Reference SNP(refSNP) Cluster Report: rs9663315

Reference SNP(refSNP) Cluster Report: rs9663315

refSNP ID: rs9663315
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
Map to Genome Build:	36.3

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

HGVS Names
NM_005539.3:c.219-662C>T
NT_017795.18:g.735733C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss13458918 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9663315 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss13458918	WI_SSAHASNP\|chr10.NT_024040.14_735733		fwd/B	C/T	gaggggccaggcagacggggcctcgtcctc	gttcatgggctccaggggtgtgcggtggcc	10/31/03	10/25/06	119	Genomic			unknown
ss75219470	ILLUMINA\|ILMN_Human_1M_rs9663315		fwd/B	C/T	gaggggccaggcagacggggcctcgtcctc	gttcatgggctccaggggtgtgcggtggcc	08/28/07	08/29/07	129	Genomic			unknown

Fasta sequence (Legend)

 TCCGTCTGTG CGTTCCTTTC GCTGTCTGGT Cacagttgca atgactgttc ccagttgctt
 tcagctcact ccgtcatttt tgcctcttcc gggtctgttt ctgttgacgg cttcttcgta
 ggatgacggg acacattcac gtggtgttgc tgcttctcat atcaagttat tttccgtagg
 atggcagaca ttgcgaatgt tacgttgttt agtgtttgag ccctgttttc ttcctttaaa
 gcgtgttgaa ggttgtgttt accaacagtt aagccacatg gggatcagtg tgggtctgtc
 aaggcattct ttGCCTTGCC CTTCTCTACT GGTGCAGTTT TATTTTCTTC AATGTGGACC
 CCCCTTCTTC CTGACACATG GACTGGCTGG ATCACAGGGT GCTGGTCTCC TCTCTCCCCA
 CTGGCTTGAA TAAGCATGCG TGGGTAGGGG GATGATGGAC TGTCTCTGTG GAGGGGCCAG
 GCAGACGGGG CCTCGTCCTC
 Y
 GTTCATGGGC TCCAGGGGTG TGCGGTGGCC TCCTGTGCAG CCATGCTTTG CGGAGATGGT
 GGTGAGCTTG TCTCCTTAAG GCCTTCCTGA TGATAAAATG TGACCAGTAG GATGAACGGT
 CGGGGACAAT GGCGTGTCCA GAGGTCCTTT CCCTCCTGTG TGGTTGCAAG GCCGTGGCAA
 CTCAACCACC ATTCTCGCTG

GeneView

GeneView via analysis of contig annotation: INPP5A inositol polyphosphate-5-phosphatase, 40kDa

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_017795->NM_005539

function

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


reference	NT_017795->NM_005539->NP_005530	735733	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9663315 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_001838014.1	1054140	128014863	plus	C	alt_assembly_8	HuRef	HuRef	view	500
10	NW_924907.1	970741	129055284	minus	G	alt_assembly_1	Celera	Celera	view	500
10	NT_017795.18	735733	134313250	plus	C	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024040

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL356603.11	AL157939.4

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss13458918	HapMap-CEU	European	106	IG	0.925	0.075	1.000	0.962	0.038

	HapMap-HCB	Asian	74	IG	0.919	0.081	1.000	0.959	0.041

	HapMap-JPT	Asian	88	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.036+/-0.129	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 .