T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers

General Information: Available

Organism	Human
Points of Interest	rs9653442; rs1160542
Karyotype Band Location	2q11.2
Chromosomal Location (GRCh37)	Chr2:100516689-101049115
Region Size	0.53 Mb
Orthologous Regions	Mouse: Human 2q11.2 Orthologous Region Mouse: Human 2q11.2 Orthologous Region Rat: Human 2q11.2 Orthologous Region
Genes in Region (4)	AFF3, CHST10, LOC150577, LONRF2

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
rs138223257	dbSNP_134	100623188	+	H/R	AFF3	3899	260
rs146038090	dbSNP_134	100623228	+	E/K	AFF3	3899	247
rs144169915	dbSNP_134	100623395	+	V/A	AFF3	3899	191
rs148995996	dbSNP_134	100623404	+	N/S	AFF3	3899	188
rs151087811	dbSNP_134	100623675	+	S/N	AFF3	3899	141
rs140526847	dbSNP_134	100623724	+	I/V	AFF3	3899	125
rs140364618	dbSNP_134	100623804	+	P/L	AFF3	3899	98
rs145368049	dbSNP_134	100625365	+	R/Q	AFF3	3899	28
rs140410536	dbSNP_134	100900770	+	R/I	LONRF2	164832	752
rs145912935	dbSNP_134	100900836	+	R/Q	LONRF2	164832	730
rs145836768	dbSNP_134	100900948	+	P/S	LONRF2	164832	693
rs115462523	dbSNP_134	100903419	+	L/S	LONRF2	164832	676
rs145208665	dbSNP_134	100903459	+	W/R	LONRF2	164832	663
rs76387809	dbSNP_134	100903495	+	A/T	LONRF2	164832	651
rs149460142	dbSNP_134	100903510	+	Y/H	LONRF2	164832	646
rs143848902	dbSNP_134	100906845	+	V/M	LONRF2	164832	599
rs111318889	dbSNP_134	100910695	+	A/T	LONRF2	164832	585
rs144370763	dbSNP_134	100910813	+	M/I	LONRF2	164832	545
rs150644363	dbSNP_134	100911925	+	I/V	LONRF2	164832	523
rs116702638	dbSNP_134	100915330	+	H/N	LONRF2	164832	482
rs138521209	dbSNP_134	100915389	+	T/M	LONRF2	164832	462
rs114250681	dbSNP_134	100915736	+	Q/P	LONRF2	164832	438
rs4851287	dbSNP_134	100915772	+	L/P	LONRF2	164832	426
rs115681175	dbSNP_134	100916221	+	D/H	LONRF2	164832	409
rs114656965	dbSNP_134	100916257	+	A/T	LONRF2	164832	397
rs116242293	dbSNP_134	100916269	+	T/A	LONRF2	164832	393
rs77688575	dbSNP_134	100917228	+	S/P	LONRF2	164832	315
rs116221236	dbSNP_134	100917240	+	E/K	LONRF2	164832	311
rs145197030	dbSNP_134	100919481	+	L/F	LONRF2	164832	275
rs112821767	dbSNP_134	100925595	+	C/R	LONRF2	164832	258
rs142007035	dbSNP_134	100925627	+	Y/C	LONRF2	164832	247
rs114378605	dbSNP_134	100925637	+	M/L	LONRF2	164832	244
rs74177694	dbSNP_134	100938226	+	D/E	LONRF2	164832	110
rs74177696	dbSNP_134	100938481	+	Q/H	LONRF2	164832	25
rs142936641	dbSNP_134	100938486	+	A/T	LONRF2	164832	24
rs147487716	dbSNP_134	101009760	+	E/K	CHST10	9486	340
rs143836571	dbSNP_134	101009765	+	R/H	CHST10	9486	338
rs139810982	dbSNP_134	101009789	+	R/Q	CHST10	9486	330
rs140261702	dbSNP_134	101009838	+	V/M	CHST10	9486	314
rs147076164	dbSNP_134	101009870	+	V/A	CHST10	9486	303
rs3748932	dbSNP_134	101010006	-	D/N	CHST10	9486	258
rs144032903	dbSNP_134	101010054	+	R/C	CHST10	9486	242
rs149656297	dbSNP_134	101010083	+	T/I	CHST10	9486	232
rs12476171	dbSNP_134	101010105	+	Y/N	CHST10	9486	225
rs149006389	dbSNP_134	101010153	+	F/V	CHST10	9486	209
rs138468060	dbSNP_134	101010221	+	F/Y	CHST10	9486	186
rs146601037	dbSNP_134	101011971	+	R/Q	CHST10	9486	178
rs141419211	dbSNP_134	101011988	+	D/E	CHST10	9486	172
rs57227647	dbSNP_134	101012068	+	S/P	CHST10	9486	146
rs148626049	dbSNP_134	101014527	+	N/K	CHST10	9486	90
rs142086595	dbSNP_134	101014586	+	P/S	CHST10	9486	71
rs138889445	dbSNP_134	101019117	+	V/A	CHST10	9486	34
rs148953500	dbSNP_134	101023061	+	T/M	CHST10	9486	26
rs141878987	dbSNP_134	101023070	+	K/T	CHST10	9486	23
rs35177621	dbSNP_134	101023080	-	V/L	CHST10	9486	20
rs150069978	dbSNP_134	101023110	+	A/T	CHST10	9486	10

Non-Synonymous SNPs in region dbSNP134:

(Human) GRCh37 - chr2:100516689..101049115 (532.43 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	rs9653442
Chr	2
Position	100825367
Strand
P-Value	7.04e-07

N/A

0.5

chr2: 100564115..101033697

LOC150577 LONRF2 AFF3 CHST10

LD Region Feature File

LD File

0.4

N/A

chr2: 100576807..100882502

LOC150577 AFF3

0.8

N/A

chr2: 100732845..100835734

LOC150577 AFF3

1

N/A

chr2: 100806514..100832155

LOC150577

Marker	rs1160542
Chr	2
Position	100832155
Strand
P-Value	7.21e-07

N/A

0.5

chr2: 100564115..101033697

LOC150577 LONRF2 AFF3 CHST10

LD Region Feature File

LD File

0.4

N/A

chr2: 100576807..100882502

LOC150577 AFF3

0.8

N/A

chr2: 100732845..100835734

LOC150577 AFF3

1

N/A

chr2: 100806514..100832155

LOC150577

Publications: 5

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
Association of the AFF3 gene and IL2/IL21 gene region with juvenile idiopathic arthritis.
Hinks A, Eyre S, Ke X, Barton A, Martin P, Flynn E, Packham J, Worthington J, Childhood Arthritis Prospective Study, UKRAG Consortium, BSPAR Study Group, Thomson W
Genes Immun. 2010
PubMed ID: 20072139
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
Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes.
Barton A, Eyre S, Ke X, Hinks A, Bowes J, Flynn E, Martin P, YEAR Consortium, BIRAC Consortium, Wilson AG, Morgan AW, Emery P, Steer S, Hocking LJ, Reid DM, Harrison P, Wordsworth P, Thomson W, Worthington J
Hum Mol Genet. 2009
PubMed ID: 19359276

Signal Clouds: Available

2q11.2