Reference SNP(refSNP) Cluster Report: rs3779419

Reference SNP(refSNP) Cluster Report: rs3779419

refSNP ID: rs3779419
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
Map to Genome Build:	36.3

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

HGVS Names
NM_005918.2:c.886-516G>A
NT_007933.14:g.929357G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss11851051 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3779419 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
ss4965486	YUSUKE\|IMS-JST135487	fwd/B	C/T	tgacattggcaaaaacaggcatctctgcca	cgtctcacctgcagaaactgagcacagttt	08/07/02	10/10/03	107	Genomic	unknown
ss11851051	WI_SSAHASNP\|chr7.NT_007933.12_929357	rev/T	A/G	aaactgtgctcagtttctgcaggtgagacg	tggcagagatgcctgtttttgccaatgtca	07/04/03	10/25/06	116	Genomic	unknown
ss23954339	PERLEGEN\|afd4396925	rev/T	A/G	aaactgtgctcagtttctgcaggtgagacg	tggcagagatgcctgtttttgccaatgtca	08/10/04	09/13/04	123	Genomic	unknown
ss67707100	ILLUMINA\|HumanHap650Yv1.0_rs3779419	fwd/B	C/T	tgacattggcaaaaacaggcatctctgcca	cgtctcacctgcagaaactgagcacagttt	11/14/06	11/14/06	127	Genomic	unknown
ss71357285	ILLUMINA\|HumanHap650Yv3.0_rs3779419	fwd/B	C/T	tgacattggcaaaaacaggcatctctgcca	cgtctcacctgcagaaactgagcacagttt	04/23/07	04/23/07	127	Genomic	unknown
ss74822351	AFFY\|SNP_M-577338	fwd/B	C/T	tgacattggcaaaaacaggcatctctgcca	cgtctcacctgcagaaactgagcacagttt	08/09/07	08/09/07	128	Genomic	unknown
ss75340956	ILLUMINA\|ILMN_Human_1M_rs3779419	fwd/B	C/T	tgacattggcaaaaacaggcatctctgcca	cgtctcacctgcagaaactgagcacagttt	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GACAATGCGA CAAGCACCTG GACGCCAGGA ACTCAATCAT CAGGAACACT TCACCGTATT
 CTCCCCAACA GAGCCTGTTT CTGGGTTCTT GTCTCTCCCC GCAGGTTGGT AAAGGACTGA
 AAACATTGTC ACAGTCACCT GAATCAGGTG TCACTAAGTA GGTAAATGTC TGACATTGGC
 AAAAACAGGC ATCTCTGCCA
 Y
 CGTCTCACCT GCAGAAACTG AGCACAGTTT GTGTGGCAAC AGCCTCAGTC CTCACCTCAA
 CTCAATTCCC TCCTACTGCT TCCCCTGGCT CAAGGGCCTA TGAGAACCGG GTGCGTCTCA
 CCTGCAGGCC CTGCCATTCC ATACACCTGC ACCGACATGG GGACAGAACT ATACCATCGA
 GTGCCTGTCT CTCACCAAGG

GeneView

GeneView via analysis of contig annotation: MDH2 malate dehydrogenase 2, NAD (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_007933->NM_005918

function

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


reference	NT_007933->NM_005918->NP_005909	929357	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3779419 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_923484.1	560356	70563602	minus	G	alt_assembly_1	Celera	Celera	view	200
7	NW_001839047.1	593773	70781633	minus	G	alt_assembly_8	HuRef	HuRef	view	200
7	NT_079595.2	929357	75028145	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	200
7	NT_007933.14	929357	75533017	minus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007933

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss11851051	HapMap-CEU	European	104	IG	0.827	0.173		0.527	0.913		0.087

	HapMap-HCB	Asian	84	IG	0.738	0.214	0.048	0.251	0.845		0.155

	HapMap-JPT	Asian	80	IG	0.550	0.350	0.100	0.479	0.725		0.275

	HapMap-YRI	Sub-Saharan African	112	IG	0.518	0.464	0.018	0.100	0.750		0.250

	CHMJ	Asian	74	IG					0.662	0.014	0.324

ss23954339	AFD_EUR_PANEL	European	48	IG	0.708	0.250	0.042	0.655	0.833		0.167

	AFD_AFR_PANEL	African American	46	IG	0.609	0.391		0.251	0.804		0.196

	AFD_CHN_PANEL	Asian	48	IG	0.625	0.292	0.083	0.403	0.771		0.229

ss4965486	JBIC-allele		1474	AF					0.690		0.310

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.310+/-0.243	332	260	9	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 .