Reference SNP(refSNP) Cluster Report: rs17524874

Reference SNP(refSNP) Cluster Report: rs17524874

refSNP ID: rs17524874
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NT_077531.3:g.4135278A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss28477580 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17524874 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
ss28477580	KYUGEN\|QH05986		fwd/T	A/G	gctcctgcgcatcctaagccccaccgcctc	cctccagtccccacagcgttcgcgctccca	07/29/04	04/14/05	123	Genomic			unknown

Fasta sequence (Legend)

 GAAGTTTCCA CATTCCTGTT ACAGGCTCTC TAAGGCTTCA GCTCCTTTTT CTAGGACTAA
 GCTGGATCTC AAGTAAACAC TAGAGAGGGG GCAGCTGAAG CTCCAGGAGT GTGTGGGGCT
 CCCTGGGGCT GGATSGCGGT GGCGGGCAGG CGAGCTGGGC TGYGCTCGGG TGTGTTACAG
 TAAAGACGCC CAGCTTGGCG CTGGCCCGGC CTTTTCACGG TTTTAGGCTC TACAGAGAGC
 GGCTGCAGAG CTCACCCGGC TGGCAGGAGC CACCGAGGCC GGACACGTGG GCGACTTATT
 GACCAAGTGG GGAGGAAGCA GCCCCGCACT GCTCTCCCGA CTGCGGACCA CYGTTGGGCT
 CCTGCGCATC CTAAGCCCCA CCGCCTC
 R
 CCTCCAGTCC CCACAGCGTT CGCGCTCCCA GCCGGGGTAA GCGGAAGAAA ACAAAGGCCC
 GGCTCCATCA GGGCACCAAT CCCGCTCGTC GGCCTCTTTC TCGGCCTCCA ATGAG

GeneView

GeneView via analysis of contig annotation: FDFT1 farnesyl-diphosphate farnesyltransferase 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_077531->NM_004462

function

HuRef

NW_001839122->NM_004462

function

Celera

NW_923873->NM_004462

function

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


reference	NT_077531->NM_004462->NP_004453	4135278	forward	5' near gene

HuRef	NW_001839122->NM_004462->NP_004453	397399	reverse	5' near gene

Celera	NW_923873->NM_004462->NP_004453	3576577	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17524874 maps exactly once on NCBI human chromosome 8

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
8	NW_001839122.2	397399	10590885	minus	T	alt_assembly_8	HuRef	HuRef	view	387
8	NW_923873.1	3576577	10789251	plus	A	alt_assembly_1	Celera	Celera	view	387
8	NT_077531.3	4135278	11697337	plus	A	ref_assembly	reference	reference	view	387

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077531.3

dbSNP Blast Analysis
GenBank HTGS Finished:
AC025857.5 AC069185.7 AF271897.2 NC_000008.9

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss28477580	CP		156	AF		1.000

	JPK2		200	AF		1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
		0	0	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	YES	YES

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Revised: May 25, 2006 1:38 PM .