Reference SNP(refSNP) Cluster Report: rs1134647

Reference SNP(refSNP) Cluster Report: rs1134647

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
Map to Genome Build:	36.3

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

HGVS Names
NM_020197.1:c.494A>G
NM_020197.2:c.494G>A
NP_064582.2:p.Gly165Glu
NT_021877.18:g.8010065G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48405195 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1134647 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
ss1535978	LEE\|663771	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	09/13/00	10/10/03	86	cDNA	unknown
ss4424320	LEE\|e663771	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	04/26/02	10/10/03	108	cDNA	unknown
ss9888353	BCM_SSAHASNP\|chr1.NT_021877.15_7928192	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	06/27/03	04/07/04	116	Genomic	unknown
ss16250338	CGAP-GAI\|1499812	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	11/18/03	11/22/03	120	cDNA	unknown
ss20463763	SSAHASNP\|WGSA-200403-chr1.chr1.NT_021877.16_7928192	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	03/18/04	03/18/04	121	Genomic	unknown
ss48405195	APPLERA_GI\|hCV25621181	rev/B	C/T	agtactacgaggctatcattgtcagggaat	cgagatgcttggagtaaaagtgatggagag	09/28/05	11/03/06	126	Genomic	unknown
ss65725330	ILLUMINA\|Human1-rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	10/10/06	10/10/06	127	Genomic	unknown
ss65923739	AFFY\|SNP_A-1754095	fwd/T	A/G	catcacttttactccaagcatctcg	attccctgacaatgatagcctcgta	10/26/06	10/26/06	127	Genomic	unknown
ss66550944	ILLUMINA\|HumanHap300v1.1_rs1134647	fwd/B	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	11/09/06	11/09/06	127	Genomic	unknown
ss66930263	ILLUMINA\|HumanHap550v1.1_rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	11/14/06	11/14/06	127	Genomic	unknown
ss67088000	ILLUMINA\|HumanHap650Yv1.0_rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	11/14/06	11/14/06	127	Genomic	unknown
ss68792445	PERLEGEN\|PGP04749008	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	01/30/07	08/14/07	127	Genomic	unknown
ss70393555	ILLUMINA\|HumanHap300v2.0_rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	04/18/07	11/18/07	127	Genomic	unknown
ss70528247	ILLUMINA\|HumanHap550v3.0__rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	04/20/07	03/30/08	130	Genomic	unknown
ss71058524	ILLUMINA\|HumanHap650Yv3.0_rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	04/23/07	04/23/07	127	Genomic	unknown
ss74809751	AFFY\|SNP_M-182701	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	08/09/07	08/09/07	128	Genomic	unknown
ss75554286	ILLUMINA\|ILMN_Human_1M_rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	08/28/07	08/29/07	129	Genomic	unknown
ss76803849	AFFY\|AFFY_6_1M_SNP_A-8665321	fwd/T	A/G	tactccaagcatctcg	attccctgacaatgat	08/28/07	08/30/07	130	Genomic	unknown
ss77534236	HGSV\|Cor12156_SNV_20070510.chr1_210880681	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	10/09/07	10/13/07	129	Genomic	unknown
ss80007178	HGSV\|Cor18507_SNV_20070510.chr1_210880681	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	11/23/07	11/24/07	130	Genomic	unknown
ss83687318	KRIBB_YJKIM\|KHS519518	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	12/04/07	12/05/07	130	Genomic	unknown
ss83912169	HGSV\|Cor19240_SNV_20070510.chr1_210880681	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	11/30/07	12/06/07	130	Genomic	unknown
ss98002642	HUMANGENOME_JCVI\|1103675333012	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	03/30/08	03/30/08	130	Genomic	unknown
ss106630737	BGI\|BGI_rs1134647	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	09/16/08	06/17/09	130	Genomic	unknown
ss108933144	1000GENOMES\|CEU.trio.12.15.2008_243454_chr1_212558909	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	12/15/08	12/16/08	130	Genomic	unknown
ss111749203	1000GENOMES\|NA19240_2008_12_16_221433_chr1_212558909	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	12/16/08	12/17/08	130	Genomic	unknown
ss119202057	ILLUMINA-UK\|NA18507_000221174_NCBI36.1_chr1_212558909	fwd/T	A/G	ctctccatcacttttactccaagcatctcg	attccctgacaatgatagcctcgtagtact	01/21/09	01/22/09	130	Genomic	99 %

