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9p24.2

General Information: Available

Organism	Human
Points of Interest	rs7020673
Karyotype Band Location	9p24.2
Chromosomal Location (GRCh37)	Chr9:4228550-4321558
Region Size	0.09 Mb
Orthologous Regions	Mouse: Human 9p24.2 Orthologous Region Rat: Human 9p24.2 Orthologous Region
Genes in Region (2)	GLIS3, LOC100287493

View this region in the Human T1D Regions table.

Non-Synonymous SNPs in region dbSNP134:

Marker	Marker Source	Start	Strand	Peptide Shift	Gene Symbol (HGNC)	Gene ID (Entrez)	Amino Acid Position
rs143425492	dbSNP_134	4286139	+	P/L	GLIS3	169792	96
rs148168366	dbSNP_134	4286194	+	R/G	GLIS3	169792	78
rs114010705	dbSNP_134	4286337	+	A/V	GLIS3	169792	30
rs113754532	dbSNP_134	4286344	+	I/V	GLIS3	169792	28
rs73641408	dbSNP_134	4299592	+	G/W	LOC100287493	100287493	60
rs142235546	dbSNP_134	4299629	+	C/Y	LOC100287493	100287493	72
rs146119120	dbSNP_134	4299836	+	P/L	LOC100287493	100287493	141
rs138857227	dbSNP_134	4300003	+	A/T	LOC100287493	100287493	197

(Human) GRCh37 - chr9:4228550..4321558 (931 kb)  View in Genome Browser

An overview of the region is provided by GBrowse. Tracks shown include gene information and study-specific data:
Immune Disease Associated Variants	Variants shown to be associated with different auto-immune diseases
P-values, -log(p)	1 degree of freedom p-values, stratified by geographic location. Generated using snpMatrix with data from the T1DGC Meta-analysis study.
HapMap Recobination Data	Genome-wide recombination rate from Phase 2 HapMap estimated from phased haplotypes in HapMap Release 22 (NCBI 36). Units are in cM/Mb, coordinates have been projected to the current build.

Genes in LD Region: Available

Summary data derived from GWA meta analysis Barrett et al. LD regions were calculated using different r² and D' threshold values, and these regions were then examined for genes. The definition of a gene location includes a 3kb flanking region either side of the gene.

Marker Data		Region Data					Links
		r2 Threshold	D' Threshold	Region	Genes
Marker rs7020673 Chr 9 Position 4291747 Strand P-Value 1.88e-09		N/A	0.5	chr9: 4211977..4298955	LOC100287493 GLIS3		LD Region Feature File LD File
		0.4	N/A	chr9: 4263055..4296430	LOC100287493 GLIS3
		0.8	N/A	chr9: 4282536..4296430	LOC100287493 GLIS3
		1	N/A	chr9: 4289050..4291747	GLIS3

Publications: 1

• Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
  Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS, The Type 1 Diabetes Genetics Consortium
  Nat Genet. 2009
  PubMed ID: 19430480
   
  

Signal Clouds: Available

Genotype data for collections is plotted to give a visual sense of the quality of clustering. The two homozygous and the heterozygous genotypes are represented by different colours; a clear separation between the clouds is indicative of good clustering.

Source: ImmunoChip

Source: WTCCC

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Printed on Fri February 10, 2012