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Reference SNP (refSNP) Cluster Report: rs6638409                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/147
Map to Genome Build:107/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
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:C=0.4976/2836 (ExAC)
T=0.3889/1468 (1000 Genomes)
HGVS Names
  • NC_000023.10:g.53659047C>T
  • NC_000023.11:g.53632095C>T
  • NG_016261.2:g.59639G>A
  • NM_031407.6:c.645+392G>A
  • NW_004070877.1:g.3345210C>T
  • XM_005261965.1:c.645+392G>A
  • XM_005261965.2:c.645+392G>A
  • XM_005261966.1:c.645+392G>A
  • XM_005261967.1:c.645+392G>A
  • XM_005261968.1:c.645+392G>A
  • XM_005261969.1:c.645+392G>A
  • XM_005261970.1:c.645+392G>A
  • XM_005261971.1:c.645+392G>A
  • XM_005261972.1:c.645+392G>A
  • XM_005277961.1:c.645+392G>A
  • XM_005277962.1:c.645+392G>A
  • XM_005277963.1:c.645+392G>A
  • XM_005277964.1:c.645+392G>A
  • XM_005277965.1:c.645+392G>A
  • XM_005277966.1:c.645+392G>A
  • XM_005277967.1:c.645+392G>A
  • XM_005277968.1:c.645+392G>A
  • XM_011530746.1:c.645+392G>A
  • XM_011530747.1:c.645+392G>A
  • XM_011530748.1:c.645+392G>A
  • XM_011530749.1:c.645+392G>A
  • XM_011530750.1:c.645+392G>A
  • XM_011530751.1:c.645+392G>A
  • XM_011530752.1:c.645+392G>A
  • XM_011530753.1:c.645+392G>A
  • XM_011530754.1:c.645+392G>A
  • XM_011530755.1:c.645+392G>A
  • XM_011530756.1:c.645+392G>A
  • XM_011530757.1:c.645+392G>A
  • XM_011530758.1:c.645+392G>A
  • XR_244463.1:n.674+392G>A
  • XR_254464.1:n.674+392G>A
  • XR_938360.1:n.1080+392G>A
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 ss283753531 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6638409 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
ss8537275SC_SNP|NT_011799.11_539636byFreqfwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact05/23/0310/25/06116Genomicunknown
ss21074252SSAHASNP|WGSA-200403-chrX.chrX.NT_011630.14_1213133fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact03/19/0403/19/04121Genomicunknown
ss24230890PERLEGEN|afd3846248byFreqfwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact08/10/0409/13/04123Genomicunknown
ss43551795ABI|hCV30150193fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact07/18/0507/18/05126Genomicunknown
ss75317055ILLUMINA|ILMN_Human_1M_rs6638409fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact08/28/0708/29/07129Genomicunknown
ss76583741AFFY|AFFY_6_1M_SNP_A-8444966fwd/BC/Tacctcctcaaacaataaaaatgaccagataat08/28/0708/30/07129Genomicunknown
ss1128889971000GENOMES|CEU.trio.12.15.2008_3868175_chrX_53675772fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact12/18/0812/18/08130Genomicunknown
ss119518595KRIBB_YJKIM|KHS1680842fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact02/04/0902/05/09131Genomicunknown
ss123259272ILLUMINA|HumanCNV370v1_C_rs6638409fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact04/14/0904/15/09131Genomicunknown
ss133963800ENSEMBL|ENSSNP3139422fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact12/08/0810/14/09131Genomicunknown
ss154372937ILLUMINA|Human610_Quadv1_B_rs6638409-127_B_F_1514287956fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact06/18/0906/20/09131Genomicunknown
ss157478645GMI|GMI_SNP_134204237fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact06/24/0906/25/09131Genomicunknown
ss163116872COMPLETE_GENOMICS|NA07022_36_chrX_53675772fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact09/29/0909/29/09132Genomicunknown
ss172164460ILLUMINA|HumanCNV370-Quadv3_C_rs6638409-127_B_F_1514287956fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact10/01/0910/04/09132Genomicunknown
ss174052956ILLUMINA|Human1M-Duov3_B_rs6638409-127_B_F_1514287956fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact10/01/0910/04/09132Genomicunknown
ss204239413BUSHMAN|BUSHMAN-chrX-53675771fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact02/16/1003/10/10132Genomicunknown
ss208905691BCM-HGSC-SUB|BCM_CMT_1011-3361126fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact03/15/1003/20/10132Genomicunknown
ss283753531GMI|GMI_AK_SNP_8073974fwd/C/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact12/16/1012/16/10137Genomicunknown
ss287612445GMI|GMI_NA10851_SNP_3625265fwd/C/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact12/17/1012/17/10138Genomicunknown
ss294451673PJP|SNP_3958031_chrX_53675772fwd/C/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact01/21/1101/21/11134Genomicunknown
ss3414884501000GENOMES|20100804_snps_240154_chrX_53659047fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact03/24/1103/24/11134Genomicunknown
ss482735065ILLUMINA|HumanOmni2.5-4v1_D_kgp22777611-0_B_F_1860528056fwd/BC/Tccaaactctttagtacctcctcaaacaataaaaatgaccagataatttaagcaggacact01/30/1202/01/12137Genomicunknown
ss484383736ILLUMINA|HumanOmni2.5-4v1_B_SNP23-53675772-0_B_F_1649800038fwd/BC/Tccaaactctttagtacctcctcaaacaataannnnnaccagataatttaagcaggacact01/30/1202/03/12137Genomicunknown
ss537373105ILLUMINA|HumanOmni5-4v1_B__rs6638409-131_B_F_1908488844fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg06/22/1208/28/15146Genomicunknown
ss566869826TISHKOFF|snp_chrX_53659047fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg11/22/1211/23/12138Genomicunknown
ss662808318SSMP|X_53659047fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg12/14/1202/14/15138Genomicunknown
ss780060976ILLUMINA|HumanOmni25Exome-8v1_A_kgp22777611-0_B_F_1860528056fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg05/30/1307/09/15146Genomicunknown
ss781860092ILLUMINA|HumanOmni2.5-4v1_H_kgp22777611-0_B_F_1860528056fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg05/30/1307/28/15146Genomicunknown
ss825658353ILLUMINA|HumanCNV370v1_C_rs6638409-126_B_F_IFB1185330552:0fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg06/24/1311/21/14144Genomicunknown
ss835542370ILLUMINA|HumanOmni2.5-8v1_A_kgp22777611-0_B_F_1860528056fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg09/18/1307/28/15146Genomicunknown
ss1082918823JMKIDD_LAB|HGDP_WGS_chrX_53659047fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg07/10/1407/12/14144Genomicunknown
ss1432044398DDI|DDI_rs6638409fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg11/04/1411/05/14144Genomicunknown
ss15544419631000GENOMES|PHASE3_chrX_1215645byFreqfwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg08/16/1408/07/15144Genomicunknown
ss1583394164EVA_GENOME_DK|EVA_GENOME_DK_snv_rs6638409fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg02/19/1502/20/15144Genomicunknown
ss1640768243EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_X_53659047_45500437fwd/C/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg03/04/1503/04/15144Genomicunknown
ss1683762276EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_X_53659047_45500437fwd/C/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg03/04/1503/04/15144Genomicunknown
ss1694527531EVA_EXAC|EVA_EXAC_10029960fwd/C/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg03/04/1503/04/15144Genomicunknown
ss1939349346WEILL_CORNELL_DGM|SNV:chrX:53659047fwd/BC/Tctctttagtacctcctcaaacaataaaaatgaccagataatttaagcagg10/16/1510/19/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6638409|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=147
 TGTAGTGTGT TACTAGTTGT CTAAAATTAA AAAAGACAAG AGAGCTGTAA GGAGTCACTG
 AACACTCTAG CTTCCCCTTC CATAGAGCTC CAAAGGGCTG TCTGAAAACC AAGATGTCAC
 CTAATAGGCT GAAGCCTAAG TGAATGCTCT TAAAATCAAG GTAAATTGAG AATCTTCCAA
 AACATCCATC TTATATGTAG AATATTCTTA GGAAAGCTCC TTTAAAACCA GTAGTATCAA
 ACTATAATGC ACATAGCCAG GCACATTTCA TATTCTTCTT TGTCCTTTTT TAACCCTCCA
 CTGACTTAAT ATCCATAGCA GTATTAATAG CAAAGACCAA ATTCATGAAA ATATTTTCTC
 TCTGAATATG TATTAGAGTT GCTTTCAAGG CAATTAAGCT AGAAAGATTA TTTATTTATT
 GAATAGTATA GGTAGAAGAG AAATTGTATT TTCACTAAGC TACTTCTAAA CCAAACTCTT
 TAGTACCTCC TCAAACAATA
 Y
 AAAATGACCA GATAATTTAA GCAGGACACT ATCCACAATA CATAAAGACT TTTGCAGGCT
 TCCTAATTAG AGAAACCTGA GCCATCACCA TCCAAACTAC TATACTACAT GTTGGAATTC
 TCAGAGACTG TGGGAAAAGC ACATAGGTCA TAGCAGTGCC TCATAATGGA TGGGACTTGC
 ATCTTTTGGC AGCTCCCAAC ATAAGACCCA ACCCTATCAG AGTTGGGGAT GCAATTAACA
 CTCCTGAGGA GCTGCTAGGT ATATTTATAG TTTGCGAGGG CAGCAGTGTA GCTCAAAACC
 ATTTATTCAT TTAACTGAGG AGTTCTAGAA GAGGCAATCC CAGTTACAGT AAATTGTAGA
 CTTTGTCAGA ACAAATCTGA ATCAGACTCA CCCTTTTCTC AATTTTGACC TCGGCCCCAG
 GATCTGCATA GAATTCAAAG TGTAGTGTAG TTGCACTGGG TGGATATTTC TGTGTATAAA
 GCACATCAAA GAATCAGACA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011799
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.
Source0/C
0/T
C/C
C/T
T
T/T
HWP0
C
T
ss133963800ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss1554441963EAS 1008AF 0.604200010.39579999
EUR 1006AF 0.571600020.42840001
AFR 1322AF 0.974300030.02570000
AMR 694AF 0.631100000.36890000
SAS 978AF 0.644199970.35580000
ss163116872CEUEuropean 1IG 1.00000000 1.00000000
ss1694527531ExAc_Aggregated_Populations 13914AF 0.590196910.40980306
ss24230890AFD_EUR_PANELEuropean 46IG0.217391300.304347810.217391300.13043478 0.130434780.150318000.260869560.391304340.34782609
AFD_AFR_PANELAfrican American 44IG0.409090910.045454550.454545470.09090909 0.740818000.227272730.704545440.06818182
AFD_CHN_PANELAsian 48IG 0.458333340.16666667 0.375000000.00250100 0.541666690.45833334
ss8537275HapMap-CEUEuropean 226IG 0.292035400.23008850 0.477876100.00100000 0.407079640.59292036
HapMap-HCBAsian 86IG 0.209302320.20930232 0.581395330.00099900 0.313953490.68604654
HapMap-JPTAsian 172IG 0.453488380.24418604 0.302325580.00100000 0.575581370.42441860
HapMap-YRISub-Saharan African 226IG 0.991150440.00884956 1.00000000 0.995575250.00442478
HAPMAP-ASW 98IG 0.816326560.16326530 0.020408160.47950000 0.897959170.10204082
HAPMAP-CHBAsian 82IG 0.390243890.24390244 0.365853670.00250100 0.512195110.48780489
HAPMAP-CHD 170IG 0.341176480.27058825 0.388235300.00100000 0.476470590.52352941
HAPMAP-GIH 176IG 0.386363630.23863636 0.375000000.00100000 0.505681810.49431819
HAPMAP-LWK 180IG 0.922222200.05555556 0.022222220.00100000 0.949999990.05000000
HAPMAP-MEX 100IG 0.340000000.18000001 0.479999990.00100000 0.430000010.56999999
HAPMAP-MKK 286IG 0.797202830.12587413 0.076923080.00100000 0.860139850.13986014
HAPMAP-TSI 176IG 0.306818190.23863636 0.454545470.00100000 0.426136370.57386363
Concordant GenotypeTotal Sample0/C0/TC/CC/TTT/T
ss13396380011
ss16311687211
ss20423941311
ss242308906712626912
ss85372751203678202303
RefSNP Genotype SummaryTotal Individual0/C0/TC/CC/TTT/T
rs663840912651267002102314
Discordant Genotypes:
Indiviudal
SampleID
SubSNP(ss)GenotypePopulation
Handle
Submitter
Population
Submitter
SampleID
SampleID
Alias
Submission
Batch
NCBI
ProbeID
188ss8537275N/NCSHL-HAPMAPHapMap-CEUNA10851CEPH1344.01r27_chX_CEU_affymetrix:genomewidesnp_6.01023807
188ss242308900/TPERLEGENAFD_EUR_PANELNA1085171_IND_CHR_X
215ss8537275N/NCSHL-HAPMAPHapMap-CEUNA10857CEPH1346.01r27_chX_CEU_affymetrix:genomewidesnp_6.01023807
215ss242308900/TPERLEGENAFD_EUR_PANELNA1085771_IND_CHR_X
348ss8537275N/NCSHL-HAPMAPHapMap-CEUNA10860CEPH1362.01r27_chX_CEU_affymetrix:genomewidesnp_6.01023807
348ss242308900/CPERLEGENAFD_EUR_PANELNA1086071_IND_CHR_X
399ss8537275C/CCSHL-HAPMAPHapMap-CEUNA10830CEPH1408.01r27_chX_CEU_affymetrix:genomewidesnp_6.01023807
399ss242308900/CPERLEGENAFD_EUR_PANELNA1083071_IND_CHR_X
Genotype data submitted for1281 samples from1265 individualsIndividual with multiple genotypes submission:16

  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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