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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs11639642          
refSNP ID: rs11639642
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_018032.3:c.366+529A>G
NM_201412.1:c.366+529A>G
NT_037887.4:g.197549T>C
Links

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 ss16695530 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11639642 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
ss16695530CSHL-HAPMAP|CSHL-HuAA-200402.chr16.NT_037887.3_197549fwd/BC/Tgaagaatatattaaaattaaaaaataatgaaaaccatgtacagaggacgaaaatggagag02/17/0403/04/04120Genomicunknown
ss21302891SSAHASNP|WGSA-200403-chr16.chr16.NT_037887.3_197549fwd/BC/Tgaagaatatattaaaattaaaaaataatgaaaaccatgtacagaggacgaaaatggagag03/19/0403/19/04121Genomicunknown
ss40674044ABI|hCV1838379fwd/BC/Tgaagaatatattaaaattaaaaaataatgaaaaccatgtacagaggacgaaaatggagag07/17/0507/17/05126Genomicunknown
ss74871087ILLUMINA|ILMN_Human_1M_rs11639642fwd/BC/Tgaagaatatattaaaattaaaaaataatgaaaaccatgtacagaggacgaaaatggagag08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11639642|allelePos=501|totalLen=991|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 attagctggg cgtggtggtg ggcacctgta gtcccagcta ctcaggaggc tgaggcagga
 gaatggcgta aacccaggag gcggagcttg cagtgagtcg agatcacgcc actgccctcc
 agcctgggcg acagaacaag actctgtctc ttaaaaaaaa aaaaaaaCCG ACAATAAttt
 ttttttcttt tgaggcaggg tctcactctg ttatccaggc tgaagcaaag tagcatgatc
 acagctcatt gaagcctcaa tctccccaag ctcaagtgat cctcccacct cagcctcctg
 agtaactggg atacacatgt gcaccaccaa gcctggctaa tatatgtatt ttttgtagag
 atggggtttc ttcatgttgc tcaggtctaa aactcctggg ctcaagcagt ctgcccccac
 cttggtgtcc caaagtgctg ggactacaag cataagccac cAAACTCAGC GAAGaatata
 ttaaaattaa aaaataatGA
 Y
 AAACCATGTA CAGAGGACGA AAATGGAGAG AATAAAAAGA CAGAGGTAGC AGCTCCTGAG
 GGATGAGAAT TCCATGACAC ATGAATGCTT GATCACAGCC CTCTATCCTT AACTGGAGTA
 AGGCAGAGAG TACTGTCCAC ACAATCAGTG CTGAGGGTCA GTTAATAGCT ATTGACAACg
 ccgggcgcgg tggctcacgc ctgtaatccc agcactttgg gaggctgagg caggcagatc
 acgaggtcag gagatcaaga ccataccggc taacacggtg aaaccccgtc tctactaaaa
 atacaaaaaa ttagccgggc atggtggcgg gcgtctgcag tcccagctac tcgggaggct
 gaggcaggag aatggcatga acccgggagg cggagcttgc actgagctga gatcatgcca
 ctgcactcca gcctgggtga cagagggaga ctccatctca aaaaaaaaaG CTATTGACAA
 GCCAGTATTT

  GeneView back to top
GeneView via analysis of contig annotation: LUC7L LUC7-like (S. cerevisiae)
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_037887->NM_018032
svfunction
referenceNT_037887->NM_201412
svfunction
HuRefNW_001838339->NM_018032
svfunction
HuRefNW_001838339->NM_201412
svfunction
CeleraNW_926018->NM_018032
svfunction
CeleraNW_926018->NM_201412
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_037887->NM_018032->NP_060502197549reverseintron
referenceNT_037887->NM_201412->NP_958815197549reverseintron
HuRefNW_001838339->NM_018032->NP_0605022448905forwardintron
HuRefNW_001838339->NM_201412->NP_9588152448905forwardintron
CeleraNW_926018->NM_018032->NP_060502172088reverseintron
CeleraNW_926018->NM_201412->NP_958815172088reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs11639642 maps exactly once on NCBI human chromosome 16
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
16NW_001838339.22448905175112minusAalt_assembly_8HuRefHuRefview500
16NT_037887.4197549197549plusTref_assemblyreferencereferenceview500
16NW_926018.1172088456438plusTalt_assembly_1CeleraCeleraview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_037887
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
NC_000016.8 Z69890.1 AC069076.3

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .