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Reference SNP (refSNP) Cluster Report: rs1053360                 
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/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0002/24 (ExAC)
A=0.0002/1 (1000 Genomes)
A=0.0002/2 (GO-ESP)
A=0.0001/15 (TOPMED)
HGVS Names
  • CM000663.2:g.25301597G>A
  • NC_000001.10:g.25628088G>A
  • NC_000001.11:g.25301597G>A
  • NG_007494.1:g.34108G>A
  • NM_001127691.2:c.712G>A
  • NM_001282867.1:c.214G>A
  • NM_001282868.1:c.712G>A
  • NM_001282869.1:c.712G>A
  • NM_001282870.1:c.712G>A
  • NM_001282871.1:c.712G>A
  • NM_001282872.1:c.712G>A
  • NM_001321772.1:c.-67+35443C>T
  • NM_016124.4:c.712G>A
  • NP_001121163.1:p.Val238Met
  • NP_001269796.1:p.Val72Met
  • NP_001269797.1:p.Val238Met
  • NP_001269798.1:p.Val238Met
  • NP_001269799.1:p.Val238Met
  • NP_001269800.1:p.Val238Met
  • NP_001269801.1:p.Val238Met
  • NP_057208.2:p.Val238Met
  • NR_135787.1:n.1215+35443C>T
  • NR_135788.1:n.277+36381C>T
  • NR_135789.1:n.1215+35443C>T
  • XP_005246016.1:p.Val238Met
  • XP_005246017.1:p.Val238Met
  • XP_005246018.1:p.Val238Met
  • XP_005246019.1:p.Val238Met
  • XP_005246020.1:p.Val238Met
  • XP_016857504.1:p.Val238Met
  • XR_946736.1:n.867G>A
  • XR_946737.1:n.867G>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 ss341945922 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053360 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
ss4419884LEE|e534368fwd/TA/Gctgagaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagcagtca04/26/0210/10/03108cDNAunknown
ss24817616SEQUENOM|sqnm216612byFreqfwd/TA/Gctgagaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagcagtca06/18/0408/05/04123cDNAunknown
ss76711596AFFY|AFFY_6_1M_SNP_A-8572935rev/BC/Ttagtaggtgttgaacaggcattcttcctttcg08/28/0708/30/07142Genomicunknown
ss341945922NHLBI-ESP|ESP2500-chr1-25628088byFreqfwd/TA/Gctgagaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagcagtca03/25/1109/05/14134Genomicunknown
ss4886579631000GENOMES|20110521_exome_5802_chr1_25628088fwd/TA/Gctgagaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagcagtca02/10/1202/13/12137Genomicunknown
ss12900894131000GENOMES|PHASE3_V1_783748fwd/A/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc08/16/1408/16/14142Genomicunknown
ss1685398832EVA_EXAC|EVA_EXAC_194655fwd/A/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc03/04/1503/04/15144Genomicunknown
ss1712318957EVA_SVP|EVA_SVP_13509fwd/TA/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc03/12/1503/12/15144Genomicunknown
ss2323023270TOPMED|1_25628088_G/Afwd/A/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc11/19/1611/19/16150Genomicunknown
ss2731264832GNOMAD|exomes_rs1053360fwd/A/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc05/17/1705/17/17151Genomicunknown
ss2746262131GNOMAD|coding_rs1053360fwd/A/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc05/17/1705/17/17151Genomicunknown
ss2752823009GNOMAD|rs1053360fwd/A/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc05/17/1705/17/17151Genomicunknown
ss3071294147TOPMED|TOPMed_freeze_5?chr1:25,301,597fwd/A/Gaagtccaatcgaaaggaagaatgcctgttcaacacctactatgctgtagc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053360|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 GTGGTTAGCT GGTATCAGCT TGAGAGCTCG GAGGGGAGAC GTGACTTCCC CATCTAACTC
 TAAGTGACAA GGCTGAGACT CTCCAGCCCT AGGATTCTCA TCCAAAACCC CTCGAGGCTC
 AGACCTTTGG AGCAGGAGTG TGATTCTGGC CAACCACCCT CTCTGGCCCC CAGGCGCCCT
 CTTCTTGTGG ATGTTCTGGC CAAGTTTCAA CTCTGCTCTG CTGAGAAGTC CAATCGAAAG
 GAAGAATGCC
 R
 TGTTCAACAC CTACTATGCT GTAGCAGTCA GCGTGGTGAC AGCCATCTCA GGGTCATCCT
 TGGCTCACCC CCAAGGGAAG ATCAGCAAGG TGAGCAGGGC GCTGCCCTTG GGCAGCACTT
 GGGTCTAACA GGACTAGCAC ACATATTTAT GCCCCTCCCC ACCCCAGGGC CAGCGTGGGT
 TGGGAGAGGG CATGCCGGGT GGTGGAGCTG TGCCTGCCTC TACAGTGGAG CTCTAGGTAG
 AATGCTGGGT

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm216612 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.
SourceA/A
A/G
G/G
HWPA
G
ss1290089413EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.000800000.99919999
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1685398832ExAc_Aggregated_Populations113228AF 0.000211960.99978805
ss24817616CEPH 184AF 0.060000000.94000006
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss341945922ESP_Cohort_Populations 4038GF 0.000990590.999009431.000000000.000495290.99950469

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0150000

  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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