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dbSNP
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Reference SNP (refSNP) Cluster Report: rs3115853                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:103/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.3598/1802 (1000 Genomes)
HGVS Names
  • CM000663.2:g.822260G>A
  • CM000663.2:g.822260G>C
  • CM000663.2:g.822260G>T
  • NC_000001.10:g.757640G>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 ss275680778 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3115853 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
ss4358503SC_JCM|AF198096.3_61090fwd/BC/Tggcaggtagtgtagacagggtggatctactggcagggaggtagtgtagacagggtggacc02/19/0210/10/03103Genomicunknown
ss6851734WI_SSAHASNP|NT_034471.1_312027rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc02/12/0310/10/03111Genomicunknown
ss19866495CSHL-HAPMAP|CSHL-HuFF-200402.chr1.NT_034471.3_236272rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc02/21/0403/04/04120Genomicunknown
ss84983519HGSV|Cor19240_SNV_20070510.chr1_797503rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc11/30/0712/08/07130Genomicunknown
ss87155738BCMHGSC_JDW|JWB-0000102rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc02/26/0802/26/08129Genomicunknown
ss97913197HUMANGENOME_JCVI|1103675000061rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc03/30/0803/30/08130Genomicunknown
ss105111664BGI|BGI_rs3115853rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc08/06/0806/16/09130Genomicunknown
ss1079382711000GENOMES|CEU.trio.12.15.2008_17_chr1_747503rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc12/15/0812/15/08130Genomicunknown
ss118438247ILLUMINA-UK|NA18507_000000033_NCBI36.1_chr1_747503rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc01/21/0901/21/09130Genomic99 %
ss137752219ENSEMBL|ENSSNP11472212rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc05/15/0905/16/09131Genomicunknown
ss154522336GMI|GMI_SNP_71795614rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc06/24/0906/24/09131Genomicunknown
ss161273412ENSEMBL|ENSSNP261806rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc09/24/0909/24/09131Genomicunknown
ss165981014COMPLETE_GENOMICS|NA20431_36_chr1_747503rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc09/30/0909/30/09132Genomicunknown
ss197885418BUSHMAN|BUSHMAN-chr1-747502byFreqrev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc02/16/1009/05/14132Genomicunknown
ss205402129BCM-HGSC-SUB|BCM_CMT_1011-180035rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc03/15/1003/15/10132Genomicunknown
ss2181903821000GENOMES|pilot_1_YRI_65_chr1_747503rev/A/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc04/22/1004/22/10132Genomicunknown
ss2303954551000GENOMES|pilot_1_CEU_84_chr1_747503rev/A/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc05/01/1005/01/10132Genomicunknown
ss2381149691000GENOMES|pilot_1_CHB+JPT_46_chr1_747503rev/A/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc05/01/1005/01/10132Genomicunknown
ss252864096BL|SNP145_1_747503rev/TA/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc08/18/1008/18/10134Genomicunknown
ss275680778GMI|GMI_AK_SNP_939rev/A/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc12/16/1012/16/10137Genomicunknown
ss283987371GMI|GMI_NA10851_SNP_137rev/A/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc12/17/1012/17/10138Genomicunknown
ss290493776PJP|SNP_134_chr1_747503rev/A/Gggtccaccctgtctacactacctccctgccagtagatccaccctgtctacactacctgcc01/21/1101/21/11134Genomicunknown
ss647516121SSMP|1_757640rev/TA/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac12/14/1202/09/15138Genomicunknown
ss974769265EVA-GONL|EVA-GONL_rs3115853rev/TA/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac04/23/1404/23/14142Genomicunknown
ss12893389421000GENOMES|PHASE3_V1_3667rev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac08/16/1408/16/14142Genomicunknown
ss1425684816DDI|DDI_rs3115853rev/TA/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac11/04/1411/04/14144Genomicunknown
ss1599378318EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_757640_209rev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac03/04/1503/04/15144Genomicunknown
ss1642372351EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_757640_209rev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac03/04/1503/04/15144Genomicunknown
ss1917960216WEILL_CORNELL_DGM|SNV:chr1:757640rev/TA/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac10/16/1510/16/15147Genomicunknown
ss2019498386JJLAB|SNP941rev/TA/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac08/29/1608/30/16149Genomicunknown
ss2147484347USC_VALOUEV|NC_000001.10:g.757640G>Arev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac11/17/1611/17/16150Genomicunknown
ss2624264755SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV348rev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac01/06/1701/06/17151Genomicunknown
ss2697374562GRF|rs3115853rev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac02/13/1702/13/17151Genomicunknown
ss2750637257GNOMAD|rs3115853rev/A/C/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac05/17/1705/17/17151Genomicunknown
ss2986148763SWEGEN|NC_000001.10:g.757640G>Arev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac05/30/1705/30/17151Genomicunknown
ss3343272488CSHL|rs3115853rev/A/Gaccctgtctacactacctccctgccagtagatccaccctgtctacactac10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3115853|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=151
 GTGGATCTGC TGGCCAGGCA GTTAGTATAG ACAGGGTGGA TCTGCTGAGC AGGCAGGTAG
 TGTAGACAGG GTAGATCTGC TGGATAGGCA GGTAGTATAG ACAGGGTGGA TCTGCTGGAC
 AGGCAGGTAG TGTAGATAGG GTGGACATGC TGGACAGGCA GCTAGTGTAG ACAGGGTGGA
 TCTGCTGGAC AAGCAGGTAG TGTAGACATG GCGCATCTTC TGGGCAGGCA GGTAGTGTAG
 ACAGGGTGGA TCTGCTGGCC AGTCAGGTAG TATAGACAGG GTGGATCTGC TGGCCAGGCA
 GGTAGTATAG ACAGGGTGGA TCTGCTGGCC AGGGAGGTAG TATAGACAGG GTGGGTCTAC
 TGGACAGGGA GGTAGTATAG ACAGCGTGGA TCTGCTAGCC AGGCAGGTAG TGTAGATAGC
 GTGCATTACT GGCAAGGAAG GTAGTGTAGA CAGGGTGGAT CTTCTGGCCA GGCAGGTAGT
 GTAGACAGGG TGGATCTACT
 N
 GGCAGGGAGG TAGTGTAGAC AGGGTGGACC TGCTGGATGG GCAGGTAGTA TAGACAGGGT
 GGATCTGCTA GACAGGCAGG TAGTATAGAC AGGGTGGATC TGCTGGATAG GCAGGTAGTG
 TAGACAGGGT GGATCTGCTG GACAGCCAGG TAGTGTAGAC AGAGTGGATT TGCTGGACAG
 GCAGGTAGTG TAGACAGGGT GGACCTGCTG GACAAGCAGG TAGAGTAGAC AGGGTGGATC
 TGCTCGCTAG GTAGGTAGTG AAGACAGGGT GGATCTGCTG GGCAGGTAGG TAGTGTAGAC
 AGGGTAGATA TGCTGGATAG GCAGGTAGTA TAGACAGGGT GGATCTTCTG GAGAGGCAGG
 TAGTGTAGAC AGGGTGGACC TGCTGGACAA GCATGTAGTG TAGACAGGGT GGATCTGGTA
 AGTCAGGTAG TGTAGATAGC GTGGATCTGC TGGCCAGGCA GGTAGAGTAG AGAGGGTCAA
 TCTGCCGGAC AGGAAGGTAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_034471 ABBA01016000 AL669831
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs3115853 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/T
T/T
HWPC
T
ss118438247YRI 2IG1.00000000 0.500000000.50000000
ss1289338942EAS 1008AF 0.267900020.73210001
EUR 1006AF 0.129200010.87079996
AFR 1322AF 0.782099960.21790001
AMR 694AF 0.255000000.74500006
SAS 978AF 0.195300000.80469996
ss137752219ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss161273412ENSEMBL_celera 2IG 1.00000000 1.00000000
ss165981014PGP 2IG1.00000000 0.500000000.50000000
ss197885418BUSHMAN_POP2 2IG1.00000000 0.500000000.50000000
BANTU 2IG1.00000000 0.500000000.50000000
ss218190382pilot_1_YRI_low_coverage_panel 118AF 0.838983060.16101696
ss230395455pilot_1_CEU_low_coverage_panel 120AF 0.108333330.89166665
ss238114969pilot_1_CHB+JPT_low_coverage_panel 120AF 0.358333320.64166665
ss97913197J. Craig Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.461+/-0.1350000

  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