Reference SNP(refSNP) Cluster Report: rs833826

Reference SNP(refSNP) Cluster Report: rs833826

refSNP ID: rs833826
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NT_029419.11:g.11494877C>A
NT_029419.11:g.11494878C>A
XM_001718260.1:c.67G>T
XP_001718312.1:p.A23S

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38905625 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs833826 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
ss1151471	KWOK\|OVLP-000804-461184	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	09/02/00	10/10/03	86	Genomic	99 %
ss2520982	SC_JCM\|AC025256.11_149884	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	11/03/00	10/10/03	92	Genomic	unknown
ss2910620	TSC-CSHL\|TSC0893157	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	01/03/01	10/25/06	92	Genomic	unknown
ss3721589	SC_JCM\|AC025256.25_166634	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	09/25/01	10/10/03	100	Genomic	unknown
ss19246960	CSHL-HAPMAP\|CSHL-HuDD-200402.chr12.NT_029419.10_11494878	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	02/20/04	03/04/04	120	Genomic	unknown
ss20919004	SSAHASNP\|WGSA-200403-chr12.chr12.NT_029419.10_11494878	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	03/19/04	03/19/04	121	Genomic	unknown
ss38905625	ABI\|hCV2023822	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	07/16/05	07/16/05	126	Genomic	unknown
ss78746228	HGSV\|Cor12878_SNV_20070510.chr12_47637839	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	10/17/07	10/20/07	129	Genomic	unknown
ss89142936	BCMHGSC_JDW\|JWB-0557440	fwd/T	A/C	agttggctgcgtaggagacgggctgggctg	ggggcccaggggctccttgggcaaagccag	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 GCGTACCCCC ACCCCCAGCC CGGGATACTT CCCACCTCCC CGATCGCGCG AGAGCTGCGC
 GGTAGCTAGC GGCAGTTCTC GCGAGACCCA TCACCATGGC AGCGGCTGCA GCACCGGCAG
 CCGGGCGCTG GAGCTGGAGT CAGGGCGGGG GCAGGTGTGG GGGCTGTGGG CGGCGGAGGC
 GGGAGCCGTG AATGGGGATG AGACAGTGAG GACTGAGGTG ACAATCCCAA GCTCCAGGGT
 TGTGCCTGGA ATTTAAGGAC TGAGGCGGCA AGTTGGCTGC GTAGGAGACG GGCTGGGCTG
 M
 GGGGCCCAGG GGCTCCTTGG GCAAAGCCAG CATCGGGATA TGGGTGAACA GTCGTTGCTG
 TGGCATGCCT TACCCAGCCA GACTTCATCT TTATTTCTTA ATCTGGGCTA GCTGCCATCC
 CCTGAAAGCC CTCACCGCAC CATTGTTGTT GCTCACTATT CCTGAGACTA GATTACTGTG
 GGGTCTGAAT CAAGAGATCC TTTCCCATAA GGAAGAGGAA GGAGAGTGAT GAACTTAAGA
 GGCTAAAGGA AAACAGCTGG ACTCTGAGCC AGTTAAGTTG GAACTTGAAA GACGGAGAGT

GeneView

GeneView via analysis of contig annotation: LOC100131446 hypothetical protein LOC100131446

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: ARF3 ADP-ribosylation factor 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_029419->XM_001718260

function

HuRef

NW_001838057->XM_001714757

function

Celera

NW_925351->XM_001714744

function

reference

NT_029419->NM_001659

function

HuRef

NW_001838057->NM_001659

function

Celera

NW_925351->NM_001659

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_029419->XM_001718260->XP_001718312	11494878	reverse	67	missense	T	Ser [S]	1	23
					contig reference	G	Ala [A]	1	23

HuRef	NW_001838057->XM_001714757->XP_001714809	8815846	reverse		intron

Celera	NW_925351->XM_001714744->XP_001714796	11691960	reverse	67	missense	T	Ser [S]	1	23
					contig reference	G	Ala [A]	1	23

reference	NT_029419->NM_001659->NP_001650	11494878	reverse		5' near gene

HuRef	NW_001838057->NM_001659->NP_001650	8815846	reverse		5' near gene

Celera	NW_925351->NM_001659->NP_001650	11691960	reverse		5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs833826 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_001838057.1	8815846	46383575	plus	A	alt_assembly_8	HuRef	HuRef	view	300
12	NT_029419.11	11494878	47637839	plus	C	ref_assembly	reference	reference	view	300
12	NW_925351.1	11691960	48146054	plus	C	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029419 AC073610 AC073610.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC025256.33 AC073610.17 NC_000012.10	AC021647.19

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	C
ss2910620	CEPH		184	AF		0.870	0.130

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.226+/-0.249	0	0	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .