Reference SNP(refSNP) Cluster Report: rs3801152

Reference SNP(refSNP) Cluster Report: rs3801152

refSNP ID: rs3801152
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001061.2:c.337-7270T>C
NM_030984.1:c.337-7270T>C
NT_007914.14:g.220272T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16336274 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3801152 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss4987537	YUSUKE\|IMS-JST159688	fwd/T	A/G	ttcatgaacacagtttagagaacatctcct	agggaagccctgttgactggacttcacccc	08/12/02	11/22/03	107	Genomic	unknown
ss12587629	RIKENSNPRC\|ssj0005737	rev/B	C/T	ggggtgaagtccagtcaacagggcttccct	aggagatgttctctaaactgtgttcatgaa	08/06/03	10/10/03	117	Genomic	unknown
ss16336274	PERLEGEN\|PS00539737	rev/B	C/T	ggggtgaagtccagtcaacagggcttccct	aggagatgttctctaaactgtgttcatgaa	11/25/03	04/07/04	123	Genomic	unknown
ss23536404	PERLEGEN\|afd0539737	rev/B	C/T	ggggtgaagtccagtcaacagggcttccct	aggagatgttctctaaactgtgttcatgaa	08/10/04	09/13/04	123	Genomic	unknown
ss65971337	AFFY\|SNP_A-1728051	rev/B	C/T	gaagtccagtcaacagggcttccct	aggagatgttctctaaactgtgttc	10/26/06	10/26/06	127	Genomic	unknown
ss75250124	ILLUMINA\|ILMN_Human_1M_rs3801152	fwd/T	A/G	ttcatgaacacagtttagagaacatctcct	agggaagccctgttgactggacttcacccc	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 TTCTCTTTCT CTGAAACTCT AGATCCCTCT CCAACCCCCT TTCTCCTTTG CCTGCTAACT
 CTTATTCACT TTCATGAACA CAGTTTAGAG AACATCTCCT
 R
 AGGGAAGCCC TGTTGACTGG ACTTCACCCC AAGGGCTTTG TGCAGATAAC AGCTTACTCC
 CATTTAAAAA AGATTTTTTA AAAAAGTGAT CCTTAGGAAC

GeneView

GeneView via analysis of contig annotation: TBXAS1 thromboxane A synthase 1 (platelet)

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_007914->NM_001061

function

reference

NT_007914->NM_030984

function

HuRef

NW_001839073->NM_001061

function

HuRef

NW_001839073->NM_030984

function

Celera

NW_923640->NM_001061

function

Celera

NW_923640->NM_030984

function

CRA_TCAGchr7v2

NT_079596->NM_001061

function

CRA_TCAGchr7v2

NT_079596->NM_030984

function

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


reference	NT_007914->NM_001061->NP_001052	220272	forward	intron

reference	NT_007914->NM_030984->NP_112246	220272	forward	intron

HuRef	NW_001839073->NM_001061->NP_001052	223340	forward	intron

HuRef	NW_001839073->NM_030984->NP_112246	223340	forward	intron

Celera	NW_923640->NM_001061->NP_001052	37109506	forward	intron

Celera	NW_923640->NM_030984->NP_112246	37109506	forward	intron

CRA_TCAGchr7v2	NT_079596->NM_001061->NP_001052	38993230	forward	intron

CRA_TCAGchr7v2	NT_079596->NM_030984->NP_112246	38993230	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3801152 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839073.1	223340	133922887	minus	T	alt_assembly_8	HuRef	HuRef	view	100
7	NW_923640.1	37109506	134350755	minus	T	alt_assembly_1	Celera	Celera	view	100
7	NT_079596.2	38993230	138957662	minus	T	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	100
7	NT_007914.14	220272	139275189	minus	T	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007798.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss16336274	AfAm	African American	12	IG	0.500	0.333	0.167	0.584	0.667	0.333

	Caucasian	European	24	IG	0.917	0.083		1.000	0.958	0.042

	Asian	Asian	12	IG	1.000				1.000

	CEPH	European	10	IG	0.800	0.200		1.000	0.900	0.100

	PDpanel	Global	48	IG	0.750	0.208	0.042	0.439	0.854	0.146

	HapMap-CEU	European	120	IG	0.983	0.017		1.000	0.992	0.008

	HapMap-HCB	Asian	90	IG	0.911	0.089		1.000	0.956	0.044

	HapMap-JPT	Asian	88	IG	0.841	0.136	0.023	0.150	0.909	0.091

	HapMap-YRI	Sub-Saharan African	120	IG	0.483	0.467	0.050	0.371	0.717	0.283

ss23536404	AFD_EUR_PANEL	European	48	IG	1.000				1.000

	AFD_AFR_PANEL	African American	46	IG	0.609	0.348	0.043	1.000	0.783	0.217

	AFD_CHN_PANEL	Asian	48	IG	0.833	0.167		0.752	0.917	0.083

ss4987537	JBIC-allele		1484	AF					0.921	0.079

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.198+/-0.244	379	306	15	0

Validation Summary:

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

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Revised: May 25, 2006 1:38 PM .