Reference SNP(refSNP) Cluster Report: rs12325267

Reference SNP(refSNP) Cluster Report: rs12325267

refSNP ID: rs12325267
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
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
NM_000512.3:c.1002+1645C>T
NT_010542.15:g.457378G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss18799571 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12325267 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss18799571	SC_SNP\|SC-CHR9-12_NA17119-200402.chr16.NT_010542.14_454582		fwd/T	A/G	gctcaggaatggggcagctactaggattgg	aaaaggcagggaacagaacatctcctggag	02/20/04	03/04/04	120	Genomic			unknown

Fasta sequence (Legend)

 CAGGCCGCTC ATCAGCGAGG CTCGAAACAG GGAGGCCAGC CTGGGTGAGC AGGGGGTGGG
 GTGGGACACA GCCACAGGGT CCTCAAAAGT GGAACAGGCg ccgggcgcgg tggctcacgc
 ctgtaatccc aacactttcg gaggccgagg cgggcagatc acgaggtcag gagattgaga
 ccatactggc caacatagtg aaactccgtc tctactaaaa atacaaaaat tagccgggca
 tggtagagca tgcctgtagt cccagctact cgggaggctg aggcaggaga atcgcttgaa
 tctgggaggt agaagttgca gtgagccgag attgcactac tgcactccag cctgggcaac
 agagtgagac ttcatctcaa aaaaaaaaaa aaaaaaaaaa aaaaCGTGGA ACAGGAAGGC
 CAGGGACAGA TGCCTGCGTg ctgctggctt tgacggtgga ggggccagga gctcaggaat
 ggggcagcta ctaggattgg
 R
 aaaaggcagg gaacagaaca tctcctggag cctccagaag gagctggccc cacgcacgtc
 ttcactcagc cccatgagcc ccatGTTGAC TCTGGCTGTC GTCATGTGTG ATGTTCCAGC
 TGCCACTGGG AGCCCCCCCC ATCCTCGTGG GGCCACTTGA AGGGGATGGC TGCCTCTGGA
 GGCCATTGGG AGGGCAAAAG ACTAAGAAAC AGTGAAGAAA CAGCGGTCGT TTACAAACAC
 CAGACTCAGC CCCGCGTGTT GATGGGTATG TCTGGCTCAA GTGCCTGT

GeneView

GeneView via analysis of contig annotation: GALNS galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio syndrome, mucopolysaccharidosis type IVA)

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	457378	reverse	intron

HuRef	NW_001838334->NM_000512->NP_000503	31586	reverse	intron

Celera	NW_926561->NM_000512->NP_000503	533343	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12325267 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	533343	73965353	plus	G	alt_assembly_1	Celera	Celera	view	500
16	NW_001838334.1	31586	74593922	plus	G	alt_assembly_8	HuRef	HuRef	view	500
16	NT_010542.15	457378	87424262	plus	G	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010542

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC092384.5 NC_000016.8	AC021125.3 AC021591.3 AC139487.1

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	HWP	G
ss18799571	HapMap-CEU	European	120	IG	1.000		1.000

	HapMap-HCB	Asian	90	IG	1.000		1.000

	HapMap-JPT	Asian	86	IG	1.000		1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
		180	150	0	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .