Reference SNP(refSNP) Cluster Report: rs8081010

Reference SNP(refSNP) Cluster Report: rs8081010

refSNP ID: rs8081010
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
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
NM_012121.4:c.-112-2924C>T
NT_010641.15:g.5211947G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14278301 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs8081010 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
ss12413485	WI_SSAHASNP\|chr17.NT_010641.13_5177836	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	07/04/03	10/10/03	116	Genomic	unknown
ss14278301	BCM_SSAHASNP\|chr17.NT_010641.14_5177836	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	11/05/03	10/25/06	119	Genomic	unknown
ss24215064	PERLEGEN\|afd2493000	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	08/10/04	09/13/04	123	Genomic	unknown
ss74836326	AFFY\|SNP_M-594082	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	08/09/07	08/09/07	128	Genomic	unknown
ss78823444	HGSV\|Cor12878_SNV_20070510.chr17_68797270	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	10/17/07	10/20/07	129	Genomic	unknown
ss86200782	HGSV\|Cor18956_SNV_20070510.chr17_68797270	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	11/30/07	12/11/07	130	Genomic	unknown
ss86208538	HGSV\|Cor18517_SNV_20070510.chr17_68797270	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	12/06/07	12/11/07	130	Genomic	unknown
ss90656146	BCMHGSC_JDW\|JWB-1047426	fwd/T	A/G	ctcatgcagctcttccgtttggctgttcct	agtcgtatcttttgtaataaaccagtaaaa	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCTCTGGGCC CCACCCTCCT GCCCCACCTC AACCTCTAAA CAATTAGACA TTGAACCGCT
 AGACCAAAGG TCAGCAAACA CTTTTTGCAA AGGGCCAGAG AGTAAATATT CTCGGCCTTG
 TGGCTGATAG GGTTTTTGTC ACAGCTACTC AACTGTCTTC TTAGTATAAA ACTAGCCGTT
 ggccgggcac agtgggtcac aactgtaatc ccagcactct gggaggctac ggcaggagga
 tcagttgagc ccaggagttc cagaccagcc tgggcaacac ggtgagaccc catctctaca
 caaaatcaaa aaAAGAAAga aaggagccat agcaacatgt aaacaagtag gcatggctat
 gttccaataa cattttattt acagaCAACT TCTGGGTTGG TGAGCAGATC GAGGTGCCAG
 GAAGGTGGTG CGTGCCCTGC CCCCCACCCC AACACTTGAC CCCACGCATC CTCATGCAGC
 TCTTCCGTTT GGCTGTTCCT
 R
 AGTCGTATCT TTTGTAATAA ACCAGTAAAA GAAAAAAAAC CACCAAAAAG CCACATcttt
 atttacaaaa gcaaacgcag gctgggtttg gcccatggac tgtagtttgc tgactcctgA
 ATATCATATA TGACCCTCTT GGCCAGCCAT GGGCTCCTAG GCAAAACTCT GAAGAAAACa
 ggaagggagg aagggaggga gggaggaagg gagggaggaa gggaggggaa ggaaaggaag
 gaaggaaagg aaataaggaa agaaaaaaag aaagagagaa agaaaaagaa aggaaagaag
 gaaaggaaag gaagagaaga aaggaagaaa ggaaaagaaa agcaaggaag gaaagaaAGA
 GAAAAAGAAG CAGCAGAAGA AAAGAAAAAG AAAAAGAGAA GGTAGACTCT GCCTCAGTCA
 CGTTGGGCAT AGAAGGGAAA AAGGCCAAGC TTCAAACGAA CTCTCGTTCC TGGCAAATCC
 TTCAGGCTTC TACTGCCACC

GeneView

GeneView via analysis of contig annotation: CDC42EP4 CDC42 effector protein (Rho GTPase binding) 4

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_010641->NM_012121

function

Celera

NW_926918->NM_012121

function

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


reference	NT_010641->NM_012121->NP_036253	5211947	reverse	intron

Celera	NW_926918->NM_012121->NP_036253	8374225	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs8081010 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_926918.1	8374225	67868824	plus	G	alt_assembly_1	Celera	Celera	view	500
17	NT_010641.15	5211947	68797270	plus	G	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010641

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC087301.8 NC_000017.9	AC026091.5

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss14278301	HapMap-CEU	European	108	IG	0.259	0.426	0.315	0.294	0.472	0.528

	HapMap-HCB	Asian	84	IG	0.333	0.405	0.262	0.251	0.536	0.464

	HapMap-JPT	Asian	72	IG	0.306	0.500	0.194	1.000	0.556	0.444

	HapMap-YRI	Sub-Saharan African	104	IG	0.077	0.538	0.385	0.200	0.346	0.654

ss24215064	AFD_EUR_PANEL	European	48	IG	0.458	0.417	0.125	1.000	0.667	0.333

	AFD_AFR_PANEL	African American	42	IG	0.381	0.381	0.238	0.317	0.571	0.429

	AFD_CHN_PANEL	Asian	48	IG	0.250	0.625	0.125	0.200	0.562	0.438

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.500+/-0.004	332	260	9	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 .