T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers

General Information: Available

Organism	Human
Points of Interest	rs12722495; rs11594656; rs12251307
Karyotype Band Location	10p15.1
Chromosomal Location (GRCh37)	Chr10:6029726-6197536
Region Size	0.17 Mb
Orthologous Regions	Mouse: Human 10p15.1 Orthologous Region Rat: Human 10p15.1 Orthologous Region
Genes in Region (4)	IL2RA, MIR3155, PFKFB3, RBM17

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
rs12722712	dbSNP_134	6054839	-	I/T	IL2RA	3559	272
rs140088691	dbSNP_134	6060023	+	R/W	IL2RA	3559	263
rs143550766	dbSNP_134	6060053	+	V/I	IL2RA	3559	253
rs113428577	dbSNP_134	6060054	+	S/R	IL2RA	3559	252
rs138764230	dbSNP_134	6061401	+	Y/X	IL2RA	3559	239
rs150060415	dbSNP_134	6061427	+	E/Q	IL2RA	3559	231
rs145428184	dbSNP_134	6061845	+	V/I	IL2RA	3559	215
rs149181289	dbSNP_134	6063462	+	M/V	IL2RA	3559	188
rs55841382	dbSNP_134	6063497	+	R/K	IL2RA	3559	176
rs147791171	dbSNP_134	6063525	+	V/I	IL2RA	3559	167
rs141246728	dbSNP_134	6063539	+	G/D	IL2RA	3559	162
rs146966522	dbSNP_134	6063540	+	G/S	IL2RA	3559	162
rs147975326	dbSNP_134	6063585	+	M/L	IL2RA	3559	147
rs141655051	dbSNP_134	6063588	+	Q/K	IL2RA	3559	146
rs138645280	dbSNP_134	6066218	+	A/V	IL2RA	3559	119
rs74162095	dbSNP_134	6066227	-	V/A	IL2RA	3559	116
rs76029930	dbSNP_134	6066236	+	M/R	IL2RA	3559	113
rs56054476	dbSNP_134	6066242	+	S/N	IL2RA	3559	111
rs36065822	dbSNP_134	6066301	+	T/I	IL2RA	3559	91
rs72650666	dbSNP_134	6066302	-	T/M	IL2RA	3559	91
rs139340259	dbSNP_134	6066311	+	R/P	IL2RA	3559	88
rs142016545	dbSNP_134	6067928	+	K/R	IL2RA	3559	42
rs146345652	dbSNP_134	6067936	+	M/I	IL2RA	3559	39
rs148505161	dbSNP_134	6067967	+	P/L	IL2RA	3559	29
rs55868253	dbSNP_134	6067977	+	D/H	IL2RA	3559	26
rs74162092	dbSNP_134	6104070	-	M/I	IL2RA	3559	15
rs141782513	dbSNP_134	6150675	+	P/S	RBM17	84991	178
rs149022692	dbSNP_134	6152003	+	K/R	RBM17	84991	206
rs145588908	dbSNP_134	6155518	+	C/R	RBM17	84991	302
rs138018241	dbSNP_134	6155525	+	T/S	RBM17	84991	304
rs76409649	dbSNP_134	6157429	+	L/F	RBM17	84991	372

Non-Synonymous SNPs in region dbSNP134:

(Human) GRCh37 - chr10:6029726..6197536 (167.81 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	rs12722495
Chr	10
Position	6097283
Strand
P-Value	0.000

N/A

0.5

chr10: 6032917..6206221

MIR3155 MIR3155B IL2RA PFKFB3 RBM17

LD Region Feature File

LD File

0.4

N/A

chr10: 6032917..6185344

IL2RA RBM17

0.8

N/A

chr10: 6078553..6122382

IL2RA

1

N/A

chr10: 6096667..6097283

IL2RA

Marker	rs11594656
Chr	10
Position	6122009
Strand
P-Value	0.000

N/A

0.5

chr10: 6033301..6184190

IL2RA RBM17

LD Region Feature File

LD File

0.4

N/A

chr10: 6058323..6184190

IL2RA RBM17

0.8

N/A

chr10: 6095410..6122009

IL2RA

1

N/A

chr10: 6118770..6122009

Marker	rs12251307
Chr	10
Position	6123495
Strand
P-Value	1.33e-13

N/A

0.5

chr10: 6032917..6206221

MIR3155 MIR3155B IL2RA PFKFB3 RBM17

LD Region Feature File

LD File

0.4

N/A

chr10: 6048112..6185344

IL2RA RBM17

0.8

N/A

chr10: 6109676..6123716

1

N/A

chr10: 6123495..6123716

Publications: 8

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
Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.
Jin Y, Birlea SA, Fain PR, Gowan K, Riccardi SL, Holland PJ, Mailloux CM, Sufit AJ, Hutton SM, Amadi-Myers A, Bennett DC, Wallace MR, McCormack WT, Kemp EH, Gawkrodger DJ, Weetman AP, Picardo M, Leone G, Taïeb A, Jouary T, Ezzedine K, van Geel N, Lambert J, Overbeck A, Spritz RA
N Engl J Med. 2010
PubMed ID: 20410501
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
IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production.
Maier LM, Lowe CE, Cooper J, Downes K, Anderson DE, Severson C, Clark PM, Healy B, Walker N, Aubin C, Oksenberg JR, Hauser SL, Compston A, Sawcer S, International Multiple Sclerosis Genetics Consortium, De Jager PL, Wicker LS, Todd JA, Hafler DA
PLoS Genet. 2009
PubMed ID: 19119414
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
Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes.
Lowe CE, Cooper JD, Brusko T, Walker NM, Smyth DJ, Bailey R, Bourget K, Plagnol V, Field S, Atkinson M, Clayton DG, Wicker LS, Todd JA
Nat Genet. 2007
PubMed ID: 17676041
Risk alleles for multiple sclerosis identified by a genomewide study.
International Multiple Sclerosis Genetics Consortium, Hafler DA, Compston A, Sawcer S, Lander ES, Daly MJ, De Jager PL, de Bakker PI, Gabriel SB, Mirel DB, Ivinson AJ, Pericak-Vance MA, Gregory SG, Rioux JD, McCauley JL, Haines JL, Barcellos LF, Cree B, Oksenberg JR, Hauser SL
N Engl J Med. 2007
PubMed ID: 17660530
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
Wellcome Trust Case Control Consortium
Nature. 2007
PubMed ID: 17554300

Signal Clouds: Available

10p15.1