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Reference SNP (refSNP) Cluster Report: rs2059612                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:94/147
Map to Genome Build:107/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=0.0194/97 (1000 Genomes)
HGVS Names
  • NC_000011.10:g.12519033C>T
  • NC_000011.9:g.12540580C>T
  • NM_018222.4:c.1162+516C>T
  • XM_005253015.1:c.910+516C>T
  • XM_005253015.3:c.910+516C>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 ss2970668 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2059612 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
ss2970668TSC-CSHL|TSC1089656fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc01/29/0110/10/0394Genomicunknown
ss10658745BCM_SSAHASNP|chr11.NT_009237.15_3941684fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc06/29/0310/10/03116Genomicunknown
ss16552326CSHL-HAPMAP|CSHL-HuAA-200402.chr11.NT_009237.16_11304520fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc02/17/0403/04/04120Genomicunknown
ss20791339SSAHASNP|WGSA-200403-chr11.chr11.NT_009237.16_11304520fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc03/19/0403/19/04121Genomicunknown
ss77691471HGSV|Cor12156_SNV_20070510.chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc10/09/0710/14/07129Genomicunknown
ss85927394HGSV|Cor18956_SNV_20070510.chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc11/30/0712/10/07130Genomicunknown
ss88470212BCMHGSC_JDW|JWB-0378634fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc02/26/0802/27/08129Genomicunknown
ss97363535HUMANGENOME_JCVI|1103649610594fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc03/29/0803/29/08130Genomicunknown
ss106722161BGI|BGI_rs2059612fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc09/16/0810/20/09130Genomicunknown
ss1100325081000GENOMES|CEU.trio.12.15.2008_2489655_chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc12/17/0812/17/08130Genomicunknown
ss1142210251000GENOMES|NA19240_2008_12_16_2244720_chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc12/18/0812/18/08130Genomicunknown
ss119683975ILLUMINA-UK|NA18507_000019670_NCBI36.1_chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc01/21/0902/05/09131Genomic99 %
ss132302461ENSEMBL|ENSSNP6588363fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc05/11/0905/13/09131Genomicunknown
ss137823488ENSEMBL|ENSSNP512002fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc12/08/0810/16/09131Genomicunknown
ss155942079GMI|GMI_SNP_33336818fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc06/24/0906/24/09131Genomicunknown
ss167849509COMPLETE_GENOMICS|NA07022_36_chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc09/30/0909/30/09132Genomicunknown
ss169113932COMPLETE_GENOMICS|NA19240_36_chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc10/01/0910/01/09132Genomicunknown
ss170508090COMPLETE_GENOMICS|NA20431_36_chr11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc10/01/0910/05/09132Genomicunknown
ss202415257BUSHMAN|BUSHMAN-chr11-12497155fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc02/16/1003/08/10132Genomicunknown
ss207614847BCM-HGSC-SUB|BCM_CMT_1011-2161852fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc03/15/1003/19/10132Genomicunknown
ss2250989601000GENOMES|pilot_1_YRI_6908643_chr11_12497156fwd/C/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc04/22/1004/22/10132Genomicunknown
ss2354520941000GENOMES|pilot_1_CEU_5056723_chr11_12497156fwd/C/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc05/01/1005/01/10132Genomicunknown
ss2421042901000GENOMES|pilot_1_CHB+JPT_3989367_chr11_12497156fwd/C/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc05/01/1005/01/10132Genomicunknown
ss254902512BL|SNP19783_11_12497156fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc08/19/1008/19/10134Genomicunknown
ss280889858GMI|GMI_AK_SNP_5210211fwd/C/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc12/16/1012/16/10137Genomicunknown
ss286319326GMI|GMI_NA10851_SNP_2332111fwd/C/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc12/17/1012/17/10138Genomicunknown
ss291181131PJP|SNP_687489_chr11_12497156fwd/C/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc01/21/1101/21/11134Genomicunknown
ss482753767ILLUMINA|HumanOmni2.5-4v1_B_SNP11-12497156-0_B_F_1619338385fwd/BC/Tatgcagaagggacaagtgcttctgcagccctnnnnnctcctgctaggagtgcacacgtgc01/30/1202/01/12137Genomicunknown
ss483873378ILLUMINA|HumanOmni2.5-4v1_D_kgp7244416-0_B_F_1797900278fwd/BC/Tatgcagaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcacacgtgc01/30/1202/03/12137Genomicunknown
ss536068627ILLUMINA|HumanOmni5-4v1_B__kgp7244416-0_B_F_1797900278fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca06/22/1208/29/15146Genomicunknown
ss562394407TISHKOFF|snp_chr11_12540580fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca11/22/1211/23/12138Genomicunknown
ss657788768SSMP|11_12540580fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca12/14/1202/12/15138Genomicunknown
ss780440557ILLUMINA|HumanOmni25Exome-8v1_A_kgp7244416-0_B_F_1797900278fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca05/30/1307/10/15146Genomicunknown
ss782380284ILLUMINA|HumanOmni2.5-4v1_H_kgp7244416-0_B_F_1797900278fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca05/30/1307/29/15146Genomicunknown
ss835930232ILLUMINA|HumanOmni2.5-8v1_A_kgp7244416-0_B_F_1797900278fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca09/18/1307/29/15146Genomicunknown
ss1077511792JMKIDD_LAB|HGDP_WGS_chr11_12540580fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca07/10/1407/12/14142Genomicunknown
ss13401633201000GENOMES|PHASE3_V1_52927555fwd/C/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca08/16/1408/16/14142Genomicunknown
ss1426541023DDI|DDI_rs2059612fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca11/04/1411/04/14144Genomicunknown
ss1575531492EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2059612fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca02/19/1502/19/15144Genomicunknown
ss1626014982EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_11_12540580_29244134fwd/C/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca03/04/1503/04/15144Genomicunknown
ss1669009015EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_11_12540580_29244134fwd/C/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca03/04/1503/04/15144Genomicunknown
ss1806699612HAMMER_LAB|Hsieh_5718875fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca07/15/1507/16/15146Genomicunknown
ss1931585803WEILL_CORNELL_DGM|SNV:chr11:12540580fwd/BC/Tgaagggacaagtgcttctgcagccctgcatactcctgctaggagtgcaca10/16/1510/17/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2059612|allelePos=437|totalLen=2583|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=147
 GGGAAGCATT TTCTGAAGCC TTCGTTGCTG GGGAAGGTGG GACTCGGTGC AGCTGCTCAG
 TCCCAGAGAC CCTTTGTGAG CTGCCAGCTG CACAGCCAGG GGAAGAAAAG AATCTGAAAT
 CCCACACATG CCATGCGTGG GATCGCGGGG ATCAGGGACC GAGCAGAACT GCTGCTGCAG
 GAACTGCCCT GTGCCCAATT TCCAGGTTTT CCTGTCCCTG CACAGGGTGC TGACCTGCCA
 AAGAGCTGTG TCCCCGCCAG TCGGGGTGAA GGTGCAGCGC AGACAGTTCT GGGCTGAGCA
 AAACTGCTTC TCTCCTTACA GATGCGGAGC TCTGCCTGCT CAGACTCTGT CTGAGGACAG
 GCCATGATTT GTGGGGTTTG GGTTGTAAAT ATAAGTCTGA GGGGAAATGC AGAAGGGACA
 AGTGCTTCTG CAGCCC
 Y
 TGCATACTCC TGCTAGGAGT GCACACGTGC ATTCGTGAGC AGAGGAGGCA CGCTTCTCTT
 AGTAGTCTTG GTACGGATGA TTGCTTTCTG CCCCTTACTG ACTGAAGTAT TCCATTTCAC
 CAGAGCTGGC AGGTCACCAC TGTGTTGCAG ATAATCTCCT GCATATGTCC CCTGGGAACA
 CTGAGAATGC CATCTGTGGC CCTTTTGCTC GCACTTTTCT GGTAGTTTAT AGGCAAGTGG
 ATGAGTAGGA ATGGTGGGCT CTCATGCCCC CTTCCTGCCT CTGCTCTGAG CTCCTCTATC
 CAAACCCCCA CCTAGTGGGG GCCATGCCCT GGTCTAGTGG GCTTGAGACC CTGTAGACCA
 TGATATAACA AGAGGGGTAA GACCTTCCTG AACCTCAAGG CACGTGTAGC CAACCAGGGA
 AGAGAAAAGT TGGAGCCAGT TAGCAAAATG AAATGACAGT CATGGGAACT GTTACGAAAG
 AGGTACAAGG AAGAGTCTGT GAGGACTGAG GAGGTGATAC CACTTCTGTC TTGGGGGAGG
 AACAGTTTGA TGGAGACAGT GGGGCTCAAC CATAAGGACC AGGTAGGGCT TTGGTGTATG
 GAGACTGGGA GAGAAGTGTG TGCATGCCAG ACAGAATGAC AGCATGAGCA AAAGTCCCCC
 CGGGGAAGAA TGGGGACCCT GTCTCATGAC TCCTTCCAGA CTCGTTATCT ATTGACTCTA
 GCCAACAAAG GTCAACTCCT GTTCTCATTT ATTACCACCT TGTCCTAAGC CCCTGGTCAA
 CTGAGACCTG GGGGAGGACC TCTAGCAAGG CTGGTGTCCC CCTGGGGCTC TCTCTTTGGC
 AAGGCCACTC CAGCCTTCCT AATGCCATTA GGAATGGACT CTTCTTGTTC TGTGGGCAGA
 TGATGAGCAC CCTGCTTCTG GGAGGACAGA CACAGTGAGA AAGTTCCGAC CATCATTTTG
 CTTCCACTTT CTTCAACCAC TTAATATGAA ACTTCCTGGT TACAGATTGG AAGTACTTCT
 GCTATTTTAG AATTGGGATA TTTCTTTCCC TTGGGACAGA TAATTTTCCC AATATAAATC
 AATCTATGGG AATATTTTGG AATATAGGTG ATATTTTTAT GCAATTATTA AGTTGCTGAA
 TGTGAAACTA ACAGACTGAT GTGGATGGAA AAACACGTGT TTTATTTGTT ATGACACAGG
 GCATTATGCC CATGCTGCAA ATTTCCAGTA CGTAAAGGGG AATGGAAATA GCATTTTATG
 AAATTGTACT TTGAAAGAAG TGAATCCCAG CATTCCGTCT GGTTTTTATG CTTCTACCTG
 GAAAGTGAGA TTTGGAAGTA AATGATGCAG ACATTTCAAA GGTGCCAATG TGGGTAATTC
 TTTGAGGGCA TTTCAAAATC AAACTGGTTG TGGTGGAGGC ATTTTTCATG GCAACATGTT
 TTTAAGGTCA GGAAAATGCA TTCTCTGCTG TGCTGTTTAA CACTCAAAGC TCTGTTGTGC
 CTTGAAATCC CCTAGAAACT GGGTTTGTAT CTGAGATGAC TTGCTGCCCA GGCTTCATGA
 CCGTTTAGTG CCTGAGTTAG TGTAAGCCAA GGGTTAGCAT CAAGTTCCTA ACCAGTGGAG
 CAGTCGAAAT AATggccagg catggaagct cacacctgta atcccaacac tttgggaggc
 caaggtgggc agacggcttg agctcaggag tttgagacca gcctgggcaa catagtgaga
 ccccacctgt acaaaaaata caaaaaaatt agccaggtgt agtggtgcat gcctgtggtc
 ccagctcctc gggaggctga ggtggaaggg atcgcttgag cctgggaggc ggaagttgca
 ccactgcact ccagcctggg caacaaagtg agaccctgtc tcaaagaaag gaaaaaagga
 aagaaaaaga aaTATTGTCA TGCAGCTGGC AGCTTTTTAT TTAGGGCATC GTGCCACATG
 TCTTCAAATG CACATGTCCA CCCTGTTATC ACCTTTCAAG TAGACTCATC ATCAATTATG
 GTTAAGACTC CAGAATAACA GGCAGGCAGG GACTCAGAAG ACATCTAGTA CCAGGCAGGA
 TTGAAGTCTG TAGGACTAAA TATCTAAAAT TTAAGGAGTC TCATAC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_009237 ABBA01061131
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.
SourceT/T
HWPC
T
ss119683975YRI 2IG1.00000000 1.00000000
ss132302461ENSEMBL_Watson 2IG1.00000000 1.00000000
ss1340163320EAS 1008AF 1.00000000
EUR 1006AF 0.001000000.99900001
AFR 1322AF 0.068799990.93119997
AMR 694AF 0.007200000.99279994
SAS 978AF 1.00000000
ss137823488ENSEMBL_Venter 2IG1.00000000 1.00000000
ENSEMBL_celera 2IG1.00000000 1.00000000
ss167849509CEUEuropean 2IG1.00000000 1.00000000
ss169113932YRISub-Saharan African 2IG1.00000000 1.00000000
ss170508090PGP 2IG1.00000000 1.00000000
ss225098960pilot_1_YRI_low_coverage_panel 118AF 0.050847460.94915253
ss235452094pilot_1_CEU_low_coverage_panel 120AF 1.00000000
ss242104290pilot_1_CHB+JPT_low_coverage_panel 120AF 1.00000000
ss2970668HapMap-CEUEuropean 118IG1.00000000 1.00000000
HapMap-HCBAsian 82IG1.00000000 1.00000000
HapMap-JPTAsian 88IG1.00000000 1.00000000
ss97363535J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.038+/-0.13235930010

  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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