Reference SNP(refSNP) Cluster Report: rs11580689

Reference SNP(refSNP) Cluster Report: rs11580689

refSNP ID: rs11580689
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_001748.4:c.307+1107G>A
NT_004559.13:g.108794G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44031803 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11580689 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
ss16407699	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_004559.11_82834	fwd/T	A/G	gtttaattcctgagctagactccctaagac	ggacctggaaaattttctagccctgaggaa	02/17/04	03/04/04	120	Genomic	unknown
ss23180762	PERLEGEN\|afd1189436	fwd/T	A/G	gtttaattcctgagctagactccctaagac	ggacctggaaaattttctagccctgaggaa	08/10/04	09/13/04	123	Genomic	unknown
ss32474601	EGP_SNPS\|CAPN2-008371	fwd/T	A/G	gtttaattcctgagctagactccctaagac	ggacctggaaaattttctagccctgaggaa	12/07/04	01/27/05	125	Genomic	unknown
ss44031803	ABI\|hCV26269343	fwd/T	A/G	gtttaattcctgagctagactccctaagac	ggacctggaaaattttctagccctgaggaa	07/18/05	11/03/06	126	Genomic	unknown
ss66862728	EGP_SNPS\|CAPN2_008371	fwd/T	A/G	rtttaattcctgagctagactccctaagac	ggacctggaaaattttctagccctgaggaa	11/09/06	03/31/08	127	Genomic	unknown

Fasta sequence (Legend)

 CTCTGATAAA CCAAAAATCT ATTTTCTGCC ATCAGCCTCA GCTGGCTGGC TCCCCAGACA
 AGTTCATCAG TAGCAAAATC AGTCAACTAG AGTTGTACCT CCTGTCCTCA CCCACCTAGC
 AGAGGTTCTG TTACTCATAT ACTCCTAATA CCAGCTGATA ACAGCTAATA TGTATCTCTA
 AGGCACCGTG ATTATTCCCA TTTTATAGAT GAGGATGCAG AGGTCTTCCT ACAGCTAAAG
 TGGTGGCTGG TACCCCTGAC CCCAGGGTAT GTTTAATTCC TGAGCTAGAC TCCCTAAGAC
 R
 GGACCTGGAA AATTTTCTAG CCCTGAGGAA TGTCAGAGCA TCATGTGAAT CATTAGGACA
 GACAGACTGT GAGGAAGAAC ATGAGCTGGG CGGGAAAGTT TGTCTGAGCT CAGGCTCTGC
 AGATTCCTGA GATGCCAGAG CACATTCTTA CCTGCAGAAA ACACTCCTTT CATTTCTTTT
 CTTCTCACCC CACAAAAGAC AGAAGATAGA GGTCCTTGAG CACCCAAGGC GGATCCTCCA
 GGAAAATCTA TTCATTAGAG AAAATGGAAT TGATGGAAAC TTTGACCAAC CCCGGGGGCT

GeneView

GeneView via analysis of contig annotation: CAPN2 calpain 2, (m/II) large subunit

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_001748

function

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


reference	NT_004559->NM_001748->NP_001739	108794	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11580689 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_001838539.2	178901	194519104	minus	C	alt_assembly_8	HuRef	HuRef	view	300
1	NW_926794.1	17228319	197062559	plus	G	alt_assembly_1	Celera	Celera	view	300
1	NT_004559.13	108794	221973263	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_004559

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
ss23180762	AFD_EUR_PANEL	European	48	IG		0.125	0.875	0.752	0.062	0.938

	AFD_AFR_PANEL	African American	46	IG		0.304	0.696	0.403	0.152	0.848

	AFD_CHN_PANEL	Asian	48	IG		0.208	0.792	0.584	0.104	0.896

ss32474601	PDR90	Global	156	IG	0.026	0.269	0.705	1.000	0.160	0.840

ss44031803	HapMap-CEU	European	120	IG		0.033	0.967	1.000	0.017	0.983

	HapMap-HCB	Asian	90	IG	0.022	0.200	0.778	0.655	0.122	0.878

	HapMap-JPT	Asian	90	IG	0.067	0.467	0.467	0.479	0.300	0.700

	HapMap-YRI	Sub-Saharan African	120	IG	0.100	0.383	0.517	0.584	0.292	0.708

ss66862728	HSP_GENO_PANEL		120	IG	0.050	0.267	0.683	0.403	0.183	0.817

	CEU_GENO_PANEL	European	120	IG		0.033	0.967	1.000	0.017	0.983

	AAM_GENO_PANEL	African American	124	IG	0.081	0.323	0.597	0.343	0.242	0.758

	CHB_GENO_PANEL	Asian	90	IG	0.022	0.200	0.778	0.655	0.122	0.878

	YRI_GENO_PANEL	Sub-Saharan African	120	IG	0.100	0.383	0.517	0.584	0.292	0.708

	JPT_GENO_PANEL	Asian	90	IG	0.067	0.467	0.467	0.479	0.300	0.700

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.289+/-0.247	545	473	218	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 .