Reference SNP(refSNP) Cluster Report: rs5746130

Reference SNP(refSNP) Cluster Report: rs5746130

refSNP ID: rs5746130
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	114/129
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_000636.2:c.523+79_523+80del2
NM_001024465.1:c.523+79_523+80del2
NM_001024466.1:c.406+79_406+80del2
NT_007422.13:g.2393147_2393148del2

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7990861 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5746130 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
ss7990861	EGP_SNPS\|SOD2-010312		fwd/T	-/CA	aagcattcaactagaaataaggaaaactaa	gtgttttaagaacatgtaataatttgcaaa	04/14/03	01/23/04	114	Genomic			unknown

Fasta sequence (Legend)

 AGTTGCTGGA AGCCATCAAA CGTGACTTTG GTTCCTTTGA CAAGTTTAAG GAGAAGCTGA
 CGGCTGCATC TGTTGGTGTC CAAGGCTCAG GTTGGGGTTG GCTTGGTTTC AATAAGGAAC
 GGGGACACTT ACAAATTGCT GCTTGTCCAA ATCAGGATCC ACTGCAAGGA ACAACAGGTT
 AGATTTAAAA ATTGTGATTT CATTTGGGAG AGATGCTCTA CTGTAAAGCA TTCAACTAGA
 AATAAGGAAA ACTAA
 N
 GTGTTTTAAG AACATGTAAT AATTTGCAAA TCTTAACAGA TAACACCCAG AGTCTTGTGT
 AAGTAAAAAT GTTTTAGAAG TCCTGATATT TCATAAAATT AAGTACACGT AATTTTATAG
 GTACATTAAC AAACATGttt tatttttatt tatttttttt gagacagatc tcactgttgc
 ccaggctgga gtgcagtggt gcgatctcgg ttcactgcaa cctccgcctc ctgggttcaa
 gtgattctcc tgcct

GeneView

GeneView via analysis of contig annotation: SOD2 superoxide dismutase 2, mitochondrial

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_007422->NM_000636

function

reference

NT_007422->NM_001024465

function

reference

NT_007422->NM_001024466

function

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


reference	NT_007422->NM_000636->NP_000627	2393147:2393148	reverse	intron

reference	NT_007422->NM_001024465->NP_001019636	2393147:2393148	reverse	intron

reference	NT_007422->NM_001024466->NP_001019637	2393147:2393148	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs5746130 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838991.2	933081..933082	157576242..157576243	plus	CA	alt_assembly_8	HuRef	HuRef	view	255
6	NT_007422.13	2393147..2393148	160025796..160025797	minus	TG	ref_assembly	reference	reference	view	255
6	NW_923184.1	92821863..92821864	160753259..160753260	minus	TG	alt_assembly_1	Celera	Celera	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY267901

dbSNP Blast Analysis
GenBank HTGS Finished:
AL135914.25

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	-/CA	CA/CA	HWP	-	CA
ss7990861	PDR90	Global	160	IG	0.013	0.988	1.000	0.006	0.994

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.012+/-0.078	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 .