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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs312887          
refSNP ID: rs312887
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:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_006640.3:c.23-35417T>C
NT_010641.15:g.9288996T>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 ss44008586 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs312887 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
ss401543KWOK|OVLP-000621-246926fwd/BC/Tgcagcccctgaccaccaccatccctgccccgccacttgctcccagggttccatcaggttg06/30/0010/10/0379Genomic99 %
ss585995SC_JCM|AC012118.2_125910byFreqfwd/BC/Tgcagcccctgaccaccaccatccctgccccgccacttgctcccagggttccatcaggttg07/12/0005/16/0480Genomicunknown
ss884413KWOK|OVLP-000804-69839fwd/BC/Tgcagcccctgaccaccaccatccctgccccgccacttgctcccagggttccatcaggttg09/01/0010/10/0386Genomic99 %
ss1915233KWOK|OVLP-000925-543487fwd/BC/Tgcagcccctgaccaccaccatccctgccccgccacttgctcccagggttccatcaggttg10/06/0010/10/0387Genomic99 %
ss3699735SC_JCM|AC023287.8_161505rev/TA/Gcaacctgatggaaccctgggagcaagtggcggggcagggatggtggtggtcaggggctgc09/24/0110/10/03100Genomicunknown
ss19363390CSHL-HAPMAP|CSHL-HuDD-200402.chr17.NT_010641.14_9254885fwd/BC/Tgcagcccctgaccaccaccatccctgccccgccacttgctcccagggttccatcaggttg02/20/0403/04/04120Genomicunknown
ss21415954SSAHASNP|WGSA-200403-chr17.chr17.NT_010641.14_9254885fwd/BC/Tgcagcccctgaccaccaccatccctgccccgccacttgctcccagggttccatcaggttg03/19/0403/20/04123Genomicunknown
ss44008586ABI|hCV958255fwd/BC/Tgcagcccctgaccaccaccatccctgccccgccacttgctcccagggttccatcaggttg07/18/0507/18/05126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs312887|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GGAACAGGAG TAGGAGGAAC GCTCTGGTCA TGGGACTGTG TGAAGAGAGA AGGATCAGGA
 AGAAAACATG AGCTATCATG TCTGGGTTAT ACCTCAGCAG AGCCGCTGGT GGCCTCCCAG
 GCATCTGAAT TTACTAATCA CAAAGCTCAC CAGGTGTGCA AATAAACAAA TGCTGTTCAG
 GAGGCACAGC CAGGGTTCTG CTGGAGAGGG ATCATCTTGG AGGGGTCATA CTTTCCACCC
 AGTCCTTCAG TCCTTCTGTC CTGTGTGTGT GCAGCCCCTG ACCACCACCA TCCCTGCCCC
 Y
 GCCACTTGCT CCCAGGGTTC CATCAGGTTG GATGTTATTG CAATAAAATG TAGCAACAGA
 AGGTCCAGGC AGTGCTGCAG TCCCTGGTGG TATCATCAGA GCCAGCAGGC AGCAGGGCTG
 GGGAACTCCA AGCTGATTCA GTCCCAAGTG CCGGAGCGGG GAGCTCGGAT GAGGTGGGGG
 TGGGGAACCG GGGAGCCATG GAGCAGAGCA TTTGCTGTGC TGAAGGCCAG GAGCCTCCTT
 GGGAGATCAT GAATTTAGAA CACTAATACT TTGTTTAAAA AGTCCCCTGC CTTGGAGATA

  GeneView back to top
GeneView via analysis of contig annotation: SEPT9 septin 9
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
referenceNT_010641->NM_006640
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010641->NM_006640->NP_0066319288996forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs312887 maps exactly once on NCBI human chromosome 17
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
17NW_001838454.211787770789345minusGalt_assembly_8HuRefHuRefview300
17NW_926918.11246389971958498plusCalt_assembly_1CeleraCeleraview300
17NT_010641.15928899672874319plusTref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010641 AC012118 AC023287 AC023287.4
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceHWPC
T
ss585995CEPH 184AF 0.730 0.270

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.394+/-0.2040000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hit
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .