Reference SNP(refSNP) Cluster Report: rs716360

Reference SNP(refSNP) Cluster Report: rs716360

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:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NT_022792.17:g.14604231G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44536999 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs716360 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
ss55497	TSC-CSHL\|TSC0005559	fwd/B	C/T	ctttttctctctctctttcttcccatagag	gcacttggggattgtctaccataataaatg	09/06/00	10/25/06	86	Genomic	95 %
ss14601085	WI_SSAHASNP\|chr4.NT_022792.16_14603812	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	11/05/03	11/22/03	119	Genomic	unknown
ss19569255	CSHL-HAPMAP\|CSHL-HuDD-200402.chr4.NT_022792.16_14603812	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	02/20/04	03/04/04	120	Genomic	unknown
ss22137236	SSAHASNP\|WGSA-200403-chr4.chr4.NT_022792.16_14603812	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	03/20/04	03/21/04	121	Genomic	unknown
ss44536999	ABI\|hCV637614	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	07/19/05	11/03/06	126	Genomic	unknown
ss68920851	PERLEGEN\|PGP13145748	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	01/30/07	08/14/07	127	Genomic	unknown
ss78561364	HGSV\|Cor18507_SNV_20070510.chr4_182567440	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	10/19/07	10/20/07	129	Genomic	unknown
ss81884149	HGSV\|Cor19240_SNV_20070510.chr4_182567440	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	11/30/07	12/01/07	130	Genomic	unknown
ss84353786	HGSV\|Cor18517_SNV_20070510.chr4_182567440	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	12/06/07	12/07/07	130	Genomic	unknown
ss92915593	BCMHGSC_JDW\|JWB-1906892	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	02/26/08	03/03/08	129	Genomic	unknown
ss98895853	HUMANGENOME_JCVI\|1103654645001	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	04/01/08	04/02/08	130	Genomic	unknown
ss108654040	1000GENOMES\|CEU.trio.12.15.2008_1166119_chr4_182429285	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	12/15/08	12/16/08	130	Genomic	unknown
ss111143591	1000GENOMES\|NA19240_2008_12_16_1047465_chr4_182429285	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	12/16/08	12/17/08	130	Genomic	unknown
ss117324384	ILLUMINA-UK\|NA18507_000244162_NCBI36.1_chr4_182429285	rev/T	A/G	catttattatggtagacaatccccaagtgc	ctctatgggaagaaagagagagagaaaaag	01/18/09	01/19/09	130	Genomic	99 %

Fasta sequence (Legend)

 AAATATCCAG TCGTGCAGTT GCACAAAACT GTCCTGCTAG TCTTAATTGC CGCTTCATCT
 CCCCGCTTTC TAATGTGGTG GAAGATATTT TTCAAGCAGC AGCATGTGGC TCAGCAGCAG
 ACACCACAGG CACTTACGCT GGGAGTTTTG AAGCTTCCTG TATATGAGGA TGCTGCTGCT
 GGGCTAGATT GTCCAGGCAA CTGTAAATGC TGAGATTTTT ACCTTCTATT CTTCTGTTCT
 TCCTGAATAC TTCATCTCTG GGGGCAGTTT CTTTTTCTCT CTCTCTTTCT TCCCATAGAG
 Y
 GCACTTGGGG ATTGTCTACC ATAATAAATG AGCGGTCTTT CAAATGAATG GTTTATCCAC
 TTTGATCCTG GTATGTCCAA TTTTAATGCT TTATGCTCTA TAACAGTGGG GGAAAATGTC
 AGAAAGCAAT TTCTAAAGAA TTTGTATACT ATTTACCTAG TAGGACAATA AAATCAAAAA
 AAGTTTCTCC CGTGTATGAA TAGGAAAGAA ACCAATCTAC AACATCTTCA TTTGACTCAT
 TTTATAGTTT TGGTTTTGAG TGTACCTTTA TTTGGTAGCT CTTTGAGAAT CTCATATGTA

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_022792 ABBA01070479

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss44536999	HapMap-CEU	European	120	IG	0.083	0.450	0.467	0.752	0.308	0.692

	HapMap-HCB	Asian	90	IG	0.111	0.356	0.533	0.371	0.289	0.711

	HapMap-JPT	Asian	88	IG	0.023	0.364	0.614	0.439	0.205	0.795

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.467	0.450	0.584	0.317	0.683

	AoD_African_American		90	AF					0.340	0.660

	AoD_Caucasian		92	AF					0.350	0.650

ss55497	TSC_42_AA		82	AF					0.293	0.707

	TSC_42_C		74	AF					0.365	0.635

	TSC_42_A		82	AF					0.268	0.732

ss68920851	HapMap-CEU	European	120	GF	0.100	0.417	0.483		0.308	0.692

	HapMap-HCB	Asian	90	GF	0.067	0.400	0.533		0.267	0.733

	HapMap-JPT	Asian	90	GF	0.067	0.333	0.600		0.233	0.767

	HapMap-YRI	Sub-Saharan African	120	GF	0.083	0.467	0.450		0.317	0.683

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss44536999	515
ss98895853	1

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs716360	526

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
214	ss44536999	A/G	CSHL-HAPMAP	HapMap-CEU	NA07345	CEPH1345.13	r27_ch4_CEU_wicgr:genotype_protocol_1
400	ss44536999	G/G	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	r27_ch4_CEU_wicgr:genotype_protocol_1
548	ss44536999	A/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch4_CEU_wicgr:genotype_protocol_1
5157	ss44536999	G/G	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	r27_ch4_CHB_wicgr:genotype_protocol_1
5160	ss44536999	G/G	CSHL-HAPMAP	HapMap-HCB	NA18545	CH18545	r27_ch4_CHB_wicgr:genotype_protocol_1
5201	ss44536999	A/G	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r27_ch4_JPT_wicgr:genotype_protocol_1
5205	ss44536999	A/G	CSHL-HAPMAP	HapMap-JPT	NA18953	JA18953	r27_ch4_JPT_wicgr:genotype_protocol_1
5245	ss44536999	G/G	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	r27_ch4_YRI_wicgr:genotype_protocol_1
5259	ss44536999	A/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r27_ch4_YRI_wicgr:genotype_protocol_1
5303	ss44536999	A/G	CSHL-HAPMAP	HapMap-YRI	NA19141	YOR071.03	r27_ch4_YRI_wicgr:genotype_protocol_1

Genotype data submitted for	526	samples from	526	individuals	Individual with multiple genotypes submission:	0

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .