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Reference SNP (refSNP) Cluster Report: rs9341296                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
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=0.0251/31 (1000 Genomes)
HGVS Names
  • CM000686.2:g.12910796C>T
  • NC_000024.10:g.12910796C>T
  • NC_000024.9:g.15022707C>T
  • NG_012831.1:g.11689C>T
  • NM_001122665.3:c.152-1044C>T
  • NM_001302552.2:c.143-1044C>T
  • NM_001324195.1:c.152-1044C>T
  • NM_004660.4:c.152-1044C>T
  • NR_136716.1:n.303-1044C>T
  • NR_136717.1:n.303-1044C>T
  • NR_136718.1:n.303-1044C>T
  • NR_136719.1:n.302+1389C>T
  • NR_136720.1:n.303-1044C>T
  • NR_136721.1:n.231-1044C>T
  • NR_136722.1:n.218-1044C>T
  • NR_136723.1:n.218-1044C>T
  • NR_136724.1:n.218-1044C>T
  • XR_001756014.1:n.266-1043C>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 ss162982085 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9341296 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
ss12724448OEFNER|M253_M254/1byFreqfwd/BC/Tttatagtattgttgatagatagcaagttgattctccaggttcttcattgaatgagtcctt10/09/0310/25/06119Genomicunknown
ss24723767PERLEGEN|afd3913289byFreqfwd/BC/Tttatagtattgttgatagatagcaagttgattctccaggttcttcattgaatgagtcctt08/10/0409/13/04123Genomicunknown
ss162982085COMPLETE_GENOMICS|NA07022_36_chrY_13532101fwd/BC/Tttatagtattgttgatagatagcaagttgattctccaggttcttcattgaatgagtcctt09/29/0909/29/09132Genomicunknown
ss491581168EXOME_CHIP|chr.Y._297394_chr_Y_15022707fwd/BC/Tttatagtattgttgatagatagcaagttgattctccaggttcttcattgaatgagtcctt03/05/1203/06/12137Genomicunknown
ss537588609ILLUMINA|HumanOmni5-4v1_B_rs9341296-131_T_R_1895867305fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag06/22/1205/19/16147Genomicunknown
ss778715828ILLUMINA|HumanOmni25Exome-8v1_A_rs9341296-131_T_R_1867868951fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag05/30/1307/09/15146Genomicunknown
ss780687377ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs9341296-131_T_R_1990494819fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag05/30/1307/09/15146Genomicunknown
ss783360930ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs9341296-131_T_R_1990494819fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag05/31/1306/19/15146Genomicunknown
ss834175106ILLUMINA|HumanOmni2.5-8v1_A_rs9341296-131_T_R_1867868951fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag09/18/1307/28/15146Genomicunknown
ss1397804275HAMMER_LAB|HAMMER_LAB_rs9341296fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag09/30/1409/30/14146Genomicunknown
ss1399956644JOBLING_UOL|SNV3919fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag10/14/1410/14/14144Genomicunknown
ss15567500831000GENOMES|PHASE3_chrY_208456byFreqfwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag08/16/1408/07/15144Genomicunknown
ss1583555664EVA_GENOME_DK|EVA_GENOME_DK_snv_rs9341296fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag02/19/1502/20/15144Genomicunknown
ss1752814363ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs9341296-131_T_R_1990494819fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag05/27/1506/09/15146Genomicunknown
ss1917716138ILLUMINA|HumanExome-12v1-1_B_exm-rs9341296-131_T_R_1990494819fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag10/16/1510/16/15147Genomicunknown
ss1945968778ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs9341296-131_T_R_1990494819fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag10/29/1510/29/15147Genomicunknown
ss1958176367ILLUMINA|JHU_Y.15022706-1_T_R_2220377081fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag11/13/1511/13/15147Genomicunknown
ss1958176368ILLUMINA|exm-rs9341296-131_T_R_1990494819fwd/BC/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag11/13/1511/13/15147Genomicunknown
ss2321407578HUMAN_LONGEVITY|HLI-Y-12910796-C-Tfwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag11/18/1611/18/16150Genomicunknown
ss2634993977ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs9341296-131_T_R_18958673fwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag02/02/1702/02/17151Genomicunknown
ss2635204606ILLUMINA|Cancer_BeadChip_11459870_A_rs9341296-128_T_R_1779348339fwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag02/02/1702/02/17151Genomicunknown
ss2711191568ILLUMINA|Consortium-OncoArray_15047405_A_chrY_15022707_C_T-100_T_R_219682fwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag03/22/1703/22/17151Genomicunknown
ss2985494870AFFY|Axiom_PsorMich_Affx-35209915fwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag05/24/1705/24/17151Genomicunknown
ss3020947386SWEGEN|NC_000024.9:g.15022707C>Tfwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag05/30/1705/30/17151Genomicunknown
ss3023053190ILLUMINA|MEGA_Consortium_v2_15070954_A2_JHU_Y.15022706-1_T_R_2220377081fwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag06/28/1706/28/17151Genomicunknown
ss3023053191ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs9341296-131_T_R_1990494819fwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag06/28/1706/28/17151Genomicunknown
ss3029947753HUMGEN|chrY_15022707fwd/C/Tgtattgttgatagatagcaagttgattctccaggttcttcattgaatgag08/09/1708/09/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9341296|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GTATACCTTA TTCTTAACGA GCATATTAAG ATTACATAGT TACTTTTGGA CTTTTAGAAT
 TTGAGGCTAT TTTAGAGGTC TGGTAGAGCA AAGTAGACAA CATGGAAATT CCTTGTTTTG
 TATTGACTAC TTCCATTTAG CTGATCTGTT TCTTTTTGGT GTTACTAGAC AAAGCTAGAT
 TTTAAAAGAT GAATTAAGAT GCTCAGCTAA CTAGTCCTGT TTATAGTATT GTTGATAGAT
 AGCAAGTTGA
 Y
 TTCTCCAGGT TCTTCATTGA ATGAGTCCTT GTTTACTATG ATGCTTGCTA CATACAGTTG
 CTACATACTA CTATGTATGA GTAGTTTTTG GTCATAAACT GCATAGAGTT GGAGCTGTTT
 TTTTTTTTTT TTTGAGACGG AGTCTTGCTG TGTTGTCCAG GCTGGAGTAC AGTGGCGCGA
 TCTCAGCTCA CTGCAAGCTC CACCTCTTGG GTTCATGCCA TTCTCCTGCC TCAGGCTCCT
 GAGTAGCTGG

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
BV088104 NC_000024.4
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
ss12724448Y2 109IG0.96330273 0.03669725 0.963302730.03669725
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss1556750083EAS 488AF 1.00000000
EUR 480AF 0.947900000.05210000
AFR 638AF 0.993699970.00630000
AMR 340AF 0.994099970.00590000
SAS 520AF 1.00000000
ss162982085CEUEuropean 1IG 1.00000000 1.00000000
ss24723767AFD_EUR_PANELEuropean 26IG 0.92307693 0.076923080.000999000.923076930.07692308
AFD_AFR_PANELAfrican American 22IG 1.00000000 1.00000000
AFD_CHN_PANELAsian 18IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.049+/-0.1490000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNYESYES

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