T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers

General Information: Available

Organism	Human
Points of Interest	rs3024505
Karyotype Band Location	1q32.1
Chromosomal Location (GRCh37)	Chr1:206802440-207049831
Region Size	0.25 Mb
Orthologous Regions	Mouse: Human 1q32.1 Orthologous Region Mouse: Human 1q32.1 Orthologous Region Rat: Human 1q32.1 Orthologous Region
Genes in Region (5)	DYRK3, IL10, IL19, IL20, MAPKAPK2

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
rs150928044	dbSNP_134	206811042	+	K/R	DYRK3	8444	42
rs141657852	dbSNP_134	206811048	+	P/L	DYRK3	8444	44
rs139024809	dbSNP_134	206820790	+	M/L	DYRK3	8444	83
rs150089955	dbSNP_134	206820793	+	K/E	DYRK3	8444	84
rs142230353	dbSNP_134	206821032	+	I/M	DYRK3	8444	163
rs78290906	dbSNP_134	206821111	+	Y/D	DYRK3	8444	190
rs55721647	dbSNP_134	206821123	+	D/Y	DYRK3	8444	194
rs35259411	dbSNP_134	206821129	+	A/T	DYRK3	8444	196
rs56079317	dbSNP_134	206821238	+	R/Q	DYRK3	8444	232
rs56374404	dbSNP_134	206821285	+	R/C	DYRK3	8444	248
rs146834595	dbSNP_134	206821286	+	R/H	DYRK3	8444	248
rs55766763	dbSNP_134	206821363	+	M/L	DYRK3	8444	274
rs17851298	dbSNP_134	206821481	+	R/H	DYRK3	8444	313
rs55982485	dbSNP_134	206821525	+	K/E	DYRK3	8444	328
rs146921314	dbSNP_134	206821533	+	K/N	DYRK3	8444	330
rs35968381	dbSNP_134	206821585	+	R/P	DYRK3	8444	348
rs1129431	dbSNP_134	206821595	+	T/I	DYRK3	8444	351
rs77980920	dbSNP_134	206821691	+	G/E	DYRK3	8444	383
rs1129432	dbSNP_134	206821729	+	G/R	DYRK3	8444	396
rs144725167	dbSNP_134	206821735	+	I/V	DYRK3	8444	398
rs140186287	dbSNP_134	206821809	+	M/I	DYRK3	8444	422
rs75807326	dbSNP_134	206821835	+	K/R	DYRK3	8444	431
rs35021645	dbSNP_134	206821856	+	R/H	DYRK3	8444	438
rs145519561	dbSNP_134	206821952	+	R/H	DYRK3	8444	470
rs137901718	dbSNP_134	206822189	+	Q/R	DYRK3	8444	549
rs141266804	dbSNP_134	206822264	+	N/S	DYRK3	8444	574
rs146073998	dbSNP_134	206858726	+	G/V	MAPKAPK2	9261	51
rs151079567	dbSNP_134	206902080	+	R/L	MAPKAPK2	9261	102
rs141946496	dbSNP_134	206902131	+	R/Q	MAPKAPK2	9261	119
rs35671930	dbSNP_134	206902774	+	A/G	MAPKAPK2	9261	173
rs149638565	dbSNP_134	206902800	+	I/V	MAPKAPK2	9261	182
rs140901506	dbSNP_134	206903357	+	I/T	MAPKAPK2	9261	202
rs74538056	dbSNP_134	206903389	+	E/K	MAPKAPK2	9261	213
rs139297717	dbSNP_134	206903392	+		MAPKAPK2	9261	214
rs142063401	dbSNP_134	206904578	+	N/S	MAPKAPK2	9261	288
rs142025224	dbSNP_134	206905223	+	R/W	MAPKAPK2	9261	340
rs140988938	dbSNP_134	206905263	+	K/R	MAPKAPK2	9261	353
rs142726516	dbSNP_134	206941989	+	R/X	IL10	3586	177
rs146520891	dbSNP_134	206942066	+	E/G	IL10	3586	151
rs150423829	dbSNP_134	206944287	+	N/Y	IL10	3586	115
rs149143243	dbSNP_134	206944314	+	K/Q	IL10	3586	106
rs141219090	dbSNP_134	206945723	+	P/S	IL10	3586	20
rs139073251	dbSNP_134	206945725	+	S/N	IL10	3586	19
rs145922845	dbSNP_134	206945738	+	G/R	IL10	3586	15
rs143483780	dbSNP_134	206972262	+	P/L	IL19	29949	8
rs148873337	dbSNP_134	206972264	+	H/Y	IL19	29949	9
rs76513170	dbSNP_134	206972307	+	H/P	IL19	29949	23
rs141906021	dbSNP_134	206972348	+	R/W	IL19	29949	37
rs149618619	dbSNP_134	207010072	+	N/S	IL19	29949	60
rs144719259	dbSNP_134	207015914	+	D/N	IL19	29949	199
rs2243191	dbSNP_134	207015957	+	F/S	IL19	29949	213
rs151121611	dbSNP_134	207039288	+	G/R	IL20	50604	31
rs148039496	dbSNP_134	207039345	+	R/G	IL20	50604	50
rs142487972	dbSNP_134	207039653	+	D/Y	IL20	50604	57
rs141716593	dbSNP_134	207039838	+	R/X	IL20	50604	79
rs35856950	dbSNP_134	207039923	-	R/Q	IL20	50604	107
rs150575323	dbSNP_134	207039973	+	R/W	IL20	50604	124
rs144756065	dbSNP_134	207040730	+	H/R	IL20	50604	127
rs139947556	dbSNP_134	207041833	+	L/P	IL20	50604	152
rs151309569	dbSNP_134	207041894	+	M/I	IL20	50604	172

Non-Synonymous SNPs in region dbSNP134:

(Human) GRCh37 - chr1:206802440..207049831 (247.39 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	rs3024505
Chr	1
Position	206939904
Strand
P-Value	2.20e-06

N/A

0.5

chr1: 206866387..207148043

IL24 IL19 IL10 IL20 PIGR FCAMR FAIM3 MAPKAPK2

LD Region Feature File

LD File

0.4

N/A

chr1: 206933517..207031859

IL19 IL10

0.8

N/A

chr1: 206939904..206955041

IL10

1

N/A

chr1: 206939904..206942413

IL10

Publications: 5

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
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R, Anderson CA, Bis JC, Bumpstead S, Ellinghaus D, Festen EM, Georges M, Green T, Haritunians T, Jostins L, Latiano A, Mathew CG, Montgomery GW, Prescott NJ, Raychaudhuri S, Rotter JI, Schumm P, Sharma Y, Simms LA, Taylor KD, Whiteman D, Wijmenga C, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Cohen A, Colombel JF, Cottone M, Stronati L, Denson T, De Vos M, D'Inca R, Dubinsky M, Edwards C, Florin T, Franchimont D, Gearry R, Glas J, Van Gossum A, Guthery SL, Halfvarson J, Verspaget HW, Hugot JP, Karban A, Laukens D, Lawrance I, Lemann M, Levine A, Libioulle C, Louis E, Mowat C, Newman W, Panés J, Phillips A, Proctor DD, Regueiro M, Russell R, Rutgeerts P, Sanderson J, Sans M, Seibold F, Steinhart AH, Stokkers PC, Torkvist L, Kullak-Ublick G, Wilson D, Walters T, Targan SR, Brant SR, Rioux JD, D'Amato M, Weersma RK, Kugathasan S, Griffiths AM, Mansfield JC, Vermeire S, Duerr RH, Silverberg MS, Satsangi J, Schreiber S, Cho JH, Annese V, Hakonarson H, Daly MJ, Parkes M
Nat Genet. 2010
PubMed ID: 21102463
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
Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility.
Franke A, Balschun T, Karlsen TH, Sventoraityte J, Nikolaus S, Mayr G, Domingues FS, Albrecht M, Nothnagel M, Ellinghaus D, Sina C, Onnie CM, Weersma RK, Stokkers PC, Wijmenga C, Gazouli M, Strachan D, McArdle WL, Vermeire S, Rutgeerts P, Rosenstiel P, Krawczak M, Vatn MH, IBSEN study group, Mathew CG, Schreiber S
Nat Genet. 2008
PubMed ID: 18836448

Signal Clouds: Available

1q32.1