Reference SNP(refSNP) Cluster Report: rs304006

Reference SNP(refSNP) Cluster Report: rs304006

refSNP ID: rs304006
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:	A
Clinical Association:	unknown

HGVS Names
NM_001099952.1:c.163+22771G>A
NM_002222.4:c.163+22771G>A
NT_022517.17:g.4525549G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16986888 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs304006 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
ss391783	KWOK\|OVLP-000621-221047	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	06/30/00	10/10/03	79	Genomic	99 %
ss579826	SC_JCM\|AC024168.2_185022	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	07/12/00	10/10/03	80	Genomic	unknown
ss975221	KWOK\|OVLP-000804-545633	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	09/01/00	10/10/03	86	Genomic	99 %
ss16986888	CSHL-HAPMAP\|CSHL-HuAA-200402.chr3.NT_022517.16_4525549	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	02/17/04	04/07/04	120	Genomic	unknown
ss22002712	SSAHASNP\|WGSA-200403-chr3.chr3.NT_022517.16_4525549	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	03/20/04	03/20/04	121	Genomic	unknown
ss66558802	ILLUMINA\|HumanHap300v1.1_rs304006	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	11/09/06	11/09/06	127	Genomic	unknown
ss67288899	ILLUMINA\|HumanHap550v1.1_rs304006	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	11/14/06	11/14/06	127	Genomic	unknown
ss67692188	ILLUMINA\|HumanHap650Yv1.0_rs304006	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	11/14/06	11/14/06	127	Genomic	unknown
ss70767472	ILLUMINA\|HumanHap550v3.0__rs304006	rev/B	C/T	caaaaagacacgattttgagactttcacta	ataagatattgcctatctctggatttctaa	04/20/07	03/30/08	130	Genomic	unknown
ss71342305	ILLUMINA\|HumanHap650Yv3.0_rs304006	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	04/23/07	04/23/07	127	Genomic	unknown
ss75553539	ILLUMINA\|ILMN_Human_1M_rs304006	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	08/28/07	08/29/07	129	Genomic	unknown
ss78966808	HGSV\|Cor18507_SNV_20070510.chr3_4560549	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	10/19/07	10/21/07	129	Genomic	unknown
ss79157451	ILLUMINA\|HumanHap300v2.0_rs304006	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	04/18/07	11/18/07	130	Genomic	unknown
ss83420080	KRIBB_YJKIM\|KHS457392	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	12/04/07	12/05/07	130	Genomic	unknown
ss91977276	BCMHGSC_JDW\|JWB-1549233	fwd/T	A/G	ttagaaatccagagataggcaatatcttat	tagtgaaagtctcaaaatcgtgtctttttg	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGGACTTGGA TTACCTGTGT TAACATGGAA GCTCCCAAGA AAACCATTTA GGCTAGACTC
 AGTTCCAaaa acaaatcaaa acaaaacaaa acaaaaacaa aaacaaaaca GGTAATAAAT
 ATACAGTCCA GGTATCCACT GTGATGGTAA TCAAGGGATA AAGAATGATA TTTgttcaag
 tgatcctctt gcctcagcct cctgagtagc tggggctata ggcacgtgcc accacgcctg
 gctaattttt gtatttttag tagagatggg gtttcaccct gttggccagg ctggtcttga
 actcctgatc tcaagtgatc tgcccacctc ggcctcccaa agtgctggga ttacaggtgt
 gagccaccat gcctggccGT ATTTAAgtct gttaggaatg attttgactg caagtaagag
 agaaaatcca cctaatagtg gcttaaaaca taagggcatt tgttgtttcc ttagaaatcc
 agagataggc aatatcttat
 R
 tagtgaaagt ctcaaaatcg tgtctttttg ctccacatcc ttagtgtatg ggtgccccca
 tccccaccat gttcttgtca cttcatggtt acaaaatagc tgcagtggtt ccaggcatcc
 tgtttgcttt cATGATAAGG AATAAGGGAC AACACAGTGA GCTCTCCTTT CATTCCTGTT
 CCTTTTTTTT TAAGACAACA AAAACTTATC TTCATGCTCC TAGCAGTCTA CTTTTATTTC
 ATTAGTCAAA ATTGGGTTTA ATGCTTATTC CTAGCTGCAG AGAGTTTGAC TGGAAGTGAG
 GTTTTGTCTT TTCAGCCTTT ATGTTAAGAA GCAGCCAGGT CACCATGTGG TGGAAATTGT
 TTGGGAGACA ACAAGCTTTC TATACTGTGG TTTATTGGTT GCACATTGAG GAATCCAAGT
 GATTCTCCTT CCATCTAGTT TTTAGTGTCT TGGTGATTGA AGAATACCAG CTT

GeneView

GeneView via analysis of contig annotation: ITPR1 inositol 1,4,5-triphosphate receptor, type 1

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_022517->NM_001099952

function

reference

NT_022517->NM_002222

function

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


reference	NT_022517->NM_001099952->NP_001093422	4525549	forward	intron

reference	NT_022517->NM_002222->NP_002213	4525549	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs304006 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_001838876.2	5823152	4519282	minus	T	alt_assembly_8	HuRef	HuRef	view	500
3	NW_921651.1	4523644	4523644	plus	A	alt_assembly_1	Celera	Celera	view	500
3	NT_022517.17	4525549	4560549	plus	G	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022517 AC025087 AC025087.3

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
ss16986888	HapMap-CEU	European	120	IG	0.300	0.483	0.217	1.000	0.542	0.458

	HapMap-HCB	Asian	90	IG	0.111	0.533	0.356	0.752	0.378	0.622

	HapMap-JPT	Asian	90	IG	0.133	0.467	0.400	0.752	0.367	0.633

	HapMap-YRI	Sub-Saharan African	120	IG	0.183	0.417	0.400	0.343	0.392	0.608

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.489+/-0.073	270	210	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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .