Reference SNP(refSNP) Cluster Report: rs15490

Reference SNP(refSNP) Cluster Report: rs15490

refSNP ID: rs15490
Organism:	human (Homo sapiens)
Molecule Type:	cDNA
Created/Updated in build:	52/129
Map to Genome Build:	36.3

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

HGVS Names
NM_005860.2:c.*1541G>T
NT_011255.14:g.623249G>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24793272 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs15490 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
ss17895	CGAP-GAI\|64240	fwd/B	G/T	gagtgtggggagcttgggcatcctcctcca	cctcctccagcccccaggcagtgccttacc	08/23/99	05/16/04	52	cDNA	99 %
ss16247789	CGAP-GAI\|1493821	rev/T	A/C	ggtaaggcactgcctgggggctggaggagg	tggaggaggatgcccaagctccccacactc	11/18/03	11/22/03	120	cDNA	unknown
ss24793272	SEQUENOM\|sqnm110065	rev/T	A/C	ggtaaggcactgcctgggggctggaggagg	tggaggaggatgcccaagctccccacactc	06/18/04	06/18/04	123	cDNA	unknown

Fasta sequence (Legend)

 ACCCAGACTC CAGCCAGACC TGCCTCACCC ACCAATGCAG CCGGGGCTGG CGACACCAGC
 CAGGTGCTGG TCTTGGGCCA GTTCTCCCAC GACGGCTCAC CCTCCCCTCC ATCTGCGTTG
 ATGCTCAGAA TCGCCTACCT GTGCCTGCGT GTAAACCACA GCCTCAGACC AGCTATGGGG
 AGAGGACAAC ACGGAGGATA TCCAGCTTCC CCGGTCTGGG GTGAGGAGTG TGGGGAGCTT
 GGGCATCCTC CTCCA
 K
 CCTCCTCCAG CCCCCAGGCA GTGCCTTACC TGTGGTGCCC AGAAAAGTGC CCCTAGGTTG
 GTGGGTCTAC AGGAGCCTCA GCCAGGCAGC CCACCCCACC CTGGGGCCCT GCCTCNCCAA
 GGAAATAAAG ACTCAAAGAA GCCATA

GeneView

GeneView via analysis of contig annotation: FSTL3 follistatin-like 3 (secreted glycoprotein)

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_011255->NM_005860

function

HuRef

NW_001838476->NM_005860

function

Celera

NW_927140->NM_005860

function

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


reference	NT_011255->NM_005860->	623249	forward	2368	3' UTR

HuRef	NW_001838476->NM_005860->	442251	forward	2368	3' UTR

Celera	NW_927140->NM_005860->	134361	reverse	2368	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs15490 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_927140.1	134361	134361	minus	C	alt_assembly_1	Celera	Celera	view	255
19	NW_001838476.1	442251	453052	plus	G	alt_assembly_8	HuRef	HuRef	view	255
19	NT_011255.14	623249	634249	plus	G	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm110065	U76702 AI918838 NM_005860

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank STS:	GenBank mRNA:
NM_005860.2	AC004156.1 AC112708.3 NC_000019.8	BV180531.1	AY358917.1 BC005839.2 BC033119.1 U76702.1

UniGene Cluster ID
529038

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	G	T
ss17895	CEPH		184	AF		0.940	0.060

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.113+/-0.209	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	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .