Reference SNP(refSNP) Cluster Report: rs10399878

Reference SNP(refSNP) Cluster Report: rs10399878

refSNP ID: rs10399878
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
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

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss87158966 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10399878 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
ss14687582	BCM_SSAHASNP\|chr1.NT_077913.2_243664	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	11/10/03	03/31/08	119	Genomic	unknown
ss19147543	CSHL-HAPMAP\|CSHL-HuDD-200402.chr1.NT_077913.2_243664	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	02/20/04	03/04/04	120	Genomic	unknown
ss19868456	CSHL-HAPMAP\|CSHL-HuFF-200402.chr1.NT_077913.2_243664	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	02/21/04	03/04/04	120	Genomic	unknown
ss20525340	SSAHASNP\|WGSA-200403-chr1.chr1.NT_077913.2_243664	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	03/18/04	03/18/04	121	Genomic	unknown
ss65744781	ILLUMINA\|Human1-rs10399878	fwd/B	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	10/10/06	10/10/06	127	Genomic	unknown
ss74884271	ILLUMINA\|ILMN_Human_1M_rs10399878	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	08/28/07	08/29/07	129	Genomic	unknown
ss77791326	HGSV\|Cor12156_SNV_20070510.chr1_1279876	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	10/09/07	10/14/07	129	Genomic	unknown
ss85118518	HGSV\|Cor19240_SNV_20070510.chr1_1279876	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	11/30/07	12/08/07	130	Genomic	unknown
ss87158966	BCMHGSC_JDW\|JWB-0000614	fwd/T	A/G	ctgcactactgcagcccatccaggtctggc	cccatgcactgtgggacagggtgggggcag	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCCGCCCCCC CAACCCCAGG CAGGCAGAGG CAGCCGCTGC TGTGCCCTCG GGGAAGAAGG
 CTGGACCAGC CTCTCCCAGG ACAGCCGGCC GCTGGGAGTC CCTCAGGGAC AGTGCCCACC
 AAGGGCTGAG CCAGCCTCAC CCGCCTCTCC TCTAGGAGTT CAGAGTCAAC CCTGGACCCA
 TCTGGAGCCC CTCAACCCTG CGGCACCTCC CCTCACCCCA CTGCACTACT GCAGCCCATC
 CAGGTCTGGC
 R
 CCCATGCACT GTGGGACAGG GTGGGGGCAG TAGGGCAGCT GCTCTCGGTC CTGGCAGCAC
 CAGGAGGACC CAGACCAGCT GGGGAGAGAC GCCCCCGGCT CCCCCAACCT CACAGCTGCA
 AGCGGCATGG TCCGCTGGAA AGACGGGTAG GCCATCCTCC TCAGAGCCCA CTCCCACCAG
 GACAGCCTGA CAGTGGGGCT GCCTGGGGAG AGAAGAGTTA AGGCATGACA TCACCAGAGA
 AGCCTCGGCG

GeneView

GeneView via analysis of contig annotation: CENTB5 ArfGAP with coiled-coil, ankyrin repeat and PH domains 3

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

Celera

NW_921350->NM_030649

function

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


Celera	NW_921350->NM_030649->NP_085152	1341188	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10399878 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838585.1	491956	511203	plus	G	alt_assembly_8	HuRef	HuRef	view	200
1	NT_004350.18	718585	1229816	plus	A	ref_assembly	reference	reference	view	200
1	NW_921350.1	1341188	1341188	minus	C	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077913

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank mRNA:
AL139287.24	AL732582.4	AB051503.1

UniGene Cluster ID
535257

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss14687582	HapMap-CEU	European	116	IG		0.086	0.914		0.043	0.957

	HapMap-HCB	Asian	90	IG	0.044	0.156	0.800		0.122	0.878

	HapMap-JPT	Asian	88	IG	0.068	0.364	0.568		0.250	0.750

	HapMap-YRI	Sub-Saharan African	116	IG	0.052	0.259	0.690		0.181	0.819

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.246+/-0.250	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 .