Reference SNP(refSNP) Cluster Report: rs4568220

Reference SNP(refSNP) Cluster Report: rs4568220

refSNP ID: rs4568220
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
NT_016354.18:g.45603597T>G
XM_001724885.1:c.317-16246T>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7897632 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4568220 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
ss6177507	SC_JCM\|NT_006302.12_1554466	fwd/B	G/T	tgtcaataaaataaaatatatatttagcaa	ttctaggcctgatcataattatttgtgtag	01/10/03	10/10/03	111	Genomic	unknown
ss7897632	DEVINE_LAB\|DB_1_339054	fwd/B	G/T	tgtcaataaaataaaatatatatttagcaa	ttctaggcctgatcataattatttgtgtag	03/16/03	08/05/04	113	Genomic	96 %
ss10169206	BCM_SSAHASNP\|chr4.NT_016354.15_45550581	fwd/B	G/T	tgtcaataaaataaaatatatatttagcaa	ttctaggcctgatcataattatttgtgtag	06/27/03	10/10/03	116	Genomic	unknown
ss22071134	SSAHASNP\|WGSA-200403-chr4.chr4.NT_016354.16_45550581	fwd/B	G/T	tgtcaataaaataaaatatatatttagcaa	ttctaggcctgatcataattatttgtgtag	03/20/04	03/20/04	121	Genomic	unknown
ss44570845	ABI\|hCV1188603	fwd/B	G/T	tgtcaataaaataaaatatatatttagcaa	ttctaggcctgatcataattatttgtgtag	07/19/05	07/19/05	126	Genomic	unknown
ss66387301	AFFY\|SNP_A-2057294	fwd/B	G/T	aatatatatttagcaa	ttctaggcctgatcat	10/29/06	03/31/08	127	Genomic	unknown
ss76125699	AFFY\|AFFY_6_1M_SNP_A-2057294	fwd/B	G/T	aatatatatttagcaa	ttctaggcctgatcat	08/28/07	08/30/07	129	Genomic	unknown
ss77165348	HGSV\|Cor12156_SNV_20070510.chr4_121413055	fwd/B	G/T	tgtcaataaaataaaatatatatttagcaa	ttctaggcctgatcataattatttgtgtag	10/09/07	10/11/07	129	Genomic	unknown

Fasta sequence (Legend)

 CTGAAAACTG CTCCATGACA AAAAAGTTCT GTTGTTATTT CCCTAAtgaa actcagagaa
 attggtaatt tttttcaaga tcacacagct attaaggtgg tagagctagg atctgaatct
 agAACTCAGA CCCTTAACCC ATACTGCCTC ATTATTTTGG TTGATATATG AATGCTTTTA
 GGTGCCAATT ACTGTGTAAG TTGAATATTT CTGAGGCCGT AGCTGCTTTG GAAAGCACAA
 TGTCTGTCTT CATTCATAAT AAGAAGATTT AATAGTGTTA TTCTAGTTTT TTGGGTTATG
 AAGAGAATAT ATATGAACAA AATATATCTC TAAATGCATA TGGTCTGTGA CAGAAGAATA
 TATACATGTC TGTCaataaa ataaaatata tatttaGCAA
 K
 TTCTAGGCCT GATCATAATT ATTTGTGTAG TTTCTAGATT CAACGAAATG ATATAATCAA
 TGTAATGTAA CCAGACTGAC TCTCTCTGTT ACATTTTCAG GAATTTTAGA ACATAGCGAA
 ATGATGATTA GTGATTCAAT TTATTTTCTA GAAGAAATAG ATATGCCTCC TCTGTGACAG
 AAATTATATA TGATCTTCCA CTCTTGTATC AAGCCCATGC CCTCAAAAGT GCTCCAAGCA
 TTGTTACTTT CCTGGATATC ATGTTATACT ATGAAAGTGT TCAGTGGGAA GTTAAGGATT
 CCACATTTTT TAAAAAATTT CTTTTATTGG AGAGTCATCA GGGCCTTCCA TATACAATGT
 ACATTAGTTT TTCAAAAGGA GTATAGATAT GTTTTATTTC

GeneView

GeneView via analysis of contig annotation: LOC100128580 hypothetical protein LOC100128580

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_016354->XM_001724885

function

HuRef

NW_001838920->XM_001716274

function

Celera

NW_922217->XM_001715828

function

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


reference	NT_016354->XM_001724885->XP_001724937	45603597	forward	intron

HuRef	NW_001838920->XM_001716274->XP_001716326	1623199	forward	intron

Celera	NW_922217->XM_001715828->XP_001715880	692366	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4568220 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838920.1	1623199	116776630	plus	G	alt_assembly_8	HuRef	HuRef	view	400
4	NW_922217.1	692366	118434887	plus	G	alt_assembly_1	Celera	Celera	view	400
4	NT_016354.18	45603597	121274900	plus	T	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016354

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss66387301	HapMap-CEU	European	118	GF	0.119	0.441	0.441		0.339	0.661

	HapMap-HCB	Asian	90	GF		0.111	0.889		0.056	0.944

	HapMap-JPT	Asian	90	GF	0.022	0.044	0.933		0.044	0.956

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.350	0.633		0.192	0.808

ss7897632	HapMap-CEU	European	120	IG	0.117	0.450	0.433	1.000	0.342	0.658

	HapMap-HCB	Asian	90	IG		0.111	0.889	0.752	0.056	0.944

	HapMap-JPT	Asian	90	IG	0.022	0.044	0.933	1.000	0.044	0.956

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.350	0.633	0.100	0.192	0.808

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss66387301	266	9	80	177
ss7897632	267	9	81	177

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs4568220	270	9	81	177

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5143	ss7897632	G/G	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	r23_ch4_YRI_affymetrix:genechip500k	432289
5143	ss66387301	G/G	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	chr4-HapMap-YRI
5229	ss7897632	G/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	r23_ch4_JPT_affymetrix:genechip500k	432289
5229	ss66387301	G/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr4-HapMap-JPT
5241	ss7897632	G/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r23_ch4_YRI_affymetrix:genechip500k	432289
5241	ss66387301	G/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	chr4-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

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 .