Reference SNP(refSNP) Cluster Report: rs685167

Reference SNP(refSNP) Cluster Report: rs685167

refSNP ID: rs685167
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_014572.2:c.476-272G>A
NT_024524.13:g.2543715C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss71642802 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs685167 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
ss858821	SC_JCM\|AL161613.4_92650	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	07/27/00	10/25/06	83	Genomic	unknown
ss1709786	KWOK\|OVLP-000925-589902	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	10/05/00	10/10/03	87	Genomic	99 %
ss2604450	SC_JCM\|AL161613.5_137513	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	11/03/00	10/10/03	92	Genomic	unknown
ss11060706	BCM_SSAHASNP\|chr13.NT_009799.12_2543715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	07/01/03	10/10/03	116	Genomic	unknown
ss12232001	WI_SSAHASNP\|chr13.NT_009799.12_2543715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	07/04/03	10/10/03	116	Genomic	unknown
ss13257877	SC_SNP\|NT_009799.12_2543715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	10/22/03	02/27/04	119	Genomic	unknown
ss16278910	SC_SNP\|NT_024524.13_2543715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	11/18/03	11/22/03	120	Genomic	unknown
ss19972220	CSHL-HAPMAP\|CSHL-HuFF-200402.chr13.NT_024524.13_2543715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	02/21/04	03/04/04	120	Genomic	unknown
ss21126009	SSAHASNP\|WGSA-200403-chr13.chr13.NT_024524.13_2543715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	03/19/04	03/19/04	121	Genomic	unknown
ss43455010	ABI\|hCV2204837	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	07/18/05	11/03/06	126	Genomic	unknown
ss66592343	ILLUMINA\|HumanHap300v1.1_rs685167	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	11/09/06	11/09/06	127	Genomic	unknown
ss67507972	ILLUMINA\|HumanHap550v1.1_rs685167	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	11/14/06	11/14/06	127	Genomic	unknown
ss67871067	ILLUMINA\|HumanHap650Yv1.0_rs685167	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	11/14/06	11/14/06	127	Genomic	unknown
ss70891349	ILLUMINA\|HumanHap550v3.0__rs685167	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	04/20/07	03/31/08	130	Genomic	unknown
ss71484364	ILLUMINA\|HumanHap650Yv3.0_rs685167	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	04/23/07	04/23/07	127	Genomic	unknown
ss71642802	SI_EXO\|NT_024524.13_2543715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	05/07/07	03/31/08	127	Genomic	unknown
ss74928524	ILLUMINA\|ILMN_Human_1M_rs685167	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	08/28/07	08/29/07	129	Genomic	unknown
ss77367627	HGSV\|Cor12156_SNV_20070510.chr13_20461715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	10/09/07	10/12/07	129	Genomic	unknown
ss79236445	ILLUMINA\|HumanHap300v2.0_rs685167	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	04/18/07	11/18/07	130	Genomic	unknown
ss83517536	KRIBB_YJKIM\|KHS480259	fwd/T	A/G	tgtggtccccagggggcagggacgcacctc	ggatgtggacgcagtcttctcttctgccct	12/04/07	12/05/07	130	Genomic	unknown
ss85041713	HGSV\|Cor19129_SNV_20070510.chr13_20461715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	12/06/07	12/08/07	130	Genomic	unknown
ss85208523	HGSV\|Cor18517_SNV_20070510.chr13_20461715	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	12/06/07	12/08/07	130	Genomic	unknown
ss89514111	BCMHGSC_JDW\|JWB-0636671	rev/B	C/T	agggcagaagagaagactgcgtccacatcc	gaggtgcgtccctgccccctggggaccaca	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGTCCTTCCT TCCGGTGTCT GTTTCAGATG AGATGTACAA AATGGAGGTC AGGATTAAGG
 TAGCAGCAGA TGAAATCAAT CTGGATATTT GTAGAGGGGT TTTGTGTGGT TTTTATTATT
 GTGTATATAT TGCTTTGTTT TAATATAGAC AAAAAAAACT AGAAAGTCTT TTAATTTGGA
 AAAGAGGTGA AAGAGAAGTG GAGCAGCTGC TGCACAGTGG ATACAGTTCT GCCCTTTCTG
 TGAGGGAGCA GCGCTTTGGG AACCGTGTGT CGGTAAACTC AGCCCCCCAC AATTTGGGCA
 TGATAGGGTT TTGAAAAAGC AAAGCTGGCT ATGCAGACGG CTCCCTAGCC TGACAGGAGA
 GTGACCCCAG TGTGGTCCCC AGGGGGCAGG GACGCACCTC
 R
 GGATGTGGAC GCAGTCTTCT CTTCTGCCCT TGGCCCTCCC ATGTGCCCTT CAGCTTGTCT
 CCACTCTGCT AACACATTAG GGCAACTGGT CCTGCTGGCA GGGCAGAGGG GAGTCCACTG
 ACCCTGTGCT GGGCAGAATG CAGCACGTCA GGGCCCAGGG TTCAAGACCC TCAGCCCCGA
 GGGCAGCGCT AGAGTGGGGA CCAGCCTGGA AGTGCCAGAA CCCACTGATC ACACCCACTC
 TGATGCTGTC TTCCTGTTTT TTCCACTGCA GGAAAGGGGC TCATGCCAAC CCCAGTGACG
 CGGAGGCCCA GCTTCGAAGG AACCGGCGAT TCGTTTGCGT CCTACCACCA GCTGAGCGGT
 ACCCCCTACG AGGGCCCAAG CTTCGGCGCT GACGGCCCCA

GeneView

GeneView via analysis of contig annotation: LATS2 LATS, large tumor suppressor, homolog 2 (Drosophila)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_024524->NM_014572

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_024524->NM_014572->NP_055387	2543715	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs685167 maps exactly once on NCBI human chromosome 13

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
13	NW_001838069.1	2366677	2366677	minus	T	alt_assembly_8	HuRef	HuRef	view	400
13	NW_925473.1	2360876	2625652	minus	T	alt_assembly_1	Celera	Celera	view	400
13	NT_024524.13	2543715	20461715	minus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024524.13 AL356285 AL356285.2

dbSNP Blast Analysis
GenBank HTGS Finished:
AL356285.9

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss43455010	HapMap-CEU	European	120	IG	0.817	0.183		0.439	0.908	0.092

	HapMap-HCB	Asian	90	IG	1.000			1.000	1.000

	HapMap-JPT	Asian	90	IG	1.000			1.000	1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.400	0.467	0.133	1.000	0.633	0.367

ss71642802	HapMap-CEU	European	120	IG	0.817	0.183			0.908	0.092

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.400	0.467	0.133		0.633	0.367

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.228+/-0.249	270	210	0	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 .