Reference SNP(refSNP) Cluster Report: rs17005568

Reference SNP(refSNP) Cluster Report: rs17005568

refSNP ID: rs17005568
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
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_005270.3:c.1519-312A>G
NT_022135.15:g.10447902A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss23693430 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17005568 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
ss23693430	PERLEGEN\|afd1308915		fwd/T	A/G	tgctgctgatttaaaaaaatagagtatgta	ctgaatacttgacatgttcccaattttggt	08/10/04	08/20/04	123	Genomic			unknown

Fasta sequence (Legend)

 CAATTCTAAC CGAGAGTGGT ACTGGGAAAC AGTTCAAAGT CATAGTTTAG AGTTTAATGA
 TATGGGAATA TGCTGCTGAT TTAAAAAA
 ATAGAGTATG TA
 R
 CTGAATACTT GA
 CATGTTCCCA ATTTTGGTTT TAAAGACATG TGGAGATGAA TTGCAGACTC ACCAGAATGA
 AACTTACCTG CGTGTCAGCA GTAGCAGC

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	10447902	forward	intron

HuRef	NW_001838848->NM_005270->NP_005261	589510	forward	intron

Celera	NW_921507->NM_005270->NP_005261	7338324	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17005568 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	589510	114062442	plus	A	alt_assembly_8	HuRef	HuRef	view	100
2	NW_921507.1	7338324	115064952	plus	A	alt_assembly_1	Celera	Celera	view	100
2	NT_022135.15	10447902	121456450	plus	A	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000002.6

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss23693430	AFD_EUR_PANEL	European	48	IG	1.000			1.000

	AFD_AFR_PANEL	African American	46	IG	0.957	0.043	1.000	0.978	0.022

	AFD_CHN_PANEL	Asian	48	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.014+/-0.082	71	50	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 .