Reference SNP(refSNP) Cluster Report: rs4975

Reference SNP(refSNP) Cluster Report: rs4975

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/130
Map to Genome Build:	36.3

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

HGVS Names
NM_000789.2:c.2548C>G
NM_000789.2:c.2550C>G
NM_152830.1:c.828C>G
NP_000780.1:p.Leu850Val
NT_010783.14:g.20218413C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48402193 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4975 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	Ancestral Allele	Success Rate
ss6412	ARAVINDA\|CHAK00021	fwd/B	C/G	gctcttccaggagctgcagccactctacct	aacctgcatgcctacgtgcgccgggccctg	06/29/99	04/07/04	52	Genomic		unknown
ss3176894	WICVAR\|WIAF-14299	fwd/B	C/G	gctcttccaggagctgcagccactctacct	aacctgcatgcctacgtgcgccgggccctg	06/28/01	04/07/04	102	cDNA	G	unknown
ss4915980	WIPGA\|WI-27766	fwd/B	C/G	gctcttccaggagctgcagccactctacct	aacctgcatgcctacgtgcgccgggccctg	07/12/02	10/25/06	126	cDNA		unknown
ss48402193	APPLERA_GI\|hCV11942563	rev/	C/G	cagggcccggcgcacgtaggcatgcaggtt	aggtagagtggctgcagctcctggaagagc	09/28/05	11/30/05	126	Genomic		unknown

Fasta sequence (Legend)

 AGTTTTACCC GAAATACGTG GAACTCATCA ACCAGGCTGC CCGGCTCAAT GGTGAGTCCC
 TGCTGCCAAC ATCACTGGCA CTTGGGTCCC TTCATTTTCC TCAAAGAGGT GCTGTGAAAC
 CCCAAGCCTA GGAAAAGGTA GATCCCTGGA GGAGGCAGGT AATGTGGTGT TGGGAGAGCC
 TGGCTGTGTC CCCTCTGTAG GCTATGTAGA TGCAGGGGAC TCGTGGAGGT CTATGTACGA
 GACACCATCC CTGGAGCAAG ACCTGGAGCG GCTCTTCCAG GAGCTGCAGC CACTCTACCT
 S
 AACCTGCATG CCTACGTGCG CCGGGCCCTG CACCGTCACT ACGGGGCCCA GCACATCAAC
 CTGGAGGGGC CCATTCCTGC TCACCTGCTG GGTAAGGGCA CATGTCGGGC CTTGAGGAGG
 GTAAAGACGG ACCACAGTGT GAGTGAGGGT TGGGACAGGG CTGACTAGAG GGTAGGGAGC
 AGGCTGGGGA CTGAGAGACT CCAGCCCTGT GGGGGATGGT TGCCCAGGCT GGAGGGGGGT
 GGGCGCTGGG AGTGGGGAGC CCCCCACTTG CATCTGGTGC CACATTCACT GCAGATCTAT

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NM_000789

dbSNP Blast Analysis

UniGene Cluster ID
298469

3D structure mapping
NP_000780 NP_690043

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	HWP	C	G
ss3176894	MITOGPOP6	multiple	68	IG	0.938	0.062	0.150	0.912	0.088

ss48402193	AGI_ASP population	multiple	30	IG	0.933	0.067	1.000	0.967	0.033

ss4915980	CEPH		184	AF				0.990	0.010

ss6412	HYP3		148	AF				0.950	0.050

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.062+/-0.165	46	46	1	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	YES	YES

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Revised: May 25, 2006 1:38 PM .