Reference SNP(refSNP) Cluster Report: rs1160312

Reference SNP(refSNP) Cluster Report: rs1160312

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/130
Map to Genome Build:	36.3
Citation:	NHGRI GWAS PubMed

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

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8359137 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1160312 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
ss1564948	TSC-CSHL\|TSC0330661	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	09/18/00	10/10/03	87	Genomic	95 %
ss5670704	SC_JCM\|NT_011387.7_21988560	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	01/10/03	10/10/03	111	Genomic	unknown
ss8359137	SC_SNP\|NT_011387.8_21990503	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	04/17/03	10/25/06	114	Genomic	unknown
ss41373780	ABI\|hCV8890069	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	07/17/05	07/17/05	126	Genomic	unknown
ss66080653	AFFY\|SNP_A-1913343	fwd/T	A/G	tgtggggtcaggactc	agtaggttggatgctg	10/27/06	08/14/07	127	Genomic	unknown
ss76021407	AFFY\|AFFY_6_1M_SNP_A-1913343	fwd/T	A/G	tgtggggtcaggactc	agtaggttggatgctg	08/28/07	08/29/07	129	Genomic	unknown
ss78965190	HGSV\|Cor18507_SNV_20070510.chr20_21998503	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	10/19/07	10/21/07	129	Genomic	unknown
ss81455707	KRIBB_YJKIM\|KHS81892	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	11/30/07	11/30/07	130	Genomic	unknown
ss85507587	HGSV\|Cor18517_SNV_20070510.chr20_21998503	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	12/06/07	12/09/07	130	Genomic	unknown
ss91666789	BCMHGSC_JDW\|JWB-1430867	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	02/26/08	03/02/08	129	Genomic	unknown
ss111862998	1000GENOMES\|CEU.trio.12.15.2008_3677330_chr20_21998503	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	12/15/08	12/17/08	130	Genomic	unknown
ss117513004	ILLUMINA-UK\|NA18507_000030359_NCBI36.1_chr20_21998503	fwd/T	A/G	gactctcctggcagtgtggggtcaggactc	agtaggttggatgctgatagcagagagtgt	01/19/09	01/19/09	130	Genomic	99 %

Fasta sequence (Legend)

 TTTAATGTGC ACACAAATCA TGCAGGATCT TTTGAAATTC ACATTCAGAC TCAGTGGGAC
 TAGATGGGGC ATGAGCCTTG CAGAGGTGAT GGGCTCACAG GCATGCCAAT GGCCTGTGGT
 CCTTGGATTG CACTCTTAAG TAGCAATGGT TTAGAATATG GTGAAAATAT GTTAGAAGGG
 GCATTGTGAA TGTATGGGGG TTCATCTGTT CAAGAAACAA CAATGAAAAA AAATGGTGAT
 TAAATGCAAC CACACCTAAA TAAGGTAGCC AGGAGGTAGA ACCAGCTTCT CCATGAACAG
 GCCACATACC ATCTCCCGGG GCTGCCTCCA GTGTCCAGCC TGGCTGTGCT CAGGCCCTCA
 GGGCTTGCTG GACTCTCCTG GCAGTGTGGG GTCAGGACTC
 R
 AGTAGGTTGG ATGCTGATAG CAGAGAGTGT GATTCTCCGG CCTGATGACC CAGAATCACT
 CCCAGGACTG GAATCCCAGC TCTCCCAGGA GGAAGGAGTC GTCCCTGGTC TCCCGCATCC
 CCCAAATGCT GATTCTGTGT CTGCATGTGG AGGGGTAACA AACAAACAAC AAAGGACCAT
 CTCAATTAAC CTGCCACACA GAGCAGAATC CCATAAAAAG TTCCAACTCT CTTTTTGGAT
 GAAGCttctt tttttttttt tttttttttt gagatggagt cttgctctgt cacccaggct
 ggagtgcagt ggtgagatct cggctcactg caacctccgc ctccttggtt caagcgattc
 tcttgcctca gcgtcccaag tagctgggac tacaggtgcA

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_011387.7

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss66080653	HapMap-CEU	European	118	GF	0.322	0.441	0.237		0.542	0.458

	HapMap-HCB	Asian	90	GF	0.089	0.378	0.533		0.278	0.722

	HapMap-JPT	Asian	90	GF	0.111	0.356	0.533		0.289	0.711

	HapMap-YRI	Sub-Saharan African	120	GF	0.050	0.317	0.633		0.208	0.792

ss76021407	ICMHP		10	IG	0.400		0.600		0.400	0.600

ss8359137	HapMap-CEU	European	120	IG	0.317	0.450	0.233	0.479	0.542	0.458

	HapMap-HCB	Asian	90	IG	0.089	0.378	0.533	0.752	0.278	0.722

	HapMap-JPT	Asian	88	IG	0.114	0.341	0.545		0.284	0.716

	HapMap-YRI	Sub-Saharan African	120	IG	0.050	0.317	0.633	1.000	0.208	0.792

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.446+/-0.155	1212	1002	269	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .