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Reference SNP (refSNP) Cluster Report: rs3093726                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:103/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
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:C=0.0391/196 (1000 Genomes)
C=0.0299/3757 (TOPMED)
HGVS Names
  • CM000668.2:g.31579012T>C
  • NC_000006.11:g.31546789T>C
  • NC_000006.12:g.31579012T>C
  • NG_007462.1:g.8440T>C
  • NT_113891.2:g.3056405T>C
  • NT_113891.3:g.3056299T>C
  • NT_167244.1:g.2861507T>C
  • NT_167244.2:g.2911591T>C
  • NT_167245.1:g.2832330C=
  • NT_167245.1:g.2832330C>T
  • NT_167245.2:g.2826745C=
  • NT_167245.2:g.2826745C>T
  • NT_167246.1:g.2889673T>C
  • NT_167246.2:g.2884053T>C
  • NT_167247.1:g.2926495T>C
  • NT_167247.2:g.2920910T>C
  • NT_167248.1:g.2840429T>C
  • NT_167248.2:g.2834833T>C
  • NT_167249.1:g.2877590T>C
  • NT_167249.2:g.2878292T>C
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 ss278727100 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3093726 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
ss4329011PGA-UW-FHCRC|TNF-004040byFreqfwd/BC/Taccgaactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg02/06/0204/07/04103Genomicunknown
ss6310601EGP_SNPS|TNF-005196byFreqfwd/BC/Taccgaactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg01/15/0304/07/04111Genomicunknown
ss11819531WI_SSAHASNP|chr6.NT_007592.13_22401365byFreqfwd/BC/Taccgaactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg07/04/0303/31/08117Genomicunknown
ss35524647SI_MHC_SNP|AL662801.7_51683_TCfwd/BC/Taccgaactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg03/24/0503/24/05125Genomicunknown
ss48297147SNP500CANCER|TNF-25byFreqfwd/BC/Taccraactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg08/19/0511/03/06126Genomicunknown
ss160609373ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3093726-128_B_F_1562986210fwd/BC/Taccgaactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg08/04/0910/04/09131Genomicunknown
ss278727100GMI|GMI_AK_SNP_3047339fwd/C/Taccgaactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg12/16/1012/16/10137Genomicunknown
ss3331844101000GENOMES|20100804_snps_4827947_chr6_31546789fwd/C/Taccgaactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggccaaggtg03/22/1103/22/11137Genomicunknown
ss481651945ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3093726-131_B_F_1863358483fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca01/30/1208/28/15146Genomicunknown
ss537160411ILLUMINA|HumanOmni5-4v1_B_rs3093726-131_B_F_1895368425fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca06/22/1208/29/15146Genomicunknown
ss559114345TISHKOFF|snp_chr6_31546789fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca11/22/1211/23/12138Genomicunknown
ss653035593SSMP|6_31546789fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca12/14/1202/11/15138Genomicunknown
ss778702760ILLUMINA|HumanOmni25Exome-8v1_A_rs3093726-131_B_F_1869424357fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca05/30/1307/09/15142Genomicunknown
ss834161762ILLUMINA|HumanOmni2.5-8v1_A_rs3093726-131_B_F_1869424357fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca09/18/1307/28/15142Genomicunknown
ss982766444EVA-GONL|EVA-GONL_rs3093726fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca04/23/1404/24/14142Genomicunknown
ss1073506049JMKIDD_LAB|HGDP_WGS_chr6_31546789fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca07/10/1407/11/14142Genomicunknown
ss13195589101000GENOMES|PHASE3_V1_31491311fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca08/16/1408/16/14142Genomicunknown
ss1592310327EVA_DECODE|EVA_DECODE_6_31654768_274365_rs3093726fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca03/02/1503/03/15144Genomicunknown
ss1615278058EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_31546789_17467630fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca03/04/1503/04/15144Genomicunknown
ss1658272091EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_31546789_17467630fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca03/04/1503/04/15144Genomicunknown
ss1804358375HAMMER_LAB|Hsieh_3368286fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca07/15/1507/15/15146Genomicunknown
ss1926018800WEILL_CORNELL_DGM|SNV:chr6:31546789fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca10/16/1510/17/15147Genomicunknown
ss1958888399ILLUMINA|6:31546789-T-C-0_B_F_2304288321fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca11/13/1511/13/15147Genomicunknown
ss2023642585JJLAB|SNP4145140fwd/BC/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca08/29/1608/30/16149Genomicunknown
ss2151809024USC_VALOUEV|NC_000006.11:g.31546789T>Cfwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca11/17/1611/17/16150Genomicunknown
ss2282946401HUMAN_LONGEVITY|HLI-6-31579012-T-Cfwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca11/18/1611/18/16150Genomicunknown
ss2451321987TOPMED|6_31546789_T/Cfwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca11/20/1611/20/16150Genomicunknown
ss2634429991ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs3093726-131_B_F_20874777fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca02/02/1702/02/17151Genomicunknown
ss2707402824GRF|rs3093726fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca02/13/1702/13/17151Genomicunknown
ss2711069585ILLUMINA|Consortium-OncoArray_15047405_A_rs3093726-131_B_F_2202431723fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca03/22/1703/22/17151Genomicunknown
ss2837429095GNOMAD|rs3093726fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca05/18/1705/18/17151Genomicunknown
ss2998796518SWEGEN|NC_000006.11:g.31546789T>Cfwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca05/30/1705/30/17151Genomicunknown
ss3022599589ILLUMINA|MEGA_Consortium_v2_15070954_A2_6:31546789-T-C-0_B_F_2304288321fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca06/28/1706/28/17151Genomicunknown
ss3493847720TOPMED|TOPMed_freeze_5?chr6:31,579,012fwd/C/Tactgccggacgtggtggcatgcaccgtaatcctaccactttgcaaggcca10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3093726|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CAGGAAACAA GAGCCTGAAC CTAATTACCT CTCCCTCAGG GCATGGGAAT TTCCAACTCT
 GGGAATTCCA ATCCTTGCTG GGAAAATCCT GCAGCTCAGG TGAGATTTCC GGCTGTTGCA
 GCTGGCCAGC AGTCCGGAGA GAGCTGGAGA GGAGCCGCAT TCTCAGGTAC CTGAATCACA
 CAGCCAAGGG ACTTCCAGAG ATTCGGGTGT CTAGGCTTCA AATCACCCTG TCCTAACTCT
 GCAACCTGAA CCAGCCACTT AACCTATCTA TCCAATGGGG ATAGGAATGT CCACCACACA
 TAGGGCATGT GAGAGAAGGC CTGACCTCCA TCAGAGGACC TCACTCAGCC CTTGGCACAG
 TGGGCACTTA GTGAATTCTG GCTTCCTTCA ACCAGTTTCC AGCTGTTCTA TCCCCTTCCA
 TTCTCTCAGT GGGTGAAATC GAAGAGACTG AGGACAATAA AGAACAAGGA ACCGAACTGC
 CGGACGTGGT GGCATGCACC
 Y
 GTAATCCTAC CACTTTGCAA GGCCAAGGTG AGAGGATCGC TTGAACCCAG GAGTTCCAGA
 GCAACCTGGG CAACATAGTG AGATCCTGTC TCTATTTTTT AAAAAAGAAT GAAACATAGG
 AATAAGATGT GGGTGAAGGA CTCACATGCC GGCTTGGTCC CACTGGTCTT TGTGGTGAAG
 GAGGGGAGAG GTGAGAGGTG GGTAATCCGG AAAGAGAAAA GCACCCCCTC CCTGGATGAA
 GGCTCTTCTG GAGAGAGTCA AAGACAAATA AGGGTGGGGC GCAGTGGCTC ATGCCTGTTA
 TCCCAACACT TTGGGAGGCT GAGGTGGGAG GACCACTTGA GCCCACTAGT TCAAGACCAG
 CCTGTGCAAC ATAGCAAGAC CTTGTTTCTA GAAAAAAAAT TAAAGATTAG TCAGGTGTAG
 TGGTGCATGC CTGTAATCCT AGCTCCTCAG GAGGCTGAGG CAGGAGGATC ACTCAAGCCC
 AGGAGTTTGA GGTTACAGTA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007592
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/T
T/T
HWPC
T
ss11819531HapMap-CEUEuropean 118IG0.084745760.915254241.000000000.042372880.95762712
HapMap-HCBAsian 88IG0.022727270.977272751.000000000.011363640.98863637
HapMap-JPTAsian 86IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss1319558910EAS 1008AF 0.011900000.98809999
EUR 1006AF 0.045700000.95430005
AFR 1322AF 0.025000000.97499996
AMR 694AF 0.018700000.98130000
SAS 978AF 0.094100000.90590000
ss4329011PGA-AFRICAN-PANELAfrican American 46IG 1.00000000 1.00000000
PGA-EUROPEAN-PANELEuropean 44IG0.136363640.863636371.000000000.068181820.93181819
ss48297147P1 204AF0.069000000.930999991.000000000.034000000.96599996
CAUC1 62AF0.032000000.967999991.000000000.016000000.98399997
AFR1 48AF0.125000000.875000001.000000000.063000000.93700004
HISP1 46AF0.087000000.913000051.000000000.043000000.95699996
PAC1 48AF0.042000000.958000001.000000000.021000000.97900003
ss6310601PDR90Global 174IG0.080459770.919540231.000000000.040229890.95977014

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.075+/-0.1790000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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