Reference SNP(refSNP) Cluster Report: rs2280539

Reference SNP(refSNP) Cluster Report: rs2280539

refSNP ID: rs2280539
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_001097610.1:c.-4C>T
NM_145651.2:c.-4T>C
NT_035113.6:g.133096T>C
NT_113933.1:g.60453G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3793527 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2280539 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
ss3218679	YUSUKE\|IMS-JST028763	fwd/T	A/G	cagcaggagggcacggctccccttcatgcc	gcagtctcaggagctgcctccagccagaat	09/05/01	11/22/03	100	Genomic	unknown
ss3793527	SC_JCM\|AC069287.4_37175	fwd/T	A/G	catcaggagggcacggctccccttcatgcc	gcagtctcaggagctgcctccagccagaat	09/25/01	10/10/03	103	Genomic	unknown
ss12149116	WI_SSAHASNP\|chr11.NT_035113.4_955769	fwd/T	A/G	cagcaggagggcacggctccccttcatgcc	gcagtctcaggagctgcctccagccagaat	07/04/03	10/10/03	116	Genomic	unknown

Fasta sequence (Legend)

 GCAGGGTCCT TGCCCACTTC TGTGACAGAA GCAGGTGGAG TGTTCACTGC AGAGGCCCGA
 TGCCAGGATT TTACCTTCTC AGGTACCCCC CACTCCCCCC CACCCCTGAA TGTTCTGGAA
 ACCCCAGTGG CACAGACTCA CGGCAGATGT AGAACAGGGG TGAGGGCCAC CATCAGGAGG
 GCACGGCTCC CCTTCATGCC
 R
 GCAGTCTCAG GAGCTGCCTC CAGCCAGAAT CCCGGGATTT TATGCCTCAC CGGACAGCAC
 CTCTCCTAGA GGGCGGACCG CACTGCCCAT TAGGACCCGG CAGCCAGCTT AGATGAGTTG
 TTCACATCCC TGCCCCCAGT GGGTGCCAAG CAGCAACAGG CATGGAGTGG CTGTGTGACA
 GGTGGTTGGC AAGCGGCTTT

GeneView

GeneView via analysis of contig annotation: LOC100130477 hypothetical protein LOC100130477

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: SCGB1C1 secretoglobin, family 1C, 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

Celera

NW_926584->XM_001713759

function

reference

NT_035113->NM_145651

function

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


Celera	NW_926584->XM_001713759->	5459	forward	17	5' UTR

reference	NT_035113->NM_145651->	133096	forward	17	5' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2280539 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
11	NW_001838015.1	12304	12304	minus	T	alt_assembly_8	HuRef	HuRef	view	200
11	NT_035113.6	133096	183096	minus	T	ref_assembly	reference	reference	view	200
17	NT_113933.1	60453	unplaced	plus	G	ref_assembly	reference	reference	view	200
17	NW_001838402.2	301586	7145	plus	G	alt_assembly_8	HuRef	HuRef	view	200
17	NW_926584.1	5459	87963	minus	T	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_035113 AF240580

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_001097610.1 NM_145651.2

UniGene Cluster ID
127059

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss3218679	JBIC-allele		1420	AF		0.578	0.422

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.488+/-0.077	0	0	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .