Reference SNP(refSNP) Cluster Report: rs3917379

Reference SNP(refSNP) Cluster Report: rs3917379

refSNP ID: rs3917379
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
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_000576.2:c.597+356A>G
NT_022135.15:g.2296436T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5111365 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3917379 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
ss5111365	PGA-UW-FHCRC\|IL1B-007154		fwd/T	A/G	actcccaaaatcaccaccactatcacctcc	gctttctcagcaaaagcttcatttccaagt	09/05/02	01/23/04	108	Genomic			unknown

Fasta sequence (Legend)

 AACAGGTCTA TTTGACAATT TTGCATTAAT GTAAATAAAT TTAACATAAT TTTTAACTGC
 GTGCAACCTT CAATCCTGCT GCAGAAAATT AAATCATTTT GCCGATGTTA TTATGTCCTA
 CCATAGTTAC AACCCCAACA GATTATATAT TGTTAGGGCT GCTCTCATTT GATAGACACC
 TTGGGAAATA GATGACTTAA AGGGTCCCAT TATCACGTCC ACTCCACTCC CAAAATCACC
 ACCACTATCA CCTCC
 R
 GCTTTCTCAG CAAAAGCTTC ATTTCCAAGT TGATGTCATT CTAGGACCAT AAGGAAAAAT
 ACAATAAAAA GCCCCTGGAA ACTAGGTACT TCAAGAAGCT CTAGCTTAAT TTTCACCCCC
 CCAAAAAAAA AAAATTCTCA CCTACATTAT GCTCCTCAGC ATTTGGCACT AAGTTTTAGA
 AAAGAAGAAG GGCTCTTTTA ATAATCACAC GGAAAGTTGG GGGCCCAGTT ACAACTCAGG
 AGTCTGGCTC CTGAT

GeneView

GeneView via analysis of contig annotation: IL1B interleukin 1, beta

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_000576

function

HuRef

NW_001838841->NM_000576

function

Celera

NW_921474->NM_000576

function

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


reference	NT_022135->NM_000576->NP_000567	2296436	reverse	intron

HuRef	NW_001838841->NM_000576->NP_000567	629321	forward	intron

Celera	NW_921474->NM_000576->NP_000567	395850	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3917379 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	629321	106043140	plus	A	alt_assembly_8	HuRef	HuRef	view	255
2	NW_921474.1	395850	106973712	minus	T	alt_assembly_1	Celera	Celera	view	255
2	NT_022135.15	2296436	113304984	minus	T	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY137079

dbSNP Blast Analysis
GenBank HTGS Finished:
AC079753.7 NC_000002.10

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss5111365	PGA-AFRICAN-PANEL	African American	48	IG	1.000			1.000

	PGA-EUROPEAN-PANEL	European	46	IG	0.957	0.043	1.000	0.978	0.022

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.021+/-0.100	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

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Revised: May 25, 2006 1:38 PM .