Reference SNP(refSNP) Cluster Report: rs2286963

Reference SNP(refSNP) Cluster Report: rs2286963

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/130
Map to Genome Build:	36.3

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

HGVS Names
NG_008002.1:g.35166A>C
NM_001608.3:c.997A>C
NP_001599.1:p.Lys333Gln

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss71646624 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2286963 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
ss3227594	YUSUKE\|IMS-JST037678	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	09/05/01	10/25/06	100	Genomic	unknown
ss24303063	PERLEGEN\|afd0726997	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	08/10/04	09/13/04	123	Genomic	unknown
ss66432338	AFFY\|SNP_A-2168774	rev/T	A/C	caagacagtgcaacat	aattagcagaattaaa	10/29/06	08/14/07	127	Genomic	unknown
ss66677216	ILLUMINA\|HumanHap300v1.1_rs2286963	fwd/T	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	11/09/06	11/09/06	127	Genomic	unknown
ss67242382	ILLUMINA\|HumanHap550v1.1_rs2286963	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	11/14/06	11/14/06	127	Genomic	unknown
ss67639166	ILLUMINA\|HumanHap650Yv1.0_rs2286963	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	11/14/06	11/14/06	127	Genomic	unknown
ss68841512	PERLEGEN\|PGP00726997	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	01/30/07	08/14/07	127	Genomic	unknown
ss70720727	ILLUMINA\|HumanHap550v3.0__rs2286963	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	04/20/07	03/30/08	130	Genomic	unknown
ss71289091	ILLUMINA\|HumanHap650Yv3.0_rs2286963	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	04/23/07	04/23/07	127	Genomic	unknown
ss71646624	SI_EXO\|NT_005403.16_61269467	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	05/07/07	03/31/08	127	Genomic	unknown
ss75577505	ILLUMINA\|ILMN_Human_1M_rs2286963	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	08/28/07	08/29/07	129	Genomic	unknown
ss76206274	AFFY\|AFFY_6_1M_SNP_A-2168774	rev/T	A/C	caagacagtgcaacat	aattagcagaattaaa	08/28/07	08/30/07	130	Genomic	unknown
ss79126692	ILLUMINA\|HumanHap300v2.0_rs2286963	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	04/18/07	11/18/07	130	Genomic	unknown
ss84022136	KRIBB_YJKIM\|KHS604548	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	12/04/07	12/06/07	130	Genomic	unknown
ss98338907	CNG\|40002045	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	03/31/08	03/31/08	130	Genomic	unknown
ss110675070	1000GENOMES\|CEU.trio.12.15.2008_572607_chr2_210768295	fwd/B	G/T	cacatatatgtgtttttaattctgctaatt	atgttgcactgtcttgaatttaaaggaaat	12/15/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTTTCCCACT CTTAATATTT TATTTTCAAT AGCAAGTTAA GAATTAAATA CTAACTTTGC
 TTGCCTATTA GGATAAAAAA ATTAAATACC AACTTGAAAC ATTTTTAGCA CATTATACAT
 ATGCTTAATG GAACTTTTTA GCATTTTTTT TTAAAGTGGA GTCTCACTTT TATTTTTCAT
 TTCACAGATT TCTTCCTTTA AGACCCTCAA GGCTGAGCTT AAAATTGGCA GAATTCCATA
 TCAGTCTGAG CACACACCGC ACTCTAATTA CTGTAGCATG CATACCAATA TTTCGCCATG
 CAAGCAGTGG CGGAGTCCAA ACGTTTCGCT TCATGCAGCT GGAGACAGTT GTCCACAAAT
 GCTCGGGTTA CACATATATG TGTTTTTAAT TCTGCTAATT
 K
 ATGTTGCACT GTCTTGAATT TAAAGGAAAT AAAAGAAAAA AGTGAGCATG GTAGAAATAT
 AAACTTCAAC CCACTTAACA TATCAGAAAT TATACAATAA AAGATCTTTA GGGCAAACAA
 AAGTGGAATT GTTGGTTTTT TCCTCCATAA AAATGGCATT TGTTACCAAA TCAGCTTAAA
 TTTAAAACTC ACTATATTTC AGTGCTAAGG AAATTTGTAC TAAAAGATGC AAAAATAGTT
 TAAAACATAA ACAATGTCTT GTTTCAGATT GTAAAATTTA GACGAGGCAA AATTCTTGAA
 AAACAGCATG ACTTTAATGT GTGAGCACCA TCTTGTGGTA CAGTTATTTA GGTACAGCCG
 TTGAAAACAC CTGTTGCTTT TTCCTCCAGA GATTAAATCC

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
NT_005403.16

dbSNP Blast Analysis

UniGene Cluster ID
471277

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	N	T
ss24303063	AFD_EUR_PANEL	European	48	IG	0.042	0.500	0.458	0.317	0.292		0.708

	AFD_AFR_PANEL	African American	46	IG		0.348	0.652	0.317	0.174		0.826

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.167	0.750	0.100	0.167		0.833

	HapMap-CEU	European	120	IG	0.200	0.350	0.450	0.050	0.375		0.625

	HapMap-HCB	Asian	90	IG	0.044	0.267	0.689	0.584	0.178		0.822

	HapMap-JPT	Asian	88	IG	0.045	0.318	0.636	1.000	0.205		0.795

	HapMap-YRI	Sub-Saharan African	120	IG		0.200	0.800	0.403	0.100		0.900

	CHMJ	Asian	74	IG					0.189	0.014	0.797

ss66432338	HapMap-CEU	European	118	GF	0.220	0.322	0.458		0.381		0.619

	HapMap-HCB	Asian	90	GF	0.044	0.267	0.689		0.178		0.822

	HapMap-JPT	Asian	90	GF	0.044	0.311	0.644		0.200		0.800

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.183	0.800		0.108		0.892

ss68841512	HapMap-CEU	European	120	GF	0.200	0.350	0.450		0.375		0.625

	HapMap-HCB	Asian	90	GF	0.044	0.267	0.689		0.178		0.822

	HapMap-JPT	Asian	90	GF	0.044	0.311	0.644		0.200		0.800

	HapMap-YRI	Sub-Saharan African	120	GF		0.200	0.800		0.100		0.900

ss71646624	HapMap-CEU	European	120	IG	0.200	0.350	0.450		0.375		0.625

	HapMap-HCB	Asian	90	IG	0.044	0.267	0.689		0.178		0.822

	HapMap-JPT	Asian	88	IG	0.045	0.318	0.636		0.205		0.795

	HapMap-YRI	Sub-Saharan African	120	IG		0.200	0.800		0.100		0.900

ss76206274	ICMHP		4	IG	1.000				1.000

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss24303063	71	3	24	44
ss68841512	267	19	73	175
ss71646624	1204	63	358	760
ss76206274	6

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs2286963	1267	66	383	811

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
213	ss68841512	G/T	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	chr2-HapMap-CEU
213	ss71646624	G/T	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	r27_ch2_CEU_illumina:human_1m_beadchip
538	ss68841512	G/G	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	chr2-HapMap-CEU
538	ss71646624	G/G	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	r27_ch2_CEU_illumina:human_1m_beadchip
5275	ss68841512	G/T	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	chr2-HapMap-YRI
5275	ss71646624	G/T	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r27_ch2_YRI_illumina:human_1m_beadchip

Genotype data submitted for	1282	samples from	1267	individuals	Individual with multiple genotypes submission:	276

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .