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Reference SNP (refSNP) Cluster Report: rs1053359                 ** 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
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:C=0.0017/187 (ExAC)
C=0.0719/360 (1000 Genomes)
C=0.0044/52 (GO-ESP)
C=0.0044/554 (TOPMED)
HGVS Names
  • CM000663.2:g.25301582G>A
  • CM000663.2:g.25301582G>C
  • NC_000001.10:g.25628073G>A
  • NC_000001.10:g.25628073G>C
  • NC_000001.11:g.25301582G>A
  • NC_000001.11:g.25301582G>C
  • NG_007494.1:g.34093G>A
  • NG_007494.1:g.34093G>C
  • NM_001127691.2:c.697G>A
  • NM_001127691.2:c.697G>C
  • NM_001282867.1:c.199G>A
  • NM_001282867.1:c.199G>C
  • NM_001282868.1:c.697G>A
  • NM_001282868.1:c.697G>C
  • NM_001282869.1:c.697G>A
  • NM_001282869.1:c.697G>C
  • NM_001282870.1:c.697G>A
  • NM_001282870.1:c.697G>C
  • NM_001282871.1:c.697G>A
  • NM_001282871.1:c.697G>C
  • NM_001282872.1:c.697G>A
  • NM_001282872.1:c.697G>C
  • NM_001321772.1:c.-67+35458C>G
  • NM_001321772.1:c.-67+35458C>T
  • NM_016124.4:c.697G>A
  • NM_016124.4:c.697G>C
  • NP_001121163.1:p.Glu233Gln
  • NP_001121163.1:p.Glu233Lys
  • NP_001269796.1:p.Glu67Gln
  • NP_001269796.1:p.Glu67Lys
  • NP_001269797.1:p.Glu233Gln
  • NP_001269797.1:p.Glu233Lys
  • NP_001269798.1:p.Glu233Gln
  • NP_001269798.1:p.Glu233Lys
  • NP_001269799.1:p.Glu233Gln
  • NP_001269799.1:p.Glu233Lys
  • NP_001269800.1:p.Glu233Gln
  • NP_001269800.1:p.Glu233Lys
  • NP_001269801.1:p.Glu233Gln
  • NP_001269801.1:p.Glu233Lys
  • NP_057208.2:p.Glu233Gln
  • NP_057208.2:p.Glu233Lys
  • NR_135787.1:n.1215+35458C>G
  • NR_135787.1:n.1215+35458C>T
  • NR_135788.1:n.277+36396C>G
  • NR_135788.1:n.277+36396C>T
  • NR_135789.1:n.1215+35458C>G
  • NR_135789.1:n.1215+35458C>T
  • XP_005246016.1:p.Glu233Gln
  • XP_005246016.1:p.Glu233Lys
  • XP_005246017.1:p.Glu233Gln
  • XP_005246017.1:p.Glu233Lys
  • XP_005246018.1:p.Glu233Gln
  • XP_005246018.1:p.Glu233Lys
  • XP_005246019.1:p.Glu233Gln
  • XP_005246019.1:p.Glu233Lys
  • XP_005246020.1:p.Glu233Gln
  • XP_005246020.1:p.Glu233Lys
  • XP_016857504.1:p.Glu233Gln
  • XP_016857504.1:p.Glu233Lys
  • XR_946736.1:n.852G>A
  • XR_946736.1:n.852G>C
  • XR_946737.1:n.852G>A
  • XR_946737.1:n.852G>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 ss341945919 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053359 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
ss4439877LEE|e1759763fwd/BC/Gttcaactctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacacctact04/26/0210/10/03108cDNAunknown
ss24814771SEQUENOM|sqnm208016byFreqfwd/BC/Gttcaactctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacacctact06/18/0408/05/04123cDNAunknown
ss76710871AFFY|AFFY_6_1M_SNP_A-8572253fwd/C/Ggctgagaagtccaatcaaaggaagaatgccgt08/28/0708/30/07129Genomicunknown
ss104835882KRIBB_YJKIM|KHS1228214fwd/C/Gttcaactctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacacctact07/10/0807/10/08130Genomicunknown
ss341945919NHLBI-ESP|ESP2500-chr1-25628073byFreqfwd/C/Gttcaactctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacacctact03/25/1109/05/14134Genomicunknown
ss4886579611000GENOMES|20110521_exome_5801_chr1_25628073fwd/C/Gttcaactctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacacctact02/10/1202/13/12137Genomicunknown
ss491289440EXOME_CHIP|nonsyn_5667_chr_1_25628073fwd/C/Gttcaactctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacacctact03/05/1203/05/12137Genomicunknown
ss553907160TISHKOFF|snp_chr1_25628073fwd/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac11/22/1211/22/12138Genomicunknown
ss12900894121000GENOMES|PHASE3_V1_783747fwd/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac08/16/1408/16/14142Genomicunknown
ss1685398828EVA_EXAC|EVA_EXAC_194650fwd/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac03/04/1503/04/15144Genomicunknown
ss1685398829EVA_EXAC|EVA_EXAC_194651fwd/A/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac03/04/1503/04/15144Genomicunknown
ss1712318956EVA_SVP|EVA_SVP_13508fwd/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac03/12/1503/12/15144Genomicunknown
ss2731264827GNOMAD|exomes_rs1053359fwd/A/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac05/17/1705/17/17151Genomicunknown
ss2746262129GNOMAD|coding_rs1053359fwd/A/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac05/17/1705/17/17151Genomicunknown
ss2752823007GNOMAD|rs1053359fwd/A/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac05/17/1705/17/17151Genomicunknown
ss3071294141TOPMED|TOPMed_freeze_5?chr1:25,301,582-01fwd/A/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac09/28/1709/28/17151Genomicunknown
ss3071294142TOPMED|TOPMed_freeze_5?chr1:25,301,582-02fwd/C/Gctctgctctgctgagaagtccaatcaaaggaagaatgccgtgttcaacac09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053359|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C/G'|mol=Genomic|build=151
 CCTTGTCTGT AAAATGTGGT TAGCTGGTAT CAGCTTGAGA GCTCGGAGGG GAGACGTGAC
 TTCCCCATCT AACTCTAAGT GACAAGGCTG AGACTCTCCA GCCCTAGGAT TCTCATCCAA
 AACCCCTCGA GGCTCAGACC TTTGGAGCAG GAGTGTGATT CTGGCCAACC ACCCTCTCTG
 GCCCCCAGGC GCCCTCTTCT TGTGGATGTT CTGGCCAAGT TTCAACTCTG CTCTGCTGAG
 AAGTCCAATC
 V
 AAAGGAAGAA TGCCGTGTTC AACACCTACT ATGCTGTAGC AGTCAGCGTG GTGACAGCCA
 TCTCAGGGTC ATCCTTGGCT CACCCCCAAG GGAAGATCAG CAAGGTGAGC AGGGCGCTGC
 CCTTGGGCAG CACTTGGGTC TAACAGGACT AGCACACATA TTTATGCCCC TCCCCACCCC
 AGGGCCAGCG TGGGTTGGGA GAGGGCATGC CGGGTGGTGG AGCTGTGCCT GCCTCTACAG
 TGGAGCTCTA

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm208016 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.
SourceC/C
C/G
G/G
HWPA
C
G
ss1290089412EAS 1008AF 1.00000000
EUR 1006AF 0.009900000.99009997
AFR 1322AF 0.109700000.89029998
AMR 694AF 0.060500000.93949997
SAS 978AF 0.166699990.83329999
ss1685398828ExAc_Aggregated_Populations113184AF 0.001767030.99823296
ss1685398829ExAc_Aggregated_Populations112996AF 0.00010620 0.99989378
ss24814771CEPH 184AF 0.080000000.92000002
ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss341945919ESP_Cohort_Populations 4032GF0.002976190.004960320.992063460.00100000 0.005456350.99454367

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.004+/-0.0430000

  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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