Reference SNP(refSNP) Cluster Report: rs9789057

Reference SNP(refSNP) Cluster Report: rs9789057

refSNP ID: rs9789057
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_005374.3:c.-34+469C>T
NT_010783.14:g.638178G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss13612104 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9789057 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
ss13612104	WI_SSAHASNP\|chr17.NT_010783.14_638178		fwd/T	A/G	ggaagcgggagaagcagcgcgcgcccttct	cggaccccctcccagggaagattgtggtgt	11/05/03	10/25/06	119	Genomic			unknown

Fasta sequence (Legend)

 GATGAGGTCA CTAAATGACT GCCCCGGCCA ACCCCCACCC CGTCTTTATC CGCACCGCCC
 CCCCCTTAAT TGACCTAACT TTCTAACCCT AGCTCTTCGC TTCTGGCACC GGTCCCCTCC
 CAAGTCTCCA GACCCTAACC CTGGCTCCCG ACCCGCCCCG CTACAGCTTG GGAAGCGGGA
 GAAGCAGCGC GCGCCCTTCT
 R
 CGGACCCCCT CCCAGGGAAG ATTGTGGTGT TAGCTGCCTA GGGGGACCAG GGGGCCACCG
 GGACCCAGCG CAACCTCTGT CTCGCTCCCC AACCCCCGGA AGCGCTAACA GCACGGTTCT
 TACGTAATGC CGGGCTTCTA AGTACCCCCA ACCCGCACAG CCCCCGGGGA GGCCGCGCAG
 ATACCGGGGC CCCTCACAGC

GeneView

GeneView via analysis of contig annotation: MPP2 membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 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_010783->NM_005374

function

HuRef

NW_001838437->NM_005374

function

Celera

NW_926839->NM_005374

function

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


reference	NT_010783->NM_005374->NP_005365	638178	reverse	intron

HuRef	NW_001838437->NM_005374->NP_005365	1549654	forward	intron

Celera	NW_926839->NM_005374->NP_005365	579451	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9789057 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838437.2	1549654	37748673	minus	C	alt_assembly_8	HuRef	HuRef	view	200
17	NW_926839.1	579451	38692410	plus	G	alt_assembly_1	Celera	Celera	view	200
17	NT_010783.14	638178	39339899	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010783

dbSNP Blast Analysis
GenBank HTGS Finished:
AC007993.15 NC_000017.9

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss13612104	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	90	IG	0.044	0.956	1.000	0.022	0.978

	HapMap-YRI	Sub-Saharan African	120	IG		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.009+/-0.068	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 .