Reference SNP(refSNP) Cluster Report: rs897958

Reference SNP(refSNP) Cluster Report: rs897958

refSNP ID: rs897958
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_000512.3:c.423-901T>C
NT_010542.15:g.465691A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43960691 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs897958 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
ss1328873	TSC-CSHL\|TSC0172365	fwd/T	A/G	ctgtccgggtttccttgcgc	gcctgtcctgtcctggaacgaatccagctt	09/06/00	10/10/03	86	Genomic	95 %
ss5012545	YUSUKE\|IMS-JST187322	rev/B	C/T	aagctggattcgttccaggacaggacaggc	gcgcaaggaaacccggacagctggcctggg	08/12/02	10/10/03	108	Genomic	unknown
ss21369292	SSAHASNP\|WGSA-200403-chr16.chr16.NT_010542.14_462895	fwd/T	A/G	cccaggccagctgtccgggtttccttgcgc	gcctgtcctgtcctggaacgaatccagctt	03/19/04	03/19/04	121	Genomic	unknown
ss43960691	ABI\|hCV7476509	fwd/T	A/G	cccaggccagctgtccgggtttccttgcgc	gcctgtcctgtcctggaacgaatccagctt	07/18/05	07/18/05	126	Genomic	unknown
ss77223670	HGSV\|Cor12156_SNV_20070510.chr16_87432575	fwd/T	A/G	cccaggccagctgtccgggtttccttgcgc	gcctgtcctgtcctggaacgaatccagctt	10/09/07	10/12/07	129	Genomic	unknown

Fasta sequence (Legend)

 GATTAGAGTG ACGACAAGAG AACGTGACAG TGTGGCCACA CTGGTGACCT CCACCAACCG
 CTCTCCTGGG ACCGGGGTTC ACCTGCTGGG AATGGCCATC GCCAGGCATC ACACCCCAGG
 CCTGTGGGAA CCCCTCCAGA CCCCGTCCCG CACTCCCCTT CTGACAATCC CCCGCAGACC
 TTGTGCTCCC ACCCTCTGGT GGCACCTAAT CTCATCCTCC GGCCCACAGC AGCCCTGCAG
 GCCACACCTC TGTGCCCACT CGCCCTGGCC CCCAGGCCAG CTGTCCGGGT TTCCTTGCGC
 R
 GCCTGTCCTG TCCTGGAACG AATCCAGCTT GCGGCTGCTC TTCAGAACGG GCTGCAGGAG
 AGGTGGTATG AGATGGCTTC TAGGCACGGC CGTGGGCGGG TCTCACGTCA GTTGCGTGTC
 GTCTGAGGAA AGTTCTTCTG CAGCTACGGC TTTGAAAGCA GCATCCCCGA CGCAGATTTC
 CCCGAGGCAG ATTTCACCAC AGCAGATTTC TGCTGCCTCC CTGGACATGG CCTCTGTACC
 CTGGACCTCC CGAGCTGCCT CTCCCCATCT CCTCTCTCAG GTAAGCACGC CTGGACCTCT

GeneView

GeneView via analysis of contig annotation: GALNS galactosamine (N-acetyl)-6-sulfate sulfatase

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_000512

function

HuRef

NW_001838334->NM_000512

function

Celera

NW_926561->NM_000512

function

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


reference	NT_010542->NM_000512->NP_000503	465691	reverse	intron

HuRef	NW_001838334->NM_000512->NP_000503	39928	reverse	intron

Celera	NW_926561->NM_000512->NP_000503	541656	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs897958 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	541656	73973666	plus	A	alt_assembly_1	Celera	Celera	view	300
16	NW_001838334.1	39928	74602264	plus	A	alt_assembly_8	HuRef	HuRef	view	300
16	NT_010542.15	465691	87432575	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010542 AC021125.3 AC021591.2 AC074303.1

dbSNP Blast Analysis

Population Diversity

There is no frequency data.

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 .