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Reference SNP (refSNP) Cluster Report: rs1053355                 ** 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:C/G (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:G=0.0051/551 (ExAC)
G=0.0152/76 (1000 Genomes)
G=0.0176/206 (GO-ESP)
G=0.0150/1879 (TOPMED)
HGVS Names
  • CM000663.2:g.25301061C>G
  • NC_000001.10:g.25627552C>G
  • NC_000001.11:g.25301061C>G
  • NG_007494.1:g.33572C>G
  • NM_001127691.2:c.602C>G
  • NM_001282867.1:c.104C>G
  • NM_001282868.1:c.602C>G
  • NM_001282869.1:c.602C>G
  • NM_001282870.1:c.602C>G
  • NM_001282871.1:c.602C>G
  • NM_001282872.1:c.602C>G
  • NM_001321772.1:c.-67+35979G>C
  • NM_016124.4:c.602C>G
  • NP_001121163.1:p.Thr201Arg
  • NP_001269796.1:p.Thr35Arg
  • NP_001269797.1:p.Thr201Arg
  • NP_001269798.1:p.Thr201Arg
  • NP_001269799.1:p.Thr201Arg
  • NP_001269800.1:p.Thr201Arg
  • NP_001269801.1:p.Thr201Arg
  • NP_057208.2:p.Thr201Arg
  • NR_135787.1:n.1215+35979G>C
  • NR_135788.1:n.277+36917G>C
  • NR_135789.1:n.1215+35979G>C
  • XP_005246016.1:p.Thr201Arg
  • XP_005246017.1:p.Thr201Arg
  • XP_005246018.1:p.Thr201Arg
  • XP_005246019.1:p.Thr201Arg
  • XP_005246020.1:p.Thr201Arg
  • XP_016857504.1:p.Thr201Arg
  • XR_946736.1:n.757C>G
  • XR_946737.1:n.757C>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 ss341945907 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053355 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
ss1530467LEE|534329fwd/TC/Gtacccaagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct09/13/0010/10/0386cDNAunknown
ss4419880LEE|e534333fwd/TC/Gtacccgagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct04/26/0210/10/03108cDNAunknown
ss24796065SEQUENOM|sqnm137556byFreqfwd/TC/Gtacccaagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct06/18/0408/05/04123cDNAunknown
ss24817615SEQUENOM|sqnm216609byFreqfwd/TC/Gtacccgagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct06/18/0408/05/04130cDNAunknown
ss35194040SSAHASNP|TA-079.chr1_25372868fwd/C/Gtacccgagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct03/11/05130Genomicunknown
ss3284846271000GENOMES|20100804_snps_128163_chr1_25627552fwd/C/Gtacccgagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct03/22/1103/22/11134Genomicunknown
ss341945907NHLBI-ESP|ESP2500-chr1-25627552byFreqfwd/C/Gtacccgagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct03/25/1109/05/14134Genomicunknown
ss4897292161000GENOMES|20110521_exome_298638_chr1_25627552fwd/C/Gtacccgagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct02/10/1202/21/12137Genomicunknown
ss491289434EXOME_CHIP|nonsyn_5661_chr_1_25627552fwd/C/Gtacccgagggaacggaggataaagatcagaagcaacgatacccagtttgtctgccatgct03/05/1203/05/12137Genomicunknown
ss491589284CLINSEQ_SNP|SNV-chr1-25500139byFreqfwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc03/06/1209/05/14137Genomicunknown
ss553907156TISHKOFF|snp_chr1_25627552fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc11/22/1211/22/12138Genomicunknown
ss974434087JMKIDD_LAB|KhoeSan_Exomes_chr1_25627552fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc03/06/1403/06/14142Genomicunknown
ss974960336EVA-GONL|EVA-GONL_rs1053355fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc04/23/1404/23/14142Genomicunknown
ss1067418345JMKIDD_LAB|HGDP_exomes_chr1_25627552fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc07/09/1407/09/14142Genomicunknown
ss1067744290JMKIDD_LAB|HGDP_WGS_chr1_25627552fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc07/10/1407/10/14142Genomicunknown
ss12900893921000GENOMES|PHASE3_V1_783725fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc08/16/1408/16/14142Genomicunknown
ss1425750452DDI|DDI_rs1053355fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc11/04/1411/04/14144Genomicunknown
ss1685398793EVA_EXAC|EVA_EXAC_194613fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc03/04/1503/04/15144Genomicunknown
ss1710896028EVA_MGP|EVA_XIMO_12780fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc03/09/1503/09/15144Genomicunknown
ss1794081806HAMMER_LAB|Hsieh_88857fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc07/15/1507/15/15146Genomicunknown
ss1918172154WEILL_CORNELL_DGM|SNV:chr1:25627552fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc10/16/1510/16/15147Genomicunknown
ss2632491841ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs1053355-131_T_F_20656485fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc02/02/1702/02/17151Genomicunknown
ss2731264777GNOMAD|exomes_rs1053355fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc05/17/1705/17/17151Genomicunknown
ss2746262116GNOMAD|coding_rs1053355fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc05/17/1705/17/17151Genomicunknown
ss2752822980GNOMAD|rs1053355fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc05/17/1705/17/17151Genomicunknown
ss3071294067TOPMED|TOPMed_freeze_5?chr1:25,301,061fwd/C/Ggagggaacggaggataaagatcagaagcaacgatacccagtttgtctgcc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053355|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=151
 TAAGCTCTGA ACACCAGTCT CATGGCTTCA AGTCACACCT CCTAAGTGAA GCTCTGAACT
 TTCTCCAAGG ACTATCAGGG CTTGCCCCGG GCAGAGGATG CCGACACTCA CTGCTCTTAC
 TGGGTTTTAT TGCAGACAGA CTACCACATG AACATGATGC ACATCTACGT GTTCGCAGCC
 TATTTTGGGC TGTCTGTGGC CTGGTGCCTG CCAAAGCCTC TACCCGAGGG AACGGAGGAT
 AAAGATCAGA
 S
 AGCAACGATA CCCAGTTTGT CTGCCATGCT GGGTAAGGAC AAGGTGGGGT GAGTGGTCTC
 CTACTTGGGC TGAGCAGAAT GGCTCAGAAA AGGCTCTGGC TGAAAAAATC TCCCTCCTTT
 ACCAAGTTCC CCTGGGTGTC TGAAGCCCTT CCATCATGAT TCATTTCTTT GAGTAGTGTT
 TGCTAAATTC ATACCTTTGA ATTAAGCACT TCACAGAGCA GGTTCAGGAG GCCTGGGGTA
 TGCAGATTTC

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm137556 sqnm216609 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.
SourceC/C
C/G
G/G
HWPC
G
ss1290089392EAS 1008AF 1.00000000
EUR 1006AF 0.997999970.00200000
AFR 1322AF 0.946299970.05370000
AMR 694AF 0.995700000.00430000
SAS 978AF 1.00000000
ss1685398793ExAc_Aggregated_Populations111802AF 0.995000060.00499991
ss24796065CEPH 184AF 0.040000000.95999998
ss24817615CEPH 184AF 0.800000010.20000000
ss341945907ESP_Cohort_Populations 4040GF0.971287130.021782180.006930690.001000000.982178210.01782178
ss491589284CSAgilent 1125GF0.99800003 0.002000000.001000000.998000030.00200000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.010+/-0.0700000

  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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