Reference SNP(refSNP) Cluster Report: rs1058999

Reference SNP(refSNP) Cluster Report: rs1058999

refSNP ID: rs1058999
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/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_021614.2:c.-101G>C
NT_034772.5:g.16113385G>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss80759788 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1058999 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
ss1541059	LEE\|798721	fwd/T	C/G	ccacgggcagcctcggcagtctgggctccg	gcccccgctctcgcaccaccaccaccaccc	09/13/00	05/16/04	86	cDNA	unknown
ss4398895	LEE\|ge798722	fwd/T	C/G	ccacgggcagcctcggcagtctgggctccg	gcccccgctctcgcaccaccaccaccaccc	04/25/02	10/10/03	106	cDNA	unknown
ss4428020	LEE\|e798722	fwd/T	C/G	ccacgggcagcctcggcagtctgggctccg	gcccccgctctcgcaccaccaccaccaccc	04/26/02	10/10/03	106	cDNA	unknown
ss24819653	SEQUENOM\|sqnm222248	fwd/T	C/G	ccacgggcagcctcggcagtctgggctccg	gcccccgctctcgcaccaccaccaccaccc	06/18/04	06/18/04	123	cDNA	unknown
ss80759788	HGSV\|Cor18507_SNV_20070510.chr5_113726271	fwd/	C/G	ccacgggcagcctcggcagtctgggctccg	gcccccgctctcgcaccaccaccaccaccc	11/26/07	11/26/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCGGCGGCGC CTTCCGGACC CGCACCTCCT CGCCGCTGTC GGGCTCGTCC TGCTGCTGCT
 GCTGCTGCTC GTCGCGCCGG GGCAGCCAGC TCAATGTGAG CGAGCTGACG CCGTCCAGCC
 ATGCCAGTGC GCTCCGGCAG CAGTACGCGC AGCAGTCCGC GCAGCAGTCG GCGTCCGCCT
 CCCAGTACCA CCAGTGCCAC AGCCTGCAGC CCGCCGCCAG CCCCACGGGC AGCCTCGGCA
 GTCTGGGCTC CG
 S
 GCCCCCGCTC TCGCACCACC ACCACCACCC GCACCCGGCG CACCACCAGC ACCACCAGCC
 CCAGGCGCGC CGCGAGAGCA ACCCCTTCAC CGAAATAGCC ATGAGCAGCT GCAGGTACAA
 CGGGGGCGTC ATGCGGCCGC TCAGCAACTT GAGCGCGTCC CGCCGGAACC TGCACGAGAT
 GGACTCAGAG GCGCAGCCCC TGCAGCCCCC CGCGTCTGTC GGAGGAGGTG GCGGCGCGTC
 CTCCCCGTCT

GeneView

GeneView via analysis of contig annotation: KCNN2 potassium intermediate/small conductance calcium-activated channel, subfamily N, 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_034772->NM_021614

function

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


reference	NT_034772->NM_021614->	16113385	forward	357	5' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1058999 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838952.2	25095670	108881038	minus	C	alt_assembly_8	HuRef	HuRef	view	100
5	NW_922751.1	14266698	109645527	plus	G	alt_assembly_1	Celera	Celera	view	100
5	NT_034772.5	16113385	113726271	plus	G	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm222248	AI339865 Hs.176305 Hs.270033

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank STS:	GenBank mRNA:
NM_021614.2	BV206914.1	AF239613.1 AK289948.1

UniGene Cluster ID
98280

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	C	G
ss1541059	CEPH		184	AF		0.020	0.980

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.039+/-0.134	0	0	0	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 .