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Reference SNP (refSNP) Cluster Report: rs117575598                 ** With Likely benign allele **
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:With Likely benign allele [ClinVar]
MAF/MinorAlleleCount:C=0.0006/74 (ExAC)
C=0.0014/7 (1000 Genomes)
C=0.0006/78 (TOPMED)
HGVS Names
  • CM000664.2:g.202514987T>C
  • NC_000002.11:g.203379710T>C
  • NC_000002.12:g.202514987T>C
  • NG_009363.1:g.143661T>C
  • NM_001204.6:c.621+8T>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 ss239018308 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs117575598 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
ss2390183081000GENOMES|pilot_1_CHB+JPT_903385_chr2_203087955fwd/C/Ttagataatctgaaactgttggaggtaagttgccgttagattatggactgttgtttctact05/01/1005/01/10132Genomicunknown
ss4898476081000GENOMES|20110521_exome_357214_chr2_203379710fwd/BC/Ttagataatctgaaactgttggaggtaagttgccgttagattatggactgttgtttctact02/10/1202/21/12137Genomicunknown
ss649825055SSMP|2_203379710fwd/BC/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt12/14/1202/10/15138Genomicunknown
ss13012527151000GENOMES|PHASE3_V1_12405500fwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt08/16/1408/16/14142Genomicunknown
ss1686688614EVA_EXAC|EVA_EXAC_1585845fwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt03/04/1503/04/15144Genomicunknown
ss2238327341HUMAN_LONGEVITY|HLI-2-202514987-T-Cfwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt11/18/1611/18/16150Genomicunknown
ss2703806876GRF|rs117575598fwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt02/13/1702/13/17151Genomicunknown
ss2733259604GNOMAD|exomes_rs117575598fwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt05/17/1705/17/17151Genomicunknown
ss2746858642GNOMAD|coding_rs117575598fwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt05/17/1705/17/17151Genomicunknown
ss2785207770GNOMAD|rs117575598fwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt05/17/1705/17/17151Genomicunknown
ss3335804311TOPMED|TOPMed_freeze_5?chr2:202,514,987fwd/C/Taatctgaaactgttggaggtaagttgccgttagattatggactgttgttt10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs117575598|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TTTCTGCAGC TCTTCTTTTT AAGTGTAATA TTATAAAAAG TGTAAAAAGA TATTCATTTT
 AAGAAAACCA TATATTAGTA ACCTGTTTCC TGTTCTTATA GGAGACCGTA AACAAGGTCT
 TCACAGTATG AACATGATGG AGGCAGCAGC ATCCGAACCC TCTCTTGATC TAGATAATCT
 GAAACTGTTG GAGGTAAGTT
 Y
 GCCGTTAGAT TATGGACTGT TGTTTCTACT GTGATACTAG ACCTGGAACA GTGACTTCAT
 TCAATCATTA AGACATTCAT TCATTTATTT AACCCTATTT ACTAAATTAC AATTTTTTGT
 CAAGGCCTAT TCTAGGCACT AGGAACATAG GTGAACAATG TCTCCTGGGG CTTCTATTTG
 AATTGGGGAG TCTACAGACA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000002
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPC
T
ss1301252715EAS 1008AF 0.006900000.99309999
EUR 1006AF 1.00000000
AFR 1322AF 1.00000000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1686688614ExAc_Aggregated_Populations121412AF 0.000609490.99939048
ss239018308pilot_1_CHB+JPT_low_coverage_panel 120AF 0.008333330.99166667

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0250000

  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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