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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6578597          
refSNP ID: rs6578597
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:A/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
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 ss88428172 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6578597 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
ss10664639BCM_SSAHASNP|chr11.NT_028310.10_406466byFreqfwd/TA/Ctggcagcaggatgacccacagcctgaagagagcagcagggcttacagcagctgcactggg06/29/0310/25/06116Genomicunknown
ss12136202WI_SSAHASNP|chr11.NT_028310.10_406466fwd/TA/Ctggcagcaggatgacccacagcctgaagagagcagcagggcttacagcagctgcactggg07/04/0310/10/03116Genomicunknown
ss84022715HGSV|Cor18956_SNV_20070510.chr11_1599460fwd/TA/Ctggcagcaggatgacccacagcctgaagagagcagcagggcttacagcagctgcactggg11/30/0712/06/07130Genomicunknown
ss85698400HGSV|Cor19129_SNV_20070510.chr11_1599460fwd/TA/Ctggcagcaggatgacccacagcctgaagagagcagcagggcttacagcagctgcactggg12/06/0712/10/07130Genomicunknown
ss88428172BCMHGSC_JDW|JWB-0362953fwd/TA/Ctggcagcaggatgacccacagcctgaagagagcagcagggcttacagcagctgcactggg02/26/0802/27/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6578597|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 GCCTCAGATC TTACACTGGC AGCACACAGG GACACAGCAA CTAGACTGGG AGCAGCAGGG
 ATTGCAGCAA CTGGACTGGC AGCAGGATGA CCCACAACCT GAGGAGGAGC AGCAGGGCTT
 ACAGCAGCTG GACTGGCAGC AGTAGGGCTT GCAGCAGCTG GACTGGCAGC AGGATGACCC
 ACAACCTGAG GAGGAGCAGC AGGGCTTACA GCAGCTGGAC TGGCAGCAGG ATGACCCACA
 GCCTGAAGAG
 M
 AGCAGCAGGG CTTACAGCAG CTGCACTGGG AGCAGCCACA AGAGCCACAG CCTCCTTTGG
 AGCCCCCACA GGAGCCACAG CCCCCCTTGG AACCCCCACA GGAGCCACAG CCCCCCTTGG
 AGCCCCCACA GGAGCCACAG CCCCCCTTGG AACCCCCACA GGAGACACAG CCCCCCTTGG
 AACCCCCACA AGAGCCATAG CCCCCCTTGG AGCCCCCACA GGAGCCACAG CTGGAGCAGG
 AACAGGCTGG

  GeneView back to top
GeneView via analysis of contig annotation: KRTAP5-4 keratin associated protein 5-4
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
CeleraNW_924962->NM_001012709
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
CeleraNW_924962->NM_001012709->NP_0010127271260059reverse665missenseTPhe [F]2207
contig referenceGCys [C]2207

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6578597 maps exactly once on NCBI human chromosome 11
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
11NW_001838017.14298511435980plusCalt_assembly_8HuRefHuRefview200
11NT_009237.174301251599460plusAref_assemblyreferencereferenceview200
11NW_924962.112600591680303plusCalt_assembly_1CeleraCeleraview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_028310
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank HTGS Finished:GenBank mRNA:
NM_001012709.1 AP006285.2 AB126073.1
UniGene Cluster ID
539087

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/C
C/C
HWPA
C
ss10664639HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 90IG 0.022 0.978 1.000 0.011 0.989
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 0.383 0.617 0.100 0.192 0.808

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.108+/-0.20627021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .