Reference SNP(refSNP) Cluster Report: rs1042565

Reference SNP(refSNP) Cluster Report: rs1042565

refSNP ID: rs1042565
Organism:	human (Homo sapiens)
Molecule Type:	cDNA
Created/Updated in build:	86/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_004168.2:c.*138T>C
NT_006576.15:g.246673T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24815764 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1042565 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
ss1509891	LEE\|25263	fwd/B	C/T	gaaggagtacattgaagggagattggcacc	agtggctgggagcttgccaggaacccagtg	09/13/00	10/10/03	86	cDNA	unknown
ss4403943	LEE\|e25263	fwd/B	C/T	gaaggagtacattgaagggagattggcacc	agtggctgggagcttgccaggaacccagtg	04/26/02	10/10/03	106	cDNA	unknown
ss24815764	SEQUENOM\|sqnm210772	fwd/B	C/T	gaaggagtacattgaagggagattggcacc	agtggctgggagcttgccaggaacccagtg	06/18/04	08/05/04	126	cDNA	unknown

Fasta sequence (Legend)

 AATTATGTAT AATAGCTCAT GCATGTGTCC ATGTCATAAC TGTCTTCATA CGCTTCTGCA
 CTCTGGGGAA GAAGGAGTAC ATTGAAGGGA GATTGGCACC
 Y
 AGTGGCTGGG AGCTTGCCAG GAACCCAGTG GCCAGGGAGC GTGGCACTTA CCTTTGTCCC
 TTGCTTCATT CTTGTGAGAT GATAAAACTG GGCACAGCTC

GeneView

GeneView via analysis of contig annotation: SDHA succinate dehydrogenase complex, subunit A, flavoprotein (Fp)

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_006576->NM_004168

function

HuRef

NW_001838923->NM_004168

function

Celera

NW_922496->NM_004168

function

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


reference	NT_006576->NM_004168->	246673	forward	2248	3' UTR

HuRef	NW_001838923->NM_004168->	1876400	reverse	2248	3' UTR

Celera	NW_922496->NM_004168->	244163	forward	2248	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1042565 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_001838923.2	1876400	246571	minus	A	alt_assembly_8	HuRef	HuRef	view	100
5	NT_006576.15	246673	309673	plus	T	ref_assembly	reference	reference	view	100
5	NW_922496.1	244163	356235	plus	T	alt_assembly_1	Celera	Celera	view	100

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm210772	AI628238 Hs.469

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank STS:	GenBank mRNA:
NM_004168.2	AC021087.5 NC_000005.8	BV167461.1 BV176805.1 BV178886.1 BV203025.1 G33146.1	AB208991.1 AK131478.1 AK291311.1 BC001380.2 BC041016.1 D30648.1 L21936.1

UniGene Cluster ID
440475

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	C	T
ss24815764	CEPH		184	AF		0.600	0.400

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.480+/-0.098	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 .