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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs4313          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:36/130
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_000789.2:c.1586+98G>C
NT_010783.14:g.20213028C>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 ss23142623 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4313 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
ss4702DEBNICK|dcp1-09222fwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag05/03/9912/23/0336Genomicunknown
ss16338631WIPGA|WI-50173byFreqfwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag12/12/0304/07/04120Genomicunknown
ss23142623PARC|ACE-008937byFreqfwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag05/07/0405/16/04126Genomicunknown
ss76875371CGM_KYOTO|717684fwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag09/12/0709/12/07129cDNAunknown
ss81154073HGSV|Cor18507_SNV_20070510.chr17_58914749fwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag11/26/0711/28/07130Genomicunknown
ss84149220PHARMGKB_PARC|PS206642_PA151793338_8937fwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag12/06/0712/10/07130Genomicunknown
ss86212067RSG_UW|ACE-008523fwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag12/12/0708/11/08129Genomicunknown
ss118097347ILLUMINA-UK|NA18507_000064292_NCBI36.1_chr17_58914749fwd/BC/Ttcctagctgcctcatccccagggcttgtcccatgctcctccagacctcaaaggcctggag01/20/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4313|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GCTAAATCCA TCTGTTTGCA ACCTCTAGGC CCTAAGACAA TTTAACCATC CTTTTCCAGA
 ACCAAGTATC AGGGGATCTG TCCTCCTGTT ACCCGAAACG AAACCCACTT TGATGCTGGA
 GCTAAGTTTC ATGTTCCAAA TGTGACACCA TACATCAGGT ATTAGCGCCC CCACCCCACC
 CACCCCCAGT ACTGTCACAC CCTCAATCCA CTTCTCCTCC TGTGATCCTA GCTGCCTCAT
 CCCCAGGGCT TGTCC
 Y
 CATGCTCCTC CAGACCTCAA AGGCCTGGAG TTAGAGTGGC CCACTCTCCT GAGCCTGTCT
 TGGGTCTCCC TTCTCCCCCA AGATAGCTTC TGGTCCAGCC TCTGCCCTGC AGGAAGCTGG
 ATGGTGCCTG GGTAAGGAAC CCCTGTTCCT GGCCCCCCAT GATCTTCCCT GACTCCCACC
 CTGTGCCTGC AGGTACTTTG TGAGTTTTGT CCTGCAGTTC CAGTTCCATG AAGCCCTGTG
 CAAGGAGGCA GGCTA

  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
NT_010783.14
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss16338631 POP-WIPGA-12-05-2003 multiple 64 IG 0.719 0.219 0.062 0.200 0.828 0.172
ss23142623 PARC-EUROPEAN-PANEL European 46 AF 0.913 0.087
ss84149220 PA151793339 92 AF 0.859 0.141
ss86212067 NEWTON_CHEH_CLINICAL_PANEL 556 AF 0.926 0.074

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.285+/-0.248 32 32 0 0

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

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Revised: May 25, 2006 1:38 PM .