Reference SNP(refSNP) Cluster Report: rs580810

Reference SNP(refSNP) Cluster Report: rs580810

refSNP ID: rs580810
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

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

HGVS Names
NM_006661.1:c.1955+12336G>A
NT_007422.13:g.8067688C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss22492433 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs580810 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
ss61501	TSC-CSHL\|TSC0046646	fwd/B	C/T	tcatatatttaggatgattgatgagaaatg	aactggccactaggataaaagttaattacc	09/06/00	10/25/06	86	Genomic	95 %
ss752352	SC_JCM\|AL117345.2_71048	rev/T	A/G	ggtaattaacttttatcctagtggccagtt	catttctcatcaatcatcctaaatatatga	07/27/00	10/10/03	83	Genomic	unknown
ss2584436	SC_JCM\|AL117345.21_71048	rev/T	A/G	ggtaattaacttttatcctagtggccagtt	catttctcatcaatcatcctaaatatatga	11/03/00	10/10/03	89	Genomic	unknown
ss13080215	SC_SNP\|NT_007422.12_8067688	fwd/B	C/T	tcatatatttaggatgattgatgagaaatg	atggccactaggataaaagttaattacctt	10/22/03	10/31/03	126	Genomic	unknown
ss22492433	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007422.12_8067688	fwd/B	C/T	tcatatatttaggatgattgatgagaaatg	aactggccactaggataaaagttaattacc	03/21/04	10/26/06	121	Genomic	unknown
ss44709802	ABI\|hCV575334	fwd/B	C/T	tcatatatttaggatgattgatgagaaatg	aactggccactaggataaaagttaattacc	07/19/05	11/03/06	126	Genomic	unknown
ss84591722	HGSV\|Cor18517_SNV_20070510.chr6_165750758	fwd/B	C/T	tcatatatttaggatgattgatgagaaatg	aactggccactaggataaaagttaattacc	12/06/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 TAAAAAGCCA AGAGACTAAA ATAAAACTTT TCAGCTGATA AAGAGTATAT AATGAAATGG
 CTAGATACTA AACAAAGTTT TAAGATTCTG GTAATCATAG AATAATAATA ATAAATTCTA
 GATAGAACTA AAAACAAATC TTGAAGATGC TGTCTAGTAC CTAAAAACTG GCGTAAGTGG
 AAGAAGATTT AAACGTTGAA AGGCAAGACC ACGTTGGGTG ACATCCTTAT TTACACAGCT
 CTTCTCCTAA GGGCATGTCA TAAATACAGC CCAAAAGAAA GTCAGGGCCC ATTGAGAAGG
 GAGAGTCTGG GGATGTCAGA GCACACACAA GTTGAGGAGG GAAATCCTAG AAAGCAGGGA
 GAACCACAGA AGTGGAAGTC CCCAAATTGG AATTCATACA AATCCCTGAC AGAGTACACC
 AAGGCCAAAA CAGAAATGGA ACCACCCAAC TAAAGCTTAA AGGAACATAC TCATATATTT
 AGGATGATTG ATGAGAAATG
 Y
 AACTGGCCAC TAGGATAAAA GTTAATTACC TTCAGAGAAA GACAAGAGCA TCCAGAAAGA
 TAATGGAGCT TGTTGCCCAT TATGTAATAT ACAAATATAA AAAAATTACT AGCCATGTAA
 AGAAACTGAA AAATGTATTA CACTGTCTAG AGTAAAATCA GTCAACAAGA CAAAACTCAT
 AGAAAACCCA GATAGTGAAA ATTCAGACAA CAATCTCTAA ATAATGTACA GATACGCTAA
 AGAATCTTCA GGAAAATATA TATTTAGAAA AGATAGGTGA AGAGATGGGG AATTTCAGGA
 GAAACATAGC AGCTATAAAA ATGAATGAAA AGGAAATCCC AGAACTTGAA AATATTACAT
 ATATATATAT ACACACACAC ATAtgtgtgt gtgtgtgtgt gtgtgcgtgc atctgtgtgt
 ATTTTCTAAA AATCACAACA TGAGGTTAAC TACAGATTGG ACAGAATATT AGGAAAAAAA
 ACAGTGAGAT TAG

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	8067688	reverse	intron

HuRef	NW_001838992->NM_006661->NP_006652	929386	forward	intron

Celera	NW_923184->NM_006661->NP_006652	98587061	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs580810 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	929386	163241843	minus	A	alt_assembly_8	HuRef	HuRef	view	500
6	NT_007422.13	8067688	165700337	plus	C	ref_assembly	reference	reference	view	500
6	NW_923184.1	98587061	166518457	plus	T	alt_assembly_1	Celera	Celera	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007422 AC046180 AL117345.20 AL354818

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC127702.2 AL117345.21 NC_000006.10	AC046180.2

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	A	C	G	T
ss22492433	HapMap-CEU	European	120	IG			0.300	0.533		0.167	0.527		0.567		0.433

	HapMap-HCB	Asian	90	IG			0.267	0.533		0.200	0.655		0.533		0.467

	HapMap-JPT	Asian	88	IG			0.295	0.545		0.159	0.479		0.568		0.432

	HapMap-YRI	Sub-Saharan African	120	IG			0.067	0.433		0.500	0.655		0.283		0.717

ss44709802	AoD_African_American		90	AF									0.430		0.570

	AoD_Caucasian		92	AF									0.650		0.350

	AoD_Chinese		90	AF									0.600		0.400

	AoD_Japanese		90	AF									0.510		0.490

ss61501	AfAm	African American	40	IG	0.200	0.600			0.200		0.371	0.500		0.500

	Caucasian	European	40	IG	0.100	0.250			0.650		0.251	0.225		0.775

	Asian	Asian	34	IG	0.059	0.647			0.294		0.150	0.382		0.618

	CEPH	European	44	IG	0.182	0.500			0.318		1.000	0.432		0.568

	PDpanel	Global	48	IG	0.458	0.208			0.333		0.005	0.562		0.438

Concordant Genotype	Total Sample	A/A	A/G	C/C	C/T	G/G	T/T
ss22492433	267			54	134		78
ss61501	102	23	44			35

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs580810	372	23	44	54	134	35	78

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
215	ss61501	G/G	AFFY	CEPH	NA10857		AFFY_071103
215	ss22492433	C/C	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r23_ch6_CEU_illumina:golden_gate_1.0.0	500285
225	ss61501	G/G	AFFY	CEPH	NA12043		AFFY_071103
225	ss22492433	C/C	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r23_ch6_CEU_illumina:golden_gate_1.0.0	500285
226	ss61501	G/G	AFFY	CEPH	NA12044		AFFY_071103
226	ss22492433	C/C	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r23_ch6_CEU_illumina:golden_gate_1.0.0	500285

Genotype data submitted for	375	samples from	372	individuals	Individual with multiple genotypes submission:	3

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .