  • NP_000448.3:p.Ala50=
  • NP_001025174.1:p.Ala28=
  • NP_001025175.1:p.Ala28=
  • NP_001245284.1:p.Ala43=
  • NP_001274111.1:p.Ala25=
  • NP_001274112.1:p.Ala25=
  • NP_001274113.1:p.Ala25=
  • NP_787110.2:p.Ala28=
  • NP_849180.1:p.Ala50=
  • NP_849181.1:p.Ala50=
  • XM_005260407.1:c.267G>A
  • XM_005260407.1:c.267G>T
  • XM_005260407.2:c.267G>A
  • XM_005260407.2:c.267G>T
  • XM_011528797.1:c.198G>A
  • XM_011528797.1:c.198G>T
  • XM_011528798.1:c.198G>A
  • XM_011528798.1:c.198G>T
  • XP_005260464.1:p.Ala89=
  • XP_011527099.1:p.Ala66=
  • XP_011527100.1:p.Ala66=
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 ss52059691 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs41282026 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
ss52059691SI_EXO|NT_011362.9_8087647fwd/TA/Ggtccccatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccctgtgt03/29/0603/29/06127Genomicunknown
ss342522507NHLBI-ESP|ESP2500-chr20-43034732byFreqfwd/TA/Ggtccccatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccctgtgt03/25/1109/05/14134Genomicunknown
ss472343394CORRELAGEN|HNF4A_150G_A_061011fwd/TA/Ggtccccatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccctgtgt11/18/1111/22/11136Genomicunknown
ss491810038CLINSEQ_SNP|SNV-chr20-42468146byFreqfwd/TA/Gcatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccc03/06/1209/05/14137Genomicunknown
ss994753804EVA-GONL|EVA-GONL_rs41282026fwd/TA/Gcatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccc04/23/1405/01/14142Genomicunknown
ss1638851663EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_20_43034732_43385907fwd/A/Gcatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccc03/04/1503/04/15144Genomicunknown
ss1681845696EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_20_43034732_43385907fwd/A/Gcatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccc03/04/1503/04/15144Genomicunknown
ss1694005295EVA_EXAC|EVA_EXAC_9469047fwd/A/Gcatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccc03/04/1503/04/15144Genomicunknown
ss1694005296EVA_EXAC|EVA_EXAC_9469048fwd/G/Tcatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccc03/04/1503/04/15144Genomicunknown
ss1698814011EVA_DECODE|EVA_DECODE_20_42468146_303790_rs41282026fwd/TA/Gcatcagaaggcaccaacctcaacgccccaacagcctgggtgtcagcgccc03/02/1503/05/15144Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs41282026|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=144
 TCTGGGGAAA ATGCAGGGGA ATGTTTCTCC CTTCCACAGC CCCCTTGCGA GTTAGGAGGC
 CGGCTCCCAC CCCAGAAGGT GGCCAGGTTT TCATGCCTTC CTAGAGAAAG CTGGGGCTCG
 TGGCCTCCAC CACAGGAAGA CGCAGACCCT CAGAAACAAG TCTGTGAAGT CACAACCAGC
 CCCAGTTTAC AGATGTGAAA CTGAAGCTCC AAAAAGTCAG GAGGTCACTG AGTGGGGAGG
 TGATGGAGTG GGAACAGCCC CCAGATCTGG CTGAGGCCGA AGCCCTGGAG AGATCCCCGC
 AAGGCTCCCT TAGATGCCTG ACATTCTGTT CTTCCTGAAG CCTCACTCCC TTCTCTCCTG
 GCGCAGACAC GTCCCCATCA GAAGGCACCA ACCTCAACGC
 D
 CCCAACAGCC TGGGTGTCAG CGCCCTGTGT GCCATCTGCG GGGACCGGGC CACGGGCAAA
 CACTACGGTG CCTCGAGCTG TGACGGCTGC AAGGGCTTCT TCCGGAGGAG CGTGCGGAAG
 AACCACATGT ACTCCTGCAG GTGAGGAGCC TCAATTTCTT CAGCTGGGAA ATGGGCACAC
 TTGGGCTCAT GGCCCCAAGG TCTGTCTTCT CCCTGAGTGG GTAGGTCCCA GAGACAGCTG
 CCCTTCAGGG CCTTCAAGGC TCTTCTGGTT TTGTAAAAGA CTTTGTGAAT CCAAGAAGAG
 CATCTATTCT AGGAACCACA TTTACTGATC ATCAAGCTAC TGGCTGCCGT TTATTGAGCT
 CTTATCATAT GCCAGGCACA ATACTAAGTC TTTGTGTGTA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011362.9
dbSNP Blast Analysis

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
T
ss1694005295ALL121411AF 0.001 0.999
ss1694005296ALL121284AF 1.000 0.000
ss342522507ESP_Cohort_Populations 4552GF 0.001 0.999 1.000 0.001 0.999
ss491810038CSAgilent 1085GF 0.004 0.996 0.002 0.998

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.002+/-0.0300000

  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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