Reference SNP(refSNP) Cluster Report: rs9282

Reference SNP(refSNP) Cluster Report: rs9282

refSNP ID: rs9282
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/129
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
NM_019034.2:c.227-812T>C
NT_009775.16:g.12789419A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss89426845 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9282 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
ss11354	CGAP-GAI\|53525	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	08/23/99	10/10/03	52	cDNA	99 %
ss1529996	LEE\|525051	rev/T	A/G	tttgcttttttcttcttcttctttataaac	attctttgtaactttttgtattgacagttt	09/13/00	10/10/03	86	cDNA	unknown
ss4419507	LEE\|e525051	rev/T	A/G	tttgcttttttcttcttcttctttataaac	attctttgtaactttttgtattgacagttt	04/26/02	10/10/03	106	cDNA	unknown
ss11028586	BCM_SSAHASNP\|chr12.NT_009487.15_187781	rev/T	A/G	tttgcttttttcttcttcttctttataaac	attctttgtaactttttgtattgacagttt	07/01/03	04/07/04	116	Genomic	unknown
ss16256688	CGAP-GAI\|1513220	fwd/B	C/T	aactgtcaatacaaaaagttacaaagaatt	gtttataaagaagaagaagaaaaaagcaaa	11/18/03	11/22/03	123	cDNA	unknown
ss23322835	PERLEGEN\|afd4230432	rev/T	A/G	tttgcttttttcttcttcttctttataaac	attctttgtaactttttgtattgacagttt	08/10/04	09/13/04	123	Genomic	unknown
ss66597590	ILLUMINA\|HumanHap300v1.1_rs9282	fwd/T	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	11/09/06	11/09/06	127	Genomic	unknown
ss67897572	ILLUMINA\|HumanHap550v1.1_rs9282	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	11/14/06	11/14/06	127	Genomic	unknown
ss68031232	ILLUMINA\|HumanHap650Yv1.0_rs9282	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	11/14/06	11/15/06	127	Genomic	unknown
ss71595886	ILLUMINA\|HumanHap650Yv3.0_rs9282	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	04/23/07	04/23/07	127	Genomic	unknown
ss74926271	ILLUMINA\|ILMN_Human_1M_rs9282	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	08/28/07	08/29/07	129	Genomic	unknown
ss79290336	ILLUMINA\|HumanHap300v2.0_rs9282	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	04/18/07	11/18/07	130	Genomic	unknown
ss83349051	KRIBB_YJKIM\|KHS440528	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	12/04/07	12/04/07	130	Genomic	unknown
ss89426845	BCMHGSC_JDW\|JWB-0618208	rev/T	A/G	tttgcttttttcttcttcttctttataaac	attctttgtaactttttgtattgacagttt	02/26/08	02/28/08	129	Genomic	unknown
ss98239033	ILLUMINA\|HumanHap550v3.0__rs9282	fwd/B	C/T	aaactgtcaatacaaaaagttacaaagaat	gtttataaagaagaagaagaaaaaagcaaa	04/20/07	03/31/08	130	Genomic	unknown

Fasta sequence (Legend)

 GGTTTCTGGG GGCTTGGGGC AGGGGAGAGA ACGCCCTTGT TCTCAGCAGA TAGGCGCTGA
 GCTAAGGGGT GAAGAGGCAG ATGTCTACAG TTACCGTGCC CTGACAGGGA GAAACAGAAG
 TGTCTGTCTC CAGATAAAGT CAGAGGGGCC AATGCAAACA GGTGGTGAAT CACAGTCAGA
 GAGCTCTTCA TACTCGTGTT GCAATTTTAC TGTAAGTTTG AAACTGTCAA TACAAAAAGT
 TACAAAGAAT
 Y
 GTTTATAAAG AAGAAGAAGA AAAAAGCAAA CCCAACCAAG CTCAAGCCTA GATCCGTATT
 TGGATTCAGC TCGTCTCGGG GCGGAGCCAG GCGTCACGGC CTCCGGATTA AAGTATCCCC
 CCAGGGAGTG TGCTCTGTGA ATCTGGGTGG GGAGGGCGCT CGGTGCTGTT CCCAGCAACC
 CACCACCCTC CTCCTAGTGC TTGCAAGAAT AGGCAGGGAA CTCAGCTGAC TGCATCAGAA
 CCTGAGAAGC

GeneView

GeneView via analysis of contig annotation: RHOF ras homolog gene family, member F (in filopodia)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: LOC100133827

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_009775->NM_019034

function

Celera

NW_925395->XM_001719076

function

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


reference	NT_009775->NM_019034->NP_061907	12789419	reverse		intron

Celera	NW_925395->XM_001719076->	69479989	forward	7121	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9282 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838063.1	10897008	119232102	minus	G	alt_assembly_8	HuRef	HuRef	view	250
12	NT_009775.16	12789419	120704293	minus	A	ref_assembly	reference	reference	view	250
12	NW_925395.1	69479989	121856160	minus	A	alt_assembly_1	Celera	Celera	view	250

NCBI Resource Links

Submitter-Referenced
GenBank
NT_009487 AI074247 Hs.106525

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
ss11028586	CEPH		184	AF					0.210	0.790

	HapMap-CEU	European	120	IG		0.333	0.667	0.150	0.167	0.833

	HapMap-HCB	Asian	90	IG	0.022	0.089	0.889	0.100	0.067	0.933

	HapMap-JPT	Asian	88	IG		0.045	0.955	1.000	0.023	0.977

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.500	0.467	0.100	0.283	0.717

ss23322835	AFD_EUR_PANEL	European	48	IG		0.208	0.792	0.584	0.104	0.896

	AFD_AFR_PANEL	African American	46	IG	0.043	0.522	0.435	0.273	0.304	0.696

	AFD_CHN_PANEL	Asian	48	IG		0.125	0.875	0.752	0.062	0.938

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.255+/-0.250	332	260	9	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 .