Reference SNP(refSNP) Cluster Report: rs4494819

Reference SNP(refSNP) Cluster Report: rs4494819

refSNP ID: rs4494819
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_014902.3:c.-72-12828T>G
NT_011362.9:g.100136T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7849524 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4494819 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
ss6049775	SC_JCM\|NT_011362.7_100136	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	01/10/03	10/10/03	111	Genomic	unknown
ss7849524	DEVINE_LAB\|DB_1_32251	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	03/16/03	10/25/06	113	Genomic	96 %
ss8418596	SC_SNP\|NT_011362.7_100136	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	04/17/03	10/10/03	114	Genomic	unknown
ss12491004	WI_SSAHASNP\|chr20.NT_011362.8_100136	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	07/04/03	10/10/03	116	Genomic	unknown
ss21785520	SSAHASNP\|WGSA-200403-chr20.chr20.NT_011362.8_100136	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	03/20/04	03/20/04	121	Genomic	unknown
ss24537203	PERLEGEN\|afd4191354	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	08/10/04	09/13/04	123	Genomic	unknown
ss67736333	ILLUMINA\|HumanHap650Yv1.0_rs4494819	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	11/14/06	11/14/06	127	Genomic	unknown
ss69240558	PERLEGEN\|PGP04191354	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	01/30/07	03/31/08	127	Genomic	unknown
ss71386498	ILLUMINA\|HumanHap650Yv3.0_rs4494819	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	04/23/07	04/23/07	127	Genomic	unknown
ss75349705	ILLUMINA\|ILMN_Human_1M_rs4494819	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	08/28/07	08/29/07	129	Genomic	unknown
ss91690171	BCMHGSC_JDW\|JWB-1438741	fwd/B	G/T	cacgtccccagcagccatggcctgctatct	gttgaccaaacaactagttgaatatcatgc	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGGGTTTTTG AAGGACAACC TTGGTTCCAT CTCTGTAGTC CCTTTGTTCT GAGAGTCTAG
 AAGACTTCAG TTCTTAGGTC TGTGTTTTCT TATCTTTTCA GTGTCTACCA CACAAAGATG
 AGTGCTGCGT ATGGAGCCCC TGTGACCCAC AGAGTCTCTG CTGAAGCCAG GCAGGTTTCA
 ATGGGGGTGG GGTCACAGAG AGGCCAAGTA AGCAGCCCTG TCCCTACCGA GCCCCCACCC
 CCTGAGGAGC TGTGACATCC ACATCCTGGG CCCTGTGTTC AGAGTTCACT GTCAGGATGG
 GCCTGGGAAT TCACTTCTCA TGGTTGTCTT CAAGTGGAGG AGGGACCCGA GGTGGGAGCA
 GTGTCAGTCA CACGTCCCCA GCAGCCATGG CCTGCTATCT
 K
 GTTGACCAAA CAACTAGTTG AATATCATGC TTTTCAGACA GTTGCTATGG ACACGGACTT
 AGGCTGGAAA CAATTCAGAC CTTGAATGCA TCAGGATTAT GGAGCTGTCT TAGATGGAAG
 GAATCCCGGA ATCTCAACTC AGCCTGGTGG GCAGGGCCAT GGGATGTGGG CTCAAGGATC
 AGGCTCGGAT TCATACCCAG CGCCACCCCC TTCTGGATGT GGGGCCTAGA GAGGTGACTT
 CAGCCATTGA GCTGCTGCTT CTCCTCTAAC ATGGGTAGAT TCGTGACCTA Tttctttctt
 tctttttttt ttcttttttt tgagataggg tcttactctt gtcacctaga ctggagtgca
 gtggcaaaat catggctcac tgtagtctcg acctccTTGA

GeneView

GeneView via analysis of contig annotation: DLGAP4 discs, large (Drosophila) homolog-associated protein 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_011362->NM_014902

function

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


reference	NT_011362->NM_014902->NP_055717	100136	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4494819 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NW_927339.1	5257400	31754291	plus	G	alt_assembly_1	Celera	Celera	view	400
20	NW_001838665.1	104944	31785033	plus	G	alt_assembly_8	HuRef	HuRef	view	400
20	NT_011362.9	100136	34480635	plus	T	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011362.7

dbSNP Blast Analysis
GenBank HTGS Finished:
AL445705.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss24537203	AFD_EUR_PANEL	European	48	IG	0.417	0.500	0.083	0.584	0.667	0.333

	AFD_AFR_PANEL	African American	46	IG	0.522	0.348	0.130	0.403	0.696	0.304

	AFD_CHN_PANEL	Asian	48	IG	0.625	0.208	0.167	0.025	0.729	0.271

ss69240558	HapMap-CEU	European	120	GF	0.400	0.483	0.117		0.642	0.358

	HapMap-HCB	Asian	90	GF	0.533	0.400	0.067		0.733	0.267

	HapMap-JPT	Asian	90	GF	0.622	0.356	0.022		0.800	0.200

	HapMap-YRI	Sub-Saharan African	120	GF	0.500	0.367	0.133		0.683	0.317

ss7849524	HapMap-CEU	European	118	IG	0.407	0.475	0.119	1.000	0.644	0.356

	HapMap-HCB	Asian	88	IG	0.545	0.386	0.068	1.000	0.739	0.261

	HapMap-JPT	Asian	90	IG	0.622	0.356	0.022		0.800	0.200

	HapMap-YRI	Sub-Saharan African	118	IG	0.492	0.373	0.136	0.273	0.678	0.322

	CHMJ	Asian	74	IG					0.662	0.338

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.415+/-0.188	332	260	270	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 .