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Reference SNP (refSNP) Cluster Report: rs146093871                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:A=0.0007/74 (ExAC)
A=0.0008/4 (1000 Genomes)
A=0.0011/13 (GO-ESP)
A=0.0006/71 (TOPMED)
HGVS Names
  • CM000663.2:g.25306719G>A
  • NC_000001.10:g.25633210G>A
  • NC_000001.11:g.25306719G>A
  • NG_007494.1:g.39230G>A
  • NM_001127691.2:c.939+3260G>A
  • NM_001282867.1:c.565G>A
  • NM_001282868.1:c.939+3260G>A
  • NM_001282869.1:c.1063G>A
  • NM_001282870.1:c.1063G>A
  • NM_001282871.1:c.1063G>A
  • NM_001282872.1:c.1063G>A
  • NM_001321772.1:c.-67+30321C>T
  • NM_016124.4:c.1063G>A
  • NP_001269796.1:p.Gly189Ser
  • NP_001269798.1:p.Gly355Ser
  • NP_001269799.1:p.Gly355Ser
  • NP_001269800.1:p.Gly355Ser
  • NP_001269801.1:p.Gly355Ser
  • NP_057208.2:p.Gly355Ser
  • NR_135787.1:n.1215+30321C>T
  • NR_135788.1:n.277+31259C>T
  • NR_135789.1:n.1215+30321C>T
  • NR_135790.1:n.1425-1898C>T
  • NR_135791.1:n.1446C>T
  • NR_135792.1:n.1216-1898C>T
  • NR_135793.1:n.1269+177C>T
  • XP_005246016.1:p.Gly355Ser
  • XP_005246017.1:p.Gly355Ser
  • XP_005246018.1:p.Gly355Ser
  • XP_005246019.1:p.Gly355Ser
  • XP_005246021.1:p.Gly204Ser
  • XP_016857504.1:p.Gly355Ser
  • XR_241226.1:n.426+177C>T
  • XR_946736.1:n.1218G>A
  • XR_946737.1:n.1094+3260G>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 ss341945952 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs146093871 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
ss3284846981000GENOMES|20100804_snps_128234_chr1_25633210fwd/A/Ggtgctgctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggcttaccc03/22/1103/22/11134Genomicunknown
ss341945952NHLBI-ESP|ESP2500-chr1-25633210byFreqfwd/TA/Ggtgctgctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggcttaccc03/25/1109/05/14134Genomicunknown
ss4897292361000GENOMES|20110521_exome_298648_chr1_25633210fwd/TA/Ggtgctgctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggcttaccc02/10/1202/21/12137Genomicunknown
ss491289456EXOME_CHIP|nonsyn_5683_chr_1_25633210fwd/TA/Ggtgctgctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggcttaccc03/05/1203/05/12137Genomicunknown
ss491589293CLINSEQ_SNP|SNV-chr1-25505797fwd/TA/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct03/06/1203/12/12137Genomicunknown
ss12900895801000GENOMES|PHASE3_V1_783924fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct08/16/1408/16/14142Genomicunknown
ss1584319176EVA_DECODE|EVA_DECODE_1_25505797_189914_rs146093871fwd/TA/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct03/02/1503/02/15144Genomicunknown
ss1599754732EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_25633210_414743fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct03/04/1503/04/15144Genomicunknown
ss1642748765EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_25633210_414743fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct03/04/1503/04/15144Genomicunknown
ss1685398949EVA_EXAC|EVA_EXAC_194775fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct03/04/1503/04/15144Genomicunknown
ss1958254332ILLUMINA|1:25633210-GA-0_T_F_2299185548fwd/TA/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct11/13/1511/13/15147Genomicunknown
ss2731265003GNOMAD|exomes_rs146093871fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct05/17/1705/17/17151Genomicunknown
ss2746262186GNOMAD|coding_rs146093871fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct05/17/1705/17/17151Genomicunknown
ss2752823457GNOMAD|rs146093871fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct05/17/1705/17/17151Genomicunknown
ss2984850854AFFY|Axiom_PsorMich_Affx-52122179fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct05/24/1705/24/17151Genomicunknown
ss2986488918SWEGEN|NC_000001.10:g.25633210G>Afwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct05/30/1705/30/17151Genomicunknown
ss3021067991ILLUMINA|MEGA_Consortium_v2_15070954_A2_1:25633210-GA-0_T_F_2299185548fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct06/28/1706/28/17151Genomicunknown
ss3071295069TOPMED|TOPMed_freeze_5?chr1:25,306,719fwd/A/Ggctggtgcttgataccgtcggagccgcaatggcatgtgggtcactgggct09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs146093871|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CTTCTTTGAG GTGAGCCTTA GTGCCCATCC CCCTTTGGTG GCCCCGGATA CCAAGGGTGT
 GTGAAAGGGG TGGGTAGGGA ATATGGGTCT CACCTGCCAA TCTGCTTATA ATAACACTTG
 TCCACAGGGG TGTTGTAACC GAGTGCTGGG GATTCCCCAC AGCTCCATCA TGGGCTACAA
 CTTCAGCTTG CTGGGTCTGC TTGGAGAGAT CATCTACATT GTGCTGCTGG TGCTTGATAC
 CGTCGGAGCC
 R
 GCAATGGCAT GTGGGTCACT GGGCTTACCC CCCATCCCCT TAACACTCCC CTCCAACTCA
 GGAAGAAATG TGTGCAGAGT CCTTAGCTGG GGCGTGTGCA CTCGGGGCCA GGTGCTCAGT
 AGGCTTCGGT GAATATTTGT TGGCTGATTT ATTCAGAAAT TCTGTCCAGC CCCTACCTTG
 GATGGATTTA TCACCTCTCC AGGCCACCTC TTCTTTCCAA ATAGGGCCAC CTAGGTATAG
 ACCAAAGACA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
3D structure mapping
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.
SourceA/A
A/G
G/G
HWPA
G
ss1290089580EAS 1008AF 1.00000000
EUR 1006AF 0.003000000.99699998
AFR 1322AF 1.00000000
AMR 694AF 0.001400000.99859995
SAS 978AF 1.00000000
ss1685398949ExAc_Aggregated_Populations112810AF 0.000700290.99929971
ss341945952ESP_Cohort_Populations 4032GF0.000496030.000992060.998511910.001000000.000992060.99900794
ss491589293CSAgilent 1063GF 0.002000000.997999971.000000000.001000000.99900001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0260000

  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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