Reference SNP(refSNP) Cluster Report: rs375511

Reference SNP(refSNP) Cluster Report: rs375511

refSNP ID: rs375511
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	80/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_003734.2:c.514C>T
NP_003725.1:p.L172L
NT_010755.15:g.4728169C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3311442 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs375511 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss480037	SC_JCM\|AC016889.6_15834		fwd/T	A/G	tctggtctatgtccaggtactcttggaaca	catggggcgtcggtgatagggcagggggcc	07/12/00	10/10/03	80	Genomic			unknown
ss3311442	TSC-CSHL\|TSC1486551		rev/B	C/T	ggccccctgccctatcaccgacgccccgtg	tgttccaagagtacctggacatagaccaga	09/20/01	05/16/04	102	Genomic			unknown

Fasta sequence (Legend)

 GGAGAAAGTC CACAGTGAGG AGGCCACTCG ACTTCCCTGG ACACTGAAGC GGGGGCCTTG
 GGGATAGAAC TGTAGAGGGG GAGCTGGACC CGGGGGCACA GGGGACTTCA GGGACCAGGA
 CCCACCTGTG CCATTGTCTG GGATCAGCAC CACATTCACC AGGCCGGCCT CAAACTGGGC
 CTCCAGCTGG GCCAGGCTGT CGTAGTAGCG GCCTTGATAG AACACCTTCT GGATAGTCCA
 GCGGGCAGGG TCAAGGGCCT TGTGGTTCAC TAGCAGCTCC AAGCCCACGT GGTGCAGGAA
 GAACCCAGCG CCCGAGATGT TGTAGTAGAG GCCAAACCAG GTGGCCCGGT CCCCTGATTG
 CAGACCACGG GGAGCCGTGG TCATTGTCAC CAGGTTCCGT CCCCGGTGCT TGTAGAAGCA
 ACAGTGGTGG AGAAGCCCAG AAGCCTGGGG CAGCTCTCTG TTGAAGATCA TCTGGTCTAT
 GTCCAGGTAC TCTTGGAACA
 R
 CACGGGGCGT CGGTGATAGG GCAGGGGGCC TCCATGACGC TCCACAGTCA CGTCCCGCAT
 GTAGGAGGGG TGAGGCAGTG GCCCCACCAC CAGCTCACTC ACGTTGGGCT GGGGTTGCCT
 GCCAAAGAAG ACGATGGCCA GTG

GeneView

GeneView via analysis of contig annotation: AOC3 amine oxidase, copper containing 3 (vascular adhesion protein 1)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: AOC2 amine oxidase, copper containing 2 (retina-specific)

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_010755->NM_003734

function

HuRef

NW_001838436->NM_003734

function

HuRef

NW_001838436->NM_001158

function

HuRef

NW_001838436->NM_009590

function

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


reference	NT_010755->NM_003734->NP_003725	4728170	forward	674	synonymous	T	Leu [L]	1	172
					contig reference	C	Leu [L]	1	172

HuRef	NW_001838436->NM_003734->NP_003725	395211	reverse	674	synonymous	T	Leu [L]	1	172
					contig reference	C	Leu [L]	1	172

HuRef	NW_001838436->NM_001158->NP_001149	395211	reverse		3' near gene

HuRef	NW_001838436->NM_009590->NP_033720	395211	reverse		3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs375511 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838436.2	395211	36768514	plus	G	alt_assembly_8	HuRef	HuRef	view	500
17	NW_926828.1	4531120	37659929	minus	T	alt_assembly_1	Celera	Celera	view	500
17	NW_926828.1	4547069	37675878	minus	T	alt_assembly_1	Celera	Celera	view	500
17	NT_010755.15	4728170	38257400	minus	C	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
AC016889 AC046171

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank mRNA:
NM_003734.2	AC016889.28 AC055866.19 NC_000017.9	AC046171.3	AF067406.1 BC050549.1 U39447.1

UniGene Cluster ID
198241

3D structure mapping
NP_003725

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss3311442	CEPH		184	AF		0.840	0.160

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.269+/-0.249	0	0	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .