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Reference SNP (refSNP) Cluster Report: rs12654739                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.0503/252 (1000 Genomes)
C=0.0429/5393 (TOPMED)
HGVS Names
  • CM000667.2:g.172985671T>C
  • NC_000005.10:g.172985671T>C
  • NC_000005.9:g.172412674T>C
  • NM_003945.3:c.104+1707T>C
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 ss20239922 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12654739 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
ss20239922CSHL-HAPMAP|CSHL-HuFF-200402.chr5.NT_023133.11_17222260byFreqfwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc02/21/0410/26/06120Genomicunknown
ss24386847PERLEGEN|afd3383365byFreqfwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc08/10/0409/13/04123Genomicunknown
ss66078236AFFY|SNP_A-1906139byFreqrev/TA/Gtggtctttaagaaaggattgtcagtgctatta10/27/0603/31/08127Genomicunknown
ss66767993ILLUMINA|HumanHap300v1.1_rs12654739fwd/TC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc11/09/0611/09/06127Genomicunknown
ss67029865ILLUMINA|HumanHap550v1.1_rs12654739fwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc11/14/0611/14/06127Genomicunknown
ss67352684ILLUMINA|HumanHap650Yv1.0_rs12654739fwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc11/14/0611/14/06127Genomicunknown
ss68959376PERLEGEN|PGP03383365byFreqfwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc01/30/0703/31/08127Genomicunknown
ss70414224ILLUMINA|HumanHap300v2.0_rs12654739fwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc04/18/0711/18/07127Genomicunknown
ss70579974ILLUMINA|HumanHap550v3.0__rs12654739rev/TA/Gggaaggggagagaatggtctttaagaaaggattgtcagtgctattagtacattaataaat04/20/0703/30/08130Genomicunknown
ss71122023ILLUMINA|HumanHap650Yv3.0_rs12654739fwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc04/23/0704/23/07127Genomicunknown
ss75771546ILLUMINA|ILMN_Human_1M_rs12654739fwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc08/28/0708/29/07129Genomicunknown
ss76015999AFFY|AFFY_6_1M_SNP_A-1906139rev/TA/Gtggtctttaagaaaggattgtcagtgctatta08/28/0708/29/07130Genomicunknown
ss85257045KRIBB_YJKIM|KHS942615fwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc12/04/0712/08/07130Genomicunknown
ss121591177ILLUMINA|HumanCNV370v1_C_rs12654739fwd/BC/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc04/14/0904/14/09131Genomicunknown
ss153259745ILLUMINA|Human610_Quadv1_B_rs12654739-127_T_R_1501639094rev/TA/Gggaaggggagagaatggtctttaagaaaggattgtcagtgctattagtacattaataaat06/18/0906/19/09131Genomicunknown
ss159229609ILLUMINA|Human660W-Quad_v1_A_rs12654739-128_T_R_1501639094rev/TA/Gggaaggggagagaatggtctttaagaaaggattgtcagtgctattagtacattaataaat07/06/0907/06/09131Genomicunknown
ss160291594ILLUMINA|HumanOmni1-Quad_v1-0_B_rs12654739-128_T_R_1501639094rev/TA/Gggaaggggagagaatggtctttaagaaaggattgtcagtgctattagtacattaataaat08/04/0910/02/09131Genomicunknown
ss170196769ILLUMINA|HumanCNV370-Quadv3_C_rs12654739-127_T_R_1501639094rev/TA/Gggaaggggagagaatggtctttaagaaaggattgtcagtgctattagtacattaataaat10/01/0910/03/09132Genomicunknown
ss172208843ILLUMINA|Human1M-Duov3_B_rs12654739-127_T_R_1501639094rev/TA/Gggaaggggagagaatggtctttaagaaaggattgtcagtgctattagtacattaataaat10/01/0910/02/09132Genomicunknown
ss2221245401000GENOMES|pilot_1_YRI_3934223_chr5_172345280fwd/C/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc04/22/1004/22/10132Genomicunknown
ss2332620051000GENOMES|pilot_1_CEU_2866634_chr5_172345280fwd/C/Tatttattaatgtactaatagcactgacaatcctttcttaaagaccattctctccccttcc05/01/1005/01/10132Genomicunknown
ss479796993ILLUMINA|HumanOmni2.5-4v1_B_rs12654739-128_T_R_1777972399fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc01/30/1210/28/16137Genomicunknown
ss479803823ILLUMINA|HumanOmniExpress-12v1_C_rs12654739-131_T_R_1857464363fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc01/30/1210/27/16137Genomicunknown
ss480383164ILLUMINA|HumanOmni1-Quad_v1-0_C_rs12654739-131_T_R_1865420397fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc01/30/1208/28/15146Genomicunknown
ss484696974ILLUMINA|HumanOmni2.5-4v1_D_rs12654739-131_T_R_1857464363fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc01/30/1210/28/16137Genomicunknown
ss536804824ILLUMINA|HumanOmni5-4v1_B_rs12654739-131_T_R_1893991005fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc06/22/1208/29/15146Genomicunknown
ss652808510SSMP|5_172412674fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc12/14/1202/11/15138Genomicunknown
ss778787779ILLUMINA|HumanOmni25Exome-8v1_A_rs12654739-131_T_R_1865420397fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc05/30/1307/09/15146Genomicunknown
ss782795257ILLUMINA|HumanOmni2.5-4v1_H_rs12654739-131_T_R_1857464363fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc05/30/1307/28/15146Genomicunknown
ss783760889ILLUMINA|HumanOmniExpressExome-8v1_A_rs12654739-131_T_R_1893991005fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc05/31/1306/19/15146Genomicunknown
ss825383498ILLUMINA|HumanCNV370v1_C_rs12654739-123_T_R_IFB1152851839:0fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc06/24/1311/21/14144Genomicunknown
ss832048126ILLUMINA|HumanOmniExpress-12v1_H_rs12654739-131_T_R_1857464363fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc09/17/1306/18/15146Genomicunknown
ss834247791ILLUMINA|HumanOmni2.5-8v1_A_rs12654739-131_T_R_1865420397fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc09/18/1307/28/15146Genomicunknown
ss982426514EVA-GONL|EVA-GONL_rs12654739fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc04/23/1404/24/14142Genomicunknown
ss1073268191JMKIDD_LAB|HGDP_WGS_chr5_172412674fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc07/10/1407/11/14142Genomicunknown
ss13183837181000GENOMES|PHASE3_V1_30260917fwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc08/16/1408/16/14142Genomicunknown
ss1581468041EVA_GENOME_DK|EVA_GENOME_DK_snv_rs12654739fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc02/19/1502/20/15144Genomicunknown
ss1591969774EVA_DECODE|EVA_DECODE_5_172345280_1300481_rs12654739fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc03/02/1503/03/15144Genomicunknown
ss1712823193EVA_SVP|EVA_SVP_517560fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc03/12/1503/12/15144Genomicunknown
ss1752564429ILLUMINA|OmniExpressExome-8v1-1_B_rs12654739-131_T_R_1893991005fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc05/27/1506/09/15146Genomicunknown
ss1925676378WEILL_CORNELL_DGM|SNV:chr5:172412674fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc10/16/1510/17/15147Genomicunknown
ss1958847466ILLUMINA|rs12654739-138_T_R_2276380850fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc11/13/1511/13/15147Genomicunknown
ss2023452320JJLAB|SNP3954875fwd/BC/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc08/29/1608/30/16149Genomicunknown
ss2151612257USC_VALOUEV|NC_000005.9:g.172412674T>Cfwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc11/17/1611/17/16150Genomicunknown
ss2280614930HUMAN_LONGEVITY|HLI-5-172985671-T-Cfwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc11/18/1611/18/16150Genomicunknown
ss2448943164TOPMED|5_172412674_T/Cfwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc11/20/1611/20/16150Genomicunknown
ss2634378075ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs12654739-131_T_R_1893991fwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc02/02/1702/02/17151Genomicunknown
ss2707189422GRF|rs12654739fwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc02/13/1702/13/17151Genomicunknown
ss2834110728GNOMAD|rs12654739fwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc05/18/1705/18/17151Genomicunknown
ss2998260348SWEGEN|NC_000005.9:g.172412674T>Cfwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc05/30/1705/30/17151Genomicunknown
ss3022557641ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs12654739-138_T_R_2276380850fwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc06/28/1706/28/17151Genomicunknown
ss3486329896TOPMED|TOPMed_freeze_5?chr5:172,985,671fwd/C/Tttaatgtactaatagcactgacaatcctttcttaaagaccattctctccc10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12654739|allelePos=201|totalLen=701|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 ACAGAGTCAG AATTCTGGCA TTATTAAAGC AATTGTATTT ACCAAAGTTA ATTAGACTTG
 TTTTTCCTAC TGGAGTTAGC GAACAACAAA GTGCTTCTTT GTTGTGTTTA TATCTTCAAC
 TGTTTCATTA CCCTACTGTC TGCCTTTATG GCCTTTGTAC TCAAAGAAGC ATTTATTAAT
 GTACTAATAG CACTGACAAT
 Y
 CCTTTCTTAA AGACCATTCT CTCCCCTTCC TTGGGATGTC ATTGCCATTA TCCAGGGTAA
 TGAAACCCAT CCTGTTTCCA CTTAGCCCTA GAGAGTGTCA TGATTCAGGT ATTTGACCAG
 CTAGTGATAT ATagacatgt gtcacttaac aaaaggacta tgtttgagaa atgtgttagt
 tgggcttttg tgtgaacaaa gagtttactt aaacagatgg tacagcctac tacacaccta
 ggctatttgg tagaacctgt tgcctctagg taggctacac acctgtacag catgttactg
 tccttaaata ctgtatagac aaatgtaaca caatggtatt tgtgtatcta aacatagaaa
 aggtacagta aaaatacata tcaaagattt aaaatggtcc acctgtgtag ggcacttacc
 atgaatggag cttgcaggac tggaaattgc tgtgagtgag tcagtgactg gtgagtgaat
 gtgaagaacc aggacattgc

  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/T
T/T
HWPC
T
ss1318383718EAS 1008AF 0.033700000.96630001
EUR 1006AF 0.050700000.94929999
AFR 1322AF 0.021200000.97880000
AMR 694AF 0.033100000.96690005
SAS 978AF 0.118600000.88139999
ss20239922HapMap-CEUEuropean 226IG 0.088495570.911504451.000000000.044247790.95575219
HapMap-HCBAsian 86IG 0.023255810.976744171.000000000.011627910.98837209
HapMap-JPTAsian 172IG 0.011627910.988372091.000000000.005813950.99418604
HapMap-YRISub-Saharan African 226IG 0.017699110.982300881.000000000.008849560.99115044
HAPMAP-ASW 98IG 0.061224490.938775541.000000000.030612250.96938777
HAPMAP-CHBAsian 82IG0.024390240.048780490.926829280.002501000.048780490.95121950
HAPMAP-CHD 170IG 0.047058820.952941181.000000000.023529410.97647059
HAPMAP-GIH 176IG0.034090910.170454550.795454560.099721000.119318180.88068181
HAPMAP-LWK 180IG 0.022222220.977777781.000000000.011111110.98888886
HAPMAP-MEX 100IG 0.060000000.940000001.000000000.030000000.97000003
HAPMAP-MKK 286IG 0.006993010.993007001.000000000.003496500.99650347
HAPMAP-TSI 176IG 0.068181820.931818191.000000000.034090910.96590906
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss222124540pilot_1_YRI_low_coverage_panel 118AF 0.016949150.98305082
ss233262005pilot_1_CEU_low_coverage_panel 120AF 0.066666670.93333334
ss24386847AFD_EUR_PANELEuropean 42IG 0.142857150.857142871.000000000.071428570.92857140
AFD_AFR_PANELAfrican American 44IG 1.00000000 1.00000000
AFD_CHN_PANELAsian 48IG 1.00000000 1.00000000
ss66078236HapMap-CEUEuropean 118IG 0.135593220.864406761.000000000.067796610.93220341
HapMap-HCBAsian 90IG 0.022222220.977777781.000000000.011111110.98888886
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 0.016666670.983333351.000000000.008333330.99166667
ss68959376HapMap-CEUEuropean 120IG 0.133333340.866666671.000000000.066666670.93333334
HapMap-HCBAsian 90IG 0.022222220.977777781.000000000.011111110.98888886
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 0.016666670.983333351.000000000.008333330.99166667
ss76015999ICMHP 6IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.096+/-0.1970000ALFRED: 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
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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