Investigating the GWAS-Implicated Loci for Rheumatoid Arthritis in the Pakistani Population

Table 4

Details of study SNPs (RegulomeDB ) with putative regulatory functions.

SNP	Chr.	Score	eQTL	Bound protein	Motifs
SYNGR1/rs909685	chr22	1b	SYNGR1	MAX, MYC, PAX5, TRIM28, EBF1	p53decamer
FADS2/rs968567	chr11	1f	NXF1	CTCF, E2F4, EP300, ETS1, FOSL2, FOXP2, GABPA, GABPB1, GATA1, HNF4A, HNF4G, MAX, MYBL2, NFIC, NFKB1, NFYB, PML, POLR2A, RAD21, REST, SIN3A, SP1, SREBF1, SREBF2, TAF1, TCF12, YY1, ZBTB7A
CD40/rs4810485	chr20	1f	CD40	POLR2A, NFKB1, NFIC, MEF2C, MEF2A, IRF1, IKZF1, FOXM1, BCL3, BATF
CCR6/rs3093023	chr6	1f	CCR6		Oct_1
HLAB/MICA/rs2596565	chr6	1f	BTN3A2, HLA-A, HLA-C, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-G, HLA-H, VARSL
HLA-DRB1/rs660895	chr6	1f	HLA-DQA2, HLA-DQA1	BCLAF1, POLR2A
GRHL2/rs678347	chr8	2a		YY1, CEBPB, EP300, FOXA2, JUND, STAT3, TCF12, USF2, SIN3A	HNF3, Foxa2, FOXF2, Freac-2, Freac-4, FOXA1, HNF3, FOXC1
PTPN22/rs2476601	chr1	2b		FOS, STAT3	Gabpa, Etv1, Elk1, Erg, Ehf, PU.1
LBH/rs10175798	chr2	2b		ATF2, FOXM1, RUNX3, NFIC, SPI1, MEF2A, BATF	STAT1:STAT1
RBPJ/rs874040	chr4	2b		GATA2, PML, TAL1	MEF-2
C5orf30/rs26232	chr5	2b		BHLHE40, CHD1, EP300, FOXM1, MAZ, NFATC1, NFIC, RUNX3, TBL1XR1, TBP, USF2, ATF2, MEF2A, MEF2C, NFKB1	ICSBP
RUNX1/rs9979383	chr21	3a		MYC, NFKB1	E47, FIGLA, ID4, MESP1, SNAI2
CTLA4/rs3087243	chr2	3a		MAX, FOS, STAT3	Bbx
IRF5/rs10488631	chr7	3a		GATA2	Nanog