Reference SNP(refSNP) Cluster Report: rs16818179

Reference SNP(refSNP) Cluster Report: rs16818179

refSNP ID: rs16818179
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	123/128
Map to Genome Build:	37.1

Allele
Variation Class:	DIP: deletion/insertion polymorphism
RefSNP Alleles:	-/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 ss24773659 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16818179 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
ss24773659	ROCHEBIO\|Esrra_JC9904_1		fwd/T	-/T	atggtttgtaaagatcttttataattatct	cttagggagaaatgagaaaagtaaggcctg	05/28/04	08/05/04	123	Genomic		-	unknown

Fasta sequence (Legend)

 gagttcctgc cttgacttcc ctcggtgagg gngtganttg agagttggaa gctgaaataa
 actcctgctc cccaagttgc ttttggtcat gttttatcac tgcaacagaa accctaaGAC
 ACCCCCATCC TGATCATGCT TCTACTTGGG CATCTGGATT GTGAAgtagt ttattgtcct
 tgaacgtact acagccacct atgaccctaa cctcccggtc ctggtttgcc tactgaatgc
 tggaattaaa gtgtgcatgg tgtttgcagt gctgaagatc aaacccaggg cttcacacat
 ggtaggcagg cactctactg agctacatcc tgagcTATGG TTTGTAAAGA TCTTTTATAA
 TTATCT
 N
 CTTAGGGAGA AATGAGAAAA GTAAGGCCTG GGTCTCAGGG TCTCACCTGT CTTCCTGGGT
 CCTCCAGCTA CTGCCAGAGG TCCAGCAGGG AAGGGGCCCG GGAAAGGCAA AGGGTCCACC
 TCTGGCCGCC GTTTGTACTT CTGCCGNCCN CCGCGGACAC GGTCCAGACG CACACCTTGA
 ATTGTAAAGC CAAACTGTTC ATGAAGTACT TGCTCCGCGC AGCTCTACTT CCCCAC

GeneView

GeneView via analysis of contig annotation: Esrra estrogen related receptor, alpha

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_001030639->NM_007953

function

C57BL/6J

NT_039687->NM_007953

function

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


Celera	NW_001030639->NM_007953->NP_031979	3690552:3690553	reverse	intron

C57BL/6J	NT_039687->NM_007953->NP_031979	100158:100159	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs16818179 maps exactly once on NCBI mouse chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001030639.1	3690552^3690553	6690552^6690553	plus	-	alt_assembly_1	Celera	Celera	view	366..366
19	NT_039687.7	100158^100159	6988263^6988264	plus	-	ref_strain	C57BL/6J	C57BL/6J	view	366..366

NCBI Resource Links

Submitter-Referenced
dbSTS
RPAMMSEQ0038681

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank STS:
AC120557.12 AC163098.4	AC147519.1 AC170181.1	BV160594.1

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	-/-	T/T
ss24773659	RPAMM		44	IG	19	3

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.236+/-0.250	22	22	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 .