Reference SNP(refSNP) Cluster Report: rs1054380

Reference SNP(refSNP) Cluster Report: rs1054380

refSNP ID: rs1054380
Organism:	human (Homo sapiens)
Molecule Type:	cDNA
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_017586.1:c.*226G>C
NT_035014.4:g.3110941G>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24817925 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1054380 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
ss1532292	LEE\|576502	fwd/T	C/G	tggacttnaggcagagcctgcagcagctgt	tggacactacccagccctactcctctgctg	09/13/00	10/10/03	86	cDNA	unknown
ss4421358	LEE\|e576500	fwd/T	C/G	tggacttgaggcagagcctgcagcagctgt	tggacactacccagccctactcctctgctg	04/26/02	10/10/03	106	cDNA	unknown
ss24817925	SEQUENOM\|sqnm217571	fwd/T	C/G	tggacttgaggcagagcctgcagcagctgt	tggacactacccagccctactcctctgctg	06/18/04	06/18/04	123	cDNA	unknown

Fasta sequence (Legend)

 TCCTCTGCTC CTTTCTCCAG ACTGGCTTAA GCCAGGAGCC ACTGGCTGCT GGTGTGAGGG
 TCTGGGCTGC TGGACTTGAG GCAGAGCCTG CAGCAGCTGT
 S
 TGGACACTAC CCAGCCCTAC TCCTCTGCTG GGTGGGTCTG CAGATCTCAC ACCACAGACA
 GGGCTGCCTG TGACCTGCTG TGACCTGGGA GCAGCTTCCC

GeneView

GeneView via analysis of contig annotation: C9orf7 chromosome 9 open reading frame 7

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_035014->NM_017586

function

HuRef

NW_001839241->NM_017586

function

Celera

NW_924573->NM_017586

function

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


reference	NT_035014->NM_017586->	3110941	forward	803	3' UTR

HuRef	NW_001839241->NM_017586->	118312	reverse	803	3' UTR

Celera	NW_924573->NM_017586->	20372466	forward	803	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1054380 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839241.2	118312	105835702	minus	C	alt_assembly_8	HuRef	HuRef	view	100
9	NW_924573.1	20372466	106884635	plus	G	alt_assembly_1	Celera	Celera	view	100
9	NT_035014.4	3110941	135323822	plus	G	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm217571	R18313 Hs.119285

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank STS:	GenBank mRNA:
NM_017586.1	AL593848.14	BV205186.1	AJ011373.1 AK074852.1 AK075416.1 AK075548.1 AY358452.1 BC030558.1

UniGene Cluster ID
62003

Population Diversity

There is no frequency data.

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 .