NCBI
dbSNP
dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
Re-designed RefSNP Report page!
Clean, modern design that makes it easy to find the information that you are looking for. Report any problems by sending us an email.
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP (refSNP) Cluster Report: rs1053356                 ** With untested allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:G=0.0121/1312 (ExAC)
G=0.0341/171 (1000 Genomes)
G=0.0340/400 (GO-ESP)
G=0.0336/4215 (TOPMED)
HGVS Names
  • CM000663.2:g.25301552T>G
  • NC_000001.10:g.25628043T>G
  • NC_000001.11:g.25301552T>G
  • NG_007494.1:g.34063T>G
  • NM_001127691.2:c.667T>G
  • NM_001282867.1:c.169T>G
  • NM_001282868.1:c.667T>G
  • NM_001282869.1:c.667T>G
  • NM_001282870.1:c.667T>G
  • NM_001282871.1:c.667T>G
  • NM_001282872.1:c.667T>G
  • NM_001321772.1:c.-67+35488A>C
  • NM_016124.4:c.667T>G
  • NP_001121163.1:p.Phe223Val
  • NP_001269796.1:p.Phe57Val
  • NP_001269797.1:p.Phe223Val
  • NP_001269798.1:p.Phe223Val
  • NP_001269799.1:p.Phe223Val
  • NP_001269800.1:p.Phe223Val
  • NP_001269801.1:p.Phe223Val
  • NP_057208.2:p.Phe223Val
  • NR_135787.1:n.1215+35488A>C
  • NR_135788.1:n.277+36426A>C
  • NR_135789.1:n.1215+35488A>C
  • XP_005246016.1:p.Phe223Val
  • XP_005246017.1:p.Phe223Val
  • XP_005246018.1:p.Phe223Val
  • XP_005246019.1:p.Phe223Val
  • XP_005246020.1:p.Phe223Val
  • XP_016857504.1:p.Phe223Val
  • XR_946736.1:n.822T>G
  • XR_946737.1:n.822T>G
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 ss489729222 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053356 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
ss1530468LEE|534336fwd/BG/Tgccctcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtccaatcc09/13/0010/10/0386cDNAunknown
ss4419881LEE|e534337fwd/BG/Tgccctcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtccaatcg04/26/0210/10/03108cDNAunknown
ss3284846321000GENOMES|20100804_snps_128168_chr1_25628043fwd/G/Tgccctcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtccaatcg03/22/1103/22/11134Genomicunknown
ss4897292221000GENOMES|20110521_exome_298641_chr1_25628043fwd/BG/Tgccctcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtccaatcg02/10/1202/21/12137Genomicunknown
ss491289437EXOME_CHIP|nonsyn_5664_chr_1_25628043fwd/BG/Tgccctcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtccaatcg03/05/1203/05/12137Genomicunknown
ss491589287CLINSEQ_SNP|SNV-chr1-25500630byFreqfwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc03/06/1209/05/14137Genomicunknown
ss712285192NHLBI-ESP|ESP6500SI-chr1-25628043fwd/BG/Tgccctcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtccaatcg02/20/1302/20/13138Genomicunknown
ss974960337EVA-GONL|EVA-GONL_rs1053356fwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc04/23/1404/23/14142Genomicunknown
ss1067744291JMKIDD_LAB|HGDP_WGS_chr1_25628043fwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc07/10/1407/10/14142Genomicunknown
ss12900894101000GENOMES|PHASE3_V1_783745fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc08/16/1408/16/14142Genomicunknown
ss1425750453DDI|DDI_rs1053356fwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc11/04/1411/04/14144Genomicunknown
ss1599754708EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_25628043_414712fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc03/04/1503/04/15144Genomicunknown
ss1642748741EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_25628043_414712fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc03/04/1503/04/15144Genomicunknown
ss1685398820EVA_EXAC|EVA_EXAC_194641fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc03/04/1503/04/15144Genomicunknown
ss1710896030EVA_MGP|EVA_XIMO_12782fwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc03/09/1503/09/15144Genomicunknown
ss1794081808HAMMER_LAB|Hsieh_88858fwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc07/15/1507/15/15146Genomicunknown
ss1918172159WEILL_CORNELL_DGM|SNV:chr1:25628043fwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc10/16/1510/16/15147Genomicunknown
ss1958254320ILLUMINA|1:25628043-TG-0_T_R_2299185527fwd/BG/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc11/13/1511/13/15147Genomicunknown
ss2731264816GNOMAD|exomes_rs1053356fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc05/17/1705/17/17151Genomicunknown
ss2746262125GNOMAD|coding_rs1053356fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc05/17/1705/17/17151Genomicunknown
ss2752823003GNOMAD|rs1053356fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc05/17/1705/17/17151Genomicunknown
ss2986488866SWEGEN|NC_000001.10:g.25628043T>Gfwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc05/30/1705/30/17151Genomicunknown
ss3021067979ILLUMINA|MEGA_Consortium_v2_15070954_A2_1:25628043-TG-0_T_R_2299185527fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc06/28/1706/28/17151Genomicunknown
ss3071294133TOPMED|TOPMed_freeze_5?chr1:25,301,552fwd/G/Tcttcttgtggatgttctggccaagttcaactctgctctgctgagaagtcc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053356|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 TAGCTGGTAT CAGCTTGAGA GCTCGGAGGG GAGACGTGAC TTCCCCATCT AACTCTAAGT
 GACAAGGCTG AGACTCTCCA GCCCTAGGAT TCTCATCCAA AACCCCTCGA GGCTCAGACC
 TTTGGAGCAG GAGTGTGATT CTGGCCAACC ACCCTCTCTG GCCCCCAGGC GCCCTCTTCT
 TGTGGATGTT CTGGCCAAGT
 K
 TCAACTCTGC TCTGCTGAGA AGTCCAATCG AAAGGAAGAA TGCCGTGTTC AACACCTACT
 ATGCTGTAGC AGTCAGCGTG GTGACAGCCA TCTCAGGGTC ATCCTTGGCT CACCCCCAAG
 GGAAGATCAG CAAGGTGAGC AGGGCGCTGC CCTTGGGCAG CACTTGGGTC TAACAGGACT
 AGCACACATA TTTATGCCCC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
Z97026 Hs.108380
dbSNP Blast Analysis
UniGene Cluster ID
269364 449968
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.
SourceG/G
T/T
HWPG
T
ss1290089410EAS 1008AF 1.00000000
EUR 1006AF 0.003000000.99699998
AFR 1322AF 0.118000000.88200003
AMR 694AF 0.014400000.98559999
SAS 978AF 0.002000000.99800003
ss1685398820ExAc_Aggregated_Populations112940AF 0.011785020.98821497
ss491589287CSAgilent 1125GF0.004000000.995999990.001000000.004000000.99599999

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.024+/-0.1070000

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

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement