Reference SNP(refSNP) Cluster Report: rs266729

Reference SNP(refSNP) Cluster Report: rs266729

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44380193 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs266729 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
ss347243	KWOK\|OVLP-000621-104893	rev/T	C/G	tcttggcacgctcatgttttgtttttgaag	gcaggatctgagccggttcttgcaagccac	06/30/00	10/10/03	79	Genomic	99 %
ss1099798	KWOK\|OVLP-000804-188111	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	09/02/00	10/10/03	86	Genomic	99 %
ss1101723	KWOK\|OVLP-000804-198038	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	09/02/00	10/10/03	86	Genomic	99 %
ss1102665	KWOK\|OVLP-000804-204030	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	09/02/00	10/10/03	86	Genomic	99 %
ss1668368	KWOK\|OVLP-000925-86396	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	10/05/00	04/07/04	87	Genomic	99 %
ss1669555	KWOK\|OVLP-000925-100797	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	10/05/00	10/10/03	87	Genomic	99 %
ss1669810	KWOK\|OVLP-000925-104474	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	10/05/00	10/10/03	87	Genomic	99 %
ss2470070	SC_JCM\|AC009863.3_99990	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	11/03/00	10/10/03	89	Genomic	unknown
ss23914895	PERLEGEN\|afd3153774	fwd/B	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	08/10/04	09/13/04	123	Genomic	unknown
ss44380193	ABI\|hCV2412786	fwd/	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	07/18/05	11/03/06	126	Genomic	unknown
ss68885544	PERLEGEN\|PGP03153774	fwd/	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	01/30/07	08/14/07	127	Genomic	unknown
ss76878288	CGM_KYOTO\|1015536	fwd/	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	09/12/07	09/12/07	129	cDNA	unknown
ss95212569	CNG\|29952148	fwd/	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	03/13/08	03/13/08	129	Genomic	unknown
ss112765747	1000GENOMES\|CEU.trio.12.15.2008_878481_chr3_188042168	fwd/	C/G	gtggcttgcaagaaccggctcagatcctgc	cttcaaaaacaaaacatgagcgtgccaaga	12/15/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 CTCTCATCTC AACGGCCTAA TGTGACTTCT CTTGAAATAT TTGGACATTA GCAGGAAGCT
 GAGGCTTTAC ATCAGATCTT TACTTTAATG GTGGACTTGA CTTTACTGGT AGATTTTTAG
 GCTCTGTGTG GACTGTGGAG ATGATATCTG GGGGGCAGGC AGACACTTGC CCTGCCTCTG
 TCTGAGAAAA TTCTGTTTTG GATGTCTTGT TGAAGTTGGT GCTGGCATCC TAAGCCCTTG
 CTGGGGTCGT AATTTAATTC ATCAGAATGT GTGGCTTGCA AGAACCGGCT CAGATCCTGC
 S
 CTTCAAAAAC AAAACATGAG CGTGCCAAGA AAGTCCAAGG TGTTGAATGT TGCCACTTCA
 AGCCTAAACT TTCTAGGAAC ACCTAAGTGG GTGGCAGCTT CCAGTTCTCC AGGCTGCTTC
 TAGGCCAGAG CTGGGTTCCA CAAGAGACAG AATAGGCATA TATATGCTTA AGGAACTGGA
 AAAACAGGCT CTCTCTCTCT CACAAACACA CACACACACA TACCAAGGTA GCTGTCAAAA
 TGTTATCCGA AATTTTGGAA CCAAAAAATC TTGAAAGATG GTATTCCAAT ATCACATTTT

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_005612.14 AC012149 AC012149.8 AC026612.3 AC072018.2 AC072018.3

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss1668368	TSC_42_AA		84	AF					0.700	0.300

	TSC_42_C		84	AF					0.700	0.300

	TSC_42_A		84	AF					0.700	0.300

	CEPH		184	AF					0.750	0.250

ss23914895	AFD_EUR_PANEL	European	48	IG	0.500	0.417	0.083	1.000	0.708	0.292

	AFD_AFR_PANEL	African American	44	IG	0.636	0.364		0.317	0.818	0.182

	AFD_CHN_PANEL	Asian	48	IG	0.542	0.292	0.167	0.150	0.688	0.312

ss44380193	HapMap-CEU	European	120	IG	0.500	0.400	0.100	0.752	0.700	0.300

	HapMap-HCB	Asian	90	IG	0.511	0.378	0.111	0.527	0.700	0.300

	HapMap-JPT	Asian	88	IG	0.477	0.432	0.091	1.000	0.693	0.307

	HapMap-YRI	Sub-Saharan African	120	IG	0.850	0.133	0.017	0.343	0.917	0.083

ss68885544	HapMap-CEU	European	120	GF	0.483	0.417	0.100		0.692	0.308

	HapMap-HCB	Asian	90	GF	0.511	0.378	0.111		0.700	0.300

	HapMap-JPT	Asian	90	GF	0.489	0.444	0.067		0.711	0.289

	HapMap-YRI	Sub-Saharan African	120	GF	0.833	0.150	0.017		0.908	0.092

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss23914895	70	39	25	5
ss44380193	348	119	48	9
ss68885544	265	159	88	18

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs266729	503	194	110	22

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
242	ss23914895	G/G	PERLEGEN	AFD_EUR_PANEL	NA10854		71_IND_CHR_3
242	ss68885544	C/G	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	chr3-HapMap-CEU
636	ss68885544	C/G	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	chr3-HapMap-CEU
5203	ss44380193	G/G	CSHL-HAPMAP	HapMap-JPT	NA18956	JA18956	r27_ch3_JPT_wicgr:genotype_protocol_1
5203	ss68885544	C/G	CSHL-HAPMAP	HapMap-JPT	NA18956	JA18956	chr3-HapMap-JPT
5227	ss44380193	C/G	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	r27_ch3_JPT_wicgr:genotype_protocol_1
5227	ss68885544	C/C	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	chr3-HapMap-JPT
5299	ss44380193	C/C	CSHL-HAPMAP	HapMap-YRI	NA19116	YOR060.02	r27_ch3_YRI_wicgr:genotype_protocol_1
5299	ss68885544	C/G	CSHL-HAPMAP	HapMap-YRI	NA19116	YOR060.02	chr3-HapMap-YRI

Genotype data submitted for	512	samples from	503	individuals	Individual with multiple genotypes submission:	189

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 .