Reference SNP(refSNP) Cluster Report: rs3724814

Reference SNP(refSNP) Cluster Report: rs3724814

refSNP ID: rs3724814
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	107/128
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 ss45988561 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3724814 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
ss5101120	WI\|WI_WGS_7_87443597	fwd/B	C/T	cagaagatcagnacagattgctagagttac	ttgatgtcaagcagaacaattcngtcagaa	08/12/02	04/07/04	107	Genomic	unknown
ss45988561	ABI\|mCV24825298	fwd/B	C/T	cagaagatcaggacagattgctagagttac	ttgatgtcaagcagaacaattcagtcagaa	07/20/05	12/22/05	125	Genomic	unknown
ss59314685	ENSEMBL\|NT_039433.5_15556656	fwd/B	C/T	cagaagatcaggacagattgctagagttac	ttgatgtcaagcagaacaattcagtcagaa	06/12/06	06/12/06	127	Genomic	unknown

Fasta sequence (Legend)

 GAATACAGAC AAGGCCTTAG TACACACCTT GAATCCCAAA TAGTGAAGGT AAAGTTAGTT
 TGTGGAAGGA AGCACCATGT TTGAAAGTGA TGTCTAGTTG AGTGGCAGAA AAAATGATCA
 AATCCGAGAA AGATTTGACC AAATAGGATA CGCCCAACCT TCGGGAGAAA AGAGGAAAGG
 AAAGCTACTG GAGAGAGCAG TTCAGAGAGA GGAAGGAGGC GGTTTTACTG GGACAGTTGT
 ACCGAGACAG GTTAGAGAAA AAGAAGGAGC CAGAAGATCA GGACAGATTG CTAGAGTTAC
 Y
 TTGATGTCAA GCAGAACAAT TCAGTCAGAA GCTGAGAGAA ACCCGATTGA GTCAGTCAGC
 TTGGAGAGGA GTTTGCACCA GAACAGCTGA GTTAAACCAG CCAGTTAGAG CTTTGAGAGA
 ACAGGAAAGG GTGAGTTTAT TCAGCAGTAA GTCTAAGTCT ATAAATATTC TATGCCTAGA
 TTAGATTGTA TGGAGGCTAG AAGCTTCCAG GATTAAGCCT AGGCTAGCAG ACAGGAATGA
 AAACTTTAGA GATGACATTA CTACAGGAGA ATAAGATACT TTTATACCCC TTGATACCAT

GeneView

GeneView via analysis of contig annotation: Clns1a chloride channel, nucleotide-sensitive, 1A

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_001030877->NM_023671

function

C57BL/6J

NT_039433->NM_023671

function

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


Celera	NW_001030877->NM_023671->NP_076160	372190	forward	intron

C57BL/6J	NT_039433->NM_023671->NP_076160	15447358	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3724814 maps exactly once on NCBI mouse chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001030877.1	372190	98018494	plus	C	alt_assembly_1	Celera	Celera	view	300
7	NT_039433.7	15447358	104847191	plus	C	ref_strain	C57BL/6J	C57BL/6J	view	300

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
G90927	NT_039433.5

dbSNP Blast Analysis
GenBank HTGS Finished:
AC123820.4 AC125323.4 AC151477.1

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	T/T
ss45988561	CRAMUS_MOUSE		8	IG	3	1

ss5101120	MOUSE		4	IG	1	1

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.500+/-0	5	5	1	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .