Reference SNP(refSNP) Cluster Report: rs8098614

Reference SNP(refSNP) Cluster Report: rs8098614

refSNP ID: rs8098614
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
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
NT_010966.13:g.25663405C>T
XM_001713754.1:c.426G>A
XP_001713806.1:p.K142K

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss12447116 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs8098614 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
ss12447116	WI_SSAHASNP\|chr18.NT_010966.13_25663406		fwd/B	C/T	tctgggtctctctcacttacttttcagccg	ttcttcctgagagacaccatctcatagagc	07/04/03	10/10/03	116	Genomic			unknown

Fasta sequence (Legend)

 ACTCTATATG GCCTGTACTT TGGAGAGTGG AGCTGCTTGG CGGGGTTGGG GGAGCTTTTT
 CCTTCCTTTC TGGAGGAGAC TTGAGAAGCA GGAGTGGACT GCCCTCATAG CTTTTGCCTA
 GTGGTCTGAC ATTCTGGCCT CTGCTGACCC TGGCTGAGAG GCCTCCAGGT TCTGGGTCTC
 TCTCACTTAC TTTTCAGCCG
 Y
 TTCTTCCTGA GAGACACCAT CTCATAGAGC TGCCTCTCAA TCAACCCATC CGCTTTCTTC
 TCATCCAGCC AGTTGCTACA AGGGAAGGTC TGCTGGATAC CAGTGAAGGG GCACAGAATC
 ACCACCTGGG GAGAGTGGAG CACAGTGTCT CCGGCATTGA GTCTCCAGTA GGGTCCTCTT
 CGTGATGTTC AGCAGGCTCC

GeneView

GeneView via analysis of contig annotation: LOXHD1 lipoxygenase homology domains 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_010966->XM_001713754

function

HuRef

NW_001838467->XM_001713755

function

Celera

NW_927095->XM_001713756

function

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


reference	NT_010966->XM_001713754->XP_001713806	25663406	reverse	573	synonymous	A	Lys [K]	3	142
					contig reference	G	Lys [K]	3	142

HuRef	NW_001838467->XM_001713755->XP_001713807	368919	forward	573	synonymous	A	Lys [K]	3	142
					contig reference	G	Lys [K]	3	142

Celera	NW_927095->XM_001713756->XP_001713808	25650304	reverse	573	synonymous	A	Lys [K]	3	142
					contig reference	G	Lys [K]	3	142

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs8098614 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_927095.1	25650304	40981899	plus	C	alt_assembly_1	Celera	Celera	view	200
18	NW_001838467.2	368919	41031883	minus	G	alt_assembly_8	HuRef	HuRef	view	200
18	NT_010966.13	25663406	42428302	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010966

dbSNP Blast Analysis
GenBank HTGS Draft:
AP001590.2

UniGene Cluster ID
345877

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	HWP	C
ss12447116	HapMap-CEU	European	118	IG	1.000		1.000

	HapMap-HCB	Asian	88	IG	1.000		1.000

	HapMap-JPT	Asian	90	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	120	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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .