Reference SNP(refSNP) Cluster Report: rs165339

Reference SNP(refSNP) Cluster Report: rs165339

refSNP ID: rs165339
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001447.1:c.12518-130C>A
NT_029289.10:g.12048724G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss93291453 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs165339 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
ss324433	KWOK\|OVLP-000621-33490	rev/T	A/C	atgttatcaacgtaagccaacagagacaac	tgcacagatgggcctatgcccacccactcc	06/30/00	10/10/03	79	Genomic	99 %
ss453925	KWOK\|OVLP-000621-384389	rev/T	A/C	atgttatcaacgtaagccaacagagacaac	tgcacagatgggcctatgcccacccactcc	06/30/00	10/10/03	79	Genomic	99 %
ss556926	SC_JCM\|AC011337.3_53893	fwd/B	G/T	ggagtgggtgggcataggcccatctgtgca	gttgtctctgttggcttacgttgataacat	07/12/00	10/25/06	80	Genomic	unknown
ss1120684	KWOK\|OVLP-000804-312936	fwd/B	G/T	ggagtgggtgggcataggcccatctgtgca	gttgtctctgttggcttacgttgataacat	09/02/00	10/10/03	86	Genomic	99 %
ss1121185	KWOK\|OVLP-000804-315059	fwd/B	G/T	ggagtgggtgggcataggcccatctgtgca	gttgtctctgttggcttacgttgataacat	09/02/00	10/10/03	86	Genomic	99 %
ss1786354	KWOK\|OVLP-000925-442361	fwd/B	G/T	ggagtgggtgggcataggcccatctgtgca	gttgtctctgttggcttacgttgataacat	10/05/00	10/10/03	87	Genomic	99 %
ss1786526	KWOK\|OVLP-000925-444408	fwd/B	G/T	ggagtgggtgggcataggcccatctgtgca	gttgtctctgttggcttacgttgataacat	10/05/00	10/10/03	87	Genomic	99 %
ss93291453	BCMHGSC_JDW\|JWB-2056491	fwd/B	G/T	ggagtgggtgggcataggcccatctgtgca	gttgtctctgttggcttacgttgataacat	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGGGTTGAGT GGCGGTGAGC CGAGGGCGGC AGAGGGCCCT GAGTCACTTC GGAGTGGGGG
 TATTCCCAGC GTTCGTTCCT GGAGTAAGTA GGGGGCCAGA CCATGGCTCC GCCAGGGTAC
 ACTGAAAGGG AACAGCAAGA TAGGGTGAGC TCATTTTCTC CCCGGAAGGT TTCAGCTGGC
 TCTATAGCAA CTATATATAA CCTAGCGAGT GGTGGAGATG GGAGTGGGTG GGCATAGGCC
 CATCTGTGCA
 K
 GTTGTCTCTG TTGGCTTACG TTGATAACAT AGAATCCAAT GGGACAAGCT CAAGGCTAGA
 GGTTTGACCT AAGGCCAGCC CATCTTGCAA ATCCCTGCCA CTAATCTGAG GGTCAGTGAA
 CAAGGGAAGG ATTTGGATGT CTCCATGCAA CCCACCCCCA CAGCTGGATA CAGTAACTCC
 ATCCCAAGTC CTACTGGTGA GTTTCATCCC CTTAACTGAA GGAAACACAC ACACAGTTTG
 GACTCACTCA

GeneView

GeneView via analysis of contig annotation: FAT2 FAT 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_029289->NM_001447

function

HuRef

NW_001838953->NM_001447

function

Celera

NW_922784->NM_001447

function

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


reference	NT_029289->NM_001447->NP_001438	12048724	reverse	intron

HuRef	NW_001838953->NM_001447->NP_001438	4251060	forward	intron

Celera	NW_922784->NM_001447->NP_001438	24595213	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs165339 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838953.2	4251060	146031185	minus	C	alt_assembly_8	HuRef	HuRef	view	250
5	NW_922784.1	24595213	146967197	plus	G	alt_assembly_1	Celera	Celera	view	250
5	NT_029289.10	12048724	150865981	plus	G	ref_assembly	reference	reference	view	250

NCBI Resource Links

Submitter-Referenced
GenBank
AC011337.3 AC025433 AC025433.4 AC034205.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC011337.5 AC034205.4 NC_000005.8	AC025433.4

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	HWP	G	T
ss556926	HapMap-CEU	European	120	IG	0.683	0.317	0.150	0.842	0.158

	HapMap-HCB	Asian	88	IG	0.932	0.068	1.000	0.966	0.034

	HapMap-JPT	Asian	90	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	116	IG	0.966	0.034	1.000	0.983	0.017

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.109+/-0.207	270	210	0	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 .