Reference SNP(refSNP) Cluster Report: rs3008024

Reference SNP(refSNP) Cluster Report: rs3008024

refSNP ID: rs3008024
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	101/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_006661.1:c.-92+41342T>C
NT_007422.13:g.8321434A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss19666615 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3008024 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
ss4233678	SC_JCM\|AL591962.10_41067		fwd/T	A/G	taaatggatggggtgcagtgtggggtggcc	aaggcagaggaagaggaaggcaggccactg	10/15/01	10/10/03	101	Genomic			unknown
ss19666615	CSHL-HAPMAP\|CSHL-HuDD-200402.chr6.NT_007422.12_8321434		fwd/T	A/G	gtaaatggatgggtgcactgtggggtggcc	aaggcagaggaagaggaaggcaggccactg	02/20/04	10/26/06	120	Genomic			unknown

Fasta sequence (Legend)

 CAATTTCCCA CCAGCCTTGC ACTTAGAGAG GCTACAAAGC ATACCAGGGA ATCTGCAGTC
 AGGTCACTGT GGAAAACCTA GCTGTTCCCT TCTTTAGAAA CAGCCGAGGA AATGGTGAAA
 CATTGTGCAG AGCCACTGAA GGCTAAGGGA AGAGAGAAAA CGATCAATAA GTAAATGGAT
 GGGTGCACTG TGGGGTGGCC
 R
 AAGGCAGAGG AAGAGGAAGG CAGGCCACTG CTTCACCTGG TGGCAAGGAT CATGGAAGAG
 CCCAGAACTC TTCTGGACTC TACCTTTGGT TCTAGAGCAG ATTAAAACAG CAGAGAAATT
 GTGTCTGTCT CTCCAGACAA AAAGGATAGA GAAGGCTGGg taatcccaac cctttgggag
 gtcgaggcgg gtggatcatg aggtcaggag atcaagacca tcctggccaa catggtgaaa
 ccccgtctct actaaaaata ctaaagttag ctgggtatga tagtgtgcac ctgtagtccc
 agctactagg gaggctgaga caggggaatc gattgaacct gggaggcaga ggttgcggtg
 agccgagatc ctgccactgc actccagcct ggcaatggag caagactctg tctcaaaaaa
 aaaaaaaaag gaagaaagaa aaaGGGTAGA GAAAGGGATA GCTGCTCACA CTATTAGTCT
 TTACTCCAGT TCTAAT

GeneView

GeneView via analysis of contig annotation: PDE10A phosphodiesterase 10A

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_007422->NM_006661

function

HuRef

NW_001838992->NM_006661

function

Celera

NW_923184->NM_006661

function

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


reference	NT_007422->NM_006661->NP_006652	8321434	reverse	intron

HuRef	NW_001838992->NM_006661->NP_006652	675104	forward	intron

Celera	NW_923184->NM_006661->NP_006652	98841379	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3008024 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838992.2	675104	163496125	minus	T	alt_assembly_8	HuRef	HuRef	view	200
6	NT_007422.13	8321434	165954083	plus	A	ref_assembly	reference	reference	view	200
6	NW_923184.1	98841379	166772775	plus	A	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007422 AL121789

dbSNP Blast Analysis
GenBank HTGS Finished:
AL121789.38

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss19666615	HapMap-CEU	European	100	IG	0.800	0.180	0.020	0.584	0.890	0.110

	HapMap-HCB	Asian	90	IG	0.867	0.111	0.022	0.150	0.922	0.078

	HapMap-JPT	Asian	90	IG	0.844	0.156			0.922	0.078

	HapMap-YRI	Sub-Saharan African	118	IG	0.288	0.559	0.153	0.294	0.568	0.432

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.309+/-0.243	270	210	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 .