Reference SNP(refSNP) Cluster Report: rs4809562

Reference SNP(refSNP) Cluster Report: rs4809562

refSNP ID: rs4809562
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_004518.3:c.690+809G>A
NM_172106.1:c.690+809G>A
NM_172107.2:c.690+809G>A
NM_172108.2:c.690+809G>A
NM_172109.1:c.690+809G>A
NT_011333.5:g.811833C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss91756126 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4809562 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
ss6638486	WI_SSAHASNP\|NT_011333.5_811833	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	02/12/03	10/10/03	111	Genomic	unknown
ss10963987	BCM_SSAHASNP\|chr20.NT_011333.5_811833	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	06/30/03	10/10/03	116	Genomic	unknown
ss12491089	WI_SSAHASNP\|chr20.NT_011333.5_811833	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	07/04/03	10/10/03	116	Genomic	unknown
ss17697377	CSHL-HAPMAP\|CSHL-HuCC-200402.chr20.NT_011333.5_811833	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	02/19/04	03/04/04	120	Genomic	unknown
ss21786100	SSAHASNP\|WGSA-200403-chr20.chr20.NT_011333.5_811833	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	03/20/04	03/20/04	121	Genomic	unknown
ss80214462	HGSV\|Cor18507_SNV_20070510.chr20_61545647	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	11/23/07	11/25/07	130	Genomic	unknown
ss85603216	HGSV\|Cor19129_SNV_20070510.chr20_61545647	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	12/06/07	12/09/07	130	Genomic	unknown
ss91756126	BCMHGSC_JDW\|JWB-1464314	fwd/B	C/T	gcctcctggcctgggcaacagtggctcgca	ggccagcccaccgtgccctccagggtcagt	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 ACCCTCACCA CCATCACCAC CCGCCACCTG CCTCCAGGAG CACTGCAGCC TCGCCAGTCA
 GCCCACTTTG GGCTCTGTCT CCAGGGATAT AGGGGCTGGA TGGACCCGTC TCCTGAGGCC
 AGCAGAGGCT CCACGCCAGG GTCGGTGGCA GGGCTGGCAC AGGGGAACCA GGAGGCGCCG
 CTGGCTTCAC CATCTTAGCT ACGGCAGCCC ATTCCCCTGA GCCTCCTGGC CTGGGCAACA
 GTGGCTCGCA
 Y
 GGCCAGCCCA CCGTGCCCTC CAGGGTCAGT AGCGTCTATT CTGGCGGCCA GCAGGGCTGG
 AGAATCTTGG GACTGTTGAG ACCCTCCCCC AACCTCCCTG AGCCTCCGGG CACAGATGTG
 AAAAGGGTGC CCACTGCAGT CAGCACTCAA CCCCCACAGC GTCCAGGGAG GGAGAGGGGC
 CACCGGGGGC TGACCCCTGC CCATTCTGCA GACAAAGCCA CCACCCTGCC AGGGCTCAAG
 AGGGAAGAAA

GeneView

GeneView via analysis of contig annotation: KCNQ2 potassium voltage-gated channel, KQT-like subfamily, member 2

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_011333->NM_004518

function

reference

NT_011333->NM_172106

function

reference

NT_011333->NM_172107

function

reference

NT_011333->NM_172108

function

reference

NT_011333->NM_172109

function

HuRef

NW_001838671->NM_172107

function

Celera

NW_927339->NM_004518

function

Celera

NW_927339->NM_172106

function

Celera

NW_927339->NM_172107

function

Celera

NW_927339->NM_172108

function

Celera

NW_927339->NM_172109

function

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


reference	NT_011333->NM_004518->NP_004509	811833	reverse	intron

reference	NT_011333->NM_172106->NP_742104	811833	reverse	intron

reference	NT_011333->NM_172107->NP_742105	811833	reverse	intron

reference	NT_011333->NM_172108->NP_742106	811833	reverse	intron

reference	NT_011333->NM_172109->NP_742107	811833	reverse	intron

HuRef	NW_001838671->NM_172107->NP_742105	823487	reverse	intron

Celera	NW_927339->NM_004518->NP_004509	32256743	reverse	intron

Celera	NW_927339->NM_172106->NP_742104	32256743	reverse	intron

Celera	NW_927339->NM_172107->NP_742105	32256743	reverse	intron

Celera	NW_927339->NM_172108->NP_742106	32256743	reverse	intron

Celera	NW_927339->NM_172109->NP_742107	32256743	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4809562 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NW_927339.1	32256743	58753634	plus	T	alt_assembly_1	Celera	Celera	view	200
20	NW_001838671.1	823487	58802833	plus	T	alt_assembly_8	HuRef	HuRef	view	200
20	NT_011333.5	811833	61545647	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011333

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL353658.33 NC_000020.9	AC210433.2

Population Diversity

There is no frequency data.

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .