Reference SNP(refSNP) Cluster Report: rs200483

Reference SNP(refSNP) Cluster Report: rs200483

refSNP ID: rs200483
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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
NT_007592.14:g.18633075G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1845484 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs200483 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
ss263413	KWOK\|OVLP-000621-124369	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	06/30/00	10/10/03	79	Genomic	97 %
ss843920	SC_JCM\|AC024428.3_91810	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	07/27/00	10/10/03	85	Genomic	unknown
ss1257512	KWOK\|OVLP-000804-591523	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	09/02/00	10/10/03	86	Genomic	97 %
ss1845484	KWOK\|OVLP-000925-712923	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	10/05/00	10/25/06	87	Genomic	97 %
ss23365538	PERLEGEN\|afd0270710	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	08/10/04	09/13/04	123	Genomic	unknown
ss65775715	ILLUMINA\|Human1-rs200483	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	10/10/06	10/10/06	127	Genomic	unknown
ss65841027	KRIBB_YJKIM\|KHS16820	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	10/17/06	12/16/06	127	Genomic	unknown
ss74976486	ILLUMINA\|ILMN_Human_1M_rs200483	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	08/28/07	08/29/07	129	Genomic	unknown
ss76718936	AFFY\|AFFY_6_1M_SNP_A-8580434	rev/B	C/T	cacttgcgcaaccaga	atgattttaaggcacg	08/28/07	08/30/07	129	Genomic	unknown
ss79783477	HGSV\|Cor18507_SNV_20070510.chr6_27882803	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	11/23/07	11/23/07	130	Genomic	unknown
ss82778490	HGSV\|Cor18555_SNV_20070510.chr6_27882803	fwd/T	A/G	ctcgggtcttttgtcgtgccttaaaatcat	tctggttgcgcaagtgagggaaaggattgg	11/27/07	12/03/07	130	Genomic	unknown

Fasta sequence (Legend)

 GAAAACAAGA AAAACTTTTA AAAATCTACT CTGGCATCTT TTGCTAGCAG GCATTGACAA
 TTAGGAGAAG GCAAGGTGTT AACTTTTACT GATCTCCCAC tttttttttt gagacaaggc
 ctggctttat cacccaggct ggagtgcagt ggtgcgatct cagctcactg taaactccgc
 ctaccaggct caagccatcc tcctacatca gccccctaag tagctgggac aacaggggcg
 cgccaccact cctggctaat ttttgtgctt tttgcagaga cggggttttg ctatgttgcc
 caggctggtt gcgaactcct gggctcaagg gatccgcccg cctccacctc ccaaagtgct
 gggattacag gcatgagcca ccgcgcccAC CCCTCTAGTT TCCAGTTTAG TCGGAAAGAT
 TAAAAACGCC AGCCTTGTTT TCCTAGTGCT GTTTTTGGTT TTTACCTCGG GTCTTTTGTC
 GTGCCTTAAA ATCAT
 R
 TCTGGTTGCG CAAGTGAGGG AAAGGATTGG GTAAAGGGGG CGCCACCGCA AGTTGCTGTG
 CAACATCCAG ACATCACCAG ACCCACCACC TGGAGCCTGG CCTGGCGGTG TCAAACGCAT
 TCTGGTCTCA TCTTTTTAGA AACCCGTGGA TGCTCAAGGA ATTTCCGGAT AACGTGATCC
 CGGATGCGCT TGACTGACTT

GeneView

GeneView via analysis of contig annotation: HIST1H2BL histone cluster 1, H2bl

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: HIST1H2AI histone cluster 1, H2ai

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_007592->NM_003519

function

reference

NT_007592->NM_003509

function

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


reference	NT_007592->NM_003519->NP_003510	18633075	reverse	3' near gene

reference	NT_007592->NM_003509->NP_003500	18633075	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs200483 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838980.1	855419	27583110	plus	G	alt_assembly_8	HuRef	HuRef	view	495
6	NT_007592.14	18633075	27882803	plus	G	ref_assembly	reference	reference	view	495
6	NW_923073.1	845183	29380862	plus	G	alt_assembly_1	Celera	Celera	view	495

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000006.6 AL009179 AL009179.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AL009179.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1845484	HapMap-CEU	European	120	IG	0.017	0.183	0.800	0.752	0.108	0.892

	HapMap-HCB	Asian	90	IG		0.178	0.822	0.527	0.089	0.911

	HapMap-JPT	Asian	88	IG		0.159	0.841	0.584	0.080	0.920

	HapMap-YRI	Sub-Saharan African	120	IG	0.100	0.283	0.617	0.100	0.242	0.758

ss23365538	AFD_EUR_PANEL	European	48	IG		0.208	0.792	0.584	0.104	0.896

	AFD_AFR_PANEL	African American	46	IG		0.304	0.696	0.403	0.152	0.848

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.083	0.875	0.050	0.083	0.917

ss65841027	KHP1		180	AF		0.122	0.878	0.584	0.061	0.939

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.201+/-0.245	332	260	9	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 .