Reference SNP(refSNP) Cluster Report: rs8254381

Reference SNP(refSNP) Cluster Report: rs8254381

refSNP ID: rs8254381
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	118/128
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 ss12750284 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs8254381 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
ss12750284	ROCHEBIO\|AF019772_DA331_5		fwd/B	C/T	caaaangctgaagagcntgactgatatcta	ctgctcaacntggccatctctgacctgctc	10/17/03	04/07/04	118	Genomic		C	unknown
ss61241837	PERLEGEN\|NES16857257		fwd/B	C/T	caaaaagctgaagagcgtgactgatatcta	ctgctcaacctggccatctctgacctgctc	06/23/06	06/23/06	127	Genomic			100 %

Fasta sequence (Legend)

 CAAGGGTCAG TTCCGACCTA TAGCTATGAC ATCGATTATG GTATGTCAGC ACCCTGCCNA
 AAAATCAATG TGAAACAAAT TGCNGCTCAG CTCCTGCCCC CACTCTACTC CCTGGTATTC
 ATCTTTGGTT TTGTGGGTAA CATGATGGTC TTCCTCATCT TGATAAGCTG CAAAANGCTG
 AAGAGCNTGA CTGATATCTA
 Y
 CTGCTCAACN TGGCCATCTC TGACCTGCTC TTCCTGCTCA CACTACCATT CTGGGCTCAC
 TATGCTG

GeneView

GeneView via analysis of contig annotation: Ccr5 chemokine (C-C motif) receptor 5

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_001030923->NM_009917

function

C57BL/6J

NT_039483->NM_009917

function

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


Celera	NW_001030923->NM_009917->NP_034047	282348	reverse	synonymous	T	Tyr [Y]	3	70
				contig reference	C	Tyr [Y]	3	70

C57BL/6J	NT_039483->NM_009917->NP_034047	206982	forward	synonymous	T	Tyr [Y]	3	70
				contig reference	C	Tyr [Y]	3	70

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs8254381 maps exactly once on NCBI mouse chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NT_039483.4	206982	124039310	plus	C	ref_strain	C57BL/6J	C57BL/6J	view	200
9	NW_001030923.1	282348	124875145	minus	G	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
RPAMMSEQ0000453	NC_000075.4

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank STS:	GenBank mRNA:
NM_009917.4	AC168021.4	BV088569.1 BV162348.1	AK141906.1 AK154595.1 AK155628.1 AK155867.1 AK170303.1 BC103574.1 BC103586.1 BC103587.1 BC105643.1 D83648.1 U47036.1 X94151.1

3D structure mapping
NP_034047

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	T/T
ss12750284	RPAMM		24	IG	10	2

ss61241837	MM_PANEL2		26	IG	10	3

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.278+/-0.248	25	25	2	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 .