Reference SNP(refSNP) Cluster Report: rs11899306

Reference SNP(refSNP) Cluster Report: rs11899306

refSNP ID: rs11899306
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

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

HGVS Names
NM_005270.3:c.149-29820G>T
NT_022135.15:g.10363039G>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss17671604 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11899306 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
ss17671604	CSHL-HAPMAP\|CSHL-HuCC-200402.chr2.NT_022135.13_10362859		fwd/B	G/T	agggcaaagattgtaggcacagggtttttg	aggccaggggattgattctgttgggtttct	02/19/04	03/04/04	120	Genomic			unknown

Fasta sequence (Legend)

 TTTTGCTCAA GAGCCTGAAC ACTACCGCTT TCCTACTAAA GGCTAAAAAT AAATTTTGAA
 GCAATAAAGG TGATCACAGT AGAGACAGTT CTCCACTTAC AATGGCTCGA CTTTACTGTG
 GGTTTACTGG GGCATGGTAA GTTGAGGAGT AAATGTGTTA CTTTGTAAGG AGGGCAAAGA
 TTGTAGGCAC AGGGTTTTTG
 K
 AGGCCAGGGG ATTGATTCTG TTGGGTTTCT AGTCTCCTCT GGATGACATC ACCAACCTGA
 AATCCCTTAC CTGTGTCATA ACAAAGGACA CTTTGTGTAA TTTTCTTAGA TACTCACATC
 TTTACCACTC TATTCTGGAA AAAAATACCC ATTTAGgcct tgccgttaac atgtctgatc
 tcaggcctga agatctctta gagactcagt ttccctttct gtacaatgag tgggtttgac
 tGATACTCAT GCTGAGCTGG TATCTTTTAT CCTGTATTTA TATAACATGG TC

GeneView

GeneView via analysis of contig annotation: GLI2 GLI-Kruppel family member GLI2

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_022135->NM_005270

function

HuRef

NW_001838848->NM_005270

function

Celera

NW_921507->NM_005270

function

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


reference	NT_022135->NM_005270->NP_005261	10363039	forward	intron

HuRef	NW_001838848->NM_005270->NP_005261	504697	forward	intron

Celera	NW_921507->NM_005270->NP_005261	7253484	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11899306 maps exactly once on NCBI human 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	NW_001838848.1	504697	113977629	plus	G	alt_assembly_8	HuRef	HuRef	view	200
2	NW_921507.1	7253484	114980112	plus	G	alt_assembly_1	Celera	Celera	view	200
2	NT_022135.15	10363039	121371587	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022135

dbSNP Blast Analysis

Population Diversity

There is no frequency data.

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 .