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

Table 1

List of selected GWAS-implicated RA SNPs examined in this study.

SNP	Locus	Chromosomal location (GRCh38)	Variant type	Gene	Reference
rs2228145	1q21	154454494	Missense variant	IL6R	[15]
rs2105325	1q25.1	173380586	Intron variant	LOC100506023	[16]
rs2843401	1p36	2596694	Intron variant	MMEL1	[15]
rs28411352	1p34.3	37812907	3 prime UTR variant	MTF1	[16]
rs883220	1p34	38151199	Intron variant	LOC105378654	[15]
rs2476601	1p13	113834946	Missense variant	PTPN22	[15]
rs6732565	2q13	110850255	Intron variant	ACOXL	[16]
rs11676922	2q11	100190478	Intergenic	AFF3	[17]
rs6715284	2q33.1	201289674	Intron variant	ALS2CR12	[16]
rs3087243	2q33	203874196	Downstream variant	CTLA4	[17]
rs34695944	2p16	60897715	Intron variant	REL	[15]
rs934734	2p14	65368452	Intron variant	SPRED2	[17]
rs13426947	2q32	191068528	Intron variant	STAT4	[15]
rs3806624	3p24.1	27723132	Upstream variant	EOMES	[16]
rs9826828	3q22.3	136683218	Intron variant	STAG1	[16]
rs4452313	3p24.3	17005540	Intron variant	PLCL2	[16]
rs13315591	3p14	58571114	Intron variant	FAM107A	[17]
rs874040	4p15	26106575	Upstream variant	RBPJ	[17]
rs2664035	4p11	48218822	Intron variant	TEC	[16]
rs71624119	5q11	56144903	Intron variant	ANKRD55	[15]
rs26232	5q21	103261019	Intron variant	C5orf30	[17]
rs3093023	6q27	167120802	Intron variant	CCR6	[16]
rs2234067	6p21.31	36387877	Upstream variant	ETV7	[16]
rs6920220	6q23	137685367	Upstream variant	TNFAIP3	[15]
rs2596565	6p21.33	31385552	Upstream variant	HLA-B/MICA	[18]
rs6910071	6p21	32315077	Intron variant	TSBP1	[17]
rs660895	6p21	32609603	Intron variant	HLA-DRB1	[14]
rs4272	7q21.2	92607515	3 prime UTR variant	CDK6	[16]
rs10488631	7q32	128954129	Downstream variant	IRF5	[17]
rs67250450	7p15.1	28135367	Intron variant	JAZF1	[16]
rs678347	8q22.3	101451374	Upstream variant	GRHL2	[16]
rs1516971	8q24.21	128529854	Intron variant	LINC00824	[16]
rs998731	8q21.13	80183160	Intron variant	TPD52	[16]
rs951005	9p13	34743684	Intergenic	CCL21	[17]
rs12764378	10q21	62040245	Intron variant	ARID5B	[15]
rs2275806	10p14	8053377	Intron variant	GATA3	[15]
rs706778	10p15	6056986	Intron variant	IL2RA	[17]
rs595158	11q12	61142109	Intron variant	VPS37C	[15]
rs4409785	11q21	95578258	Intergenic/unknown	CEP57	[16]
rs773125	12q13.2	56001170	Intron variant	SUOX	[16]
rs1950897	14q24.1	68293424	Intron variant	RAD51B	[16]
rs8043085	15q14	38535939	Intron variant	RASGRP1	[15]
rs8026898	15q23	69699078	Intergenic/unknown	TLE3	[15]
rs13330176	16q24	85985481	Intergenic/unknown	IRF8	[15]
rs4780401	16p13.13	11745470	Upstream variant	TXNDC11	[16]
rs12936409	17q12	39887396	Intergenic/unknown	IKZF3	[15]
rs34536443	19p13	10352442	Missense variant	TYK2	[15]
rs4810485	20q13	46119308	Intron variant	CD40	[17]
rs9979383	21q22	35343463	Intron variant	RUNX1	[15]
rs1893592	21q22.3	42434957	Intron variant	UBASH3A	[16]
rs909685	22q13.1	39351666	Intron variant	SYNGR1	[16]
rs2240336	1p36	17347907	Intron variant	PADI4	[16]
rs10175798	2p23.1	30226728	Upstream variant	LBH	[16]
rs968567	11q12.2	61828092	Intron variant	FADS2	[16]
rs10774624	12q24.12	111395984	Upstream variant	LINC02356	[16]
rs9603616	13q14.11	39793932	Downstream variant	COG6	[16]
rs73194058	21q22.11	33391982	Intergenic/unknown	IFNGR2	[16]
rs2834512	21q22	34539301	Intron variant	RCAN1	[15]