Table 1: Putative causal genes identified by our new method FOGS in the GWAS risk loci that contained at least one genome-wide significant SNP.

FOGS identified 22 putative causal genes with their chromosomes (CHR), transcription start sites (TSS) and relevant previous studies (Reported) in the GWAS Catalog [23]. For comparison, we also list the p-values of TWAS [14, 16] and the posterior probabilities of FOCUS [24]

Gene	CHR	Position	FOGS	TWAS	FOCUS	Reported
PTPRF	1	43990858	< 1.0 × 10−7	2.2 × 10−2	0.00	[15, 22, 31, 37]
MED8	1	43849578	9.0 × 10−7	1.1 × 10−11	1.00	[15, 31, 37]
THOC7	3	63819545	1.7 × 10−6	2.7 × 10−11	1.00	[15, 31, 37]
FAM114A2	5	153371268	5.0 × 10−7	5.3 × 10−6	0.78
BTN2A1	6	26458152	< 1.0 × 10−7	2.8 × 10−4	0.00	[37]
HIST1H2BJ	6	27093676	< 1.0 × 10−7	5.5 × 10−1	0.00
HIST1H4L	6	27840926	< 1.0 × 10−7	< 1.0 × 10−17	1.00
TRIM27	6	28870779	< 1.0 × 10−7	< 1.0 × 10−17	0.00
HLA-F-AS1	6	29696142	5.0 × 10−7	8.1 × 10−1	0.00
MICE	6	29709508	< 1.0 × 10−7	1.9 × 10−1	0.00
ZFP57	6	29640168	< 1.0 × 10−7	< 1.0 × 10−17	1.00	[15, 37]
PPP1R18	6	30644166	< 1.0 × 10−7	< 1.0 × 10−17	1.00
FLOT1	6	30695486	< 1.0 × 10−7	1.3 × 10−8	0.00
IER3	6	30710979	< 1.0 × 10−7	< 1.0 × 10−17	0.54
C4A	6	31949801	< 1.0 × 10−7	< 1.0 × 10−17	1.00
PRRT1	6	32116136	2.0 × 10−7	7.4 × 10−2	0.00	[37]
OPCML	11	132284874	< 1.0 × 10−7	1.2 × 10−6	0.94
IGSF9B	11	133778459	< 1.0 × 10−7	3.4 × 10−11	1.00	[15]
B3GAT1	11	134248397	< 1.0 × 10−7	3.3 × 10−3	0.01	[15]
RGS6	14	72398816	< 1.0 × 10−7	2.8 × 10−2	0.00	[15, 31, 37]
HYKK	15	78799906	< 1.0 × 10−7	6.0 × 10−2	0.27
FURIN	15	91411884	4.0 × 10−7	2.3 × 10−12	1.00	[15, 31]