Chunk #3 — GENOME-WIDE ASSOCIATION STUDIES AND ‘THE MISSING HERITABILITY'

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Synthetic associations in the context of genome-wide association scan signals.

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yes

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for type 2 diabetes (T2D) (10), their established susceptibility loci would contribute ∼33–47%, 55.6%, 10–12.6% and 11.9% of the total heritability, respectively (Table 1). Table 1.Established susceptibility loci for RA, T1D, CD and T2DChromosomeSNPPositionRegion/geneRAFORλsReferenceRheumatoid arthritis 1p36rs38907452553624TNFSFR140.681.121.003(16) 1p13rs2476601114377568PTPN220.101.941.068(16) 1p13rs11586238117263138CD2, CD580.241.131.003(16) 1q23rs12746613161467042FCGR2A0.121.131.002(16) 1q31rs10919563198700442PTPRC0.871.141.002(16) 2p16rs1303123761136129REL0.371.131.004(16) 2p14rs93473465595586SPRED20.491.131.004(16) 2q11rs10865035100835734AFF30.471.121.003(16) 2q32rs7574865191964633STAT40.221.161.004(16) 2q33rs1980422204610396CD280.241.121.002(16) 2q33rs3087243204738919CTLA40.561.151.005(16) 3p14rs1331559158556841PXK0.091.291.007(16) 4p15rs87404026108197RBPJ0.301.141.004(16) 4q27rs6822844123509421IL2, IL210.821.111.002(16) 5q11rs685921955438580ANKRD55, IL6ST0.791.281.009(16) 5q21rs26232102596720C5orf130.681.141.004(16) 6p21HLA1.800(70,71) 6q21rs548234106568034PRDM10.331.101.002(16) 6q23rs10499194138002637TNFAIP30.731.101.002(16) 6q23rs6920220138006504TNFAIP30.221.221.008(16) 6q23rs5029937138195151TNFAIP30.041.401.006(16) 6q25rs394581159482521TAGAP0.701.101.002(16) 6q27rs3093023167534290CCR60.431.131.004(16) 7q32rs10488631128594183IRF50.111.191.003(16) 8p23rs273634011343973BLK0.251.121.003(16) 9p13rs281237834710260CCL210.341.101.002(16) 9q33rs3761847123690239TRAF1, C50.431.131.004(16) 10p15rs21042866099045IL2RA0.731.091.001(16) 10p15rs47503166393260PRKCQ0.811.151.003(16) 11p12rs54038636525293TRAF60.861.141.002(16) 12q13rs167854257968715KIF5A0.621.101.002(16) 20q13rs481048544747947CD400.751.181.005(16) 22q12rs321825337544810IL2RB0.261.091.001(16)Type 1 diabetes 1p31rs226924164108771PGM10.191.101.001(15) 1p13rs2476601114377568PTPN220.142.051.104(15) 1q31rs2816316192536813RGS10.821.121.002(15) 1q32rs3024505206939904IL100.831.191.004(15) 2p25rs1534422126407412p250.461.081.001(15) 2q12rs917997103070568IL18RAP0.781.201.005(15) 2q24rs1990760163124051IFIH10.601.161.005(15) 2q33rs3087243204738919CTLA40.551.141.004(15) 3p21rs33346345611CCR50.881.181.003(15) 4p15rs10517086260855114p150.301.091.002(15) 4q27rs17388568123132492IL20.261.261.011(15) 5p13rs689793235874575IL7R0.731.121.002(15) 6p21MHC3.058(72) 6q15rs1175552790958231BACH20.471.131.004(15) 6q22rs9388489126698719C6orf1730.451.171.006(15) 6q23rs6920220137973068TNFAIP30.221.091.001(15) 6q25rs1738074159465977TAGAP0.561.091.002(15) 7p15rs7804356268916657p150.761.141.003(15) 7p12rs494808851027194COBL0.951.301.002(15) 9p24rs70206734291747GLIS30.501.141.004(15) 10p15rs115946566,62015IL2RA0.751.191.005(15) 10p15rs127224956137289IL2RA0.891.591.015(15) 10p15rs9474746430456PRKCQ0.811.101.001(15) 10q23rs1050954090023033C10orf590.721.331.015(15) 11p15rs6892138800INS0.712.301.096(15) 12p13rs47638799910164CD690.371.091.002(15) 12q13rs229223956482180ERBB30.341.311.018(15) 12q13rs167853657979190Multiple0.721.121.002(15) 12q24rs3184504111884608SH2B30.491.281.015(15) 14q24rs14657886926359914q240.711.161.004(15) 14q32rs49003849849895114q320.291.091.002(15) 15q25rs382593279235446CTSH0.681.161.005(15) 16p13rs1270871611179873CLEC16A0.651.231.009(15) 16p12rs124442682034257216p120.301.101.002(15) 16p11rs478808428539848IL270.581.161.005(15) 16q23rs72028777524724516q230.101.131.001(15) 17p13rs16956936763369217p130.871.091.001(15) 17q12rs229040038066240ORMDL30.511.151.005(15) 17q21rs72211093877028617q210.651.051.001(15) 18p11rs189321712809340PTPN20.171.131.002(15) 18q22rs76336167531642CD2260.471.161.006(15) 19q13rs4251054720848119q130.841.161.003(15) 20p13rs2281808161055120p130.641.111.002(15) 21q22rs1120320343836186UBASH3A0.431.131.004(15) 22q12rs57530373058172222q120.391.101.002(15) 22q13rs22954137591318C1QTNF60.431.111.003(15) Xq28rs2664170153945602Xq280.321.161.005(15)Crohn's disease 1p31rs1146580467475114IL23R0.932.501.025(14) 1p13rs2476601114179091PTPN220.901.311.005(14) 1q23rs2274910159118670ITLN10.681.141.004(14) 1q24rs92868791711288571q240.241.191.006(14) 1q32rs115843831992024891q320.701.181.005(14) 2q27rs3828309233845149ATG16L10.531.281.015(14) 3p21rs319799949696536MST10.271.201.007(14) 5p13rs461376340428485PTGER40.131.321.010(14) 5q31rs21889621317987045q310.431.251.013(14) 5q33rs11747270150239060IRGM0.091.331.008(14) 5q33rs10045431158747111IL12B0.711.111.002(14) 6p22rs690842520836710CDKAL10.781.211.006(14) 6q21rs77460821065419626q210.291.171.005(14) 6q27rs2301436167357978CCR60.461.211.009(14) 7p12rs1456893502402187p120.681.201.007(14) 8q24rs15513981266092338q240.621.081.001(14) 9p24rs107586694971602JAK20.351.121.003(14) 9q32rs4263839116606261TNFSF150.681.221.008(14) 10p11rs175824163532765610p110.351.161.005(14) 10q21rs1099527164108492ZNF3650.391.251.012(14) 10q24rs11190140101281583NKX2-30.481.201.008(14) 11q13rs792789475978964C11orf300.391.161.005(14) 12q12rs1117559338888207LRRK2, MUC190.021.541.005(14) 13q14rs37641474335592513q140.221.251.010(14) 16q12rs206684749321280NOD20.023.991.147(14) 17q21rs287250735294289ORMDL30.471.121.003(14) 17q21rs74416637767727STAT30.571.181.007(14) 18p11rs254215112769947PTPN20.151.351.014(14) 21q21rs17361351572709121q210.571.181.007(14) 21q22rs76242144439989ICOSLG0.391.131.004(14)Type 2 diabetes 1p13–p11rs10923931120319482NOTCH20.111.091.001(73) 1q32rs340874212225879PROX10.561.071.001(18) 2p23rs78009427594741GCKR0.611.061.001(18) 2p21rs757859743586327THADA0.901.151.002(73) 2p16rs24302160438323BCL11A0.461.081.001(74) 2q26rs7578326226728897IRS10.641.111.002(74) 3p25rs180128212368125PPARG0.851.231.005(73) 3p14rs460710364686944ADAMTS90.761.101.002(73) 3q13–q21rs11708067124548468ADCY50.771.121.002(18) 3q27rs4402960186994381IGF2BP20.311.111.002(73) 4p16rs100101316343816WFS10.591.141.004(73) 5q13rs445705376460705ZBED30.261.081.001(74) 6p22rs1094639820769013CDKAL10.331.091.002(73) 7p21rs219134915030834DGKB/TMEM1950.471.061.001(18) 7p15rs86474528147081JAZF10.501.081.001(73) 7p15rs460751744202193GCK0.21.071.001(18) 7q32rs972283130117394KLF140.551.071.001(74) 8q22rs89685496029687TP53INP10.481.061.001(74) 8q24rs13266634118253964SLC30A80.681.121.003(73) 9p21rs1081166122124094CDKN2A/B0.841.171.003(73) 9q21rs1329213681141948CHCHD90.931.111.001(74) 10p13rs1277979012368016CDC123/CAMK1D0.181.111.002(73) 10q23rs501548094455539HHEX/IDE0.591.101.002(73) 11p15rs23344991653428DUSP80.411.081.001(32) 11p15rs2313622648047KCNQ10.521.081.001(74) 11p15rs22378922796327KCNQ10.341.421.031(73) 11p15rs521917366148KCNJ110.391.151.005(73) 11q13rs155222472110746CENTD20.881.141.002(74) 11q21rs1083096392348358MTNR1B0.301.091.001(73) 12q14rs153134364461161HMGA20.11.11.001(74) 12q14–q21rs796158169949369TSPAN8/LGR50.271.061.001(73) 12q24rs7957197119945069HNF1A0.851.071.001(74) 15q25rs1163439778219277ZFAND60.61.061.001(74) 15q26rs804268089322341PRC10.221.071.001(74) 16q12rs805013652373776FTO0.381.211.009(73) 17cen–q21.3rs75721033170628HNF1B (TCF2)0.381.101.002(73) Xq28rs5945326152553116DUSP90.211.271.011(74)RA, rheumatoid arthritis; T1D, type 1 diabetes; CD,