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Reference SNP (refSNP) Cluster Report: rs12629971                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
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:T=0.1879/941 (1000 Genomes)
T=0.1797/22568 (TOPMED)
HGVS Names
  • CM000665.2:g.71734167C>T
  • NC_000003.11:g.71783318C>T
  • NC_000003.12:g.71734167C>T
  • NM_001134649.2:c.-290-5544G>A
  • NM_001282886.1:c.-290-5544G>A
  • NM_173359.4:c.-290-5544G>A
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 ss277178712 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12629971 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
ss20150003CSHL-HAPMAP|CSHL-HuFF-200402.chr3.NT_022459.13_5477482fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg02/21/0410/26/06120Genomicunknown
ss44396178ABI|hCV11331386byFreqfwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg07/18/0511/03/06126Genomicunknown
ss66637351ILLUMINA|HumanHap300v1.1_rs12629971fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg11/09/0611/09/06127Genomicunknown
ss67026945ILLUMINA|HumanHap550v1.1_rs12629971fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg11/14/0611/14/06127Genomicunknown
ss67349328ILLUMINA|HumanHap650Yv1.0_rs12629971fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg11/14/0611/14/06127Genomicunknown
ss70413573ILLUMINA|HumanHap300v2.0_rs12629971fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg04/18/0711/18/07127Genomicunknown
ss70578477ILLUMINA|HumanHap550v3.0__rs12629971rev/TA/Gcatctttttagcctctgggaataagatacttcttaccacaaacactaagaaaatttaaag04/20/0703/30/08130Genomicunknown
ss71120311ILLUMINA|HumanHap650Yv3.0_rs12629971fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg04/23/0704/23/07127Genomicunknown
ss75522773ILLUMINA|ILMN_Human_1M_rs12629971fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg08/28/0708/29/07129Genomicunknown
ss84925369HGSV|Cor19240_SNV_20070510.chr3_71866008fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg11/30/0712/08/07130Genomicunknown
ss85252549KRIBB_YJKIM|KHS941334fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg12/04/0712/08/07130Genomicunknown
ss92136507BCMHGSC_JDW|JWB-1611227fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg02/26/0803/02/08129Genomicunknown
ss1103468391000GENOMES|NA19240_2008_12_16_649928_chr3_71866008fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg12/17/0812/17/08130Genomicunknown
ss1119294281000GENOMES|CEU.trio.12.15.2008_726467_chr3_71866008fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg12/17/0812/17/08130Genomicunknown
ss121587327ILLUMINA|HumanCNV370v1_C_rs12629971fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg04/14/0904/14/09131Genomicunknown
ss138933517ENSEMBL|ENSSNP5891792fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg05/18/0905/18/09131Genomicunknown
ss153251615ILLUMINA|Human610_Quadv1_B_rs12629971-128_T_R_1501645713rev/TA/Gcatctttttagcctctgggaataagatacttcttaccacaaacactaagaaaatttaaag06/18/0906/19/09131Genomicunknown
ss159228027ILLUMINA|Human660W-Quad_v1_A_rs12629971-128_T_R_1501645713rev/TA/Gcatctttttagcctctgggaataagatacttcttaccacaaacactaagaaaatttaaag07/06/0907/06/09131Genomicunknown
ss161463533ENSEMBL|ENSSNP2198501fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg09/24/0909/24/09131Genomicunknown
ss163545446COMPLETE_GENOMICS|NA19240_36_chr3_71866008fwd/BC/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg09/29/0909/29/09132Genomicunknown
ss170186343ILLUMINA|HumanCNV370-Quadv3_C_rs12629971-128_T_R_1501645713rev/TA/Gcatctttttagcctctgggaataagatacttcttaccacaaacactaagaaaatttaaag10/01/0910/03/09132Genomicunknown
ss172193965ILLUMINA|Human1M-Duov3_B_rs12629971-128_T_R_1501645713rev/TA/Gcatctttttagcctctgggaataagatacttcttaccacaaacactaagaaaatttaaag10/01/0910/02/09132Genomicunknown
ss2202116251000GENOMES|pilot_1_YRI_2021308_chr3_71866008fwd/C/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg04/22/1004/22/10132Genomicunknown
ss2318746181000GENOMES|pilot_1_CEU_1479247_chr3_71866008fwd/C/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg05/01/1005/01/10132Genomicunknown
ss2392779581000GENOMES|pilot_1_CHB+JPT_1163035_chr3_71866008fwd/C/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg05/01/1005/01/10132Genomicunknown
ss244277072ILLUMINA|CVDSNP55v1_A_rs12629971rev/TA/Gcatctttttagcctctgggaataagatacttcttaccacaaacactaagaaaatttaaag06/10/1006/10/10132Genomicunknown
ss277178712GMI|GMI_AK_SNP_1498921fwd/C/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg12/16/1012/16/10137Genomicunknown
ss292822481PJP|SNP_2328839_chr3_71866008fwd/C/Tctttaaattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaaagatg01/21/1101/21/11134Genomicunknown
ss536801872ILLUMINA|HumanOmni5-4v1_B_rs12629971-131_T_R_1885497605fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa06/22/1208/28/15146Genomicunknown
ss556703481TISHKOFF|snp_chr3_71783318fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa11/22/1211/23/12138Genomicunknown
ss650385920SSMP|3_71783318fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa12/14/1202/10/15138Genomicunknown
ss825382847ILLUMINA|HumanCNV370v1_C_rs12629971-126_T_R_IFB1135509412:0fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa06/24/1311/21/14144Genomicunknown
ss978737743EVA-GONL|EVA-GONL_rs12629971fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa04/23/1404/24/14142Genomicunknown
ss1070518536JMKIDD_LAB|HGDP_WGS_chr3_71783318fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa07/10/1407/10/14142Genomicunknown
ss13045549851000GENOMES|PHASE3_V1_15841248fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa08/16/1408/16/14142Genomicunknown
ss1397342760HAMMER_LAB|HAMMER_LAB_rs12629971fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa09/30/1409/30/14146Genomicunknown
ss1429462065DDI|DDI_rs12629971fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa11/04/1411/05/14144Genomicunknown
ss1580019776EVA_GENOME_DK|EVA_GENOME_DK_snv_rs12629971fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa02/19/1502/20/15144Genomicunknown
ss1588209516EVA_DECODE|EVA_DECODE_3_71866008_587149_rs12629971fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa03/02/1503/03/15144Genomicunknown
ss1607371120EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_3_71783318_8778008fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa03/04/1503/04/15144Genomicunknown
ss1650365153EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_3_71783318_8778008fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa03/04/1503/04/15144Genomicunknown
ss1712587039EVA_SVP|EVA_SVP_281584fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa03/12/1503/12/15144Genomicunknown
ss1799477862HAMMER_LAB|Hsieh_1671948fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa07/15/1507/15/15146Genomicunknown
ss1921972764WEILL_CORNELL_DGM|SNV:chr3:71783318fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa10/16/1510/17/15147Genomicunknown
ss2021547915JJLAB|SNP2050470fwd/BC/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa08/29/1608/30/16149Genomicunknown
ss2149624266USC_VALOUEV|NC_000003.11:g.71783318C>Tfwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa11/17/1611/17/16150Genomicunknown
ss2252736904HUMAN_LONGEVITY|HLI-3-71734167-C-Tfwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa11/18/1611/18/16150Genomicunknown
ss2419806708TOPMED|3_71783318_C/Tfwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa11/19/1611/19/16150Genomicunknown
ss2625273125SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV1283504fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa01/06/1701/06/17151Genomicunknown
ss2635120370ILLUMINA|Cancer_BeadChip_11459870_A_rs12629971-128_T_R_1782916359fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa02/02/1702/02/17151Genomicunknown
ss2705005015GRF|rs12629971fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa02/13/1702/13/17151Genomicunknown
ss2794515289GNOMAD|rs12629971fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa05/18/1705/18/17151Genomicunknown
ss2992532854SWEGEN|NC_000003.11:g.71783318C>Tfwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa05/30/1705/30/17151Genomicunknown
ss3024538099BIOINF_KMB_FNS_UNIBA|3.71734167C>Tfwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa07/05/1707/05/17151Genomicunknown
ss3345081037CSHL|rs12629971fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa10/02/1710/02/17151Genomicunknown
ss3394173203TOPMED|TOPMed_freeze_5?chr3:71,734,167fwd/C/Taattttcttagtgtttgtggtaagaagtatcttattcccagaggctaaaa10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12629971|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TACTGCTCAT GTACTGGGAA GTCAATAAAT ATCTGAATAA TGAATCCTTC TGTGATTTAA
 AACCATTCAT TAAAGTGTAG ATTGAAATAC TTTATAAGTC ATTTACTTCT TAAGAGCTAA
 GTACACTAAA GTTTGAGAAG CCATTATCAA TTGATGAACA ATTAGTAAAG GAAAATAAAG
 CAATTCTTGA AAGGAAGCTG CATTATTTGT TTTCTAAAAA AAATCATAAT TACATGACAT
 TTTTAGAACT CTAACTACTG TGCAAAATGC ACCATTCAGA AACAGAAGGA CACTTGCAGT
 GTTTAGGCCA ATGAGACCCC TTCAGTTACT GAATCTCTTT TGTTTTACCA TCAGCAGGAA
 TTGCATACTC ACAATACAGA AAGATCCTGT TAATTTTTCA CTCTTTTCCT GTTCATTCTT
 ATTAGTTACA TATTATCTAC ATAATGGCAG GTTGCACCTT ATGGTATTTG CTTTAAATTT
 TCTTAGTGTT TGTGGTAAGA
 Y
 AGTATCTTAT TCCCAGAGGC TAAAAAGATG CACATATTGA TCATACTAGG TCATCATTAC
 AAAAGAGGAG CTCTCATGGA GGCTATGATG AACATGGTAT CCCTCAGATG ACTTTATACA
 AGTATTTGAT GTCACAAATA TATACTGTGG TTGACAATGA TCTTGGAGAT AGCTGAGTCA
 CTTTCGTCCT TTCAAAACCT ACCAGGTCAC TCAGAAATAC ACTGTGAATT ATCCTAAATT
 TGGGATGAGT CCCTATCATT CCTAAAATGC CTAAGGGTCA TGTCTGCTTG CCTTATTGGA
 CTAAAATATT TTATAACACA TGAAACATAA ATTTGTCAAT TAAATGCAGT ATCATGTTTT
 TCATAGTTTG CAAAAGCACA GTTAATGATG CAAATAATTT CCTATTTTTC ATTCTGAGGG
 AAAATCATTA ATAAAACCAA ACTCCTTATT AGAATTGAAA TTCAGCAGTA AGAGGGCACA
 AGCCACCCAT AAAGGCAAGA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022459
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
ss1304554985EAS 1008AF 0.678600010.32139999
EUR 1006AF 0.859799980.14020000
AFR 1322AF 0.809400020.19060001
AMR 694AF 0.854500000.14549999
SAS 978AF 0.874199990.12580000
ss138933517ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss161463533ENSEMBL_celera 2IG 1.00000000 1.00000000
ss163545446YRISub-Saharan African 2IG 1.00000000 1.00000000
ss220211625pilot_1_YRI_low_coverage_panel 118AF 0.847457650.15254237
ss231874618pilot_1_CEU_low_coverage_panel 120AF 0.858333350.14166667
ss239277958pilot_1_CHB+JPT_low_coverage_panel 120AF 0.666666690.33333334
ss44396178HapMap-CEUEuropean 226IG0.796460150.20353982 0.654721000.898230080.10176991
HapMap-HCBAsian 86IG0.465116290.465116290.069767450.527089000.697674390.30232558
HapMap-JPTAsian 172IG0.430232550.406976730.162790700.254213000.633720930.36627907
HapMap-YRISub-Saharan African 226IG0.663716790.300884960.035398231.000000000.814159270.18584071
AoD_African_American 90AF 0.850000020.15000001
AoD_Caucasian 92AF 0.889999990.11000000
AoD_Chinese 90AF 0.630000000.37000000
AoD_Japanese 90AF 0.769999920.23000000
HAPMAP-ASW 98IG0.632653060.346938790.020408160.479500000.806122420.19387755
HAPMAP-CHBAsian 82IG0.439024390.365853670.195121940.200325000.621951220.37804878
HAPMAP-CHD 170IG0.517647090.411764710.070588241.000000000.723529400.27647060
HAPMAP-GIH 176IG0.761363630.227272730.011363640.751830000.875000000.12500000
HAPMAP-LWK 178IG0.629213510.337078660.033707860.751830000.797752800.20224719
HAPMAP-MEX 100IG0.740000010.220000000.040000000.342782000.850000020.15000001
HAPMAP-MKK 286IG0.664335670.286713270.048951050.371093000.807692290.19230770
HAPMAP-TSI 176IG0.806818190.170454550.022727270.294266000.892045440.10795455
ENSEMBL_Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.305+/-0.2440000ALFRED: 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
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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