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Reference SNP (refSNP) Cluster Report: rs1053341                 
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 (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.0003/28 (ExAC)
C=0.0006/3 (1000 Genomes)
C=0.0004/45 (TOPMED)
HGVS Names
  • CM000663.2:g.25284602A>C
  • NC_000001.10:g.25611093A>C
  • NC_000001.11:g.25284602A>C
  • NG_007494.1:g.17113A>C
  • NM_001127691.2:c.178A>C
  • NM_001282867.1:c.-317A>C
  • NM_001282868.1:c.178A>C
  • NM_001282869.1:c.178A>C
  • NM_001282870.1:c.178A>C
  • NM_001282871.1:c.178A>C
  • NM_001282872.1:c.178A>C
  • NM_001321772.1:c.-66-37573T>G
  • NM_016124.4:c.178A>C
  • NP_001121163.1:p.Ile60Leu
  • NP_001269797.1:p.Ile60Leu
  • NP_001269798.1:p.Ile60Leu
  • NP_001269799.1:p.Ile60Leu
  • NP_001269800.1:p.Ile60Leu
  • NP_001269801.1:p.Ile60Leu
  • NP_057208.2:p.Ile60Leu
  • NR_135787.1:n.1216-37573T>G
  • NR_135788.1:n.278-37573T>G
  • NR_135789.1:n.1216-37573T>G
  • XP_005246016.1:p.Ile60Leu
  • XP_005246017.1:p.Ile60Leu
  • XP_005246018.1:p.Ile60Leu
  • XP_005246019.1:p.Ile60Leu
  • XP_005246020.1:p.Ile60Leu
  • XP_005246021.1:p.Ile60Leu
  • XP_016857504.1:p.Ile60Leu
  • XR_946736.1:n.333A>C
  • XR_946737.1:n.333A>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 ss71642852 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053341 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
ss1530449LEE|534184fwd/TA/Cgttggccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgagtttcc09/13/0010/10/0386cDNAunknown
ss4419861LEE|e534184fwd/TA/Cgttggccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgagtttcc04/26/0210/10/03106cDNAunknown
ss71642852SI_EXO|NT_004610.18_8435435fwd/TA/Cgttggccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgagtttcc05/07/0705/07/07127Genomicunknown
ss159137034ILLUMINA|Human660W-Quad_v1_A_rs1053341-128_B_R_1539595699rev/BG/Tggaaactcgaggtgaggaagcccaagccaaggccgccatcacggtcagatcttggccaac07/06/0907/06/09131Genomicunknown
ss491289423EXOME_CHIP|nonsyn_5650_chr_1_25611093fwd/TA/Cgttggccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgagtttcc03/05/1203/05/12137Genomicunknown
ss12900889171000GENOMES|PHASE3_V1_783241fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag08/16/1408/16/14142Genomicunknown
ss1685398658EVA_EXAC|EVA_EXAC_194465fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag03/04/1503/04/15144Genomicunknown
ss1918171983WEILL_CORNELL_DGM|SNV:chr1:25611093fwd/TA/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag10/16/1510/16/15147Genomicunknown
ss1958254298ILLUMINA|1:25611093-AC-0_B_R_2299185503fwd/TA/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag11/13/1511/13/15147Genomicunknown
ss2731264590GNOMAD|exomes_rs1053341fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag05/17/1705/17/17151Genomicunknown
ss2746262051GNOMAD|coding_rs1053341fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag05/17/1705/17/17151Genomicunknown
ss2752821590GNOMAD|rs1053341fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag05/17/1705/17/17151Genomicunknown
ss2984850834AFFY|Axiom_PsorMich_Affx-8214165fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag05/24/1705/24/17151Genomicunknown
ss3021067954ILLUMINA|MEGA_Consortium_v2_15070954_A2_1:25611093-AC-0_B_R_2299185503fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag06/28/1706/28/17151Genomicunknown
ss3071291159TOPMED|TOPMed_freeze_5?chr1:25,284,602fwd/A/Cccaagatctgaccgtgatggcggccttggcttgggcttcctcacctcgag09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053341|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 AGCAGCAATG ACCTTTACTG AGTGTCCATG TGCGTCAAGC ACGTGTGCTT TACACTTGTT
 CTTATTATTA GGTTTAATAA TAGAATAATT GCCACATTTA CTGAGCACTC ATTATGGGCC
 AGGCCCTGCC CTAAGTGCTT AATTAGCTTT AGCTCCTCTA ATCCTTATCT TATCCCCACA
 CGGCATGTTA TGTTATCCCC ATTATTCAGT TGAGAACATT GAGGCTCAAA GAGGCAAAGT
 AACTTGACCA AATACTTGTA AACGATCTTG CATGCCCCTT CCAGCTGCCA TTTAGTAAGA
 CTCTAATTTC ATACCACCCT AAATCTCGTC TGCTTCCCCC TCGTCCTTCT CGCCATCTCC
 CCACCGAGCA GTTGGCCAAG ATCTGACCGT GATGGCGGCC
 M
 TTGGCTTGGG CTTCCTCACC TCGAGTTTCC GGAGACACAG CTGGAGCAGT GTGGCCTTCA
 ACCTCTTCAT GCTGGCGCTT GGTGTGCAGT GGGCAATCCT GCTGGACGGC TTCCTGAGCC
 AGTTCCCTTC TGGGAAGGTG GTCATCACAC TGTTCAGGTA TTGGGATGGT GGCTGGATCA
 CTTCTGGGTC ATAGAGGGAA TGGACCCCGA AAGGACAGGT TCCAGAAGAT CTGGGATATT
 GCCCCCTCTC TGTCTAGCAC CAGTGCTGTG CAATATTTAG GACATCCTTA TACTAAAAGA
 TTATTCATTG TTTAAAATTC AAATTAACTG GGCATCCTGT ATTTTACTGG ACAGCCCTAC
 TCCGTGTATC ACAAGGAATC CAGGCCTACA TTCCTCCTGC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
X54534 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
HWPA
C
ss1290088917EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.997699980.00230000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1685398658ExAc_Aggregated_Populations111194AF 0.999730230.00026980
ss71642852ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0160000

  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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