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Reference SNP (refSNP) Cluster Report: rs12513649                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.0216/108 (1000 Genomes)
G=0.0131/1642 (TOPMED)
HGVS Names
  • CM000667.2:g.173045049C>G
  • CM000667.2:g.173045049C>T
  • NC_000005.9:g.172472052C>G
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 ss278592004 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12513649 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
ss19608988CSHL-HAPMAP|CSHL-HuDD-200402.chr5.NT_023133.11_17281638byFreqfwd/TC/Gggtaaaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggccacac02/20/0410/26/06120Genomicunknown
ss44604361ABI|hCV26692451fwd/C/Gggtaaaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggccacac07/19/0507/19/05126Genomicunknown
ss76815887AFFY|AFFY_6_1M_SNP_A-8677315fwd/C/Gctttacccatcgatgaggtcttgtagccttag08/28/0708/30/07129Genomicunknown
ss105058408KRIBB_YJKIM|KHS1450731fwd/C/Gggtaaaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggccacac07/10/0807/11/08130Genomicunknown
ss2403613831000GENOMES|pilot_1_CHB+JPT_2246460_chr5_172404658fwd/C/Gggtaaaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggccacac05/01/1005/01/10132Genomicunknown
ss278592004GMI|GMI_AK_SNP_2912243fwd/C/Gggtaaaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggccacac12/16/1012/16/10137Genomicunknown
ss482505557ILLUMINA|HumanOmni2.5-4v1_D_kgp22303571-0_T_F_1840500803fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc01/30/1210/28/16137Genomicunknown
ss484992758ILLUMINA|HumanOmni2.5-4v1_B_SNP5-172404658-0_T_F_1624545917fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc01/30/1210/28/16137Genomicunknown
ss534678970ILLUMINA|HumanOmni5-4v1_B_kgp22303571-0_T_F_1840500803fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc06/22/1208/29/15146Genomicunknown
ss652808760SSMP|5_172472052fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc12/14/1202/11/15138Genomicunknown
ss779125436ILLUMINA|HumanOmni25Exome-8v1_A_kgp22303571-0_T_F_1840500803fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc05/30/1307/09/15142Genomicunknown
ss781783908ILLUMINA|HumanOmni2.5-4v1_H_kgp22303571-0_T_F_1840500803fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc05/30/1307/28/15142Genomicunknown
ss834589841ILLUMINA|HumanOmni2.5-8v1_A_kgp22303571-0_T_F_1840500803fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc09/18/1307/28/15142Genomicunknown
ss1073268515JMKIDD_LAB|HGDP_WGS_chr5_172472052fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc07/10/1407/11/14142Genomicunknown
ss13183853361000GENOMES|PHASE3_V1_30262624fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc08/16/1408/16/14142Genomicunknown
ss1614643082EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_172472052_16762234fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc03/04/1503/04/15144Genomicunknown
ss1657637115EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_172472052_16762234fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc03/04/1503/04/15144Genomicunknown
ss1712823209EVA_SVP|EVA_SVP_517576fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc03/12/1503/12/15144Genomicunknown
ss1925676844WEILL_CORNELL_DGM|SNV:chr5:172472052fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc10/16/1510/17/15147Genomicunknown
ss2023452572JJLAB|SNP3955127fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc08/29/1608/30/16149Genomicunknown
ss2151612437USC_VALOUEV|NC_000005.9:g.172472052C>Gfwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc11/17/1611/17/16150Genomicunknown
ss2280618260HUMAN_LONGEVITY|HLI-5-173045049-C-G,Tfwd/C/G/Taattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc11/18/1611/18/16150Genomicunknown
ss2448946503TOPMED|5_172472052_C/Gfwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc11/20/1611/20/16150Genomicunknown
ss2634378107ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp22303571-0_T_F_18405008fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc02/02/1702/02/17151Genomicunknown
ss2707189623GRF|rs12513649fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc02/13/1702/13/17151Genomicunknown
ss2834115646GNOMAD|rs12513649fwd/C/G/Taattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc05/18/1705/18/17151Genomicunknown
ss2998261060SWEGEN|NC_000005.9:g.172472052C>Gfwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc05/30/1705/30/17151Genomicunknown
ss3022557673ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs12513649-138_B_R_2287082830fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc06/28/1706/28/17151Genomicunknown
ss3486340872TOPMED|TOPMed_freeze_5?chr5:173,045,049-01fwd/C/Gaattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc10/04/1710/04/17151Genomicunknown
ss3486340873TOPMED|TOPMed_freeze_5?chr5:173,045,049-02fwd/C/Taattcctcactttacccatcgatgaggtcttgtagccttagtttcttggc10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12513649|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/G/T'|mol=Genomic|build=151
 TTTTTTATTT TTATTTTTTG AGATGGAGTT TCGCTCTTGT TGCCCAGGCT GGAGTGCAAT
 GGCGCAATCT CGGCTCACTG CAACCTCCGC CTCCCAGTTT CAAGCAATTC TCCTGCCTCG
 GCCTCCTGAG TAGCTGAGAT TACAGGCATG CACCACCACG CCCGGCTAAT TTTGTATTTT
 GAGTAGAGAC GGGGTTTCGC CATGTTGGGG CTGGTCTCGA ACTCCTGACC TCAGGTGATC
 CGCCTGCCTC AGCCTCCCAA AGTGCTGGGA TTACAGGCGT CAGCCACCGT GCCCGGCCCT
 CCATTTTGAT TTTTAGCCTG GTCTGTCGGG GCCTAATGCA GGAGCTTATT CCAAAACAAT
 GGCCTCCTAT AATGGTTTAT TTAACAGTGT TAATTAGAGG AAATGGGGTT TAAACCCAGG
 GGAGTCCGAC TTTAGGGTTC AGGGCTGTCA CTGAGGCTCC ATTTTTCTGA GGTAAAATTC
 CTCACTTTAC CCATCGATGA
 B
 GGTCTTGTAG CCTTAGTTTC TTGGCCACAC CTTCAACCTT TCAGTGCCTA TGGTTGTTCC
 TAGCCCCAAA AGGTCACATG GTTCTTCTAA TACCTTCCAT TAAGAAGCCA ATAGCTTTCT
 GAAAATGAGG CCAGAGGCCA TTTGGAGAAT CCTAAACCTA CTACCTGGGA ACGGGCAGGG
 TCTTGTGGTT CTGAATGTCC TCAGAATGAA TTTCCTGCCA TCCCTGGGAT TCCAGCTCCC
 CTCTCTCCAC AGCTCCCCAC AAGACAGGGT TGGAATTGCT AATCCCCTGC CTTTGGGGCA
 GACTATCAGA CCCAAAGGTA GTTCTTTGTG TTTTTTTTTT TTCCGGTGAC ACTTCAATGC
 CCTCATGCAA TAAAGGGGCC TTCCTTGATT TTCCTGAGTT GCCCAAGGGG GCCGGCACCT
 GCAAGTCCCA GGGAGGGTGA GCACTTCATG CTCTCTGCCA GCGTTTCTGA AGCATGGGGT
 CGGAATGGGA TTTTCCAGTG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023133
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/G
G/G
HWPC
G
ss1318385336EAS 1008AF 0.937500000.06250000
EUR 1006AF 1.00000000
AFR 1322AF 0.999199990.00080000
AMR 694AF 0.940900030.05910000
SAS 978AF 0.996900020.00310000
ss19608988HapMap-CEUEuropean 120IG1.00000000 1.00000000
HapMap-HCBAsian 86IG0.860465110.13953489 1.000000000.930232580.06976745
HapMap-JPTAsian 172IG0.837209280.16279070 0.751830000.918604670.08139535
HapMap-YRISub-Saharan African 120IG1.00000000 1.00000000
HAPMAP-CHBAsian 82IG0.829268280.17073171 1.000000000.914634170.08536585
HAPMAP-CHD 170IG0.835294130.152941180.011764710.654721000.911764680.08823530
HAPMAP-MEX 100IG0.819999990.18000001 1.000000000.910000030.09000000
ENSEMBL_Watson 2IG1.00000000 1.00000000
ss240361383pilot_1_CHB+JPT_low_coverage_panel 120AF 0.933333340.06666667

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.042+/-0.1390000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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