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Reference SNP (refSNP) Cluster Report: rs12720065                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.0012/150 (ExAC)
G=0.0064/32 (1000 Genomes)
G=0.0043/56 (GO-ESP)
G=0.0038/477 (TOPMED)
HGVS Names
  • CM000670.2:g.18400406C>G
  • NC_000008.10:g.18257916C>G
  • NC_000008.11:g.18400406C>G
  • NG_012246.1:g.14162C>G
  • NM_000015.2:c.403C>G
  • NP_000006.2:p.Leu135Val
  • XP_016868427.1:p.Leu135Val
Links , Linkout
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 ss105440017 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12720065 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
ss20398860POLYGENYX|NAT2-409fwd/BC/Gtctggaagctcctcccagatgtggcagccttagaattwatttctgggaaggatcagcctc02/23/0403/04/04121Genomicunknown
ss69042398PERLEGEN|PGP07586564fwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc01/30/0701/30/07127Genomicunknown
ss76869171CGM_KYOTO|11625fwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc09/12/0709/12/07129cDNAunknown
ss86244080CORNELL|hCV25604708fwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc01/21/0809/29/10129Genomicunknown
ss105440017SNP500CANCER|NAT2-19byFreqfwd/C/Gtctggaagctcctcccagatgtggcagccttagaattwatttctgggaaggatcagcctc09/05/0809/05/14130Genomicunknown
ss120036970ILLUMINA|GS0007123-OPA_Ober-rs12720065fwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc02/24/0902/24/09131Genomicunknown
ss160296881ILLUMINA|HumanOmni1-Quad_v1-0_B_rs12720065-128_T_R_1562279613rev/C/Ggaggctgatccttcccagaaattaattctaaggctgccacatctgggaggagcttccaga08/04/0910/02/09131Genomicunknown
ss342253606NHLBI-ESP|ESP2500-chr8-18257916byFreqfwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc03/25/1109/05/14134Genomicunknown
ss4602566261000GENOMES|20101123_snps_6423856_chr8_18257916fwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc07/20/1107/20/11135Genomicunknown
ss480404307ILLUMINA|HumanOmni1-Quad_v1-0_C_rs12720065-128_T_R_1776603172fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca01/30/1208/28/15146Genomicunknown
ss4909607211000GENOMES|20110521_exome_468519_chr8_18257916fwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc02/10/1202/21/12137Genomicunknown
ss491410758EXOME_CHIP|nonsyn_126984_chr_8_18257916fwd/C/Gtctggaagctcctcccagatgtggcagccttagaattaatttctgggaaggatcagcctc03/05/1203/05/12137Genomicunknown
ss560588641TISHKOFF|snp_chr8_18257916fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca11/22/1211/23/12138Genomicunknown
ss780867823ILLUMINA|HumanOmni25Exome-8v1_A_exm685672-0_T_R_1922984080fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca05/30/1307/10/15142Genomicunknown
ss783552754ILLUMINA|HumanOmniExpressExome-8v1_A_exm685672-0_T_R_1922984080fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca05/31/1306/19/15142Genomicunknown
ss13288539011000GENOMES|PHASE3_V1_41164985fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca08/16/1408/16/14142Genomicunknown
ss1689107855EVA_EXAC|EVA_EXAC_4197275fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca03/04/1503/04/15144Genomicunknown
ss1752722184ILLUMINA|OmniExpressExome-8v1-1_B_exm685672-0_T_R_2060141827fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca05/27/1506/09/15146Genomicunknown
ss1917826204ILLUMINA|HumanExome-12v1-1_B_exm685672-0_T_R_2060141827fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca10/16/1510/16/15147Genomicunknown
ss1946231108ILLUMINA|HumanCoreExome-12v1-0_C_exm685672-0_T_R_2060141827fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca10/29/1510/29/15147Genomicunknown
ss1959092402ILLUMINA|exm685672-0_T_R_1922984080fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca11/13/1511/13/15147Genomicunknown
ss2301164550HUMAN_LONGEVITY|HLI-8-18400406-C-Gfwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca11/18/1611/18/16150Genomicunknown
ss2470822143TOPMED|8_18257916_C/Gfwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca11/20/1611/20/16150Genomicunknown
ss2737016679GNOMAD|exomes_rs12720065fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca05/17/1705/17/17151Genomicunknown
ss2748005933GNOMAD|coding_rs12720065fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca05/17/1705/17/17151Genomicunknown
ss2863932591GNOMAD|rs12720065fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca05/19/1705/19/17151Genomicunknown
ss2985432612AFFY|Axiom_PsorMich_Affx-31859120fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca05/24/1705/24/17151Genomicunknown
ss3022824452ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm685672-0_T_R_1922984080fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca06/28/1706/28/17151Genomicunknown
ss3029637977CSIRBIOHTS|NM_000015.2:g.18257916C>Gfwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca07/28/1707/28/17151Genomicunknown
ss3555514735TOPMED|TOPMed_freeze_5?chr8:18,400,406fwd/C/Gaagctcctcccagatgtggcagccttagaattaatttctgggaaggatca10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12720065|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=151
 GTTCCCTTYG AGAACCTTAA CATGCATTGT GGGCAAGCCA TGGAGTTGGG CTTAGAGGCT
 ATTTTTGATC ACATTGTAAG AAGAAACYRG GGTGGGTGGT GTCTCCAGGT CAATCAACTT
 CTGTACTGGG CTCTGACCAC AATCGGTTTT CAGACCACAA TGTTAGGAGG GTATTTTTAY
 ATCCCTCCAG TTAACAAATA CAGCACTGGC ATGGTTCACC TTCTCCTGCA GGTGACCAYT
 GAYGGCAGGA ATTACATTGT CRATGCTGGG TCTGGAAGCT CCTCCCAGAT GTGGCAGCCT
 S
 TAGAATTWAT TTCTGGGAAG GATCAGCCTC MGGTGCCTTG CATTTTCTGC TTGACAGAAG
 AGAGAGGAAT CTGGTACYTG GACCAAATCA GGAGAGAGCA GTATATTACA AACAAAGAAT
 TTCTTAATTC TCATCTCCTG CCAAAGAAGA AACACCAAAA AATATACTTA TTTACGCTTG
 AACCTCRAAC AATTGAAGAT TTTGAKTCTW TGAATACATA CCTGCAGACG TCTCCAACAT
 CTTCATTTAT AACCACATCA TTTTGTTCCT TGCAGACCCY AGAAGGGGTT TACTGTTTGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_030737.9
dbSNP Blast Analysis
UniGene Cluster ID
2
3D structure mapping
NP_000006  

  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/G
G/G
HWPC
G
ss105440017HapMap-CEUEuropean 106IG0.981132090.01886792 1.000000000.990566020.00943396
HapMap-HCBAsian 88IG1.00000000 1.00000000
HapMap-JPTAsian 90IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 118IG1.00000000 1.00000000
P2 420GF0.995238070.00476190 1.000000000.997619030.00238095
CAUC2 120GF1.00000000 1.00000000
AFR2 120GF0.983333350.01666667 1.000000000.991666670.00833333
P3 558GF0.982078850.01792115 1.000000000.991039450.00896057
CAUC3 132GF1.00000000 1.00000000
AFR3 150GF0.933333340.06666667 1.000000000.966666640.03333334
HISP3 98GF1.00000000 1.00000000
PAC3 178GF1.00000000 1.00000000
ASI2 180GF1.00000000 1.00000000
ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss1328853901EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.976599990.02340000
AMR 694AF 0.998599950.00140000
SAS 978AF 1.00000000
ss1689107855ExAc_Aggregated_Populations121408AF 0.998764510.00123550
ss342253606ESP_Cohort_Populations 4524GF0.988063630.011494250.000442090.002501000.993810770.00618921
ss86244080AGI_ASP_populationmultiple 66IG0.969697000.03030303 1.000000000.984848500.01515152

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.002+/-0.0350000ALFRED: The Allele Frequency Database

  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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