Reference SNP(refSNP) Cluster Report: rs27615560

Reference SNP(refSNP) Cluster Report: rs27615560

refSNP ID: rs27615560
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 ss37803781 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs27615560 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
ss37803781	PERLEGEN\|NES09117679		fwd/B	C/T	cttttttcacctatggagcagctattttgg	ttctttgctgcacccgtttcattcccttga	04/27/05	07/28/05	125	Genomic			100 %

Fasta sequence (Legend)

 AGCCCGCCCC ACCCCCATAG CTTCTCTCTG CTTTCCCGAG ACAGCCTTGG CAGTTGGAAA
 TAAACTTTTT CTTTTTTCAC CTATGGAG
 CAGCTATTTT GG
 Y
 TTCTTTGCTG CA
 CCCGTTTCAT TCCCTTGAAA GCCAGTCTCA CCTGGAACTC TACATAGCAA GTTTTAGGCC
 ATCCAGGGAT GTACAGCAAG GCACTGTC

GeneView

GeneView via analysis of contig annotation: Frap1 FK506 binding protein 12-rapamycin associated protein 1

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_001030773->NM_020009

function

C57BL/6J

NT_039268->NM_020009

function

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


Celera	NW_001030773->NM_020009->NP_064393	687000	forward	5' near gene

C57BL/6J	NT_039268->NM_020009->NP_064393	2281094	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs27615560 maps exactly once on NCBI mouse chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NT_039268.5	2281094	147820972	plus	T	ref_strain	C57BL/6J	C57BL/6J	view	100
4	NW_001030773.1	687000	150707615	plus	T	alt_assembly_1	Celera	Celera	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000070.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC108508.2 AL731654.7 CU210865.6	AL626777.8

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	T/T
ss37803781	MM_PANEL2		14	IG	1	6

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

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Revised: May 25, 2006 1:38 PM .