Table 3 H3K27ac HiChIP target genes and nominated target genes for the 27 systemic sclerosis association signals

From: GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways

Ch	Locus	SNP PP Max	HiChIP target genes with SNP PP Max	Nominated genes by H3K27ac HiChIP + eQTL validation	Nominated genes by CHi-C + eQTL validation	Prioritized genes by DEPICT/other criteria
1	IL12RB2	rs3790567	*IL12RB2* , IL23R	IL12RB2	IL12RB2, SERBP1	IL12RB2
1	CD247	rs2056626	*CD247* , POU2F1, TADA1, GPA33, MAEL, DUSP27, CREG1, RCSD1, MPZL1, DCAF6, MPC2	CD247	CD247	CD247
1	TNFSF4- LOC100506023 -PRDX6	rs2022449				TNFSF4
1	TNFSF4- LOC100506023 -PRDX6	rs11576547				TNFSF4 ^a
2	NAB1	rs716254	*NAB1* , GLS, TMEM194B, MFSD6	NAB1		NAB1, TMEM194B
2	STAT4	rs3821236	STAT4, STAT1, GLS, MYO1B, NABP1, SDPR	STAT4, STAT1**		STAT4
2	STAT4	rs4853458	STAT4, STAT1, GLS, MYO1B, NABP1, SDPR	STAT4, STAT1**
3	FLNB -DNASE1L3-PXK	rs7355798			PXK, FLNB, RPP14	FLNB-AS1
3	FLNB-DNASE1L3- PXK	rs7653734			PXK, RPP14	PXK, DNASE1L3 ^b
3	POGLUT1-TIMMDC1-CD80- ARHGAP31	rs9884090			POGLUT1, TIMMDC1	CD80, ARHGAP31, POGLUT1
3	IL12A	rs589446	*IL12A*	IL12A	IL12A
4	DGKQ	rs11724804			DGKQ, GAK, TMEM175
4	NFKB1	rs230517	*NFKB1, MANBA* , UBE2D3, CISD2, SLC9B1, SLC39A8	NFKB1, MANBA	NFKB1, MANBA, BDH2	NFKB1
5	TNIP1	rs3792783	*TNIP1*, GPX3, CD71, RPS14, RMB22, DCTN4, IRGM, SMIM3,*ANXA6*, GM2A, SLC36A3	TNIP1, ANXA6	TNIP1, ANXA6	TNIP1
6	ATG5	rs633724				ATG5 ^b
7	IRF5- TNPO3*	rs36073657	TNPO3, *IRF5*	IRF5	IRF5, FAM71F2
7	IRF5- TNPO3*	rs12155080	*TNPO3, IRF5*	TNPO3, IRF5	TNPO3	IRF5
8	FAM167A,BLK	rs2736340			BLK, RP11-481A20.11, FDFT1, NEIL2	BLK, C8orf14
8	RAB2A-CHD7	rs6987084	CHD7, *RAB2A*, CLVS1	RAB2A
11	CDHR5 -IRF7	rs6598008	*IRF7*, RIC8A, BET1L, PSMD13, SIRT3, NLRP6, PTDSS2, *RNH1, HRAS*, RASSF7, *PHRF1, DEAF1, DRD4*, TALDO1, PDDC1, CEND1, *EPS8L2*	IRF7, RNH1, HRAS, PHRF1, DRD4, EPS8L2	DRD4, C11orf35, IRF7, PHRF1, RNH1	IRF7
11	TSPAN32,CD81-AS1	rs2651804			CD81, ASCL2	TSPAN32
11	DDX6	rs10892286	*DDX6*, KMT2A, *TREH*, CXCR5, BCL9L, UPK2, ATP5L, TRAPPC4, FOXR1, VPS11	DDX6, TREH	PHLDB1, TREH
15	CSK	rs1378942	*CSK*, PML, STOML1, ARID3B, SEMA7A, CLK3, EDC3, *CYP1A1, LMAN1L, CPLX3, ULK3, SCAMP2, MPI*, COX5A, *RPP25, PPCDC*, GOLGA6C, MAN2C1, NEIL1, SIN3A, SNUPN, SNX33	CSK, CYP1A1, LMAN1L, CPLX3, ULK3, SCAMP2, MPI, RPP25, PPCDC	CPLX3, CSK, CYP1A1, FAM219B, LMAN1L, MPI, PPCDC, RPP25, SCAMP2, SCAMP5, ULK3	CSK, SCAMP2, ULK3
16	IRF8	rs11117422	*IRF8* , COX4I1, EMC8, FOXF1	IRF8**		IRF8
17	IKZF3- GSDMB	rs9303277	*GSDMB, IKZF3, ZPBP2, GRB7, MED1, CDK12, PPP1R1B,PNMT, PGAP3*, ERBB2, *ORMDL3*, NEUROD2, STARD3, TCAP, MIEN1, RPL19, CACNB1, FBXL20, LRRC3C, *GSDMA, PSMD3*, THRA, NR1D1, MSL1, RARA, GJD3, TNS4, IGFBP4, CCR7, SMARCE1, KRTAP17, KRT33A	GSDMB, IKZF3, ZPBP2, PNMT, PGAP3, ORMDL3, GSDMA, PSMD3	IKZF3, ZPBP2, GSDMB, ORMDL3	GSDMB, IKZF3, ORMDL3
17	NUP85- GRB2	rs1005714	*NUP85, MRPS7*, ATP5H, ICT1	NUP85, MRPS7	ARMC7, GGA3, SLC16A5, MRPS7, NT5C, NUP85	ARMC7, GGA3, NT5C
19	IL12RB1	rs2305743	*IL12RB1*, MAST3, ARRDC2, ISYNA1, ELL, SSBP4, LSM4, JUND, RAB3A, PDE4C, *KIAA1683*, MPV17L2, IFI30, PIK3R2, B3GNT3, FCHO1, INSL3, JAK3, RPL18A, SLC5A	IL12RB1, KIAA1683	KIAA1683	IL12RB1, MAST3

In column ‘HiChIP Target Genes withSNP PP Max’, genes with HiChIP and eQTL signals are highlighted in bold
Ch, chromosome; PP, posterior probability from the statistical fine-mapping; SNP, single-nucleotide polymorphism
*Credible set not feasible
**NO eQTL signals found but strong HiChIP signal
^aGene nominated by proximity
^bGenes nominated according to the results from the first Immunochip in systemic sclerosis (9)

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Table 3 H3K27ac HiChIP target genes and nominated target genes for the 27 systemic sclerosis association signals

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