Reference SNP(refSNP) Cluster Report: rs1152377

Reference SNP(refSNP) Cluster Report: rs1152377

refSNP ID: rs1152377
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_007039.3:c.932+170G>A
NT_026437.11:g.69962340C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43664543 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1152377 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
ss2031240	KWOK\|OVLP-000925-688571	rev/B	C/T	cttgtaactagttgaaataaatcttagagg	atacaatgtagttattacaagttggtccaa	10/06/00	10/10/03	87	Genomic	99 %
ss2031439	KWOK\|OVLP-000925-690311	fwd/T	A/G	ttggaccaacttgtaataactacattgtat	cctctaagatttatttcaactagttacaag	10/06/00	10/10/03	87	Genomic	99 %
ss2606280	SC_JCM\|AL162171.2_152830	fwd/T	A/G	ttggaccaacttgtaataactacattgtat	cctctaagatttatttcaactagttacaag	11/03/00	04/07/04	92	Genomic	unknown
ss3241457	YUSUKE\|IMS-JST051542	fwd/T	A/G	ttggaccaacttgtaataactacattgtat	cctctaagatttatttcaactagttacaag	09/05/01	10/10/03	100	Genomic	unknown
ss16637153	CSHL-HAPMAP\|CSHL-HuAA-200402.chr14.NT_026437.10_68882628	rev/B	C/T	cttgtaactagttgaaataaatcttagagg	atacaatgtagttattacaagttggtccaa	02/17/04	03/04/04	120	Genomic	unknown
ss21176229	SSAHASNP\|WGSA-200403-chr14.chr14.NT_026437.10_68882628	rev/B	C/T	cttgtaactagttgaaataaatcttagagg	atacaatgtagttattacaagttggtccaa	03/19/04	03/19/04	121	Genomic	unknown
ss24218220	PERLEGEN\|afd1467211	rev/B	C/T	cttgtaactagttgaaataaatcttagagg	atacaatgtagttattacaagttggtccaa	08/10/04	09/13/04	123	Genomic	unknown
ss43664543	ABI\|hCV9595850	rev/B	C/T	cttgtaactagttgaaataaatcttagagg	atacaatgtagttattacaagttggtccaa	07/18/05	07/18/05	126	Genomic	unknown
ss76896815	SI_EXO\|NT_026437.11_69962340	rev/B	C/T	cttgtaactagttgaaataaatcttagagg	atacaatgtagttattacaagttggtccaa	09/20/07	09/20/07	129	Genomic	unknown
ss90029917	BCMHGSC_JDW\|JWB-0807164	rev/B	C/T	cttgtaactagttgaaataaatcttagagg	atacaatgtagttattacaagttggtccaa	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCAAGTTGTA TGTGTGCTTT CATATTGCTT TATGCCTATT TTGTTTGCTA GGAAGACATG
 GAAACAGCAA AATACATTTG GAGACTCTGT GTTGCGCGAC ACAAGTTTTA CAGACTAAAC
 CAGTGTAACC TGTAAGTATG TCCTGCTCAT GGAAATTATC AAAAATAATG AATTTAGAAA
 TTGTAATCTT GAGTATACTG TATCATCAAG AAAGACATTT TATCAGTTGA CATCTTTTCT
 TGATCCTATA GCTGTTTTCC TATTTTAGCT TTGGACCAAC TTGTAATAAC TACATTGTAT
 R
 CCTCTAAGAT TTATTTCAAC TAGTTACAAG AACCATTGTA ATTCTTGAAA GGTAAAAAGG
 GAATAATATC CTTTATTTGT TTAAATCAAT CCTCTGGTAA GCATTTTGAG TCATTAAAGA
 TTATTCAGCT TTTCCAGCTA TCTGAAGAAT TTTTGCCCCT CCTTCCTGGT GTGCATTTTT
 CTTAGCCCAC ATGGGTTTCT TACTGTTTGC CAGATCAATA AAGCACACGG TGATATTGCA
 CATATAAAAT ATTGTCCTTC ATCTATACTC CCCTCCAGCC TCTGCACCAT ATCTCTGCTT

GeneView

GeneView via analysis of contig annotation: PTPN21 protein tyrosine phosphatase, non-receptor type 21

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_026437->NM_007039

function

HuRef

NW_001838113->NM_007039

function

Celera

NW_925561->NM_007039

function

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


reference	NT_026437->NM_007039->NP_008970	69962340	reverse	intron

HuRef	NW_001838113->NM_007039->NP_008970	6775655	forward	intron

Celera	NW_925561->NM_007039->NP_008970	35762711	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1152377 maps exactly once on NCBI human chromosome 14

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
14	NW_925561.1	35762711	69008181	minus	T	alt_assembly_1	Celera	Celera	view	300
14	NW_001838113.2	6775655	69132887	plus	A	alt_assembly_8	HuRef	HuRef	view	300
14	NT_026437.11	69962340	88032340	minus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_026437.11 AC011190 AL138975 AL353786 AL353786.8

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL162171.4 AL353786.16 NC_000014.7	AC011190.3 AL138975.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24218220	AFD_EUR_PANEL	European	48	IG	0.333	0.583	0.083	0.251	0.625	0.375

	AFD_AFR_PANEL	African American	42	IG	0.048	0.381	0.571	1.000	0.238	0.762

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.542	0.125	0.527	0.604	0.396

ss2606280	SC_12_A	Asian	14	IG	0.714	0.143	0.143	0.150	0.786	0.214

	SC_12_C	European	14	IG	0.571	0.286	0.143	0.439	0.714	0.286

ss3241457	JBIC-allele		1484	AF					0.636	0.364

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.496+/-0.042	95	63	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .