Reference SNP(refSNP) Cluster Report: rs519507

Reference SNP(refSNP) Cluster Report: rs519507

refSNP ID: rs519507
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_005187.4:c.379+886C>T
NM_175931.1:c.121+4312C>T
NT_010542.15:g.524217G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss689813 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs519507 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
ss689813	SC_JCM\|AC021125.2_120482	fwd/T	A/G	ctttgccatccataagatcacagagtggat	acaagagccactgtccaggagctgcacgcc	07/27/00	10/25/06	83	Genomic	unknown
ss1276034	KWOK\|OVLP-000804-538599	fwd/T	A/G	ctttgccatccataagatcacagagtggat	acaagagccactgtccaggagctgcacgcc	09/02/00	10/10/03	86	Genomic	94 %
ss1653260	KWOK\|OVLP-000925-92087	fwd/T	A/G	ctttgccatccataagatcacagagtggat	acaagagccactgtccaggagctgcacgcc	10/05/00	10/10/03	87	Genomic	94 %
ss66140255	AFFY\|SNP_A-2101063	fwd/T	A/G	agatcacagagtggat	acaagagccactgtcc	10/27/06	10/27/06	127	Genomic	unknown
ss76157227	AFFY\|AFFY_6_1M_SNP_A-2101063	fwd/T	A/G	agatcacagagtggat	acaagagccactgtcc	08/28/07	08/30/07	129	Genomic	unknown
ss85616377	HGSV\|Cor19129_SNV_20070510.chr16_87491101	fwd/T	A/G	ctttgccatccataagatcacagagtggat	acaagagccactgtccaggagctgcacgcc	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 ACGCACACGA GTCCCCAGCT GAGGATTGGG GGCACACGCG AGCACCCCCG CGGCTCCCCC
 AGCCTCAGAG CCTTGGTGGG GGGGTCAGAT GCGACAGAGG CACCCTAACG CAGCCCCTCC
 TGTCACCCCT GCTCCTTGCT GTGGGGGCTC CGGGATCTGG GATTCACCAA CTTTGCCATC
 CATAAGATCA CAGAGTGGAT
 R
 ACAAGAGCCA CTGTCCAGGA GCTGCACGCC AGGCGCGAGT GCGTGGCCAG GCCCATCACA
 GAATAATGGC TGTGAAAAGG ACAGCCCTGT GCAACAGAAA CAACGCACAG TTGTTCTGCT
 GCCCTCGTTC TTAGAGCCGG GAGTGCCACG ACAGCCACAC CTGGGCCATG CTGCCAGGCT
 GGCTGGTAGT GATGGACCGG

GeneView

GeneView via analysis of contig annotation: CBFA2T3 core-binding factor, runt domain, alpha subunit 2; translocated to, 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_010542->NM_005187

function

reference

NT_010542->NM_175931

function

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


reference	NT_010542->NM_005187->NP_005178	524217	reverse	intron

reference	NT_010542->NM_175931->NP_787127	524217	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs519507 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_926561.1	600836	74032846	plus	G	alt_assembly_1	Celera	Celera	view	200
16	NW_001838334.1	99133	74661469	plus	G	alt_assembly_8	HuRef	HuRef	view	200
16	NT_010542.15	524217	87491101	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AC021125 AC009149 AC021125.3

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss689813	CEPH		184	AF					1.000

	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	90	IG	0.022	0.978	1.000	0.011	0.989

	HapMap-YRI	Sub-Saharan African	120	IG	0.367	0.633	0.100	0.183	0.817

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.104+/-0.203	270	210	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .