T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers

General Information: Available

Organism	Human
Points of Interest	rs2069763; rs4505848
Karyotype Band Location	4q27
Chromosomal Location (GRCh37)	Chr4:122909415-123614282
Region Size	0.70 Mb
Orthologous Regions	Mouse: Human 4q27 Orthologous Region Rat: Human 4q27 Orthologous Region
Genes in Region (4)	ADAD1, IL2, IL21, KIAA1109

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
rs35291174	dbSNP_134	123108626	+	W/V	KIAA1109	84162	196
rs76912349	dbSNP_134	123108631	+	R/S	KIAA1109	84162	197
rs76417860	dbSNP_134	123109066	+	G/E	KIAA1109	84162	215
rs74643640	dbSNP_134	123113428	+	S/G	KIAA1109	84162	316
rs118054489	dbSNP_134	123113464	+	C/R	KIAA1109	84162	328
rs78972292	dbSNP_134	123118355	+	T/K	KIAA1109	84162	405
rs72925924	dbSNP_134	123130479	+	V/I	KIAA1109	84162	640
rs77013769	dbSNP_134	123132159	+	P/Q	KIAA1109	84162	719
rs138206785	dbSNP_134	123132217	+	Y/X	KIAA1109	84162	738
rs140431038	dbSNP_134	123140520	+	M/K	KIAA1109	84162	758
rs78196909	dbSNP_134	123145825	+	A/V	KIAA1109	84162	929
rs6848868	dbSNP_134	123150286	+	I/T	KIAA1109	84162	978
rs76255955	dbSNP_134	123156013	+	G/C	KIAA1109	84162	1137
rs78724860	dbSNP_134	123159501	+	A/P	KIAA1109	84162	1277
rs76067900	dbSNP_134	123160682	+	E/G	KIAA1109	84162	1282
rs75959726	dbSNP_134	123161078	+	P/Q	KIAA1109	84162	1414
rs111840903	dbSNP_134	123161375	+	I/T	KIAA1109	84162	1513
rs80142599	dbSNP_134	123161395	+	P/T	KIAA1109	84162	1520
rs75923324	dbSNP_134	123167847	+	C/R	KIAA1109	84162	1732
rs56363411	dbSNP_134	123171659	+	D/E	KIAA1109	84162	1951
rs75111065	dbSNP_134	123175434	+	I/V	KIAA1109	84162	2003
rs74664188	dbSNP_134	123175468	+	T/N	KIAA1109	84162	2014
rs45510500	dbSNP_134	123179900	+	R/W	KIAA1109	84162	2222
rs78442674	dbSNP_134	123184597	+	G/E	KIAA1109	84162	2328
rs74701285	dbSNP_134	123184753	+	T/I	KIAA1109	84162	2380
rs77991335	dbSNP_134	123185416	+	P/H	KIAA1109	84162	2384
rs146497178	dbSNP_134	123185528	+		KIAA1109	84162	2421
rs148822396	dbSNP_134	123192228	+	T/S	KIAA1109	84162	2517
rs45608936	dbSNP_134	123192240	+	S/R	KIAA1109	84162	2521
rs76824913	dbSNP_134	123192392	+	L/F	KIAA1109	84162	2571
rs115036597	dbSNP_134	123202841	+	M/I	KIAA1109	84162	2983
rs34234630	dbSNP_134	123207826	+	G/G	KIAA1109	84162	3056
rs79067453	dbSNP_134	123207867	+	V/G	KIAA1109	84162	3070
rs147165699	dbSNP_134	123207880	+	D/E	KIAA1109	84162	3074
rs45511998	dbSNP_134	123207926	+	R/S	KIAA1109	84162	3090
rs76336753	dbSNP_134	123225959	+	Q/K	KIAA1109	84162	3165
rs74831924	dbSNP_134	123225965	+	T/P	KIAA1109	84162	3167
rs35465874	dbSNP_134	123230458	+	L/F	KIAA1109	84162	3364
rs78266497	dbSNP_134	123239373	+	V/G	KIAA1109	84162	3581
rs62321684	dbSNP_134	123239423	+	R/W	KIAA1109	84162	3598
rs80118871	dbSNP_134	123245617	+	Y/X	KIAA1109	84162	3610
rs79101308	dbSNP_134	123245628	+	Y/S	KIAA1109	84162	3614
rs149346321	dbSNP_134	123249358	+	P/T	KIAA1109	84162	3699
rs75040092	dbSNP_134	123249392	+	P/L	KIAA1109	84162	3710
rs115275370	dbSNP_134	123249462	+	E/D	KIAA1109	84162	3733
rs77586875	dbSNP_134	123252539	+	R/C	KIAA1109	84162	3770
rs78864045	dbSNP_134	123265655	+	F/L	KIAA1109	84162	4224
rs2306369	dbSNP_134	123268859	+	T/A	KIAA1109	84162	4352
rs80304474	dbSNP_134	123269728	+	L/P	KIAA1109	84162	4379
rs34290998	dbSNP_134	123270399	+	G/E	KIAA1109	84162	4456
rs141798602	dbSNP_134	123275109	+	P/S	KIAA1109	84162	4748
rs10017270	dbSNP_134	123277001	+	T/A	KIAA1109	84162	4786
rs35817975	dbSNP_134	123283255	+	F/F	KIAA1109	84162	4957
rs13106366	dbSNP_134	123301235	+	N/T	ADAD1	132612	4
rs139643444	dbSNP_134	123301250	+	Q/R	ADAD1	132612	9
rs145257122	dbSNP_134	123301267	+	S/G	ADAD1	132612	15
rs13106730	dbSNP_134	123301310	+	A/G	ADAD1	132612	29
rs13106561	dbSNP_134	123301312	+	T/P	ADAD1	132612	30
rs114035595	dbSNP_134	123301381	+	V/I	ADAD1	132612	53
rs62000437	dbSNP_134	123302179	+	L/V	ADAD1	132612	69
rs76510705	dbSNP_134	123302209	+	P/T	ADAD1	132612	79
rs140553056	dbSNP_134	123302240	+	K/T	ADAD1	132612	89
rs146584990	dbSNP_134	123302249	+	R/H	ADAD1	132612	92
rs74486351	dbSNP_134	123302255	+	E/G	ADAD1	132612	94
rs78087673	dbSNP_134	123305104	+	R/Q	ADAD1	132612	171
rs113377246	dbSNP_134	123317479	+	R/H	ADAD1	132612	224
rs75377620	dbSNP_134	123317520	+	I/L	ADAD1	132612	238
rs150494354	dbSNP_134	123329105	+	N/S	ADAD1	132612	256
rs138644891	dbSNP_134	123329182	+	L/F	ADAD1	132612	282
rs143785712	dbSNP_134	123332504	+	M/V	ADAD1	132612	326
rs147371432	dbSNP_134	123336536	+	D/N	ADAD1	132612	418
rs139575725	dbSNP_134	123336569	+	I/V	ADAD1	132612	429
rs142214661	dbSNP_134	123342477	+	R/W	ADAD1	132612	517
rs76874072	dbSNP_134	123342486	+	L/M	ADAD1	132612	520
rs55924141	dbSNP_134	123350835	+	Q/X	ADAD1	132612	558
rs144212663	dbSNP_134	123350875	+	I/T	ADAD1	132612	571
rs146270985	dbSNP_134	123374990	+	L/F	IL2	3558	76
rs146566026	dbSNP_134	123377467	+	M/I	IL2	3558	43
rs3087209	dbSNP_134	123377483	-	L/R	IL2	3558	38
rs77806995	dbSNP_134	123377516	+	T/K	IL2	3558	27
rs145809792	dbSNP_134	123536860	+	G/R	IL21	59067	113
rs148990483	dbSNP_134	123536862	+	A/V	IL21	59067	112
rs143807041	dbSNP_134	123536880	+	K/R	IL21	59067	106
rs141748932	dbSNP_134	123542048	+	R/H	IL21	59067	40
rs137963779	dbSNP_134	123542072	+	Q/L	IL21	59067	32

Non-Synonymous SNPs in region dbSNP134:

(Human) GRCh37 - chr4:122909415..123614282 (704.87 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	rs2069763
Chr	4
Position	123377482
Strand
P-Value	0.000

N/A

0.5

chr4: 122901933..123564458

ADAD1 IL2 IL21 KIAA1109

LD Region Feature File

LD File

0.4

N/A

chr4: 123026869..123557236

ADAD1 IL2 IL21 KIAA1109

0.8

N/A

chr4: 123067808..123475979

ADAD1 IL2 KIAA1109

1

N/A

chr4: 123067808..123377482

ADAD1 IL2 KIAA1109

Marker	rs4505848
Chr	4
Position	123132492
Strand
P-Value	4.68e-13

N/A

0.5

chr4: 122901933..123564458

ADAD1 IL2 IL21 KIAA1109

LD Region Feature File

LD File

0.4

N/A

chr4: 123026869..123557236

ADAD1 IL2 IL21 KIAA1109

0.8

N/A

chr4: 123067808..123475979

ADAD1 IL2 KIAA1109

1

N/A

chr4: 123067808..123377482

ADAD1 IL2 KIAA1109

Publications: 6

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagacé C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Colombel JF, Denson LA, De Vos M, Dubinsky M, Edwards C, Ellinghaus D, Fehrmann RS, Floyd JA, Florin T, Franchimont D, Franke L, Georges M, Glas J, Glazer NL, Guthery SL, Haritunians T, Hayward NK, Hugot JP, Jobin G, Laukens D, Lawrance I, Lémann M, Levine A, Libioulle C, Louis E, McGovern DP, Milla M, Montgomery GW, Morley KI, Mowat C, Ng A, Newman W, Ophoff RA, Papi L, Palmieri O, Peyrin-Biroulet L, Panés J, Phillips A, Prescott NJ, Proctor DD, Roberts R, Russell R, Rutgeerts P, Sanderson J, Sans M, Schumm P, Seibold F, Sharma Y, Simms LA, Seielstad M, Steinhart AH, Targan SR, van den Berg LH, Vatn M, Verspaget H, Walters T, Wijmenga C, Wilson DC, Westra HJ, Xavier RJ, Zhao ZZ, Ponsioen CY, Andersen V, Torkvist L, Gazouli M, Anagnou NP, Karlsen TH, Kupcinskas L, Sventoraityte J, Mansfield JC, Kugathasan S, Silverberg MS, Halfvarson J, Rotter JI, Mathew CG, Griffiths AM, Gearry R, Ahmad T, Brant SR, Chamaillard M, Satsangi J, Cho JH, Schreiber S, Daly MJ, Barrett JC, Parkes M, Annese V, Hakonarson H, Radford-Smith G, Duerr RH, Vermeire S, Weersma RK, Rioux JD
Nat Genet. 2011
PubMed ID: 21297633
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
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
A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21.
van Heel DA, Franke L, Hunt KA, Gwilliam R, Zhernakova A, Inouye M, Wapenaar MC, Barnardo MC, Bethel G, Holmes GK, Feighery C, Jewell D, Kelleher D, Kumar P, Travis S, Walters JR, Sanders DS, Howdle P, Swift J, Playford RJ, McLaren WM, Mearin ML, Mulder CJ, McManus R, McGinnis R, Cardon LR, Deloukas P, Wijmenga C
Nat Genet. 2007
PubMed ID: 17558408
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, Bailey R, Nejentsev S, Field SF, Payne F, Lowe CE, Szeszko JS, Hafler JP, Zeitels L, Yang JH, Vella A, Nutland S, Stevens HE, Schuilenburg H, Coleman G, Maisuria M, Meadows W, Smink LJ, Healy B, Burren OS, Lam AA, Ovington NR, Allen J, Adlem E, Leung HT, Wallace C, Howson JM, Guja C, Ionescu-Tîrgovişte C, Genetics of Type 1 Diabetes in Finland, Simmonds MJ, Heward JM, Gough SC, Wellcome Trust Case Control Consortium, Dunger DB, Wicker LS, Clayton DG
Nat Genet. 2007
PubMed ID: 17554260

Signal Clouds: Available

4q27