Reference SNP(refSNP) Cluster Report: rs6106986

Reference SNP(refSNP) Cluster Report: rs6106986

refSNP ID: rs6106986
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	114/129
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_032501.2:c.1108+163A>G
NT_011387.8:g.24941862T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8433290 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6106986 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
ss8433290	SC_SNP\|NT_011387.8_24941862		fwd/B	C/T	gctgctgcctgtcagatctttctgaagacc	ggggcctggccccaccgggcatttcgacag	04/17/03	10/25/06	114	Genomic			unknown
ss91675643	BCMHGSC_JDW\|JWB-1434479		fwd/B	C/T	gctgctgcctgtcagatctttctgaagacc	ggggcctggccccaccgggcatttcgacag	02/26/08	03/02/08	129	Genomic			unknown

Fasta sequence (Legend)

 CTTTGGGCAG AGCCACCATG ATCTGCTTAC ATTAAAGAAA ATATTTGAAG ACACTGTGCT
 GTGTGGGAGG ACGATGCCCA AGGGAGCCAG TCATCACCTT GTCTTCAAAG TGATCTCAAT
 TTAATGGAGA TGGTTCTAGG CCATGCCTAA CATGGTTTGA GGGACAGCCC TGAAGGCTCA
 GGGGCAGGGC TGGGGACACA GAAGTGGCGG GCAGCTGGCC CTGGCTTTGA GAAAGGGCTG
 GATCTGGGCA AGCAGCCTAG AGGTGAGAAG GATGCCAAAG CGATGGCCTG AGGCCGGCAG
 TTTAAGTCAG AGGGCAGGAG TGCAGGAGCA GGGGCCTTGA GATGTCCTCC AGCACCAAGT
 CAGACTCCCT GCTGCTGCCT GTCAGATCTT TCTGAAGACC
 Y
 GGGGCCTGGC CCCACCGGGC ATTTCGACAG CAGGACCTGG AGAGCCACAC CCTCACCAGA
 ACCCAGGCGT CCCCCTTCCA TGAACCTCTC CACAAGCCTC GAGCCTCAGG CTCTCTCCCC
 TGACACCAGC ATGGGGTCCC AAACAGGGTT CACCATCCTT ACCAGCATTG GGATAAACTG
 GGGTGCTCTC AAAAAGGACG CTGGTGGCAC CATTGCAGAG AGGCCCATAC ACCACGTAGC
 TGTGTCCTGT AATCCAACCG ATGTCGGCCA CACAGCCAAA GATGTCACCT GGCTGGTGGT
 CAAACACAAG CTGCAGAGAC AGGAAAGGAG CATCAGGAGC TTGTCCCCCC ACTCCACCAT
 GTTCACACCA GGTCACTAGG AAATAGGCAT GCATAGGCTG

GeneView

GeneView via analysis of contig annotation: ACSS1 acyl-CoA synthetase short-chain family member 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_011387->NM_032501

function

HuRef

NW_001838659->NM_032501

function

Celera

NW_927317->NM_032501

function

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


reference	NT_011387->NM_032501->NP_115890	24941862	reverse	intron

HuRef	NW_001838659->NM_032501->NP_115890	758267	forward	intron

Celera	NW_927317->NM_032501->NP_115890	24932844	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6106986 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NT_011387.8	24941862	24949862	plus	T	ref_assembly	reference	reference	view	400
20	NW_001838659.2	758267	24958699	minus	A	alt_assembly_8	HuRef	HuRef	view	400
20	NW_927317.1	24932844	25075668	plus	T	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011387

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank mRNA:
AL035661.16 NC_000020.9	AK024424.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss8433290	HapMap-CEU	European	120	IG	0.017	0.283	0.700	0.655	0.158	0.842

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	114	IG	0.018	0.263	0.719	1.000	0.149	0.851

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.159+/-0.233	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 .