Fasta sequence (Legend)

 GAGGGAGAGA AGGAAGAAAT GGCTTGCTTT CTTTCCTTAG GGTTTGTCAG TTAAACCAAG
 TAATGGGGAA GAATGTTCTC TGGGGGTTCA ACATGTTAGT TTTGGGTTTT TTTTTTTTCG
 CCCGTTCCTT TCCTCTGTAT CATTTACAGC AAAAATAGGA TGTAGCTAGA AATCCCACGC
 TTTCTACTGG GTGAATAATG GATTATTTAT CCACAGATCT GGATAAGTTA GACAATGAGA
 AGAAGGATTT GATTCAGAGT GACATAGCTG CTCTCCATCA CTTTTACTCC AAGCATCTCG
 R
 ATTCCCTGAC AATGATAGCC TCGTAGTACT CTTTGCACAG GTAAGGACGC TGGCAGCAGG
 TAACACTCAG TCTGGCCTTT CCCTCTCCAA GGCCCTCTCC CTAGCAAGCA CTCAGTGAAG
 ATGAATGCAA ATAGAATGAT GGCATCTTCC TGACAACGAA GCTCTGAGCC AATTGGACCG
 TGTGTTGCCA TAGCCTTGCT CAGTGACCTT GAGCAGATCA AGGTCCCCTC TGCTGGCCCT
 CATTGATGGG TGGAGTGTAG GAAATTCGCC TCTGCCTCTG CCTCACAAAG AGTTCATGAA

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_021877 ABBA01048148 BI598885 Hs.66170

dbSNP Blast Analysis

UniGene Cluster ID
66170

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss48405195	HapMap-CEU	European	120	IG	0.867	0.133		0.584	0.933	0.067

	HapMap-HCB	Asian	88	IG	0.318	0.500	0.182	1.000	0.568	0.432

	HapMap-JPT	Asian	88	IG	0.250	0.523	0.227	1.000	0.511	0.489

	HapMap-YRI	Sub-Saharan African	120	IG	0.983	0.017		1.000	0.992	0.008

	AGI_ASP population	multiple	76	IG	0.763	0.211	0.026	0.655	0.868	0.132

ss68792445	HapMap-CEU	European	120	GF	0.867	0.133			0.933	0.067

	HapMap-HCB	Asian	90	GF	0.311	0.511	0.178		0.567	0.433

	HapMap-JPT	Asian	90	GF	0.267	0.511	0.222		0.522	0.478

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

ss9888353	AfAm	African American	10	IG	1.000				1.000

	Caucasian	European	24	IG	0.750	0.250		0.655	0.875	0.125

	Asian	Asian	10	IG	0.200	0.400	0.400	0.752	0.400	0.600

	CEPH	European	10	IG	0.800		0.200	0.050	0.800	0.200

	PDpanel	Global	46	IG	0.696	0.261	0.043	0.752	0.826	0.174

	CEPH		184	AF					0.930	0.070

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss48405195	1154
ss68792445	269	195	56	18
ss98002642	1	1
ss9888353	50	35	11	4

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1134647	1206	231	67	22

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5143	ss48405195	C/T	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	r27_ch1_YRI_illumina:golden_gate_1.0.0	272683
5143	ss68792445	A/A	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	chr1-HapMap-YRI

Genotype data submitted for	1206	samples from	1206	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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .