Supplementary table 1. Known genetic susceptibility loci in extra-intestinal manifestations and complications of inflammatory bowel disease included in the pathway analyses.
EIM Locus SNPs Reported Genes* p value# References Overlap IBD CRC 1q41 rs6691170;rs6687758 DUSP10 9,60E-10 10 no
CRC 3q26 rs10936599 MYNN/ARPM1 3,40E-08 10 no
CRC 6q25 rs7758229 SLC22A3 7,90E-09 11 no
CRC 8q23 rs16892766;rs11986063 EIF3H 3,30E-18 12,13 no CRC 8q24 rs7014346;rs10505477; POU5F1P1/
8,60E-26 12,13,
14,15,16 no rs6983267;rs7837328 DQ515897
CRC 10p14 rs10795668 - 2,50E-13 12 no
CRC 11q23 rs11213809;rs3802842
LOC120376/
5,20E-13 13,16 no FLJ45803/
c11orf53/POU2AF1
CRC 12q13 rs7136702;rs11169552 LARP4/DIP2 1,90E-10 10 no
CRC 14q22 rs4444235 BMP4 8,10E-10 13 no
CRC 15q13 rs4779584;rs10318 SCG5/GREM1/FMN1 4,40E-14 13,17 no
CRC 16q22 rs9929218 CDH1 1,20E-08 13 yes
CRC 18q21 rs4939827;rs12953717 SMAD7 7,80E-28 13,16,18 yes
CRC 19q13 rs10411210 RHPN2 4,60E-09 13 yes
CRC 20p12 rs355527;rs961253 BMP2 2,00E-10 13 no
CRC 20q13 rs4925386 LAMA5 1,90E-10 10 no
BMD 1p36 rs6696981;rs7524102;
rs6426749 ZBTB40/WNT4 5,00E-16 19,20 yes
BMD 1p31 rs1430742;rs2566755 GPR177 2,50E-12 20 no
BMD 3p22 rs87938 CTNNB1 3,40E-09 20 no
BMD 5q14 rs1366594 MEF2C 1,10E-12 20 no
BMD 6q25
rs9479055;rs4870044;
rs1038304;rs6929137;
rs2941740; ESR1/ C6orf7 1,60E-11 19,20 no rs1999805;rs2504063
BMD 7p14 rs1524058 STARD3NL 5,20E-09 20 no
BMD 7q21 rs4729260;rs7781370 FLJ42280 2,90E-11 20 no
BMD 7q31 rs7776725 FAM3C 1,0E–11 21 no
BMD 8q24
rs4355801;rs2062377;
rs11995824;rs6469804;
rs6993813
TNFRSF11B 5,70E-15 19,20,22 no
BMD 11p15 rs9630182 PTH 4,00E-07 23 no
BMD 11p15 rs7117858 SOX6 2,70E-09 20 no
BMD 11p13 rs16921914 DCDC5 1,00E-08 20 no
BMD 11p11 rs7932354 ARHGAP1 1,50E-08 20 no
BMD 11q13 rs3736228 LRP5 6,30E-12 22 no
BMD 12q13 rs2016266;rs10876432 SP7 9,90E-11 24 no BMD 13q14 rs9533090;rs9594738;
rs9594759;rs1021188 TNFSF11 4,60E-23 19,20,23 no
BMD 14q32 rs2010281 MARK3 1,80E-09 25 no
BMD 16p12 rs8057551 IL21R 2,30E-06 23 no
BMD 16q23 rs11859065;rs11864477;
ADAMTS18 2,10E-08 26 no
rs16945612
BMD 17q21 rs7220711;rs1513670 SOST 2,10E-08 25 no
BMD 17q21 rs9303521 CRHR1 5,00E-08 20 no
BMD 18q21 rs884205 TNFRSF11A 3,80E-08 20 no
BMD 20p12 rs2273061 JAG1 8,50E-09 27 no
AS 1p36 rs11249215 RUNX3 9,20E-11 28 no
AS 1p31 rs11209026;rs11465804 IL23R 2,30E-17 28,29,30 yes AS 1q32 rs11584383;rs2297909 KIF21B 5,20E-12 28,30 yes AS 2p15 rs4672495;rs10865331 B3GNT2 6,50E-34 28,29 yes
AS 4q21 rs4389526 ANTXR2 9,40E-08 28 no
AS 5p13 rs10440635 PTGER4 2,60E-07 28 yes
AS 5q15
rs27434;rs2287987;
rs27037;
ERAP1 1,80E-27 28,29,31 yes rs30187;rs10050860;
rs17482078
AS 5q33 rs6556416;rs10045431 IL12B 1,90E-08 28,30 yes AS 6p21 rs4349859;rs7743761 MHC 5,00E-304 28,29 yes
AS 6p22 rs6908425 CDKAL1 1,10E-04 30 yes
AS 6p22 rs3734523 HLA 1,60E-08 29 no
AS 9p24 rs10758669 JAK2 2,90E-04 30 yes
AS 9q34 rs10781500 CARD9 1,10E-06 28 yes
AS 12p13 rs11616188 LTBR/TNFRSF1A 4,10E-12 28 no
AS 12q12 rs11175593 LRRK2/MUC19 9,90E-05 30 yes
AS 17q21 rs6503695;rs744166 STAT3 2,60E-05 30 yes
AS 17q21 rs8070463 TBKBP1 5,30E-08 28 no
AS 21q22 rs2242944;rs378108 PSMG1 8,30E-20 28,29 yes PSC 1p36 rs3748816 TNFRSF14/MMEL1 2,10E-08 32 yes
PSC 2p25 rs11682163 ALLC 7,60E-06 32 no
PSC 2p16 rs13017599;rs6706689 REL 1,90E-04 32,33 yes
PSC 2q13 rs6720394 BCL2L11 4,10E-08 34 no
PSC 2q35 rs12612347 GPBAR1 8,80E-03 35 yes
PSC 3p21 rs3197999 MST1 1,10E-16 34,35 yes PSC 4q27 rs13132245;rs6822844;
IL2/IL21 9,90E-08 32,33 yes rs11936230;rs13119723
PSC 6p21 rs3134792;rs2844559;
HLA 6,80E-49 34,35 yes
rs3099844
PSC 9q34 rs4077515 CARD9 7,60E-05 32,33 yes
PSC 10p15 rs10905718 IL2RA 2,40E-07 34 yes
PSC 13q31 rs9524260 GPC6 2,70E-04 35 no
PSC 16p13 rs2903692 CLEC16A 6,40E-06 32 yes
PSC 19q13 rs281377;rs601338;
FUT2 1,90E-06 32 yes
rs602662
PSC 21q22 rs9976767;rs11203203 UBASH3A 2,90E-05 32 no GS 2p21 rs11887534;rs4299376 ABCG8 1,40E-14 36 no
KS 21q22
rs219781;rs219780;
rs219779; CLDN14 1,70E-12 37 no
rs219778
VT 1q24 rs1208134;rs2420371 F5 8,10E-10 38 no
VT 9q34 rs657152;rs505922;
rs630014 ABO 1,50E-14 38 no
* candidate gene(s) as reported in referred literature
# p value of most associated SNP in literature reference(s)
EIM = extra-intestinal manifestation; SNP = single nucleotide polymorphism; IBD = inflammatory bowel disease; AS = ankylosing spondylitis; PSC = primary sclerosing cholangitis; CRC = colorectal cancer; BMD = bone mineral density; GS = gallstones; KS = kidney stones; VT = Venous thrombosis.
