Reference SNP(refSNP) Cluster Report: rs16819635

Reference SNP(refSNP) Cluster Report: rs16819635

refSNP ID: rs16819635
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	123/128
Map to Genome Build:	37.1

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
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 ss24775173 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16819635 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
ss24775173	ROCHEBIO\|Nr5a1_JC9999_8		fwd/T	A/G	agggagatgcctggggacaatatgcagagt	atgtcagtgannggtggccacagggtggag	05/28/04	08/05/04	123	Genomic		G	unknown

Fasta sequence (Legend)

 TTTGCAATAC ATCTGCTGAT GCTCCGGATG GTCTTGATTG TCAAGTATNC ATGGTGACAA
 CAGCAATGAT NACTGGGCCA GTGATATGGT TTAGCGGTTG GTGATGGTGG CGGCCATACT
 GATAGACAGG GATTTTCTAg gtncagtggc acatgcatta gtccacttgg gaggcagaga
 gaagcaagtg ggtccagacc agccagggag anatagtgag atccggtctn gaaaaggaaa
 gaaaATAAAC AAACAAAACA AANNNGACAA AGAAAGCACA GGGAGATGCC TGGGGACAAT
 ATGCAGAGT
 R
 ATGTCAGTGA NNGGTGGCCA CAGGGTGGAG GTGGGGAGGC TGCCATTGAG AGGCTCATAG
 CAGTCTCTGC ACCCACAGGC TGGTATCCTC TGGGAATGTG GTATGGTGCT GGTAATACTG
 GTGACTGTGT CAGCCCAACT TTGTTGGTNG CACAGTGACA AGAGGGTGAT GGGCTGCTCC
 CGTTGCAGAT GTGAAATTCC TGAACAACCA CAGCCTCGTA AAGGACGCCC AGGANAAGGC
 CAACGCTGCC CTGTTGGATT ACACCTTNTG TCACTACCCA CACTGCGGGG ACAAATTCCA
 GCAGTTGCTA TTGTGCCTGG

GeneView

GeneView via analysis of contig annotation: Nr5a1 nuclear receptor subfamily 5, group A, member 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_001030694->NM_139051

function

C57BL/6J

NT_039206->NM_139051

function

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


Celera	NW_001030694->NM_139051->NP_620639	313936	reverse	intron

C57BL/6J	NT_039206->NM_139051->NP_620639	16152721	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs16819635 maps exactly once on NCBI mouse chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NT_039206.7	16152721	38549973	minus	C	ref_strain	C57BL/6J	C57BL/6J	view	309
2	NW_001030694.1	313936	40418642	minus	C	alt_assembly_1	Celera	Celera	view	309

NCBI Resource Links

Submitter-Referenced
dbSTS
RPAMMSEQ0038854

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank STS:
AL844842.29	BV160784.1

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	G/G
ss24775173	RPAMM		46	IG	1	22

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.083+/-0.186	23	23	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 .