T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers

General Information: Available

Organism	Human
Points of Interest	rs3087243
Karyotype Band Location	2q33.2
Chromosomal Location (GRCh37)	Chr2:204672809-204820058
Region Size	0.15 Mb
Orthologous Regions	Mouse: Human 2q33.2 Orthologous Region Rat: Human 2q33.2 Orthologous Region
Genes in Region (2)	CTLA4, ICOS

View this region in the Human T1D Regions table.

Marker	Marker Source	Start	Strand	Peptide Shift	Gene Symbol (HGNC)	Gene ID (Entrez)	Amino Acid Position
rs138279736	dbSNP_134	204732688	+	R/Q	CTLA4	1493	8
rs146541851	dbSNP_134	204732693	+	K/E	CTLA4	1493	10
rs231775	dbSNP_134	204732714	+	T/A	CTLA4	1493	17
rs1065442	dbSNP_134	204735471	+	M/T	CTLA4	1493	91
rs144988077	dbSNP_134	204735525	+	G/E	CTLA4	1493	109
rs77411896	dbSNP_134	204801577	+	R/C	ICOS	29851	14

Non-Synonymous SNPs in region dbSNP134:

(Human) GRCh37 - chr2:204672809..204820058 (147.25 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	rs3087243
Chr	2
Position	204738919
Strand
P-Value	1.21e-15

N/A

0.5

chr2: 204461526..204819551

CTLA4 ICOS CD28

LD Region Feature File

LD File

0.4

N/A

chr2: 204690355..204796094

CTLA4

0.8

N/A

chr2: 204691538..204777818

CTLA4

1

N/A

Publications: 6

Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers.
Plant D, Flynn E, Mbarek H, Dieudé P, Cornelis F, Arlestig L, Dahlqvist SR, Goulielmos G, Boumpas DT, Sidiropoulos P, Johansen JS, Ørnbjerg LM, Hetland ML, Klareskog L, Filer A, Buckley CD, Raza K, Witte T, Schmidt RE, Worthington J
Ann Rheum Dis. 2010
PubMed ID: 20498205
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
Stahl EA, Raychaudhuri S, Remmers EF, Xie G, Eyre S, Thomson BP, Li Y, Kurreeman FA, Zhernakova A, Hinks A, Guiducci C, Chen R, Alfredsson L, Amos CI, Ardlie KG, BIRAC Consortium, Barton A, Bowes J, Brouwer E, Burtt NP, Catanese JJ, Coblyn J, Coenen MJ, Costenbader KH, Criswell LA, Crusius JB, Cui J, de Bakker PI, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Lee AT, Liu X, Martin P, Morgan AW, Padyukov L, Posthumus MD, Radstake TR, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, van der Schoot CE, van Riel PL, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth BP, YEAR Consortium, Wijmenga C, Karlson EW, Toes RE, de Vries N, Begovich AB, Worthington J, Siminovitch KA, Gregersen PK, Klareskog L, Plenge RM
Nat Genet. 2010
PubMed ID: 20453842
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
Shared and distinct genetic variants in type 1 diabetes and celiac disease.
Smyth DJ, Plagnol V, Walker NM, Cooper JD, Downes K, Yang JH, Howson JM, Stevens H, McManus R, Wijmenga C, Heap GA, Dubois PC, Clayton DG, Hunt KA, van Heel DA, Todd JA
N Engl J Med. 2008
PubMed ID: 19073967
Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease.
Ueda H, Howson JM, Esposito L, Heward J, Snook H, Chamberlain G, Rainbow DB, Hunter KM, Smith AN, Di Genova G, Herr MH, Dahlman I, Payne F, Smyth D, Lowe C, Twells RC, Howlett S, Healy B, Nutland S, Rance HE, Everett V, Smink LJ, Lam AC, Cordell HJ, Walker NM, Bordin C, Hulme J, Motzo C, Cucca F, Hess JF, Metzker ML, Rogers J, Gregory S, Allahabadia A, Nithiyananthan R, Tuomilehto-Wolf E, Tuomilehto J, Bingley P, Gillespie KM, Undlien DE, Rønningen KS, Guja C, Ionescu-Tîrgovişte C, Savage DA, Maxwell AP, Carson DJ, Patterson CC, Franklyn JA, Clayton DG, Peterson LB, Wicker LS, Todd JA, Gough SC
Nature. 2003
PubMed ID: 12724780
The CTLA-4 gene region of chromosome 2q33 is linked to, and associated with, type 1 diabetes. Belgian Diabetes Registry.
Nisticò L, Buzzetti R, Pritchard LE, Van der Auwera B, Giovannini C, Bosi E, Larrad MT, Rios MS, Chow CC, Cockram CS, Jacobs K, Mijovic C, Bain SC, Barnett AH, Vandewalle CL, Schuit F, Gorus FK, Tosi R, Pozzilli P, Todd JA
Hum Mol Genet. 1996
PubMed ID: 8817351

Signal Clouds: Available

2q33.2