Reference SNP(refSNP) Cluster Report: rs1234213

Reference SNP(refSNP) Cluster Report: rs1234213

refSNP ID: rs1234213
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
Map to Genome Build:	36.3
Citation:	PubMed

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_000314.4:c.210-1482G>A
NT_030059.12:g.8437837G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38349773 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1234213 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
ss1846084	KWOK\|OVLP-000925-722591	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	10/05/00	05/16/04	87	Genomic	97 %
ss2575963	SC_JCM\|AF067844.1_87533	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	11/03/00	04/07/04	92	Genomic	unknown
ss10639707	BCM_SSAHASNP\|chr10.NT_030059.10_8127869	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	06/29/03	10/10/03	116	Genomic	unknown
ss16083268	SC_SNP\|NT_030059.11_8437837	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	11/18/03	11/22/03	120	Genomic	unknown
ss24106854	PERLEGEN\|afd0803408	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	08/10/04	09/13/04	123	Genomic	unknown
ss38349773	EGP_SNPS\|PTEN-068061	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	07/07/05	11/02/06	126	Genomic	unknown
ss69086722	PERLEGEN\|PGP00803408	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	01/30/07	08/14/07	127	Genomic	unknown
ss80744487	KRIBB_YJKIM\|KHS1003202	fwd/T	A/G	tcagtcctctttttcctgtttttcatgtca	tgggtatgaaattactagcaaggatgcata	11/26/07	11/26/07	130	Genomic	unknown

Fasta sequence (Legend)

 GTTCTGGGAT CCTGAGAAAG TAGGGGAAGT TTAGAGAACT GAAGCTGCAC AAAACTAATG
 TTTATTTTCT GTTGTGTTGT CCTGAGACCA GCTTCTTAGA TTGTGTTTCC TAGTCCTACA
 TCTCTGATTC CTTATAAAAT ATTCCATTAT GAATTCTTCA CTATTGACAA TTTCTCCCCT
 TTTATCTTAA AAGTACCAAA GAAAGTGTAA AATGTGACTG TCTTGTCAGT CCTCTTTTTC
 CTGTTTTTCA TGTCA
 R
 TGGGTATGAA ATTACTAGCA AGGATGCATA TATGTGCATA TGTCATTACT AAATGCATTT
 TCTTTCTAGA AAAACTCAAT ATACTAAATT GTACTAAAAA GGAAAAGCTT GTTTTGTTTT
 GAGTGGTAGT ATGAAAGTTG TTTTATTTTA GGTCTGACCA GTTAGAAACC AATGGATTGT
 AGTTTATTTA TAATTAGTTA AACCTTCATG TGAATTTGGT TTTGAATTAC CTTTAAGGTA
 GAGAAGAAAC TATAT

GeneView

GeneView via analysis of contig annotation: PTEN phosphatase and tensin homolog

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_030059->NM_000314

function

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


reference	NT_030059->NM_000314->NP_000305	8437837	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1234213 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_001838005.2	10795715	83324107	minus	C	alt_assembly_8	HuRef	HuRef	view	255
10	NW_924884.1	438586	83435769	plus	G	alt_assembly_1	Celera	Celera	view	255
10	NT_030059.12	8437837	89679301	plus	G	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030059 AC022016 AF067844.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AF067844.1 CU041290.5

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1846084	CEPH		184	AF					0.330	0.670

ss24106854	AFD_EUR_PANEL	European	46	IG	0.087	0.478	0.435	0.752	0.326	0.674

	AFD_AFR_PANEL	African American	38	IG	0.105	0.421	0.474	1.000	0.316	0.684

	AFD_CHN_PANEL	Asian	48	IG	0.292	0.583	0.125	0.343	0.583	0.417

ss2575963	SC_12_AA	African American	16	IG	0.500	0.125	0.375	0.050	0.562	0.438

	SC_12_C	European	12	IG		0.667	0.333	0.251	0.333	0.667

ss38349773	HapMap-CEU	European	120	IG	0.133	0.517	0.350	0.527	0.392	0.608

	HapMap-HCB	Asian	90	IG	0.222	0.600	0.178	0.200	0.522	0.478

	HapMap-JPT	Asian	88	IG	0.295	0.500	0.205	1.000	0.545	0.455

	HapMap-YRI	Sub-Saharan African	120	IG	0.167	0.450	0.383	0.752	0.392	0.608

	EGP_YORUB-PANEL	Sub-Saharan African	24	AF	0.167	0.250	0.583	0.200	0.292	0.708

	EGP_HISP-PANEL	Hispanic	44	AF	0.273	0.455	0.273	0.752	0.500	0.500

	EGP_CEPH-PANEL	European	44	AF	0.182	0.409	0.409	0.527	0.386	0.614

	EGP_AD-PANEL	African American	30	AF	0.067	0.533	0.400	0.479	0.333	0.667

	EGP_ASIAN-PANEL	Asian	46	AF	0.217	0.565	0.217	0.584	0.500	0.500

ss69086722	HapMap-CEU	European	120	GF	0.150	0.483	0.367		0.392	0.608

	HapMap-HCB	Asian	90	GF	0.222	0.622	0.156		0.533	0.467

	HapMap-JPT	Asian	90	GF	0.289	0.511	0.200		0.544	0.456

	HapMap-YRI	Sub-Saharan African	120	GF	0.167	0.450	0.383		0.392	0.608

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24106854	71	11	33	22
ss2575963	23	4	6	8
ss38349773	303	55	156	90
ss69086722	265	48	139	78

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1234213	371	67	184	111

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
213	ss38349773	A/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	r23_ch10_CEU_illumina:golden_gate_1.0.0	764164
213	ss69086722	G/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	chr10-HapMap-CEU
262	ss38349773	A/G	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r23_ch10_CEU_illumina:golden_gate_1.0.0	764164
262	ss69086722	A/A	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	chr10-HapMap-CEU
429	ss2575963	A/G	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
429	ss38349773	G/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r23_ch10_CEU_illumina:golden_gate_1.0.0	764164
429	ss69086722	G/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr10-HapMap-CEU
5148	ss38349773	G/G	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	r23_ch10_HCB_illumina:golden_gate_1.0.0	764164
5148	ss69086722	A/G	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	chr10-HapMap-HCB
5148	ss38349773	G/G	EGP_SNPS	EGP_ASIAN-PANEL	X101	NA18526	PTEN-EGP_ASIAN-060105	764164
5259	ss38349773	A/A	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	764164
5259	ss69086722	A/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr10-HapMap-YRI

Genotype data submitted for	460	samples from	371	individuals	Individual with multiple genotypes submission:	286

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

YES

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Revised: May 25, 2006 1:38 PM .