Reference SNP(refSNP) Cluster Report: rs1801279

Reference SNP(refSNP) Cluster Report: rs1801279

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_000015.2:c.191G>A
NP_000006.2:p.Arg64Gln
NT_030737.9:g.6102632G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5586796 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1801279 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
ss2421518	HGBASE\|SNP000003453	fwd/T	A/G	tttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaat	11/07/00	10/10/03	89	cDNA	unknown
ss5586796	SNP500CANCER\|NAT2-04	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacy	gggtgggtggtgtctccaggtcaatcaact	09/26/02	04/07/04	113	Genomic	unknown
ss24796682	SEQUENOM\|sqnm142275	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	06/18/04	06/18/04	123	cDNA	unknown
ss66858966	EGP_SNPS\|NAT2_010261	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	11/09/06	12/16/06	127	Genomic	unknown
ss69042396	PERLEGEN\|PGP04652196	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	01/30/07	08/14/07	127	Genomic	unknown
ss70456612	EGP_SNPS\|NAT2-010261	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	04/19/07	08/14/07	127	Genomic	unknown
ss74813623	AFFY\|SNP_M-289727	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	08/09/07	08/09/07	128	Genomic	unknown
ss74867512	ILLUMINA\|ILMN_Human_1M_rs1801279	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacy	gggtgggtggtgtctccaggtcaatcaact	08/28/07	08/29/07	129	Genomic	unknown
ss76869168	CGM_KYOTO\|11622	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	09/12/07	09/12/07	129	cDNA	unknown
ss86271257	CORNELL\|hCV572771	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	01/21/08	01/21/08	129	Genomic	unknown
ss115075062	1000GENOMES\|NA19240_2008_12_16_1752285_chr8_18301984	fwd/T	A/G	ctatttttgatcacattgtaagaagaaacc	gggtgggtggtgtctccaggtcaatcaact	12/18/08	12/19/08	130	Genomic	unknown

Fasta sequence (Legend)

 ATTGTGTTTT TACGTATTTA AAATACGTTA TACCTATAAT TAGTCACACG AGGAAATCAA
 ATGCTAAAGT ATGATATGTT TTTATGTTTT GTTTTTCTTG CTTAGGGGAT CATGGACATT
 GAAGCATATT TTGAAAGAAT TGGCTATAAG AACTCTAGGA ACAAATTGGA CTTGGAAACA
 TTAACTGACA TTCTTGAGCA CCAGATCCGG GCTGTTCCCT TTGAGAACCT TAACATGCAT
 TGTGGGCAAG CCATGGAGTT GGGCTTAGAG GCTATTTTTG ATCACATTGT AAGAAGAAAC
 Y
 R
 GGGTGGGTGG TGTCTCCAGG TCAATCAACT TCTGTACTGG GCTCTGACCA CAATCGGTTT
 TCAGACCACA ATGTTAGGAG GGTATTTTTA YATCCCTCCA GTTAACAAAT ACAGCACTGG
 CATGGTTCAC CTTCTCCTGC AGGTGACCAT TGACGGCAGG AATTACATTG TCGATGCTGG
 GTCTGGAAGC TCCTCCCAGA TGTGGCAGCC TCTAGAATTA ATTTCTGGGA AGGATCAGCC
 TCAGGTGCCT TGCATTTTCT GCTTGACAGA AGAGAGAGGA ATCTGGTACC TGGACCAAA

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
dbSTS	GenBank
sqnm142275	X14672

dbSNP Blast Analysis

UniGene Cluster ID
2

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss5586796	P1		202	GF			0.010	0.035	0.965

	CAUC1		62	GF					1.000

	AFR1		48	GF			0.752	0.083	0.917

	HISP1		46	GF			0.003	0.065	0.936

	PAC1		46	GF					1.000

	CEPH		184	AF					1.000

	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	88	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.183	0.817	0.439	0.092	0.908

	Brazilian Population		620	AF				0.220	0.780

ss66858966	HSP_GENO_PANEL		54	IG	0.037	0.963	1.000	0.019	0.981

	CEU_GENO_PANEL	European	68	IG		1.000			1.000

	AAM_GENO_PANEL	African American	124	IG	0.161	0.839	0.527	0.081	0.919

	CHB_GENO_PANEL	Asian	90	IG		1.000			1.000

	YRI_GENO_PANEL	Sub-Saharan African	120	IG	0.183	0.817	0.439	0.092	0.908

	JPT_GENO_PANEL	Asian	24	IG		1.000			1.000

ss69042396	HapMap-CEU	European	120	GF		1.000			1.000

	HapMap-HCB	Asian	90	GF		1.000			1.000

	HapMap-JPT	Asian	90	GF		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.183	0.817		0.092	0.908

ss70456612	PDR90-PANEL		174	AF				0.023	0.977

Concordant Genotype	Total Sample	A/G	G/G
ss5586796	1118	84	964
ss66858966	332	22	218
ss69042396	269	17	252

RefSNP Genotype Summary	Total Individual	A/G	G/G
rs1801279	1242	97	1065

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5259	ss5586796	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r27_ch8_YRI_illumina:human_1m_beadchip	668249
5259	ss69042396	A/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr8-HapMap-YRI

Genotype data submitted for	1451	samples from	1242	individuals	Individual with multiple genotypes submission:	270

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 .