Reference SNP(refSNP) Cluster Report: rs4353

Reference SNP(refSNP) Cluster Report: rs4353

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	36/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_000789.2:c.2913-375G>A
NM_152830.1:c.1191-375G>A
NT_010783.14:g.20222433A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss90499 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4353 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
ss4742	DEBNICK\|dcp1-18912	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	05/03/99	12/23/03	36	Genomic	unknown
ss90499	TSC-CSHL\|TSC0109264	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	09/06/00	04/07/04	92	Genomic	95 %
ss6877014	WI_SSAHASNP\|NT_035428.2_994975	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	02/12/03	10/10/03	111	Genomic	unknown
ss23142663	PARC\|ACE-018342	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	05/07/04	05/16/04	126	Genomic	unknown
ss24456408	PERLEGEN\|afd4165168	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	08/10/04	09/13/04	123	Genomic	unknown
ss44011767	ABI\|hCV589818	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	07/18/05	11/03/06	126	Genomic	unknown
ss65718744	ILLUMINA\|Human1-rs4353	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	10/10/06	10/10/06	127	Genomic	unknown
ss67329221	ILLUMINA\|HumanHap550v1.1_rs4353	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	11/14/06	11/14/06	127	Genomic	unknown
ss67729789	ILLUMINA\|HumanHap650Yv1.0_rs4353	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	11/14/06	11/14/06	127	Genomic	unknown
ss68227995	ILLUMINA\|HumanHap250Sv1.0_rs4353	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	12/06/06	12/07/06	127	Genomic	unknown
ss70801096	ILLUMINA\|HumanHap550v3.0__rs4353	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	04/20/07	03/30/08	130	Genomic	unknown
ss71379940	ILLUMINA\|HumanHap650Yv3.0_rs4353	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	04/23/07	04/23/07	127	Genomic	unknown
ss75915917	ILLUMINA\|ILMN_Human_1M_rs4353	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	08/28/07	08/29/07	129	Genomic	unknown
ss78187380	HGSV\|Cor12878_SNV_20070510.chr17_58924154	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	10/17/07	10/18/07	129	Genomic	unknown
ss82754448	HGSV\|Cor19240_SNV_20070510.chr17_58924154	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	11/30/07	12/03/07	130	Genomic	unknown
ss83346413	KRIBB_YJKIM\|KHS439891	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	12/04/07	12/04/07	130	Genomic	unknown
ss84149615	PHARMGKB_PARC\|PS206642_PA151798079_18342	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	12/06/07	12/10/07	130	Genomic	unknown
ss90634048	BCMHGSC_JDW\|JWB-1038663	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	02/26/08	02/29/08	129	Genomic	unknown
ss109855951	1000GENOMES\|CEU.trio.12.15.2008_3421273_chr17_58924154	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	12/15/08	12/16/08	130	Genomic	unknown
ss113710691	1000GENOMES\|NA19240_2008_12_16_3080159_chr17_58924154	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	12/18/08	12/18/08	130	Genomic	unknown
ss118097392	ILLUMINA-UK\|NA18507_000064314_NCBI36.1_chr17_58924154	fwd/T	A/G	agaaacagttgtttccttcagggagcctcc	tcttgggagataaagcatgtgtacatggga	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 CCATTCATCC TGGCCATAAG AATTCTTGGG GTGAATAAGT TTGTCGCTGT TGGGCCGCAT
 GAGATGCAGA ATCGCCCACT CTCACCCCTG ACAGAAACAG TTGTTTCCTT CAGGGAGCCT
 CC
 R
 TCTTGGGAGA TAAAGCATGT GTACATGGGA ACCCACTGGC CACACATTCT CTAGAAAGTA
 CACAATGTCC CAGTGCCTCT AGAGCAAGCA CTTTGTACAG TCAGAAAGCA ACAGGTGGTG
 GGGGCTGGAG TCATTCAGGA AAATGGGAGG CAGAGGAATG GCCTGAACGG CCCGATGCTA
 GGGGCTTCTG CCCCCAGATT CCCTCTTACG CACACTCAGT GGTTGCCCTT CCCCTCCCTC
 CCCACAGTGC TGTGTCCCCT GCATGCTGCA GTGCTGGGGT CTGCCCTGGG TATAGCAAGG
 CCCACTGTTC CCTTATGCCC AGGGCTTCTC ACTGTCCTCT CCCAACACCC TCTCCCCCAC
 TCCACTATTC CTAGGATCAA GCAGTGCACC ACCGTGAACT TGGAGGACCT GGTGGTGGCC
 CACCACGAAA TGGGCCACAT CCAGTATTTC ATGCAGTACA AAGACTTACC TGTGGCCTTG
 AGGGAGGTGC CAACCCCGGC TTACATGAGG CCATTGGGGA CGTGCTAGCC CTCTGATGTC
 TACGCCCAAG CACCTGCACA GTCTAACCTG CTGAGCATGA GGGTGGCACA CCGTGAGAAG
 AACG

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
NC_000017.6 AF118569.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	A	G
ss23142663	PARC-EUROPEAN-PANEL	European	42	AF								0.619	0.381

ss24456408	AFD_EUR_PANEL	European	42	IG	0.381	0.429			0.190		0.655	0.595	0.405

	AFD_AFR_PANEL	African American	44	IG	0.455	0.409			0.136		0.752	0.659	0.341

	AFD_CHN_PANEL	Asian	28	IG	0.214	0.286			0.500		0.200	0.357	0.643

ss44011767	AoD_African_American		90	AF								0.590	0.410

	AoD_Caucasian		92	AF								0.550	0.450

	AoD_Chinese		90	AF								0.390	0.610

	AoD_Japanese		90	AF								0.420	0.580

ss84149615	PA151798080		84	AF								0.631	0.369

ss90499	SC_12_A	Asian	24	AF			0.417	0.333		0.250	0.001	0.420	0.580

	SC_12_AA	African American	24	AF			0.167	0.333		0.500	0.001	0.670	0.330

	SC_12_C	European	24	AF			0.286	0.571		0.143	0.010	0.376	0.624

	SC_95_C	European	94	IG	0.255	0.362			0.383		0.100	0.436	0.564

	HapMap-CEU	European	120	IG	0.283	0.400			0.317		0.150	0.483	0.517

	HapMap-HCB	Asian	90	IG	0.044	0.422			0.533		0.479	0.256	0.744

	HapMap-JPT	Asian	88	IG	0.182	0.659			0.159		0.050	0.511	0.489

	HapMap-YRI	Sub-Saharan African	120	IG	0.350	0.467			0.183		1.000	0.583	0.417

Concordant Genotype	Total Sample	A/A	A/G	C/C	C/T	G/G	T/T
ss24456408	66	18	20			14
ss90499	1279	369	565	12	7	290	7

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs4353	1327	382	578	12	7	301	7

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
114	ss90499	A/A	TSC-CSHL	SC_95_C	CEPH1331.12		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844879
114	ss90499	T/T	TSC-CSHL	SC_12_C	CEPH1331.12		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844879
229	ss90499	C/T	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844879
229	ss90499	G/G	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844879
229	ss90499	G/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r27_ch17_CEU_illumina:human_1m_beadchip	844879
231	ss90499	A/G	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844879
231	ss90499	C/T	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844879
429	ss90499	A/A	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844879
429	ss90499	C/T	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844879
429	ss90499	A/A	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r27_ch17_CEU_illumina:human_1m_beadchip	844879
430	ss90499	C/T	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844879
430	ss90499	G/G	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844879
840	ss90499	T/T	TSC-CSHL	SC_12_AA	NA17109		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	844879
840	ss24456408	A/A	PERLEGEN	AFD_AFR_PANEL	NA17109		71_IND_CHR_17
842	ss90499	T/T	TSC-CSHL	SC_12_AA	NA17111		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	844879
842	ss24456408	A/A	PERLEGEN	AFD_AFR_PANEL	NA17111		71_IND_CHR_17
845	ss90499	C/T	TSC-CSHL	SC_12_AA	NA17114		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	844879
845	ss24456408	A/G	PERLEGEN	AFD_AFR_PANEL	NA17114		71_IND_CHR_17
865	ss90499	C/T	TSC-CSHL	SC_12_AA	NA17134		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	844879
865	ss24456408	A/G	PERLEGEN	AFD_AFR_PANEL	NA17134		71_IND_CHR_17
867	ss90499	T/T	TSC-CSHL	SC_12_AA	NA17136		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	844879
867	ss24456408	A/A	PERLEGEN	AFD_AFR_PANEL	NA17136		71_IND_CHR_17

Genotype data submitted for	1409	samples from	1327	individuals	Individual with multiple genotypes submission:	72

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .