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Reference SNP (refSNP) Cluster Report: rs12720461                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0006/3 (1000 Genomes)
T=0.0017/214 (TOPMED)
HGVS Names
  • CM000677.2:g.74749010C>T
  • NC_000015.10:g.74749010C>T
  • NC_000015.9:g.75041351C>T
  • NG_008431.2:g.31469C>T
  • NG_055245.1:g.4680C>T
  • NM_000761.4:c.-10+113C>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 ss20418281 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12720461 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
ss20418281WRAYLAB|CYP1A2-730byFreqfwd/BC/Tgcctgggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgacttctgt02/25/0410/26/06121Genomicunknown
ss32475100BIOVENTURES|BV02004fwd/BC/Tgcctgggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgacttctgt12/10/04125Genomicunknown
ss48293714SNP500CANCER|CYP1A2-27byFreqfwd/BC/Tgcctgggctaggtgtaggggkcctgasttcgggctttgctacccagctcttgacttctgt08/19/0511/03/06126Genomicunknown
ss75235230ILLUMINA|ILMN_Human_1M_rs12720461fwd/BC/Tgcctgggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgacttctgt08/28/0708/29/07129Genomicunknown
ss84158700PHARMGKB_AB_DME|PS206191_PA149535152_301fwd/BC/Tgcctgggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgacttctgt12/06/0712/10/07130Genomicunknown
ss119808382KRIBB_YJKIM|KHS1854088fwd/BC/Tgcctgggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgacttctgt02/04/0902/05/09131Genomicunknown
ss153275061ILLUMINA|Human610_Quadv1_B_rs12720461-128_T_R_1514203200rev/TA/Gacagaagtcaagagctgggtagcaaagcccgaactcaggacccctacacctagcccaggc06/18/0906/19/09131Genomicunknown
ss159232839ILLUMINA|Human660W-Quad_v1_A_rs12720461-128_T_R_1514203200rev/TA/Gacagaagtcaagagctgggtagcaaagcccgaactcaggacccctacacctagcccaggc07/06/0907/06/09131Genomicunknown
ss160296911ILLUMINA|HumanOmni1-Quad_v1-0_B_rs12720461-128_T_R_1514203200rev/TA/Gacagaagtcaagagctgggtagcaaagcccgaactcaggacccctacacctagcccaggc08/04/0910/02/09131Genomicunknown
ss172232549ILLUMINA|Human1M-Duov3_B_rs12720461-128_T_R_1514203200rev/TA/Gacagaagtcaagagctgggtagcaaagcccgaactcaggacccctacacctagcccaggc10/01/0910/02/09132Genomicunknown
ss3388916241000GENOMES|20100804_snps_10535165_chr15_75041351fwd/C/Tgcctgggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgacttctgt03/22/1103/22/11134Genomicunknown
ss479812540ILLUMINA|HumanOmni2.5-4v1_B_rs12720461-128_T_R_1616886775fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact01/30/1210/28/16137Genomicunknown
ss479819658ILLUMINA|HumanOmniExpress-12v1_C_rs12720461-131_T_R_1857476361fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact01/30/1210/27/16137Genomicunknown
ss480404424ILLUMINA|HumanOmni1-Quad_v1-0_C_rs12720461-131_T_R_1865767036fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact01/30/1208/28/15146Genomicunknown
ss484704763ILLUMINA|HumanOmni2.5-4v1_D_rs12720461-131_T_R_1857476361fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact01/30/1210/27/16137Genomicunknown
ss536810794ILLUMINA|HumanOmni5-4v1_B_rs12720461-131_T_R_1889943058fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact06/22/1208/29/15146Genomicunknown
ss778789425ILLUMINA|HumanOmni25Exome-8v1_A_rs12720461-131_T_R_1865767036fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/30/1307/10/15146Genomicunknown
ss782799150ILLUMINA|HumanOmni2.5-4v1_H_rs12720461-131_T_R_1857476361fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/30/1307/29/15146Genomicunknown
ss783764706ILLUMINA|HumanOmniExpressExome-8v1_A_rs12720461-131_T_R_1889943058fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/31/1306/18/15146Genomicunknown
ss832052100ILLUMINA|HumanOmniExpress-12v1_H_rs12720461-131_T_R_1857476361fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact09/17/1306/18/15146Genomicunknown
ss834249455ILLUMINA|HumanOmni2.5-8v1_A_rs12720461-131_T_R_1865767036fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact09/18/1307/29/15146Genomicunknown
ss991955438EVA-GONL|EVA-GONL_rs12720461fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact04/23/1404/30/14142Genomicunknown
ss13541273651000GENOMES|PHASE3_V1_67486823fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact08/16/1408/16/14142Genomicunknown
ss1633356812EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_15_75041351_37331430fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact03/04/1503/04/15144Genomicunknown
ss1676350845EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_15_75041351_37331430fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact03/04/1503/04/15144Genomicunknown
ss1713502764EVA_SVP|EVA_SVP_1197131fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact03/12/1503/12/15144Genomicunknown
ss1752171274ILLUMINA|OmniExpressExome-8v1-1_B_rs12720461-131_T_R_1889943058fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/27/1506/09/15146Genomicunknown
ss1935358588WEILL_CORNELL_DGM|SNV:chr15:75041351fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact10/16/1510/18/15147Genomicunknown
ss1959626384ILLUMINA|15:75041351-C-T-0_T_R_2304290264fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact11/13/1511/13/15147Genomicunknown
ss2028461524JJLAB|SNP8964079fwd/BC/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact08/29/1608/31/16149Genomicunknown
ss2208164815HUMAN_LONGEVITY|HLI-15-74749010-C-Tfwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact11/18/1611/18/16150Genomicunknown
ss2372617246TOPMED|15_75041351_C/Tfwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact11/19/1611/19/16150Genomicunknown
ss2633251309ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs12720461-131_T_R_1889943fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact02/02/1702/02/17151Genomicunknown
ss2710820366ILLUMINA|Consortium-OncoArray_15047405_A_rs12720461-131_T_R_1889943058fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact03/22/1703/22/17151Genomicunknown
ss2936801928GNOMAD|rs12720461fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/23/1705/23/17151Genomicunknown
ss2985046784AFFY|Axiom_PsorMich_Affx-11968835fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/24/1705/24/17151Genomicunknown
ss2985680242AFFY|Axiom_Smokesc1_Affx-11968835fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/24/1705/24/17151Genomicunknown
ss3013550578SWEGEN|NC_000015.9:g.75041351C>Tfwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact05/30/1705/30/17151Genomicunknown
ss3021649404ILLUMINA|MEGA_Consortium_v2_15070954_A2_15:75041351-C-T-0_T_R_2304290264fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact06/28/1706/28/17151Genomicunknown
ss3232003707TOPMED|TOPMed_freeze_5?chr15:74,749,010fwd/C/Tggctaggtgtaggggtcctgagttcgggctttgctacccagctcttgact10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12720461|allelePos=320|totalLen=702|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GTAGTAGGTG GAGCTGAGGG ATAATGGCCC AAGGCCAAGA GTTGATCCTT CCAACTTTGT
 TCAGTGATCC AGCTTTCATA TCAGGTGATC AGGACAACCA GGCCAATCTG ATAGGGGGCG
 GTGTTTATAA AAAGGCCACT CACCTAGAGC CAGAAGCTCC ACACCAGCCA TTACAACCCT
 GCCAATCTCA AGCACCTGCC TCTACAGGTA CCTTTCTTGG GACCAATTTA CAATCTCTGG
 GATCCCCAAC TATAGAACCT GGAAGCTAGT GGGGACAGAA AGACGGGGAG CCTGGGCTAG
 GTGTAGGGGT CCTGAGTTC
 Y
 GGGCTTTGCT ACCCAGCTCT TGACTTCTGT TTCCCGATTT TAAATGAGCA GTTTGGACTA
 AGCCATTTTT AAGGAGAGCG ATGGGGAGGG CTTCCCCCTT AGCACAAGGG CAGCCCTGGC
 CCTGGCTGAA GCCCAACCCC AACCTCCAAG ACTGTGAGAG GATGGGGACT CATCCCTGGA
 GGAGGTGCCC CTCCTGGTAT TGATAAAGAA TGCCCTGGGG AGGGGGCATC ACAGGCTATT
 TGAACCAGCC CTGGGACCTT GGCCACCTCA GTGTCACTGG GTAGGGGGAA CTCCTGGTCC
 CTTGGGTATA TGGAAGGTAT CAGCAGAAAG CCAGCACTGG CAGGGACTCT TTGGTACAAT
 ACCCAGCATG CATGCTGTGC CA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010194
dbSNP Blast Analysis

  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
ss1354127365EAS 1008AF 1.00000000
EUR 1006AF 0.996999980.00300000
AFR 1322AF 1.00000000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss20418281HapMap-CEUEuropean 120IG1.00000000 1.00000000
HapMap-HCBAsian 88IG0.97727275 0.022727270.001000000.977272750.02272727
HapMap-JPTAsian 90IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 118IG1.00000000 1.00000000
HAPMAP-GIH 176IG0.988636370.01136364 1.000000000.994318190.00568182
HAPMAP-MKK 286IG0.993007000.00699301 1.000000000.996503470.00349650
HAPMAP-TSI 176IG0.965909060.03409091 1.000000000.982954560.01704546
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss48293714P1 204AF0.980000020.02000000 1.000000000.990000010.01000000
CAUC1 62AF0.935000000.06500001 1.000000000.967999990.03200000
AFR1 48AF1.00000000 1.00000000
HISP1 46AF1.00000000 1.00000000
PAC1 48AF1.00000000 1.00000000
ss84158700PA149535153 358AF 0.997206690.00279330

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0240000

  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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