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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs17005979          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_173650.1:c.11T>G
NP_775921.1:p.Val4Gly
NT_022184.14:g.6315540T>G
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 ss48413007 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17005979 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
ss23191641PERLEGEN|afd1241906fwd/BG/Tcttctcctctggctcagatcatgtctactggaaggaagcagcacaccggctgtccaaaag08/10/0408/20/04123Genomicunknown
ss48413007APPLERA_GI|hCV25652450byFreqrev/TA/Ccttttggacagccggtgtgctgcttccttccagtagacatgatctgagccagaggagaag09/28/0511/03/06126Genomicunknown
ss68807501PERLEGEN|PGP01241906byFreqfwd/BG/Tcttctcctctggctcagatcatgtctactggaaggaagcagcacaccggctgtccaaaag01/30/0703/31/08127Genomicunknown
ss74868815ILLUMINA|ILMN_Human_1M_rs17005979fwd/BG/Tcttctcctctggctcagatcatgtctactggaaggaagcagcacaccggctgtccaaaag08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17005979|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=129
 CCTGCTTACA ACACCTCTAG GATGTGGGAT ATCTAGAGGT CTGTGTAGCT GGAGGATGCT
 GGGAAATGTG AGGAGAAGAT GTTTCCTCCT TAAAATTGGA ATCTTTCTGA TCACCTGAAT
 TCTCCTGCTA GCCACAAATC CCACTCACTC TTATCTTATC CTTGTCCTTC TGTCATCGTT
 TACCTGCCTA ATCCCTGAAG GTAGTGAGTT TCCTGTCACT GGAAGTGCAC TTCTCGGTAC
 CCTTACTTGT AGAAGTTCTC ACAGATGCTG CTTCTCCTCT GGCTCAGATC ATGTCTACTG
 K
 GAAGGAAGCA GCACACCGGC TGTCCAAAAG TGAGATGAGC CTCTATGCAG TGCTGGATCT
 TAAGAAGGGC GCCTCACCTG AAGACTTCAA AAAATCCTAC AGGTTCAGAC CTCAGCCCTT
 TATTGATCCT TGGAATTTCC CCCTTAAACC TTTTTCTTTC TGTATCTCTT TTGCTATCTG
 ACTCTTTTTT TTTTTTTTTT TTTTTGAGAG GAAGTCTCGT CCTGTCACAG AGCAGAGACA
 GAGACTATTG AGAGTGCAGT GGCACGATCT TGGCTTACTG CAACCTCTGC CTCCCAGGTT

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NC_000002.9
dbSNP Blast Analysis
UniGene Cluster ID
116303

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source G/T
 T/T
 HWP G
 T
ss23191641 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.043 0.957 1.000 0.022 0.978
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
ss48413007 HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 90 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.067 0.933 1.000 0.033 0.967
AGI_ASP population multiple 74 IG 0.027 0.973 1.000 0.014 0.986
ss68807501 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.067 0.933 0.033 0.967

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.019+/-0.095 872 688 15 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .