Reference SNP(refSNP) Cluster Report: rs284691

Reference SNP(refSNP) Cluster Report: rs284691

refSNP ID: rs284691
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:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_022467.3:c.131-31278T>C
NT_011109.15:g.6499258T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1966538 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs284691 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
ss368882	KWOK\|OVLP-000621-160763	rev/T	A/G	tctccacttggggctcctacagcttgctga	tggctttagcatagcctcgtatttgcatca	06/30/00	10/10/03	79	Genomic	99 %
ss553242	SC_JCM\|AC011519.6_24678	rev/T	A/G	tctccacttggggctcctacagcttgctga	tggctttagcatagcctcgtatttgcatca	07/12/00	10/10/03	80	Genomic	unknown
ss1248725	KWOK\|OVLP-000804-507698	fwd/B	C/T	tgatgcaaatacgaggctatgctaaagcca	tcagcaagctgtaggagccccaagtggaga	09/02/00	10/10/03	86	Genomic	97 %
ss1966538	KWOK\|OVLP-000925-717013	fwd/B	C/T	tgatgcaaatacgaggctatgctaaagcca	tcagcaagctgtaggagccccaagtggaga	10/06/00	10/25/06	87	Genomic	97 %
ss6632304	WI_SSAHASNP\|NT_011196.11_6279716	fwd/B	C/T	tgatgcaaatacgaggctatgctaaagcca	tcagcaagctgtaggagccccaagtggaga	02/12/03	10/10/03	111	Genomic	unknown
ss19398589	CSHL-HAPMAP\|CSHL-HuDD-200402.chr19.NT_011109.15_6499258	fwd/B	C/T	tgatgcaaatacgaggctatgctaaagcca	tcagcaagctgtaggagccccaagtggaga	02/20/04	03/04/04	120	Genomic	unknown
ss21507712	SSAHASNP\|WGSA-200403-chr19.chr19.NT_011109.15_6499258	fwd/B	C/T	tgatgcaaatacgaggctatgctaaagcca	tcagcaagctgtaggagccccaagtggaga	03/20/04	03/20/04	121	Genomic	unknown
ss24525660	PERLEGEN\|afd1608892	fwd/B	C/T	tgatgcaaatacgaggctatgctaaagcca	tcagcaagctgtaggagccccaagtggaga	08/10/04	09/13/04	123	Genomic	unknown
ss76440433	AFFY\|AFFY_6_1M_SNP_A-8301299	fwd/B	C/T	ggctatgctaaagcca	tcagcaagctgtagga	08/28/07	08/30/07	130	Genomic	unknown
ss81202389	HGSV\|Cor18507_SNV_20070510.chr19_38922880	fwd/B	C/T	tgatgcaaatacgaggctatgctaaagcca	tcagcaagctgtaggagccccaagtggaga	11/26/07	11/28/07	130	Genomic	unknown

Fasta sequence (Legend)

 GGCTCTGGGC ATCTCTCAAA AAGAGATGGT CAAAGAATCT GATGAGGTCT GCTGAAAAGG
 AAGGGTGCCA TAGAGAACCA GACCAGCCCC CATCCTGGTG AGCGGTGCCT CCTCACACAA
 AAAGCTAATG GTTTGGGTTG GTGTGGTCAG AGGAGAGCAG CTCTCAGAGA CAGAGGTGAG
 GATGGAGGCC CTTTCATTTT CCTGGTGAGT CTTTCCATAC TACTTTTTAA AAGAAAGTCG
 GTACTTTAAA ATATTTTGTA AGTCAATTTG TCCAGGATGC CTGCAAGTTT TCCTGGAATT
 TGATGCAAAT ACGAGGCTAT GCTAAAGCCA
 Y
 TCAGCAAGCT GTAGGAGCCC CAAGTGGAGA AACTCAAACT AGTTCACAGG AGCAAACATC
 ATGCAGCTCC CTCCAAGGCT ACATCACTCG TGGGTTGTGG TGTTTCTTTG TGGAAGTCCC
 CAAGCTCTTA GGGTGAGAGG GCTCTTCAGT GACGCCCAGG GACCTTTCTC AAGGCTGTGG
 GCATCGGTTT GCAGAACCGT

GeneView

GeneView via analysis of contig annotation: CHST8 carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8

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_011109->NM_022467

function

HuRef

NW_001838493->NM_022467

function

Celera

NW_927206->NM_022467

function

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


reference	NT_011109->NM_022467->NP_071912	6499258	forward	intron

HuRef	NW_001838493->NM_022467->NP_071912	280444	forward	intron

Celera	NW_927206->NM_022467->NP_071912	6496213	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs284691 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838493.1	280444	30730605	plus	C	alt_assembly_8	HuRef	HuRef	view	330
19	NW_927206.1	6496213	30924645	plus	C	alt_assembly_1	Celera	Celera	view	330
19	NT_011109.15	6499258	38922880	plus	T	ref_assembly	reference	reference	view	330

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011109 AC067911 AC067911.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC011519.7 NC_000019.8	AC067911.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1966538	HapMap-CEU	European	120	IG	0.217	0.400	0.383		0.417	0.583

	HapMap-HCB	Asian	90	IG	0.156	0.400	0.444		0.356	0.644

	HapMap-JPT	Asian	90	IG	0.022	0.467	0.511		0.256	0.744

	CHMJ	Asian	74	IG					0.257	0.743

ss24525660	AFD_EUR_PANEL	European	48	IG	0.250	0.500	0.250	1.000	0.500	0.500

	AFD_AFR_PANEL	African American	46	IG	0.130	0.522	0.348	0.655	0.391	0.609

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.500	0.417	0.584	0.333	0.667

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.466+/-0.127	242	200	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

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .