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Reference SNP (refSNP) Cluster Report: rs117706971                 **Clinical Channel**
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:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0621/311 (1000 Genomes)
A=0.0127/1590 (TOPMED)
HGVS Names
  • CM000668.2:g.32660615G>A
  • NC_000006.11:g.32628392G>A
  • NC_000006.12:g.32660615G>A
  • NG_029922.1:g.11448C>T
  • NM_001243961.1:c.796+245C>T
  • NM_001243962.1:c.773-367C>T
  • NM_002123.4:c.773-367C>T
  • NR_133907.1:n.438G>A
  • NT_113891.2:g.4073664G>A
  • NT_113891.3:g.4073558G>A
  • NT_167245.1:g.3907030G>A
  • NT_167245.2:g.3901445G>A
  • NT_167246.1:g.4083687G>A
  • NT_167246.2:g.4078067G>A
  • NT_167247.1:g.3962568G>A
  • NT_167247.2:g.3956983G>A
  • NT_167248.1:g.3860118G>A
  • NT_167248.2:g.3854522G>A
  • NT_167249.1:g.4057146G>A
  • NT_167249.2:g.4057848G>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 ss240480744 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs117706971 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
ss2404807441000GENOMES|pilot_1_CHB+JPT_2365821_chr6_32736370fwd/A/Gcatgtggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctggctcca05/01/1005/01/10132Genomicunknown
ss539209889DBMHC|NG_029922.1:g.11448C>Trev/BC/Ttggagccagaaccacggcttaaatgttagaactaggatgatgcccactttgtgccacatg10/01/1210/01/12137Genomicunknown
ss653050026SSMP|6_32628392fwd/TA/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg12/14/1202/11/15138Genomicunknown
ss13195943841000GENOMES|PHASE3_V1_31528440fwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg08/16/1408/16/14142Genomicunknown
ss1592319693EVA_DECODE|EVA_DECODE_6_32736370_283731_rs117706971fwd/TA/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg03/02/1503/03/15144Genomicunknown
ss1926040792WEILL_CORNELL_DGM|SNV:chr6:32628392fwd/TA/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg10/16/1510/17/15147Genomicunknown
ss2151829578USC_VALOUEV|NC_000006.11:g.32628392G>Afwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg11/17/1611/17/16150Genomicunknown
ss2282990382HUMAN_LONGEVITY|HLI-6-32660615-G-Afwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg11/18/1611/18/16150Genomicunknown
ss2451370481TOPMED|6_32628392_G/Afwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg11/20/1611/20/16150Genomicunknown
ss2707423933GRF|rs117706971fwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg02/13/1702/13/17151Genomicunknown
ss2837514216GNOMAD|rs117706971fwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg05/18/1705/18/17151Genomicunknown
ss2998836774SWEGEN|NC_000006.11:g.32628392G>Afwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg05/30/1705/30/17151Genomicunknown
ss3494040964TOPMED|TOPMed_freeze_5?chr6:32,660,615fwd/A/Gggcacaaagtgggcatcatcctagttctaacatttaagctgtggttctgg10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs117706971|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 AGGACACAGA ACTTCAGCTT GATGCAGATG TGTGGGAGGT GGGGAACAGC TGTTATTCTT
 CTGGGGAATA TGAAGGGTTC AGTCTTTTTA GGAAATTGGA TGATATCTCT TCCCGACCAC
 TAGCAGCCTC TTTCAGTCAC TGGAAAATGC TTACAGGCAG TAGCCACCAT CATGTGGCAC
 AAAGTGGGCA TCATCCTAGT
 R
 TCTAACATTT AAGCTGTGGT TCTGGCTCCA CATTTCACAA GAAGATGCCA CCAAAGTTAA
 GGCTTGGTTC TGGGGAACAA TGTCTGGAGA TTCCTAGAAA CTGGCAAACT TCTCCCCTAA
 GTCTTGATCC TCATAGCAGC AAATAGGCCA TGAACATGGA CCACTGTGGT CAGGTACACT
 CAGCTCATGC TCTTCCCTCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000006
dbSNP Blast Analysis

dbMHC locus: HLA-DQB1
  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPA
G
ss1319594384EAS 1008AF 0.128000010.87200004
EUR 1006AF 0.003000000.99699998
AFR 1322AF 0.000800000.99919999
AMR 694AF 0.010100000.98989999
SAS 978AF 0.174800010.82520002
ss240480744pilot_1_CHB+JPT_low_coverage_panel 120AF 0.116666670.88333333

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.116+/-0.2110000

  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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