Table 2.

Genome-Wide Significant (P < 5.0 × 10 ⁸) Variants Associated With Inflammatory Bowel Disease After Analysis Conditioned on the HLA-DRB1 Single-Nucleotide Polymorphism rs9270299 (From the Ulcerative Colitis Analysis)

Phenotype	Chr	Position (hg19)	Nearest gene	SNP name	A1	A2	Combined Freq	Unconditional		Conditional		MAF				African subpopulation with highest MAF
								OR	P value	OR	P value	YRI	EAS	EUR	SAS
IBD	6	32594240	HLA-DQA1	rs139282044a	T	A	0.031	1.93	9.43E-08	2.08	5.78E-09	0.04 (A)	0 (A)	0 (A)	0 (A)	ESN 0.08 (A)
	6	32367297	BTNL2	rs144540865a	A	G	0.032	1.88	1.41E-07	2.01	1.25E-08	0 (G)	0 (G)	0 (G)	0 (G)	LWK 0.03 (G)
	6	32590316	HLA-DQA1	rs75441240a	C	T	0.032	1.84	2.89E-07	1.97	1.91E-08	0.04 (T)	0 (T)	0 (T)	0 (T)	ESN 0.08 (T)
	6	32572195	HLA-DRB1	rs140435271a	A	G	0.033	1.82	4.51E-07	1.95	2.97E-08	0.04 (G)	0 (G)	0 (G)	0 (G)	ESN 0.08 (G)
	6	32415572	HLA-DRA	rs114243387a	G	C	0.038	1.69	4.92E-07	1.80	3.25E-08	0.04 (C)	0 (C)	0 (C)	0 (C)	ESN 0.08 (C)
	6	32553401	HLA-DRB1	rs144404284	G	A	0.048	1.66	8.14E-07	1.79	3.54E-08	0.05 (A)	0.02 (A)	0.05 (A)	0.01 (A)	—
	6	32589502	HLA-DQA1	rs114210446	A	G	0.033	1.80	5.73E-07	1.92	4.11E-08	0.05 (G)	0 (G)	0.01 (G)	0 (G)	—
	6	32425875	HLA-DRA	rs140228374a	C	T	0.036	1.75	6.46E-07	1.87	4.17E-08	0.04 (T)	0 (T)	0 (T)	0 (T)	ESNa0.08 (T)
	6	32543575	HLA-DRB1	rs41294271	C	T	0.210	1.36	2.72E-06	1.45	4.27E-08	0.09 (T)	Observed variant without frequency or population information			—

A1, tested allele; A2, alternate allele; Chr, chromosome; EAS, East Asian; ESN, Esan in Nigeria; (data from 1000 genome phase 3); EUR, European; Freq, frequency; LWK, Luhya in Webuye, Kenya; MAF, minor allele frequency; SAS, South Asian; YRI, Yoruba in Ibadan, Nigeria.

^aAfrican-specific SNP (monomorphic in EAS, EUR, and SAS).