Reference SNP(refSNP) Cluster Report: rs1382602

Reference SNP(refSNP) Cluster Report: rs1382602

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/130
Map to Genome Build:	36.3

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

HGVS Names
NM_001134734.1:c.703C>G
NM_032884.2:c.133C>G
NM_032884.3:c.133C>G
NP_001128206.1:p.Gln235Glu
NP_116273.2:p.Gln45Glu
NT_032977.8:g.4635126C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43842236 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1382602 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
ss2173397	TSC-CSHL\|TSC0544922	fwd/T	C/G	gtgggaactgggacagaagcttgctgactt	caagttggagtcacctaggatgcggcccct	10/19/00	04/07/04	88	Genomic	95 %
ss2506147	SC_JCM\|AC022251.2_61373	fwd/T	C/G	gtgggaactgggacagaagcttgctgactt	caagttggagtcacctaggatgcggcccct	11/03/00	10/10/03	89	Genomic	unknown
ss4981790	YUSUKE\|IMS-JST153195	rev/B	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	08/12/02	10/10/03	108	Genomic	unknown
ss5559306	TSC-CSHL\|TSC0610021	fwd/T	C/G	gtgggaactgggacagaagcttgctgactt	caagttggagtcacctaggatgcggcccct	09/21/02	05/16/04	108	Genomic	unknown
ss6240702	SC_JCM\|NT_004511.12_1967220	rev/B	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	01/10/03	10/10/03	111	Genomic	unknown
ss23180484	PERLEGEN\|afd1008443	rev/B	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	08/10/04	09/13/04	123	Genomic	unknown
ss28497508	MGC_GENOME_DIFF\|37548184-C4601575G	rev/B	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	08/20/04	08/20/04	126	cDNA	unknown
ss28512225	MGC_GENOME_DIFF\|BC007637x37548184-C4601575G	rev/B	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	08/25/04	08/25/04	126	cDNA	unknown
ss43842236	ABI\|hCV8702316	rev/	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	07/18/05	11/03/06	126	Genomic	unknown
ss65725621	ILLUMINA\|Human1-rs1382602	fwd/T	C/G	gtgggaactgggacagaagcttgctgactt	caagttggagtcacctaggatgcggcccct	10/10/06	10/10/06	127	Genomic	unknown
ss68763206	PERLEGEN\|PGP01008443	rev/	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	01/30/07	08/14/07	127	Genomic	unknown
ss74808091	AFFY\|SNP_M-179701	fwd/T	C/G	gtgggaactgggacagaagcttgctgactt	caagttggagtcacctaggatgcggcccct	08/09/07	08/09/07	128	Genomic	unknown
ss81285723	HGSV\|Cor18507_SNV_20070510.chr1_34332301	rev/	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	11/26/07	11/29/07	130	Genomic	unknown
ss86272114	CORNELL\|hCV8702316	rev/	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	01/21/08	01/21/08	129	Genomic	unknown
ss99199431	HUMANGENOME_JCVI\|1103675065168	rev/	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	04/03/08	04/03/08	130	Genomic	unknown
ss118613565	ILLUMINA-UK\|NA18507_000041058_NCBI36.1_chr1_34435795	rev/	C/G	aggggccgcatcctaggtgactccaacttg	aagtcagcaagcttctgtcccagttcccac	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 AGTGGTGCCT CTCCACAGCA GGGTCAGCCT TGGGCTTGGA ACAGATCTTG GCAAACACTG
 GGAGCTGCCT CTTCTGAGCA GGGAGCTCAG GGAGCTTGTC AGGACGTGCA GGAGGAGGTC
 GGGGAGGCAG CAGCAGAAAT GGGCTCAGCC CTGTGGGCTC CTTGGGTCCA GGGCCACTGA
 ACAGGTTGTC CTGTAGGAAG TCCTTGGTGA CCCTTGTCTT GTCCAGCACA TTCTTGTTGT
 CAGGGACCTT GGATGTCTCA GTGGACTTCA GTGGGAACTG GGACAGAAGC TTGCTGACTT
 S
 CAAGTTGGAG TCACCTAGGA TGCGGCCCCT GTCCTCTGTC CCCTTGCTGC TCTTGACCTC
 GGCGGCACAC AGAATGTCTG TGACAGTAGA AGTGGCAGAA TCACAGTCCT GCCTGCTGCT
 GATAACGGGC ATGGCCACCT TCTGCTTCAG AAGCTTGTCT CCGACAATGA TGGAGGCTCT
 GGGGCGCTCA TTACTGCCTG CCACTAGAGG AGGGGCAAGA ATGCAGGGAG CCAGCTCTCT
 GGTCCCCTCG GGAGAGCTGC CGGGTACCTC CAGCTCCCCA GAACTCTCTT CGACCAGGAT

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_004511.6 ABBA01023367 AL359498 BC007637

dbSNP Blast Analysis

UniGene Cluster ID
194610

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G	N
ss2173397	AfAm	African American	40	IG	0.400	0.500	0.100	0.752	0.650	0.350

	Caucasian	European	26	IG	0.077	0.462	0.462	1.000	0.308	0.692

	Asian	Asian	40	IG		0.250	0.750	0.527	0.125	0.875

	CEPH	European	34	IG	0.176	0.412	0.412	0.655	0.382	0.618

	PDpanel	Global	42	IG	0.238	0.190	0.571	0.010	0.333	0.667

ss23180484	AFD_EUR_PANEL	European	48	IG	0.083	0.292	0.625	0.403	0.229	0.771

	AFD_AFR_PANEL	African American	44	IG	0.500	0.364	0.136	0.479	0.682	0.318

	AFD_CHN_PANEL	Asian	46	IG		0.261	0.739	0.479	0.130	0.870

ss43842236	HapMap-CEU	European	118	IG	0.051	0.288	0.661	0.584	0.195	0.805

	HapMap-HCB	Asian	90	IG	0.022	0.222	0.756	1.000	0.133	0.867

	HapMap-JPT	Asian	88	IG	0.045	0.295	0.659	0.752	0.193	0.807

	HapMap-YRI	Sub-Saharan African	120	IG	0.683	0.267	0.050	0.403	0.817	0.183

ss5559306	CEPH		184	AF					0.160	0.840

	CHMJ	Asian	74	IG					0.676	0.176	0.149

ss68763206	HapMap-CEU	European	120	GF	0.050	0.283	0.667		0.192	0.808

	HapMap-HCB	Asian	90	GF	0.022	0.267	0.711		0.156	0.844

	HapMap-JPT	Asian	90	GF	0.044	0.289	0.667		0.189	0.811

	HapMap-YRI	Sub-Saharan African	120	GF	0.683	0.267	0.050		0.817	0.183

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss2173397	93	17	34	42
ss23180484	71	35	21	13
ss43842236	523	123	77	66
ss99199431	1		1

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs1382602	660	170	121	121

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5171	ss43842236	C/C	CSHL-HAPMAP	HapMap-HCB	NA18563	CH18563	r27_ch1_CHB_bcm:genotype_0002	226515
5180	ss43842236	C/C	CSHL-HAPMAP	HapMap-HCB	NA18623	CH18623	r27_ch1_CHB_bcm:genotype_0002	226515

Genotype data submitted for	690	samples from	660	individuals	Individual with multiple genotypes submission:	29

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .