Reference SNP(refSNP) Cluster Report: rs1051162

Reference SNP(refSNP) Cluster Report: rs1051162

refSNP ID: rs1051162
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_020192.2:c.90G>A
NP_064577.1:p.A30A
NT_007819.16:g.39095064G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44833775 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1051162 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
ss1526472	LEE\|442376	fwd/T	A/G	tgacgaagaagcagacgagtcgctcctggc	cagcgggaatggcagagtaacatgcaaaga	09/13/00	05/16/04	86	cDNA	unknown
ss23759081	PERLEGEN\|afd0496425	fwd/T	A/G	tgacgaagaagcagacgagtcgctcctggc	cagcgggaatggcagagtaacatgcaaaga	08/10/04	09/13/04	123	Genomic	unknown
ss44833775	ABI\|hCV8855661	fwd/T	A/G	tgacgaagaagcagacgagtcgctcctggc	cagcgggaatggcagagtaacatgcaaaga	07/19/05	11/03/06	126	Genomic	unknown
ss48410289	APPLERA_GI\|hCV8855661	fwd/T	A/G	tgacgaagaagcagacgagtcgctcctggc	cagcgggaatggcagagtaacatgcaaaga	09/28/05	11/30/05	126	Genomic	unknown
ss75004358	ILLUMINA\|ILMN_Human_1M_rs1051162	fwd/T	A/G	tgacgaagaagcagacgagtcgctcctggc	cagcgggaatggcagagtaacatgcaaaga	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 CTCACAACTC ACAGGCACAC ATCAACACTG CCAACCGAGG GAGCCCAAAA TCACCGCAAG
 CGAAAGGCTC CGGCGGCGGC CACGGGCCAC AGCCCGCCTC CGCGCACACG CAGCCCCTCC
 CGAGCCTCCA CTCGCCGTCT TCGCCCCGCC TTCGGACCGG AAGGAGTTGT TGGCGCTTCC
 GGTGGCCTGC GACCCCGTAA TTGCCTCGGT GATGTCGTGG GTTCAAGCAG CCTCCTTGAT
 CCAGGGCCCT GGAGACAAAG GGGACGTGTT TGACGAAGAA GCAGACGAGT CGCTCCTGGC
 R
 CAGCGGGAAT GGCAGAGTAA CATGCAAAGA CGAGTCAAAG TAAACGTGGT GTGGACGGCG
 CGGGGTGCTG GGTTGTGGGA AGAGGCGCGG AGTTGTGAAG AAGCTGGGTC CAGAGTGGCC
 CCAGCCTGGC CCGGCGCTGC TCTCTTTATC CCTAGGGACC CGGTCCGACC CGCGTCTTGC
 TAGGATTTCT CGATGGTTAC TTGAAAGCGT GTAAAACAAC AAGACGCATT CTTTGAGCGC
 CTACGGGATG CGTTAGAAAC TGAGGACCGA CCAAAATTAA CTATGTGTAG ACTTTGAACA

GeneView

GeneView via analysis of contig annotation: C7orf36 chromosome 7 open reading frame 36

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_007819->NM_020192

function

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


reference	NT_007819->NM_020192->NP_064577	39095065	forward	99	synonymous	A	Ala [A]	3	30
					contig reference	G	Ala [A]	3	30

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1051162 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_001839004.1	306106	39490184	plus	G	alt_assembly_8	HuRef	HuRef	view	300
7	NT_007819.16	39095065	39572632	plus	G	ref_assembly	reference	reference	view	300
7	NW_923240.1	32764508	39593643	plus	G	alt_assembly_1	Celera	Celera	view	300
7	NT_079592.2	39593995	39643995	plus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000007.8 Hs.83313

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_020192.2

UniGene Cluster ID
83313

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1526472	CEPH		184	AF					0.180	0.820

ss23759081	AFD_EUR_PANEL	European	48	IG		0.167	0.833	0.752	0.083	0.917

	AFD_AFR_PANEL	African American	46	IG	0.043	0.522	0.435	0.273	0.304	0.696

	AFD_CHN_PANEL	Asian	48	IG		0.292	0.708	0.439	0.146	0.854

ss44833775	HapMap-CEU	European	104	IG		0.231	0.769	0.371	0.115	0.885

	HapMap-HCB	Asian	68	IG		0.294	0.706	0.317	0.147	0.853

	HapMap-JPT	Asian	82	IG	0.024	0.341	0.634		0.195	0.805

	HapMap-YRI	Sub-Saharan African	110	IG	0.091	0.473	0.436	0.655	0.327	0.673

	AoD_African_American		90	AF					0.290	0.710

	AoD_Caucasian		92	AF					0.160	0.840

	AoD_Chinese		90	AF					0.060	0.940

	AoD_Japanese		90	AF					0.150	0.850

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.315+/-0.241	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .