T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers

General Information: Available

Organism	Human
Points of Interest	rs6752770
Karyotype Band Location	2q32.2
Chromosomal Location (GRCh37)	Chr2:191888224-192030553
Region Size	0.14 Mb
Orthologous Regions	Mouse: Human 2q32.2 Orthologous Region Rat: Human 2q32.2 Orthologous Region
Genes in Region (1)	STAT4

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
rs111535990	dbSNP_134	191895798	+	D/G	STAT4	6775	707
rs149089413	dbSNP_134	191897833	+	R/Q	STAT4	6775	632
rs3024933	dbSNP_134	191898318	-	R/W	STAT4	6775	584
rs144091208	dbSNP_134	191898712	+	S/L	STAT4	6775	547
rs147007636	dbSNP_134	191900922	+	D/V	STAT4	6775	513
rs149621054	dbSNP_134	191900987	+	L/F	STAT4	6775	491
rs146386562	dbSNP_134	191903935	+	N/S	STAT4	6775	475
rs141331848	dbSNP_134	191904022	+	T/I	STAT4	6775	446
rs66818798	dbSNP_134	191905797	+		STAT4	6775	443
rs143642103	dbSNP_134	191926530	+	R/Q	STAT4	6775	320
rs142125913	dbSNP_134	191927591	+	E/K	STAT4	6775	280
rs35279173	dbSNP_134	191927624	-	L/I	STAT4	6775	269
rs113436186	dbSNP_134	191929537	+	N/D	STAT4	6775	260
rs61756200	dbSNP_134	191929596	+	R/Q	STAT4	6775	240
rs145218540	dbSNP_134	191929675	+	S/G	STAT4	6775	214
rs144713478	dbSNP_134	191931174	+	S/R	STAT4	6775	204
rs140675301	dbSNP_134	191937906	+	E/V	STAT4	6775	128
rs3024839	dbSNP_134	191940982	-	I/V	STAT4	6775	115

Non-Synonymous SNPs in region dbSNP134:

(Human) GRCh37 - chr2:191888224..192030553 (142.33 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	rs6752770
Chr	2
Position	191973563
Strand
P-Value	9.32e-06

N/A

0.5

chr2: 191973563..192005729

STAT4

LD Region Feature File

LD File

0.4

N/A

chr2: 191973563..191982205

STAT4

0.8

N/A

1

N/A

Publications: 7

STAT4 is a confirmed genetic risk factor for Sjögren's syndrome and could be involved in type 1 interferon pathway signaling.
Gestermann N, Mekinian A, Comets E, Loiseau P, Puechal X, Hachulla E, Gottenberg JE, Mariette X, Miceli-Richard C
Genes Immun. 2010
PubMed ID: 20535138
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 of systemic sclerosis identifies CD247 as a new susceptibility locus.
Radstake TR, Gorlova O, Rueda B, Martin JE, Alizadeh BZ, Palomino-Morales R, Coenen MJ, Vonk MC, Voskuyl AE, Schuerwegh AJ, Broen JC, van Riel PL, van 't Slot R, Italiaander A, Ophoff RA, Riemekasten G, Hunzelmann N, Simeon CP, Ortego-Centeno N, González-Gay MA, González-Escribano MF, Spanish Scleroderma Group, Airo P, van Laar J, Herrick A, Worthington J, Hesselstrand R, Smith V, de Keyser F, Houssiau F, Chee MM, Madhok R, Shiels P, Westhovens R, Kreuter A, Kiener H, de Baere E, Witte T, Padykov L, Klareskog L, Beretta L, Scorza R, Lie BA, Hoffmann-Vold AM, Carreira P, Varga J, Hinchcliff M, Gregersen PK, Lee AT, Ying J, Han Y, Weng SF, Amos CI, Wigley FM, Hummers L, Nelson JL, Agarwal SK, Assassi S, Gourh P, Tan FK, Koeleman BP, Arnett FC, Martin J, Mayes MD
Nat Genet. 2010
PubMed ID: 20383147
A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.
Gateva V, Sandling JK, Hom G, Taylor KE, Chung SA, Sun X, Ortmann W, Kosoy R, Ferreira RC, Nordmark G, Gunnarsson I, Svenungsson E, Padyukov L, Sturfelt G, Jönsen A, Bengtsson AA, Rantapää-Dahlqvist S, Baechler EC, Brown EE, Alarcón GS, Edberg JC, Ramsey-Goldman R, McGwin G, Reveille JD, Vilá LM, Kimberly RP, Manzi S, Petri MA, Lee A, Gregersen PK, Seldin MF, Rönnblom L, Criswell LA, Syvänen AC, Behrens TW, Graham RR
Nat Genet. 2009
PubMed ID: 19838195
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
Analysis of 17 autoimmune disease-associated variants in type 1 diabetes identifies 6q23/TNFAIP3 as a susceptibility locus.
Fung EY, Smyth DJ, Howson JM, Cooper JD, Walker NM, Stevens H, Wicker LS, Todd JA
Genes Immun. 2009
PubMed ID: 19110536
STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus.
Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, Behrens TW, de Bakker PI, Le JM, Lee HS, Batliwalla F, Li W, Masters SL, Booty MG, Carulli JP, Padyukov L, Alfredsson L, Klareskog L, Chen WV, Amos CI, Criswell LA, Seldin MF, Kastner DL, Gregersen PK
N Engl J Med. 2007
PubMed ID: 17804842

Signal Clouds: Available

2q32.2