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Reference SNP (refSNP) Cluster Report: rs56172717                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/T (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0024/292 (ExAC)
T=0.0012/6 (1000 Genomes)
T=0.0024/31 (GO-ESP)
T=0.0018/231 (TOPMED)
HGVS Names
  • CM000670.2:g.18222799A>T
  • NC_000008.10:g.18080308A>T
  • NC_000008.11:g.18222799A>T
  • NG_012245.2:g.57338A>T
  • NM_000662.7:c.752A>T
  • NM_001160170.3:c.752A>T
  • NM_001160171.3:c.752A>T
  • NM_001160172.3:c.752A>T
  • NM_001160173.3:c.752A>T
  • NM_001160174.2:c.752A>T
  • NM_001160175.3:c.938A>T
  • NM_001160176.3:c.938A>T
  • NM_001160179.2:c.752A>T
  • NM_001291962.1:c.938A>T
  • NP_000653.3:p.Asp251Val
  • NP_001153642.1:p.Asp251Val
  • NP_001153643.1:p.Asp251Val
  • NP_001153644.1:p.Asp251Val
  • NP_001153645.1:p.Asp251Val
  • NP_001153646.1:p.Asp251Val
  • NP_001153647.1:p.Asp313Val
  • NP_001153648.1:p.Asp313Val
  • NP_001153651.1:p.Asp251Val
  • NP_001278891.1:p.Asp313Val
  • XP_005273734.1:p.Asp313Val
  • XP_005273735.1:p.Asp251Val
  • XP_005273736.1:p.Asp251Val
  • XP_006716473.1:p.Asp251Val
  • XP_011542989.1:p.Asp313Val
  • XP_011542990.1:p.Asp313Val
  • XP_011542991.1:p.Asp251Val
  • XP_016869436.1:p.Asp313Val
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 ss342253590 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs56172717 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
ss75261833ILLUMINA|ILMN_Human_1M_SNP36fwd/A/Tataggagattcaattataaggacaatacagtctaatagagttcaagactctgagtgagga08/28/0708/29/07129Genomicunknown
ss105434756AFFY_DM3_1|DMET3B14982fwd/A/Tataggagattcaattataaggacaatacagtctaatagagttcaagactctgagtgagga09/03/0809/03/08130Genomicunknown
ss161079685ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP36-0_B_F_1514230367fwd/A/Tataggagattcaattataaggacaatacagtctaatagagttcaagactctgagtgagga08/04/0910/05/09131Genomicunknown
ss169136297ILLUMINA|Human1M-Duov3_B_SNP36-unknown_B_F_1514230367fwd/A/Tataggagattcaattataaggacaatacagtctaatagagttcaagactctgagtgagga10/01/0910/01/09132Genomicunknown
ss342253590NHLBI-ESP|ESP2500-chr8-18080308byFreqfwd/A/Tataggagattcaattataaggacaatacagtctaatagagttcaagactctgagtgagga03/25/1109/05/14134Genomicunknown
ss483025687ILLUMINA|HumanOmni1-Quad_v1-0_C_SNP36-0_B_F_1853007728fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt01/30/1208/28/15146Genomicunknown
ss4888833891000GENOMES|20110521_exome_116801_chr8_18080308fwd/A/Tataggagattcaattataaggacaatacagtctaatagagttcaagactctgagtgagga02/10/1202/13/12137Genomicunknown
ss491410746EXOME_CHIP|nonsyn_126972_chr_8_18080308fwd/A/Tataggagattcaattataaggacaatacagtctaatagagttcaagactctgagtgagga03/05/1203/05/12137Genomicunknown
ss491921833CLINSEQ_SNP|SNV-chr8-18124588byFreqfwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt03/06/1209/05/14137Genomicunknown
ss537652775ILLUMINA|HumanOmni5-4v1_B_SNP36-0_B_F_1853007728fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt06/22/1208/29/15146Genomicunknown
ss780867815ILLUMINA|HumanOmni25Exome-8v1_A_exm685642-0_B_F_1922923285fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/30/1307/10/15142Genomicunknown
ss783552746ILLUMINA|HumanOmniExpressExome-8v1_A_exm685642-0_B_F_1922923285fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/31/1306/19/15142Genomicunknown
ss985254183EVA-GONL|EVA-GONL_rs56172717fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt04/23/1404/25/14142Genomicunknown
ss13288471241000GENOMES|PHASE3_V1_41157963fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt08/16/1408/16/14142Genomicunknown
ss1584057285EVA_FINRISK|EVA_FINRISK_rs56172717fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt02/27/1502/27/15144Genomicunknown
ss1620096464EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_8_18080308_22757071fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt03/04/1503/04/15144Genomicunknown
ss1663090497EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_8_18080308_22757071fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt03/04/1503/04/15144Genomicunknown
ss1689107723EVA_EXAC|EVA_EXAC_4197135fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt03/04/1503/04/15144Genomicunknown
ss1711194380EVA_MGP|EVA_XIMO_310140fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt03/09/1503/09/15144Genomicunknown
ss1752722041ILLUMINA|OmniExpressExome-8v1-1_B_exm685642-0_B_F_1922923285fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/27/1506/09/15146Genomicunknown
ss1917826196ILLUMINA|HumanExome-12v1-1_B_exm685642-0_B_F_1922923285fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt10/16/1510/16/15147Genomicunknown
ss1946231057ILLUMINA|HumanCoreExome-12v1-0_C_exm685642-0_B_F_1922923285fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt10/29/1510/29/15147Genomicunknown
ss1959092256ILLUMINA|exm685642-0_B_F_1922923285fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt11/13/1511/13/15147Genomicunknown
ss2301150684HUMAN_LONGEVITY|HLI-8-18222799-A-Tfwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt11/18/1611/18/16150Genomicunknown
ss2470808532TOPMED|8_18080308_A/Tfwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt11/20/1611/20/16150Genomicunknown
ss2634717610ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SNP36-0_B_F_1853007728fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt02/02/1702/02/17151Genomicunknown
ss2711131561ILLUMINA|Consortium-OncoArray_15047405_A_rs56172717-131_B_F_1889936296fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt03/22/1703/22/17151Genomicunknown
ss2737016494GNOMAD|exomes_rs56172717fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/17/1705/17/17151Genomicunknown
ss2748005878GNOMAD|coding_rs56172717fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/17/1705/17/17151Genomicunknown
ss2863915053GNOMAD|rs56172717fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/19/1705/19/17151Genomicunknown
ss2985432576AFFY|Axiom_PsorMich_Affx-31855749fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/24/1705/24/17151Genomicunknown
ss2986074627AFFY|Axiom_Smokesc1_Affx-31855749fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/24/1705/24/17151Genomicunknown
ss3002777611SWEGEN|NC_000008.10:g.18080308A>Tfwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt05/30/1705/30/17151Genomicunknown
ss3022824296ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm685642-0_B_F_1922923285fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt06/28/1706/28/17151Genomicunknown
ss3555475173TOPMED|TOPMed_freeze_5?chr8:18,222,799fwd/A/Tagattcaattataaggacaatacagtctaatagagttcaagactctgagt10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs56172717|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=151
 CAGTACATTC CAAATGAAGA ATTTCTTCAT TCTGATCTCC TAGAAGACAG CAAATACCGA
 AAAATCTACT CCTTTACTCT TAAGCCTCGA ACAATTGAAG ATTTTGAGTC TATGAATACA
 TACCTGCAGA CATCTCCATC ATCTGTGTTT ACTAGTAAAT CATTTTGTTC CTTGCAGACC
 CCAGATGGGG TTCACTGTTT GGTGGGCTTC ACCCTCACCC ATAGGAGATT CAATTATAAG
 GACAATACAG
 W
 TCTAATAGAG TTCAAGACTC TGAGTGAGGA AGAAATAGAA AAAGTGCTGA AAAATATATT
 TAATATTTCC TTGCAGAGAA AGCTTGTGCC CAAACATGGT GATAGATTTT TTACTATTTA
 GAATAAGGAG TAAAACAATC TTGTCTATTT GTCATCCAGC TCACCAGTTA TCAACTGACG
 ACCTATCATG TATCTTCTGT ACCCTTACCT TATTTTGAAG AAAATCCTAG ACATCAAATC
 ATTTCACCTA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000008
dbSNP Blast Analysis
3D structure mapping
NP_000653  NP_001153642  NP_001153643  NP_001153644  NP_001153645  NP_001153646  NP_001153647  NP_001153648  NP_001153651  

  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/T
T/T
HWPA
T
ss1328847124EAS 1008AF 1.00000000
EUR 1006AF 0.994999950.00500000
AFR 1322AF 1.00000000
AMR 694AF 0.998599950.00140000
SAS 978AF 1.00000000
ss1689107723ExAc_Aggregated_Populations121406AF 0.997594830.00240515
ss342253590ESP_Cohort_Populations 4476GF0.998212700.00178731 1.000000000.999106350.00089366
ss491921833CSAgilent 1215GF0.995000060.00500000 1.000000000.997500000.00250000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.005+/-0.0490000

  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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