Reference SNP(refSNP) Cluster Report: rs31610698

Reference SNP(refSNP) Cluster Report: rs31610698

refSNP ID: rs31610698
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 ss46125242 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs31610698 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
ss46125242	ABI\|mCV24825629	fwd/B	C/T	ctcccaggtgctgacgtgttagcatgctgc	atctaaaaagcagtctttggtgatactcag	07/20/05	12/22/05	125	Genomic	unknown
ss47070861	PERLEGEN\|NES11628927	fwd/B	C/T	ctcccaggtgctgacgtgttagcatgctgc	atctaaaaagcagtctttggtgatactcag	08/11/05	08/11/05	125	Genomic	100 %
ss59314886	ENSEMBL\|NT_039433.5_15563876	fwd/B	C/T	ctcccaggtgctgacgtgttagcatgctgc	atctaaaaagcagtctttggtgatactcag	06/12/06	06/12/06	127	Genomic	unknown

Fasta sequence (Legend)

 CCTGGTTAGA TGGTTCGGGA TTAGGATTCT CACTGGAATA CCCCACCATT AGTTTACATG
 CGGTGTCCAG GGATCCAAAC GCTTACCCTC AAGAGCATTT GTATGTTATG GTGAATGCCA
 AGCTTGGAGG TATGTATGGA CAACTTACTC TAGTGCTGCC TCTGACAGCA GTGTGTATTT
 TAAAGGGCAA TGTTTGTTTG TTTGTTTGTT TGTTTGTTTG AGATGAGGTC TTCAGGCTGC
 TCAGGTTGGC CCTGAGCTCC AGGGCTTGCT CTCCCAGGTG CTGACGTGTT AGCATGCTGC
 Y
 ATCTAAAAAG CAGTCTTTGG TGATACTCAG TGTAAAACTG AAGCCATTGG TCCACATTGG
 ATAGTAATGT ATTAAGCTGA ATTAATTATC TAAAATAATT TGACCACTTG AATTTCTTCT
 AATGGGCACT GGCTTTCTAT GTGTCTGCAT ATATTCACAC TTAGAGGTCT TCTGTTAATA
 TGCTTATCTT CCTATTTCTT AACTGCCTTC TTCTAAAGGC ATTTCAGAGA TGTGAACCAG
 TATATTCTGT CTTTCCAAAA ATTTACGATA GATTATATAT ATATATTTTT ATTTATTTTA

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	379422	forward	intron

C57BL/6J	NT_039433->NM_023671->NP_076160	15454578	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs31610698 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	379422	98025726	plus	T	alt_assembly_1	Celera	Celera	view	300
7	NT_039433.7	15454578	104854411	plus	C	ref_strain	C57BL/6J	C57BL/6J	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
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
ss46125242	CRAMUS_MOUSE		8	IG	1	3

ss47070861	MM_PANEL2		20	IG	1	9

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 .