Reference SNP(refSNP) Cluster Report: rs1147497

Reference SNP(refSNP) Cluster Report: rs1147497

refSNP ID: rs1147497
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002851.2:c.5081-401T>G
NT_007933.14:g.46854703T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1697179 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1147497 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
ss1697179	KWOK\|OVLP-000925-418313	rev/T	A/C	ataatatagtttcaattttagtgtggacca	gcataataaatagtgtaatttcggttttgt	10/05/00	10/25/06	87	Genomic	99 %
ss1734625	KWOK\|OVLP-000925-410659	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaaattgaaactatattat	10/05/00	10/10/03	87	Genomic	97 %
ss2564028	SC_JCM\|AC073471.3_112814	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaattgaaactatattatt	11/03/00	10/10/03	92	Genomic	unknown
ss19726037	CSHL-HAPMAP\|CSHL-HuDD-200402.chr7.NT_007933.13_46847817	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaaattgaaactatattat	02/20/04	03/04/04	120	Genomic	unknown
ss22589243	SSAHASNP\|WGSA-200403-chr7.chr7.NT_007933.13_46847817	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaaattgaaactatattat	03/21/04	03/21/04	121	Genomic	unknown
ss22893272	SSAHASNP\|AACC-200403.chr7.NT_007933.13_46847817	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaaattgaaactatattat	03/22/04	03/22/04	121	Genomic	unknown
ss24467314	PERLEGEN\|afd0564579	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaaattgaaactatattat	08/10/04	09/13/04	123	Genomic	unknown
ss66524199	AFFY\|SNP_A-4228475	rev/T	A/C	attttagtgtggacca	gcataataaatagtgt	10/29/06	08/14/07	127	Genomic	unknown
ss69026861	PERLEGEN\|PGP00564579	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaaattgaaactatattat	01/30/07	08/14/07	127	Genomic	unknown
ss76346839	AFFY\|AFFY_6_1M_SNP_A-4228475	rev/T	A/C	attttagtgtggacca	gcataataaatagtgt	08/28/07	08/30/07	129	Genomic	unknown
ss93756587	BCMHGSC_JDW\|JWB-2366055	fwd/B	G/T	acaaaaccgaaattacactatttattatgc	tggtccacactaaaattgaaactatattat	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 TTCAAGTTAG AATTCTTGAA ATTTTACAGA TTAAAAGTCC CAAAGGCTTT TGACATTATC
 CTTAATGAAA TTCTCCATAT AAATGTTTTC TATTATTTAC AGAGAGAAGG AAAAAATGTT
 TTCAAATGTA AACATCTATT TGACTGTAAG ACATTAAATT GTACAGTTTT ACAAAACCGA
 AATTACACTA TTTATTATGC
 K
 TGGTCCACAC TAAAATTGAA ACTATATTAT TTCTACATTT TTTCTCAGAA TTTACATGCA
 ACATCCAGGC ATGTTAAAGA AAGTTGTCCA TCAAAAGATG CAGTCCACTG ATAAGGAGTG
 GGGCTATGGT GGTATTTATA AATTAACATT GAAAATAAGT GATTTTATCT TTAGGTATAG
 ATGGAAAAGA GATTGCTGAA

GeneView

GeneView via analysis of contig annotation: PTPRZ1 protein tyrosine phosphatase, receptor-type, Z polypeptide 1

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_007933->NM_002851

function

HuRef

NW_001839071->NM_002851

function

Celera

NW_923640->NM_002851

function

CRA_TCAGchr7v2

NT_079596->NM_002851

function

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


reference	NT_007933->NM_002851->NP_002842	46854703	forward	intron

HuRef	NW_001839071->NM_002851->NP_002842	9620333	reverse	intron

Celera	NW_923640->NM_002851->NP_002842	19239101	forward	intron

CRA_TCAGchr7v2	NT_079596->NM_002851->NP_002842	21101364	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1147497 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839071.2	9620333	116034181	minus	C	alt_assembly_8	HuRef	HuRef	view	200
7	NW_923640.1	19239101	116480350	plus	G	alt_assembly_1	Celera	Celera	view	200
7	NT_079596.2	21101364	121065796	plus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	200
7	NT_007933.14	46854703	121458363	plus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007933 AC006020 AC073095 AC073471.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC006020.2 NC_000007.12	AC073471.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss1697179	HapMap-CEU	European	120	IG	0.117	0.517	0.367	0.439	0.375	0.625

	HapMap-HCB	Asian	90	IG	0.111	0.578	0.311	0.200	0.400	0.600

	HapMap-JPT	Asian	90	IG	0.133	0.378	0.489		0.322	0.678

	HapMap-YRI	Sub-Saharan African	120	IG	0.250	0.550	0.200	0.439	0.525	0.475

ss24467314	AFD_EUR_PANEL	European	48	IG	0.208	0.417	0.375	0.527	0.417	0.583

	AFD_AFR_PANEL	African American	46	IG	0.130	0.348	0.522	0.403	0.304	0.696

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.375	0.583	1.000	0.229	0.771

ss66524199	HapMap-CEU	European	118	GF	0.119	0.525	0.356		0.381	0.619

	HapMap-HCB	Asian	90	GF	0.111	0.578	0.311		0.400	0.600

	HapMap-JPT	Asian	90	GF	0.133	0.378	0.489		0.322	0.678

	HapMap-YRI	Sub-Saharan African	120	GF	0.250	0.550	0.200		0.525	0.475

ss69026861	HapMap-CEU	European	120	GF	0.117	0.517	0.367		0.375	0.625

	HapMap-HCB	Asian	90	GF	0.111	0.578	0.311		0.400	0.600

	HapMap-JPT	Asian	90	GF	0.133	0.378	0.489		0.322	0.678

	HapMap-YRI	Sub-Saharan African	120	GF	0.250	0.550	0.200		0.525	0.475

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.481+/-0.095	332	260	270	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 .