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Reference SNP (refSNP) Cluster Report: rs17426593                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/151
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=0.1645/824 (1000 Genomes)
C=0.0477/5995 (TOPMED)
HGVS Names
  • CM000668.2:g.32640300T>C
  • NC_000006.11:g.32608077T>C
  • NC_000006.12:g.32640300T>C
  • NG_032876.1:g.7895T>C
  • NM_002122.3:c.83-1010T>C
  • NT_113891.2:g.4058502T>C
  • NT_113891.3:g.4058396T>C
  • NT_167245.2:g.3884157T>C
  • NT_167246.2:g.4058555T>C
  • NT_167247.2:g.3941302C=
  • NT_167247.2:g.3941302C>T
  • NT_167248.1:g.3844961T>C
  • NT_167248.2:g.3839365T>C
  • NT_167249.2:g.4042171C=
  • NT_167249.2:g.4042171C>T
  • XR_001744085.1:n.268A>G
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 ss278738837 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17426593 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
ss24651660PERLEGEN|afd0293591byFreqfwd/BC/Ttttgttccttaatggtagaccatgcctgatggtgttttacacatcccctgctatgtctga08/10/0409/13/04123Genomicunknown
ss43528953ABI|hCV32864912byFreqrev/TA/Gtcagacatagcaggggatgtgtaaaacaccatcaggcatggtctaccattaaggaacaaa07/18/0511/03/06126Genomicunknown
ss50398026UWGC|HLA-71745byFreqrev/TA/Gtcagacatagcaggggatgtgtaaaacaccatcaggcatggtctaccattaaggaacaaa02/02/0611/03/06130Genomicunknown
ss52050531SI_MHC_SNP|AL662789.11_52194_TCbyFreqfwd/BC/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga03/24/0609/05/14130Genomicunknown
ss76495110AFFY|AFFY_6_1M_SNP_A-8356019rev/TA/Gggatgtgtaaaacaccatcaggcatggtctac08/28/0708/30/07129Genomicunknown
ss105100945KRIBB_YJKIM|KHS1493268fwd/BC/Ttttgttccttaatggtagaccatgcctgatggtgttttacacatcccctgctatgtctga07/10/0807/11/08130Genomicunknown
ss162212478COMPLETE_GENOMICS|NA07022_36_chr6_32716055fwd/BC/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga09/28/0909/28/09132Genomicunknown
ss201645876BUSHMAN|BUSHMAN-chr6-32716054fwd/BC/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga02/16/1003/08/10132Genomicunknown
ss207751672BCM-HGSC-SUB|BCM_CMT_1011-1383203fwd/BC/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga03/15/1003/19/10132Genomicunknown
ss2223151501000GENOMES|pilot_1_YRI_4124833_chr6_32716055fwd/C/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga04/22/1004/22/10132Genomicunknown
ss2334123191000GENOMES|pilot_1_CEU_3016948_chr6_32716055fwd/C/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga05/01/1005/01/10132Genomicunknown
ss2404798791000GENOMES|pilot_1_CHB+JPT_2364956_chr6_32716055fwd/C/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga05/01/1005/01/10132Genomicunknown
ss244283661ILLUMINA|CVDSNP55v1_A_rs17426593rev/TA/Gtcagacatagcaggggatgtgtaaaacaccatcaggcatggtctaccattaaggaacaaa06/10/1006/10/10142Genomicunknown
ss278738837GMI|GMI_AK_SNP_3059078fwd/C/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga12/16/1012/16/10137Genomicunknown
ss285379362GMI|GMI_NA10851_SNP_1392135fwd/C/Ttttgttccttaatagtagaccatgcctgatggtgttttacacatctccggctatgtctga12/17/1012/17/10138Genomicunknown
ss653049207SSMP|6_32608077fwd/BC/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg12/14/1202/11/15138Genomicunknown
ss982782873EVA-GONL|EVA-GONL_rs17426593fwd/BC/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg04/23/1404/24/14142Genomicunknown
ss13195929371000GENOMES|PHASE3_V1_31526960fwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg08/16/1408/16/14142Genomicunknown
ss1712852398EVA_SVP|EVA_SVP_546765fwd/BC/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg03/12/1503/12/15144Genomicunknown
ss1926039560WEILL_CORNELL_DGM|SNV:chr6:32608077fwd/BC/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg10/16/1510/17/15147Genomicunknown
ss2023653573JJLAB|SNP4156128fwd/BC/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg08/29/1608/30/16149Genomicunknown
ss2095179837ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs17426593-138_B_F_2260348877fwd/BC/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg09/27/1609/27/16150Genomicunknown
ss2151828300USC_VALOUEV|NC_000006.11:g.32608077T>Cfwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg11/17/1611/17/16150Genomicunknown
ss2282989705HUMAN_LONGEVITY|HLI-6-32640300-T-Cfwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg11/18/1611/18/16150Genomicunknown
ss2451369283TOPMED|6_32608077_T/Cfwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg11/20/1611/20/16150Genomicunknown
ss2707422740GRF|rs17426593fwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg02/13/1702/13/17151Genomicunknown
ss2711072103ILLUMINA|Consortium-OncoArray_15047405_A_chr6_32608077_C_T-100_B_F_219878fwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg03/22/1703/22/17151Genomicunknown
ss2837511443GNOMAD|rs17426593fwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg05/18/1705/18/17151Genomicunknown
ss2998834850SWEGEN|NC_000006.11:g.32608077T>Cfwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg05/30/1705/30/17151Genomicunknown
ss3494036717TOPMED|TOPMed_freeze_5?chr6:32,640,300fwd/C/Ttccttaatagtagaccatgcctgatggtgttttacacatctccggctatg10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17426593|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TATATTCATG TTTGAACAAG GAGTCAAGAT TTATGGCAAG GATAAGGAGG CTTTGTTGGT
 GACCTGTTAA GACCAACCAG GGCAGTCATG CTGGATAGGG AAGAAGGTGA GCTGGAAGAG
 GAACAGACAA CTTGGACAGC CAGATGTTGA GACGGAGGGG TTGGAGGTCA TAATGTGGTC
 AAAAACATGT TGATGAGAGG ACTCAGCTAC AAAGTTGTTA ACTTAAGCAG AAACCTCAAG
 GATGGATTTT AGAATTTCTC CAGGAAGTCC TAAAAGATAA TTCCATTTCA GGGAGAAAAA
 CAACAGACCA CTGCAAAGAC CAGGGAACAT GAAAGGATAA TGTAGTTTGT CTTGCTTGGC
 AGATACTTTT GAAGGATGTT GGACTGTAAG GCTGTCGATA TCCTCCTCAG AGAACTTACT
 ACAGTACATT GTATCTGTTC CCTTACCTAC CTGACTCTTC CACTATTCAG TTTGTTCCTT
 AATAGTAGAC CATGCCTGAT
 Y
 GGTGTTTTAC ACATCTCCGG CTATGTCTGA CACTTGTGGA TGCTCAGAAA GTGGGGAAGG
 AAGGAAAGAT ACGATGGTAA AAGGCTTACA CATGTCTTGA CAAAAAAGTC CAGTTTGGCT
 CATTTGGCTG GAGTCGTACT GCATGGCTGC CATTCTGCTC TGGCATCCTC AGACAAGCAC
 ACTGCCCATT AGAGGAAAAA GTGTGATATA AGTGTTGAGT CAGAATGCTG TAGACATTTA
 GTAATCTCCT TCACAGGAAA AAAAAAAAAA AGGTGGGGGG AATGACAGAA ATCCAAAAAC
 TAGTAGAGCT TCCACTTTTC ATTTCAGAAG AAATCAGTTG CTCTCCTCTA AGGACCATTA
 CTATTAACAA AACAGAGACC TTAGAAGGAG GCATTGTTTA TTTATTATAT ATTTTGTAAT
 GTTATTACCA ATCTTGTTAT ACTCTTTCTT ATACCCTACA ATTGTTAGCA GAAATTATTT
 TAAATTAATA AGATCCTGCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000006.6
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
ss1319592937EAS 1008AF 0.250000000.75000000
EUR 1006AF 0.160000010.83999997
AFR 1322AF 0.095300000.90470004
AMR 694AF 0.270899980.72909999
SAS 978AF 0.099200000.90080005
ss162212478CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss201645876BANTU 2IG 1.00000000 0.500000000.50000000
ss222315150pilot_1_YRI_low_coverage_panel 118AF 0.042372880.95762712
ss233412319pilot_1_CEU_low_coverage_panel 120AF 0.266666680.73333335
ss240479879pilot_1_CHB+JPT_low_coverage_panel 120AF 0.333333340.66666669
ss52050531HapMap-CEUEuropean 224IG0.071428570.366071430.562500000.751830000.254464300.74553573
HapMap-HCBAsian 86IG0.069767450.534883740.395348850.200325000.337209310.66279072
HapMap-JPTAsian 172IG0.139534890.488372090.372093021.000000000.383720930.61627907
HapMap-YRISub-Saharan African 226IG0.008849560.132743360.858407080.654721000.075221240.92477876
HAPMAP-ASW 98IG0.040816330.163265300.795918350.099721000.122448980.87755102
HAPMAP-CHBAsian 82IG0.024390240.390243890.585365830.402784000.219512190.78048778
HAPMAP-CHD 168IG0.119047620.464285700.416666661.000000000.351190480.64880955
HAPMAP-GIH 176IG0.022727270.170454550.806818190.294266000.107954550.89204544
HAPMAP-LWK 180IG 0.066666670.933333341.000000000.033333340.96666664
HAPMAP-MEX 100IG0.040000000.360000010.600000020.751830000.220000000.77999997
HAPMAP-MKK 280IG0.014285710.250000000.735714260.654721000.139285710.86071426
HAPMAP-TSI 176IG0.011363640.113636370.875000000.342782000.068181820.93181819

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.275+/-0.2490000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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