Reference SNP(refSNP) Cluster Report: rs17790638

Reference SNP(refSNP) Cluster Report: rs17790638

refSNP ID: rs17790638
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:	G
Clinical Association:	unknown

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24708107 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17790638 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
ss24708107	PERLEGEN\|afd0932539		fwd/T	A/G	aagatccaagaagctcagaaagaggaagct	tttatatggttcagtgatggtattgattgg	08/10/04	09/13/04	123	Genomic			unknown

Fasta sequence (Legend)

 AGGTGTGGGA CAAGGAGGGG GAGATGGAGG TGGCCATGCA GAAAGTCAAC ACGATGTGGC
 AGGAGAGCTG AAGATCCAAG AAGCTCAG
 AAAGAGGAAG CT
 R
 TTTATATGGT TC
 AGTGATGGTA TTGATTGGAC TTTTTAAAAT GTTTCATTAT TACACTTTAA GTTCTGGGGT
 ACTTTGTATG ACCTTAATAA AACATCTT

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17790638 maps exactly once on NCBI human chromosome 13

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
13	NW_001838069.1	566581	566581	plus	A	alt_assembly_8	HuRef	HuRef	view	100
13	NW_925473.1	558670	823446	plus	A	alt_assembly_1	Celera	Celera	view	100
13	NT_024524.13	741496	18659496	plus	A	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000013.6

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL139327.18	AL162715.12 AL590046.3

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss24708107	AFD_EUR_PANEL	European	48	IG	0.875	0.125	0.752	0.938	0.062

	AFD_AFR_PANEL	African American	46	IG	0.913	0.087	1.000	0.957	0.043

	AFD_CHN_PANEL	Asian	48	IG	0.958	0.042	1.000	0.979	0.021

	HapMap-CEU	European	118	IG	0.847	0.153	0.527	0.924	0.076

	HapMap-HCB	Asian	88	IG	0.932	0.068	1.000	0.966	0.034

	HapMap-JPT	Asian	88	IG	0.932	0.068	1.000	0.966	0.034

	HapMap-YRI	Sub-Saharan African	120	IG	0.933	0.067	1.000	0.967	0.033

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.086+/-0.189	332	260	9	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 .