Reference SNP(refSNP) Cluster Report: rs29040856

Reference SNP(refSNP) Cluster Report: rs29040856

refSNP ID: rs29040856
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	125/128
Map to Genome Build:	37.1

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Strain:	not submitted
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38364198 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs29040856 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
ss38364198	PERLEGEN\|NES09691130		fwd/B	C/T	ggcctggcagcatggctggaggtgggaaaa	ccgtgctggttgcaggataagggtctggac	07/12/05	01/20/06	125	Genomic			100 %

Fasta sequence (Legend)

 GCCCCAAGAA GCCCCCAAGC ATACCCCAGG CAGCTGGCAG AAGGTGGTGC CATGCATTTC
 TCATAGATGG GGCCTGGCAG CATGGCTG
 GAGGTGGGAA AA
 Y
 CCGTGCTGGT TG
 CAGGATAAGG GTCTGGACCA GCTGGTTCAC TCGGCCTTGC AAGGCTACTG GGTCTTGCCC
 AGCAGGCACA GGCAACAGTG TAGGCCCA

GeneView

GeneView via analysis of contig annotation: Arhgap4 Rho GTPase activating protein 4

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

Celera

NW_001035173->NM_138630

function

C57BL/6J

NT_039706->NM_138630

function

129/SvEvTac

NT_039745->NM_138630

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


Celera	NW_001035173->NM_138630->NP_619536	743648	reverse	missense	G	Val [V]	1	705
				contig reference	A	Ile [I]	1	705

C57BL/6J	NT_039706->NM_138630->NP_619536	18726751	reverse	missense	G	Val [V]	1	705
				contig reference	A	Ile [I]	1	705

129/SvEvTac	NT_039745->NM_138630->NP_619536	515590	reverse	missense	G	Val [V]	1	705
				contig reference	A	Ile [I]	1	705

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs29040856 maps exactly once on NCBI mouse chromosome X

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
X	NW_001035173.1	743648	65149735	plus	T	alt_assembly_1	Celera	Celera	view	100
X	NT_039745.3	515590	71141771	plus	T	alt_strain_1	129/SvEvTac	129/SvEvTac	view	100
X	NT_039706.7	18726751	71142644	plus	T	ref_strain	C57BL/6J	C57BL/6J	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000086.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AC091472.2 AF133093.2 AL672002.14

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	T/T
ss38364198	MM_PANEL2		30	IG	3	12

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	-1.000+/-0	15	15	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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .