Reference SNP(refSNP) Cluster Report: rs833067

Reference SNP(refSNP) Cluster Report: rs833067

refSNP ID: rs833067
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001025366.1:c.606+940C>T
NM_001025367.1:c.606+940C>T
NM_001025368.1:c.606+940C>T
NM_001025369.1:c.606+940C>T
NM_001025370.1:c.606+940C>T
NM_001033756.1:c.606+940C>T
NM_003376.4:c.606+940C>T
NT_007592.14:g.34598239C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44753627 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs833067 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
ss1148469	KWOK\|OVLP-000804-448385	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	09/02/00	10/10/03	86	Genomic	99 %
ss1767521	KWOK\|OVLP-000925-161730	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	10/05/00	10/10/03	87	Genomic	99 %
ss2590299	SC_JCM\|AL136131.14_137973	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	11/03/00	10/10/03	89	Genomic	unknown
ss2765252	TSC-CSHL\|TSC0902637	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	01/02/01	04/07/04	92	Genomic	unknown
ss4986333	YUSUKE\|IMS-JST158331	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	08/12/02	10/10/03	108	Genomic	unknown
ss6497119	WI_SSAHASNP\|NT_007592.11_34537115	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	02/12/03	10/10/03	111	Genomic	unknown
ss12834708	SC_SNP\|NT_007592.13_34537116	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	10/21/03	11/17/03	119	Genomic	unknown
ss22508977	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007592.13_34537116	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	03/21/04	03/21/04	121	Genomic	unknown
ss44753627	ABI\|hCV8311624	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	07/19/05	08/14/07	126	Genomic	unknown
ss84152959	HGSV\|Cor19240_SNV_20070510.chr6_43847967	fwd/B	C/T	ttagcctggagagaagcccctgtcaccccg	ttattttcatttctctctgcggagaagatc	11/30/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 GCCGGGTGCG CGCGGCGCGG AGCCGATTAC ATCAGCCCGG GCCTGGCCGG CCGCGTGTTC
 CCGGAGCCTC GGCTGCCCGA ATGGGGAGCC CAGAGTGGCG AGCGGCACCC CTCCCCCCGC
 CAGCCCTCCG CGGGAAGGTG ACCTCTCGAG GTAGCCCCAG CCCGGGGATC CAGAGAACCA
 TCCCTACCCC TTCCTACTGT CTCCAGACCC TACCTCTGCC CAGTGCTAGG AGGAATTTCC
 TGACGCCCCT TCTCTTCACC CATTTCCTTT TTAGCCTGGA GAGAAGCCCC TGTCACCCCG
 Y
 TTATTTTCAT TTCTCTCTGC GGAGAAGATC CATCTAACCC CTTTCTGGCC CCAGAGTCCA
 GGGAAAGGAT GATCACTGTC AGAAGTCGTG GCGCGGGAGC CCACTGGGCG CTTTGTCACA
 TTCCACCGAA AGTCCCGACT TGGTGACAGT GTGCTTCCCT TCCCTCGCCA ACAGTTCCGA
 GTGAGCTGTG CTTTAGCTCT CGTGGGGGTG GGTCAAGGGA GGATTTGAAG AGTCATTGCC
 CCACTTTACC CTTTTGGAGA AATGGCTTGA AATTTGCTGT GACACGGGCA GCATGGGAAT

GeneView

GeneView via analysis of contig annotation: VEGFA vascular endothelial growth factor A

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_007592->NM_001025366

function

reference

NT_007592->NM_001025367

function

reference

NT_007592->NM_001025368

function

reference

NT_007592->NM_001025369

function

reference

NT_007592->NM_001025370

function

reference

NT_007592->NM_001033756

function

reference

NT_007592->NM_003376

function

HuRef

NW_001838981->NM_001025366

function

HuRef

NW_001838981->NM_001025367

function

HuRef

NW_001838981->NM_001025368

function

HuRef

NW_001838981->NM_001025369

function

HuRef

NW_001838981->NM_001025370

function

HuRef

NW_001838981->NM_001033756

function

HuRef

NW_001838981->NM_003376

function

Celera

NW_923073->NM_001025366

function

Celera

NW_923073->NM_001025367

function

Celera

NW_923073->NM_001025368

function

Celera

NW_923073->NM_001025369

function

Celera

NW_923073->NM_001025370

function

Celera

NW_923073->NM_001033756

function

Celera

NW_923073->NM_003376

function

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


reference	NT_007592->NM_001025366->NP_001020537	34598239	forward	intron

reference	NT_007592->NM_001025367->NP_001020538	34598239	forward	intron

reference	NT_007592->NM_001025368->NP_001020539	34598239	forward	intron

reference	NT_007592->NM_001025369->NP_001020540	34598239	forward	intron

reference	NT_007592->NM_001025370->NP_001020541	34598239	forward	intron

reference	NT_007592->NM_001033756->NP_001028928	34598239	forward	intron

reference	NT_007592->NM_003376->NP_003367	34598239	forward	intron

HuRef	NW_001838981->NM_001025366->NP_001020537	13807749	reverse	intron

HuRef	NW_001838981->NM_001025367->NP_001020538	13807749	reverse	intron

HuRef	NW_001838981->NM_001025368->NP_001020539	13807749	reverse	intron

HuRef	NW_001838981->NM_001025369->NP_001020540	13807749	reverse	intron

HuRef	NW_001838981->NM_001025370->NP_001020541	13807749	reverse	intron

HuRef	NW_001838981->NM_001033756->NP_001028928	13807749	reverse	intron

HuRef	NW_001838981->NM_003376->NP_003367	13807749	reverse	intron

Celera	NW_923073->NM_001025366->NP_001020537	16755934	forward	intron

Celera	NW_923073->NM_001025367->NP_001020538	16755934	forward	intron

Celera	NW_923073->NM_001025368->NP_001020539	16755934	forward	intron

Celera	NW_923073->NM_001025369->NP_001020540	16755934	forward	intron

Celera	NW_923073->NM_001025370->NP_001020541	16755934	forward	intron

Celera	NW_923073->NM_001033756->NP_001028928	16755934	forward	intron

Celera	NW_923073->NM_003376->NP_003367	16755934	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs833067 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838981.2	13807749	43460149	minus	A	alt_assembly_8	HuRef	HuRef	view	300
6	NT_007592.14	34598239	43847967	plus	C	ref_assembly	reference	reference	view	300
6	NW_923073.1	16755934	45291613	plus	T	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592 AL355349 AL355349.1 AL355349.2

dbSNP Blast Analysis
GenBank HTGS Finished:
AL136131.15 NC_000006.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss2765252	SC_12_A	Asian	24	IG		0.583	0.417	0.200	0.292	0.708

	SC_12_AA	African American	20	IG	0.200	0.300	0.500	0.294	0.350	0.650

	SC_12_C	European	12	IG	0.167	0.667	0.167	0.439	0.500	0.500

	WICGR8_asian_pooled		84	AF					0.390	0.610

	WICGR6_caucasian_pooled		96	AF					0.470	0.530

	CEPH		184	AF					0.560	0.440

ss44753627	7		65	AF					0.269	0.731

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.459+/-0.137	36	25	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .