Reference SNP(refSNP) Cluster Report: rs598119

Reference SNP(refSNP) Cluster Report: rs598119

refSNP ID: rs598119
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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
NM_001037334.1:c.299+5015T>G
NM_005151.3:c.404+5015T>G
NT_010859.14:g.175354T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1390751 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs598119 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
ss770019	SC_JCM\|AP001022.2_86689		rev/T	A/C	ggattttgaaaccagccttgacaatatagc	aaacccgtctctactaaaaatacaaaaatt	07/27/00	10/10/03	83	Genomic			unknown
ss1390751	TSC-CSHL\|TSC0373305		fwd/B	G/T	aattttggtatttttagtagagacgggttt	gctatattgtcaaggctggtttcaaaatcc	06/14/01	10/10/03	108	Genomic			unknown

Fasta sequence (Legend)

 TTAGAACCTA GAGTGAAAAC TATATGTTAT AAAAAAATCA TCCTAAAATT CTATAAATTA
 CTCCTCAAAA GACAGTATCA CATGGCCGTA TCTGTTGTAT TGGAGACTGG CAAGCCCCAG
 CTCTCAATAT ACACAGTGTT AACAGTTACT AGGTTGCTGA TTTTCTTTCA tttttttttt
 tcttattttt tatttattta ttttcgagac agagtctcac tccctcaccc aggctgcagt
 gcagtggtgc gatctcagct cactgcagcc tctgcctccc ggcttgagca attcttctgt
 ctcagcctcc caagtagctg gaattacagg tgtgtgccac catgcctgac taattttggt
 atttttagta gagacgggtt t
 K
 gctatattgt caaggctggt ttcaaaatcc tcacaagtca tctgcccgcc tcagcctccc
 aaagtgctgg gattacaggt gtgagccact gtgcctggct GAAAATATTT GTCTGTTAAC
 ACTAGCGTCT CATTCAGTTC AGTGAGATGC TCATATTATG AGAGGCATGC AAGAACTGAG
 ACACTCGGAG AGAACAGAAA AGCCC

GeneView

GeneView via analysis of contig annotation: USP14 ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)

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_010859->NM_001037334

function

reference

NT_010859->NM_005151

function

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


reference	NT_010859->NM_001037334->NP_001032411	175354	forward	intron

reference	NT_010859->NM_005151->NP_005142	175354	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs598119 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_926940.1	60502	60502	plus	T	alt_assembly_1	Celera	Celera	view	381
18	NW_001838461.1	133422	145062	plus	T	alt_assembly_8	HuRef	HuRef	view	381
18	NT_010859.14	175354	175354	plus	T	ref_assembly	reference	reference	view	381

NCBI Resource Links

Submitter-Referenced
GenBank
AP001022 AP000845 AP000939

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP000845.4	AP000939.3 AP001022.2

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	T/T	HWP	T
ss1390751	HapMap-CEU	European	118	IG	1.000		1.000

	HapMap-HCB	Asian	88	IG	1.000		1.000

	HapMap-JPT	Asian	90	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000		1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
		270	210	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .