Table 3.

Association of White Blood Cell Trait Variants with Immune-Mediated Diseases and Clinical Phenotypes in Previous Genome-wide Association Studies

Trait (Population)	dbSNP ID	Chr	Pos	Alt/Ref	Gene	Phenotype	Sample Size	p Valuea
WBC (EA)	rs1260328	2	27,730,940	C/T	GCKR	inflammatory bowel disease	96,486	1.27 × 10−4
LYM (EA)	rs2229094b	6	31,540,556	C/T	LTA	Crohn disease	69,268	7.81 × 10−7
LYM (EA)	rs2229094b	6	31,540,556	C/T	LTA	systemic lupus erythematosus	23,209	3.09 × 10−7
LYM (EA)	rs2229094b	6	31,540,556	C/T	LTA	primary biliary cirrhosis	21,216	1.31 × 10−5
WBC (All)	rs185819	6	32,050,067	C/T	TNXB	multiple sclerosisc	22,850	2.16 × 10−6
WBC (All)	rs185819	6	32,050,067	C/T	TNXB	type 1 diabetes	33,394	3.29 × 10−9
WBC (All)	rs185819	6	32,050,067	C/T	TNXB	ulcerative colitis	72,647	2.91 × 10−6
WBC (All)	rs185819	6	32,050,067	C/T	TNXB	systemic lupus erythematosusc	23,209	2.32 × 10−37
WBC (All)	rs185819	6	32,050,067	C/T	TNXB	rheumatoid arthritis	103,558	3.90 × 10−53
MON (All)	rs4917014	7	50,305,863	G/T	C7orf72-IKZF1	systemic lupus erythematosus	32,444	8.10 × 10−5
MON (All)	rs4917014	7	50,305,863	G/T	C7orf72-IKZF1	inflammatory bowel disease	96,486	4.59 × 10−5
MON (All)	rs4917014	7	50,305,863	G/T	C7orf72-IKZF1	Crohn disease	69,268	1.49 × 10−4
MON (All)	rs4917014	7	50,305,863	G/T	C7orf72-IKZF1	Stevens-Johnson syndrome/toxic epidermal necrolysis	1,129	8.00 × 10−11
MON (All)	rs4917014	7	50,305,863	G/T	C7orf72-IKZF1	selective immunoglobulin a deficiency	2,748	2.80 × 10−23
LYM (EA)	rs4763879	12	9,910,164	A/G	CD69	type 1 diabetes	38,522	1.90 × 10−11
LYM (EA)	rs4763879	12	9,910,164	A/G	CD69	multiple sclerosis	38,135	2.18 × 10−5
LYM (EA)	rs4763879	12	9,910,164	A/G	CD69	selective immunoglobulin A deficiency	2,748	1.90 × 10−11
MON (EA)	rs11642873	16	85,991,705	C/A	IRF8-LINC01082	systemic lupus erythematosus	23,209	3.56 × 10−10
MON (EA)	rs11642873	16	85,991,705	C/A	IRF8-LINC01082	systemic sclerosis	14,853	2.30 × 10−12
WBC (EA); MON (All)	rs1292053	17	57,963,537	G/A	TUBD1	multiple sclerosis	38,135	7.47 × 10−6
WBC (EA); MON (All)	rs1292053	17	57,963,537	G/A	TUBD1	Crohn disease	96,486	8.53 × 10−6
WBC (EA); MON (All)	rs1292053	17	57,963,537	G/A	TUBD1	inflammatory bowel disease	96,486	9.61 × 10−5
WBC (EA); NEU (EA)	rs4760	19	44,153,100	G/A	CD87 (PLAUR)	ulcerative colitis	72,647	1.51 × 10−4
WBC (EA)	rs3865444	19	51,727,962	A/C	CD33	Alzheimer disease	59,716	1.60 × 10−9
BAS (EA)	rs2295764	20	31,025,163	G/A	ASXL1	somatic mutations in MDS, CML, and ICUS	–	–
WBC (All)	rs2836878	21	40,465,534	A/G	ETS2-PSMG1	ankylosing spondylitis	9,609	4.90 × 10−12
WBC (All)	rs2836878	21	40,465,534	A/G	ETS2-PSMG1	Crohn disease	69,268	2.43 × 10−6
WBC (All)	rs2836878	21	40,465,534	A/G	ETS2-PSMG1	ulcerative colitis	72,647	2.05 × 10−20
WBC (All)	rs2836878	21	40,465,534	A/G	ETS2-PSMG1	inflammatory bowel disease	96,486	3.70 × 10−22
WBC (All)	rs2836878	21	40,465,534	A/G	ETS2-PSMG1	selective immunoglobulin A deficiency	2,748	1.40 × 10−8

Abbreviations: Chr, chromosome; Pos, basepair position; Alt, effect allele; Ref, reference allele; CML, chronic myelogenous leukemia; ICUS, Idiopathic cytopenia of undetermined significance; MDS, myelodysplastic syndrome, WBC, white blood cell; NEU, neutrophil; MON, monocyte; LYM, lymphocyte; BAS, basophil.

^aSignificant results are shown after correcting for multiple testing of 16 variants and 15 diseases (p < 2.08 × 10⁻⁴). When multiple studies report the same variant-trait associations, results from the largest sample size are presented here.

^bLD r² between rs2229094 and rs1799964 is 0.75.

^cPhenome-wide association results. Permutation p value for association with multiple sclerosis was 0.0122.