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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs4332          
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.2218-66T>C
NM_152830.1:c.496-66T>C
NT_010783.14:g.20216292T>C
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 ss23142644 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4332 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
ss4721DEBNICK|dcp1-12486fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa05/03/9912/23/0336Genomicunknown
ss2990976YUSUKE|IMS-JST003566fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa05/24/0110/10/0396Genomicunknown
ss4915976WIPGA|WI-27762fwd/BC/Tccccacctgccagcccatggggctngggggagtgcaggccccagagagaccaagtgcaaa07/12/0210/10/03108cDNAunknown
ss10865082BCM_SSAHASNP|chr17.NT_010783.13_16856213fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa06/30/0310/10/03116Genomicunknown
ss22886488IMCJ-GDT|IMCJ-ACE_6-ctbyFreqfwd/BC/Tccccacctgccagcccatggggcnngggggagtgcaggccccagagagaccaagtgcaaa03/22/0410/26/06123Genomicunknown
ss23142644PARC|ACE-012202byFreqfwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa05/07/0405/16/04126Genomicunknown
ss76866564CGM_KYOTO|7874fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa09/12/0709/12/07129cDNAunknown
ss80769984HGSV|Cor18507_SNV_20070510.chr17_58918013fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa11/26/0711/26/07130Genomicunknown
ss84149371PHARMGKB_PARC|PS206642_PA151795316_12202fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa12/06/0712/10/07130Genomicunknown
ss86212083RSG_UW|ACE-011788fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa12/12/0708/11/08129Genomicunknown
ss90634019BCMHGSC_JDW|JWB-1038651fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa02/26/0802/29/08129Genomicunknown
ss95210620CNG|17444962fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa03/13/0803/13/08129Genomicunknown
ss1098559031000GENOMES|CEU.trio.12.15.2008_3421261_chr17_58918013fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa12/15/0812/16/08130Genomicunknown
ss118097370ILLUMINA-UK|NA18507_000064303_NCBI36.1_chr17_58918013fwd/BC/Tccccacctgccagcccatggggcctgggggagtgcaggccccagagagaccaagtgcaaa01/20/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4332|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AAGGTTCAGG ACCTAGAACG GGCAGCACTG CCTGCCCAGG AGCTGGAGGA GGTGTGTGGC
 TCGCAAGGTA CAGGGAGAGG GGAATCCTGG GGCAGTGAGC CCAACACAGG GTCTGGCCTG
 GCCTTCACGC TGCTTCCTCT TCCTCGTTGT ATCAAGTCAT GGCATCTGCC ATGCGATGTG
 CACCTCAGAA CTGCTGAGAG GGCAGCGCTC CCCAGCTCCC TGGCTCCCCA CCTGCCAGCC
 CATGGGGCCT GGGGG
 Y
 AGTGCAGGCC CCAGAGAGAC CAAGTGCAAA GGAGTACAGC TCATTGCCTC TCCTTCCTCC
 TGCAGTACAA CAAGATCCTG TTGGATATGG AAACCACCTA CAGCGTGGCC ACTGTGTGCC
 ACCCGAATGG CAGCTGCCTG CAGCTCGAGC CAGGTGAGAG CTCATGTGCA GGCTGAGTGA
 GAGGCGAGGG CTGGGACTGG CATGGGGCCC GGGGGTGCTG GGTGAGAGCA CAGAGTTGGG
 TTCCCCTCGC TCTTG

  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 AscertainmentGenotypesAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source HWP C
 T
ss22886488 IMCJ-JP2 92 AF 0.696 0.304
IMCJ-AA1 198 AF 0.414 0.586
IMCJ-CA1 196 AF 0.495 0.505
IMCJ-JP1 128 AF 0.672 0.328
ss23142644 PARC-EUROPEAN-PANEL European 44 AF 0.386 0.614
ss84149371 PA151795317 88 AF 0.398 0.602
ss86212083 NEWTON_CHEH_CLINICAL_PANEL 510 AF 0.435 0.565

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.499+/-0.020 0 0 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
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN YES YES

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Revised: May 25, 2006 1:38 PM .