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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs8039584          
refSNP ID: rs8039584
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_002675.3:c.603-9203C>T
NM_033238.2:c.603-9203C>T
NM_033239.2:c.603-9203C>T
NM_033240.2:c.603-9203C>T
NM_033244.3:c.603-9203C>T
NM_033246.2:c.603-9203C>T
NM_033247.2:c.603-9203C>T
NM_033249.2:c.603-9203C>T
NM_033250.2:c.603-9203C>T
NT_010194.16:g.45096284C>T
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss12338516 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs8039584 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
ss12338516WI_SSAHASNP|chr15.NT_010194.15_45092364byFreqfwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata07/04/0310/25/06116Genomicunknown
ss67863810ILLUMINA|HumanHap550v1.1_rs8039584fwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata11/14/0611/14/06127Genomicunknown
ss68011707ILLUMINA|HumanHap650Yv1.0_rs8039584fwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata11/14/0611/15/06127Genomicunknown
ss68293927ILLUMINA|HumanHap250Sv1.0_rs8039584fwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata12/06/0612/07/06127Genomicunknown
ss70966493ILLUMINA|HumanHap550v3.0__rs8039584fwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata04/20/0703/31/08130Genomicunknown
ss71576303ILLUMINA|HumanHap650Yv3.0_rs8039584fwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata04/23/0704/23/07127Genomicunknown
ss75696887ILLUMINA|ILMN_Human_1M_rs8039584fwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata08/28/0708/29/07129Genomicunknown
ss76847486AFFY|AFFY_6_1M_SNP_A-8708964rev/TA/Ggcagctcttctattcatcatgccaaatttgaa08/28/0708/30/07129Genomicunknown
ss84774700KRIBB_YJKIM|KHS806027fwd/BC/Tagtaggtgaggtgtttcaaatttggcatgatgaatagaagagctgcccgttctcaccata12/04/0712/07/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs8039584|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TGAGAATATC AGAATTATTT ATGTCACACA AGGAGTTACT GCCTGTTTTC TGTGTCACCA
 GATTCTATTA ACATTTAATG ATTACCTTTA CTCTTTGAAT TTTGAATTTT GTAACAAATT
 CCTGCTGTGG CATATTTTGC AATTTGGTTA TGTTCTGCCA AAGCTGTAAC AGTAGGTGAG
 GTGTTTCAAA TTTGGCATGA
 Y
 TGAATAGAAG AGCTGCCCGT TCTCACCATA TGTTACTCAA CTCATATATT GCTATGTTAT
 TTTTACCTTA CTCATCAAAT TATCTTTTCT CTTATACATG GCTTTAATTA ATTGATTATT
 TTAGGTATTT CCATCTCTGG ACATTTCATG TACTGAAAAT AGATCAGATT TAAATAAAAT
 AGCTTTATAA TCAGTATTTA

  GeneView back to top
GeneView via analysis of contig annotation: PML promyelocytic leukemia
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_010194->NM_002675
svfunction
referenceNT_010194->NM_033238
svfunction
referenceNT_010194->NM_033239
svfunction
referenceNT_010194->NM_033240
svfunction
referenceNT_010194->NM_033244
svfunction
referenceNT_010194->NM_033246
svfunction
referenceNT_010194->NM_033247
svfunction
referenceNT_010194->NM_033249
svfunction
referenceNT_010194->NM_033250
svfunction
HuRefNW_001838218->NM_002675
svfunction
HuRefNW_001838218->NM_033238
svfunction
HuRefNW_001838218->NM_033239
svfunction
HuRefNW_001838218->NM_033240
svfunction
HuRefNW_001838218->NM_033244
svfunction
HuRefNW_001838218->NM_033246
svfunction
HuRefNW_001838218->NM_033247
svfunction
HuRefNW_001838218->NM_033249
svfunction
HuRefNW_001838218->NM_033250
svfunction
CeleraNW_925884->NM_033244
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010194->NM_002675->NP_00266645096284forwardintron
referenceNT_010194->NM_033238->NP_15024145096284forwardintron
referenceNT_010194->NM_033239->NP_15024245096284forwardintron
referenceNT_010194->NM_033240->NP_15024345096284forwardintron
referenceNT_010194->NM_033244->NP_15024745096284forwardintron
referenceNT_010194->NM_033246->NP_15024945096284forwardintron
referenceNT_010194->NM_033247->NP_15025045096284forwardintron
referenceNT_010194->NM_033249->NP_15025245096284forwardintron
referenceNT_010194->NM_033250->NP_15025345096284forwardintron
HuRefNW_001838218->NM_002675->NP_00266653213reverseintron
HuRefNW_001838218->NM_033238->NP_15024153213reverseintron
HuRefNW_001838218->NM_033239->NP_15024253213reverseintron
HuRefNW_001838218->NM_033240->NP_15024353213reverseintron
HuRefNW_001838218->NM_033244->NP_15024753213reverseintron
HuRefNW_001838218->NM_033246->NP_15024953213reverseintron
HuRefNW_001838218->NM_033247->NP_15025053213reverseintron
HuRefNW_001838218->NM_033249->NP_15025253213reverseintron
HuRefNW_001838218->NM_033250->NP_15025353213reverseintron
CeleraNW_925884->NM_033244->NP_15024730281104forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs8039584 maps exactly once on NCBI human chromosome 15
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
15NW_001838218.25321351137797minusGalt_assembly_8HuRefHuRefview200
15NW_925884.13028110451183287plusCalt_assembly_1CeleraCeleraview200
15NT_010194.164509628472093019plusCref_assemblyreferencereferenceview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010194
dbSNP Blast Analysis
GenBank HTGS Finished:
AC013486.12 AC108137.8 NC_000015.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
HWPC
T
ss12338516HapMap-CEUEuropean 120IG 0.900 0.100 0.752 0.950 0.050
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 118IG 0.814 0.186 0.439 0.907 0.093

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.078+/-0.18127021000

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

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Revised: May 25, 2006 1:38 PM .