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Type 1 Diabetes Loci

Overview
 

A table of human loci associated with T1D. Cytogenetic bands are defined using data from UCSC genome browser, protein coding and non-coding genes were extracted from EnsEMBL v52. Loci were defined using the method described in Barrett et al. SNPs were extracted from dbSNP129. The 'Immune Diseases' column was populated by including studies where a convincing p-value (P < 5 x 10-8) was available for a large study and in T1D the combined p-value was less that 10-4 (Smyth DJ et al.). It is expected that this column will change considerably in the near future as more results become publicly available. The SNPs defined here are the strongest associated in a given LD region.


Version 1, 2009-02-12 09:52:11 		 
 
T1D Loci
 

Last updated 27th January 2010

The table below is available for download as a text file or pdf file.
Chromosome
SNP
OR Minor Allele
(95% CI)
MAF
Immune Diseases
Causal Gene Candidate
Protein Coding Genes in LD Region
Non-Coding Genes in LD Region
Protein Coding Genes +/-0.5Mb of Region
Non-Coding Genes +/-0.5Mb of Region
Publications
1
2.05 (1.90-2.20)
0.142‡
 AITD21, Crohn's21, MS21, RA35,37,38, SLE21 MAGI3, PHTF1, RSBN1, PTPN22, HIPK1, C1orf178, AP4B1, DCLRE1B, OLFML3, SYT6 AL391058.25, RP11-473L1.1, RP4-730K3.3, RP4-590F24.2 SLC16A1, LRIG2, SYT6, TRIM33, BCAS2, DENND2C RP3-522D1.2, RP4-580L15.2, RP11-389O22.3, RP11-389O22.4, RPS15P1, RP4-591B8.2, RP11-343L14.1, Y_RNA, RP11-343L14.2 Bottini N et al. (PMID:15004560)
2
SLE
LAMC2, NMNAT2, SMG7, NCF2 RP11-548N1.1 NPL, DHX9, C1orf14, LAMC1, LAMC2, NCF2, ARPC5, RGL1, APOBEC4, GLT25D2, TSEN15 RP11-505O17.3, 5S_rRNA, RP11-505O17.1, KRT18P28, U6
3
0.89 (0.84-0.95)
0.182†
 Coeliac22
RGS1 RGS18, RGS21, RGS13, RGS2, UCHL5, TROVE2 RP11-142L4.3, RP11-142L4.2, AL136987.11, RP11-92K2.2, RP3-419C19.3, RP3-419C19.2, 7SK, RP11-101E13.1 Smyth DJ et al. (PMID:19073967)
4
0.84 (0.77-0.91)
0.169†
 Crohn's18, SLE
DYRK3, MAPKAPK2, IL10, IL19, IL20 RP11-343H5.4, Y_RNA AVPR1B, C1orf186, CTSE, SRGAP2, IKBKE, RASSF5, LGTN, DYRK3, IL24, FAIM3, PIGR, FCAMR, C1orf116, YOD1, PFKFB2, C4BPB, C4BPA, CD55 RP11-421E17.4, RP11-534L20.4, RPL13AP8, AC098935.2-1, AC098935.2-2, RP11-164O23.5, RP11-164O23.6, RP11-6J21.1 Barrett JC et al. (PMID:19430480)
5
JIA1
AFF3, LONRF2, CHST10 AC012493.9 REV1, AFF3, NMS, PDCL3, NPAS2 AC018690.5, AC068538.8
1.11 (1.07-1.16)
0.464‡
 RA9
6
0.83 (0.72-0.96)
0.221†
 Coeliac13,22 IL1RL2, IL1RL1, IL18R1, IL18RAP, SLC9A4 AC007248.4 MAP4K4, IL1R2, IL1R1, IL1RL2, SLC9A2, MFSD9, TMEM182 AC007239.3 Smyth DJ et al. (PMID:19073967)
7
0.86 (0.82-0.90)
0.400†
 AITD33, SLE GCG, FAP, IFIH1, GCA, KCNH7 5S_rRNA SLC4A10, DPP4, KCNH7 Smyth DJ et al. (PMID:16699517)
8
1.11
SLE STAT4 U6 TMEM194B, NAB1, GLS, STAT1, MYO1B AC108047.4, AC068056.7 Fung EY et al. (PMID:19110536)
1.10 (1.04-1.15)
0.240†
 RA43, SLE43
9
0.88 (0.83-0.93)
0.452†
 JIA1, RA36 CTLA4, ICOS ABI2, RAPH1, CD28, ICOS AC080075.7, AC125238.5-1, AC125238.5-2, AC010138.6-1, U6 Nistico L et al. (PMID:8817351), Smyth DJ et al. (PMID:19073967), Ueda H et al. (PMID:12724780)
10
FYCO1, CXCR6, XCR1, CCR1, CCR3, CCR2, CCR5, CCRL2, LTF, RTP3, LRRC2, TDGF1 LARS2, LIMD1, SACM1L, SLC6A20, LZTFL1, CCR9, FYCO1, ALS2CL, TMIE, TSP50, AC109583.2, MYL3, PTH1R, CCDC12, SETD2 SRP_euk_arch, Y_RNA, AC104304.2 Smyth DJ et al. (PMID:19073967)
0.85 (0.80-0.92)
0.119†
 Coeliac14
11
1.09 (1.02-1.17)
0.299†
SLC34A2, AC092436.5-6, AC133961.3, RBPSUH, CCKAR, TBC1D19 AC092436.5-1, AC092436.5-2, AC092436.5-3, AC092436.5-4, AC092436.5-5 Barrett JC et al. (PMID:19430480)
12
1.13 (1.08-1.18)
KIAA1109, ADAD1, IL2, IL21 AC097533.1, AC097533.2 ANXA5, TMEM155, EXOSC9, CCNA2, BBS7, TRPC3, BBS12, FGF2, NUDT6, SPATA5 AC079341.6, AC108930.3, AC053545.4, AC109357.3 Todd JA et al. (PMID:17554260), Cooper JD et al. (PMID:18978792)
13
0.89 (0.84-0.94)
JIA1, MS28 SPEF2, IL7R, CAPSL, UGT3A1, UGT3A2 SPEF2, UGT3A2, LMBRD2, SKP2, C5orf33, RANBP3L U3, hsa-mir-580, U6, 5S_rRNA Todd JA et al. (PMID:17554260)
14
AITD, Coeliac14, MS11, RA, SLE
,
Too many to list.
Please see GBrowse or the MHC Overview for more details.
Nejentsev S et al. (PMID:18004301)
15
1.13 (1.09-1.18)
0.465†
 BACH2 RP3-453I5.2 ANKRD6, LYRM2, MDN1, CASP8AP2, GJA10, BACH2, MAP3K7 RP11-29C12.1, RP11-63K6.1, AL353692.14-1, Y_RNA, RP11-63K6.4, RP11-63K6.5, Y_RNA, 7SK, AL121787.22-1 Cooper JD et al. (PMID:18978792)
16
1.17 (1.10-1.24)
0.452†
C6orf173 AC020559.4, hsa-mir-588, U6, RP11-162L10.1, RP11-753G20.1, RP1-179E13.1 HEY2, ESNA1, HINT3, TRMT11, RSPO3, RNF146, ECHDC1, C6orf174, AL096711.9, C6orf58 AL136163.15-1, 7SK, AL035689.26, AL109939.13-1, AL109939.13-2, RP3-351K20.4, RP1-177A13.1, RP3-403A15.1 Barrett JC et al. (PMID:19430480)
17
0.90 (0.86-0.95)
0.270†
 RA8,12, SLE12
TNFAIP3 RP11-95M15.2, Y_RNA, RP11-240M16.2 IL22RA2, IFNGR1, OLIG3, PERP, KIAA1244, PBOV1, HEBP2 AL023580.1, RP3-422G23.3, RP3-422G23.2 Fung EY et al. (PMID:19110536)
1.09 (1.04-1.15)
0.220†
 RA8,12,31, SLE12
18
0.92 (0.88-0.96)
0.437†
 Coeliac14,22 C6orf99, RSPH3, TAGAP AL627422.12-1, U6 TULP4, TMEM181, DYNLT1, SYTL3, VIL2, OSTCL, C6orf99, FNDC1 AL360169.17-1, AL360169.17-2, SRP_euk_arch, RP11-107N4.1, RP11-114M11.2, RP11-507C10.4, RP3-393E18.1 Smyth DJ et al. (PMID:19073967)
19
0.88 (0.82-0.94)
0.238†
AC003999.3, SKAP2, HOXA1, HOXA2, HOXA3, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9 AC073472.6-1, AC073472.6-2, AC004079.1-1, AC004079.1-2 NFE2L3, HNRPA2B1, CBX3, SNX10, KIAA0087, HOXA9, HOXA10, HOXA11, HOXA13, EVX1, HIBADH AC004540.1, hsa-mir-196b, AC004996.1, AC004996.1, AC073150.7-1, AC073150.7-2, AC007130.2 Barrett JC et al. (PMID:19430480)
20
0.77 (0.67-0.90)
0.047†
COBL SNORA4 IKZF1, FIGNL1, DDC, GRB10 AC124014.3, U6, AC006478.2 Barrett JC et al. (PMID:19430480)
21
0.88 (0.83-0.93)
0.502†
 GLIS3 GLIS3, SLC1A1, C9orf68, PPAPDC2, CDC37L1, AK3, RCL1 AL162419.34-1, U6, RP11-6J24.3, RP11-307I14.2, SSU_rRNA_5, RP11-307I14.3 Barrett JC et al. (PMID:19430480)
22
0.87 (0.82-0.92)
0.246†
 MS11, SLE10 IL2RA, RBM17, PFKFB3 AL137186.18, AL157395.17-1, 7SK ASB13, C10orf18, GDI2, ANKRD16, FBXO18, IL15RA, PFKFB3, AL137145.13-2, PRKCQ RP11-336A10.7, SRP_euk_arch, AL365356.13-1, AL157395.17-2, RP11-298K24.2 Lowe CE et al. (PMID:17676041)
0.62 (0.57-0.68)
0.113†
23
0.84 (0.79-0.90)
0.242‡
PRKCQ FBXO18, IL15RA, IL2RA, RBM17, PFKFB3, AL137145.13-2, PRKCQ AL137186.18, AL157395.17-1, 7SK, AL157395.17-2, RP11-298K24.2 Cooper JD et al. (PMID:18978792)
0.88 (0.83-0.93)
0.187†
24
IBD4
ZMIZ1 ZMIZ1, PPIF, ZCCHC24, SFTPA2, SFTPA1, FAM22B RP11-342M3.2, EIF5AP1, RP11-589B3.1, BX248123.5, RP11-589B3.3, RP11-119F19.4
25
0.75 (0.70-0.80)
0.285†
RNLS AFDC1, PTEN, C10orf59, LIPJ, LIPF, LIPK, LIPN, LIPM, ANKRD22, STAMBPL1, AL157394.15, ACTA2, FAS AC022016.7-1, AC022016.7-2, RP11-380G5.3, SNORD74, RP11-380G5.4, Y_RNA, RPL7P34, RP11-186O14.5, RP11-186O14.4, RP11-399O19.6 Barrett JC et al. (PMID:19430480)
26
0.42 (0.41-0.46)
IGF2, IGF2AS, INS, TH, ASCL2 hsa-mir-483 DUSP8, KRTAP5-1, KRTAP5-2, KRTAP5-3, KRTAP5-4, KRTAP5-5, KRTAP5-6, CTSD, SYT8, TNNI2, LSP1, TNNT3, MRPL23, TSPAN32, CD81, TSSC4, TRPM5, KCNQ1 AP006285.2-1, AC139143.1, AC139143.2, hsa-mir-675, U6, AC129929.5-1, Y_RNA, AC013791.2 Bell GI et al. (PMID:6363172)
0.317‡
27
1.09 (1.02-1.16)
0.368†
AC006432.15-2, KLRB1, CLEC2D, CLECL1, CD69 U6 KLRG1, A2M, PZP, AC137766.2, DDX12, KLRF1, CLEC2B, CLEC12A, CLEC1B, CLEC9A, CLEC1A, CLEC7A, OLR1, C12orf59, GABARAPL3, KLRD1 AC007436.1-2, AC007436.1-1, AC007436.1-3, SNORA75, SNORA75, AC091814.10, 7SK Barrett JC et al. (PMID:19430480)
28
1.31 (1.22-1.34)
0.340†
 SILV, CDK2, RAB5B, SUOX, IKZF4, RPS26P53, ERBB3, PA2G4P4, ZC3H10, FAM62A, MYL6B, MYL6, SMARCC2, RNF41, OBFC2B, SLC39A5, ANKRD52, COQ10A, CS, CNPY2, PAN2, IL23A, STAT2, APOF AC034102.32 OR6C70, OR6C68, OR6C4, OR10P1, METTL7B, ITGA7, BLOC1S1, RDH5, CD63, GDF11, AC073487.34, ORMDL2, DNAJC14, AC023055.40-3, MMP19, WIBG, DGKA, SILV, TIMELESS, MIP, SPRYD4, GLS2, RBMS2P, BAZ2A, ATP5B, PTGES3, NACA, PRIM1, HSD17B6 AC023055.40-1, U1, U6, SNORD59, SNORD59, AC117378.8, AC121758.14-1, AC121758.14-2, SNORA48 Todd JA et al. (PMID:17554260), Hakonarson H et al. (PMID:18198356)
29
0.89 (0.82-0.97)
0.278†
RBMS2P, BAZ2A, ATP5B, PTGES3, NACA, PRIM1, HSD17B6, SDR9C7, RDH16, GPR182, ZBTB39, TAC3, MYO1A, TMEM194A, NAB2, STAT6, LRP1, NXPH4, SHMT2, NDUFA4L2, STAC3, R3HDM2, INHBC, INHBE, GLI1, ARHGAP9, MARS, DDIT3, MBD6, DCTN2, KIF5A, PIP4K2C, DTX3, GEFT, B4GALNT1, OS9, AGAP2, TSPAN31, CDK4, MARCH9, CYP27B1, METTL1, FAM119B, TSFM, AVIL, CTDSP2, XRCC6BP1 U6, SNORD59, SNORD59, AC117378.8, AC121758.14-1, AC121758.14-2, SNORA48, AC137628.3, hsa-mir-1228, Y_RNA, U6, hsa-mir-616, U6, hsa-mir-26a-2, AC083805.17, 7SK, AC084033.33-1 ERBB3, PA2G4P4, ZC3H10, FAM62A, MYL6B, MYL6, SMARCC2, RNF41, OBFC2B, SLC39A5, ANKRD52, COQ10A, CS, CNPY2, PAN2, IL23A, STAT2, APOF, TIMELESS, MIP, SPRYD4, GLS2, RBMS2P Fung EY et al. (PMID:19110536)
0.92 (0.88-0.96)
0.360†
 RA19
30
1.28 (1.22-1.35)
0.488†
 Coeliac22 CCDC63, MYL2, AC002351.2, CUX2, FAM109A, SH2B3, ATXN2, BRAP, ACAD10, ALDH2, MAPKAPK5, TMEM116, ERP29, C12orf30, TRAFD1, C12orf51, RPL6P27, PTPN11, RPH3A AC002978.1, AC002979.14, AC005805.12, AC137055.12, Y_RNA, Y_RNA, 7SK, AC004217.1-1, hsa-mir-1302-1 ATP2A2, ANAPC7, ARPC3, GPN3, C12orf24, VPS29, RAD9B, PPTC7, TCTN1, HVCN1, PPP1CC, CCDC63, RPH3A, OAS1, OAS3, OAS2, DTX1, RASAL1, AC089999.20-1, DDX54, C12orf52, IQCD, AC010178.40-2, SLC24A6 SRP_euk_arch, SNORD50, AC144522.12, Y_RNA, Y_RNA, AC010178.40-1 Todd JA et al. (PMID:17554260)
31
0.86 (0.80-0.91)
0.287†
ZFP36L1, C14orf181 U6 RAD51L1, ACTN1, WDR22, EXDL2, GALNTL1 AL136294.4, AL122013.5-1, AL122013.5-2, AL132986.4-1, Y_RNA Barrett JC et al. (PMID:19430480)
32
1.09 (1.02-1.16)
0.288†
AL163872.2, AL355097.5 AL355098.3-1, SRP_euk_arch, AL163760.4-2, AL163760.4-1, SRP_euk_arch Barrett JC et al. (PMID:19430480)
33
0.90 (0.86-0.94)
AL117190.6-4 hsa-mir-770 C14orf68, WARS, WDR25, BEGAIN, DLK1, RTL1 hsa-mir-493, hsa-mir-337, hsa-mir-665, hsa-mir-431, hsa-mir-433, hsa-mir-127, hsa-mir-432, hsa-mir-136, AL117190.6-5, hsa-mir-370, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, SNORD113, hsa-mir-379, hsa-mir-411, hsa-mir-299, hsa-mir-380, hsa-mir-1197, hsa-mir-323, hsa-mir-758, hsa-mir-329-1, hsa-mir-329-2, hsa-mir-494, AL132709.5-3, hsa-mir-543, hsa-mir-495, hsa-mir-654, hsa-mir-300, hsa-mir-1185-1, hsa-mir-1185-2, hsa-mir-381, hsa-mir-487b, hsa-mir-539, hsa-mir-889, hsa-mir-544, hsa-mir-655, hsa-mir-487a, hsa-mir-382, hsa-mir-134, hsa-mir-668, hsa-mir-485, hsa-mir-453, hsa-mir-154, hsa-mir-496, hsa-mir-377, hsa-mir-541, hsa-mir-409, hsa-mir-412, hsa-mir-369, hsa-mir-410, hsa-mir-656, U3 Wallace C et al. (PMID:19966805)
34
1.21 (1.14-1.30)
0.209†
RASGRP1, C15orf53 Y_RNA SPRED1, FAM98B, RASGRP1 AC087878.7 Qu HQ et al. (PMID:19465406)
35
0.86 (0.82-0.90)
0.318†
ADAMTS7, MORF4L1, CTSH, RASGRF1 AC103975.9, AC011944.12-2 ACSBG1, DNAJA4, WDR61, CRABP1, IREB2, AC027228.16, PSMA4, CHRNA5, CHRNA3, CHRNB4, RASGRF1, TMED3, KIAA1024 AC011944.12-1, hsa-mir-184 Cooper JD et al. (PMID:18978792)
36
0.81 (0.77-0.86)
0.322†
 MS15, SLE
CIITA, DEXI, CLEC16A, SOCS1, TNP2, PRM3, PRM2, PRM1, C16orf75, LITAF AC009121.8-1, SNORA48, AC009121.8-2, hsa-mir-548h-2, Y_RNA ATF7IP2, EMP2, TEKT5, NUBP1, FAM18A, CIITA, LITAF, SNN, TXNDC11, ZC3H7A, RSL1D1, GSPT1, TNFRSF17, RUNDC2A, SNX29 U6, AC007595.9-1, AC007595.9-2, AC007595.9-3, AC007595.9-4, AC007595.9-5, AC074136.4, AC099489.2-1, AC007216.2 Todd JA et al. (PMID:17554260), Hakonarson H et al. (PMID:17632545)
37
0.86 (0.81-0.91)
0.424†
 SBK1, EIF3CL, CLN3, AC138894.2-3, IL27, AC130449.1, CCDC101, SULT1A2, SULT1A1, EIF3S8, ATXN2L, TUFM, SH2B1, ATP2A1, RABEP2, CD19, NFATC2IP, SPNS1, LAT KIAA0556, GSG1L, XPO6, AC009093.10-3, RUNDC2B, AC025279.6, BOLA2, GIYD1, SULT1A4 U6, U6, SNORA25, Y_RNA, AC109460.3, AC112166.3-1, AC009093.10-1, AC133555.3-1 Barrett JC et al. (PMID:19430480)
38
1.28 (1.17-1.41)
0.096†
ZFP1, CTRB2, CTRB1, BCAR1, CFDP1, TMEM170A, CHST6 AC009078.6 MLKL, FA2H, WDR59, ZNRF1, LDHD, ZFP1, CHST6, CHST5, AC009163.6, GABARAPL2, ADAT1, KARS, TERF2IP AC025287.8-1, AC025287.8-2, 5S_rRNA Barrett JC et al. (PMID:19430480)
39
STAC2, FBXL20, PPARBP, CRKRS, NEUROD2, PPP1R1B, STARD3, TCAP, PNMT, PERLD1, ERBB2, C17orf37, GRB7, IKZF3, ZPBP2, GSDMB, ORMDL3, GSDMA, PSMD3, CSF3, THRAP4, THRA, NR1D1 U6, AC009283.6-1, U6, AC079199.2, AC068669.21-1 MLLT6, PCGF2, PSMB3, PIP5K2B, CCDC49, C17orf98, RPL23, LASP1, FBXO47, PLXDC1, ARL5C, CACNB1, RPL19, STAC2, NR1D1, MSL1, CASC3, RAPGEFL1, WIPF2, CDC6, RARA, IGFBP4, TNS4, CCR7 5S_rRNA, SNORA21, AC091178.7-2, AC068669.21-2, AC068669.21-3, Y_RNA, AC080112.15-1, Y_RNA Barrett JC et al. (PMID:19430480)
0.87 (0.82-0.93)
0.495†
 Asthma26
40
0.95 (0.89-1.01)
0.353†
SMARCE1, KRT222P, KRT24 AC004585.1-1, AC004585.1-2, AC090283.3 THRA, NR1D1, MSL1, CASC3, RAPGEFL1, WIPF2, CDC6, RARA, IGFBP4, TNS4, CCR7, KRT25, KRT26, KRT27, KRT28, KRT10, TMEM99, KRT12, KRT20, KRT23, KRT39, KRT40, KRTAP3-3, KRTAP3-2, KRTAP3-1, KRTAP1-5, KRTAP1-3, KRTAP1-1, AC007455.8, KRTAP2-2, KRTAP2-1, KRTAP2-4, KRTAP4-8, AC100808.6, KRTAP4-14, KRTAP4-12, KRTAP4-6, KRTAP4-5, KRTAP4-4, KRTAP4-3, KRTAP4-2, KRTAP4-1, KRTAP9-1 AC068669.21-1, AC068669.21-2, AC068669.21-3, Y_RNA, AC080112.15-1, Y_RNA, AC007455.9, AC100808.10, AC006070.12, AC006070.11 Barrett JC et al. (PMID:19430480)
41
PTPN2 Y_RNA CIDEA, TUBB6, AFG3L2, C18orf43, SPIRE1, CEP76, TNFSF5IP1, SEH1L, CEP192, C18orf1 U6, AP005264.3-2, AP001029.5-1, AP001029.5-2, AP001029.5-3, AP001357.5-2, AP001357.5-1 Todd JA et al. (PMID:17554260)
1.28 (1.21-1.36)
0.166†
 Coeliac32
0.83 (0.79-0.88)
0.449†
 Coeliac32, Crohn's32
42
1.16 (1.10-1.22)
0.465†
 JIA1, MS15, RA17 DOK6, CD226 DOK6, CD226, RTTN, SOCS6 Todd JA et al. (PMID:17554260)
43
0.86 (0.82-0.90)
ICAM1, ICAM4, ICAM5, AC011511.11, FDX1L, RAVER1, ICAM3, TYK2, CDC37, PDE4A, KEAP1, S1PR5 hsa-mir-1181 FBXL12, UBL5, PIN1, OLFM2, COL5A3, RDH8, C19orf66, ANGPTL6, PPAN, AC020931.6-2, P2RY11, EIF3G, DNMT1, S1PR2, MRPL4, ICAM1, ATG4D, KRI1, CDKN2D, AP1M2, SLC44A2, ILF3, QTRT1, DNM2, TMED1, C19orf38, CARM1, YIPF2, C19orf52, SMARCA4 SNORA70, AC008752.6-1, SNORD105, hsa-mir-1238, AC011475.6, hsa-mir-638, hsa-mir-199a-1, AC011442.5-1, SRP_euk_arch Wallace C et al. (PMID:19966805)
44
0.86 (0.79-0.93)
0.162†
DACT3, PRKD2, STRN4, FKRP, SLC1A5 AC093503.2-1, SRP_euk_arch, AC008635.6-4, AC008635.6-1, Y_RNA, AC008635.6-2 IGFL2, IGFL1, HIF3A, PPP5C, CCDC8, PNMAL1, CALM3, PTGIR, GNG8, DACT3, AP2S1, GRLF1, NPAS1, TMEM160, ZC3H4, SAE1, BBC3, CCDC9, C5AR1 U6 Barrett JC et al. (PMID:19430480)
45
0.90 (0.84-0.95)
0.362†
SIRPD, SIRPB1, SIRPG AL049634.8, RP4-673D20.1, AL109809.18 PSMF1, C20orf46, RP4-545L17.10, RAD21L1, SDCBP2, FKBP1A, NSFL1C, SIRPB2, SIRPA, PDYN, STK35 AL031665.19, AL136531.16, RPL7P2 Barrett JC et al. (PMID:19430480)
46
TMPRSS3, UBASH3A AP001624.1 C2CD2, ZNF295, UMODL1, ABCG1, TFF3, TFF2, TFF1, TMPRSS3, TSGA2, SLC37A1, PDE9A, WDR4, NDUFV3 AP001619.1-1, 5S_rRNA, AP001622.1-1, AP001623.1, AP001629.1 Concannon P et al. (PMID:18647951)
1.13 (1.08-1.18)
0.367‡
47
1.10 (1.04-1.17)
0.391†
RFPL1, NEFH, THOC5, NIPSNAP1, NF2, CABP7, ZMAT5, UCRC, ASCC2, MTMR3, HORMAD2, LIF, OSM AC000041.8, Y_RNA, U6, AC003681.1, CTA-85E5.8, CTA-85E5.7, CTA-85E5.6 ZNRF3, C22orf31, KREMEN1, EMID1, RHBDD3, EWSR1, GAS2L1, RASL10A, AP1B1, RP1-130H16.13, TBC1D10A, SF3A1, CCDC157, RNF215, SEC14L2, MTP18, SEC14L3, SEC14L4, RP4-539M6.17, GAL3ST1, PES1, TCN2, SLC35E4, DUSP18, OSBP2 AL021393.1-1, U6, Z95116.1-1, U6, AC004832.3-1, AC004832.3-3, RP4-539M6.18, SDC4P, AC004832.3-2 Barrett JC et al. (PMID:19430480)
48
RA5
IL2RB CACNG2, RABL4, PVALB, NCF4, CSF2RB, C22orf33, TST, MPST, KCTD17, TMPRSS6, IL2RB, C1QTNF6, SSTR3, RAC2, CYTH4, LRRC62, MFNG, CARD10, CDC42EP1, LGALS2, GGA1, SH3BP1, PDXP Z82185.1, AL133392.1, CITF22-45C1.3, 7SK, RP1-151B14.9, Z94160.1
49
1.12 (1.07-1.17)
0.427†
C1QTNF6, SSTR3, RAC2 RP1-151B14.9 CACNG2, RABL4, PVALB, NCF4, CSF2RB, C22orf33, TST, MPST, KCTD17, TMPRSS6, IL2RB, CYTH4, LRRC62, MFNG, CARD10, CDC42EP1, LGALS2, GGA1, SH3BP1, PDXP, LGALS1, NOL12, TRIOBP Z82185.1, AL133392.1, CITF22-45C1.3, 7SK, Z94160.1, Z83844.5-1 Cooper JD et al. (PMID:18978792)
50
0.84 (0.73-0.96)
SLE TLR8, TMSB4X FRMPD4, PRPS2, TLR7, FAM9C, ATXN3L RP11-2N21.2, 7SK, AC119619.5-1, GS1-324M7.3, GS1-324M7.4, GS1-600G8.4, RP11-142G7.1 Cooper JD et al. (PMID:19956107)
51
1.16 (1.07-1.24)
0.316†
CTAG1B, CTAG2, GAB3, DKC1, MPP1, F8, H2AFB1, F8A1, FUNDC2, MTCP1NB, MTCP1NB, BRCC3, VBP1 AF277315.19, AF277315.6-1, AF277315.10, AF277315.13, OR3B1P, SNORA36, SNORA56, hsa-mir-1184, CTD-2183H9.7, CTD-2183H9.4, CTD-2183H9.3, RP11-143H17.1, RP13-228J13.9 MECP2, OPN1LW, TEX28P2, OPN1MW, TEX28P1, OPN1MW2, TEX28, TKTL1, FLNA, EMD, RPL10, DNASE1L1, TAZ, ATP6AP1, GDI1, FAM50A, PLXNA3, LAGE3, UBL4A, SLC10A3, FAM3A, G6PD, IKBKG, CXorf52, CTAG1A, VBP1, RAB39B, CLIC2, H2AFB2, F8A2, F8A3, H2AFB3, TMLHE SNORA70, BX936347.3, SRP_euk_arch, SRP_euk_arch, ATF4P, RP13-228J13.6, RP13-228J13.8, RP13-228J13.10, RP13-228J13.5, BX682237.6, hsa-mir-1184, hsa-mir-1184, BX276110.5 Barrett JC et al. (PMID:19430480)

Key: RA - rheumatoid arthritis, SLE - systematic lupus erythemastosus, AITD - autoimmune thyroid disease, MS - multiple sclerosis, JIA - Juvenile Idiopathic Arthritis.
* rs876498 could not be typed with taqman assay, so used a SNP in R2=1 was used instead (rs3788013).

† MAF sourced from referenced publication
‡ MAF sourced from HapMap (CEU population).
# Data provided from a combined study - pelase see publication for further information.


Version 54, 2010-02-23 13:17:37 		 
 
Publications
 
  1. 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 (CAPS), UKRAG Consortium, BSPAR Study Group, Thomson WT
    Genes Immun. 2010
    PubMed ID: 20072139
  2. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes.
    Wallace C, Smyth DJ, Maisuria-Armer M, Walker NM, Todd JA, Clayton DGT
    Nat Genet. 2010
    PubMed ID: 19966805
  3. Follow-up of 1715 SNPs from the Wellcome Trust Case Control Consortium genome-wide association study in type I diabetes families.
    Cooper JD, Walker NM, Smyth DJ, Downes K, Healy BC, Todd JA, Type I Diabetes Genetics ConsortiumT
    Genes Immun. 2009
    PubMed ID: 19956107
  4. Common variants at five new loci associated with early-onset inflammatory bowel disease.
    Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, Western Regional Alliance for Pediatric IBD, Silber G, Wrobel I, Quiros A, International IBD Genetics Consortium, Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, NIDDK IBD Genetics Consortium, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Belgian-French IBD Consortium, Wellcome Trust Case Control Consortium, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwillam R, Tremelling M, Delukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ, Heyman MB, Ferry GD, Kirschner B, Lee J, Essers J, Grand R, Stephens M, Levine A, Piccoli D, Van Limbergen J, Cucchiara S, Monos DS, Guthery SL, Denson L, Wilson DC, Grant SF, Daly M, Silverberg MS, Satsangi J, Hakonarson HT
    Nat Genet. 2009
    PubMed ID: 19915574
  5. Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk.
    Raychaudhuri S, Thomson BP, Remmers EF, Eyre S, Hinks A, Guiducci C, Catanese JJ, Xie G, Stahl EA, Chen R, Alfredsson L, Amos CI, Ardlie KG, BIRAC Consortium, Barton A, Bowes J, Burtt NP, Chang M, Coblyn J, Costenbader KH, Criswell LA, Crusius JB, Cui J, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Kurreeman FA, Lee AT, Liu X, Li Y, Martin P, Morgan AW, Padyukov L, 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, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth P, YEAR Consortium, Altshuler D, Karlson EW, Toes RE, de Vries N, Begovich AB, Siminovitch KA, Worthington J, Klareskog L, Gregersen PK, Daly MJ, Plenge RMT
    Nat Genet. 2009
    PubMed ID: 19898481
  6. Association of RASGRP1 with type 1 diabetes is revealed by combined follow-up of two genome-wide studies.
    Qu HQ, Grant SF, Bradfield JP, Kim C, Frackelton E, Hakonarson H, Polychronakos CT
    J Med Genet. 2009
    PubMed ID: 19465406
  7. 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 ConsortiumT
    Nat Genet. 2009
    PubMed ID: 19430480
  8. Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23.
    Orozco G, Hinks A, Eyre S, Ke X, Gibbons LJ, Bowes J, Flynn E, Martin P, Wellcome Trust Case Control Consortium, YEAR consortium, Wilson AG, Bax DE, Morgan AW, Emery P, Steer S, Hocking L, Reid DM, Wordsworth P, Harrison P, Thomson W, Barton A, Worthington JT
    Hum Mol Genet. 2009
    PubMed ID: 19417005
  9. 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 JT
    Hum Mol Genet. 2009
    PubMed ID: 19359276
  10. Contrasting genetic association of IL2RA with SLE and ANCA-associated vasculitis.
    Carr EJ, Clatworthy MR, Lowe CE, Todd JA, Wong A, Vyse TJ, Kamesh L, Watts RA, Lyons PA, Smith KGT
    BMC Med Genet. 2009
    PubMed ID: 19265545
  11. 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 DAT
    PLoS Genet. 2009
    PubMed ID: 19119414
  12. 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 JAT
    Genes Immun. 2009
    PubMed ID: 19110536
  13. Association study of the IL18RAP locus in three European populations with coeliac disease.
    Koskinen LL, Einarsdottir E, Dukes E, Heap GA, Dubois P, Korponay-Szabo IR, Kaukinen K, Kurppa K, Ziberna F, Vatta S, Not T, Ventura A, Sistonen P, Adány R, Pocsai Z, Széles G, Mäki M, Kere J, Wijmenga C, van Heel DA, Saavalainen PT
    Hum Mol Genet. 2009
    PubMed ID: 19103669
  14. 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 JAT
    N Engl J Med. 2008
    PubMed ID: 19073967
  15. The expanding genetic overlap between multiple sclerosis and type I diabetes.
    International Multiple Sclerosis Genetics Consortium (IMSGC)T
    Genes Immun. 2009
    PubMed ID: 18987646
  16. Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
    Cooper JD, Smyth DJ, Smiles AM, Plagnol V, Walker NM, Allen JE, Downes K, Barrett JC, Healy BC, Mychaleckyj JC, Warram JH, Todd JAT
    Nat Genet. 2008
    PubMed ID: 18978792
  17. CD226 Gly307Ser association with multiple autoimmune diseases.
    Hafler JP, Maier LM, Cooper JD, Plagnol V, Hinks A, Simmonds MJ, Stevens HE, Walker NM, Healy B, Howson JM, Maisuria M, Duley S, Coleman G, Gough SC, The International Multiple Sclerosis Genetics Consortium (IMSGC), Worthington J, Kuchroo VK, Wicker LS, Todd JAT
    Genes Immun. 2008
    PubMed ID: 18971939
  18. 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 ST
    Nat Genet. 2008
    PubMed ID: 18836448
  19. Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
    Raychaudhuri S, Remmers EF, Lee AT, Hackett R, Guiducci C, Burtt NP, Gianniny L, Korman BD, Padyukov L, Kurreeman FA, Chang M, Catanese JJ, Ding B, Wong S, van der Helm-van Mil AH, Neale BM, Coblyn J, Cui J, Tak PP, Wolbink GJ, Crusius JB, van der Horst-Bruinsma IE, Criswell LA, Amos CI, Seldin MF, Kastner DL, Ardlie KG, Alfredsson L, Costenbader KH, Altshuler D, Huizinga TW, Shadick NA, Weinblatt ME, de Vries N, Worthington J, Seielstad M, Toes RE, Karlson EW, Begovich AB, Klareskog L, Gregersen PK, Daly MJ, Plenge RMT
    Nat Genet. 2008
    PubMed ID: 18794853
  20. A human type 1 diabetes susceptibility locus maps to chromosome 21q22.3.
    Concannon P, Onengut-Gumuscu S, Todd JA, Smyth DJ, Pociot F, Bergholdt R, Akolkar B, Erlich HA, Hilner JE, Julier C, Morahan G, Nerup J, Nierras CR, Chen WM, Rich SS, the Type 1 Diabetes Genetics ConsortiumT
    Diabetes. 2008
    PubMed ID: 18647951
  21. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, NIDDK IBD Genetics Consortium, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Belgian-French IBD Consortium, Wellcome Trust Case Control Consortium, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJT
    Nat Genet. 2008
    PubMed ID: 18587394
  22. Newly identified genetic risk variants for celiac disease related to the immune response.
    Hunt KA, Zhernakova A, Turner G, Heap GA, Franke L, Bruinenberg M, Romanos J, Dinesen LC, Ryan AW, Panesar D, Gwilliam R, Takeuchi F, McLaren WM, Holmes GK, Howdle PD, Walters JR, Sanders DS, Playford RJ, Trynka G, Mulder CJ, Mearin ML, Verbeek WH, Trimble V, Stevens FM, O'Morain C, Kennedy NP, Kelleher D, Pennington DJ, Strachan DP, McArdle WL, Mein CA, Wapenaar MC, Deloukas P, McGinnis R, McManus R, Wijmenga C, van Heel DAT
    Nat Genet. 2008
    PubMed ID: 18311140
  23. A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study.
    Hakonarson H, Qu HQ, Bradfield JP, Marchand L, Kim CE, Glessner JT, Grabs R, Casalunovo T, Taback SP, Frackelton EC, Eckert AW, Annaiah K, Lawson ML, Otieno FG, Santa E, Shaner JL, Smith RM, Onyiah CC, Skraban R, Chiavacci RM, Robinson LJ, Stanley CA, Kirsch SE, Devoto M, Monos DS, Grant SF, Polychronakos CT
    Diabetes. 2008
    PubMed ID: 18198356
  24. Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A.
    Nejentsev S, Howson JM, Walker NM, Szeszko J, Field SF, Stevens HE, Reynolds P, Hardy M, King E, Masters J, Hulme J, Maier LM, Smyth D, Bailey R, Cooper JD, Ribas G, Campbell RD, Clayton DG, Todd JA, Wellcome Trust Case Control ConsortiumT
    Nature. 2007
    PubMed ID: 18004301
  25. Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A.
    Nejentsev S, Howson JM, Walker NM, Szeszko J, Field SF, Stevens HE, Reynolds P, Hardy M, King E, Masters J, Hulme J, Maier LM, Smyth D, Bailey R, Cooper JD, Ribas G, Campbell RD, Clayton DG, Todd JA, Wellcome Trust Case Control ConsortiumT
    Nature. 2007
    PubMed ID: 18004301
  26. Replication of an association between 17q21 SNPs and asthma in a French-Canadian familial collection.
    Madore AM, Tremblay K, Hudson TJ, Laprise CT
    Hum Genet. 2008
    PubMed ID: 17992541
  27. 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 JAT
    Nat Genet. 2007
    PubMed ID: 17676041
  28. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis.
    Gregory SG, Schmidt S, Seth P, Oksenberg JR, Hart J, Prokop A, Caillier SJ, Ban M, Goris A, Barcellos LF, Lincoln R, McCauley JL, Sawcer SJ, Compston DA, Dubois B, Hauser SL, Garcia-Blanco MA, Pericak-Vance MA, Haines JL, Multiple Sclerosis Genetics GroupT
    Nat Genet. 2007
    PubMed ID: 17660817
  29. 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 SLT
    N Engl J Med. 2007
    PubMed ID: 17660530
  30. A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene.
    Hakonarson H, Grant SF, Bradfield JP, Marchand L, Kim CE, Glessner JT, Grabs R, Casalunovo T, Taback SP, Frackelton EC, Lawson ML, Robinson LJ, Skraban R, Lu Y, Chiavacci RM, Stanley CA, Kirsch SE, Rappaport EF, Orange JS, Monos DS, Devoto M, Qu HQ, Polychronakos CT
    Nature. 2007
    PubMed ID: 17632545
  31. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    Wellcome Trust Case Control ConsortiumT
    Nature. 2007
    PubMed ID: 17554300
  32. 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 DGT
    Nat Genet. 2007
    PubMed ID: 17554260
  33. Genomic polymorphism at the interferon-induced helicase (IFIH1) locus contributes to Graves' disease susceptibility.
    Sutherland A, Davies J, Owen CJ, Vaikkakara S, Walker C, Cheetham TD, James RA, Perros P, Donaldson PT, Cordell HJ, Quinton R, Pearce SHT
    J Clin Endocrinol Metab. 2007
    PubMed ID: 17535987
  34. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region.
    Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ, Guja C, Ionescu-Tirgoviste C, Widmer B, Dunger DB, Savage DA, Walker NM, Clayton DG, Todd JAT
    Nat Genet. 2006
    PubMed ID: 16699517
  35. Effects of PTPN22 C1858T polymorphism on susceptibility and clinical characteristics of British Caucasian rheumatoid arthritis patients.
    Harrison P, Pointon JJ, Farrar C, Brown MA, Wordsworth BPT
    Rheumatology (Oxford). 2006
    PubMed ID: 16490755
  36. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4.
    Plenge RM, Padyukov L, Remmers EF, Purcell S, Lee AT, Karlson EW, Wolfe F, Kastner DL, Alfredsson L, Altshuler D, Gregersen PK, Klareskog L, Rioux JDT
    Am J Hum Genet. 2005
    PubMed ID: 16380915
  37. The PTPN22 R620W polymorphism associates with RF positive rheumatoid arthritis in a dose-dependent manner but not with HLA-SE status.
    Lee AT, Li W, Liew A, Bombardier C, Weisman M, Massarotti EM, Kent J, Wolfe F, Begovich AB, Gregersen PKT
    Genes Immun. 2005
    PubMed ID: 15674368
  38. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis.
    Begovich AB, Carlton VE, Honigberg LA, Schrodi SJ, Chokkalingam AP, Alexander HC, Ardlie KG, Huang Q, Smith AM, Spoerke JM, Conn MT, Chang M, Chang SY, Saiki RK, Catanese JJ, Leong DU, Garcia VE, McAllister LB, Jeffery DA, Lee AT, Batliwalla F, Remmers E, Criswell LA, Seldin MF, Kastner DL, Amos CI, Sninsky JJ, Gregersen PKT
    Am J Hum Genet. 2004
    PubMed ID: 15208781
  39. A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes.
    Bottini N, Musumeci L, Alonso A, Rahmouni S, Nika K, Rostamkhani M, MacMurray J, Meloni GF, Lucarelli P, Pellecchia M, Eisenbarth GS, Comings D, Mustelin TT
    Nat Genet. 2004
    PubMed ID: 15004560
  40. Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease.
    Ueda H, Howson JM, Esposito L, Heward J, Snook H, Chamberlain G, Rainbow DB, Hunter KM, Smith AN, Di Genova G, Herr MH, Dahlman I, Payne F, Smyth D, Lowe C, Twells RC, Howlett S, Healy B, Nutland S, Rance HE, Everett V, Smink LJ, Lam AC, Cordell HJ, Walker NM, Bordin C, Hulme J, Motzo C, Cucca F, Hess JF, Metzker ML, Rogers J, Gregory S, Allahabadia A, Nithiyananthan R, Tuomilehto-Wolf E, Tuomilehto J, Bingley P, Gillespie KM, Undlien DE, Rønningen KS, Guja C, Ionescu-Tîrgovişte C, Savage DA, Maxwell AP, Carson DJ, Patterson CC, Franklyn JA, Clayton DG, Peterson LB, Wicker LS, Todd JA, Gough SCT
    Nature. 2003
    PubMed ID: 12724780
  41. The CTLA-4 gene region of chromosome 2q33 is linked to, and associated with, type 1 diabetes. Belgian Diabetes Registry.
    Nistico L, Buzzetti R, Pritchard LE, Van der Auwera B, Giovannini C, Bosi E, Larrad MT, Rios MS, Chow CC, Cockram CS, Jacobs K, Mijovic C, Bain SC, Barnett AH, Vandewalle CL, Schuit F, Gorus FK, Tosi R, Pozzilli P, Todd JAT
    Hum Mol Genet. 1996
    PubMed ID: 8817351
  42. A polymorphic locus near the human insulin gene is associated with insulin-dependent diabetes mellitus.
    Bell GI, Horita S, Karam JHT
    Diabetes. 1984
    PubMed ID: 6363172
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    Kristensen OT
    Tidsskr Nor Laegeforen. 1991
    PubMed ID: 1780842

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