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Reference SNP (refSNP) Cluster Report: rs6532059                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
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=0.0351/176 (1000 Genomes)
T=0.0661/8294 (TOPMED)
HGVS Names
  • CM000666.2:g.88242771C>T
  • NC_000004.11:g.89163923C>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 ss10135007 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6532059 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
ss10135007BCM_SSAHASNP|chr4.NT_016354.15_13658628byFreqfwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc06/27/0308/05/04116Genomicunknown
ss11644542WI_SSAHASNP|chr4.NT_016354.15_13658628fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc07/03/0310/10/03116Genomicunknown
ss66846661ILLUMINA|HumanHap300v1.1_rs6532059fwd/TC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc11/09/0611/09/06127Genomicunknown
ss67467516ILLUMINA|HumanHap550v1.1_rs6532059fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc11/14/0611/14/06127Genomicunknown
ss67821991ILLUMINA|HumanHap650Yv1.0_rs6532059fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc11/14/0611/14/06127Genomicunknown
ss70870893ILLUMINA|HumanHap550v3.0__rs6532059fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc04/20/0703/31/08130Genomicunknown
ss71459744ILLUMINA|HumanHap650Yv3.0_rs6532059fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc04/23/0704/23/07127Genomicunknown
ss75893565ILLUMINA|ILMN_Human_1M_rs6532059fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc08/28/0708/29/07129Genomicunknown
ss79224459ILLUMINA|HumanHap300v2.0_rs6532059fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc04/18/0711/18/07130Genomicunknown
ss80315174HGSV|Cor18507_SNV_20070510.chr4_89521102fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc11/23/0711/25/07130Genomicunknown
ss84496894KRIBB_YJKIM|KHS726142fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc12/04/0712/07/07130Genomicunknown
ss92678229BCMHGSC_JDW|JWB-1815688fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc02/26/0803/03/08129Genomicunknown
ss1081209701000GENOMES|CEU.trio.12.15.2008_1030064_chr4_89382947fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc12/15/0812/15/08130Genomicunknown
ss117084601ILLUMINA-UK|NA18507_000124807_NCBI36.1_chr4_89382947fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc01/18/0901/18/09130Genomic99 %
ss122562171ILLUMINA|HumanCNV370v1_C_rs6532059fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc04/14/0904/15/09131Genomicunknown
ss154366123ILLUMINA|Human610_Quadv1_B_rs6532059-127_B_F_1501812601fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc06/18/0906/20/09131Genomicunknown
ss159542290ILLUMINA|Human660W-Quad_v1_A_rs6532059-128_B_F_1501812601fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc07/06/0907/07/09131Genomicunknown
ss160783613ILLUMINA|HumanOmni1-Quad_v1-0_B_rs6532059-128_B_F_1501812601fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc08/04/0910/04/09131Genomicunknown
ss172142965ILLUMINA|HumanCNV370-Quadv3_C_rs6532059-127_B_F_1501812601fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc10/01/0910/04/09132Genomicunknown
ss174026622ILLUMINA|Human1M-Duov3_B_rs6532059-127_B_F_1501812601fwd/BC/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc10/01/0910/04/09132Genomicunknown
ss2324857231000GENOMES|pilot_1_CEU_2090352_chr4_89382947fwd/C/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc05/01/1005/01/10132Genomicunknown
ss293122160PJP|SNP_2628518_chr4_89382947fwd/C/Tttgagctgaaggcacttgagaaagagctgagcaggaagggctctctgacctccccttttc01/21/1101/21/11134Genomicunknown
ss481272656ILLUMINA|HumanOmni2.5-4v1_B_rs6532059-128_B_F_1782923344fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc01/30/1210/28/16137Genomicunknown
ss481297139ILLUMINA|HumanOmniExpress-12v1_C_rs6532059-131_B_F_1856980166fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc01/30/1210/27/16137Genomicunknown
ss482280689ILLUMINA|HumanOmni1-Quad_v1-0_C_rs6532059-131_B_F_1865337442fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc01/30/1208/28/15146Genomicunknown
ss485431630ILLUMINA|HumanOmni2.5-4v1_D_rs6532059-131_B_F_1856980166fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc01/30/1210/28/16137Genomicunknown
ss537360706ILLUMINA|HumanOmni5-4v1_B_rs6532059-131_B_F_1894827521fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc06/22/1208/28/15146Genomicunknown
ss557672395TISHKOFF|snp_chr4_89163923fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc11/22/1211/23/12138Genomicunknown
ss778943082ILLUMINA|HumanOmni25Exome-8v1_A_rs6532059-131_B_F_1865337442fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc05/30/1307/09/15146Genomicunknown
ss783161254ILLUMINA|HumanOmni2.5-4v1_H_rs6532059-131_B_F_1856980166fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc05/30/1307/28/15146Genomicunknown
ss784117009ILLUMINA|HumanOmniExpressExome-8v1_A_rs6532059-131_B_F_1894827521fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc05/31/1306/19/15146Genomicunknown
ss825554977ILLUMINA|HumanCNV370v1_C_rs6532059-116_B_F_IFB1137691494:0fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc06/24/1311/21/14144Genomicunknown
ss832420625ILLUMINA|HumanOmniExpress-12v1_H_rs6532059-131_B_F_1856980166fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc09/17/1306/18/15146Genomicunknown
ss834404826ILLUMINA|HumanOmni2.5-8v1_A_rs6532059-131_B_F_1865337442fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc09/18/1307/28/15146Genomicunknown
ss980363767EVA-GONL|EVA-GONL_rs6532059fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc04/23/1404/24/14142Genomicunknown
ss13106707971000GENOMES|PHASE3_V1_22215369fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc08/16/1408/16/14142Genomicunknown
ss1580656262EVA_GENOME_DK|EVA_GENOME_DK_snv_rs6532059fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc02/19/1502/20/15144Genomicunknown
ss1589865782EVA_DECODE|EVA_DECODE_4_89382947_710010_rs6532059fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc03/02/1503/03/15144Genomicunknown
ss1610572164EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_4_89163923_12292662fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc03/04/1503/04/15144Genomicunknown
ss1653566197EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_4_89163923_12292662fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc03/04/1503/04/15144Genomicunknown
ss1712688282EVA_SVP|EVA_SVP_382649fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc03/12/1503/12/15144Genomicunknown
ss1752536459ILLUMINA|OmniExpressExome-8v1-1_B_rs6532059-131_B_F_1894827521fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc05/27/1506/09/15146Genomicunknown
ss1923608211WEILL_CORNELL_DGM|SNV:chr4:89163923fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc10/16/1510/17/15147Genomicunknown
ss2022389215JJLAB|SNP2891770fwd/BC/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc08/29/1608/30/16149Genomicunknown
ss2264768069HUMAN_LONGEVITY|HLI-4-88242771-C-Tfwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc11/18/1611/18/16150Genomicunknown
ss2432570713TOPMED|4_89163923_C/Tfwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc11/20/1611/20/16150Genomicunknown
ss2634146262ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs6532059-131_B_F_18948275fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc02/02/1702/02/17151Genomicunknown
ss2635134139ILLUMINA|Cancer_BeadChip_11459870_A_rs6532059-128_B_F_1782923344fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc02/02/1702/02/17151Genomicunknown
ss2811961547GNOMAD|rs6532059fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc05/18/1705/18/17151Genomicunknown
ss2995083163SWEGEN|NC_000004.11:g.89163923C>Tfwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc05/30/1705/30/17151Genomicunknown
ss3024970744BIOINF_KMB_FNS_UNIBA|4.88242771C>Tfwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc07/05/1707/05/17151Genomicunknown
ss3345827625CSHL|rs6532059fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc10/02/1710/02/17151Genomicunknown
ss3435180540TOPMED|TOPMed_freeze_5?chr4:88,242,771fwd/C/Tctgaaggcacttgagaaagagctgagcaggaagggctctctgacctcccc10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6532059|allelePos=287|totalLen=1107|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GAGAAACTGG GCTCCAGCTC TCATGATTTC CATCTATTCC AGAATAATAA ATGTTAGATA
 AATCCTTCGT TAAGAAGTAA CCAAAGACTT TTTTTCCTTT GGGGCAAATC TAAATGATTC
 CAATTTAGAA AACACATACT TTTTTTTCTG ACAGAAGATA ACACAAGCTT TAATTTTCAA
 ATTTCCTCCC ATGTTTCATG tgaaggagtt aaggtcatgc tgccccaaaa tatgctgctt
 tggcatgtta actattttga gctgaaggca cttgagaaag agctga
 Y
 gcaggaaggg ctctctgacc tccccttttc tatttaagaa taggccataa aacttcccat
 gaggaaggtg ccctccttat accagaaaga caagaaatcc ttatcaccag agactgggaa
 tcgacattga aatggatctg cataaacaaa cttaataaat aatccttata tcttactagt
 tttaccccca ttcatatatc tcccagtcat ttccccacaa tttattacct ccagtccaaa
 cccctttatc ttgttatttc ttcataaatg tataatttct ttgtcaaaaa tgtttagaaa
 gatttctgct ctagtcactt ctttagagcg tcatgtgaaa gcccatgtac atgtaaaaat
 ttaataaagc ttgtctactt ttctcctgtt tatccatctt atgtctgttt aattcttagt
 cccaaccaga gaatcTGAGA AGGTAGAGGA TAATGTGTTT CCTCCTCAAC AGATGTAACA
 CGTTATTTTA TGTTATTAAA TATACTATTA AGACCATTGT AATTCAATAT AGAAAGGTAG
 AAAAGAAAGG AAAGAAGGAA AAACTAGAAC CTAAATGCTT ATCTCCAAGG GTACGAGTAA
 ATAAAATGCA GCAAATGCAT ACAATAGAAT GTTATGCAAC AGTTTGAGAT AGAAATACAT
 GTGCTATATT GACAAAGACC TCCAATACAT ATTAATTGAA AACAGCAAGC TGCTAATTAA
 CACAGGGCAT ATAAATTCAT TGATATTAAA AGACACACAC AGacaGACAC ACATACACAC
 ACCTCACAGA ACAAAAATAT ATATTTCTGT ATGTATCTAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_016354
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
ss10135007HapMap-CEUEuropean 120IG0.766666650.23333333 0.654721000.883333330.11666667
HapMap-HCBAsian 80IG0.899999980.10000000 1.000000000.949999990.05000000
HapMap-JPTAsian 86IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 222IG0.936936910.06306306 1.000000000.968468490.03153153
HAPMAP-ASW 96IG0.937500000.06250000 1.000000000.968750000.03125000
HAPMAP-CHBAsian 80IG1.00000000 1.00000000
HAPMAP-GIH 168IG0.988095220.01190476 1.000000000.994047640.00595238
HAPMAP-MEX 94IG0.787234070.191489370.021276600.654721000.882978740.11702128
HAPMAP-MKK 274IG0.905109470.087591240.007299270.273322000.948905110.05109489
HAPMAP-TSI 174IG0.816091950.172413800.011494251.000000000.902298870.09770115
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss117084601YRI 2IG 1.00000000 0.500000000.50000000
ss1310670797EAS 1008AF 1.00000000
EUR 1006AF 0.905600010.09440000
AFR 1322AF 0.989400030.01060000
AMR 694AF 0.935200040.06480000
SAS 978AF 0.977500020.02250000
ss232485723pilot_1_CEU_low_coverage_panel 120AF 0.883333330.11666667

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.068+/-0.1710000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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