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Reference SNP (refSNP) Cluster Report: rs113982491                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:132/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0067/721 (ExAC)
T=0.0216/108 (1000 Genomes)
T=0.0245/291 (GO-ESP)
T=0.0199/2503 (TOPMED)
HGVS Names
  • CM000663.2:g.25290715C>T
  • NC_000001.10:g.25617206C>T
  • NC_000001.11:g.25290715C>T
  • NG_007494.1:g.23226C>T
  • NM_001127691.2:c.410C>T
  • NM_001282867.1:c.-85C>T
  • NM_001282868.1:c.410C>T
  • NM_001282869.1:c.410C>T
  • NM_001282870.1:c.410C>T
  • NM_001282871.1:c.410C>T
  • NM_001282872.1:c.410C>T
  • NM_001321772.1:c.-66-43686G>A
  • NM_016124.4:c.410C>T
  • NP_001121163.1:p.Ala137Val
  • NP_001269797.1:p.Ala137Val
  • NP_001269798.1:p.Ala137Val
  • NP_001269799.1:p.Ala137Val
  • NP_001269800.1:p.Ala137Val
  • NP_001269801.1:p.Ala137Val
  • NP_057208.2:p.Ala137Val
  • NR_135787.1:n.1216-43686G>A
  • NR_135788.1:n.278-43686G>A
  • NR_135789.1:n.1216-43686G>A
  • XP_005246016.1:p.Ala137Val
  • XP_005246017.1:p.Ala137Val
  • XP_005246018.1:p.Ala137Val
  • XP_005246019.1:p.Ala137Val
  • XP_005246020.1:p.Ala137Val
  • XP_005246021.1:p.Ala137Val
  • XP_016857504.1:p.Ala137Val
  • XR_946736.1:n.565C>T
  • XR_946737.1:n.565C>T
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 ss341945885 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs113982491 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
ss198190817BUSHMAN|BUSHMAN-chr1-25489792byFreqfwd/BC/Ttggatgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtggaggt02/16/1009/05/14132Genomicunknown
ss3284845121000GENOMES|20100804_snps_128048_chr1_25617206fwd/C/Ttggatgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtggaggt03/22/1103/22/11134Genomicunknown
ss341945885NHLBI-ESP|ESP2500-chr1-25617206byFreqfwd/BC/Ttggatgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtggaggt03/25/1109/05/14134Genomicunknown
ss480822742ILLUMINA|HumanOmni2.5-4v1_D_kgp15326551-0_B_F_1836296972fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg01/30/1210/27/16137Genomicunknown
ss482303430ILLUMINA|HumanOmni2.5-4v1_B_SNP1-25489793-0_B_F_1642751861fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg01/30/1210/28/16137Genomicunknown
ss4897292081000GENOMES|20110521_exome_298634_chr1_25617206fwd/BC/Ttggatgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtggaggt02/10/1202/21/12137Genomicunknown
ss491289429EXOME_CHIP|nonsyn_5656_chr_1_25617206fwd/BC/Ttggatgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtggaggt03/05/1203/05/12137Genomicunknown
ss491589280CLINSEQ_SNP|SNV-chr1-25489793byFreqfwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg03/06/1209/05/14137Genomicunknown
ss533965765ILLUMINA|HumanOmni5-4v1_B_kgp15326551-0_B_F_1836296972fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg06/22/1208/28/15146Genomicunknown
ss780643505ILLUMINA|HumanOmni25Exome-8v1_A_kgp15326551-0_B_F_1836296972fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg05/30/1307/09/15146Genomicunknown
ss781326979ILLUMINA|HumanOmni2.5-4v1_H_kgp15326551-0_B_F_1836296972fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg05/30/1307/28/15146Genomicunknown
ss836138001ILLUMINA|HumanOmni2.5-8v1_A_kgp15326551-0_B_F_1836296972fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg09/18/1307/28/15146Genomicunknown
ss1067418344JMKIDD_LAB|HGDP_exomes_chr1_25617206fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg07/09/1407/09/14142Genomicunknown
ss12900891171000GENOMES|PHASE3_V1_783444fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg08/16/1408/16/14142Genomicunknown
ss1425750409DDI|DDI_rs113982491fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg11/04/1411/04/14144Genomicunknown
ss1685398725EVA_EXAC|EVA_EXAC_194535fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg03/04/1503/04/15144Genomicunknown
ss1710896021EVA_MGP|EVA_XIMO_12773fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg03/09/1503/09/15144Genomicunknown
ss1918172060WEILL_CORNELL_DGM|SNV:chr1:25617206fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg10/16/1510/16/15147Genomicunknown
ss1958254305ILLUMINA|1:25617206-CT-0_B_F_2299185512fwd/BC/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg11/13/1511/13/15147Genomicunknown
ss2632491840ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp15326551-0_B_F_18362969fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg02/02/1702/02/17151Genomicunknown
ss2731264692GNOMAD|exomes_rs113982491fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg05/17/1705/17/17151Genomicunknown
ss2746262089GNOMAD|coding_rs113982491fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg05/17/1705/17/17151Genomicunknown
ss2752822166GNOMAD|rs113982491fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg05/17/1705/17/17151Genomicunknown
ss2984850840AFFY|Axiom_PsorMich_Affx-8214840fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg05/24/1705/24/17151Genomicunknown
ss3021067962ILLUMINA|MEGA_Consortium_v2_15070954_A2_1:25617206-CT-0_B_F_2299185512fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg06/28/1706/28/17151Genomicunknown
ss3071292313TOPMED|TOPMed_freeze_5?chr1:25,290,715fwd/C/Tgctgtcttggggaaggtcaacttgggcagttggtggtgatggtgctggtg09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs113982491|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CACTCCACTC TGCAGCATCA GCGCCCAGGT GGGTAGAAAT CTTGTCTTCT ATTCCCACAG
 AAAGTAGGTG CCCAACAGTG TTTGTTGAAA GAATGAATGA ATGAATGAAT GAATGAATGA
 ATGAGTGAGA GGCATCCTTC CTTCTCAGTC GTCCTGGCTC TCCCTCTCTC CCCCAGTATT
 CGGCTGGCCA CCATGAGTGC TTTGTCGGTG CTGATCTCAG TGGATGCTGT CTTGGGGAAG
 GTCAACTTGG
 Y
 GCAGTTGGTG GTGATGGTGC TGGTGGAGGT GACAGCTTTA GGCAACCTGA GGATGGTCAT
 CAGTAATATC TTCAACGTGA GTCATGGTGC TGGGAGGAGG GACCTGGGAG AAAAGGGCCA
 AAAGCTCCAT TTGGTGGGGT TTCCAGGGTT TTGAAAAATA AAGACAACCT GTAATCCCAG
 CTACTTGGGA GGTTGAGGAG GGAAGATCAC TTGAGGCCAG GAGTTTGAGA CCAGCCTGGG
 CATCATAGCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
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/T
T/T
HWPC
T
ss1290089117EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.922800060.07720000
AMR 694AF 0.992799940.00720000
SAS 978AF 0.998999950.00100000
ss1685398725ExAc_Aggregated_Populations112232AF 0.993531230.00646874
ss198190817BUSHMAN_POP 2IG 1.00000000 0.500000000.50000000
BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss341945885ESP_Cohort_Populations 4068GF0.956735490.033923310.009341200.001000000.973697130.02630285
ss491589280CSAgilent 1125GF0.995999990.00400000 1.000000000.998000030.00200000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.013+/-0.0800000

  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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