Reference SNP(refSNP) Cluster Report: rs2802319

Reference SNP(refSNP) Cluster Report: rs2802319

refSNP ID: rs2802319
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_004455.2:c.1341+291C>T
NT_004610.18:g.9182690C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3970451 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2802319 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
ss3970451	SC_JCM\|AL391650.8_157409		fwd/T	A/G	cagaatccttccttactttttatctgctca	ccttaagcccagggcctagtgctcagaaaa	09/25/01	10/10/03	100	Genomic			unknown

Fasta sequence (Legend)

 GACTCCCAGC CCAGCTCAAT GGCCTGTTTG GAGCCTTCCT GTGTGCACCC TGGCTGAGCT
 AACTGCTTCA CTTCCTCTAC AAGGACTCTT ATTAATCTAT CTGGCTTCTC TAGAAGTAAG
 ATTTGACAGT CTGTGTGCTG GAAAATGCTA ACCCAGTCTG ACTCTCTGGG CAGAATCCTT
 CCTTACTTTT TATCTGCTCA
 R
 CCTTAAGCCC AGGGCCTAGT GCTCAGAAAA TGACTGCTGA GTAAAGGAAT GAATGTTTCC
 TTCTCCAGCC TCCCCAAGAG ACATCTGCTT TTCACGTGGC TTCATCAATT TCCATGGGGA
 AAAGGCAACA GAATCTTGGG ACTTACAGGA GGCAGCAAGA ACACTTGGAA ATCTTCCCCG
 TGCCTCCCCT CAAATAGTGG

GeneView

GeneView via analysis of contig annotation: EXTL1 exostoses (multiple)-like 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_004610->NM_004455

function

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


reference	NT_004610->NM_004455->NP_004446	9182690	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2802319 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838576.1	257278	24612456	minus	C	alt_assembly_8	HuRef	HuRef	view	200
1	NW_921351.1	615883	24755025	minus	C	alt_assembly_1	Celera	Celera	view	200
1	NT_004610.18	9182690	26230935	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AL391650 AF153980

dbSNP Blast Analysis
GenBank HTGS Finished:
AL391650.18

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	HWP	G
ss3970451	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	114	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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .