Reference SNP(refSNP) Cluster Report: rs563153

Reference SNP(refSNP) Cluster Report: rs563153

refSNP ID: rs563153
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:	A/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_020935.1:c.863+5763T>A
NT_005403.16:g.69598332A>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1887040 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs563153 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
ss734313	SC_JCM\|AC064861.1_170521	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	07/27/00	10/10/03	83	Genomic	unknown
ss1147326	KWOK\|OVLP-000804-443138	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	09/02/00	10/10/03	86	Genomic	99 %
ss1148600	KWOK\|OVLP-000804-449093	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	09/02/00	10/10/03	86	Genomic	99 %
ss1886712	KWOK\|OVLP-000925-263142	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	10/06/00	10/10/03	87	Genomic	99 %
ss1887040	KWOK\|OVLP-000925-268191	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	10/06/00	10/10/03	87	Genomic	99 %
ss3345415	TSC-CSHL\|TSC1574794	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	09/20/01	10/10/03	100	Genomic	unknown
ss3829850	SC_JCM\|AC079810.1_71623	rev/B	A/T	atatgagaagagaaaattatagtttttcac	tatgaacacagaaaaatccaaaataaaatt	09/25/01	10/10/03	100	Genomic	unknown
ss9934647	BCM_SSAHASNP\|chr2.NT_005403.13_69548250	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	06/27/03	10/10/03	116	Genomic	unknown
ss11457586	WI_SSAHASNP\|chr2.NT_005403.13_69548250	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	07/03/03	10/10/03	116	Genomic	unknown
ss16819775	CSHL-HAPMAP\|CSHL-HuAA-200402.chr2.NT_005403.14_69598329	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	02/17/04	03/04/04	120	Genomic	unknown
ss17635633	CSHL-HAPMAP\|CSHL-HuCC-200402.chr2.NT_005403.14_69598329	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	02/19/04	03/04/04	120	Genomic	unknown
ss21612155	SSAHASNP\|WGSA-200403-chr2.chr2.NT_005403.14_69598329	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	03/20/04	03/20/04	121	Genomic	unknown
ss23168616	PERLEGEN\|afd4008916	fwd/T	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	08/10/04	10/21/04	123	Genomic	unknown
ss44165888	ABI\|hCV1042174	fwd/	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	07/18/05	07/18/05	126	Genomic	unknown
ss81217207	HGSV\|Cor18507_SNV_20070510.chr2_219214421	fwd/	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	11/26/07	11/28/07	130	Genomic	unknown
ss81474746	HGSV\|Cor18555_SNV_20070510.chr2_219214421	fwd/	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	11/27/07	11/30/07	130	Genomic	unknown
ss81910225	HGSV\|Cor18956_SNV_20070510.chr2_219214421	fwd/	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	11/30/07	12/01/07	130	Genomic	unknown
ss91551334	BCMHGSC_JDW\|JWB-1385702	fwd/	A/T	aattttattttggatttttctgtgttcata	gtgaaaaactataattttctcttctcatat	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 ACAGTTTACA TTTTATTATT GCTGGATTTA GAAACACCAT TAATTTTGTG AATTGATCTT
 GTATTCCAGA AACCTTATAA AGCTGTTTTT TGGCAGGGGG gtcttttttc atcctttttc
 tgtggagaac aggatgttac tatgttgccc aggcaggtct tgaactcctg ggctcaagct
 atccccctgc ctttgccccc ttaagtactg tgataatagg tgtgagccac tgaacccggc
 cTAGAGCACT TTaatttgtt ttaataacct ctggtgattc tctttgtgtt aaatatttaa
 cagatcacac agtctgcaaa ttatgacaat tctgtttttc ccctttccaa tccccaaacc
 tctttatttc attttcttgt cctactgcat tggctaaaac cttcagaaca atatCACCCT
 GTTCTTGACT TTGATGGGAA TACTTCTCAA AGTTTCATAA TTGTAATGTG ATTTAAGTTT
 TTGACAGATA ACTTTTTATC AAACTAGGAA CATAATGCTC TGTTCCTAAT ATGCTAAAAG
 TAGGTATCAT CAATGGCTAT CAAATAGTTT TAAAAATCTA CCACAATCCC AAAAGAGTTT
 TCTAATGTTT ACTTTTGCAT TTCTGGGATA TACCCTACTC AGTCACTGTG TATCATTTTC
 AATGCCCTAT TAGATTCAAC TGTTAAAATT TTATTTTGGA TTTTTCTGTG TTCATA
 W
 GTGAAAAACT ATAATTTTCT CTTCTCATAT TGCTGTTACA AGGTTTTATT AAATTCCTAG
 ATTAGTTATG TAGCCTTTCC TGttttgtag agatgggggt cttgctatct tgccaagact
 agtcttgaac tcctggattc aagtgatcct cccacctagt cctcccaaag tgctgagatt
 ataggtgtga accactgctc cACTCCCAGC CATCTTTAAC TTTTTAATAT GTCTATGTAA
 TTGCAGCCTC CTCTGAAACT AAAGCTTGAA ATATTTTAAT TTCCCTGAAT CTTCTCCACT
 CCTGTATTTC TTTTGTCCAA TGTTTTATTA AGTATTGGCT TTTAATCCAA CAACATCCTC
 CTTTGATAGA AAATATCAAG ACGTATTTAC

GeneView

GeneView via analysis of contig annotation: USP37 ubiquitin specific peptidase 37

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_005403->NM_020935

function

HuRef

NW_001838865->NM_020935

function

Celera

NW_921618->NM_020935

function

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


reference	NT_005403->NM_020935->NP_065986	69598332	reverse	intron

HuRef	NW_001838865->NM_020935->NP_065986	7117981	forward	intron

Celera	NW_921618->NM_020935->NP_065986	24070054	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs563153 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838865.2	7117981	211241795	minus	A	alt_assembly_8	HuRef	HuRef	view	716
2	NW_921618.1	24070054	213155524	plus	T	alt_assembly_1	Celera	Celera	view	716
2	NT_005403.16	69598332	219097160	plus	A	ref_assembly	reference	reference	view	716

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005403 AC012510 AC064861 AC064861.1 AC073838 AC073838.2 AC073838.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC073838.6 NC_000002.10	AC064861.2

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/T	T/T	HWP	A	T
ss23168616	AFD_EUR_PANEL	European	48	IG		1.000			1.000

	AFD_AFR_PANEL	African American	46	IG	0.043	0.957	1.000	0.022	0.978

	AFD_CHN_PANEL	Asian	46	IG		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.014+/-0.083	71	50	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

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Revised: May 25, 2006 1:38 PM .