Reference SNP(refSNP) Cluster Report: rs7935124

Reference SNP(refSNP) Cluster Report: rs7935124

refSNP ID: rs7935124
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_003957.2:c.1987+290G>A
NT_009237.17:g.268000G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38687440 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7935124 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
ss12140096	WI_SSAHASNP\|chr11.NT_028310.10_244304	fwd/T	A/G	ctcccaaggcctgaagccagtgagggtccc	ctggtcccactggtgcaggctgtggcctag	07/04/03	10/25/06	116	Genomic	unknown
ss17438528	CSHL-HAPMAP\|CSHL-HuCC-200402.chr11.NT_009237.16_247471	fwd/T	A/G	ctcccaaggcctgaagccagtgagggtccc	ctggtcccactggtgcaggctgtggcctag	02/19/04	03/04/04	120	Genomic	unknown
ss38687440	ABI\|hCV306931	fwd/T	A/G	ctcccaaggcctgaagccagtgagggtccc	ctggtcccactggtgcaggctgtggcctag	07/16/05	11/02/06	126	Genomic	unknown
ss81033759	HGSV\|Cor18555_SNV_20070510.chr11_1437335	fwd/T	A/G	ctcccaaggcctgaagccagtgagggtccc	ctggtcccactggtgcaggctgtggcctag	11/27/07	11/27/07	130	Genomic	unknown

Fasta sequence (Legend)

 TTCCAAATGT GGTAAGAATC CCCCACGCTC ACCTGGCACC TCCACCTGCC ACTTCACCGC
 TCACCCTCAG CCCGCTGTGG CCGCCACCTG CCGCCCGGGT TGTCCCGGCC TCCCTGTGTA
 GATGTAGGCA CCCAGCAGCC CAGATGTCCC CGGCCCCATC CTCTACCAGG AGCAGCCCCC
 GTCGCTCCCC TACCACAGCA AGCCCAGGCG GGGTTCCTGG CCAGACTCAC CTCTGCCAGG
 CCCTAGGATC AGGGCAGGCC CAAGAAGGGG CTCCCAAGGC CTGAAGCCAG TGAGGGTCCC
 R
 CTGGTCCCAC TGGTGCAGGC TGTGGCCTAG GGGAGGGGCC GGTGCCCATC CCTCTGTCCA
 CTGGAGGCTG TGCCTGGCAG GGAGCGGAGG GGCCCACAGC TCAGGGCTCA GGTGGGGGTT
 AGGCTTAGGA AGTGGGATTG AGGGGCCTCC ATCGACACAC CTGGGCAGTG AGCACAGGGC
 CCCAAGAAGG GTGGGCTCCC CATTTCCGCC CCTCTTCTCA GGACTGCCCC CATCCCAGGG
 ACCCGGGACA TGACTCTAGC TGCTTGCCCC CAGCCCCCCA GCCTGCCTCC CACATCCACC

GeneView

GeneView via analysis of contig annotation: BRSK2 BR serine/threonine kinase 2

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

reference

NT_009237->NM_003957

function

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


reference	NT_009237->NM_003957->NP_003948	268000	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs7935124 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838017.1	262649	1268778	plus	G	alt_assembly_8	HuRef	HuRef	view	300
11	NT_009237.17	268000	1437335	plus	G	ref_assembly	reference	reference	view	300
11	NW_924962.1	1092325	1512569	plus	G	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_028310

dbSNP Blast Analysis
GenBank mRNA:
AF533878.1

UniGene Cluster ID
170819

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss38687440	HapMap-CEU	European	118	IG	0.254	0.746	0.273	0.127	0.873

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.222+/-0.248	90	60	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .