Reference SNP(refSNP) Cluster Report: rs12108288

Reference SNP(refSNP) Cluster Report: rs12108288

refSNP ID: rs12108288
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001083.3:c.1131+966T>C
NM_033430.2:c.1005+966T>C
NM_033437.2:c.975+966T>C
NT_016354.18:g.45031167A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss18231229 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12108288 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
ss18231229	SC_SNP\|SC-CHR1_NA17109-200402.chr4.NT_016354.16_44978151	fwd/T	A/G	ccaaatggttgagatgttgggtcatacagt	tagtccttatatctaaatcaactaaaattt	02/20/04	10/26/06	120	Genomic	unknown
ss23285192	PERLEGEN\|afd3523074	fwd/T	A/G	ccaaatggttgagatgttgggtcatacagt	tagtccttatatctaaatcaactaaaattt	08/10/04	09/13/04	123	Genomic	unknown
ss74853471	AFFY\|SNP_M-613241	fwd/T	A/G	ccaaatggttgagatgttgggtcatacagt	tagtccttatatctaaatcaactaaaattt	08/09/07	08/09/07	128	Genomic	unknown

Fasta sequence (Legend)

 CATGGCTACT ATATTAAAAT CACCTCTATA TTAAGGATTT TATAACTGAT TGAAAAATAT
 GAAATAGTAT CTATGAAAAT ACTGATTACC TTTTAGCCTA CTGAGTTCTC ATTTGATATT
 AATCAGAATT TTGTATTAAA CAATGCATTC ATCTGACACA TATACACATC CCAAATGGTT
 GAGATGTTGG GTCATACAGT
 R
 TAGTCCTTAT ATCTAAATCA ACTAAAATTT CTTAATATAA ATTAAGTACT GAATACCTTT
 TATTATTCTA CTTTGCCCCA AAACATAACT TCGGATATCA TATGTAGATT ATAATTGACC
 TATACAAGTG ATAGTGCACG CTCTCTTTCC TATTAATCCA CAAATGAACA ACCTATTCTT
 AGGGACTAAA GGAAAAAGAA

GeneView

GeneView via analysis of contig annotation: PDE5A phosphodiesterase 5A, cGMP-specific

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_016354->NM_001083

function

reference

NT_016354->NM_033430

function

reference

NT_016354->NM_033437

function

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


reference	NT_016354->NM_001083->NP_001074	45031167	reverse	intron

reference	NT_016354->NM_033430->NP_236914	45031167	reverse	intron

reference	NT_016354->NM_033437->NP_246273	45031167	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12108288 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838920.1	1050678	116204109	plus	A	alt_assembly_8	HuRef	HuRef	view	200
4	NW_922217.1	120038	117862559	plus	A	alt_assembly_1	Celera	Celera	view	200
4	NT_016354.18	45031167	120702470	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016354

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss18231229	HapMap-CEU	European	116	IG	0.914	0.086		0.752	0.957	0.043

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	0.956	0.044		1.000	0.978	0.022

	HapMap-YRI	Sub-Saharan African	112	IG	0.911	0.071	0.018	0.050	0.946	0.054

ss23285192	AFD_EUR_PANEL	European	46	IG	0.870	0.130		0.752	0.935	0.065

	AFD_AFR_PANEL	African American	44	IG	0.818	0.182		0.655	0.909	0.091

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.071+/-0.174	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 .