Reference SNP(refSNP) Cluster Report: rs3783579

Reference SNP(refSNP) Cluster Report: rs3783579

refSNP ID: rs3783579
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
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
NM_000575.3:c.319+631A>G
NT_022135.15:g.2246473T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss4969932 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3783579 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
ss4969932	PGA-UW-FHCRC\|IL1A-009548		fwd/T	A/G	ctgtcacccaggctggagtgcagtggcgca	tctcggctcactgcaagctctgcctcctgg	08/09/02	02/03/05	107	Genomic			unknown

Fasta sequence (Legend)

 ATCAGAATCC CCCACTCATT GGATTGTTGT AAAGATTAAG AGTCTCAGGC TTTACAGACT
 GAGCTAGCTG GGCCCTCCTG ACTGTTATAA AGATTAAATG AGTCAACATC CCCTAACTTC
 TGGACTAGAA TAATGTCTGG TACAAAGTAA GCACCCAATA AATGTTAGCT ATTACTATCA
 TTATTATTAT TATTTTATTT TATTTTTTTG AGATGGAGTC TGGCTCTGTC ACCCAGGCTG
 GAGTGCAGTG GCGCA
 R
 TCTCGGCTCA CTGCAAGCTC TGCCTCCTGG GTTCATGCCA TTCTCCTGCC TCAGCCTCCC
 GAGTAGCTGG GAATACAGGC ACCCGCCACT GTTCCCGGCT AATTTTTTGT ATTTTTAGTA
 GAGACGGAGT TTCACCGTGG TCTCCATCTC CTCGTGATCC ACCCACCTTG GCCTCCCAAA
 GTGCCGGGAT TACAGGCGTG AGCCACCGCG CCCGGCCTAT GATTATTATT ATTATTACTA
 CTACTACTAC CTATA

GeneView

GeneView via analysis of contig annotation: IL1A interleukin 1, alpha

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_022135->NM_000575

function

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


reference	NT_022135->NM_000575->NP_000566	2246473	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3783579 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838841.2	679335	105993126	plus	A	alt_assembly_8	HuRef	HuRef	view	255
2	NW_921474.1	345850	106923712	minus	T	alt_assembly_1	Celera	Celera	view	255
2	NT_022135.15	2246473	113255021	minus	T	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AF536338

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss4969932	PGA-AFRICAN-PANEL	African American	48	IG	0.958	0.042	1.000	0.979	0.021

	PGA-EUROPEAN-PANEL	European	44	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.022+/-0.101	47	26	0	0

Validation Summary:

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .