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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs311075          
refSNP ID: rs311075
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:Not available
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 ss1583714 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs311075 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
ss399522KWOK|OVLP-000621-241484fwd/TA/Ggcttatgtctcagtcatagtcccattcaactcaagaagtggagaagggctgggcacggtg06/30/0010/10/0379Genomic99 %
ss875857KWOK|OVLP-000804-28047fwd/TA/Ggcttatgtctcagtcatagtcccattcaactcaagaagtggagaagggctgggcacggtg09/01/0010/10/0386Genomic99 %
ss1583714KWOK|OVLP-000925-181807byFreqfwd/TA/Ggcttatgtctcagtcatagtcccattcaactcaagaagtggagaagggctgggcacggtg10/04/0008/14/0787Genomic99 %
ss2513634SC_JCM|AC023670.4_61066fwd/TA/Ggcttatgtctcagtcatagtcccattcaactcaagaagtggagaagggctgggcacggtg11/03/0010/10/0389Genomicunknown
ss66232247AFFY|SNP_A-4261576rev/BC/Tcttctccacttcttgagttgaatgggactatg10/27/0610/28/06127Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs311075|allelePos=201|totalLen=703|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=127
 TCAGAGGGGG CAGCCTAGGC AGAGGCCTGA CGGGGCCAAA AGTGTGTTTC ATATGAGAAA
 TGTGAACAGC CTTTCAGCCA TCAATCCGGT GTCTCTCCTT CTCATGCATA GATCTCGGGC
 TCTGAAAAGG GCAGTTTTTC TCCTAACTTT GCCATTCTCC TGCCTTCCTG GCTTATGTCT
 CAGTCATAGT CCCATTCAAC
 R
 TCAAGAAGTG GAGAAGggct gggcacggtg gctcaagcct gtcatcccag cactttggga
 ggacgaggtg ggtggatcac ctgaggtcag gagttcgaga ccaacctggc caacgtggtg
 aaaccccatc tctgctaaaa atacaaaaaa ttagccggga gtgatggcat gcacctgtaa
 gcccagctac tcgggaggct gaggcaggag aatcgcttga acccaggagg cagaggttgt
 ggtgaacgga gaccacacca ttgcactcca gcttgggtaa cagagcaaga cttggtctca
 aaaaaaaaaa aaaaagaaGT GGAGAAGGGG CTCCTGGTCT CTGTGGAAAC CATGGCCGGT
 AGCAGCCTCT GTGTCTGTCT TCTGGGCTCA AGAGTCGTTG TATAAACCTC AGCTCGGTGT
 GGGCAGGTGA GAAAAAACAA TGCTAAAAAC ATTCTCCGAC TGTTTCCAAG AAAATGAAAC
 ATCCTTAACC ACAAAAGAGT TG

  GeneView back to top
GeneView via analysis of contig annotation: CD99 CD99 molecule
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
HuRefNW_001842356->NM_002414
function
CeleraNW_927700->NM_002414
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
HuRefNW_001842356->NM_002414->NP_002405576983forwardintron
CeleraNW_927700->NM_002414->NP_0024051313800forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer: rs311075 was not linked to the human genome 36.3 because it aligned to more than 2 locations on the genome.
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
XNW_001842356.1576983576983plusGalt_assembly_8HuRefHuRefview200
XNT_011757.155168512645089plusGref_assemblyreferencereferenceview200
XNW_927700.113138006915518plusGalt_assembly_1CeleraCeleraview200
YNT_113973.15168512645089plusGref_parreferencePARview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AC023670 AC006209 AC023670.4
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss1583714HapMap-CEUEuropean 90IG 0.500 1.000
HapMap-HCBAsian 68IG 0.511 1.000
HapMap-JPTAsian 66IG 0.500 1.000
HapMap-YRISub-Saharan African 97IG 0.067 0.267 0.283 0.527 0.289 0.711

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.191+/-0.2430000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .