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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2233903          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/130
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_003008.2:c.835C>T
NP_002999.1:p.His279Tyr
NT_011362.9:g.8904023C>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 ss117555316 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2233903 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
ss3181392GENAISSANCE|GEN3075byFreqfwd/BC/Tcagacaaaaaatctcagtcaagatcaagagatggccggaaggcacataaaatatcatacc07/19/0110/25/0698Genomicunknown
ss69242433PERLEGEN|PGP04778029byFreqfwd/BC/Tcagacaaaaaatctcagtcaagatcaagagatggccggaaggcacataaaatatcatacc01/30/0708/14/07127Genomicunknown
ss74818033AFFY|SNP_M-316646fwd/BC/Tcagacaaaaaatctcagtcaagatcaagagatggccggaaggcacataaaatatcatacc08/09/0708/09/07128Genomicunknown
ss74857844ILLUMINA|ILMN_Human_1M_rs2233903fwd/BC/Tcagacaaaaaatctcagtcaagatcaagagatggccggaaggcacataaaatatcatacc08/28/0708/29/07129Genomicunknown
ss76738987AFFY|AFFY_6_1M_SNP_A-8600311fwd/BC/Tcagtcaagatcaagagatggccggaaggcaca08/28/0708/30/07129Genomicunknown
ss86239537CORNELL|hCV15947264fwd/BC/Tcagacaaaaaatctcagtcaagatcaagagatggccggaaggcacataaaatatcatacc01/21/0801/21/08129Genomicunknown
ss104866886KRIBB_YJKIM|KHS1259204fwd/BC/Tcagacaaaaaatctcagtcaagatcaagagatggccggaaggcacataaaatatcatacc07/10/0807/10/08130Genomicunknown
ss117555316ILLUMINA-UK|NA18507_000051817_NCBI36.1_chr20_43284522fwd/BC/Tcagacaaaaaatctcagtcaagatcaagagatggccggaaggcacataaaatatcatacc01/19/0901/19/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2233903|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TCTCCAAACT GAAGAACTAG TAGTTAACAA ACAACAACGT GAGACTAAAA ATTCTCATCA
 AAATAAAGGG CATTACCAAA ATGTGGTTGA CGTGAGAGAG GAACATTCAA GTAAACTACA
 AACTTCACTC CATCCTGCAC ATCAAGACAG ACTCCAACAT GGACCCAAAG ACATTTTTAC
 TACCCAAGAT GAGCTCCTAG TATATAACAA GAATCAACAC CAGACAAAAA ATCTCAGTCA
 AGATCAAGAG
 Y
 ATGGCCGGAA GGCACATAAA ATATCATACC CGTCTTCACG TACAGAAGAA AGACAACTTC
 ACCATGGAGA AAAGAGTGTA CAGAAAGATG TATCCAAAGG CAGCATTTCT ATCCAAACTG
 AAGAGAAAAT ACATGGCAAG TCTCAAAACC AGGTAACAAT TCATAGTCAA GATCAAGAGC
 ATGGCCATAA GGAAAATAAA ATATCATACC AATCTTCAAG TACAGAAGAA AGACATCTCA
 ACTGTGGAGA

  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
dbSNP Blast Analysis
UniGene Cluster ID
537218

  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
ss3181392 HapMap-CEU European 120 IG 0.950 0.050 1.000 0.975 0.025
HapMap-HCB Asian 90 IG 0.867 0.133 0.655 0.933 0.067
HapMap-JPT Asian 88 IG 0.932 0.068 1.000 0.966 0.034
HapMap-YRI Sub-Saharan African 120 IG 0.750 0.250 0.273 0.875 0.125
ss69242433 HapMap-CEU European 120 GF 0.950 0.050 0.975 0.025
HapMap-HCB Asian 90 GF 0.867 0.133 0.933 0.067
HapMap-JPT Asian 90 GF 0.911 0.067 0.022 0.944 0.056
HapMap-YRI Sub-Saharan African 120 GF 0.750 0.250 0.875 0.125

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.125+/-0.216 1207 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 .