Reference SNP(refSNP) Cluster Report: rs1060946

Reference SNP(refSNP) Cluster Report: rs1060946

refSNP ID: rs1060946
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:	G/T
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_002373.5:c.5068G>T
NP_002364.5:p.A1690S
NT_010194.16:g.14609295G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3632192 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1060946 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
ss1545319	LEE\|888644	fwd/B	G/T	aataggtattggaggggcagagaggatgtg	ccttggaacaggacacatactggagggagc	09/13/00	10/10/03	86	cDNA	unknown
ss3632192	SC_JCM\|AC015664.5_139167	fwd/B	G/T	aataggtattggaggggcagagaggatgtg	ccttggaacaggacacatactggagggagc	09/24/01	10/10/03	100	Genomic	unknown
ss4430969	LEE\|e888643	fwd/B	G/T	aataggtattggaggggcagagaggatgtg	ccttggaacaggacacatactggagggagc	04/26/02	10/10/03	106	cDNA	unknown
ss74816816	AFFY\|SNP_M-313680	fwd/B	G/T	aataggtattggaggggcagagaggatgtg	ccttggaacaggacacatactggagggagc	08/09/07	08/09/07	128	Genomic	unknown
ss74901615	ILLUMINA\|ILMN_Human_1M_rs1060946	fwd/B	G/T	aataggtattggaggggcagagaggatgtg	ccttggaacaggacacatactggagggagc	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 TGGAAGAGAG CCTAGTGCAG GAGGGCAGGG CCAGAGAGCA GGAAGAAAAG TACTGGAGGG
 GGCAGGATGT GGTCCAGGAG TGGCAAGAAA CATCTCCTAC CAGAGAGGAG CCGGCTGGAG
 AACAGAAAGA GCTTGCCCCG GCATGGGAGG ACACATCTCC TGAGCAGGAC AATAGGTATT
 GGAGGGGCAG AGAGGATGTG
 K
 CCTTGGAACA GGACACATAC TGGAGGGAGC TAAGCTGTGA GCGGAAGGTC TGGTTCCCTC
 ACGAGCTGGA TGGCCAGGGG GCCCGCCCAC ACTACACTGA GGAACGGGAA AGCACTTTCC
 TAGATGAGGG CCCAGATGAT GAGCAAGAAG TACCCCTGCG GGAACACGCA ACCCGGAGCC
 CCTGGGCCTC AGACTTCAAG

GeneView

GeneView via analysis of contig annotation: MAP1A microtubule-associated protein 1A

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_010194->NM_002373

function

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


reference	NT_010194->NM_002373->NP_002364	14609296	forward	5535	missense	T	Ser [S]	1	1690
					contig reference	G	Ala [A]	1	1690

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1060946 maps exactly once on NCBI human chromosome 15

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
15	NW_925840.1	10872180	20589411	plus	G	alt_assembly_1	Celera	Celera	view	200
15	NW_001838214.2	52336	20666676	minus	C	alt_assembly_8	HuRef	HuRef	view	200
15	NT_010194.16	14609296	41606031	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
U38291 AC015663 AC019011 Hs.194301 U38291

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank mRNA:
NM_002373.5	AF200415.2 U14577.1

UniGene Cluster ID
194301

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	HWP	G	T
ss3632192	CEPH		184	AF				1.000

	HapMap-CEU	European	116	IG	1.000			1.000

	HapMap-HCB	Asian	88	IG	0.977	0.023		0.989	0.011

	HapMap-JPT	Asian	86	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	116	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.005+/-0.049	270	210	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 .