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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs8108278          
refSNP ID: rs8108278
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_001040134.1:c.503-4084C>T
NM_002579.2:c.634+1718C>T
NT_011255.14:g.682201C>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 ss12464406 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs8108278 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
ss12464406WI_SSAHASNP|chr19.NT_011255.13_682201fwd/BC/Tggagagaagccccatccccatcagctgtcattcctgtcccctccccagtcagcgtcactc07/04/0310/10/03116Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs8108278|allelePos=532|totalLen=1636|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=116
 CTGAGGGCTT TGGGAAGCCT TGGGTGCGTT GGGTCCTGAC GGTGCTGAGG TCTAATTTGG
 TTTTAAGGGC TCCTCCTAGA GGTCAAGAGG CAAACAGGCT GTGGGAGATG CCAGGGACCC
 CAGGAGGAGG AGGGAAGCTC CACACTGAAG CCCCACTCTC TCTCtttctt tttcttttta
 tttatttact ttctgaagaa agagtttcac tctgtcgccc ggcccgcagt gcagcgatgc
 catcacagct cactgcagcc tccagctcct gggctcaggc gatcctcctg cctcggcctc
 ccgaaatgct gagaccacag gcatgagtca ctgcacccgg cCTCTTTTTC Ttttatgaga
 tataattcgc agaccataaa attccgcctt AATGggaggc tcatctgggc ccgggacatt
 gaggctgcaa tgagctatga tggcacccct gcactccagc ctgggccaca gaccaagacc
 ctgtctcaaa aacaagaaag aggagagaaG CCCCATCCCC ATCAGCTGTC A
 Y
 TTCCTGTccc ctccccagtc agcgtcactc cctatcccct ccccagctct ggcacccacg
 catcccctcc tgtctctctg gattggcctg tcctggacat ttcatagaaa tgagatcaca
 cggccgggtg cggtggctca cacctgtaat cccggcactt tgggaggccg aggcgggtgg
 atcacctgag gtcaggagtt cgagaccagc ctggccaaca tggagaaccc ccgtctctgc
 taaaaataca aaaattagct ggacgtggtg gcggacgcct gtaatcccag atactttgga
 ggctgaagca ggagaatcac ttgaacccag gaggcggagg ttgcagtgag ccgagatcgc
 gccactgctc tccagcctgt gcgacaagag tgaaactctg tctcaaaaaa aaaaaaaaga
 aagaaaagag aataaatggg gtcacacact gcacgtggcc ttctgtgtct ggcgtctctc
 actgggcgtg acgtccccaa ggtgcatcgg cactgtggcc tgggtcggag cctgactcct
 tttcatggct gaatactatt ccacgggttg ggtgggccat ggtgggttta tcccttcttc
 catctgtaga cagttgggct gtttctaccc tttggctgca gtgagtagca tgctggggaa
 tttgtgtgca agtatttgtt cacgcccctg ctttcgaggc ctttgggtgt acacgtagga
 gtgaactgct gggtcctgag gcgactgtgt ggagctccgt gaggacctgc tgttttccac
 ggaggctgca ccgtcccgtt cccacaggtc gtggatgagg gcccagtttc tccacgtcct
 caccagcgct cgtagcccat tctcgtggct gtcctggtgg cgtgacgtgg ggtctccctg
 tggtttggat tCCCAAAGCC TTCTGTTCTC AGAGGCAGCT TGGCCTCTGC GGTGCCCCAG
 ATGCTGTCAG AGGGGTCCCC GCAGCCCAGC TCTGGAGTGG CTTTGGGGTG TGGCGTTGGT
 GGCATCTCAG CTCTAGCTCT CCCCAGCTGT GTGGCCCTGG GAAGTCCCCA TGCCTCGTCT
 TCCGGATGAG GTCCTCACCC CCAT

  GeneView back to top
GeneView via analysis of contig annotation: PALM paralemmin
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_011255->NM_001040134
svfunction
referenceNT_011255->NM_002579
svfunction
HuRefNW_001838476->NM_002579
svfunction
CeleraNW_927140->NM_001040134
svfunction
CeleraNW_927140->NM_002579
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011255->NM_001040134->NP_001035224682201forwardintron
referenceNT_011255->NM_002579->NP_002570682201forwardintron
HuRefNW_001838476->NM_002579->NP_002570501057forwardintron
CeleraNW_927140->NM_001040134->NP_00103522474168reverseintron
CeleraNW_927140->NM_002579->NP_00257074168reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs8108278 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
19NW_927140.17416874168minusGalt_assembly_1CeleraCeleraview531
19NW_001838476.1501057511858plusCalt_assembly_8HuRefHuRefview531
19NT_011255.14682201693201plusCref_assemblyreferencereferenceview531

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011255
dbSNP Blast Analysis
GenBank HTGS Finished:
AC004030.2 NC_000019.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
HWPC
ss12464406HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 84IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 110IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
27021000

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

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Revised: May 25, 2006 1:38 PM .