Reference SNP(refSNP) Cluster Report: rs3215651

Reference SNP(refSNP) Cluster Report: rs3215651

refSNP ID: rs3215651
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	106/129
Map to Genome Build:	36.3

Allele
Variation Class:	DIP: deletion/insertion polymorphism
RefSNP Alleles:	-/CA
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_004518.3:c.1548-182_1548-181del2
NM_172106.1:c.1578-182_1578-181del2
NM_172107.2:c.1632-182_1632-181del2
NM_172108.2:c.1539-182_1539-181del2
NT_011333.5:g.781745_781746del2

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss77837833 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3215651 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
ss4476617	YUSUKE\|IMS-JST077195	fwd/T	-/CA	ggcctttatgtggccctgctctgcccggga	ggtggggcttgcaggcctggccatgccccc	06/06/02	10/10/03	106	Genomic	unknown
ss77837833	HGSV\|Cor12156_DIV_20070510.chr20_61515558-61515561_1	fwd/	-/CA	ggcctttatgtggccctgctctgcccggga	ggtggggcttgcaggcctggccatgccccc	10/15/07	10/15/07	129	Genomic	unknown
ss77892060	HGSV\|Cor12156_DIV_20070510.chr20_61515558-61515561_2	fwd/	-/CA	ggcctttatgtggccctgctctgcccggga	ggtggggcttgcaggcctggccatgccccc	10/15/07	10/15/07	129	Genomic	unknown

Fasta sequence (Legend)

 ACACCAGGAA CCGCATGACA CTGCAGGGGG GTGGGTGGGG CTGTGAGCCC TGGGCCAGAG
 ACCCCCGGCC ACAGGCACCA GGACCTTCCT AGCACCTCTG AGACCTCGGC GCCTGGAGAT
 GGCTGGACTT GCCCCTCTTG TCTGCCGCCC ACCAGCTCCA CACACAGAAG GGCCTTTATG
 TGGCCCTGCT CTGCCCGGGA
 N
 GGTGGGGCTT GCAGGCCTGG CCATGCCCCC TTGGACTCCA TGCCACAGCA GGCAGAAGGT
 GGCTGAGTTG CTTCCTAAGC CAGGTGGAGC CCGGCCTCAG GCCTCTTGCT GAACCGGCAT
 CCCACCCGAA ACCCGCCTGA GTCCCAGAGG AGTGCACTCC AGGACATTCA GCCAGGTCCA
 CCCGTGTCTT AGCCCTTTCT

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

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


reference	NT_011333->NM_004518->NP_004509	781745:781746	reverse	intron

reference	NT_011333->NM_172106->NP_742104	781745:781746	reverse	intron

reference	NT_011333->NM_172107->NP_742105	781745:781746	reverse	intron

reference	NT_011333->NM_172108->NP_742106	781745:781746	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3215651 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	32225463..32225464	58722354..58722355	plus	CA	alt_assembly_1	Celera	Celera	view	60
20	NW_001838671.1	791806..791807	58771152..58771153	plus	CA	alt_assembly_8	HuRef	HuRef	view	60
20	NT_011333.5	781745..781746	61515559..61515560	plus	CA	ref_assembly	reference	reference	view	60

NCBI Resource Links

Submitter-Referenced
GenBank
AL121827.13

dbSNP Blast Analysis
GenBank HTGS Finished:
AL121827.34

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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .