Reference SNP(refSNP) Cluster Report: rs11836098

Reference SNP(refSNP) Cluster Report: rs11836098

refSNP ID: rs11836098
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:	G
Clinical Association:	unknown

HGVS Names
NM_005895.3:c.407-949C>T
NT_024477.13:g.583962G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss17473665 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11836098 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
ss17473665	CSHL-HAPMAP\|CSHL-HuCC-200402.chr12.NT_024477.12_385427	fwd/T	A/G	acaacagaaagaactgggttcaaagctgga	ccgtgccgagcactctgaggcaggctcagc	02/19/04	10/26/06	120	Genomic	unknown
ss38880805	ABI\|hCV1859905	fwd/T	A/G	acaacagaaagaactgggttcaaagctgga	ccgtgccgagcactctgaggcaggctcagc	07/16/05	11/02/06	126	Genomic	unknown
ss67125513	ILLUMINA\|HumanHap650Yv1.0_rs11836098	fwd/T	A/G	acaacagaaagaactgggttcaaagctgga	ccgtgccgagcactctgaggcaggctcagc	11/14/06	11/14/06	127	Genomic	unknown
ss71077597	ILLUMINA\|HumanHap650Yv3.0_rs11836098	fwd/T	A/G	acaacagaaagaactgggttcaaagctgga	ccgtgccgagcactctgaggcaggctcagc	04/23/07	04/23/07	127	Genomic	unknown
ss75390633	ILLUMINA\|ILMN_Human_1M_rs11836098	fwd/T	A/G	acaacagaaagaactgggttcaaagctgga	ccgtgccgagcactctgaggcaggctcagc	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 gcgcccgcca ccacgcctgg ctaatttttt gtatttttag tagagacggg gtttcaccat
 gttagtcagg atggtctcga tctcctgacc tcatgatcca cccgcctcgg cctcccaaag
 tgctgggatt acaggcgtga gccaccgcgc ccggcctttt tttttttttt ttttgagacg
 gagtttcatt cttgttgccc aggctggagt gcaatggtgc gatctcggct caccacaacc
 tctgcctcct gggttcaagc gattctcctg ccacagcctc ctgagtaggt gggattacag
 gcatgcaaca cgacccctga cgactttggt atttttagta gagacagggt ttctccatgt
 tggtcaggct ggtctcgaac tcccgacctg aggtgatccg cccacctcgg cctctcaaag
 tgctgagatt atgggcctga gccaccgtgc ccggcAGCAA GTGCCTTTTA ACAACAGAAA
 GAACTGGGTT CAAAGCTGGA
 R
 CCGTGCCGAG CACTCTGAGG CAGGCTCAGC TCTCACCACG CTGCAACTTG CCCTGGCTTC
 ACAGCAGGTT CTCGTGACCC CGCTGGGAGA ACCTGAAACG CCGGCACCGT GGAGTTACAG
 GCAGTACCCA GCCACAGGAG CTCAGCCGTC GTGGGGTCAC GAGACCCCGA GTGCATTTCT
 TTGCTCAGTT ACATTTGGGG

GeneView

GeneView via analysis of contig annotation: GOLGA3 golgi autoantigen, golgin subfamily a, 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

reference

NT_024477->NM_005895

function

HuRef

NW_001838068->NM_005895

function

Celera

NW_925428->NM_005895

function

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


reference	NT_024477->NM_005895->NP_005886	583962	reverse	intron

HuRef	NW_001838068->NM_005895->NP_005886	449578	forward	intron

Celera	NW_925428->NM_005895->NP_005886	542031	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11836098 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838068.2	449578	130168279	minus	C	alt_assembly_8	HuRef	HuRef	view	500
12	NT_024477.13	583962	131901027	plus	G	ref_assembly	reference	reference	view	500
12	NW_925428.1	542031	133089927	plus	G	alt_assembly_1	Celera	Celera	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024477

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC127070.10 NC_000012.10	AC023047.19

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss17473665	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	90	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	116	IG	0.034	0.276	0.690	1.000	0.172	0.828

ss38880805	AoD_African_American		90	AF					0.070	0.930

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.092+/-0.193	270	210	0	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 .