Reference SNP(refSNP) Cluster Report: rs2162869

Reference SNP(refSNP) Cluster Report: rs2162869

refSNP ID: rs2162869
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_004168.2:c.1794+209A>G
NT_006576.15:g.241792A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3095294 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2162869 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
ss3095294	TSC-CSHL\|TSC1195181	fwd/B	C/T	ttggcttggagatgccactgctggcatcag	ggatgccgacccaaagcaaggaaaaggtca	06/07/01	04/07/04	96	Genomic	unknown
ss5211951	TSC-CSHL\|TSC1203872	fwd/B	C/T	ttggcttggagatgccactgctggcatcag	ggatgccgacccaaagcaaggaaaaggtca	09/20/02	10/10/03	108	Genomic	unknown
ss5972100	SC_JCM\|NT_034766.1_242446	rev/T	A/G	tgaccttttccttgctttgggtcggcatcc	ctgatgccagcagtggcatctccaagccaa	01/10/03	10/10/03	111	Genomic	unknown

Fasta sequence (Legend)

 CTAACAGCAA AGCACATTGG CTTGGAGATG CCACTGCTGG CATCAG
 Y
 GGATGCCGAC CCAAAGCAAG GAAAAGGTCA CAGTGATCCA GAAGATGGCG AGAACCCAGG
 GATCAAAGTT ACCAGGGGGG AAAAAGGCAT TTTTTGGATT TACTTTTGGG GCAACGAAAG
 AAAATGCAGA GAAAATGCAG GGGTGGGGCT GAGTCCCACC AGGTGGCAGG AAAAGGCAGG
 TGCAGGTGGG CGTGGTGAGA AGGCCCACCT TGTAGTCTTC CCTGGCATGC GCGCCCCGTG
 ACTCCTTCCG TGCCTCTGCT CCGTAGATGG TCTGCAGCGC ACACAGCATC AGGTTCTGCA
 GCTCCAGGGT CTCCACCAGG TCCGTGTTCC AGACCATTCC TGGGGACACA AAAAGTTCCA
 TCAGGGGCAG GCGGGACCCA GTCACATGGG CCCTCCGAGC TGTCAGCCTG GGCCTGCTAG
 TCCATGGAGT CACTGGTTGT GGCTTTATAG CTGTGGGCCA GGACCCATCC AGACAGCAAG
 CACGGAACTA AGTCAGCACT GAC

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	Function


reference	NT_006576->NM_004168->NP_004159	241792	forward	intron

HuRef	NW_001838923->NM_004168->NP_004159	1881280	reverse	intron

Celera	NW_922496->NM_004168->NP_004159	239282	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2162869 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	1881280	241691	plus	T	alt_assembly_8	HuRef	HuRef	view	46
5	NT_006576.15	241792	304792	minus	A	ref_assembly	reference	reference	view	46
5	NW_922496.1	239282	351354	minus	A	alt_assembly_1	Celera	Celera	view	46

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034766.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AC021087.5 NC_000005.8

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/T	T/T	HWP	C	T
ss3095294	WICGR8_asian_pooled		84	AF				0.010	0.990

	WICGR6_caucasian_pooled		96	AF				0.030	0.970

	HapMap-CEU	European	118	IG	0.220	0.780	0.343	0.110	0.890

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.196+/-0.244	90	60	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 .