Reference SNP(refSNP) Cluster Report: rs11676792

Reference SNP(refSNP) Cluster Report: rs11676792

refSNP ID: rs11676792
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
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
NT_005120.15:g.665070A>G
XM_291007.7:c.4234A>G
XP_291007.6:p.M1412V

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss41559660 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11676792 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
ss16820037	CSHL-HAPMAP\|CSHL-HuAA-200402.chr2.NT_005120.14_662851	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	02/17/04	03/04/04	120	Genomic	unknown
ss21613578	SSAHASNP\|WGSA-200403-chr2.chr2.NT_005120.14_662851	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	03/20/04	03/20/04	121	Genomic	unknown
ss28520155	BROAD\|BI141197	fwd/T	A/G	cgcatcagcagcacagcggtctgcntggaa	tgaggcaccgggtgtgggcggggtgcaagc	08/20/04	10/04/04	124	Genomic	unknown
ss41559660	ABI\|hCV2669249	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	07/17/05	11/03/06	126	Genomic	unknown
ss65834950	KRIBB_YJKIM\|KHS10742	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	10/17/06	12/16/06	127	Genomic	unknown
ss78861744	HGSV\|Cor18507_SNV_20070510.chr2_234514317	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	10/19/07	10/21/07	129	Genomic	unknown
ss84995831	HGSV\|Cor19129_SNV_20070510.chr2_234514317	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	12/06/07	12/08/07	130	Genomic	unknown
ss110966091	1000GENOMES\|CEU.trio.12.15.2008_608274_chr2_234397056	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	12/15/08	12/17/08	130	Genomic	unknown
ss111825874	1000GENOMES\|NA19240_2008_12_16_543999_chr2_234397056	fwd/T	A/G	cgcatcagcagcacagcggtctgcgtggaa	tgaggcaccgggtgtgggcggggtgcaagc	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 GATTCACTGA CAACCTCAAC CAAGTCCCCA GGAAGAGGAG GGAGAAACCC AGAGATGTTA
 CGACATCTTT CCGGGGTTAT CTTGCCACCA GGGTCCAGGC ACCGATGTGG CCCTGCCCAG
 CTCTTGGCAA ACGTCAGGCA GGGGTGGGGC CGCCTCCACG ACCTGGCACT GTCTCTCCTC
 TGCAGGCTGT GCATGCAGCA CGTGGAGGGC CACAGGCAGA GGCTGGCCGA GCTGGTGCTC
 AGGGGCATGG ACTCAGAAGT CCTGAGCTGC CGCATCAGCA GCACAGCGGT CTGCGTGGAA
 R
 TGAGGCACCG GGTGTGGGCG GGGTGCAAGC GGAGGGGATG GGGTCCCTGG ATTCTTCTGG
 GGATGGCTTG TCTCCAAGGC ATGGGAGTCG GGGGGACAGG CGAGCGCCCC TCCTCTGAGT
 GCTCATTCTC TCATCTGCTC CTTCATTCAT TCATCACATG AGTAGTGCAG GGCAGGCCCT
 GCTGGAAAGA CAGGCTGAGC CCTGCAGCAT TGCAGTTAAC TGATGTGTGA CCCAGGCAAG
 TACAGTGACC CAGGGGACCC AGGGAGGGCA CCTGGGTTCT CGCTGGGGCA GGCTTCCTGC

GeneView

GeneView via analysis of contig annotation: LOC339766 HEAT repeat containing 7B1

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_005120->XM_291007

function

HuRef

NW_001838868->XM_001721240

function

Celera

NW_921618->XM_939706

function

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


reference	NT_005120->XM_291007->XP_291007	665071	forward	4310	missense	G	Val [V]	1	1412
					contig reference	A	Met [M]	1	1412

HuRef	NW_001838868->XM_001721240->XP_001721292	677504	forward		donor

Celera	NW_921618->XM_939706->XP_944799	39367257	forward		donor

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11676792 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838868.1	677504	226531962	plus	G	alt_assembly_8	HuRef	HuRef	view	300
2	NW_921618.1	39367257	228452727	plus	G	alt_assembly_1	Celera	Celera	view	300
2	NT_005120.15	665071	234397056	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005120

dbSNP Blast Analysis

UniGene Cluster ID
361778

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss41559660	HapMap-CEU	European	120	IG	0.283	0.500	0.217	1.000	0.533	0.467

	HapMap-HCB	Asian	90	IG	0.200	0.511	0.289	1.000	0.456	0.544

	HapMap-JPT	Asian	88	IG	0.295	0.523	0.182	0.752	0.557	0.443

	HapMap-YRI	Sub-Saharan African	120	IG		0.150	0.850	0.584	0.075	0.925

ss65834950	KHP1		160	AF	0.412	0.400	0.188	0.200	0.613	0.387

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.495+/-0.048	270	210	0	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .