Reference SNP(refSNP) Cluster Report: rs30019389

Reference SNP(refSNP) Cluster Report: rs30019389

refSNP ID: rs30019389
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:	A/C
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 ss45887590 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs30019389 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss45887590	ABI\|mCV23184252	fwd/T	A/C	cacaccagcaatacaatggttttaagaacg	gagcgtagctcaggggcgcagcaactgctt	07/20/05	12/22/05	125	Genomic	unknown
ss48082864	PERLEGEN\|NES11864712	fwd/T	A/C	cacaccagcaatacaatggttttaagaacg	gagcgtagctcaggggcgcagcaactgctt	08/12/05	08/12/05	125	Genomic	100 %
ss58015053	ENSEMBL\|NT_094510.3_11793701	fwd/T	A/C	cacaccagcaatacaatggttttaagaacg	gagcgtagctcaggggcgcagcaactgctt	06/12/06	06/12/06	127	Genomic	unknown

Fasta sequence (Legend)

 AGCCTGGCAT GGCCCTCAGC CTGGCCTAGA ACTTGACGTT CAGGCAAGAA CGGTCTTCCC
 TTCTGATCCT CCTGCCTCCA CTGTCCGGGT GTTGGGTCTA CAGATGCCAA CCTCTGTGCC
 TGGTTTCTGC CAGCTGTCCT GTATCTCCAG CCCTTTCTTT GGGCTTTGGA GACAAGTTCT
 TACTATGAAG CCCAGGCTTG CTTTGAAACT TGTTCTCCTT CTCATTCCTG CCTTGGCCTG
 CCAAGTGCTG GCATCACAGA CTTGACCCAC CACACCAGCA ATACAATGGT TTTAAGAACG
 M
 GAGCGTAGCT CAGGGGCGCA GCAACTGCTT AGTGGGCAAA GGTTTCTGCC TTTAACCATT
 AGCACAGAAA GTAATCTTGC CAAAGGGTGG TGTGGAAAAG GGCGTGTGCA CCATGCCACT
 GAAGCTGCCC ATCCCTGGGG CCTCACTAGG CCTGCAGAAG ATGGCTGTCC TGGTTGTCTG
 AGGCCTATAA GATACAGAGA CCTGCTTTCC CTCCCTACCC AGGACCGAGG CTTCTGAAAT
 ATCTAAGCAT TGGGTGGGAC AAGATGGCTA GCAGAAAGGG AGTCAGATGT CCTAAGGGTG

GeneView

GeneView via analysis of contig annotation: Bid BH3 interacting domain death agonist

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_001030811->NM_007544

function

C57BL/6J

NT_039353->NM_007544

function

129/Sv

NT_039382->NM_007544

function

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


Celera	NW_001030811->NM_007544->NP_031570	62551310	reverse	intron

C57BL/6J	NT_039353->NM_007544->NP_031570	73174341	reverse	intron

129/Sv	NT_039382->NM_007544->NP_031570	100140	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs30019389 maps exactly once on NCBI mouse chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NT_039382.3	100140	120858201	minus	G	alt_strain_15	129/Sv	129/Sv	view	300
6	NT_039353.7	73174341	120861379	plus	A	ref_strain	C57BL/6J	C57BL/6J	view	300
6	NW_001030811.1	62551310	122755183	plus	C	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_094510.3

dbSNP Blast Analysis
GenBank HTGS Finished:
AC006404.25 AC006945.17 AC083894.21

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	C/C
ss45887590	CRAMUS_MOUSE		8	IG	2	2

ss48082864	MM_PANEL2		12	IG	3	3

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	-1.000+/-0	17	17	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 .