Reference SNP(refSNP) Cluster Report: rs1052418

Reference SNP(refSNP) Cluster Report: rs1052418

refSNP ID: rs1052418
Organism:	human (Homo sapiens)
Molecule Type:	cDNA
Created/Updated in build:	86/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_006001.1:c.1167T>C
NP_005992.1:p.A389A
NT_024524.13:g.728188A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24817375 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1052418 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
ss1528716	LEE\|495093	fwd/B	C/T	caacaccacggccatcgcggaggcctgggc	cgcctggaccataagttcgatctcatgtat	09/13/00	10/10/03	86	cDNA	unknown
ss4395328	LEE\|ge495093	fwd/B	C/T	caacaccacggccatcgcggaggcctgggc	cgcctggaccataagttcgatctcatgtat	04/25/02	10/10/03	106	cDNA	unknown
ss4418496	LEE\|e495093	fwd/B	C/T	caacaccacggccatcgcggaggcctgggc	cgcctggaccataagttcgatctcatgtat	04/26/02	10/10/03	106	cDNA	unknown
ss24817375	SEQUENOM\|sqnm215827	fwd/B	C/T	caacaccacggccatcgcggaggcctgggc	cgcctggaccataagttcgatctcatgtat	06/18/04	08/05/04	123	cDNA	unknown
ss28505084	MGC_GENOME_DIFF\|BC011721x37546841-G728189A	rev/T	A/G	atacatgagatcgaacttatggtccaggcg	gcccaggcctccgcgatggccgtggtgttg	08/25/04	08/25/04	126	cDNA	unknown

Fasta sequence (Legend)

 ACTACCAGCC CCCCACGGTG GTCCCTGGGG GAGACCTGGC CAAGGTGCAG CGGGCTGTGT
 GCATGCTGAG CAACACCACG GCCATCGCGG AGGCCTGGGC
 Y
 CGCCTGGACC ATAAGTTCGA TCTCATGTAT GCCAAGCGGG CCTTTGTGCA CTGGTACGTG
 GGAGAAGGCA TGGAGGAGGG GGAGTTCTCT GAGGCCCGCG

GeneView

GeneView via analysis of contig annotation: TUBA3C tubulin, alpha 3c

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_024524->NM_006001

function

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


reference	NT_024524->NM_006001->NP_005992	728189	reverse	1216	synonymous	C	Ala [A]	3	389
					contig reference	T	Ala [A]	3	389

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1052418 maps exactly once on NCBI human chromosome 13

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
13	NW_925473.1	545353	810129	minus	A	alt_assembly_1	Celera	Celera	view	100
13	NT_024524.13	728189	18646189	minus	A	ref_assembly	reference	reference	view	100
2	NW_001838859.2	17455666	124233690	minus	G	alt_assembly_8	HuRef	HuRef	view	100

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm215827	AL042663 BC011721 Hs.98102

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank STS:	GenBank mRNA:
NM_006001.1 NM_080386.2	AL139327.18	AL162715.12 AL590046.3	BV204636.1	L11645.1

UniGene Cluster ID
349695

3D structure mapping
NP_005992 NP_525125

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	C	T
ss24817375	CEPH		184	AF		0.130	0.870

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.226+/-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 .