Reference SNP(refSNP) Cluster Report: rs1047039

Reference SNP(refSNP) Cluster Report: rs1047039

refSNP ID: rs1047039
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/T
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NT_029419.11:g.17487234A>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss40147928 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1047039 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
ss1518766	LEE\|255390	fwd/B	A/T	agctgcatgcacaaagaccttaggcacatc	cttcatttctctgtacactggtttctctac	09/13/00	10/10/03	86	cDNA	unknown
ss2422295	HGBASE\|SNP000009204	fwd/B	A/T	catgcacaaagaccttaggcacatc	cttcatttctctgtacactggtttc	11/07/00	10/10/03	89	cDNA	unknown
ss3053637	TSC-CSHL\|TSC1139540	fwd/B	A/T	agctgcatgcacaaagaccttaggcacatc	cttcatttctctgtacactggtttctctac	06/07/01	10/10/03	96	Genomic	unknown
ss4410916	LEE\|e255390	fwd/B	A/T	agctgcatgcacaaagaccttaggcacatc	cttcatttctctgtacactggtttctctac	04/26/02	10/10/03	106	cDNA	unknown
ss16233050	CGAP-GAI\|1474260	rev/T	A/T	gtagagaaaccagtgtacagagaaatgaag	gatgtgcctaaggtctttgtgcatgcagct	11/18/03	11/22/03	120	cDNA	unknown
ss40147928	ABI\|hCV11964757	rev/	A/T	gtagagaaaccagtgtacagagaaatgaag	gatgtgcctaaggtctttgtgcatgcagct	07/16/05	11/02/06	126	Genomic	unknown
ss76599482	AFFY\|AFFY_6_1M_SNP_A-8460554	fwd/	A/T	agaccttaggcacatc	cttcatttctctgtac	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 ACCCAAAGTT GTTTAAAAAA TGCATGATAT GTATCTTTTT TATTCCCATT GCAGGCTTTC
 TCCACCACCA CAACAGCATG TGGTCTGACA GAATTGGCTT CAAAGAAGAA ACTAAAAGCC
 ACCTCTTGCA GGAAACTGCA CTGCCCTCAA CATCCAGCCC CTACTCCTTG GTCCTCCAAA
 CCCCCAAACT CTGCAGGAGA AAGGCAGCAT GGTACATGGG GAGGAAGACC AGACTGAGCG
 ATTTGGAATC CACATCCTAA TGCTGCCACA AGCTGCATGC ACAAAGACCT TAGGCACATC
 W
 CTTCATTTCT CTGTACACTG GTTTCTCTAC TATGTGTGTA TTAAAATATA TAATGTGGAT
 GATAGTAAAC TGAACAAAGC CTTAATTTTC TCCCAAGCTT TGACATTGCC AAGGGCAGTT
 AGGAGACTTC AGGATCAAGT TTAGGGGACA AGTTTTTTTC TAATACTTTC AAAAGGCCCA
 AGTGAAGAGA GGAAGGACAC CTCACTTTCT GGCTCTAAAA GCATGGTACA TCTCACACTA
 GGATTCCCTC TGCACCTCTG TTCATCCCTG TATTCCTAAC TAAATTCCAG AAAATCTTCC

GeneView

GeneView via analysis of contig annotation: KIAA0748 KIAA0748

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_029419->NM_001098815

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_029419->NM_001098815->NP_001092285	17487234	reverse	3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1047039 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_001838059.1	2608945	52382785	minus	A	alt_assembly_8	HuRef	HuRef	view	300
12	NT_029419.11	17487234	53630195	minus	A	ref_assembly	reference	reference	view	300
12	NW_925395.1	2619617	54995788	minus	A	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
H43688 BI820476 Hs.33187

dbSNP Blast Analysis

UniGene Cluster ID
33187

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss40147928	HapMap-HCB	Asian	82	IG	0.488	0.415	0.098	1.000	0.695	0.305

	HapMap-JPT	Asian	84	IG	0.524	0.429	0.048	0.527	0.738	0.262

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.406+/-0.195	90	90	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .