Table 2.

Genome-wide significant (P < 5 × 10⁻⁸) non-HLA susceptibility variants identified by two (hypothesis-free) GWAS for AIH and several genome-wide meta-analyses (GWMA) for PBC and PSC. Susceptibility variants for PBC and PSC from monocentric studies and studies with candidate gene are not listed. Variant: dbSNP name of the variant. Chromosome:position: human genome build hg37. Candidate gene: candidate gene from the respective publication. Fine-mapped to single variant: In cases where loci could be resolved to a single variant by Bayesian fine-mapping with high probability as causal (posterior probability > 50%), the name of the variant is indicated. NA: fine-mapping results not yet available

Disease	Variant	Chromosome:position	Candidate gene	Population	Fine-mapped to single variant	Reference
AIH	rs3184504	12:111,884,608	SH2B3	Netherlands/Germany	NA	De Boer et al. (2014) [27]
AIH	rs72929257	2:204,982,643	CTLA4	China	NA	Li et al. (2022) [33]
AIH	rs6809477	3:63,563,282	SYNPR	China	NA	Li et al. (2022) [33]
PBC	rs867436	1:2,523,723	MMEL1	European ancestry	rs867436	Cordell et al. (2021) [53]
PBC	rs6679356	1:67,820,194	IL12RB2	European ancestry	rs6679356	Cordell et al. (2021) [53]
PBC	rs10802191	1:117,065,083	CD58	European ancestry	rs10802191	Cordell et al. (2021) [53]
PBC	rs945635	1:157,670,290	FCRL3	European ancestry	rs945635	Cordell et al. (2021) [53]
PBC	rs12123169	1:197,780,966	DENND1B	European ancestry	rs12123169	Cordell et al. (2021) [53]
PBC	rs55734382	1:201,019,059	INAVA	European ancestry	rs55734382	Cordell et al. (2021) [53]
PBC	rs34655300	2:25,514,333	DNMT3A	European ancestry	rs891058	Cordell et al. (2021) [53]
PBC	rs859767	2:135,341,200	TMEM163	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs3771317	2:191,543,962	STAT4	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs9876137	3:16,961,265	PLCL2	European ancestry	rs9876137	Cordell et al. (2021) [53]
PBC	rs6550965	3:25,383,587	RARB	European ancestry	rs6550965	Cordell et al. (2021) [53]
PBC	rs2293370	3:119,219,934	CD80	European ancestry	rs2293370	Cordell et al. (2021) [53]
PBC	rs589446	3:159,733,527	IL12A	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs7674640	4:103,540,780	NFKB1	European ancestry	rs7674640	Cordell et al. (2021) [53]
PBC	rs7663401	4:106,128,954	TET2	European ancestry	rs7663401	Cordell et al. (2021) [53]
PBC	rs35467801	5:35,881,130	IL7R	European ancestry	rs35467801	Cordell et al. (2021) [53]
PBC	rs2546890	5:158,759,900	IL12B	European ancestry	rs2546890	Cordell et al. (2021) [53]
PBC	rs2327832	6:137,973,068	TNFAIP3	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs7805218	7:20,378,801	ITGB8	European ancestry	rs7805218	Cordell et al. (2021) [53]
PBC	rs60600003	7:37,382,465	ELMO1	European ancestry	rs60600003	Cordell et al. (2021) [53]
PBC	rs12531711	7:128,617,466	IRF5	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs370193557	7:138,729,543	ZC3HAV1L	European ancestry	rs370193557	Cordell et al. (2021) [53]
PBC	rs11390003	9:100,741,912	TRIM14	European ancestry	rs11390003	Cordell et al. (2021) [53]
PBC	rs7097397	10:50,025,396	WDFY4	European ancestry	rs7097397	Cordell et al. (2021) [53]
PBC	rs58523027	11:646,986	IRF7	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs11601860	11:64,110,422	CCDC88B	European ancestry	rs11601860	Cordell et al. (2021) [53]
PBC	rs12419634	11:111,239,365	POU2AF1	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs201150316	11:118,740,104	CXCR5	European ancestry	rs201150316	Cordell et al. (2021) [53]
PBC	rs1800693	12:6,440,009	TNFRSF1A	European ancestry	rs1800693	Cordell et al. (2021) [53]
PBC	rs35350651	12:111,907,431	SH2B3	European ancestry	rs35350651	Cordell et al. (2021) [53]
PBC	rs9533122	13:43,055,002	TNFSF11	European ancestry	rs9533122	Cordell et al. (2021) [53]
PBC	rs9591325	13:50,811,220	DLEU1	European ancestry	rs9591325	Cordell et al. (2021) [53]
PBC	rs3784099	14:68,749,927	RAD51B	European ancestry	rs3784099	Cordell et al. (2021) [53]
PBC	rs72699866	14:93,114,787	RIN3	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs59643720	14:103,564,807	TNFAIP2	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs9652601	16:11,174,365	CLEC16A	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs1119132	16:27,403,469	IL21R	European ancestry	rs1119132	Cordell et al. (2021) [53]
PBC	rs79577483	16:68,036,939	DPEP3	European ancestry	rs79577483	Cordell et al. (2021) [53]
PBC	rs11117432	16:86,019,271	IRF8	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs33938760	17:38,044,893	IKZF3	European ancestry	rs33938760	Cordell et al. (2021) [53]
PBC	rs1029464	17:44,149,348	MAPT	European ancestry	rs1029464	Cordell et al. (2021) [53]
PBC	rs1808094	18:67,526,026	CD226	European ancestry	rs1808094	Cordell et al. (2021) [53]
PBC	rs2304256	19:10,475,652	TYK2	European ancestry	rs2304256	Cordell et al. (2021) [53]
PBC	rs3745516	19:50,926,742	SPIB	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs137687	22:39,740,078	SYNGR1	European ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs10802190	1:117,061,384	CD58	China/Japan	rs10802190	Cordell et al. (2021) [53]
PBC	rs842349	2:135,342,452	TMEM163	China/Japan	rs842349	Cordell et al. (2021) [53]
PBC	rs11889341	2:191,943,742	STAT4	China/Japan	Several signals	Cordell et al. (2021) [53]
PBC	rs4675370	2:204,646,499	CD28	China/Japan	rs4675370	Cordell et al. (2021) [53]
PBC	rs12695386	3:119,209,027	POGLUT1	China/Japan	rs12695386	Cordell et al. (2021) [53]
PBC	rs230534	4:103,449,041	NFKB1	China/Japan	rs230534	Cordell et al. (2021) [53]
PBC	rs34463936	5:35,850,149	LOC105374724	China/Japan	rs34463936	Cordell et al. (2021) [53]
PBC	rs4709148	6:167,521,676	CCR6	China/Japan	rs4709148	Cordell et al. (2021) [53]
PBC	rs56211063	9:117,585,897	TNFSF15	China/Japan	Several signals	Cordell et al. (2021) [53]
PBC	rs4938534	11:111,275,133	BTG4	China/Japan	rs4938534	Cordell et al. (2021) [53]
PBC	rs480958	11:118,577,990	LOC105369519	China/Japan	Several signals	Cordell et al. (2021) [53]
PBC	rs12942330	17:37,939,839	IKZF3	China/Japan	rs12942330	Cordell et al. (2021) [53]
PBC	rs13416555	2:8,441,735	ID2	European + Asian ancestry	rs891058	Cordell et al. (2021) [53]
PBC	rs10581773	2:204,660,748	CD28	European + Asian ancestry	rs10581773	Cordell et al. (2021) [53]
PBC	rs60643069	5:100,238,073	ST8SIA4	European + Asian ancestry	rs141002831	Cordell et al. (2021) [53]
PBC	rs6874308	5:141,506,911	NDFIP1	European + Asian ancestry	rs10062349	Cordell et al. (2021) [53]
PBC	rs742108	6:106,582,920	PRDM1	European + Asian ancestry	Several signals	Cordell et al. (2021) [53]
PBC	rs968334	6:167,526,096	CCR6	European + Asian ancestry	rs3093024	Cordell et al. (2021) [53]
PBC	rs4733851	8:129,264,420	PVT1	European + Asian ancestry	several signals	Cordell et al. (2021) [53]
PBC	rs1322057	9:117,578,374	TNFSF15	European + Asian ancestry	rs6478109	Cordell et al. (2021) [53]
PBC	rs10893872	11:128,325,553	ETS1	European + Asian ancestry	rs10893872	Cordell et al. (2021) [53]
PBC	rs799469	14:35,444,425	FAM177A1	European + Asian ancestry	rs712315	Cordell et al. (2021) [53]
PBC	rs7059064	X:48,837,087	GRIPAP1	China/Japan	NA	Asselta et al. (2021) [61]
PSC	rs7556897	2:228,660,112	AC073065.3	European ancestry	NA	Ellinghaus et al. (2016) [54]
PSC	rs17032705	4:103,432,974	NFKB1	European ancestry	NA	Ellinghaus et al. (2016) [54]
PSC	rs12369214	12:107,198,611	RIC8B	European ancestry	NA	Ellinghaus et al. (2016) [54]
PSC	rs11649613	16:11,319,357	RP11-396B14.2	European ancestry	NA	Ellinghaus et al. (2016) [54]
PSC	rs3748816	1:2,526,746	MMEL1	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs72837826	2:111,933,001	BCL2L11	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs7426056	2:204,612,058	CD28	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs3749171	2:241,569,692	GPR35	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs3197999	3:49,721,532	MST1	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs80060485	3:71,153,890	FOXP1	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs13140464	4:123,499,745	IL21	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs56258221	6:91,030,441	BACH2	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs4147359	10:6,108,439	IL2RA	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs663743	11:64,107,735	CCDC88B	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs7937682	11:111,579,939	SIK2	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs11168249	12:48,208,368	HDAC7	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs3184504	12:111,884,608	SH2B3	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs725613	16:11,169,683	CLEC16A	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs1788097	18:67,543,688	CD226	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs60652743	19:47,205,707	PRKD2	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs2836883	21:40,466,744	PSMG1	European ancestry	NA	Ji et al. (2016) [55]
PSC	rs1893592	21:43,855,067	UBASH3A	European ancestry	NA	Ji et al. (2016) [55]