Reference SNP(refSNP) Cluster Report: rs1045496

Reference SNP(refSNP) Cluster Report: rs1045496

refSNP ID: rs1045496
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:	Not available
Clinical Association:	unknown

HGVS Names
NM_152269.2:c.400G>A
NP_689482.1:p.A134T
NT_009755.18:g.1151409G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss74813525 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1045496 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
ss1515739	LEE\|174413	fwd/T	A/G	aacagtcctgttcacaaagaaaaacgagaa	cggcgaagaaaaaacaagaaaggaaaaaaa	09/13/00	05/16/04	86	cDNA	unknown
ss4408511	LEE\|e174413	fwd/T	A/G	aacagtcctgttcacaaagaaaaacgagaa	cggcgaagaaaaaacaagaaaggaaaaaaa	04/26/02	10/10/03	106	cDNA	unknown
ss24796460	SEQUENOM\|sqnm140493	fwd/T	A/G	aacagtcctgttcacaaagaaaaacgagaa	cggcgaagaaaaaacaagaaaggaaaaaaa	06/18/04	06/18/04	123	cDNA	unknown
ss74813525	AFFY\|SNP_M-289825	fwd/T	A/G	aacagtcctgttcacaaagaaaaacgagaa	cggcgaagaaaaaacaagaaaggaaaaaaa	08/09/07	08/09/07	128	Genomic	unknown

Fasta sequence (Legend)

 AGTTGATCAG AACAGAAAGC TAGCTCGGAA AATCCTACAA GAGAAAGTAG ATGTTTTCTA
 CAATGGTGAA AACAGTCCTG TTCACAAAGA AAAACGAGAA
 R
 CGGCGAAGAA AAAACAAGAA AGGAAAAAAA GAGCAAAGGA AACCCTGGAA AAAAAGAAGC
 TACTTAAAGA ACTGTGGGAG TCAAGTAAAA AGGTCCACTG

GeneView

GeneView via analysis of contig annotation: C12orf65 chromosome 12 open reading frame 65

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_009755->NM_152269

function

HuRef

NW_001838064->NM_152269

function

Celera

NW_925395->NM_152269

function

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


reference	NT_009755->NM_152269->NP_689482	1151410	forward	1044	missense	A	Thr [T]	1	134
					contig reference	G	Ala [A]	1	134

HuRef	NW_001838064->NM_152269->NP_689482	5241116	reverse	1044	missense	A	Thr [T]	1	134
					contig reference	G	Ala [A]	1	134

Celera	NW_925395->NM_152269->NP_689482	70956884	forward	1044	missense	A	Thr [T]	1	134
					contig reference	G	Ala [A]	1	134

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1045496 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838064.2	5241116	120702662	minus	C	alt_assembly_8	HuRef	HuRef	view	100
12	NT_009755.18	1151410	122307430	plus	G	ref_assembly	reference	reference	view	100
12	NW_925395.1	70956884	123333055	plus	G	alt_assembly_1	Celera	Celera	view	100

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm140493	AI082864 Hs.19772

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_152269.2	AC068768.31 NC_000012.10	AF061733.1 AK095982.1 BC018145.1 BC062329.1

UniGene Cluster ID
319128

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss1515739	CEPH		184	AF		0.040	0.960

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.077+/-0.180	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 .