Reference SNP(refSNP) Cluster Report: rs11612594

Reference SNP(refSNP) Cluster Report: rs11612594

refSNP ID: rs11612594
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_020845.2:c.2570-34C>T
NT_009755.18:g.884462G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38987724 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11612594 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
ss16582869	CSHL-HAPMAP\|CSHL-HuAA-200402.chr12.NT_009755.16_868109	fwd/T	A/G	agaagcaagagcaatggatggctcagccac	cggggatgaccgcactgccacgtctaccag	02/17/04	03/04/04	120	Genomic	unknown
ss38987724	ABI\|hCV1427532	fwd/T	A/G	agaagcaagagcaatggatggctcagccac	cggggatgaccgcactgccacgtctaccag	07/16/05	07/16/05	126	Genomic	unknown
ss74989430	ILLUMINA\|ILMN_Human_1M_rs11612594	fwd/T	A/G	agaagcaagagcaatggatggctcagccac	cggggatgaccgcactgccacgtctaccag	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 CTCCCTGTTA GGCCGAAGCG GGGGTCTAGG TGGGCAGAGC CTGGCAGTGA GGGGTGCTCA
 GCAGCAGAGT GACCCCCAGT GAGGGGAAAG TGTGTGGGGT GGTACCTTCT CCAATGTCCA
 GCTCAGGGAG GCCAGGGGCC CTCTCCAGGC CAGGGCTTGC CTTCCTGGCT GGAGGGTGGG
 GGCCAGGGGT GGTGGGGCTG GGGGCGGGCA GGGCGAGCAG GGACAGACGC CTGACGCTGG
 GGGTATGGCT GAGCGCATCG GGGGCCTCTG AGAAGCAAGA GCAATGGATG GCTCAGCCAC
 R
 CGGGGATGAC CGCACTGCCA CGTCTACCAG GGGCCAGGCA GGACACTGGG ACAGTGCCAG
 GCCTGGAGCT ATCAAGGGCG AGCCCATTGG CCCTCCTCAC GGATGAACAC AACTGCCAGC
 AACCCCCACC CCAGCCTCAG CTCCTGCATG GCCACCCTGA CCACAGCTGC GAGAATCCCT
 GGCCCAGCAC GGGGCGCAGC CCCTGGCGGG GACTGAGAAG GGAACCCGGG CTGTGCTTCA
 AGCACCAAGA GGCTTCATGC AGGAGCTAAG CATGAGGAAG GCGGGGCCCT TACTAATGCG

GeneView

GeneView via analysis of contig annotation: PITPNM2 phosphatidylinositol transfer protein, membrane-associated 2

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_009755->NM_020845

function

HuRef

NW_001838064->NM_020845

function

Celera

NW_925395->NM_020845

function

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


reference	NT_009755->NM_020845->NP_065896	884462	reverse	intron

HuRef	NW_001838064->NM_020845->NP_065896	5508109	forward	intron

Celera	NW_925395->NM_020845->NP_065896	70691151	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11612594 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_001838064.2	5508109	120435669	minus	C	alt_assembly_8	HuRef	HuRef	view	300
12	NT_009755.18	884462	122040482	plus	G	ref_assembly	reference	reference	view	300
12	NW_925395.1	70691151	123067322	plus	G	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_009755

dbSNP Blast Analysis
GenBank HTGS Finished:
AC026362.38 NC_000012.10

Population Diversity

There is no frequency data.

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 .