Reference SNP(refSNP) Cluster Report: rs3803430

Reference SNP(refSNP) Cluster Report: rs3803430

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/130
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_000693.2:c.1156A>G
NP_000684.2:p.Met386Val

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48424588 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3803430 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
ss4989817	YUSUKE\|IMS-JST162260	fwd/B	C/T	tgggtttgatgaagagccccttgtcttcca	ggctgagcccccgcattccagcttggcccc	08/12/02	10/10/03	107	Genomic	unknown
ss6311955	RIKENSNPRC\|ssj0004337	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	01/15/03	10/10/03	111	Genomic	unknown
ss12343035	WI_SSAHASNP\|chr15.NT_035325.4_2887552	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	07/04/03	10/10/03	116	Genomic	unknown
ss23641698	PERLEGEN\|afd4394104	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	08/10/04	09/13/04	123	Genomic	unknown
ss48424588	APPLERA_GI\|hCV25767417	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	09/28/05	11/03/06	126	Genomic	unknown
ss65727942	ILLUMINA\|Human1-rs3803430	fwd/B	C/T	tgggtttgatgaagagccccttgtcttcca	ggctgagcccccgcattccagcttggcccc	10/10/06	10/10/06	127	Genomic	unknown
ss74806623	AFFY\|SNP_M-176422	fwd/B	C/T	tgggtttgatgaagagccccttgtcttcca	ggctgagcccccgcattccagcttggcccc	08/09/07	08/09/07	128	Genomic	unknown
ss74896543	ILLUMINA\|ILMN_Human_1M_rs3803430	fwd/B	C/T	tgggtttgatgaagagccccttgtcttcca	ggctgagcccccgcattccagcttggcccc	08/28/07	08/29/07	129	Genomic	unknown
ss84160438	PHARMGKB_AB_DME\|PS206162_PA150153309_301	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	12/06/07	12/10/07	130	Genomic	unknown
ss86348215	CANCER-GENOME\|16766	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	01/25/08	01/25/08	129	Genomic	unknown
ss105439657	SNP500CANCER\|ALDH1A3-02	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	09/05/08	09/05/08	130	Genomic	unknown
ss114669584	1000GENOMES\|NA19240_2008_12_16_2901680_chr15_99263338	rev/T	A/G	ggggccaagctggaatgcgggggctcagcc	tggaagacaaggggctcttcatcaaaccca	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 GCTGTATCAT GCTTGGAGTT CGCCAGAGGC AGGACAAAAC GGCTTCCCTA GGGACCCCAA
 AGGAGAGGGG AAAGACCACA CAGAAAAAAC AACAACGACA ACAACAGCAA CAAAAACAAA
 AAAACACTCA GATCACAAGG ATTTCTGGGA TCCCTGGGCC CTAGGGAAGG ACTCGTGTTT
 GAAAGGCCCC GCAAGTCGTA GCCTTGCCAC AGCCCCCTTG TACCTCCTCT TTGGCAATCC
 GCATGTTGTC TGTGACTTCT GAGAAGACAG TGGGTTTGAT GAAGAGCCCC TTGTCTTCCA
 Y
 GGCTGAGCCC CCGCATTCCA GCTTGGCCCC TTCCTTCTTC CCACTCTCGA TCAGCTCTAA
 GATTTTGTCG AACTGCTTTT GATCAATCTG CAAGACACAA ACAAGAAGTA CAGCCTGGCT
 TCCTTCTGGG CAGTGGCTGC CATCTCATGT TTTCAGTGGC CTTCAACATG ATCAGCCATC
 CTCCCTCTGC ATGTTCTTGT CAAGCCATGA TCCATGTAAC TAATGAGCCT TGCAGGCAAA
 TATTCCTCTG ATGCACAGAG CTGGGCTCTT TGGAGCAGGG GAGAGATGGG GAGATAGACT

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_035325

dbSNP Blast Analysis

UniGene Cluster ID
459538

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss105439657	P1		204	GF	0.029	0.108	0.863		0.083	0.917

	CAUC1		62	GF		0.065	0.935		0.032	0.968

	AFR1		48	GF	0.125	0.208	0.667		0.229	0.771

	HISP1		46	GF		0.087	0.913		0.043	0.957

	PAC1		48	GF		0.083	0.917		0.042	0.958

	P2		420	GF	0.043	0.176	0.781		0.131	0.869

	CAUC2		120	GF		0.017	0.983		0.008	0.992

	AFR2		120	GF	0.150	0.383	0.467		0.342	0.658

	P3		558	GF	0.043	0.158	0.799		0.122	0.878

	CAUC3		132	GF		0.015	0.985		0.008	0.992

	AFR3		150	GF	0.160	0.453	0.387		0.387	0.613

	HISP3		98	GF			1.000			1.000

	PAC3		178	GF		0.101	0.899		0.051	0.949

	ASI2		180	GF		0.144	0.856		0.072	0.928

ss23641698	AFD_EUR_PANEL	European	46	IG		0.043	0.957	1.000	0.022	0.978

	AFD_AFR_PANEL	African American	46	IG		0.565	0.435	0.100	0.283	0.717

	AFD_CHN_PANEL	Asian	46	IG		0.130	0.870	0.752	0.065	0.935

ss48424588	HapMap-CEU	European	120	IG		0.017	0.983	1.000	0.008	0.992

	HapMap-HCB	Asian	90	IG		0.156	0.844	0.584	0.078	0.922

	HapMap-JPT	Asian	88	IG		0.136	0.864	0.655	0.068	0.932

	HapMap-YRI	Sub-Saharan African	118	IG	0.153	0.390	0.458	0.254	0.347	0.653

	AGI_ASP population	multiple	76	IG	0.053	0.184	0.763	0.150	0.145	0.855

ss4989817	JBIC-allele		1496	AF					0.078	0.922

ss84160438	PA150153310		356	AF					0.110	0.890

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.213+/-0.247	1302	1091	15	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .