Reference SNP(refSNP) Cluster Report: rs1052067

Reference SNP(refSNP) Cluster Report: rs1052067

refSNP ID: rs1052067
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_007221.2:c.411G>A
NP_009152.2:p.M137I
NT_004487.18:g.6696475G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44127204 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1052067 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
ss1528110	LEE\|482129	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	09/13/00	10/10/03	86	cDNA	unknown
ss3239836	YUSUKE\|IMS-JST049921	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	09/05/01	10/10/03	100	Genomic	unknown
ss3863214	SC_JCM\|AF141309.1_17455	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	09/25/01	04/07/04	100	Genomic	unknown
ss16228905	CGAP-GAI\|1465921	rev/B	C/T	ggtgtcccgttgctgcaggaagtagggtgc	ataacactgtgcagatccttctctgggatc	11/18/03	11/22/03	120	cDNA	unknown
ss16248104	CGAP-GAI\|1494496	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	11/18/03	11/22/03	120	cDNA	unknown
ss17355226	CSHL-HAPMAP\|CSHL-HuCC-200402.chr1.NT_079484.1_2655953	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	02/19/04	03/04/04	120	Genomic	unknown
ss24638412	PERLEGEN\|afd0689631	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	08/10/04	09/13/04	123	Genomic	unknown
ss24791800	SEQUENOM\|sqnm103701	rev/B	C/T	ggtgtcccgttgctgcaggaagtagggtgc	ataacactgtgcagatccttctctgggatc	06/18/04	11/02/06	130	cDNA	unknown
ss28510250	MGC_GENOME_DIFF\|BC065031x37549803-G2655953A	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	08/25/04	08/25/04	126	cDNA	unknown
ss44127204	ABI\|hCV11181965	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	07/18/05	11/03/06	126	Genomic	unknown
ss48410223	APPLERA_GI\|hCV11181965	rev/B	C/T	ggtgtcccgttgctgcaggaagtagggtgc	ataacactgtgcagatccttctctgggatc	09/28/05	11/03/06	126	Genomic	unknown
ss65730351	ILLUMINA\|Human1-rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	10/10/06	10/10/06	127	Genomic	unknown
ss66480936	AFFY\|SNP_A-2293963	rev/B	C/T	gcaggaagtagggtgc	ataacactgtgcagat	10/29/06	08/14/07	127	Genomic	unknown
ss66666431	ILLUMINA\|HumanHap300v1.1_rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	11/09/06	11/09/06	127	Genomic	unknown
ss66895702	ILLUMINA\|HumanHap550v1.1_rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	11/14/06	11/14/06	127	Genomic	unknown
ss67004820	ILLUMINA\|HumanHap650Yv1.0_rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	11/14/06	11/14/06	127	Genomic	unknown
ss68427445	CSHL-HAPMAP\|sanger:assay:423372:1	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	01/11/07	01/16/07	127	NA	unknown
ss68780740	PERLEGEN\|PGP00689631	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	01/30/07	08/14/07	127	Genomic	unknown
ss70376413	ILLUMINA\|HumanHap300v2.0_rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	04/18/07	11/18/07	127	Genomic	unknown
ss70491748	ILLUMINA\|HumanHap550v3.0__rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	04/20/07	03/30/08	130	Genomic	unknown
ss71016371	ILLUMINA\|HumanHap650Yv3.0_rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	04/23/07	04/23/07	127	Genomic	unknown
ss75579235	ILLUMINA\|ILMN_Human_1M_rs1052067	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	08/28/07	08/29/07	129	Genomic	unknown
ss76296540	AFFY\|AFFY_6_1M_SNP_A-2293963	rev/B	C/T	gcaggaagtagggtgc	ataacactgtgcagat	08/28/07	08/30/07	129	Genomic	unknown
ss81478547	HGSV\|Cor18555_SNV_20070510.chr1_153019194	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	11/27/07	11/30/07	130	Genomic	unknown
ss83674282	KRIBB_YJKIM\|KHS516341	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	12/04/07	12/05/07	130	Genomic	unknown
ss87827069	BCMHGSC_JDW\|JWB-0129096	fwd/T	A/G	gatcccagagaaggatctgcacagtgttat	gcaccctacttcctgcagcaacgggacacc	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGTCGGGAAG GCTAAGATAG GGGCTGAAGT GAGAAGGGGG AGAGGTGGAC CCCTAAGCAT
 TGAAACCCAG GGAAAGGAAG TGTGCATTCC TACGAGGAAC AGGTCTTGGG AGGTGAGAGG
 GACCACAGGA GAGACCTGGG AAGCCAGCCC AACTTGGGAC AAGGTGGGCA TGTCACCGAG
 TGTGGGCTTG GAAGCTGAAC CTTCTTCCAC AAGGGCCTTC CGCCTCCTTC ATTCCTTGTG
 CCCCGTGTGG CCCTCCAGGC GCCCCAGCGG GATCCCAGAG AAGGATCTGC ACAGTGTTAT
 R
 GCACCCTACT TCCTGCAGCA ACGGGACACC CTGCGGCGCC ATGTGCAGAA ACAGGAGGCC
 GAGAACCAGC AGCTGGCAGA TGCCGTCCTG GCAGGGCGGA GGCAGGTGGA GGAGCTGCAG
 CTACAGGTCC AGGCCCAGCA GCAGGCCTGG CAGGTCAGTG TCCCAGCCTG CCTCTTCCTC
 TTCCTTCTCT AATGGGCCCT CTGAGATCCG CAAATTGGTG GCTTCCTCCA TTCCAACACA
 GGGGACCCCC ACAGGGGGTA GGAGAGCTTG CCCCCTGGGG AACAGTCATG AATTACCTCT

GeneView

GeneView via analysis of contig annotation: PMF1 polyamine-modulated factor 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_004487->NM_007221

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_004487->NM_007221->NP_009152	6696476	forward	434	missense	A	Ile [I]	3	137
					contig reference	G	Met [M]	3	137

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1052067 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838531.2	5199243	127567214	minus	C	alt_assembly_8	HuRef	HuRef	view	300
1	NW_925683.1	6315927	129279101	plus	G	alt_assembly_1	Celera	Celera	view	300
1	NT_004487.18	6696476	154472745	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm103701	NT_079484 AC007227 AL135927 AL589685 AX078379 BC065031 BM549553 BU554050 Hs.94446

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_007221.2	AL135927.14

UniGene Cluster ID
530479

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24638412	AFD_EUR_PANEL	European	48	IG	0.042	0.417	0.542	0.655	0.250	0.750

	AFD_AFR_PANEL	African American	46	IG		0.261	0.739	0.479	0.130	0.870

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.208	0.750	0.439	0.146	0.854

ss24791800	CEPH		184	AF					0.400	0.600

ss3239836	JBIC-allele		1484	AF					0.267	0.733

ss3863214	CEPH		184	AF					0.470	0.530

	CHMJ	Asian	74	IG					0.122	0.878

ss44127204	HapMap-CEU	European	120	IG	0.050	0.417	0.533	0.527	0.258	0.742

	HapMap-HCB	Asian	90	IG		0.267	0.733	0.317	0.133	0.867

	HapMap-JPT	Asian	88	IG	0.114	0.318	0.568	0.200	0.273	0.727

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.233	0.733	0.527	0.150	0.850

	AoD_African_American		90	AF					0.180	0.820

	AoD_Caucasian		92	AF					0.260	0.740

	AoD_Chinese		90	AF					0.200	0.800

	AoD_Japanese		90	AF					0.260	0.740

ss48410223	AGI_ASP population	multiple	78	IG		0.333	0.667	0.251	0.167	0.833

ss66480936	HapMap-CEU	European	118	GF	0.051	0.424	0.525		0.263	0.737

	HapMap-HCB	Asian	90	GF		0.267	0.733		0.133	0.867

	HapMap-JPT	Asian	90	GF	0.111	0.311	0.578		0.267	0.733

	HapMap-YRI	Sub-Saharan African	120	GF	0.033	0.233	0.733		0.150	0.850

ss68780740	HapMap-CEU	European	120	GF	0.050	0.417	0.533		0.258	0.742

	HapMap-HCB	Asian	90	GF		0.267	0.733		0.133	0.867

	HapMap-JPT	Asian	90	GF	0.111	0.311	0.578		0.267	0.733

	HapMap-YRI	Sub-Saharan African	120	GF	0.033	0.233	0.733		0.150	0.850

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.318+/-0.241	371	299	270	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 .