Reference SNP(refSNP) Cluster Report: rs5017481

Reference SNP(refSNP) Cluster Report: rs5017481

refSNP ID: rs5017481
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	113/129
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_198834.1:c.39-25720C>A
NM_198839.1:c.-350C>A
NT_078100.1:g.996682G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7941536 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5017481 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
ss7941536	DEVINE_LAB\|DB_1_618088		fwd/B	G/T	gtcagtgccttgcccacaactgtggctcca	ttgtgatataaaagaaaaataagacacaaa	03/16/03	10/10/03	113	Genomic			96 %
ss75064043	ILLUMINA\|ILMN_Human_1M_rs5017481		fwd/B	G/T	gtcagtgccttgcccacaactgtggctcca	ttgtgatataaaagaaaaataagacacaaa	08/28/07	08/29/07	129	Genomic			unknown

Fasta sequence (Legend)

 Cctcaaatga tcctcccacc tctgcctccc aaaatgctgg gattacaggt gtgagccacc
 atgcctggcc CACAGTTCAG AATTTAATTA GGATATATTT TTTTGTCTGC ATACTGGTTT
 TAGCTCTCCA GTTAAATCCT GAAGGCAGAG ACCATCTCTT ATAGTTTGCT ACCCCCTTTT
 ATAGCTCTTC AAGTAGGACT AGGTATTTCT ATTAGTAAGC GCTTCATTGA CTGAAATAAA
 GATTAGCTCT GTACCTGAGA GGCCACTCTG CTCCTGATGC CTGCTTATCC GTCTTCACGT
 TGTCTCTGAG AGGCAAAGCC TCCAGTGGGA TATATAGCTG CTTTACAGAT GGACAGAATT
 CATCAAGAAA GTCAGTGCCT TGCCCACAAC TGTGGCTCCA
 K
 TTGTGATATA AAAGAAAAAT AAGACACAAA GTCCTTATCT GAATACTATG TCTCTTTGCT
 CTTGTTAATC ACTCCAGTTT ATCCAGAATT AAGAGCCTGA AGGAACTTCA TACCATAAGG
 TCAGAAAATC TCCTCAGGAA GGCCACTTCA TAAGTCTGGT CCTAATGATG AAAGGTAGAA
 TTGCACAATG AAGGACAGCA TGAGTAGTAG AGACTCCCCA CGATGTTTTC ACATGGACAC
 AGGGTTTTCA CATGGCATTT CTGCTCTCAC TCCTTCCTTA TCCAATGGCA AACACTTCCA
 GTCTCTATAC TTCAGCCAGT TACCAAATCT TAACTTCTTC CTCCATGACA CCTCCAATAT
 ATATGTTTTT AAGATCCCTT TCTAAGTCCT ACACACCTCA

GeneView

GeneView via analysis of contig annotation: ACACA acetyl-Coenzyme A carboxylase alpha

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: LOC100134390 similar to acetyl-CoA carboxylase 1

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_078100->NM_198834

function

reference

NT_078100->NM_198839

function

Celera

NW_926817->NM_198834

function

Celera

NW_926817->NM_198839

function

HuRef

NW_001838434->XM_001718762

function

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


reference	NT_078100->NM_198834->NP_942131	996682	reverse		intron

reference	NT_078100->NM_198839->	996682	reverse	949	5' UTR

Celera	NW_926817->NM_198834->NP_942131	912987	reverse		intron

Celera	NW_926817->NM_198839->	912987	reverse	949	5' UTR

HuRef	NW_001838434->XM_001718762->XP_001718814	542043	forward		5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs5017481 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_001838434.2	542043	31660509	minus	C	alt_assembly_8	HuRef	HuRef	view	400
17	NW_926817.1	912987	32545018	plus	G	alt_assembly_1	Celera	Celera	view	400
17	NT_078100.1	996682	32796643	plus	G	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010795

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC068400.10 AC068447.16 NC_000017.9	AC002346.1

UniGene Cluster ID
160556

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	HWP	G
ss7941536	HapMap-CEU	European	112	IG	1.000		1.000

	HapMap-HCB	Asian	84	IG	1.000		1.000

	HapMap-JPT	Asian	86	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	114	IG	1.000		1.000

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