Reference SNP(refSNP) Cluster Report: rs28359672

Reference SNP(refSNP) Cluster Report: rs28359672

refSNP ID: rs28359672
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	125/129
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_006615.2:c.953+1706A>G
NM_016452.1:c.876-2636A>G
NT_004559.13:g.7114237A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss32479170 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28359672 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss32479170	EGP_SNPS\|CAPN9-030741		fwd/T	A/G	cacctcccaaaggccccacctcctgacact	ctacttcgagggttaggattcaacatatga	01/06/05	11/02/06	125	Genomic			unknown

Fasta sequence (Legend)

 GGCTTACAAA GAACAGGAAT TTATTTCTCA CAGTTCTAGA TACCAGGAAG TCCAAGAAGA
 TGACACAGGC AGTACCTATA TCTGTGGAGG GCCCTGTTTC TGATTTATAG ATGGATCCTT
 CTCACTCTGT CCTCACATGG TAGAAAGAGG GCAAGGCAGC TCTCTGGGGC CTCTTTTATA
 ATGGCACTAA CCCCATCCAT GAGGGCTCCA CCCTCACAAC CTAGTCACCT CCCAAAGGCC
 CCACCTCCTG ACACT
 R
 CTACTTCGAG GGTTAGGATT CAACATATGA ATTTAGGGGA GACCACAAAC ATTCAGTCCA
 TAACAACATG CAACAGATTT ACCCAATGTT TTGCCACTGC ATAACATAGA TAACCATTTT
 CCAGCTCGAA CAGTTCCATG ATCCCTCTTG CTCAACTGCT AACATATTTT AGAATTTCGT
 TGTGGCAGTT CTGTAATTCA AGGCACCAAT GACTCAAGGT AACACTAGCT GCAGTAGTGA
 ATAGACCCCA AATAT

GeneView

GeneView via analysis of contig annotation: CAPN9 calpain 9

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_004559->NM_006615

function

reference

NT_004559->NM_016452

function

HuRef

NW_001838549->NM_006615

function

HuRef

NW_001838549->NM_016452

function

Celera

NW_927128->NM_006615

function

Celera

NW_927128->NM_016452

function

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


reference	NT_004559->NM_006615->NP_006606	7114237	forward	intron

reference	NT_004559->NM_016452->NP_057536	7114237	forward	intron

HuRef	NW_001838549->NM_006615->NP_006606	440355	forward	intron

HuRef	NW_001838549->NM_016452->NP_057536	440355	forward	intron

Celera	NW_927128->NM_006615->NP_006606	6759241	forward	intron

Celera	NW_927128->NM_016452->NP_057536	6759241	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs28359672 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838549.1	440355	201396785	plus	A	alt_assembly_8	HuRef	HuRef	view	255
1	NW_927128.1	6759241	204178071	plus	A	alt_assembly_1	Celera	Celera	view	255
1	NT_004559.13	7114237	228978706	plus	A	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY874864

dbSNP Blast Analysis
GenBank HTGS Finished:
AL591291.1 NC_000001.9

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss32479170	PDR90	Global	170	IG	0.976	0.024	1.000	0.988	0.012

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.023+/-0.105	90	90	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .