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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2233896          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_003008.2:c.127C>A
NP_002999.1:p.Gln43Lys
NT_011362.9:g.8903315C>A
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 ss76897381 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2233896 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
ss3181385GENAISSANCE|GEN3068fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag07/19/0110/10/0398Genomicunknown
ss44225490ABI|hCV25618988byFreqfwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag07/18/0511/03/06126Genomicunknown
ss69242430PERLEGEN|PGP04769307byFreqfwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag01/30/0708/14/07127Genomicunknown
ss74818584AFFY|SNP_M-318014fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag08/09/0708/09/07128Genomicunknown
ss74868585ILLUMINA|ILMN_Human_1M_rs2233896fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag08/28/0708/29/07129Genomicunknown
ss76897381SI_EXO|NT_011362.9_8903315fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag09/20/0709/20/07129Genomicunknown
ss78724340HGSV|Cor18507_SNV_20070510.chr20_43283814fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag10/19/0710/20/07129Genomicunknown
ss86242230CORNELL|hCV2530128fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag01/21/0801/21/08129Genomicunknown
ss96245833HUMANGENOME_JCVI|1103643207533fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag03/25/0803/25/08130Genomicunknown
ss117555310ILLUMINA-UK|NA18507_000051814_NCBI36.1_chr20_43283814fwd/TA/Cccaagcggatcttcccaatttccacatggaaaaagggccagcactattttggacaaaaag01/19/0901/19/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2233896|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 CTCAGTTCTC AGACAAGATT TTTCAAGCAA GATGAAGTCC ATCATCCTCT TTGTCCTTTC
 CCTGCTCCTT ATCTTGGAGA AGCAAGCAGC TGTGATGGGA CAAAAAGGTG AGTGGAGAGG
 GTAAGCCTTG GGGAAAGCTA CTTTAAAAAA ATGGCCTCTA AGGATATTCA GGGTGCAAAC
 AGTAACCTGT TCAGGCACAG ATTCTTCTCC TTGATGAGAA TTGATTTTTC TCCACCCAAC
 GCTGTAGGCT TTTGGAAATA TCAGAAATTT GTTGGGAAAA GGTGGGAGGT AAGAGTTGCA
 AGAGAGCTTT GGAGATAATG AATGCATACA TTTCTATTAT CAATTACCAG GTGGATCAAA
 AGGCCAATTG CCAAGCGGAT CTTCCCAATT TCCACATGGA
 M
 AAAAGGGCCA GCACTATTTT GGACAAAAAG ACCAACAACA TACTAAATCC AAAGGCAGTT
 TTTCTATTCA ACACACATAT CATGTAGACA TCAATGATCA TGACTGGACC CGAAAAAGTC
 AGCAATATGA TTTGAATGCC CTACATAAGG CGACAAAATC AAAACAACAC CTAGGTGGAA
 GTCAACAACT GCTCAATTAT AAACAAGAAG GCAGAGACCA TGATAAATCA AAAGGTCATT
 TTCACATGAT AGTTATACAT CATAAAGGAG GCCAAGCTCA TCATGGGACA CAAAATCCTT
 CTCAAGATCA GGGGAATAGC CCATCTGGAA AGGGATTATC CAGTCAATGT TCAAACACAG
 AAAAAAGGCT ATGGGTTCAT GGACTAAGTA AAGAACAAGC

  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
Z47556.1 ABBA01052657
dbSNP Blast Analysis
UniGene Cluster ID
537218

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/C
 C/C
 HWP A
 C
ss44225490 HapMap-CEU European 120 IG 0.267 0.733 0.251 0.133 0.867
HapMap-HCB Asian 90 IG 0.022 0.978 1.000 0.011 0.989
HapMap-JPT Asian 90 IG 0.022 0.978 1.000 0.011 0.989
HapMap-YRI Sub-Saharan African 120 IG 0.133 0.867 0.584 0.067 0.933
ss69242430 HapMap-CEU European 120 GF 0.267 0.733 0.133 0.867
HapMap-HCB Asian 90 GF 0.022 0.978 0.011 0.989
HapMap-JPT Asian 90 GF 0.022 0.978 0.011 0.989
HapMap-YRI Sub-Saharan African 120 GF 0.133 0.867 0.067 0.933

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.116+/-0.211 1208 1002 270 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 .