Reference SNP(refSNP) Cluster Report: rs3738321

Reference SNP(refSNP) Cluster Report: rs3738321

refSNP ID: rs3738321
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
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
NT_004487.18:g.398969G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss4924321 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3738321 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
ss4924321	YUSUKE\|IMS-JST084054		fwd/B	C/T	ctaacacccctcttctcaacaagactcagc	tctccccgaggtgggtgagcatccttgagg	07/24/02	10/10/03	107	Genomic			unknown
ss75124841	ILLUMINA\|ILMN_Human_1M_rs3738321		fwd/B	C/T	ctaacacccctcttctcaacaagactcagc	tctccccgaggtgggtgagcatccttgagg	08/28/07	08/29/07	129	Genomic			unknown

Fasta sequence (Legend)

 TCCCTTGTGT CCAACCCCCT ACCCCTCTCC CTAACACCCC TCTTCTCAAC AAGACTCAGC
 Y
 TCTCCCCGAG GTGGGTGAGC ATCCTTGAGG TTTCCCACCC TTAACTGCTG TGTCCCCGGA

GeneView

GeneView via analysis of contig annotation: MTMR11 myotubularin related protein 11

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_004487->NM_181873

function

HuRef

NW_001838529->NM_181873

function

Celera

NW_925683->NM_181873

function

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


reference	NT_004487->NM_181873->NP_870988	398969	reverse	5' near gene

HuRef	NW_001838529->NM_181873->NP_870988	106929	reverse	5' near gene

Celera	NW_925683->NM_181873->NP_870988	61410	reverse	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3738321 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838529.1	106929	121289098	minus	G	alt_assembly_8	HuRef	HuRef	view	60
1	NW_925683.1	61410	123024584	minus	G	alt_assembly_1	Celera	Celera	view	60
1	NT_004487.18	398969	148175238	minus	G	ref_assembly	reference	reference	view	60

NCBI Resource Links

Submitter-Referenced
GenBank
NT_004705.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank mRNA:
AL590487.20 NC_000001.9	AC018785.3	BC094756.1 U78556.1 U78557.1

UniGene Cluster ID
425144

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss4924321	JBIC-allele		1486	AF				0.968	0.032

	HapMap-CEU	European	120	IG	1.000			1.000

	HapMap-HCB	Asian	90	IG	1.000			1.000

	HapMap-JPT	Asian	88	IG	0.955	0.045	1.000	0.977	0.023

	HapMap-YRI	Sub-Saharan African	120	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.010+/-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 .