Reference SNP(refSNP) Cluster Report: rs10306118

Reference SNP(refSNP) Cluster Report: rs10306118

refSNP ID: rs10306118
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_000962.2:c.94+690G>T
NM_080591.1:c.94+690G>T
NT_008470.18:g.32455446G>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14327260 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10306118 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss14327260	PGA-UW-FHCRC\|PTGS1-002937		fwd/B	G/T	cagaaagctgcttctacccacaatggaccc	gagccactctgggtttcatgggggaggttg	11/07/03	10/25/06	119	Genomic			unknown

Fasta sequence (Legend)

 CAGTGGAGAA GGTCTCCCCT GGTGAAGACT TCGGGAGAAC ATGGGAGATG GAAATACATT
 TAGGAGCCGG GATGCTTCAT CTGGGGTTTA AGAGATCCCC ATTGAGCAAA TGAGGAAACC
 GAGGCTCAGT AGGTGCCATG ATTCCCCAAG CTCACAAAAT ACATGGTGGG CCCAGGATCT
 GAACTCAGGT CTGTCTGCGT CCACACACTT CGCAAGGTCT TTCCACAGAA AGCTGCTTCT
 ACCCACAATG GACCC
 K
 GAGCCACTCT GGGTTTCATG GGGGAGGTTG ATGGGGAAAT TCCGCCCTTC CCTCCCCCAT
 GCATGTGCCA GGTTCCAGGT GAAGGAATTC AGCTCCTCGC TCAGCCAACC TTCCTCCCCC
 AGCTCGCTGC TTGTGTGTGT GCGTGTGTGT GAGCATGTGT CCCAGTTGGA TATAGTTTCC
 TCCACCACCT AGCTGTGTAA AATCTCTAAA ATGAGGCCCA GAGAGGGCAG GAGGGAGCAG
 AGGGAGTCCG CACTT

GeneView

GeneView via analysis of contig annotation: PTGS1 prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_008470->NM_000962

function

reference

NT_008470->NM_080591

function

HuRef

NW_001839239->NM_000962

function

HuRef

NW_001839239->NM_080591

function

Celera

NW_924573->NM_000962

function

Celera

NW_924573->NM_080591

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_008470->NM_000962->NP_000953	32455446	forward	intron

reference	NT_008470->NM_080591->NP_542158	32455446	forward	intron

HuRef	NW_001839239->NM_000962->NP_000953	476272	forward	intron

HuRef	NW_001839239->NM_080591->NP_542158	476272	forward	intron

Celera	NW_924573->NM_000962->NP_000953	9270392	forward	intron

Celera	NW_924573->NM_080591->NP_542158	9270392	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10306118 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839239.1	476272	94748964	plus	G	alt_assembly_8	HuRef	HuRef	view	255
9	NW_924573.1	9270392	95782561	plus	G	alt_assembly_1	Celera	Celera	view	255
9	NT_008470.18	32455446	124174062	plus	G	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY449688

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL162424.20 NC_000009.10	AL353767.14

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss14327260	PGA-AFRICAN-PANEL	African American	46	IG	0.696	0.261	0.043	0.752	0.826	0.174

	PGA-EUROPEAN-PANEL	European	46	IG	1.000				1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.159+/-0.233	47	26	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .